The 2023 MDPI Annual Report has
been released!
 
17 pages, 1345 KiB  
Review
Machine Learning and Deep Learning Strategies for Chinese Hamster Ovary Cell Bioprocess Optimization
by Tiffany-Marie D. Baako, Sahil Kaushik Kulkarni, Jerome L. McClendon, Sarah W. Harcum and Jordon Gilmore
Fermentation 2024, 10(5), 234; https://doi.org/10.3390/fermentation10050234 (registering DOI) - 27 Apr 2024
Abstract
The use of machine learning and deep learning has become prominent within various fields of bioprocessing for countless modeling and prediction tasks. Previous reviews have emphasized machine learning applications in various fields of bioprocessing, including biomanufacturing. This comprehensive review highlights many of the [...] Read more.
The use of machine learning and deep learning has become prominent within various fields of bioprocessing for countless modeling and prediction tasks. Previous reviews have emphasized machine learning applications in various fields of bioprocessing, including biomanufacturing. This comprehensive review highlights many of the different machine learning and multivariate analysis techniques that have been utilized within Chinese hamster ovary cell biomanufacturing, specifically due to their rising significance in the industry. Applications of machine and deep learning within other bioprocessing industries are also briefly discussed. Full article
(This article belongs to the Special Issue Feature Review Papers in Fermentation Process Design 2023)
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12 pages, 3292 KiB  
Article
Spatial Distribution of Macrophage and Lymphocyte Subtypes within Tumor Microenvironment to Predict Recurrence of Non-Muscle-Invasive Papillary Urothelial Carcinoma after BCG Immunotherapy
by Julius Drachneris, Mindaugas Morkunas, Mantas Fabijonavicius, Albertas Cekauskas, Feliksas Jankevicius and Arvydas Laurinavicius
Int. J. Mol. Sci. 2024, 25(9), 4776; https://doi.org/10.3390/ijms25094776 (registering DOI) - 27 Apr 2024
Abstract
Non-muscle-invasive papillary urothelial carcinoma (NMIPUC) of the urinary bladder is the most common type of bladder cancer. Intravesical Bacille Calmette–Guerin (BCG) immunotherapy is applied in patients with a high risk of recurrence and progression of NMIPUC to muscle-invasive disease. However, the tumor relapses [...] Read more.
Non-muscle-invasive papillary urothelial carcinoma (NMIPUC) of the urinary bladder is the most common type of bladder cancer. Intravesical Bacille Calmette–Guerin (BCG) immunotherapy is applied in patients with a high risk of recurrence and progression of NMIPUC to muscle-invasive disease. However, the tumor relapses in about 30% of patients despite the treatment, raising the need for better risk stratification. We explored the potential of spatial distributions of immune cell subtypes (CD20, CD11c, CD163, ICOS, and CD8) within the tumor microenvironment to predict NMIPUC recurrence following BCG immunotherapy. Based on analyses of digital whole-slide images, we assessed the densities of the immune cells in the epithelial–stromal interface zone compartments and their distribution, represented by an epithelial–stromal interface density ratio (IDR). While the densities of any cell type did not predict recurrence, a higher IDR of CD11c (HR: 0.0012, p-value = 0.0002), CD8 (HR: 0.0379, p-value = 0.005), and ICOS (HR: 0.0768, p-value = 0.0388) was associated with longer recurrence-free survival (RFS) based on the univariate Cox regression. The history of positive repeated TUR (re-TUR) (HR: 4.93, p-value = 0.0001) and T1 tumor stage (HR: 2.04, p-value = 0.0159) were associated with shorter RFS, while G3 tumor grade according to the 1973 WHO classification showed borderline significance (HR: 1.83, p-value = 0.0522). In a multivariate analysis, the two models with a concordance index exceeding 0.7 included the CD11c IDR in combination with either a history of positive re-TUR or tumor stage. We conclude that the CD11c IDR is the most informative predictor of NMIPUC recurrence after BCG immunotherapy. Our findings highlight the importance of assessment of the spatial distribution of immune cells in the tumor microenvironment. Full article
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23 pages, 739 KiB  
Article
An Innovative Probiotic-Based Supplement to Mitigate Molecular Factors Connected to Depression and Anxiety: An In Vitro Study
by Sara Ferrari, Simone Mulè, Giorgia Rosso, Francesca Parini, Rebecca Galla, Claudio Molinari and Francesca Uberti
Int. J. Mol. Sci. 2024, 25(9), 4774; https://doi.org/10.3390/ijms25094774 (registering DOI) - 27 Apr 2024
Abstract
The gut–brain axis is a bidirectional relationship between the microbiota and the brain; genes related to the brain and gut synaptic formation are similar. Research on the causal effects of gut microbiota on human behavior, brain development, and function, as well as the [...] Read more.
The gut–brain axis is a bidirectional relationship between the microbiota and the brain; genes related to the brain and gut synaptic formation are similar. Research on the causal effects of gut microbiota on human behavior, brain development, and function, as well as the underlying molecular processes, has emerged in recent decades. Probiotics have been shown in several trials to help reduce anxiety and depressive symptoms. Because of this, probiotic combinations have been tested in in vitro models to see whether they might modulate the gut and alleviate depression and anxiety. Therefore, we sought to determine whether a novel formulation might affect the pathways controlling anxiety and depression states and alter gut barrier activities in a 3D model without having harmful side effects. Our findings indicate that B. bifidum novaBBF7 10 mg/mL, B. longum novaBLG2 5 mg/mL, and L. paracasei TJB8 10 mg/mL may influence the intestinal barrier and enhance the synthesis of short-chain fatty acids. Additionally, the probiotics studied did not cause neuronal damage and, in combination, exert a protective effect against the condition of anxiety and depression triggered by L-Glutamate. All these findings show that probiotics can affect gut function to alter the pathways underlying anxiety and depression. Full article
(This article belongs to the Special Issue Molecular Pharmacology of Antidepressants)
16 pages, 6529 KiB  
Article
Numerical Simulation of Stress Disturbance Mechanism Caused by Hydraulic Fracturing of Shale Formation
by Yinghui Zhu, Heng Zheng, Yi Liao and Ruiquan Liao
Processes 2024, 12(5), 886; https://doi.org/10.3390/pr12050886 (registering DOI) - 27 Apr 2024
Abstract
Characterizing changes in rock properties is essential for the hydraulic fracture and re-fracture parameter optimization of shale formations. This paper proposed a hydraulic fracturing model to investigate the changes in rock properties during hydraulic fracturing using SPH, and the changes in the stress [...] Read more.
Characterizing changes in rock properties is essential for the hydraulic fracture and re-fracture parameter optimization of shale formations. This paper proposed a hydraulic fracturing model to investigate the changes in rock properties during hydraulic fracturing using SPH, and the changes in the stress field and rock properties were quantitatively characterized. The simulation results indicated that the minimum horizontal principal stress increased by 10 MPa~15 MPa during fracture propagation, which is the main reason for the uneven propagation in multi-fracture propagation. Affected by the stress disturbance, the stimulated area was divided into four parts based on the changes in Young’s modulus and permeability; the more seriously the stress disturbance was affected, the higher the permeability of the stimulated zone was, and the smaller the stimulated zone was. Meanwhile, a zone with reduced permeability appeared due to the compression effect caused by the high injection pressure, and this increased with the increase in stress disturbance. The main reason for this was that strain formed because of the compression effect from the high injection pressure. The higher the stress disturbance, the higher the accumulated strain. This new model provides a new method for fracture parameter optimization, which also provides a foundation for the re-fracture parameter optimization of shale formations. Full article
(This article belongs to the Special Issue Advanced Fracturing Technology for Oil and Gas Reservoir Stimulation)
19 pages, 949 KiB  
Article
Nutritional Quality of Conventional, Organic, and Hydroponic Tomatoes Commercialized in Quito, Ecuador
by Pamela Y. Vélez-Terreros, David Romero-Estévez, Hugo Navarrete and Gabriela S. Yánez-Jácome
Foods 2024, 13(9), 1348; https://doi.org/10.3390/foods13091348 (registering DOI) - 27 Apr 2024
Abstract
The consumption of natural foods is increasingly high, and in recent years, consumers have preferred foods from systems with responsible management of natural resources (organic, hydroponic). However, there are still contradictions regarding the nutritional content of products from these different types of crops. [...] Read more.
The consumption of natural foods is increasingly high, and in recent years, consumers have preferred foods from systems with responsible management of natural resources (organic, hydroponic). However, there are still contradictions regarding the nutritional content of products from these different types of crops. Our study aims to compare, for the first time, the content of antioxidants (ascorbic acid, lycopene, total phenolics, essential fatty acids), micronutrients (copper, iron, manganese, zinc), contaminants (cadmium and lead), and free radical scavenging activity between conventional, organic, and hydroponic tomatoes (Solanum lycopersicum) sold in markets in Quito, Ecuador. Ascorbic acid and lycopene were determined by HPLC/UV-Vis. Total phenolics (Folin–Ciocalteu method) and free-radical scavenging activity (2,2-diphenyl-1-picrylhydrazyl method) were determined via UV-Vis spectrophotometry. Lipid profiles were determined as fatty acid methyl esters through a GC-FID. Trace metals were determined using FAAS (micronutrients), and GFAAS (pollutants). No significant differences (p > 0.05) between antioxidant and micronutrient content among the three types of tomatoes were found. Regarding cadmium and lead, the contents were below the Codex Alimentarius threshold limits. Finally, free radical scavenging activity varied slightly (organic > hydroponic > conventional). Although the samples showed certain differences in antioxidant content, none of the tomato types could be considered nutritionally better because of the high variability of the results. Full article
(This article belongs to the Special Issue Analysis of Nutrients and Contaminants in Foods)
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8 pages, 611 KiB  
Article
Hazard Flagging as a Risk Mitigation Strategy for Violence against Emergency Medical Services
by Justin Mausz, Dan Piquette, Robert Bradford, Mandy Johnston, Alan M. Batt and Elizabeth A. Donnelly
Healthcare 2024, 12(9), 909; https://doi.org/10.3390/healthcare12090909 (registering DOI) - 27 Apr 2024
Abstract
Paramedics are increasingly being subjected to violence, creating the potential for significant physical and psychological harm. Where a patient has a history of violent behavior, hazard flags—applied either to the individual, their residential address, or phone number—can alert paramedics to the possibility of [...] Read more.
Paramedics are increasingly being subjected to violence, creating the potential for significant physical and psychological harm. Where a patient has a history of violent behavior, hazard flags—applied either to the individual, their residential address, or phone number—can alert paramedics to the possibility of violence, potentially reducing the risk of injury. Leveraging a novel violence reporting process embedded in the electronic patient care record, we reviewed violence reports filed over a thirteen-month period since its inception in February 2021 to assess the effectiveness of hazard flagging as a potential risk mitigation strategy. Upon reviewing a report, paramedic supervisors can generate a hazard flag if recurrent violent behavior from the patient is anticipated. In all, 502 violence reports were filed, for which paramedic supervisors generated hazard flags in 20% of cases (n = 99). In general, cases were not flagged either because the incident occurred at a location not amenable to flagging or because the supervisors felt that a hazard flag was not warranted based on the details in the report. Hazard flagging was associated with an increased risk of violence during subsequent paramedic attendance (Odds Ratio [OR] 6.21, p < 0.001). Nevertheless, the process appears to reliably identify persons who may be violent towards paramedics. Full article
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21 pages, 6591 KiB  
Article
Design and Evaluation of Novel Submerged Floating Tunnel Models Based on Dynamic Similarity
by Hongyu Ren, Tong Guo, Zhongxiang Liu, Guoliang Zhi and Xiangyang Xu
Appl. Sci. 2024, 14(9), 3724; https://doi.org/10.3390/app14093724 (registering DOI) - 27 Apr 2024
Abstract
Submerged floating tunnels (SFTs), also known as the Archimedes Bridge, are new transportation structures designed for crossing deep waters. Compared with cross-sea bridges and subsea tunnels, SFTs offer superior environmental adaptability, reduced construction costs, and an enhanced spanning capacity, highlighting their significant development [...] Read more.
Submerged floating tunnels (SFTs), also known as the Archimedes Bridge, are new transportation structures designed for crossing deep waters. Compared with cross-sea bridges and subsea tunnels, SFTs offer superior environmental adaptability, reduced construction costs, and an enhanced spanning capacity, highlighting their significant development potential and research value. This paper introduces a new type of SFT scale model for hydrodynamic experiments, adhering to the criteria for geometric similarity, motion similarity, and dynamic similarity principles, including the Froude and Cauchy similarity principles. This model enables the accurate simulation of the elastic deformation of the tunnel body and complex hydrodynamic phenomena, such as fluid–structure interactions and vortex–induced vibrations. Moreover, this paper details the design methodology, fabrication process, and method for similarity evaluation, covering the mass, deflection under load, natural frequency in air, and the natural frequency of the various underwater motion freedoms of the model. The results of our experiments and numerical simulations demonstrate a close alignment, proving the reliability of the new SFT scale model. The frequency distribution observed in the white noise wave tests indicates that the SFT equipped with inclined mooring cables experiences a coupled interaction between horizontal motion, vertical motion, and rotation. Furthermore, the design methodology of this model can be applied to other types of SFTs, potentially advancing technical progress in scale modeling of SFTs and enhancing the depth of SFT research through hydrodynamic experiments. Full article
(This article belongs to the Special Issue Advances in Intelligent Bridge: Maintenance and Monitoring)
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28 pages, 11577 KiB  
Article
Improved Finite Element Model Updating of a Highway Viaduct Using Acceleration and Strain Data
by Doron Hekič, Diogo Ribeiro, Andrej Anžlin, Aleš Žnidarič and Peter Češarek
Sensors 2024, 24(9), 2788; https://doi.org/10.3390/s24092788 (registering DOI) - 27 Apr 2024
Abstract
Most finite element model updating (FEMU) studies on bridges are acceleration-based due to their lower cost and ease of use compared to strain- or displacement-based methods, which entail costly experiments and traffic disruptions. This leads to a scarcity of comprehensive studies incorporating strain [...] Read more.
Most finite element model updating (FEMU) studies on bridges are acceleration-based due to their lower cost and ease of use compared to strain- or displacement-based methods, which entail costly experiments and traffic disruptions. This leads to a scarcity of comprehensive studies incorporating strain measurements. This study employed the strain- and acceleration-based FEMU analyses performed on a more than 50-year-old multi-span concrete highway viaduct. Mid-span strains under heavy vehicles were considered for the strain-based FEMU, and frequencies and mode shapes for the acceleration-based FEMU. The analyses were performed separately for up to three variables, representing Young’s modulus adjustment factors for different groups of structural elements. FEMU studies considered residual minimisation and the error-domain model falsification (EDMF) methodology. The residual minimisation utilised four different single-objective optimisations focusing on strains, frequencies, and mode shapes. Strain- and frequency-based FEMU analyses resulted in an approximately 20% increase in the overall superstructure’s design stiffness. This study shows the benefits of the intuitive EDMF over residual minimisation for FEMU, where information gained from the strain data, in addition to the acceleration data, manifests more sensible updated variables. EDMF finally resulted in a 25–50% overestimated design stiffness of internal main girders. Full article
28 pages, 13189 KiB  
Article
WLI, XPS and SEM/FIB/EDS Surface Characterization of an Electrically Fluted Bearing Raceway
by Omid Safdarzadeh, Alireza Farahi, Andreas Binder, Hikmet Sezen and Jan Philipp Hofmann
Lubricants 2024, 12(5), 148; https://doi.org/10.3390/lubricants12050148 (registering DOI) - 27 Apr 2024
Abstract
Electrical bearing currents may disturb the performance of the bearings via electro-corrosion if they surpass a limit of ca. 0.1 to 0.3 A/mm2. A continuous current flow, or, after a longer time span, an alternating current or a repeating impulse-like current, [...] Read more.
Electrical bearing currents may disturb the performance of the bearings via electro-corrosion if they surpass a limit of ca. 0.1 to 0.3 A/mm2. A continuous current flow, or, after a longer time span, an alternating current or a repeating impulse-like current, damages the raceway surface, leading in many cases to a fluting pattern on the raceway. Increased bearing vibration, audible noise, and decreased bearing lubrication as a result may demand a replacement of the bearings. Here, an electrically corroded axial ball bearing (type 51208) with fluting patterns is investigated. The bearing was lubricated with grease lubrication and was exposed to 4 A DC current flow. It is shown that the electric current flow causes higher concentrations of iron oxides and iron carbides on the bearing raceway surface together with increased surface roughness, leading to a mixed lubrication also at elevated bearing speeds up to 1500 rpm. The “electrically insulating” iron oxide layer and the “mechanically hard” iron carbide layer on the bearing steel are analysed by WLI, XPS, SEM, and EDS. White Light Interferometry (WLI) is used to provide an accurate measurement of the surface topography and roughness. X-ray Photoelectron Spectroscopy (XPS) measurements are conducted to analyze the chemical surface composition and oxidation states. Scanning Electron Microscopy (SEM) is applied for high-resolution imaging of the surface morphology, while the Focused Ion Beam (FIB) is used to cut a trench into the bearing surface to inspect the surface layers. With the Energy Dispersive X-ray spectrometry (EDS), the presence of composing elements is identified, determining their relative concentrations. The electrically-caused iron oxide and iron carbide may develop periodically along the raceway due to the perpendicular vibrations of the rolling ball on the raceway, leading gradually to the fluting pattern. Still, a simulation of this vibration-induced fluting-generation process from the start with the first surface craters—of the molten local contact spots—to the final fluting pattern is missing. Full article
(This article belongs to the Special Issue Tribological Characteristics of Bearing System, 2nd Edition)
20 pages, 5291 KiB  
Article
Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms—A Comparative Study
by Jirina Markova, Denisa Langova, Vladimir Babak and Iveta Kostovova
Microorganisms 2024, 12(5), 875; https://doi.org/10.3390/microorganisms12050875 (registering DOI) - 27 Apr 2024
Abstract
Caseous lymphadenitis (CLA) is a worldwide disease of small ruminants caused by Corynebacterium pseudotuberculosis, a facultative intracellular pathogen that is able to survive and multiply in certain white blood cells of the host. In this study, 33 strains of C. pseudotuberculosis were [...] Read more.
Caseous lymphadenitis (CLA) is a worldwide disease of small ruminants caused by Corynebacterium pseudotuberculosis, a facultative intracellular pathogen that is able to survive and multiply in certain white blood cells of the host. In this study, 33 strains of C. pseudotuberculosis were isolated from sheep and goats suffering from CLA on nine farms in the Czech Republic. All these strains were tested for their antibiotic susceptibility, ability to form a biofilm and resistance to the effects of commonly used disinfectant agents. To better understand the virulence of C. pseudotuberculosis, the genomes of strains were sequenced and comparative genomic analysis was performed with another 123 genomes of the same species, including ovis and equi biovars, downloaded from the NCBI. The genetic determinants for the virulence factors responsible for adherence and virulence factors specialized for iron uptake and exotoxin phospholipase D were revealed in every analyzed genome. Carbohydrate-Active Enzymes were compared, revealing the presence of genetic determinants encoding exo-α-sialidase (GH33) and the CP40 protein in most of the analyzed genomes. Thirty-three Czech strains of C. pseudotuberculosis were identified as the biovar ovis on the basis of comparative genome analysis. All the compared genomes of the biovar ovis strains were highly similar regardless of their country of origin or host, reflecting their clonal behavior. Full article
(This article belongs to the Special Issue Bacterial Infections and Antimicrobial Resistance in Animals)
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13 pages, 2560 KiB  
Article
Facile Synthesis of Fe-Doped, Algae Residue-Derived Carbon Aerogels for Electrochemical Dopamine Biosensors
by Hao Wu, Qin Wen, Xin Luan, Weiwei Yang, Lei Guo and Gang Wei
Sensors 2024, 24(9), 2787; https://doi.org/10.3390/s24092787 (registering DOI) - 27 Apr 2024
Abstract
An abnormal level of dopamine (DA), a kind of neurotransmitter, correlates with a series of diseases, including Parkinson’s disease, Willis-Ekbom disease, attention deficit hyperactivity disorder, and schizophrenia. Hence, it is imperative to achieve a precise, rapid detection method in clinical medicine. In this [...] Read more.
An abnormal level of dopamine (DA), a kind of neurotransmitter, correlates with a series of diseases, including Parkinson’s disease, Willis-Ekbom disease, attention deficit hyperactivity disorder, and schizophrenia. Hence, it is imperative to achieve a precise, rapid detection method in clinical medicine. In this study, we synthesized nanocomposite carbon aerogels (CAs) doped with iron and iron carbide, based on algae residue-derived biomass materials, using Fe(NO3)3 as the iron source. The modified glassy carbon electrode (GCE) for DA detection, denoted as CAs-Fe/GCE, was prepared through surface modification with this composite material. X-ray photoelectron spectroscopy and X-ray diffraction characterization confirmed the successful doping of iron into the as-prepared CAs. Additionally, the electrochemical behavior of DA on the modified electrode surface was investigated and the results demonstrate that the addition of the CAs-Fe promoted the electron transfer rate, thereby enhancing their sensing performance. The fabricated electrochemical DA biosensor exhibits an accurate detection of DA in the concentration within the range of 0.01~200 µM, with a detection limit of 0.0033 µM. Furthermore, the proposed biosensor is validated in real samples, showing its high applicability for the detection of DA in beverages. Full article
(This article belongs to the Special Issue Recent Advances in Nanomaterial-Based Electrochemical Sensors)
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16 pages, 6756 KiB  
Article
Uncovering the Effect of CeO2 on the Microstructure and Properties of TiAl/WC Coatings on Titanium Alloy
by Xinmeng Sui, Yitao Weng, Lin Zhang, Jian Lu, Xiangbiao Huang, Fuquan Long and Weiping Zhang
Coatings 2024, 14(5), 543; https://doi.org/10.3390/coatings14050543 (registering DOI) - 27 Apr 2024
Abstract
It remains a popular question whether rare earth oxides encourage reinforcing phases to the uniform distribution in cermet coating to improve the mechanical properties. This study applied laser cladding to prepare the TiAl/WC/CeO2 MMC cermet coatings on the TC21 alloy substrate. The [...] Read more.
It remains a popular question whether rare earth oxides encourage reinforcing phases to the uniform distribution in cermet coating to improve the mechanical properties. This study applied laser cladding to prepare the TiAl/WC/CeO2 MMC cermet coatings on the TC21 alloy substrate. The effects of CeO2 content on the phase composition, microstructure formation, evolution mechanism, and properties of cermet coatings were investigated. Results show that the incorporation of CeO2 did not change the phase of composite coating, but the shape of the TiC phase has a close relation to the CeO2 content. CeO2 enhanced the fluidity of the molten pool, which further encouraged the TiC/Ti2AlC core-shell reinforcement phase. With the increase in CeO2 content, the optimized coating contributed to homogenous microstructure distribution and fine grain size. Owing to the hard phases strengthening and dispersion strengthening effects of CeO2, the microhardness of the composite coatings was all significantly higher (almost 1.6 times) than that of the substrate. Importantly, the addition of CeO2 significantly improved the wear resistance of the composite coating. This work provides a certain reference value for the study of surface strengthening of key parts in the aerospace field. Full article
14 pages, 3305 KiB  
Communication
Microbial Community and Metabolome Analysis of the Porcine Intestinal Damage Model Induced by the IPEC-J2 Cell Culture-Adapted Porcine Deltacoronavirus (PDCoV) Infection
by Ying Shi, Benqiang Li, Jinghua Cheng, Jie Tao, Pan Tang, Jiajie Jiao and Huili Liu
Microorganisms 2024, 12(5), 874; https://doi.org/10.3390/microorganisms12050874 (registering DOI) - 27 Apr 2024
Abstract
This study was conducted to elucidate the intestinal damage induced by the IPEC-J2 cell culture-passaged PDCoV. The results showed that PDCoV disrupted the intestinal structure and increased intestinal permeability, causing abnormalities in mucosal pathology. Additionally, PDCoV induced an imbalance in the intestinal flora [...] Read more.
This study was conducted to elucidate the intestinal damage induced by the IPEC-J2 cell culture-passaged PDCoV. The results showed that PDCoV disrupted the intestinal structure and increased intestinal permeability, causing abnormalities in mucosal pathology. Additionally, PDCoV induced an imbalance in the intestinal flora and disturbed its stability. Microbial community profiling revealed bacterial enrichment (e.g., Proteobacteria) and reduction (e.g., Firmicutes and Bacteroidetes) in the PDCoV-inoculated piglet model. In addition, metabolomics analysis indicated that 82 named differential metabolites were successfully quantified, including 37 up-regulated and 45 down-regulated metabolites. Chenodeoxycholic acid, sphingosine, and oleanolic aldehyde levels were reduced in PDCoV-inoculated piglets, while phenylacetylglycine and geranylgeranyl-PP levels were elevated. Correlation analysis indicated a negative correlation between Escherichia-Shigella and choline, succinic acid, creatine, phenyllactate, and hippuric acid. Meanwhile, Escherichia-Shigella was positively correlated with acetylcholine, L-Glutamicacid, and N-Acetylmuramate. Roseburia, Lachnospiraceae_UCG-010, Blautia, and Limosilactobacillus were negatively and positively correlated with sphingosine, respectively. These data suggested PDCoV-inoculated piglets exhibited significant taxonomic perturbations in the gut microbiome, which may result in a significantly altered metabolomic profile. Full article
(This article belongs to the Section Veterinary Microbiology)
19 pages, 2761 KiB  
Review
Two-Dimensional Nanomaterials in Hydrogels and Their Potential Bio-Applications
by Zhongnan Wang, Hui Guo, Ji Zhang, Yi Qian and Yanfei Liu
Lubricants 2024, 12(5), 149; https://doi.org/10.3390/lubricants12050149 (registering DOI) - 27 Apr 2024
Abstract
Hydrogels with high hydrophilicity and excellent biocompatibility have been considered as potential candidates for various applications, including biomimetics, sensors and wearable devices. However, their high water content will lead to poor load-bearing and high friction. Currently, two-dimensional (2D) materials have been widely investigated [...] Read more.
Hydrogels with high hydrophilicity and excellent biocompatibility have been considered as potential candidates for various applications, including biomimetics, sensors and wearable devices. However, their high water content will lead to poor load-bearing and high friction. Currently, two-dimensional (2D) materials have been widely investigated as promising nanofillers to improve the mechanical and lubrication performances of hydrogels because of their unique physical–chemical properties. On one hand, 2D materials can participate in the cross-linking of hydrogels, leading to enhanced load-bearing capacity and fatigue resistance, etc.; on the other hand, using 2D materials as nanofillers also brings unique biomedical properties. The combination of hydrogels and 2D materials shows bright prospects for bioapplications. This review focusses on the recent development of high-strength and low-friction hydrogels with the addition of 2D nanomaterials. Functional properties and the underlying mechanisms of 2D nanomaterials are firstly overviewed. Subsequently, the mechanical and friction properties of hydrogels with 2D nanomaterials including graphene oxide, black phosphorus, MXenes, boron nitride, and others are summarized in detail. Finally, the current challenges and potential applications of using 2D nanomaterials in hydrogel, as well as future research, are also discussed. Full article
(This article belongs to the Special Issue Tribology of 2D Nanomaterials)
11 pages, 2605 KiB  
Article
Application of Deep Learning for Real-Time Ablation Zone Measurement in Ultrasound Imaging
by Corinna Zimmermann, Adrian Michelmann, Yannick Daniel, Markus D. Enderle, Nermin Salkic and Walter Linzenbold
Cancers 2024, 16(9), 1700; https://doi.org/10.3390/cancers16091700 (registering DOI) - 27 Apr 2024
Abstract
Background: The accurate delineation of ablation zones (AZs) is crucial for assessing radiofrequency ablation (RFA) therapy’s efficacy. Manual measurement, the current standard, is subject to variability and potential inaccuracies. Aim: This study aims to assess the effectiveness of Artificial Intelligence (AI) in automating [...] Read more.
Background: The accurate delineation of ablation zones (AZs) is crucial for assessing radiofrequency ablation (RFA) therapy’s efficacy. Manual measurement, the current standard, is subject to variability and potential inaccuracies. Aim: This study aims to assess the effectiveness of Artificial Intelligence (AI) in automating AZ measurements in ultrasound images and compare its accuracy with manual measurements in ultrasound images. Methods: An in vitro study was conducted using chicken breast and liver samples subjected to bipolar RFA. Ultrasound images were captured every 15 s, with the AI model Mask2Former trained for AZ segmentation. The measurements were compared across all methods, focusing on short-axis (SA) metrics. Results: We performed 308 RFA procedures, generating 7275 ultrasound images across liver and chicken breast tissues. Manual and AI measurement comparisons for ablation zone diameters revealed no significant differences, with correlation coefficients exceeding 0.96 in both tissues (p < 0.001). Bland–Altman plots and a Deming regression analysis demonstrated a very close alignment between AI predictions and manual measurements, with the average difference between the two methods being −0.259 and −0.243 mm, for bovine liver and chicken breast tissue, respectively. Conclusion: The study validates the Mask2Former model as a promising tool for automating AZ measurement in RFA research, offering a significant step towards reducing manual measurement variability. Full article
(This article belongs to the Special Issue Endoscopic Ultrasound in Cancer Research)
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26 pages, 4076 KiB  
Article
New Insights into Tetraplosphaeriaceae Based on Taxonomic Investigations of Bambusicolous Fungi and Freshwater Fungi
by Hai-Jun Zhao, Mingkwan Doilom, Ausana Mapook, Gennuo Wang, Kevin D. Hyde and Wei Dong
J. Fungi 2024, 10(5), 319; https://doi.org/10.3390/jof10050319 (registering DOI) - 27 Apr 2024
Abstract
Species within Tetraplosphaeriaceae have been frequently documented in recent years with the extensive investigations of microfungi along a latitudinal gradient from north to south in the Asian/Australian region. Both bamboo substrates and freshwater habitats serve as extensive reservoirs, hosting a rich diversity of [...] Read more.
Species within Tetraplosphaeriaceae have been frequently documented in recent years with the extensive investigations of microfungi along a latitudinal gradient from north to south in the Asian/Australian region. Both bamboo substrates and freshwater habitats serve as extensive reservoirs, hosting a rich diversity of fungi that exhibit broad geographical distributions. The most common fungi in these two environments are generally distributed in distinct families. However, our statistics have revealed an intriguingly distinct preference of Tetraplosphaeriaceae species for inhabiting both bamboo substrates and freshwater habitats. The genera Pseudotetraploa (100%) and Triplosphaeria (100%) exhibit a strong preference, followed by Shrungabeeja (71%) and Quadricrura (67%). Our taxonomic and phylogenetic study of microfungi in southern China have identified four additional novel species, viz., Aquatisphaeria bambusae sp. nov., Pseudotetraploa phyllostachydis sp. nov., Pseudotetraploa yangjiangensis sp. nov., and Tetraploa submersa sp. nov. from bamboo substrates and freshwater habitats. In addition, Aquatisphaeria thailandica has previously been documented from freshwater habitats in Thailand; however, we have once again isolated this species from decaying bamboo substrates in Guangdong, China. The new findings substantiate our hypothesis that the preference of Tetraplosphaeriaceae species for colonizing bamboo substrates and freshwater habitats will be more evident through more extensive investigations conducted in such environments. Full article
(This article belongs to the Special Issue Freshwater Fungal Diversity)
15 pages, 8106 KiB  
Article
Tribological Performance Study of Low-Friction PEEK Composites under Different Lubrication Conditions
by Shibo Wu, Zhijun Yan, Haocheng Sun, Ze Liu, Lixia Xue and Tao Sun
Appl. Sci. 2024, 14(9), 3723; https://doi.org/10.3390/app14093723 (registering DOI) - 27 Apr 2024
Abstract
This study introduces a low-friction composite based on PEEK to improve its friction and wear properties. The composite incorporates PTFE as a solid lubricant and utilizes PPTA as a reinforcing material within the PEEK matrix. These components were prepared utilizing a compression molding [...] Read more.
This study introduces a low-friction composite based on PEEK to improve its friction and wear properties. The composite incorporates PTFE as a solid lubricant and utilizes PPTA as a reinforcing material within the PEEK matrix. These components were prepared utilizing a compression molding method, followed by a series of exploratory experiments to identify the optimal preparation conditions for PEEK. This research assesses how the PTFE/PPTA/PEEK composites perform in terms of friction and wear under dry and oil-lubricated conditions. By examining wear tracks using scanning electron microscopy and white light interference microscopy, this study aims to uncover the wear mechanisms of PEEK and its composites under different lubrication scenarios. Results show that the main wear mechanisms for the PTFE/PPTA/PEEK composites and bearing steel are ploughing and adhesive wear. The presence of PPTA helps reduce wear by leveraging its strong fibers and thermal stability, while the coefficient of friction decreases as PTFE creates a smooth, solid lubricating film on the surface. Notably, PEEK composites containing 25 wt% PTFE and 6 wt% PPTA demonstrate the lowest wear rates and reduced coefficient of friction in both dry and oil-lubricated conditions. Full article
(This article belongs to the Special Issue Advanced Composites and Hybrid Materials)
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24 pages, 8810 KiB  
Article
Spatiotemporal Evolution and Transformation Regulation Strategies of Rural Residential Land on the Grand Canal (China)
by Jintao Li and Lei Chu
Land 2024, 13(5), 578; https://doi.org/10.3390/land13050578 (registering DOI) - 27 Apr 2024
Abstract
Land use is an embodiment of human socio-economic activities and represents a bridge between these activities and natural systems. Rural residential land represents a space for rural residents to reside in and exhibits spatial characteristics that evolve over time, which is proof of [...] Read more.
Land use is an embodiment of human socio-economic activities and represents a bridge between these activities and natural systems. Rural residential land represents a space for rural residents to reside in and exhibits spatial characteristics that evolve over time, which is proof of rural socio-economic development. As one of the most developed regions in China, cities along the Beijing–Hangzhou Canal experienced significant changes in rural residential land use from 1990 to 2020. This paper analyses the spatial differentiation of rural residential land in 21 cities on the Grand Canal. Then, it explores the driving factors of this land using spatial grid analysis and the geographic detector model. According to the spatial differentiation characteristics and the driving factors of rural residential land, the study proposed an improved potential model for rural residential land improvement. Lastly, it proposes three different forms of rural residential land based on the results. The study found that (1) the change in rural residential land in the northern part of the Grand Canal was more volatile than that in the southern part. The change in rural residential land from 1990 to 2020 conformed to the pattern of cultivated land–rural residential land–urban construction land. (2) Based on the driving factors of rural residential land, the land is divided into one-dimensional cities, two-dimensional cities, and three-dimensional cities. Circular, linear, and scattered cities of different sizes were affected by socio-economic factors, transportation accessibility, and the natural environment, respectively. (3) Based on the potential scale of rural residential land consolidation, different types of development strategies were proposed through research, including constructing large-scale villages, relocating and reconstructing new villages, and constructing high-quality villages, respectively. Enhancing the scientific planning of rural residential land and its efficiency and tapping into the potential of land consolidation can offer the protection of agricultural land and the integration of urban and rural areas in the new era. Full article
11 pages, 271 KiB  
Article
Chemical Composition and Elements Concentration of Fillet, Spine and Bones of Common Carp (Cyprinus carpio) in Relation to Nutrient Requirements for Minerals
by Agnieszka Kaliniak-Dziura, Piotr Skałecki, Mariusz Florek, Monika Kędzierska-Matysek and Paweł Sobczak
Animals 2024, 14(9), 1311; https://doi.org/10.3390/ani14091311 (registering DOI) - 27 Apr 2024
Abstract
The aim of the study was to compare the content of major components, selected elements and heavy metals in the fillet, spine and bones of a carp (Cyprinus carpio). Moreover, the extent to which a prepared portion of carp tissue (100 [...] Read more.
The aim of the study was to compare the content of major components, selected elements and heavy metals in the fillet, spine and bones of a carp (Cyprinus carpio). Moreover, the extent to which a prepared portion of carp tissue (100 g of fillet and 10 g of carp spine or bones) met the requirements for analyzed elements in adults (women and men) and children was calculated. The proximate composition (total protein, total lipid, ash, moisture) and mineral content of the fish samples were determined. The nutrient composition presented fluctuations among the different tissues. Moisture was the main constituent in the fillet and in the spine with 77.8% and 56.0%, respectively, whereas in bones, the main ingredient was ash (36.2%). All carp tissues were good sources of protein, with 16.5%, 21.0% and 17.0% in spine, bones and fillet, respectively. The most abundant main elements were the potassium in the fillet (4005 mg kg−1) and calcium in the bones (116,463 mg kg−1). The most abundant trace elements were iron in fillet and zinc in bones and spine. Carp meat can be considered a safe foodstuff in terms of concentrations of Hg, Pb and Cd, as the levels of these contaminants were less than FAO and European Commission maximum guidelines. Full article
(This article belongs to the Section Animal Nutrition)
24 pages, 49122 KiB  
Article
Integrated Remote Sensing for Geological and Mineralogical Mapping of Pb-Zn Deposits: A Case Study of Jbel Bou Dahar Region Using Multi-Sensor Imagery
by Marouane Chniouar, Amina Wafik, Youssef Daafi and Daniela Guglietta
Mining 2024, 4(2), 302-325; https://doi.org/10.3390/mining4020018 (registering DOI) - 27 Apr 2024
Abstract
This research applies remote sensing methodologies for the first time to comprehensively explore the geological and mineralogical characteristics of the Jbel Bou Dahar region. An integrated approach with multi-sensor satellite images, including ASTER, Landsat-8, and Sentinel-2 was applied with the aim to discriminate [...] Read more.
This research applies remote sensing methodologies for the first time to comprehensively explore the geological and mineralogical characteristics of the Jbel Bou Dahar region. An integrated approach with multi-sensor satellite images, including ASTER, Landsat-8, and Sentinel-2 was applied with the aim to discriminate the different lithological units in the study area. We implemented a suite of well-established image processing techniques, including Band Ratios, Principal Component Analysis, and Spectral Angle Mapper, to successfully identify, classify, and map the spatial distribution of carbonate minerals, OH-bearing minerals, and iron oxide minerals. Due to its high spectral resolution in the short-wave infrared region (SWIR), the ASTER sensor provided the most accurate results for mapping carbonate and OH-bearing minerals compared to the Sentinel-2 and Landsat-8 sensors. Conversely, Sentinel-2 offers high spectral and spatial resolution in visible and near-infrared (VNIR) corresponding to the regions where iron oxide minerals exhibit their characteristic absorption peaks. The results confirm the advantages of remote sensing technologies in the geological and mineralogical exploration of the study area and the importance of selecting the appropriate sensors for specific mapping objectives. Full article
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9 pages, 1055 KiB  
Communication
Advancing Evidence Generation for Circulating Tumor DNA: Lessons Learned from A Multi-Assay Study of Baseline Circulating Tumor DNA Levels across Cancer Types and Stages
by Brittany A. McKelvey, Hillary S. Andrews, Frederick L. Baehner, James Chen, Carin R. Espenschied, David Fabrizio, Vanessa Gorton, Claire Gould, Justin Guinney, Greg Jones, Xiangyang Lv, Michael S. Nahorski, Melanie R. Palomares, Gary A. Pestano, Mark Sausen, Alain Silk, Nicole Zhang, Zhihong Zhang, Mark D. Stewart and Jeff D. Allen
Diagnostics 2024, 14(9), 912; https://doi.org/10.3390/diagnostics14090912 (registering DOI) - 27 Apr 2024
Abstract
Circulating tumor DNA (ctDNA) holds promise as a biomarker for predicting clinical responses to therapy in solid tumors, and multiple ctDNA assays are in development. However, the heterogeneity in ctDNA levels prior to treatment (baseline) across different cancer types and stages and across [...] Read more.
Circulating tumor DNA (ctDNA) holds promise as a biomarker for predicting clinical responses to therapy in solid tumors, and multiple ctDNA assays are in development. However, the heterogeneity in ctDNA levels prior to treatment (baseline) across different cancer types and stages and across ctDNA assays has not been widely studied. Friends of Cancer Research formed a collaboration across multiple commercial ctDNA assay developers to assess baseline ctDNA levels across five cancer types in early- and late-stage disease. This retrospective study included eight commercial ctDNA assay developers providing summary-level de-identified data for patients with non-small cell lung cancer (NSCLC), bladder, breast, prostate, and head and neck squamous cell carcinoma following a common analysis protocol. Baseline ctDNA levels across late-stage cancer types were similarly detected, highlighting the potential use of ctDNA as a biomarker in these cancer types. Variability was observed in ctDNA levels across assays in early-stage NSCLC, indicative of the contribution of assay analytical performance and methodology on variability. We identified key data elements, including assay characteristics and clinicopathological metadata, that need to be standardized for future meta-analyses across multiple assays. This work facilitates evidence generation opportunities to support the use of ctDNA as a biomarker for clinical response. Full article
(This article belongs to the Special Issue Emerging Biomarkers of Clinical Diagnosis)
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15 pages, 1335 KiB  
Article
Embedding Secret Data in a Vector Quantization Codebook Using a Novel Thresholding Scheme
by Yijie Lin, Jui-Chuan Liu, Ching-Chun Chang and Chin-Chen Chang
Mathematics 2024, 12(9), 1332; https://doi.org/10.3390/math12091332 (registering DOI) - 27 Apr 2024
Abstract
In recent decades, information security has become increasingly valued, including many aspects of privacy protection, copyright protection, and digital forensics. Therefore, many data hiding schemes have been proposed and applied to various carriers such as text, images, audio, and videos. Vector Quantization (VQ) [...] Read more.
In recent decades, information security has become increasingly valued, including many aspects of privacy protection, copyright protection, and digital forensics. Therefore, many data hiding schemes have been proposed and applied to various carriers such as text, images, audio, and videos. Vector Quantization (VQ) compression is a well-known method for compressing images. In previous research, most methods related to VQ compressed images have focused on hiding information in index tables, while only a few of the latest studies have explored embedding data in codebooks. We propose a data hiding scheme for VQ codebooks. With our approach, a sender XORs most of the pixel values in a codebook and then applies a threshold to control data embedding. The auxiliary information generated during this process is embedded alongside secret data in the index reordering phase. Upon receiving the stego codebook and the reordered index table, the recipient can extract the data and reconstruct the VQ-compressed image using the reverse process. Experimental results demonstrate that our scheme significantly improves embedding capacity compared to the most recent codebook-based methods. Specifically, we observe an improvement rate of 223.66% in a small codebook of size 64 and an improvement rate of 85.19% in a codebook of size 1024. Full article
24 pages, 1506 KiB  
Article
Study on the Mechanism of Exogenous 5-Aminolevulinic Acid (ALA) in Regulating the Photosynthetic Efficiency of Pear Leaves
by Xinqing Wang, Jianting Zhang and Liangju Wang
Forests 2024, 15(5), 769; https://doi.org/10.3390/f15050769 (registering DOI) - 27 Apr 2024
Abstract
To provide a theoretical basis for the application of ALA in pear production, the effects of exogenous 5-aminolevulinic acid (ALA) treatment on leaf photosynthetic gas exchange parameters, chlorophyll fast fluorescence properties, and relative expression of the related genes were investigated using pear ( [...] Read more.
To provide a theoretical basis for the application of ALA in pear production, the effects of exogenous 5-aminolevulinic acid (ALA) treatment on leaf photosynthetic gas exchange parameters, chlorophyll fast fluorescence properties, and relative expression of the related genes were investigated using pear (Pyrus pyrifolia Nakai cv. ‘Whasan’) as a material in the study. The results show that exogenous ALA treatment improved the photosynthetic gas exchange parameters of pear leaves, upregulated the expression of multiple key genes which are related to ALA biosynthesis, metabolism, and transformation into chlorophylls. GUS staining in tobacco leaves showed that exogenous ALA activated the promoter activity of PypHEMA and PypCHLH genes, implying that the synthesis of endogenous ALA and chlorophylls was promoted by exogenous ALA. Furthermore, ALA promoted the expression of the genes encoding photosystem II (PSII) reaction center proteins, such as core protein D1, inner light-harvesting pigment proteins CP43 and CP47, and cytochrome b559. This led to increased PSII reaction center activity. In addition, ALA alleviated the donor side oxygen-evolving complex inhibition and reduced the closure rate on the receptor side, allowing for increased photochemical electron transfer and reduced heat dissipation while improving the photosynthetic performance index PIabs and PItotal. The findings of this study contribute to a better understanding of ALA’s promotion of plant photosynthetic efficiency, providing valuable insights for further research and potential applications in pear production. Full article
(This article belongs to the Section Forest Ecophysiology and Biology)

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