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17 pages, 3234 KB

Open AccessArticle

Transcription Factor BnaC04.MYB89 Negatively Regulates Seed Fatty Acid Biosynthesis in Brassica napus

by Dong Li, Xumin Wang, Yujiao Song, Jianchao Sun, Shuhan Yu, Bowei Zhu, Xin Liu, Guodong Zhao, Tongsheng Zhao, Limin Wang, Yuting Sheng and Hongxia Zhang

Plants 2025, 14(22), 3495; https://doi.org/10.3390/plants14223495 (registering DOI) - 16 Nov 2025

Abstract

Seed oil content and fatty acid (FA) composition collectively determine the quality and economic value of Brassica napus. Little is known about the role of R2R3-MYB transcription factors (TFs) in regulating FA biosynthesis in B. napus. Here, BnaC04.MYB89 was found to [...] Read more.

Seed oil content and fatty acid (FA) composition collectively determine the quality and economic value of Brassica napus. Little is known about the role of R2R3-MYB transcription factors (TFs) in regulating FA biosynthesis in B. napus. Here, BnaC04.MYB89 was found to be expressed primarily in developing seeds. Overexpression of BnaC04.MYB89 consistently decreased FA levels, as evidenced by its effect in both the Arabidopsis thaliana myb89-1 mutant and B. napus seeds. RNA-seq of developing seeds at 30 DAP (days after pollination) revealed marked suppression of FA biosynthetic genes in BnaC04.MYB89-overexpressing plants compared to the K407 control. ChIP (Chromatin immunoprecipitation) analysis revealed that BnaC04.MYB89 directly inhibited the expression of BnaA03.BCCP1 and BnaC03.HD while indirectly regulating that of BnaA09.BADC1, BnaA03.BADC3, BnaA03.MOD1, and BnaA08.FAT8, thereby reducing seed FA accumulation. Collectively, these results elucidate the role for BnaC04.MYB89 and provide new insights into the transcriptional regulatory network controlling seed oil accumulation in B. napus. Full article

(This article belongs to the Special Issue Plant Organ Development and Stress Response)

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25 pages, 4862 KB

Open AccessReview

Comparative Efficacy of Platelet-Rich Fibrin, Freeze-Dried Bone Allograft, or Spontaneous Healing for Alveolar Ridge Preservation: Systematic Review and Meta-Analysis

by Abeer S. Al-Zawawi, Amani M. Basudan, Rand Osama Alkhani, Lamis Khalid Alraddadi, Shikha Fahad Bin-Muhayya, Layan Abdullah Alzuwayyid, Deemah Alsaeed, Eithar Ibrahim Alrosaa, Lana Mohammed Alrasheed, Muneerah Abduaziz Alfahad, Ghadeer Mohammed Almutairi, Jana Alawad, Wasan Saeed Koaban, Munirah Naeem Alsubaie and Sundar Ramalingam

Bioengineering 2025, 12(11), 1253; https://doi.org/10.3390/bioengineering12111253 (registering DOI) - 16 Nov 2025

Abstract

Alveolar ridge preservation (ARP) is crucial for maintaining bone and soft-tissue integrity after tooth extraction, thereby facilitating future implant placement. Among various biomaterials, platelet-rich fibrin (PRF) and freeze-dried bone allograft (FDBA) are commonly used; however, their comparative effectiveness remains unclear. This systematic review [...] Read more.

Alveolar ridge preservation (ARP) is crucial for maintaining bone and soft-tissue integrity after tooth extraction, thereby facilitating future implant placement. Among various biomaterials, platelet-rich fibrin (PRF) and freeze-dried bone allograft (FDBA) are commonly used; however, their comparative effectiveness remains unclear. This systematic review and meta-analysis aimed to evaluate and compare the outcomes of PRF, FDBA, and spontaneous healing with blood clot in ARP, incorporating recent randomized controlled trials and comparative studies published up to June 2025. Electronic searches were conducted across multiple databases following the PRISMA 2020 guidelines, and the risk of bias was assessed using RoB-2 and ROBINS-I tools. Primary outcomes included changes in alveolar ridge height and width, while secondary outcomes encompassed histological, radiographic, implant-related, and patient-centered measures. Twenty studies were included for qualitative synthesis and sixteen for quantitative analysis. Meta-analyses showed no significant difference between PRF and FDBA in ridge height (SMD = −0.24; 95% CI: −0.56 to 0.08; p = 0.145) or width preservation (SMD = −0.16; 95% CI: −0.73 to 0.42; p = 0.597). PRF significantly reduced ridge height loss compared to spontaneous healing (SMD = −0.79; 95% CI: −1.33 to −0.25; p = 0.004) and enhanced histologic new bone formation (SMD = 1.43; 95% CI: 0.39 to 2.47; p = 0.007), while FDBA showed a non-significant trend toward benefit (SMD = −0.37; 95% CI: −0.86 to 0.11; p = 0.129). Moderate risk-of-bias and heterogeneity were observed among included studies. In conclusion, PRF and FDBA are both effective for alveolar ridge preservation, outperforming spontaneous healing. PRF offers biologically driven benefits in bone quality and soft-tissue healing, whereas FDBA provides greater structural stability. These findings suggest a promising clinical potential for PRF in improving bone quality at the implant site. Moreover, considering cost, preparation complexity, and site-specific needs, PRF may serve as a cost-effective, clinically favorable option for ARP. Future multi-center randomized trials with standardized PRF protocols and long-term follow-up are recommended. Full article

(This article belongs to the Special Issue Periodontics and Implant Dentistry)

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18 pages, 616 KB

Open AccessArticle

Does Resistance Indicate Malposition? A Standardized Comparison of Pedicle Screw Placement

by Sascha Kurz, Benjamin Fischer, Janine Schultze, Florian Metzner, Toni Wendler, Christoph-Eckhard Heyde and Stefan Schleifenbaum

Bioengineering 2025, 12(11), 1254; https://doi.org/10.3390/bioengineering12111254 (registering DOI) - 16 Nov 2025

Abstract

Pedicle screw malpositioning remains a frequent complication, with reported rates from 2% to 15%, often leading to revision surgeries. Analyzing mechanical resistance and torque encountered during screw insertion has been implicated as a promising approach for real-time detection. Five fresh-frozen human thoracolumbar spine [...] Read more.

Pedicle screw malpositioning remains a frequent complication, with reported rates from 2% to 15%, often leading to revision surgeries. Analyzing mechanical resistance and torque encountered during screw insertion has been implicated as a promising approach for real-time detection. Five fresh-frozen human thoracolumbar spine specimens were utilized in this study. Using 3D-printed templates, correct trajectories were systematically compared against four defined malpositions (medial, lateral, superior, superolateral), with offsets ranging from 2.0 mm to 3.5 mm. Drilling, tapping, and insertion phases were conducted at a constant speed and defined feed force. Contrary to the anticipated behavior, malpositioned trajectories showed no statistically significant difference in peak torque compared to correct trajectories across all phases (e.g., tapping

p = 0.944

,

r = 0.01

; insertion

p = 0.693

,

r = 0.05

). Regional stratification between thoracic and lumbar spine also failed to yield significant differences. The only statistically significant difference was observed between the correct trajectory and the superolateral malposition during drilling (

p = 0.038

). Under the tested standardized conditions, torque-based mechanical resistance during pedicle screw placement is generally not a reliable and consistent real-time indicator of malposition. Full article

(This article belongs to the Special Issue Spine Biomechanics)

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25 pages, 16835 KB

Open AccessArticle

Thermochemical Degradation of a Polyacrylamide Gel as a Dual-Function Strategy for Enhanced Oil Recovery and Reservoir Remediation

by Jiaying Wang, Renbao Zhao, Yuan Yuan, Yunpeng Zhang, Guangsen Zhu, Jingtong Tian, Haiyang Zhang, Haitao Ren, Guanghui Zhou and Bin Liao

Gels 2025, 11(11), 915; https://doi.org/10.3390/gels11110915 (registering DOI) - 16 Nov 2025

Abstract

The accumulation of residual hydrolyzed polyacrylamide (HPAM) gel or molecular-based solutions in reservoirs after polymer flooding poses dual challenges: irreversible formation damage and long-term environmental risk issues. However, existing research mainly focuses on treating polymers in surface-produced water, neglecting both in situ decomposition [...] Read more.

The accumulation of residual hydrolyzed polyacrylamide (HPAM) gel or molecular-based solutions in reservoirs after polymer flooding poses dual challenges: irreversible formation damage and long-term environmental risk issues. However, existing research mainly focuses on treating polymers in surface-produced water, neglecting both in situ decomposition of residual polymer gel or molecular-based solutions in reservoirs and the degradation of HPAM gels under high temperatures from in situ combustion (ISC). This work investigates the thermochemical behavior of HPAM gel during ISC and its dual-function role in enhanced oil recovery (EOR) and reservoir remediation. It was demonstrated that the residual gel and/or molecular-based solutions undergo efficient degradation, serving as an in situ fuel that significantly reduces the activation energy for crude oil oxidation by up to 58.4% in the low-temperature stage and 75.2% in the high-temperature stage. Factors influencing the gel’s degradation and the combustion process, including its molecular weight, ionic type, and crude oil viscosity, were systematically evaluated. Optimal conditions achieved over 90% gel degradation. Combustion tube experiments validated the dual benefits of this approach: an incremental oil recovery of 68.6% and an average HPAM gel removal efficiency of 64.8%. This work presents a novel strategy for utilizing retained gels in situ to simultaneously enhance oil recovery and mitigate gel-induced formation damage, offering significant insights for the management of mature gel-treated reservoirs. Full article

(This article belongs to the Special Issue Applications of Gels for Enhanced Oil Recovery)

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42 pages, 1195 KB

Open AccessReview

Prebiotic and Functional Fibers from Micro- and Macroalgae: Gut Microbiota Modulation, Health Benefits, and Food Applications

by Nurdeniz Deniz, Sümeyye Sarıtaş, Mikhael Bechelany and Sercan Karav

Int. J. Mol. Sci. 2025, 26(22), 11082; https://doi.org/10.3390/ijms262211082 (registering DOI) - 16 Nov 2025

Abstract

Micro- and macro-algae are natural resources that attract attention in terms of their prebiotic potential and functional food applications due to their rich polysaccharide diversity. In this review, the regulatory effects of dietary fibers and polysaccharides from algae on gut microbiota, their health [...] Read more.

Micro- and macro-algae are natural resources that attract attention in terms of their prebiotic potential and functional food applications due to their rich polysaccharide diversity. In this review, the regulatory effects of dietary fibers and polysaccharides from algae on gut microbiota, their health benefits and their potential functions in foods are discussed in detail. Compounds such as fucoidan, laminarin, alginate, porphyran, agar, carrageenan and exopolysaccharides are examined for their interactions with the microbiota and how they support digestive health, immunity and metabolic balance through the production of short chain fatty acids. In contrast to earlier reviews, this paper offers a comprehensive comparison between sulfated and non-sulfated algal polysaccharides, incorporates updated insights on their regulatory status and safety, and highlights emerging direction for developing next-generation prebiotic formulation. The review also examines their applications in functional foods, nutraceutical effects and protective roles, and includes preclinical and clinical studies. However, some limitations such as safety of consumption, risk of heavy metal accumulation, bioavailability issues and regulatory restrictions are also addressed. New nutritional approaches, next generation prebiotic formulations and biotechnological studies are included. This review aims to comprehensively highlight the versatile potential of algal polysaccharides as functional fibers and prebiotics. While numerous studies have examined algal polysaccharides, their heterogeneous structures and safety. This review emphasized these critical gaps and proposed a rational evaluation framework for future research and functional food development. Full article

(This article belongs to the Collection 30th Anniversary of IJMS: Updates and Advances in Biochemistry)

14 pages, 2397 KB

Open AccessArticle

Cellular Uptake and Tissue Retention of Microplastics in Black Soldier Fly Larvae

by Claudiu-Nicusor Ionica, Romelia Pop, Dragos Hodor, Irina Constantin, Ana Hiruta, Alexia-Teodora Hota, Alexandru Flaviu Tabaran, Sorana Daina, Andrei-Radu Szakacs and Adrian Macri

Insects 2025, 16(11), 1169; https://doi.org/10.3390/insects16111169 (registering DOI) - 16 Nov 2025

Abstract

Microplastic pollution is a pressing global concern, yet its immunotoxicological impacts on invertebrates remain poorly understood. The Black Soldier Fly (Hermetia illucens) larva has gained attention for its role in waste management and potential bioremediation, making it essential to evaluate its [...] Read more.

Microplastic pollution is a pressing global concern, yet its immunotoxicological impacts on invertebrates remain poorly understood. The Black Soldier Fly (Hermetia illucens) larva has gained attention for its role in waste management and potential bioremediation, making it essential to evaluate its interactions with microplastics. In this study, fluorescent carboxylate-modified polystyrene microbeads were directly injected into the hemocoel of larvae to bypass gut-associated variables and investigate systemic immune responses. Experimental groups were analyzed at multiple time points (1 h, 6 h, 24 h, 48 h, and 7 days) using histopathology, cytology, and confocal laser scanning microscopy. Results confirmed the persistence and systemic distribution of microplastics in hemolymph and tissues, with hemocytes exhibiting active phagocytosis of particles. Microplastics were retained within tissues for up to seven days, indicating long-term sequestration. Histological observations further highlighted their close association with metabolically active organs such as the fat body and Malpighian tubules, suggesting possible effects on detoxification and metabolism. These findings demonstrate that microplastics elicit measurable immune responses and are subject to cellular uptake and retention in insect larvae. The study provides novel insights into the immunological and histopathological consequences of microplastic contamination in H. illucens larvae, with implications for their safe use in bioconversion and bioremediation applications. Full article

(This article belongs to the Section Role of Insects in Human Society)

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18 pages, 5310 KB

Open AccessArticle

Enhanced Energy Storage Properties in Lead-Free (1−x)(BNT–5BT)–xBCZT Ceramics: Comparative Study of Direct and Indirect Synthesis Routes

by Mauro Difeo, Leandro Ramajo and Miriam Castro

Micro 2025, 5(4), 51; https://doi.org/10.3390/micro5040051 (registering DOI) - 16 Nov 2025

Abstract

This work presents a comparative study on the structural, microstructural, and functional properties of a novel lead-free solid solution based on (1–x)(0.95(Bi₀.₅Na₀.₅)TiO₃–0.05BaTiO₃)–x(0.5Ba₀.₇Ca₀.₃TiO₃ [...] Read more.

This work presents a comparative study on the structural, microstructural, and functional properties of a novel lead-free solid solution based on (1–x)(0.95(Bi₀.₅Na₀.₅)TiO₃–0.05BaTiO₃)–x(0.5Ba₀.₇Ca₀.₃TiO₃–0.5BaTi₀.₈Zr₀.₂O₃), abbreviated as (1−x)(BNT–5BT)–xBCZT, with x values ranging from 0 to 0.20. Two different synthesis routes were evaluated: a direct route, where all raw materials were mixed and processed in a single step, and an indirect route, where BNT–5BT and BCZT were pre-synthesized separately and later combined. X-ray diffraction (XRD) and Raman spectroscopy confirmed the formation of single-phase perovskite structures, with progressively increasing tetragonality as x increased. Field-emission scanning electron microscopy (FE-SEM/EDS) revealed dense microstructures and secondary rod-like phases whose morphology and amount evolved with composition. Dielectric measurements indicated an enhanced relaxor behavior with increasing BCZT content, evidenced by a shift in the T_F–R with frequency. The direct route resulted in more efficient dopant incorporation, leading to stronger dielectric relaxation, reduced hysteresis losses, and improved energy storage performance. The maximum energy efficiency (η) reached 43.7% for x = 0.075 via the direct route, compared to 38.0% for the same composition prepared by the indirect route. The maximum recoverable energy density (W_rec) reached 0.42 J·cm⁻³ for x = 0.075 via the direct route (vs. 0.40 J·cm⁻³ for the indirect route), with corresponding peak energy efficiencies of 43.7% and 38.0%, respectively. These findings demonstrate that (1−x)(BNT–5BT)–xBCZT ceramics synthesized via the direct route constitute a promising and scalable approach for high-efficiency, lead-free dielectric capacitors. Full article

(This article belongs to the Special Issue Nanomaterials for Sustainable Waste Conversion, Energy Production, and Environmental Applications)

23 pages, 3931 KB

Open AccessArticle

Enhanced 3D Gaussian Splatting for Real-Scene Reconstruction via Depth Priors, Adaptive Densification, and Denoising

by Haixing Shang, Mengyu Chen, Kenan Feng, Shiyuan Li, Zhiyuan Zhang, Songhua Xu, Chaofeng Ren and Jiangbo Xi

Sensors 2025, 25(22), 6999; https://doi.org/10.3390/s25226999 (registering DOI) - 16 Nov 2025

Abstract

The application prospects of photorealistic 3D reconstruction are broad in smart cities, cultural heritage preservation, and related domains. However, existing methods face persistent challenges in balancing reconstruction accuracy, computational efficiency, and robustness, particularly in complex scenes characterized by reflective surfaces, vegetation, sparse viewpoints, [...] Read more.

The application prospects of photorealistic 3D reconstruction are broad in smart cities, cultural heritage preservation, and related domains. However, existing methods face persistent challenges in balancing reconstruction accuracy, computational efficiency, and robustness, particularly in complex scenes characterized by reflective surfaces, vegetation, sparse viewpoints, or large-scale structures. In this study, an enhanced 3D Gaussian Splatting (3DGS) framework that integrates three key innovations is proposed: (i) a depth-aware regularization module that leverages metric depth priors from the pre-trained Depth-Anything V2 model, enabling geometrically informed optimization through a dynamically weighted hybrid loss; (ii) a gradient-driven adaptive densification mechanism that triggers Gaussian adjustments based on local gradient saliency, reducing redundant computation; and (iii) a neighborhood density-based floating artifact detection method that filters outliers using spatial distribution and opacity thresholds. Extensive evaluations are conducted across four diverse datasets—ranging from architectures, urban scenes, natural landscapes with water bodies, and long-range linear infrastructures. Our method achieves state-of-the-art performance in both reconstruction quality and efficiency, attaining a PSNR of 34.15 dB and SSIM of 0.9382 on medium-sized scenes, with real-time rendering speeds exceeding 170 FPS at a resolution of 1600 × 900. It demonstrates superior generalization on challenging materials such as water and foliage, while exhibiting reduced overfitting compared to baseline approaches. Ablation studies confirm the critical contributions of depth regularization and gradient-sensitive adaptation, with the latter improving training efficiency by 38% over depth supervision alone. Furthermore, we analyze the impact of input resolution and depth model selection, revealing non-trivial trade-offs between quantitative metrics and visual fidelity. While aggressive downsampling inflates PSNR and SSIM, it leads to loss of high-frequency detail; we identify 1/4–1/2 resolution scaling as an optimal balance for practical deployment. Among depth models, Vitb achieves the best reconstruction stability. Despite these advances, memory consumption remains a challenge in large-scale scenarios. Future work will focus on lightweight model design, efficient point cloud preprocessing, and dynamic memory management to enhance scalability for industrial applications. Full article

(This article belongs to the Special Issue Intelligent Point Cloud Processing, Sensing and Understanding—Third Edition)

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22 pages, 1574 KB

Open AccessArticle

Maternal Dietary Choices Might Impact Intrauterine Healing Processes and Postnatal Phenotype and Function in Human Fetuses with Spina Bifida Aperta—Early Clinical Observations and Implications from a Retrospective Cohort Study

by Thomas Kohl

Biomedicines 2025, 13(11), 2791; https://doi.org/10.3390/biomedicines13112791 (registering DOI) - 16 Nov 2025

Abstract

Background: The severity of postnatal symptoms in patients with spina bifida aperta (SBA) is also determined by secondary factors that damage the exposed neural tissue throughout gestation. The purpose of this report is to present clinical cases, from 2010 to 2025, and a [...] Read more.

Background: The severity of postnatal symptoms in patients with spina bifida aperta (SBA) is also determined by secondary factors that damage the exposed neural tissue throughout gestation. The purpose of this report is to present clinical cases, from 2010 to 2025, and a new hypothesis for a nonsurgical means of prenatal secondary prophylaxis. Patients: Eight fetuses underwent minimally invasive fetoscopic patch closure of SBA. After delivery, an unusual degree of prenatal patch healing was observed. Furthermore, time to complete postnatal skin closure was shorter (mean ± SD: 22.00 ± 6.53 days) than in 31 contemporary patients without dietary restrictions (Mean ± SD: 44.35 ± 11.91 days; p < 0.001). Four of the eight prenatally operated women reported that they ate plant-based food most of the time but also some meat throughout gestation; the other four were strict vegetarians. Two other fetuses with SBA at the level of the second and third lumbar vertebrae, respectively, had not undergone prenatal surgery. Following delivery, they presented with a markedly preserved surface of the neural cord and exhibited L5 motor function. One mother of the postnatally operated patients was on a vegetarian diet; the other one on a vegan diet. Conclusions: These early clinical observations point to the possibility that maternal plant-based diets might ameliorate the loss of neurological function and facilitate wound healing in human fetuses with SBA. If this impact of maternal dietary habits holds true, it opens the door to a far-reaching, easily available, non-invasive secondary prophylaxis in prenatally operated and unoperated fetuses with SBA and some other malformations. Full article

(This article belongs to the Special Issue Advances in Fetal Medicine and Neonatology)

29 pages, 1013 KB

Open AccessArticle

Multi-Port Liner Ship Routing and Scheduling Optimization Using Machine Learning Forecast and Branch-And-Price Algorithm

by Zhichao Cao, Tao Qian, Silin Zhang, Haibo Song and Yaxin Tian

J. Mar. Sci. Eng. 2025, 13(11), 2163; https://doi.org/10.3390/jmse13112163 (registering DOI) - 16 Nov 2025

Abstract

This study focuses on an integrated three-level multi-port liner ship vessel routing and scheduling optimization problem. Specifically, the three-level multi-port network consists of hub ports, feeder ports, and cargo source points, which provide the demands’ loading/unloading at each port. Considering vessel-specific constraints such [...] Read more.

This study focuses on an integrated three-level multi-port liner ship vessel routing and scheduling optimization problem. Specifically, the three-level multi-port network consists of hub ports, feeder ports, and cargo source points, which provide the demands’ loading/unloading at each port. Considering vessel-specific constraints such as speed, capacity, and cost, we formulate the multi-port liner ship routing and scheduling optimization problem as a mixed integer linear programming model with the objective of minimizing total voyage cost and operating time. First, we employ machine learning models to forecast the short-term demand at different ports as the input. There are multiple feasible routes generated and allowed to be elected. Second, to ensure both computational efficiency and solution quality, we devise and compare genetic algorithm (GA), simulated annealing (SA), Gurobi and the branch-and-price (B&P) algorithm to optimize scheduling plans. Experimental results demonstrate that the proposed predict-then-optimization framework effectively addresses the complexity of multi-port scheduling and routing problems, achieving a reduction in total transportation cost by 0.81% to 8.08% and a decrease in computation time by 16.86% to 24.7% compared to baseline methods, particularly with the SA + B&P hybrid approach. This leads to overall efficiency and cost-saving ocean vessel operations. Full article

(This article belongs to the Special Issue New Trends in Engineering and Operational Research on Container Supply Chain Management for Resilience, Digitalization, Intelligence and Sustainability)

14 pages, 534 KB

Open AccessFeature PaperArticle

Affine Invariance of Bézier Curves on Digital Grid

by Miklós Hoffmann and Ede Troll

Mathematics 2025, 13(22), 3672; https://doi.org/10.3390/math13223672 (registering DOI) - 16 Nov 2025

Abstract

Affine invariance is one of the most fundamental properties of free-form curves, ensuring that transformations such as translation, scaling, rotation, and shearing preserve the essential characteristics of the geometric shape. It is exploited by almost every software that uses such curves. However, this [...] Read more.

Affine invariance is one of the most fundamental properties of free-form curves, ensuring that transformations such as translation, scaling, rotation, and shearing preserve the essential characteristics of the geometric shape. It is exploited by almost every software that uses such curves. However, this property only holds in a theoretical, mathematical sense. The transformation of a curve calculated and displayed on computers using finite precision arithmetic and representation may not be fully identical to the curve calculated from the transformed control points. This deviation, even pixel-level inaccuracy, can cause problems in various applications, such as Computer-Aided Geometric Design, medical image processing, numerical computations, and font design, where this level of error can have serious consequences. In this paper, we study and demonstrate the extent and nature of this deviation using geometric and statistical tools on a cubic Bézier curve. We provide practical methods to mitigate this inaccuracy and decrease the error level using fast and simple alternative computations of the curve, taking advantage of the symmetry of the basis functions, elevating the degree of the curve, and using reparametrization to evaluate the curve on integer values. The effectiveness of these alternatives is evaluated by statistical methods based on 500,000 transformations. Full article

(This article belongs to the Special Issue Image Processing and Generation, Pattern Recognition, and Data Visualization)

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20 pages, 3020 KB

Open AccessReview

Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies

by Qinyu Ge, Yuqi Sheng, Yuting Shan, Yuwei Yang, Haohan Jiang and Ruyue Wang

Int. J. Mol. Sci. 2025, 26(22), 11076; https://doi.org/10.3390/ijms262211076 (registering DOI) - 16 Nov 2025

Abstract

Spatial transcriptomics technology represents a groundbreaking advancement in the life sciences, enabling the analysis of gene expression patterns within their native spatial context. However, inefficiencies in RNA capture from tissue samples have historically limited its effective application. This article presents a systematic review [...] Read more.

Spatial transcriptomics technology represents a groundbreaking advancement in the life sciences, enabling the analysis of gene expression patterns within their native spatial context. However, inefficiencies in RNA capture from tissue samples have historically limited its effective application. This article presents a systematic review of innovative technologies and strategies that have enhanced the efficiency of spatial transcriptome RNA capture in recent years. These strategies include nanomaterial-enhanced capture, optimization of microfluidic chips, advancements in molecular biology techniques, and computationally assisted prediction methods, among others. Through a comparative analysis of cutting-edge technologies such as Decoder-seq, Stereo-seq V2, MAGIC-seq, and MSN-seq, this article summarizes progress made in addressing challenges related to RNA diffusion, probe density, and tissue processing. Particular emphasis is placed on optimization approaches for formalin-fixed paraffin-embedded (FFPE) clinical samples and computational prediction methodologies that integrate artificial intelligence. These innovations provide valuable references for future technological development. The objective of this review is to provide researchers with a comprehensive understanding of how to enhance spatial transcriptome capture efficiency while promoting the utility of this technology in both basic research and clinical applications. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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40 pages, 8122 KB

Open AccessReview

Rational Design of Covalent Organic Frameworks for Enhanced Reticular Electrochemiluminescence and Biosensing Applications

by Bing Sun and Lin Cui

Biosensors 2025, 15(11), 760; https://doi.org/10.3390/bios15110760 (registering DOI) - 16 Nov 2025

Abstract

Electrochemiluminescence (ECL) has evolved into a powerful analytical technique due to its ultra-high sensitivity, low background noise, and precise electrochemical control. The development of efficient ECL emitters is central to advancing this technology for practical applications. Covalent organic frameworks (COFs) have recently emerged [...] Read more.

Electrochemiluminescence (ECL) has evolved into a powerful analytical technique due to its ultra-high sensitivity, low background noise, and precise electrochemical control. The development of efficient ECL emitters is central to advancing this technology for practical applications. Covalent organic frameworks (COFs) have recently emerged as promising candidates for constructing high-performance ECL systems. The tunable porosity, ordered π-conjugated structures, and versatile modular functionalities of COFs provide fast massive transport, effective electron transfer, rapid interfacial electrochemical reaction, and enhanced ECL emission performance. This review provides a comprehensive overview of the rational design strategies and structural engineering for COF-based ECL materials at the molecular level. Linkage chemistry, monomer selection (luminophores and π-conjugated non-ECL motifs), precise framework regulation, post-synthetic modification, composite formation, and other ECL enhancement strategies were discussed for developing COF-based ECL emitter. Both the incorporation of aggregation-induced emission and intramolecular charge transfer mechanisms are included to enhance ECL efficiency. Donor–acceptor conjugation, heteroatom element content, isomerism, substitution, and dimensional direction were regarded as effective strategies to regulate the electronic structure and band diagrams for designing high-performance ECL systems. The role of COFs as both active emitters and functional scaffolds for signal amplification is critically examined. Furthermore, their diverse analytical applications across biosensing, food safety, environmental monitoring, and chiral recognition are highlighted. By correlating structural features with ECL performance, this review offers insights into the design principles of next-generation reticular ECL materials and outlines future directions for their practical deployment in sensitive and selective sensing platforms. Full article

(This article belongs to the Special Issue Progress in Electrochemiluminescence Biosensors)

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20 pages, 1265 KB

Open AccessArticle

Adaptive Remaining Useful Life Estimation of Rolling Bearings Using an Incremental Unscented Kalman Filter with Nonlinear Degradation Tracking

by Xiangdian Shang, Junxing Li, Taishan Lou, Zhihua Wang, Xiaoxu Pang and Zhiwen Zhang

Machines 2025, 13(11), 1058; https://doi.org/10.3390/machines13111058 (registering DOI) - 16 Nov 2025

Abstract

In consideration of the characteristics of two-stage (stable and degraded), nonlinearity and non-stationary randomness in the full life-cycle evolution process of the rolling bearing health indicator (HI), a novel remaining useful life (RUL) prediction method for rolling bearings is proposed based on long [...] Read more.

In consideration of the characteristics of two-stage (stable and degraded), nonlinearity and non-stationary randomness in the full life-cycle evolution process of the rolling bearing health indicator (HI), a novel remaining useful life (RUL) prediction method for rolling bearings is proposed based on long short-term memory network–Mahalanobis distance (LSTM-MD) and an incremental unscented Kalman filter (IUKF). First, an LSTM-MD hybrid algorithm is developed to precisely identify the critical change point (CP) between stable operation and incipient degradation in bearing HI trajectories, effectively mitigating the susceptibility of conventional threshold-based methods to HI fluctuations. Second, during the degradation stage, a degradation analysis model based on the nonlinear Wiener process is constructed. Simultaneously, an IUKF-based RUL prediction method for bearings is proposed, which overcomes the implicit assumption of the traditional UKF method that one-step prediction can replace state prediction, particularly in scenarios with significant HI fluctuations, thereby significantly reducing prediction errors. Finally, the proposed method is validated through comparisons with traditional methods using both the XJTU-SY public dataset and a self-built bearing test dataset. The results demonstrate that compared to traditional methods, the accuracy of initial degradation change point identification is improved by 32.6%, and the root mean square error (MSE) of RUL prediction is decreased by 41.8%. Full article

(This article belongs to the Special Issue Data-Driven RUL Prediction: Innovations in Generalization, Uncertainty, and Efficiency for Industrial PHM)

21 pages, 1794 KB

Open AccessArticle

Groundwater Recharge Estimation Based on Environmental Isotopes, Chloride Mass Balance and SWAT Model in Arid Lands, Southwestern Saudi Arabia

by Milad Masoud, Maged El Osta, Jalal Basahi, Burhan Niyazi, Nassir Al-Amri, Michael Schneider, Abdulaziz Alqarawy and Riyadh Halawani

Hydrology 2025, 12(11), 306; https://doi.org/10.3390/hydrology12110306 (registering DOI) - 16 Nov 2025

Abstract

Estimated groundwater recharge is considered the essential factor for groundwater management and sustainability, especially in arid lands such as the Kingdom of Saudi Arabia (KSA). Consequently, assessing groundwater recharge is a key process for forecasting groundwater accessibility to sustain safe withdrawal. So, this [...] Read more.

Estimated groundwater recharge is considered the essential factor for groundwater management and sustainability, especially in arid lands such as the Kingdom of Saudi Arabia (KSA). Consequently, assessing groundwater recharge is a key process for forecasting groundwater accessibility to sustain safe withdrawal. So, this study focused on environmental isotopes, the chloride mass balance (CMB) method, and a SWAT model by integrating GIS with hydrological and hydrochemical techniques to detect the origin of coastal aquifer groundwater and to compute the recharging rate in the study area. This study is based on the results of chemical analysis of 78 groundwater samples and environmentally stable isotopes, including deuterium (²H) and oxygen-¹⁸O, in 29 representative samples. The results revealed that the origin of groundwater recharge comes through precipitation, where the ranges of δ¹⁸O and δ²H isotopes in the analyzed groundwater were from −1.10‰ to +1.03‰ and from −0.63‰ to 11.63‰, respectively. The CMB finding for estimating the average recharge is 3.57% of rainfall, which agrees with a previous study conducted in the wadi Qanunah basin (north of the study area), where the estimated average value of recharge was 4.25% of rainfall. Meanwhile, the estimated annual recharge using a SWAT model ranged between 1 mm and 16.5 mm/year at an average value of approximately 8.75 mm/year. The results obtained by the two techniques are different due to some reasons such as the presence of additional chloride sources, as well as evaporation. Outputs of this study will be valuable for the local community, officials, and decision-makers who are concerned with groundwater resources. Full article

16 pages, 1629 KB

Open AccessArticle

Dried Sourdough as a Functional Tool for Enhancing Carob-Enriched Wheat Bread

by Jana Zahorec, Dragana Šoronja-Simović, Jovana Petrović, Ljubica Dokić, Ivana Lončarević and Ivana Nikolić

Processes 2025, 13(11), 3699; https://doi.org/10.3390/pr13113699 (registering DOI) - 16 Nov 2025

Abstract

Functional bread development with clean-label ingredients remains a technological challenge due to the negative effects of certain functional additives on dough rheology and bread quality. The aim of this study was to evaluate the effectiveness of dried sourdough as a natural improver in [...] Read more.

Functional bread development with clean-label ingredients remains a technological challenge due to the negative effects of certain functional additives on dough rheology and bread quality. The aim of this study was to evaluate the effectiveness of dried sourdough as a natural improver in carob-enriched bread. Dough formulations included 10–20% carob flour as a partial replacement of wheat flour, with dried sourdough added as a dough improver at 5–10%. The results demonstrated that the addition of 10% dried sourdough increased maximum creep compliance of dough with 10% and 15% carob flour by 26% and 56%, respectively. The addition of 5% and 10% dried sourdough to dough with 10% carob flour decreased its Newtonian viscosity by 24% and 36%, resulting in improved dough handling. Crumb pore structure was enhanced by the addition of 5% dried sourdough, with average pore surface area increasing around 2.5 times in breads with 15% and 20% carob flour. Incorporation of dried sourdough reduced bread hardness and chewiness by up to 40% in samples with 15% carob flour and by 20–30% in samples with 20% carob flour. Sensory properties of crumb structure (crumb development, pore fineness, elasticity and crumbliness), which were adversely affected by carob flour addition, showed varying levels of improvement by the addition of dried sourdough. These results demonstrate the feasibility of using dried sourdough as a natural improver in functional bakery formulations, supporting the development of clean-label products without synthetic additives. Full article

(This article belongs to the Section Food Process Engineering)

20 pages, 4333 KB

Open AccessArticle

Hydrogen Storage Capacity and Optoelectronic Response of Mechanically and Thermally Stable Lithium-Based Tetrahydrates (LiXH₄, X = B, Al, Mn), a DFT Approach

by Ahmad Hussain, Nawishta Jabeen, Ali Yaqoob, Aseel Smerat, Muhammad Adnan Qaiser and Naflaa A. Aldawsari

Crystals 2025, 15(11), 990; https://doi.org/10.3390/cryst15110990 (registering DOI) - 16 Nov 2025

Abstract

In this work, density functional theory (DFT)-based first-principles investigations are performed by Generalized Gradient Approximation (GGA) with the Perdew–Burke–Ernzerhof (PBE) functional in the CASTEP code. These simulations provide the insights of the structural, electronic, optical, thermodynamic, mechanical and hydrogen storage gravimetric ratios of [...] Read more.

In this work, density functional theory (DFT)-based first-principles investigations are performed by Generalized Gradient Approximation (GGA) with the Perdew–Burke–Ernzerhof (PBE) functional in the CASTEP code. These simulations provide the insights of the structural, electronic, optical, thermodynamic, mechanical and hydrogen storage gravimetric ratios of lithium-based tetrahydrides (LiBH₄, LiAlH₄, and LiMnH₄) for hydrogen storage and photovoltaic (PV) applications. All these structures crystallize in orthorhombic Cmcm (No. 63) geometry with different lattice parameters and bonding strengths. Thermodynamic stabilities of hydrides are obtained by dispersion of phonons and phonon density of states. The measured band gaps of hydrides are 3.81 eV (LiBH₄), 4.60 eV (LiAlH₄), and 0.53 eV (LiMnH₄), which are calculated by GGA-PBE approach. Moreover, the optical characteristics with strong optical activity are observed from visible to ultraviolet (2 eV to 6 eV) regions. High dielectric response between 6 and 8 and absorption coefficient up to 10⁵ cm⁻¹ for hydrides are observed. Debye temperature has exceeded from 300 K to 600 K for all hydrides and saturation occurred closer to Dulong–Petit limit ~75 J mol⁻¹ K⁻¹. Mechanical stability in hydrides has been observed by Born-Hung mechanical stability criterion, demonstrating ductile nature. These natural hydrides have shown exceptional hydrogen storage capacities, as 18.5 wt% for LiBH₄, 10.6 wt% for LiAlH₄, and 6.1 wt% for LiMnH₄, are measured; these values have exceeded the U.S department of energy (DOE) targets (5.5 wt% H₂). These analyses prove that LiXH₄ (X = B, Al, Mn) hydrides are promising candidates for solid state hydrogen storage materials. Full article

(This article belongs to the Section Materials for Energy Applications)

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18 pages, 3290 KB

Open AccessArticle

Screening-Identified Oxazole-4-Carboxamide KB-2777 Exhibits In Vitro Anti-Coronavirus Activity

by Bud Jung, Woonsung Na, Minjoo Yeom, Jong-Woo Lim, Hai Quynh Do, Geonhee Jang, Min-A Ban, Ji-eun Yang, Youngjoo Byun and Daesub Song

Pharmaceutics 2025, 17(11), 1477; https://doi.org/10.3390/pharmaceutics17111477 (registering DOI) - 16 Nov 2025

Abstract

Background/Objectives: Direct-acting antivirals vary by lineage and face rapid resistance. We identified the oxazole-4-carboxamide lead KB-2777 and aimed to define its in vitro activity across α/β-coronaviruses, time-of-addition (TOA) profile, host-response signatures, and combinability with benchmark DAAs. Methods: We tested KB-2777 (≤25 μM) against [...] Read more.

Background/Objectives: Direct-acting antivirals vary by lineage and face rapid resistance. We identified the oxazole-4-carboxamide lead KB-2777 and aimed to define its in vitro activity across α/β-coronaviruses, time-of-addition (TOA) profile, host-response signatures, and combinability with benchmark DAAs. Methods: We tested KB-2777 (≤25 μM) against HCoV-NL63 (LLC-MK2), HCoV-OC43 (Vero E6; MRC-5 for transcript profiling), and PEDV (Vero E6). We quantified extracellular viral RNA by RT-qPCR at 72 h (n = 3) and confirmed activity by spike-protein immunofluorescence (IFA), cytopathic effect (CPE) protection, and TCID₅₀. We compared TOA regimens (full, pre, co, post), evaluated combinations with nirmatrelvir (NL63) or GS-441524 (OC43) using ZIP scores, and profiled infection-context transcripts (IL6, IFNB1, ISG15, NRF2/antioxidant, UPR). Results: KB-2777 reduced viral RNA with EC₅₀ 5.27 μM (NL63), 1.83 μM (OC43), and 1.59 μM (PEDV) without cytotoxicity in the tested range. In NL63 post-treatment, inhibition was minimal at 24 h but clear at 48–72 h (EC₅₀ 2.42 μM at 48 h; 5.25 μM at 72 h). TCID₅₀ decreased at 48 h (12.5–25 μM, n = 3, p < 0.0001), and IFA/CPE corroborated antiviral activity. TOA ranked full > pre ≈ post > co. Combinations were additive to synergistic (ZIP 5.16 with nirmatrelvir; 8.40 with GS-441524). In OC43-infected MRC-5 cells, KB-2777 attenuated IL6, IFNB1, ISG15, and selected UPR transcripts, with limited changes in uninfected cells (n = 3). Conclusions: KB-2777 shows reproducible cell-based anti-coronavirus activity across α/β lineages, a TOA signature consistent with early post-entry host modulation, and favorable, non-antagonistic combinability with DAAs. These findings support target deconvolution, SAR/ADME optimization, and evaluation in primary airway and in vivo models. Full article

(This article belongs to the Special Issue Recent Advances in Nanotechnology Therapeutics)

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18 pages, 381 KB

Open AccessArticle

Examining Coherence in Preservice Mathematics Teachers’ Noticing of Students’ Thinking About Classification in Geometry

by Hélia Oliveira, Fernanda Caroline Cybulski and Márcia Cristina de Costa Trindade Cyrino

Educ. Sci. 2025, 15(11), 1543; https://doi.org/10.3390/educsci15111543 (registering DOI) - 16 Nov 2025

Abstract

This study aims to examine the thematic coherence among preservice mathematics teachers’ noticing components when analysing students’ thinking about classification in geometry, as well as the actions they propose to respond to those students. The research was conducted within an instructional module on [...] Read more.

This study aims to examine the thematic coherence among preservice mathematics teachers’ noticing components when analysing students’ thinking about classification in geometry, as well as the actions they propose to respond to those students. The research was conducted within an instructional module on the teaching of geometry, embedded in a mathematics methods course of a master’s programme. The module was designed to foster preservice secondary mathematics teachers’ pedagogical content knowledge alongside their noticing skills. Considering the mathematics education literature about the process of classification in geometry and the components of noticing, an analytical framework was developed to identify the thematic coherence of preservice mathematics teachers’ noticing of students’ thinking from two fictitious classroom episodes. Data came from individual written responses of 12 preservice mathematics teachers to an instructional task. The results overall patterns reveal strong thematic coherence in attending and interpreting, with responding also showing substantial, though comparatively lower, coherence. The findings also indicate that preservice teachers frequently proposed coherent responses that were both specific and may foster students’ conceptual understanding. This study highlights that promoting coherence in professional noticing, particularly within the responding component, is vital for cultivating teaching practices that are both responsive and conceptually grounded. Full article

(This article belongs to the Special Issue Different Approaches in Mathematics Teacher Education)

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12 pages, 212 KB

Open AccessArticle

Facilitators and Barriers to the Implementation of Family Integrated Care in Ontario Level II Neonatal Intensive Care Units

by Ayah Al Bizri, Mariana Bueno, Vibhuti Shah, Fabiana Bacchini, Douglas M. Campbell, Karen M. Benzies and Karel O’Brien

Children 2025, 12(11), 1548; https://doi.org/10.3390/children12111548 (registering DOI) - 16 Nov 2025

Abstract

Background/Objectives: In Ontario, approximately 8% (11,000) of infants are born preterm (22–<37 weeks gestation) each year. Many of these infants are cared for in a Level II Neonatal Intensive Care Unit (NICU). Family Integrated Care (FICare), an innovative model of care, aims [...] Read more.

Background/Objectives: In Ontario, approximately 8% (11,000) of infants are born preterm (22–<37 weeks gestation) each year. Many of these infants are cared for in a Level II Neonatal Intensive Care Unit (NICU). Family Integrated Care (FICare), an innovative model of care, aims to facilitate the involvement of parents in the care of their infants in NICUs. The aim of this study was to gain a better understanding of the general and specific needs of Level II NICUs in Ontario prior to implementation of FICare. Methods: Using a cross-sectional study design, two surveys (leadership and site resources) were developed using the Consolidated Framework for Implementation Science Research’s innovation, inner setting, and outer setting constructs and distributed to Level II NICUs medical and nursing leaders. Results: The surveys were sent to 44 Level II NICUs in Ontario, of which 24 hospitals (55%) responded. Key facilitators to implementation of FICare in Level II hospitals in Ontario were leadership interest, availability of staff and parent volunteers, and existing policies to support implementation. The identified barriers were lack of financial resources for new initiatives, skepticism in FICare’s ability to save costs, need for tailored implementation due to variability in NICU characteristics, and the lack of environmental support for prolonged parental presence. Conclusions: This study has confirmed the interest of many Ontario level II NICUs in implementing FICare and variability in their readiness for implementation based on the identified facilitators and barriers. Full article

(This article belongs to the Section Pediatric Neonatology)

24 pages, 5398 KB

Open AccessArticle

Robust Dolphin Whistle Detection Based on Dually-Regularized Non-Negative Matrix Factorization in Passive Acoustic Monitoring

by Lei Li, Xinrui Shao, Shuping Huang, Xuerong Cui, Jiang Zhu and Songzuo Liu

J. Mar. Sci. Eng. 2025, 13(11), 2164; https://doi.org/10.3390/jmse13112164 (registering DOI) - 16 Nov 2025

Abstract

Underwater passive acoustic monitoring (PAM) serves as a core approach pervasively applied to the long-term, non-invasive detection of biological acoustic signals. Dolphin whistles serve as a fundamental aspect of vocal communication, exhibiting intricate frequency-modulated structures. Robust detection of these whistles is essential for [...] Read more.

Underwater passive acoustic monitoring (PAM) serves as a core approach pervasively applied to the long-term, non-invasive detection of biological acoustic signals. Dolphin whistles serve as a fundamental aspect of vocal communication, exhibiting intricate frequency-modulated structures. Robust detection of these whistles is essential for dolphin species diversity conservation, yet performance is frequently compromised by underwater background noise, leading to significant degradation in detection reliability. To address this issue, this paper presents an unsupervised enhancement method based on Dually-Regularized Non-Negative Matrix Factorization (DR-NMF). Beyond a standard data fidelity term, the proposed framework integrates two specialized regularizers, including Overlapping Group Shrinkage and Group Lasso. The former promotes time–frequency continuity of whistle ridges, while the latter adaptively eliminates redundant bases, achieving an improved trade-off between structural integrity and noise suppression. The optimization procedure employed a combination of majorization–minimization, iteratively reweighted least squares, and proximal gradient techniques, all of which were implemented within an alternating minimization scheme featuring nested inner–outer iterations. This architecture ensures stable convergence and computational practicality. Extensive experimental evaluations under diverse low signal-to-noise ratio (SNR) conditions reveal that the proposed method achieves a substantial improvement in recall without compromising precision, resulting in consistent enhancements in frame-level

F_{1}

-scores. When applied to real-world dolphin whistle recordings, our method outperforms existing baseline approaches, demonstrating remarkable robustness in detecting whistle signals when amidst challenging marine environmental noise. Full article

(This article belongs to the Section Ocean Engineering)

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21 pages, 5613 KB

Open AccessArticle

Thermo-Economic Investigation of an ORC-Based Carnot Battery Driven by the Ocean Temperature Gradient

by Liuchen Liu, Yining Yang and Jiarui Dai

Energies 2025, 18(22), 6005; https://doi.org/10.3390/en18226005 (registering DOI) - 16 Nov 2025

Abstract

Carnot Batteries with thermal integration stand as one of the most promising approaches to tackling contemporary global energy problems. Currently, research on Carnot Battery systems utilizing the ocean thermal gradient is still in its early stages. This paper establishes a holistic thermo-economic model [...] Read more.

Carnot Batteries with thermal integration stand as one of the most promising approaches to tackling contemporary global energy problems. Currently, research on Carnot Battery systems utilizing the ocean thermal gradient is still in its early stages. This paper establishes a holistic thermo-economic model to assess the system’s performance. Through working fluid screening and subsequent multi-objective optimization, this study identifies the optimal working fluid and clarifies the system’s thermal economy at the optimal design point. With round-trip efficiency and total cost as metrics, a sensitivity analysis identified key parameter effects on the system. This was followed by a multi-objective optimization, where the TOPSIS method selected the optimal solution. It was found that, when Ammonia and R1234yf were used as the working fluids in the RC and ORC sub-cycles, respectively, the system can achieve peak performances of 71.79% round-trip efficiency and 36.24% exergy efficiency. Moreover, the RC evaporation temperature exerts the most significant influence on the overall thermodynamic performance. Multi-objective optimization successfully identified a balanced thermo-economic design, yielding an optimal solution with a round-trip efficiency of 65.30% at a total cost of USD 65.90 M. These results offer critical insights for the design and optimization of this promising ocean thermal-powered Carnot Battery system. Full article

(This article belongs to the Section K: State-of-the-Art Energy Related Technologies)

21 pages, 1177 KB

Open AccessArticle

Altered Co-Expression Patterns of Mitochondrial NADH-Dehydrogenase Genes in the Prefrontal Cortex of Rodent ADHD Models

by Polina A. Sylko, Arina A. Gromova, Zoia S. Fesenko, Evgeny V. Kanov, Anna B. Volnova, Raul R. Gainetdinov and Anastasia N. Vaganova

Int. J. Mol. Sci. 2025, 26(22), 11079; https://doi.org/10.3390/ijms262211079 (registering DOI) - 16 Nov 2025

Abstract

Altered mitochondrial function is implicated in disorders characterized by prefrontal cortex activation deficits, including attention deficit hyperactivity disorder (ADHD). The expression of mitochondrial DNA-coded respiratory chain complex I genes (ND1–ND6) in the prefrontal cortex of ADHD animal models was estimated in [...] Read more.

Altered mitochondrial function is implicated in disorders characterized by prefrontal cortex activation deficits, including attention deficit hyperactivity disorder (ADHD). The expression of mitochondrial DNA-coded respiratory chain complex I genes (ND1–ND6) in the prefrontal cortex of ADHD animal models was estimated in the present study. ND gene expression was assessed in two publicly available datasets: GSE117357 (Adgrl3 knockout mice) and GSE173926 (MYT1L heterozygous knockout mice). Additionally, we measured NDs gene expression via qPCR in dopamine transporter knockout (DAT-KO) rats and their heterozygous (DAT-Het) littermates. Transcriptomic analysis revealed consistent ND1–ND6 expression profiles across both datasets, and co-expression among ND genes was significantly enhanced in ADHD models compared to wild-type controls. Whole-transcriptome analysis identified associations between ND3 and ND4L expression and genes involved in neural tissue-specific processes, exclusively in ADHD models. In DAT-KO and DAT-Het rats, NDs gene co-expression increased. Furthermore, in DAT-Het rats, which do not exhibit hyperactivity, the upregulation of ND4L expression relative to wild-type littermates was demonstrated. The observed changes in mitochondrial complex I gene co-expression in ADHD models suggest mitochondria may serve as a prospective target for adjuvant therapy. These findings highlight the need for further investigation into mitochondrial contributions to ADHD pathophysiology. Full article

(This article belongs to the Special Issue New Insights in Translational Bioinformatics: Second Edition)

16 pages, 1775 KB

Open AccessArticle

Algae-Derived C-Phycocyanin Mitigates AGE–RAGE-Induced ER Stress and Mitochondrial Apoptosis: Implications for Diabetes-Associated Neurodegeneration

by Mei Chou Lai, Wayne Young Liu, Yu-Cheng Tzeng and I-Min Liu

Int. J. Mol. Sci. 2025, 26(22), 11077; https://doi.org/10.3390/ijms262211077 (registering DOI) - 16 Nov 2025

Abstract

Impaired glucose metabolism elevates the risk of neurodegenerative diseases by activating the receptor for advanced glycation end products (RAGE), thereby promoting oxidative and endoplasmic reticulum (ER) stress that leads to neuronal apoptosis. C-phycocyanin (C-PC), a natural pigment–protein complex derived from algae, possesses potent [...] Read more.

Impaired glucose metabolism elevates the risk of neurodegenerative diseases by activating the receptor for advanced glycation end products (RAGE), thereby promoting oxidative and endoplasmic reticulum (ER) stress that leads to neuronal apoptosis. C-phycocyanin (C-PC), a natural pigment–protein complex derived from algae, possesses potent antioxidant and antiglycation properties; however, its capacity to modulate RAGE-mediated neurotoxicity remains to be fully elucidated. In this study, we established a RAGE-driven neuronal injury model by exposing differentiated SH-SY5Y cells to advanced glycation end products (AGEs; 300 μg/mL). Pretreatment with C-PC (15–50 μmol/L) improved cell viability, preserved neuronal morphology, and attenuated AGEs-induced oxidative stress, as indicated by reduced intracellular reactive oxygen species and mitochondrial superoxide levels. Furthermore, C-PC inhibited activation of the PERK-CHOP pathway, and upregulated Bcl-2 while downregulating Bax, thereby preventing cytochrome c release and reducing caspase-9/3 activation as well as apoptotic DNA fragmentation. These neuroprotective effects of C-PC were comparable to those observed with the selective RAGE antagonist FPS-ZM1. In conclusion, our findings demonstrate that C-PC confers robust protection against AGEs-induced neuronal injury by suppressing oxidative and ER stress pathways downstream of RAGE activation, highlighting its potential as a natural modulator of the AGE–RAGE axis for the prevention or treatment of diabetes-associated neurodegeneration. Full article

(This article belongs to the Special Issue Algae-Derived Bioactives: Key Molecular Interactions Govern High-Value Applications)

38 pages, 5160 KB

Open AccessArticle

YOLOv11-Safe: An Explainable AI Framework for Data-Driven Building Safety Evaluation and Design Optimization in University Campuses

by Jing Hou, Yanfeng Hu, Bingchun Jiang, Zhoulin Chang, Mingjie Cao and Beili Wang

Buildings 2025, 15(22), 4125; https://doi.org/10.3390/buildings15224125 (registering DOI) - 16 Nov 2025

Abstract

Campus buildings often present hidden safety risks such as falls and wheelchair instabilities, which are closely related to architectural layout, material selection, and accessibility design. This study develops YOLOv11-Safe, an attention-enhanced and geometry-aware framework that functions as both a detection model and a [...] Read more.

Campus buildings often present hidden safety risks such as falls and wheelchair instabilities, which are closely related to architectural layout, material selection, and accessibility design. This study develops YOLOv11-Safe, an attention-enhanced and geometry-aware framework that functions as both a detection model and a spatial diagnostic tool for building safety assessment. The framework integrates a modified SimAM attention mechanism and a normalized Wasserstein distance (NWD) loss to improve detection accuracy in complex indoor environments, trained on a dataset of 1000 annotated images covering fall and wheelchair accident scenarios. To interpret spatial risk patterns, a Random Forest classifier combined with SHAP analysis was applied to quantify the contribution of five architectural–behavioral variables: body–ground contact ratio (BGCR), accessibility index (AI), event duration (D), body posture angle (PA), and spatial density (SD). Results show that BGCR and AI dominate the risk-level prediction, while D, PA, and SD refine boundary conditions. Scene-based verification further demonstrated that the framework accurately localized unsafe features—such as uneven drainage edges and discontinuous handrails—and translated them into actionable design feedback. The proposed approach thus links deep-learning detection with interpretable spatial analysis, offering a quantitative foundation for evidence-based architectural safety optimization in university campuses. Full article

(This article belongs to the Special Issue Practice and Application of Artificial Intelligence in Built Environment)

24 pages, 3095 KB

Open AccessArticle

Sustainable Stabilization of Expansive Soils Using Metakaolin and Cement: Evaluation Through Soil–Water Characteristic Curve Analysis

by Grzegorz Kacprzak, Muluager Bewket Demlew, Semachew Molla Kassa and Betelhem Zewdu Wubineh

Sustainability 2025, 17(22), 10249; https://doi.org/10.3390/su172210249 (registering DOI) - 16 Nov 2025

Abstract

The study examines the use of environmentally friendly materials, such as metakaolin and cement, in various proportions to stabilize expansive plastic soils and assess their effects on the soil–water characteristic curve (SWCC). Metakaolin, a supplementary cementitious material with a lower carbon footprint than [...] Read more.

The study examines the use of environmentally friendly materials, such as metakaolin and cement, in various proportions to stabilize expansive plastic soils and assess their effects on the soil–water characteristic curve (SWCC). Metakaolin, a supplementary cementitious material with a lower carbon footprint than ordinary cement, enhances soil behavior through pozzolanic reactions. The incorporation of metakaolin and cement reduced the fitting parameter “a,” linked to the air-entry value (AEV), indicating that treated soils desaturate at lower suction values due to improved aggregate formation and pore structure. With increasing stabilizer content, the SWCC shifted toward lower suction values, reflecting improved hydraulic performance and reduced moisture sensitivity. The fitting parameter “n,” representing desaturation capacity and pore size distribution, increased with stabilizer content, suggesting a more uniform and durable soil structure. Overall, using metakaolin and cement enhances expansive soils’ structural and hydraulic behavior while conserving cement and reducing CO₂ emissions. Machine learning models, Random Forest (RF), Decision Tree (DT), and Artificial Neural Network (ANN), were developed to predict SWCC. The RF model achieved the best accuracy (R² = 0.9063, adjusted R² = 0.8631), demonstrating the reliability of ML in evaluating green soil stabilization methods. Full article

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29 pages, 19578 KB

Open AccessArticle

Effect of Sedimentary Environment on Mudrock Lithofacies and Organic Matter Enrichment in a Freshwater Lacustrine Basin: Insight from the Triassic Chang 7 Member in the Ordos Basin, China

by Meizhou Zhang, Xiaomin Zhu, Wenming Ji, Xingyue Lin and Lei Ye

Sustainability 2025, 17(22), 10248; https://doi.org/10.3390/su172210248 (registering DOI) - 16 Nov 2025

Abstract

Gradually replacing fossil fuels with renewable energy constitutes a long-term strategy for achieving sustainable development. In the short term, it is necessary to explore unconventional oil and gas resources to support current economic sustainability and to secure essential time for the energy transition. [...] Read more.

Gradually replacing fossil fuels with renewable energy constitutes a long-term strategy for achieving sustainable development. In the short term, it is necessary to explore unconventional oil and gas resources to support current economic sustainability and to secure essential time for the energy transition. With the continuous growth in global energy demand, unconventional resources such as shale oil and shale gas have become important alternative energy sources. Lacustrine mudrock successions demonstrate significant potential for unconventional oil and gas resources. However, the unclear understanding of how paleoenvironmental evolution influences lithofacies and organic matter enrichment restricts the optimization of shale oil reservoirs and evaluation of shale oil resources, thereby hindering the progress of lacustrine shale oil exploration and development. The mudrocks in the Chang 7 Member of the Triassic Yanchang Formation, Ordos Basin, were deposited in a pro-delta to a deep lacustrine environment and are rich in shale oil resources. Through petrographic, sedimentological, sequence stratigraphic, and geochemical analyses, this study reveals how the evolution of the paleoenvironment controlled the development of mudrocks and the enrichment of organic matter, and establishes a sedimentary model for freshwater lacustrine systems. Six lithofacies have been identified within the mudrock interval of the Chang 7 Member. According to the T-R (transgressive–regressive) sequence model, the Chang 7 Member can be subdivided into three fourth-order sequences, termed Parasequence Set 1–3 (PPS1–3). Mudrock is predominantly developed in the fourth-order sequences PSS1 and PSS2. The PSS1 and the lower part of PSS2 consist of lithofacies 1–4, representing semi-deep to deep lacustrine deposits. The upper part of PSS2 develops lithofacies 5, representing shallow lacustrine to pro-delta deposits. Fluctuations of the lake level controlled the vertical stacking of lithofacies and the transition in depositional mechanisms. During lake-level rise, bottom currents shifted to suspension settling, whereas the opposite occurred during lake-level fall. The organic matter is derived from algae, and its enrichment is jointly controlled by productivity and the redox conditions. Volcanic–hydrothermal activity and a humid climate promoted high productivity in the water body. This high productivity promotes dyoxic conditions in the bottom water. Fourth-order relative lake-level fluctuations also influence organic matter enrichment. During lake-level rise, increased productivity coupled with reduced consumption and dilution favors organic matter enrichment. Conversely, organic matter accumulation is inhibited during lake-level fall. Ultimately, a depositional model for a freshwater lacustrine basin under a humid to semi-humid climatic background was established. This paper elucidates the influence of sedimentary environment on mudrock lithofacies and organic matter enrichment, providing a theoretical basis for optimizing shale oil reservoir selection and resource assessment, thereby promoting efficient exploration and low-carbon development of shale oil in lacustrine basins. Full article

(This article belongs to the Topic Global Unconventional Shale Oil and Gas: Geological Mechanisms, Technological Innovations, and Economic–Environmental Sustainability Assessment)

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