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by Zhiwei Tian, Zhongqi Zhao, Marco Aoqi Rausch, Christian Behm, Dino Tur, Hassan Ali Shokoohi-Tabrizi, Oleh Andrukhov and Xiaohui Rausch-Fan

Int. J. Mol. Sci. 2025, 26(2), 672; https://doi.org/10.3390/ijms26020672 (registering DOI) - 15 Jan 2025

Abstract

Over the past few years, biomaterial-based periodontal tissue engineering has gained popularity. An ideal biomaterial for treating periodontal defects is expected to stimulate periodontal-derived cells, allowing them to contribute most efficiently to tissue reconstruction. The present study focuses on evaluating the in vitro behavior of human periodontal ligament-derived stromal cells (hPDL-MSCs) when cultured on gelatin/Polycaprolactone prototype (GPP) and volume-stable collagen matrix (VSCM). Cells were cultured onto the GPP, VSCM, or tissue culture plate (TCP) for 3, 7, and 14 days. Cell morphology, adhesion, proliferation/viability, the gene expression of Collagen type I, alpha1 (COL1A1), Vascular endothelial growth factor A (VEGF-A), Periostin (POSTN), Cementum protein 1 (CEMP1), Cementum attachment protein (CAP), Interleukin 8 (IL-8) and Osteocalcin (OCN), and the levels of VEGF-A and IL-8 proteins were investigated. hPDL-MSCs attached to both biomaterials exhibited a different morphology compared to TCP. GPP exhibited stronger capabilities in enhancing cell viability and metabolic activity compared to VSCM. In most cases, the expression of all investigated genes, except POSTN, was stimulated by both materials, with GPP having a superior effect on COL1A1 and VEGF-A, and VSCM on OCN. The IL-8 protein production was slightly higher in cells grown on VSCM. GPP also exhibited the ability to absorb VEGF-A protein. The gene expression of POSTN was promoted by GPP and slightly suppressed by VSCM. In summary, our findings indicate that GPP electrospun nanofibers effectively promote the functional performance of PDLSCs in periodontal regeneration, particularly in the periodontal ligament and cementum compartment. Full article

(This article belongs to the Special Issue Periodontitis: Advances in Mechanisms, Treatment and Prevention)

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Colonization and patterns of cells observation on two scaffolds through SEM. hPDL-MSCs were grown on GPP (a–f) or VSCM (g–l) for 3, 7, or 14 days. The images were taken at magnification 400-fold (left panels) or 1500-fold (right panels). Scale bars correspond to 100 µm and 20 µm, respectively. The yellow arrows indicate cells. GPP demonstrated nanoscale, microscale fiber, and VSCM a porous structure; cell attachment and growth were well-established on both substrates. Full article ">Figure 2
The morphological characteristics of hPDL-MSCs observed on different surface types. hPDL-MSCs were grown on GPP (a,d,g), VSCM (b,e,h) or TCP (c,f,i) for 3, 7, or 14 days and stained with a focal adhesion staining kit. F-actin was stained with TRITC-conjugated phalloidin (red) and the nucleus with DAPI (blue).The images were captured at 100-fold magnification; scale bars correspond to 50 µm. The cells exhibited different morphologies and distributions on the three different materials. Full article ">Figure 3
Assessment of the proliferation/viability of hPDL-MSCs when cultured on GPP, VSCM, and TCP surfaces. Cells were cultured on different substrates for 3, 7, and 14 days, and their proliferation/viability was measured using a CCK-8 assay. The Y-axis shows the OD values measured at 450 nm. Data are presented as mean ± SD of five independent experiments with hPDL-MSCs isolated from five different donors. * and **—significantly different between substrates with p < 0.05 and 0.01, respectively. #—significantly different between day 3 and day 7 on the same substrate. †—significantly different between day 7 and day 14 on the same substrate. Full article ">Figure 4
Metabolic activity of hPDL-MSCs grown on GPP, VSCM, and TCP. Cells were cultured on different substrates for 3, 7, and 14 days, and their metabolic activity was measured using a resazurin-based assay. The Y-axis shows the fluorescence measured with the excitation settings at 540/34 nm and emission at 600/40 nm. Data are presented as mean ± SD of five independent experiments with hPDL-MSCs isolated from five different donors. * and **—significantly different between substrates with p < 0.05 and 0.01, respectively. #—significantly different between day 3 and day 7 on the same substrate. †—significantly different between day 7 and day 14 on the same substrate. Full article ">Figure 5
Analysis of gene expression for diverse biomarkers in hPDL-MSCs cultured on different types of materials. hPDL-MSCs were cultured on different substrates for 3, 7, and 14 days, and the gene expression of COL1A1 (a), POSTN (b), CEMP-1 (c), CAP (d), VEGF-A (e), IL-8 (f), and OCN (g) was measured by qPCR. Y-axes show n-fold expression of the corresponding gene in relation to that measured on tissue culture plastic on day 3 and calculated by a 2−ΔΔCt method using GAPDH as a housekeeping gene. Comparison results of OCN was ultimately limited to day 14, as its values were too low for reliable detection at early time points. Data are presented as mean ± SD of five independent experiments with hPDL-MSCs isolated from five different donors. * and **—significantly different between substrates with p < 0.05 and 0.01, respectively. Full article ">Figure 6
IL-8 protein production by hPDL-MSCs grown on three types of substrates. The content of IL-8 in the conditioned media was measured by ELISA after 3, 7, and 14 days of culture. Data are presented as mean ± SD of five independent experiments with hPDL-MSCs isolated from five different donors. * and **—significantly different between substrates with p < 0.05 and 0.01, respectively. Full article ">Figure 7
VEGF protein production by cells and absorption by materials. (a)—hPDL-MSCs were cultured on different substrates for 3, 7, and 14 days, and the content of VEGF in conditioned media was measured by ELISA. (b)—the scaffolds were incubated in a medium containing 10 ng/mL recombinant VEGF protein for 6 h at 37 °C, and the content of VEGF in conditioned media was determined by ELISA at the end of the incubation. (c)—after incubation with recombinant VEGF, the scaffolds were incubated for an additional 24 h in a medium, and the amount of released VEGF was measured by ELISA. Data are presented as mean ± SD of five independent experiments with hPDL-MSCs isolated from five different donors. * and **—significantly different between substrates with p < 0.05 and 0.01, respectively. Full article ">

24 pages, 21684 KiB

Open AccessArticle

An Effective Iterative Process Utilizing Transcendental Sine Functions for the Generation of Julia and Mandelbrot Sets

by Khairul Habib Alam, Yumnam Rohen, Anita Tomar, Naeem Saleem, Maggie Aphane and Asima Razzaque

Fractal Fract. 2025, 9(1), 40; https://doi.org/10.3390/fractalfract9010040 (registering DOI) - 15 Jan 2025

Abstract

This study presents an innovative iterative method designed to approximate common fixed points of generalized contractive mappings. We provide theorems that confirm the convergence and stability of the proposed iteration scheme, further illustrated through examples and visual demonstrations. Moreover, we apply s-convexity to the iteration procedure to construct orbits under convexity conditions, and we present a theorem that determines the condition when a sequence diverges to infinity, known as the escape criterion, for the transcendental sine function

sin (u^{m}) - α u + β

, where

u, α,

β \in C

and

m \geq 2

. Additionally, we generate chaotic fractals for this orbit, governed by escape criteria, with numerical examples implemented using MATHEMATICA software. Visual representations are included to demonstrate how various parameters influence the coloration and dynamics of the fractals. Furthermore, we observe that enlarging the Mandelbrot set near its petal edges reveals the Julia set, indicating that every point in the Mandelbrot set contains substantial data corresponding to the Julia set’s structure. Full article

(This article belongs to the Special Issue Fixed Point Theory and Fractals)

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12 pages, 862 KiB

Open AccessArticle

The Feasibility of an Online Lifestyle Intervention During the COVID-19 Pandemic on the BMI Z-Score of Mexican Schoolchildren: A Pilot Randomized Controlled Trial

by Diana L. Ramírez-Rivera, Teresita Martínez-Contreras, Alma L. Ruelas, Trinidad Quizán-Plata, Julián Esparza-Romero, Michelle M. Haby and Rolando G. Díaz-Zavala

Obesities 2025, 5(1), 3; https://doi.org/10.3390/obesities5010003 (registering DOI) - 15 Jan 2025

Abstract

The COVID-19 pandemic was a risky period for childhood obesity, due to the increase in unhealthy behaviors. Online interventions could prevent this problem. The aim of this study was to evaluate the feasibility and explore the effect of an online program on the BMI z-score of Mexican schoolchildren at 4 months during the pandemic. A pilot randomized controlled trial was conducted with 54 children. The intervention included three online sessions per week of nutrition and physical activity, as well as nutrition information for parents during 4 months. The control group received one nutrition digital brochure. Of the schoolchildren enrolled, 87% completed the study, and the intervention group attended 46% of the classes. At the end of the intervention, no significant difference between groups in the BMI z-score was observed (−0.02, 95% CI −0.19 to 0.15). However, the intervention group improved their quality of life and daily fruit consumption. This online intervention implemented during the COVID-19 pandemic was feasible, and the exploratory analysis showed positive trends in quality of life and daily fruit consumption but not in the BMI z-score and other secondary variables of Mexican schoolchildren. Additional strategies may be needed to improve attendance in online interventions and their impact on BMI in this age group. Full article

(This article belongs to the Special Issue Obesity and Its Comorbidities: Prevention and Therapy)

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Flow diagram of participants recruited for the 4-month pilot randomized controlled trial during the COVID-19 pandemic. Full article ">Figure 2
Changes in BMI z-score at four months of intervention. Note: means and CI 95% were used to build this figure. Full article ">

23 pages, 2583 KiB

Open AccessArticle

Pearl Millet Cover Crop Extract Inhibits the Development of the Weed Ipomoea grandifolia by Inducing Oxidative Stress in Primary Roots and Affecting Photosynthesis Efficiency

by Gislaine Cristiane Mantovanelli, Adriano Antônio Silva, Letycia Lopes Ricardo, Fernanda Lima Kagami, Jéssica Dario de Almeida, Mauro Cezar Barbosa, Márcio Shigueaki Mito, Isabela de Carvalho Contesoto, Paulo Vinicius Moreira da Costa Menezes, Gabriel Felipe Stulp, Beatriz Pereira Moreno, Francielli Alana Pereira Valeze, Rubem Silvério de Oliveira Junior, Debora Cristina Baldoqui and Emy Luiza Ishii Iwamoto

Plants 2025, 14(2), 222; https://doi.org/10.3390/plants14020222 (registering DOI) - 15 Jan 2025

Abstract

The cover crop Pennisetum glaucum (L.) R.Br. (pearl millet) reduces the emergence of weed species in the field through a mechanism that is not fully known. The identification of the allelopathic activity of pearl millet can contribute to the development of no-tillage techniques to produce crops without or with low doses of herbicides. This issue was investigated by testing the effects of extracts from the aerial parts of pearl millet on the germination and growth of the weeds Bidens pilosa L., Euphorbia heterophylla L., and Ipomoea grandifolia (Dammer) O’Donell under laboratory conditions. The ethyl acetate fraction (EAF) at a concentration of 2000 µg mL⁻¹ was inactive on Bidens pilosa; it inhibited root length (−72%) and seedling fresh weight (−41%) of E. heterophylla, and in I. grandifolia the length of primary root and aerial parts and the fresh and dry weight of seedlings were reduced by 63%, 32%, 25%, and 12%, respectively. In roots of I. grandifolia seedlings, at the initial development stage, EAF induced oxidative stress and increased electrolyte leakage. At the juvenile vegetative stage, a lower concentration of EAF (250 µg mL⁻¹) induced a stimulus in seedling growth (+60% in root length and +23% in aerial parts length) that was associated with increased photosynthetic efficiency. However, at higher concentrations (1000 µg mL⁻¹), it induced the opposite effects, inhibiting the growth of root (−41%) and aerial parts (−25%), with reduced superoxide dismutase activity and photosynthetic efficiency. The stilbenoid pallidol was identified as the main compound in EAF. The allelopathic activity of pearl millet may be attributed, at least in part, to the impairment of energy metabolism and the induction of oxidative stress in weed seedlings, with pallidol possibly involved in this action. Such findings demonstrated that the application of the EAF extract from pearl millet can be a natural and renewable alternative tool for weed control. Full article

(This article belongs to the Special Issue Allelopathy in Agroecosystems)

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18 pages, 22026 KiB

Open AccessArticle

The Effects of Pilot Structure on the Lean Ignition Characteristics of the Internally Staged Combustor

by Zhengyan Guo, Yan Lu, Jingtao Yuan, Pimin Chen, Qibin Zhang and Wei Fan

Energies 2025, 18(2), 349; https://doi.org/10.3390/en18020349 (registering DOI) - 15 Jan 2025

Abstract

In order to explore the influence of pilot structure on the lean ignition characteristics in a certain type of internally staged combustor, the current study was conducted on the effects of the auxiliary fuel nozzle diameter, the rotating direction of the pilot swirler, and the swirl number on the lean ignition fuel–gas ratio limit, combining numerical simulation and experimental validation. The optimization potential of the mixing structure of this type of internally staged combustor was further explored. It indicated that the lean ignition fuel–gas ratio limit was significantly influenced by the diameter of the auxiliary fuel nozzles the swirl number of the pilot swirler and the combination of the same rotating direction for both pilot swirlers, while the mass flow rate of air was constant. Increasing the diameter of the auxiliary fuel path nozzles (0.4~0.6 mm) and having excessively higher or lower swirl numbers of the pilot module primary swirlers are not conducive to broadening the lean ignition boundary. Compared with the two-stage pilot swirler with the same rotation combination, the fuel–gas ignition performance of the two-stage pilot swirler with the opposite rotation combination is better. Under the typical working conditions (the air mass flow rate is 46.7 g/s and the ignition energy is 4 J), for a pilot swirler with a rotating direction opposite to the main swirler, the diameter of the auxiliary fuel nozzles is 0.2 mm, the swirl number of first-stage of pilot swirler is 1.4, and the lean ignition fuel–air ratio was reduced to 0.0121, which is 32.78% lower than the baseline scheme, which further broadens the lean ignition boundary of the centrally staged combustion chamber. Full article

(This article belongs to the Section I2: Energy and Combustion Science)

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16 pages, 7348 KiB

Open AccessArticle

Optimization of Urban Fire Emergency Resource Allocation Based on Pre-Allocated Swarm Algorithm

by Xiaolei Zhang, Kaigong Zhao, Shang Gao and Changming Li

Fire 2025, 8(1), 27; https://doi.org/10.3390/fire8010027 (registering DOI) - 15 Jan 2025

Abstract

As a high-frequency disaster with potentially devastating consequences, urban fires not only threaten the lives of city residents but can also lead to severe property losses, especially for hazardous chemical leaking scenarios. Quick and scientific decision-making regarding resource allocation during urban fire emergency responses is crucial for reducing disaster damages. Based on several key factors such as the number of trapped individuals and hazardous chemical leaks during the early stages of an incident, an emergency weight system for resource allocation is proposed to effectively address complex situations. In addition, a multi-objective optimization model is built to achieve the shortest response time for emergency rescue teams and the lowest cost for material transportation. Additionally, a pre-allocated bee swarm algorithm is introduced to mitigate the issue of local incident points being unable to participate in rescue due to low weights, and a comparison of traditional genetic algorithms and particle swarm optimization algorithms is conducted. Experiments conducted in a virtual urban fire scenario validate the effectiveness of the proposed model. The results demonstrate that the proposed model can effectively achieve the dual goals of minimizing transportation time and costs. Furthermore, the bee swarm algorithm exhibits advantages in convergence speed, allowing for the faster identification of ideal solutions, thereby providing a scientific basis for the rapid allocation of resources in urban fire emergency rescues. Full article

(This article belongs to the Special Issue Advances in Industrial Fire and Urban Fire Research: 2nd Edition)

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22 pages, 3116 KiB

Open AccessArticle

Verification and Usability of Indoor Air Quality Monitoring Tools in the Framework of Health-Related Studies

by Alicia Aguado, Sandra Rodríguez-Sufuentes, Francisco Verdugo, Alberto Rodríguez-López, María Figols, Johannes Dalheimer, Alba Gómez-López, Rubèn González-Colom, Artur Badyda and Jose Fermoso

Air 2025, 3(1), 3; https://doi.org/10.3390/air3010003 - 14 Jan 2025

Abstract

Indoor air quality (IAQ) significantly impacts human health, particularly in enclosed spaces where people spend most of their time. This study evaluates the performance of low-cost IAQ sensors, focusing on their ability to measure carbon dioxide (CO₂) and particulate matter (PM) under real-world conditions. Measurements provided by these sensors were verified against calibrated reference equipment. The study utilized two commercial devices from inBiot and Kaiterra, comparing their outputs to a reference sensor across a range of CO₂ concentrations (500–1200 ppm) and environmental conditions (21–25 °C, 27–92% RH). Data were analyzed for relative error, temporal stability, and reproducibility. Results indicate strong correlation between low-cost sensors (LCSs) and the reference sensor at lower CO₂ concentrations, with minor deviations at higher levels. Environmental conditions had minimal impact on sensor performance, highlighting robustness to temperature and humidity within the tested ranges. For PM measurements, low-cost sensors effectively tracked trends, but inaccuracies increased with particle concentration. Overall, these findings support the feasibility of using low-cost sensors for non-critical IAQ monitoring, offering an affordable alternative for tracking CO₂ and PM trends. Additionally, LCSs can assess long-term exposure to contaminants, providing insights into potential health risks and useful information for non-expert users. Full article

(This article belongs to the Special Issue Indoor Air Quality: Airborne Disease Measurement, Control, Mitigation and Disinfection)

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23 pages, 20381 KiB

Open AccessArticle

In and out of Replication Stress: PCNA/RPA1-Based Dynamics of Fork Stalling and Restart in the Same Cell

by Teodora Dyankova-Danovska, Sonya Uzunova, Georgi Danovski, Rumen Stamatov, Petar-Bogomil Kanev, Aleksandar Atemin, Aneliya Ivanova, Radoslav Aleksandrov and Stoyno Stoynov

Int. J. Mol. Sci. 2025, 26(2), 667; https://doi.org/10.3390/ijms26020667 - 14 Jan 2025

Abstract

Replication forks encounter various impediments, which induce fork stalling and threaten genome stability, yet the precise dynamics of fork stalling and restart at the single-cell level remain elusive. Herein, we devise a live-cell microscopy-based approach to follow hydroxyurea-induced fork stalling and subsequent restart at 30 s resolution. We measure two distinct processes during fork stalling. One is rapid PCNA removal, which reflects the drop in DNA synthesis. The other is gradual RPA1 accumulation up to 2400 nt of ssDNA per fork despite an active intra-S checkpoint. Restoring the nucleotide pool enables a prompt restart without post-replicative ssDNA and a smooth cell cycle progression. ATR, but not ATM inhibition, accelerates hydroxyurea-induced RPA1 accumulation nine-fold, leading to RPA1 exhaustion within 20 min. Fork restart under ATR inhibition led to the persistence of ~600 nt ssDNA per fork after S-phase, which reached 2500 nt under ATR/ATM co-inhibition, with both scenarios leading to mitotic catastrophe. MRE11 inhibition had no effect on PCNA/RPA1 dynamics regardless of ATR activity. E3 ligase RAD18 was recruited at stalled replication forks in parallel to PCNA removal. Our results shed light on fork dynamics during nucleotide depletion and provide a valuable tool for interrogating the effects of replication stress-inducing anti-cancer agents. Full article

(This article belongs to the Special Issue DNA Damage and DNA Repair Pathways in Cancer Development)

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26 pages, 1837 KiB

Open AccessArticle

A Proposal for a Zero-Trust-Based Multi-Level Security Model and Its Security Controls

by Jun-Hyung Park, Sung-Chae Park and Heung-Youl Youm

Appl. Sci. 2025, 15(2), 785; https://doi.org/10.3390/app15020785 - 14 Jan 2025

Abstract

The rapid advancement of technology and increasing data utilisation have underscored the need for new models to manage and secure big data effectively. However, the constraints of isolated network environments and the limitations of existing security frameworks hinder the adoption of cutting-edge technologies such as AI and cloud computing, as well as the safe utilisation of data. To address these challenges, this study proposes an enhanced security model that integrates the concepts of Multi-Level Security (MLS) and Zero Trust (ZT). The proposed model classifies data into the following three sensitivity levels: “Classified,” “Sensitive,” and “Open.” It applies tailored security requirements and dynamic controls to each level, enhancing both data security and usability. Furthermore, the model overcomes the static access control limitations of MLS by incorporating ZT’s automated dynamic access capabilities, significantly improving responsiveness to anomalous behaviours. This study contributes to the design and evaluation of a new security model that ensures secure data protection and utilisation, even in isolated network environments such as those of military and governmental organisations. It also provides a foundation for the future development of advanced security frameworks. Full article

(This article belongs to the Special Issue Advanced Cybersecurity Applications: Solutions to Counteract Cyber Threats)

21 pages, 978 KiB

Open AccessArticle

Enhanced Polar Lights Optimization with Cryptobiosis and Differential Evolution for Global Optimization and Feature Selection

by Yang Gao and Liang Cheng

Biomimetics 2025, 10(1), 53; https://doi.org/10.3390/biomimetics10010053 - 14 Jan 2025

Abstract

Optimization algorithms play a crucial role in solving complex problems across various fields, including global optimization and feature selection (FS). This paper presents the enhanced polar lights optimization with cryptobiosis and differential evolution (CPLODE), a novel improvement upon the original polar lights optimization (PLO) algorithm. CPLODE integrates a cryptobiosis mechanism and differential evolution (DE) operators to enhance PLO’s search capabilities. The original PLO’s particle collision strategy is replaced with DE’s mutation and crossover operators, enabling a more effective global exploration and using a dynamic crossover rate to improve convergence. Furthermore, a cryptobiosis mechanism records and reuses historically successful solutions, thereby improving the greedy selection process. The experimental results on 29 CEC 2017 benchmark functions demonstrate CPLODE’s superior performance compared to eight classical optimization algorithms, with higher average ranks and faster convergence. Moreover, CPLODE achieved competitive results in feature selection on ten real-world datasets, outperforming several well-known binary metaheuristic algorithms in classification accuracy and feature reduction. These results highlight CPLODE’s effectiveness for both global optimization and feature selection. Full article

(This article belongs to the Special Issue Bio-Inspired Optimization Algorithms and Designs for Engineering Applications: 2nd Edition)

14 pages, 4480 KiB

Open AccessArticle

Calcium Phosphate (CaP) Composite Nanostructures on Polycaprolactone (PCL): Synergistic Effects on Antibacterial Activity and Osteoblast Behavior

by Suvd Erdene Ganbaatar, Hee-Kyeong Kim, Nae-Un Kang, Eun Chae Kim, Hye Jin U, Young-Sam Cho and Hyun-Ha Park

Polymers 2025, 17(2), 200; https://doi.org/10.3390/polym17020200 - 14 Jan 2025

Abstract

Bone tissue engineering aims to develop biomaterials that are capable of effectively repairing and regenerating damaged bone tissue. Among the various polymers used in this field, polycaprolactone (PCL) is one of the most widely utilized. As a biocompatible polymer, PCL is easy to fabricate, cost-effective, and offers consistent quality control, making it a popular choice for biomedical applications. However, PCL lacks inherent antibacterial properties, making it susceptible to bacterial adhesion and biofilm formation, which can lead to implant failure. To address this issue, this study aims to enhance the antibacterial properties of PCL by incorporating calcium phosphate composite (PCL_CaP) nanostructures onto its surface via hydrothermal synthesis. The resulting “PCL_CaP” nanostructured surfaces exhibited improved wettability and demonstrated mechano-bactericidal potential against Escherichia coli and Bacillus subtilis. The flake-like morphology of the fabricated CaP nanostructures effectively disrupted bacteria membranes, inhibiting bacterial growth. Furthermore, the “PCL_CaP” surfaces supported the adhesion, proliferation, and differentiation of pre-osteoblasts, indicating their potential for bone tissue engineering applications. This study demonstrates the promise of calcium phosphate composite nanostructures as an effective antibacterial coating for implants and medical devices, with further research required to evaluate their long-term stability and in vivo performance. Full article

(This article belongs to the Section Polymer Applications)

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(a) Schematic diagram of the preparation of “PCL_CaP” nanostructured surfaces. (b) Representative SEM images showing the (i) surface of “PCL bare”, (ii) surface of “PCL_CaP”, and (iii) cross section of “PCL_CaP.” (c) Surface roughness for the “PCL_CaP” nanostructured surface. Full article ">Figure 2
(a) EDS images; (b) WCA of the “PCL_CaP” nanostructured surface; (c) FT-IR spectra (including PCL, β-Tri-Calcium Phosphate, hydroxyapatite, and “PCL_CaP”). Full article ">Figure 3
Confocal microscopy images of (a) E. coli and (b) B. subtilis cultured on the “PCL bare” surface and the “PCL_CaP” nanostructured surface (green: live cells; red: dead cells). CFU of (c) E. coli and (d) B. subtilis cultured on the “PCL bare” surface and the “PCL_CaP” nanostructured surface. Full article ">Figure 4
SEM images of (a) E. coli and (b) B. subtilis cultured on the “PCL bare” surface and “PCL_CaP” nanostructured surface. Full article ">Figure 5
Assessment of pre-osteoblast proliferation and differentiation. (a) CCK-8 assay (proliferation); (b) ALP activity (differentiation). (ns; not significant, *; p < 0.05, ***; p < 0.001). Full article ">

17 pages, 6455 KiB

Open AccessArticle

A Novel Mesoscale Eddy Identification Method Using Enhanced Interpolation and A Posteriori Guidance

by Lei Zhang, Xiaodong Ma, Weishuai Xu, Xiang Wan and Qiyun Chen

Sensors 2025, 25(2), 457; https://doi.org/10.3390/s25020457 - 14 Jan 2025

Abstract

Mesoscale eddies are pivotal oceanographic phenomena affecting marine environments. Accurate and stable identification of these eddies is essential for advancing research on their dynamics and effects. Current methods primarily focus on identifying Cyclonic and Anticyclonic eddies (CE, AE), with anomalous eddy identification often requiring secondary analyses of sea surface height anomalies and eddy center properties, leading to segmented data interpretations. This study introduces a deep learning model integrating multi-source fusion data with a Squeeze-and-Excitation (SE) attention mechanism to enhance the identification accuracy for both normal and anomalous eddies. Comparative ablation experiments validate the model’s effectiveness, demonstrating its potential for more nuanced, multi-source, and multi-class mesoscale eddy identification. This approach offers a promising framework for advancing mesoscale eddy identification through deep learning. Full article

(This article belongs to the Special Issue Artificial Intelligence-Based Target Recognition and Remote Sensing Data Processing)

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Schematic of the methodological framework. Full article ">Figure 2
Schematic of the study area. Full article ">Figure 3
Probability distribution of extreme thermohaline anomaly (left) and corresponding depth (right) in the KE region. Full article ">Figure 4
Schematic of the sea surface multi-channel fusion model for mesoscale eddy identification with integrated SE attention mechanism. Full article ">Figure 5
Trends in evaluation metrics during model training and verification. Full article ">Figure 6
Confusion matrix for model predictions of normal and abnormal eddies against background field. Full article ">Figure 7
(a) Visualization of identification results using 5113 days of daily multi-source remote-sensing superimposed data (2007–2020) based on a sample of 8 consecutive days. (Note: Normal and abnormal eddies are marked without consideration of eddy polarity). (b) Visualization of identification results using single sea surface height data. Full article ">

18 pages, 1136 KiB

Open AccessArticle

Carbon Dioxide Micro-Nano Bubbles Aeration Improves Carbon Fixation Efficiency for Succinic Acid Synthesis by Escherichia coli

by Ying Chen, Hao Wu, Qianqian Huang, Jingwen Liao, Liuqing Wang, Yue Pan, Anming Xu, Wenming Zhang and Min Jiang

Fermentation 2025, 11(1), 31; https://doi.org/10.3390/fermentation11010031 - 14 Jan 2025

Abstract

The low solubility of CO₂ in water leads to massive CO₂ emission and extremely low CO₂ utilization in succinic acid (SA) biosynthesis. To enhance microbial CO₂ utilization, micro-nano bubbles (MNBs) were induced in SA biosynthesis by E. coli Suc260 in this study. The results showed that MNB aeration decreased CO₂ emissions and increased CO₂solubility in the medium significantly. The CO₂ utilization of MNB aeration was 129.69% higher than that of bubble aeration in atmospheric fermentation. However, MNBs showed a significant inhibitory effect on bacterial growth in the pressurized environment, although a two-stage aerobic–anaerobic fermentation strategy weakened the inhibition. The biofilm-enhanced strain E. coli Suc260-CsgA showed a strong tolerance to MNBs. In pressurized fermentation with MNB aeration, the actual CO₂ utilization of E. coli Suc260-CsgA was 30.63% at 0.18 MPa, which was a 6.49-times improvement. The CO₂ requirement for SA synthesis decreased by 83.4%, and the fugitive emission of CO₂ was successfully controlled. The activities of key enzymes within the SA synthesis pathway were also maintained or enhanced in the fermentation process with MNB aeration. These results indicated that the biofilm-enhanced strain and CO₂-MNBs could improve carbon fixation efficiency in microbial carbon sequestration. Full article

(This article belongs to the Section Fermentation Process Design)

13 pages, 1991 KiB

Open AccessArticle

Outcomes of Broader Genomic Profiling in Metastatic Colorectal Cancer: A Portuguese Cohort Study

by Ricardo Roque, Rita Santos, Luís Guilherme Santos, Rita Coelho, Isabel Fernandes, Gonçalo Cunha, Marta Gonçalves, Teresa Fraga, Judy Paulo and Nuno Bonito

DNA 2025, 5(1), 4; https://doi.org/10.3390/dna5010004 (registering DOI) - 14 Jan 2025

Abstract

Background: Colorectal cancer (CRC) is the third most diagnosed cancer globally and the second leading cause of cancer-related deaths. Despite advancements, metastatic CRC (mCRC) has a five-year survival rate below 20%. Next-generation sequencing (NGS) is recommended nowadays to guide mCRC treatment; however, its clinical utility when compared with traditional molecular testing in mCRC is debated due to limited survival improvement and cost-effectiveness concerns. Methods: This retrospective study included mCRC patients (≥18 years) treated at a single oncology centre who underwent NGS during treatment planning. Tumour samples were analysed using either a 52-gene Oncomine™ Focus Assay or a 500+-gene Oncomine™ Comprehensive Assay Plus. Variants were classified by clinical significance (ESMO ESCAT) and potential benefit (ESMO-MCBS and OncoKBTM). The Mann–Whitney and Chi square tests were used to compare characteristics of different groups, with significance at p < 0.05. Results: Eighty-six metastatic colorectal cancer (mCRC) patients were analysed, all being MMR proficient. Most cases (73.3%) underwent sequencing at diagnosis of metastatic disease, using primary tumour samples (74.4%) and a focused NGS assay (75.6%). A total of 206 somatic variants were detected in 86.0% of patients, 31.1% of which were classified as clinically significant, predominantly KRAS mutations (76.6%), with G12D and G12V variants as the most frequent. Among 33.7% RAS/BRAF wild-type patients, 65.5% received anti-EGFR therapies. Eleven patients (12.8%) had other actionable variants which were ESCAT level I-II, including four identified as TMB-high, four KRAS G12C, two BRAF V600E, and one HER2 amplification. Four received therapies classified as OncoKbTM level 1–2 and ESMO-MCBS score 4, leading to disease control in three cases. Conclusions: NGS enables the detection of rare variants, supports personalised treatments, and expands therapeutic options. As new drugs emerge and genomic data integration improves, NGS is poised to enhance real-world mCRC management. Full article

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Figure 1
Diagram illustrating the patient selection process and the main results influencing treatment strategies. Full article ">Figure 2
(a) Relative frequency of all detected variants (n = 206). Forty-nine variants of uncertain significance (VUSs), which occurred only once in the sample and in different genes, are excluded from this graph. (b) Prevalence of variants in the 86 included patients. (c) Heatmap showing the distribution of variants based on their clinical significance for each of the 74 patients with detectable variants. Graphs (b,c) include only genes that overlap between the two NGS assays. Full article ">Figure 3
Relative frequencies of each KRAS variant according to stage at diagnosis (a) or location of the primary tumour (b). Graphic (c) displays a box plot showing the distribution of the median allele frequency for each KRAS variant. Full article ">Figure 4
Absolute frequency of PIK3CA (a) and APC (b) variants distributed by affected exon. Heatmap (c) showing relative frequency of variants, classified according to amino acid change, for each of the most commonly altered genes overlapping between the two panels. Full article ">Figure 5
The table (left) presents four patients treated with targeted therapies in subsequent lines of systemic treatment for mCRC. The variant-matched treatment is scored according to its potential clinical benefit using the ESMO Magnitude of Clinical Benefit Scale (ESMO-MCBS) in the non-curative setting and OncoKBTM therapeutic level. The bars (right) display the median progression-free survival (in months) and the best response to treatment: progression (red) or partial response/disease stability (blue). One patient died (†) and two are still on treatment (◊). ND—not defined. Full article ">

22 pages, 10534 KiB

Open AccessArticle

Integrated Metabolome, Transcriptome, and Physiological Analysis of the Flavonoid and Phenylethanol Glycosides Accumulation in Wild Phlomoides rotata Roots from Different Habitats

by Zuxia Li, Guigong Geng, Chongxin Yin, Lianyu Zhou, Xiaozhuo Wu, Jianxia Ma, Rui Su, Zirui Wang, Feng Qiao and Huichun Xie

Int. J. Mol. Sci. 2025, 26(2), 668; https://doi.org/10.3390/ijms26020668 - 14 Jan 2025

Abstract

Phlomoides rotata, a traditional medicinal plant, is commonly found on the Tibetan Plateau at altitudes of 3100–5200 m. Its primary active medicinal compounds, flavonoids and phenylethanol glycosides (PhGs), exhibit various pharmacological effects, including hemostatic, anti-inflammatory, antitumor, immunomodulatory, and antioxidant activities. This study analyzed flavonoid and PhG metabolites in the roots of P. rotata collected from Henan County (HN), Guoluo County (GL), Yushu County (YS), and Chengduo County (CD) in Qinghai Province. A total of differentially abundant metabolites (DAMs) including 38 flavonoids and 21 PhGs were identified. Six genes (UFGT1, CHS1, COMT2, C4H3, C4H8, and C4H5) and four enzymes (4CL, C4H, PPO, and ALDH) were found to play key roles in regulating flavonoid and PhG biosynthesis in P. rotata roots. With increasing altitude, the relative content of 15 metabolites, the expression of seven genes, and the activity of four enzymes associated with flavonoid and PhG metabolism increased. These findings enhance our understanding of the regulatory mechanisms of flavonoid and PhG metabolism in P. rotata and provide insights into the potential pharmaceutical applications of its bioactive compounds. Full article

(This article belongs to the Special Issue Plant Metabolomics: Uncovering the Hidden World of Plant Secondary Metabolites)

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