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Search Results (221)

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30 pages, 6897 KiB  
Article
Research on UAV Autonomous Recognition and Approach Method for Linear Target Splicing Sleeves Based on Deep Learning and Active Stereo Vision
by Guocai Zhang, Guixiong Liu and Fei Zhong
Electronics 2024, 13(24), 4872; https://doi.org/10.3390/electronics13244872 (registering DOI) - 10 Dec 2024
Viewed by 307
Abstract
This study proposes an autonomous recognition and approach method for unmanned aerial vehicles (UAVs) targeting linear splicing sleeves. By integrating deep learning and active stereo vision, this method addresses the navigation challenges faced by UAVs during the identification, localization, and docking of splicing [...] Read more.
This study proposes an autonomous recognition and approach method for unmanned aerial vehicles (UAVs) targeting linear splicing sleeves. By integrating deep learning and active stereo vision, this method addresses the navigation challenges faced by UAVs during the identification, localization, and docking of splicing sleeves on overhead power transmission lines. First, a two-stage localization strategy, LC (Local Clustering)-RB (Reparameterization Block)-YOLO (You Only Look Once)v8n (OBB (Oriented Bounding Box)), is developed for linear target splicing sleeves. This strategy ensures rapid, accurate, and reliable recognition and localization while generating precise waypoints for UAV docking with splicing sleeves. Next, virtual reality technology is utilized to expand the splicing sleeve dataset, creating the DSS dataset tailored to diverse scenarios. This enhancement improves the robustness and generalization capability of the recognition model. Finally, a UAV approach splicing sleeve (UAV-ASS) visual navigation simulation platform is developed using the Robot Operating System (ROS), the PX4 open-source flight control system, and the GAZEBO 3D robotics simulator. This platform simulates the UAV’s final approach to the splicing sleeves. Experimental results demonstrate that, on the DSS dataset, the RB-YOLOv8n(OBB) model achieves a mean average precision (mAP0.5) of 96.4%, with an image inference speed of 86.41 frames per second. By incorporating the LC-based fine localization method, the five rotational bounding box parameters (x, y, w, h, and angle) of the splicing sleeve achieve a mean relative error (MRE) ranging from 3.39% to 4.21%. Additionally, the correlation coefficients (ρ) with manually annotated positions improve to 0.99, 0.99, 0.98, 0.95, and 0.98, respectively. These improvements significantly enhance the accuracy and stability of splicing sleeve localization. Moreover, the developed UAV-ASS visual navigation simulation platform effectively validates high-risk algorithms for UAV autonomous recognition and docking with splicing sleeves on power transmission lines, reducing testing costs and associated safety risks. Full article
(This article belongs to the Section Computer Science & Engineering)
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Figure 1

Figure 1
<p>UAV carrying DR equipment approaches and docks with the splicing sleeve on overhead transmission lines. (<b>a</b>) Splicing sleeve; (<b>b</b>) DR; (<b>c</b>) UAV; (<b>d</b>) Approaching; (<b>e</b>) Docking/Hanging.</p>
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<p>Aerial views of splicing sleeves on overhead transmission lines. (<b>a</b>) Distant view; (<b>b</b>) Medium-distance view; (<b>c</b>) Close-up view; (<b>d</b>) Third-person aerial view showing the UAV inspecting the transmission line and splicing sleeves.</p>
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<p>Block Diagram of UAV-ASS Method.</p>
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<p>The network architecture diagram of the RB-YOLOv8(OBB) model.</p>
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<p>Structure and Reparameterization Process of the RepBlock Module.</p>
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<p>Schematic Diagram of the Rotated Bounding Box Output for the Splicing Sleeve from Rapid Localization.</p>
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<p>Diagram of the Fine Localization Principle for Rotational Object Detection Using LC. (<b>a</b>) Boundary calculation of the coarsely localized rectangular box for the splicing sleeve in the local region <span class="html-italic">R</span><sub>DE</sub>; (<b>b</b>) Boundary calculation of the coarsely localized rectangular box for the splicing sleeve in the local region <span class="html-italic">R</span><sub>DE</sub>, and clustering and fitting of the depth values <span class="html-italic">D</span><sub>R</sub> in region <span class="html-italic">R</span><sub>DE</sub>; (<b>c</b>) Fine localization of the splicing sleeve’s rotated bounding box B<sub>F_RGB</sub>.</p>
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<p>Rules for obtaining <span class="html-italic">D</span><sub>UAV-SS.</sub></p>
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<p>UAV-ASS Coordinate system.</p>
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<p>Schematic Diagram of UAV Approaching the Splicing Sleeve.</p>
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<p>Virtual Scenario of Splicing Sleeve for Dataset Augmentation.</p>
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<p>Comparison of Model Size, mAP0.5, and Speed for Different Rotational Object Detection Models. (<b>a</b>) Model Size (MB) vs. FPS; (<b>b</b>) mAP0.5 (%) vs. FPS.</p>
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<p>Different scene recognition effect diagrams, with (<b>a</b>–<b>c</b>), (<b>d</b>–<b>f</b>), and (<b>g</b>–<b>i</b>) corresponding to the hazy static, real/virtual, and UAV aerial dynamic scenarios, respectively.</p>
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<p>Diagram of Localization Using Three Methods.</p>
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<p>Comparison of Five Coordinate Parameters Using Different Methods Across Various Metrics. (<b>a</b>) MAE of Parameters; (<b>b</b>) MRE of Parameters; (<b>c</b>) RMSE of Parameters; (<b>d</b>) <span class="html-italic">ρ</span> of Parameters.</p>
Full article ">Figure 15 Cont.
<p>Comparison of Five Coordinate Parameters Using Different Methods Across Various Metrics. (<b>a</b>) MAE of Parameters; (<b>b</b>) MRE of Parameters; (<b>c</b>) RMSE of Parameters; (<b>d</b>) <span class="html-italic">ρ</span> of Parameters.</p>
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<p>Positioning results of B<sub>C_RGB</sub> and B<sub>F_RGB</sub>, B<sub>F_Depth</sub>. Panels (<b>a</b>–<b>c</b>), as well as (<b>d</b>–<b>f</b>), represent the B<sub>C_RGB</sub>, B<sub>F_RGB</sub>, and the B<sub>F_Depth</sub> results when the distance between the UAV and the splicing sleeve is 4.8 m and 1.2 m, respectively. Panels (<b>g</b>–<b>i</b>) display the positioning results of B<sub>C_RGB</sub>, B<sub>F_RGB</sub>, and B<sub>F_Depth</sub> using an Intel D455 depth camera in a laboratosry environment. The resolution of the images in panels (<b>a</b>–<b>f</b>) is 848 × 480, while the resolution in panels (<b>g</b>–<b>i</b>) is 640 × 480.</p>
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<p>UAV-ASS visual simulation system.</p>
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<p>UAV-ASS visual simulation system interface. (<b>a</b>) Main interface of the UAV-ASS simulation; (<b>b</b>) resulting RGB image of the UAV’s visual recognition and localization of the splicing sleeve; (<b>c</b>) depth map of the UAV’s visual recognition and localization of the splicing sleeve.</p>
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<p>UAV calculating <span class="html-italic">D</span><sub>UAV-SS</sub> using B<sub>C_Depth</sub> and B<sub>F_ Depth</sub> for splicing sleeve localization. (<b>a</b>) UAV Fixed-Point Rotation; (<b>b</b>) <span class="html-italic">D</span><sub>UAV-SS</sub> extraction using B<sub>C_Depth</sub> localization; (<b>c</b>) <span class="html-italic">D</span><sub>UAV-SS</sub> extraction using B<sub>F_Depth</sub> localization.</p>
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<p>Video screenshots of the UAV body coordinate trajectory and B<sub>F_RGB</sub>-located splicing sleeve position during the UAV recognition and docking process.</p>
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<p>Video screenshots of the UAV body coordinate trajectory and B<sub>F_RGB</sub>-located splicing sleeve position during the UAV recognition and docking process.</p>
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<p>Changes in the UAV Pose Adjustment Process during Approach and Docking.</p>
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<p>UAV Initial Positions at Different Starting Points.</p>
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37 pages, 5363 KiB  
Article
Design, Synthesis, Antimicrobial Activity, and Molecular Docking of Novel Thiazoles, Pyrazoles, 1,3-Thiazepinones, and 1,2,4-Triazolopyrimidines Derived from Quinoline-Pyrido[2,3-d] Pyrimidinones
by Ameen Ali Abu-Hashem and Sami A. Al-Hussain
Pharmaceuticals 2024, 17(12), 1632; https://doi.org/10.3390/ph17121632 - 4 Dec 2024
Viewed by 666
Abstract
Background: Recently, pyrido[2,3-d] pyrimidine, triazolopyrimidine, thiazolopyrimidine, quinoline, and pyrazole derivatives have gained attention due to their diverse biological activities, including antimicrobial, antioxidant, antitubercular, antitumor, anti-inflammatory, and antiviral effects. Objective: The synthesis of new heterocyclic compounds including 5-quinoline-pyrido[2,3-d] pyrimidinone ( [...] Read more.
Background: Recently, pyrido[2,3-d] pyrimidine, triazolopyrimidine, thiazolopyrimidine, quinoline, and pyrazole derivatives have gained attention due to their diverse biological activities, including antimicrobial, antioxidant, antitubercular, antitumor, anti-inflammatory, and antiviral effects. Objective: The synthesis of new heterocyclic compounds including 5-quinoline-pyrido[2,3-d] pyrimidinone (12, 4, 67), 6-quinoline-pyrido[2,3-d]thiazolo[3,2-a]pyrimidinone (3, 5, 810), 1,2,4-triazole-6-quinoline-pyrido[2,3-d]thiazolo[3,2-a]pyrimidinone (1113), and pyrido[2,3-d]thiazolo[3,2-a]pyrimidine-ethyl-(pyridine)-9-thiaazabenzo[cd]azulenone (14) derivatives was performed with high yields while evaluating antimicrobial activities. Methods: A new series of quinoline-pyrido[2,3-d]thiazolo[3,2-a]pyrimidine derivatives were prepared using a modern style and advanced technology, resulting in high yields of these new compounds. Various reagents were utilized, specifically tailored to the production needs of each compound, through reactions that included alkylation, addition, condensation, acylation, the formation of Schiff bases, and intramolecular cyclization. Results: The chemical structures of the new compounds were determined using spectroscopy analyses, including IR, NMR, and MS, achieving good yields ranging from 68% to 90% under mild conditions in a regular system. All compounds were tested for in vitro antimicrobial activity and compared to standard drugs, specifically cefotaxime sodium and nystatin. The results showed that compounds 10 to 14 exhibited excellent antimicrobial activity, with a minimum inhibitory concentration (MIC) of 1 to 5 µmol/mL, compared to that of the standard drugs, which had MIC values of 1 to 3 µmol/mL. Furthermore, molecular docking studies were conducted to explore the interactions of specific compounds with antimicrobial target proteins. The findings revealed that compounds 10 to 14 displayed significant binding energies, with ΔG values ranging from −7.20 to −11.70 kcal/mol, indicating effective binding to the active sites of antimicrobial protein receptors. Conclusions: The SAR study confirmed a relationship between antimicrobial activity and the tested compounds. Molecular docking demonstrated that compounds 10, 11, 12, 13, and 14 exhibited significant binding energy, effectively interacting with the active sites of antimicrobial protein receptors. This consistent finding supports that these new compounds’ practical and theoretical studies align regarding their antimicrobial activity. Full article
(This article belongs to the Section Medicinal Chemistry)
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Figure 1

Figure 1
<p>Some drugs with interesting molecules of Pyrido[2,3-<span class="html-italic">d</span>] pyrimidine derivatives (all of these drugs contain the Pyrido[2,3-<span class="html-italic">d</span>] pyrimidine moiety, so this moiety is red, and all the nitrogen atoms are blue.).</p>
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<p>Certain drugs contain derivatives of quinoline (all of these drugs contain the quinoline moiety, so this moiety is red, and all the nitrogen atoms are blue).</p>
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<p>Three-dimensional representations of the compound at the binding pocket of dihydropteroate synthase of <span class="html-italic">S. aureus</span> (PDB: ID 1AD4): (<b>a</b>,<b>b</b>) <b>10</b>; (<b>c</b>,<b>d</b>) <b>11</b>; (<b>e</b>,<b>f</b>) <b>12</b>; (<b>g</b>,<b>h</b>) <b>13;</b> (<b>i</b>,<b>j</b>) <b>14;</b> and (<b>k</b>,<b>l</b>) cefotaxime.</p>
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<p>Three-dimensional representations of compounds at the binding pocket of DNA gyrase of <span class="html-italic">E. coli</span> (PDB: ID 7P2M): (<b>a</b>,<b>b</b>) <b>10</b>; (<b>c</b>,<b>d</b>) <b>11</b>; (<b>e</b>,<b>f</b>) <b>12</b>; (<b>g</b>,<b>h</b>) <b>13;</b> (<b>i</b>,<b>j</b>) <b>14;</b> and (<b>k</b>,<b>l</b>) cefotaxime.</p>
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<p>Three-dimensional representations of the compound at the binding pocket of Sortase A in <span class="html-italic">S. pyogenes</span> (PDB: ID 8T8G): (<b>a</b>,<b>b</b>) <b>10</b>; (<b>c</b>,<b>d</b>) <b>11</b>; (<b>e</b>,<b>f</b>) <b>12</b>; (<b>g</b>,<b>h</b>) <b>13</b>; (<b>i</b>,<b>j</b>) <b>14</b>; and (<b>k</b>,<b>l</b>) cefotaxime.</p>
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<p>Three-dimensional representations of compounds at the binding pocket of KPC-2 carbapenemase of <span class="html-italic">K. pneumoniae</span> (PDB: ID 2OV5): (<b>a</b>,<b>b</b>) <b>10</b>; (<b>c</b>,<b>d</b>) <b>11</b>; (<b>e</b>,<b>f</b>) <b>12</b>; (<b>g</b>,<b>h</b>) <b>13</b>; (<b>i</b>,<b>j</b>) <b>14</b>; and (<b>k</b>,<b>l</b>) cefotaxime.</p>
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<p>Three-dimensional representations of compound conformations at the binding pocket of sterol 14-alpha demethylase of <span class="html-italic">C. albicans</span> (PDB: ID 5TZ1): (<b>a</b>,<b>b</b>) <b>10</b>; (<b>c</b>,<b>d</b>) <b>11</b>; (<b>e</b>,<b>f</b>) <b>12</b>; (<b>g</b>,<b>h</b>) <b>13</b>; (<b>i</b>,<b>j</b>) <b>14</b>; and (<b>k</b>,<b>l</b>) nystatin.</p>
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<p>Three-dimensional representations of compound conformations at the binding pocket of the fdc1of <span class="html-italic">A. niger</span> (PDB: ID 4ZA5): (<b>a</b>,<b>b</b>) <b>10</b>; (<b>c</b>,<b>d</b>) <b>11</b>; (<b>e</b>,<b>f</b>) <b>12</b>; (<b>g</b>,<b>h</b>) <b>13;</b> (<b>i</b>,<b>j</b>) <b>14;</b> and (<b>k</b>,<b>l</b>) nystatin.</p>
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<p>Three-dimensional representations of compound conformations at the binding pocket of AaTPS of <span class="html-italic">Alternaria alternata</span> (PDB: ID 6LCD): (<b>a</b>,<b>b</b>) <b>10</b>; (<b>c</b>,<b>d</b>) <b>11</b>; (<b>e</b>,<b>f</b>) <b>12</b>; (<b>g</b>,<b>h</b>) <b>13</b>; (<b>i</b>,<b>j</b>) <b>14</b> and (<b>k</b>,<b>l</b>) nystatin.</p>
Full article ">Scheme 1
<p>Synthesis of 3-sub-phenyl-6-(quinoline)-pyrido[2,3-<span class="html-italic">d</span>]thiazolo[3,2-<span class="html-italic">a</span>]pyrimidinones (to clarify the type of reagents, one contains chlorine, and the other contains bromine; therefore, they are represented in different colours).</p>
Full article ">Scheme 2
<p>Synthesis of thiazole, pyrazole, and thioxopyrimidine with quinoline-pyrido[2,3-<span class="html-italic">d</span>] pyrimidinone derivatives.</p>
Full article ">Scheme 3
<p>Synthesis of hydroxyimino, 4-sub-(phenyl) acryloyl, and hydrazine-1-carbothio-amide linked to quinoline-pyrido[2,3-<span class="html-italic">d</span>]thiazolo[3,2-<span class="html-italic">a</span>] pyrimidine derivatives.</p>
Full article ">Scheme 4
<p>Synthesis of 1,3-thiazepinone and 1,2,4-triazolopyrimidine linked to quinoline-pyrido[2,3-<span class="html-italic">d</span>]thiazolo[3,2-<span class="html-italic">a</span>] pyrimidine derivatives (arrows illustrate the reaction mechanism and the formation direction of the product).</p>
Full article ">
22 pages, 19618 KiB  
Article
Advanced PROTAC and Quantitative Proteomics Strategy Reveals Bax Inhibitor-1 as a Critical Target of Icaritin in Burkitt Lymphoma
by Peixi Zhang, Ziqing Zhang, Jie Li, Meng Xu, Weiming Lu, Ming Chen, Jiaqi Shi, Qiaolai Wang, Hengyuan Zhang, Shi Huang, Chenlei Lian, Jia Liu, Junjie Ma and Jieqing Liu
Int. J. Mol. Sci. 2024, 25(23), 12944; https://doi.org/10.3390/ijms252312944 - 2 Dec 2024
Viewed by 430
Abstract
Understanding the molecular targets of natural products is crucial for elucidating their mechanisms of action, mitigating toxicity, and uncovering potential therapeutic pathways. Icaritin (ICT), a bioactive flavonoid, demonstrates significant anti-tumor activity but lacks defined molecular targets. This study employs an advanced strategy integrating [...] Read more.
Understanding the molecular targets of natural products is crucial for elucidating their mechanisms of action, mitigating toxicity, and uncovering potential therapeutic pathways. Icaritin (ICT), a bioactive flavonoid, demonstrates significant anti-tumor activity but lacks defined molecular targets. This study employs an advanced strategy integrating proteolysis targeting chimera (PROTAC) technology with quantitative proteomics to identify ICT’s key targets. A library of 22 ICT-based PROTAC derivatives were synthesized, among which LJ-41 exhibited a superior IC50 of 5.52 μM against Burkitt lymphoma (CA-46) cells. Then, differential proteomic analysis identified Bax inhibitor-1 (BI-1) as a potential target. Target validation techniques, including cellular thermal shift assay (CETSA), drug affinity responsive target stability (DARTS) assay, surface plasmon resonance (SPR) assay, and molecular docking, confirmed LJ-41’s high specificity for BI-1. Mechanistic investigations revealed that LJ-41 induces apoptosis through BI-1 degradation, triggering endoplasmic reticulum stress and activating inositol-requiring enzyme 1 α (IRE1α), activating transcription factor 6 (ATF6), and nuclear factor erythroid 2-related factor transcription factor heme oxygenase 1 (NRF2-HO-1) signaling pathways. This study establishes a refined methodological framework for natural product target discovery and highlights ICT-PROTAC derivatives’ potential for clinical application in Burkitt lymphoma treatment. Full article
(This article belongs to the Section Molecular Oncology)
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Figure 1

Figure 1
<p>The design of ICT PROTACs. (<b>A</b>) Chemical structure diagram of ICT and POI ligands designed on its basis. (<b>B</b>) Diagram of the mechanism of PROTACs-induced degradation of target proteins. (<b>C</b>) The chemical structure of each component of ICT-PROTACs.</p>
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<p>Cell viability (%) after compound action. (<b>A</b>) The effect of compounds on the viability of SH-SY5Y cells. (<b>B</b>) Effects of compounds on the activity of MCF-7 cells. (<b>C</b>) The effect of compounds on the viability of CA-46 cells. Data are presented as mean ± SEM.</p>
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<p>TMT differential proteomics reveals that BI-1 is a potential target of anti-CA-46 cell action for <b>LJ-41</b>. (<b>A</b>) Structure of compound <b>LJ-41</b>. (<b>B</b>) The downregulated (blue) and upregulated (red) proteins associated with the tumor were plotted as fold change (<b>LJ-41</b>/Control) versus −Log10 of the <span class="html-italic">p</span>-value (<span class="html-italic">t</span>-test). (<b>C</b>) The downregulated(blue) and upregulated (red) proteins associated with the tumor were plotted as fold change (<b>LJ-41</b>/<b>1a</b>) versus −Log10 of the <span class="html-italic">p</span>-value (<span class="html-italic">t</span>-test). (<b>D</b>) The fold change in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment after 48 h treatment of <b>LJ-41</b> or DMSO control. (<b>E</b>) The fold change in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment after 48 h treatment of <b>LJ-41</b> or <b>1a</b>. (<b>F</b>) Classification histogram for GO enrichment analysis of differentially expressed proteins after 48 h treatment of <b>LJ-41</b> or DMSO control. (<b>G</b>) Classification histogram for GO enrichment analysis of differentially expressed proteins after 48 h treatment of <b>LJ-41</b> or <b>1a</b>. (<b>H</b>) Differentially expressed proteins were analyzed by hierarchical clustering and visualized by heat maps to visualize the changing patterns of differences found between experimental groups of differentially expressed proteins.</p>
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<p>BI-1 is a degradation target of <b>LJ-41</b>. (<b>A</b>) Immunoblot analysis of concentration-dependent degradation of BI-1 protein in CA-46 cells. (<b>B</b>) Immunoblot analysis of time-dependent degradation of BI-1 protein in CA-46 cells. (<b>C</b>) Immunoblot analysis of BI-1 protein in CA-46 cells pre-treated with MG132 for 12 h and subsequently treated with either DMSO or <b>LJ-41</b> for 48 h. (<b>D</b>) Immunoblot analysis of BI-1 protein in CA-46 cells treated by <b>LJ-41</b> together with either 1a or Lenalidomide for 48 h. Immunoblot analysis data were normalized with β-Actin. Data are presented as mean ± SEM. <sup>ns</sup> <span class="html-italic">p</span> &gt; 0.05, * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.005, *** <span class="html-italic">p</span> &lt; 0.001 compared with the 0 μM control group.</p>
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<p><b>1a</b> directly binds to BI-1. (<b>A</b>) Fitted plot of affinity determination of <b>LJ-41</b> with BI-1. (<b>B</b>) CETSA to detect the thermal stability of cellular BI-1 protein. (<b>C</b>) DARTS assay to test the stability of cellular BI-1 protein under enzyme degradation. Data are presented as mean ± SEM. * <span class="html-italic">p</span> &lt; 0.05 compared with the control group.</p>
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<p>Molecular docking simulation. (<b>A</b>) Binding pattern of compound a with the target protein BI-1 (UniProtKB/Swiss-Prot: P55061), compound a is a green rod-like structure. (<b>B</b>) Diagram of the binding pattern of ICT to the target protein BI-1, ICT is a blue rod-like structure. (<b>C</b>) Schematic simulation of molecular docking between ICT and BI-1, and ICT is represented as an orange rod-like structure, the green solid line indicates Pi–Pi stacking, and the gray dashed line represents hydrophobic interactions. (<b>D</b>) Schematic diagram of molecular docking simulation of ICT-PROTAC (<b>LJ-41</b>) with BI-1, and ICT-PROTAC (<b>LJ-41</b>) is represented as an orange rod-like structure, the green solid line indicates Pi–Pi stacking, and the gray dashed line represents hydrophobic interactions.</p>
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<p><b>LJ-41</b> promotes apoptosis by degrading the BI-1 induced ERS pathway. (<b>A</b>) Immunoblot analysis of ATF6, BIP, CHOP, Caspase-9 and Cleaved-caspase 9. (<b>B</b>) Immunoblot analysis of P-IRE1, IRE1, Caspase 12 and P38. (<b>C</b>) Immunoblot analysis of NRF2 and HO-1. Data are presented as mean ± SEM. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.005, *** <span class="html-italic">p</span> &lt; 0.001 compared with the control group.</p>
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<p>Mechanism of <b>LJ-41</b>-induced CA-46 cell death through BI-1 degradation.</p>
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16 pages, 21217 KiB  
Article
Global Identification of Anti-Melanoma Cellular Targets by Photochemically Induced Coupling of L-Shikonin Reactions on the Surface of Magnetic Particles
by Min Li, Wenying Li, Fang Xu, Yiping Pu and Jianguang Li
Pharmaceutics 2024, 16(12), 1543; https://doi.org/10.3390/pharmaceutics16121543 - 2 Dec 2024
Viewed by 572
Abstract
Background: L-Shikonin, an active component of Arnebia euchroma (Royle) Johnst., has remarkable pharmacological effects, particularly in its anti-tumour activity. Nonetheless, the specific targets and mechanisms of action remain to be further explored. Methods: A novel Fe3O4@L-Shikonin [...] Read more.
Background: L-Shikonin, an active component of Arnebia euchroma (Royle) Johnst., has remarkable pharmacological effects, particularly in its anti-tumour activity. Nonetheless, the specific targets and mechanisms of action remain to be further explored. Methods: A novel Fe3O4@L-Shikonin was designed and synthesized in this study by linking Fe3O4 and L-Shikonin through benzophenone. Fe3O4@L-Shikonin was characterized using several techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR), and drug removal methods, to determine the content of L-Shikonin on the surface of the magnetic particles. Target hooking technology was utilized to identify the target proteins of the compound in melanoma. The synthesized Fe3O4@L-Shikonin was co-incubated with A375 cell lysate, followed by the target proteins, which were purified by magnetic enrichment using magnetic microspheres and identified by high-resolution mass spectrometry. Results: AutoDock Vina software was employed for molecular docking analysis, where it was found that L-Shikonin targets RPN1, CPEB4, and HNRNPUL1 proteins. Subsequently, A375 cells were treated with L-Shikonin at different concentrations (2.5, 5.0, 10.0 μM) for 48 h, and the expressions of the three proteins were observed. The results showed a significant reduction in the relative expression of CPEB4 in the high-dose group compared to the control group (p < 0.01). Moreover, the relative expression of HNRNPUL1 was decreased in the medium- and high-dose groups (p < 0.05). Conclusions: This study initially revealed from the source that L-Shikonin may regulate melanoma-specific markers, melanosomes, tyrosine kinases related to abnormal tyrosine metabolism, and melanoma through multiple targets such as CPEB4 and HNRNPUL1. Proliferation and metastasis work together to exert an anti-melanoma mechanism, which provides a new idea for the follow-up study of the molecular pharmacological mechanism of the complex system of total naphthoquinones in Arnebia euchroma (Royle) Johns. Full article
(This article belongs to the Special Issue Applications of Nanotechnology for Melanoma Treatment and Diagnosis)
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Figure 1

Figure 1
<p><span class="html-italic">L-Shikonin</span> structure.</p>
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<p>Schematic diagram of the Fe<sub>3</sub>O<sub>4</sub>@<span class="html-italic">L-Shikonin</span> structure exhibits the ability to detect cellular targets. On the surface of Fe<sub>3</sub>O<sub>4</sub>-SH, sulfhydryl groups react with the isocyanate groups of 2-isocyanatoethyl 2,6-diisocuanatohexanoate (LTI) via click chemistry. Subsequently, a condensation reaction occurs between the isocyanate groups at the opposite end of LTI and the hydroxyl groups of hydroxyl-containing 4,4′-dihydroxybenzophenone (DHBP), culminating in the creation of Fe<sub>3</sub>O<sub>4</sub>@<span class="html-italic">L-Shikonin.</span></p>
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<p>(<b>A</b>) Synthesis of Fe<sub>3</sub>O<sub>4</sub>-BP photosensitive magnetic particles through a polymerization reaction. (<b>B</b>) <span class="html-italic">L-Shikonin</span> binds to the surface of magnetic particles (Fe<sub>3</sub>O<sub>4</sub>-BP) to form drug-conjugated magnetic particles (Fe<sub>3</sub>O<sub>4</sub>-BP-<span class="html-italic">L-Shikonin</span>). BP in the chemical structure denotes benzophenone.</p>
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<p>The cell viability of A375 cells treated by <span class="html-italic">L-Shikonin</span> was measured by CCK-8 assay. ** <span class="html-italic">p</span> &lt; 0.01 vs. Con, n = 3.</p>
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<p>(<b>A</b>) Cell apoptosis was analysed via Annexin-V/PI staining. Cells shown in the lower right and upper right represent the percentages of early and late apoptosis, respectively. (<b>B</b>) Percentage of cells showing live and apoptosis. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01 vs. Con, n = 3.</p>
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<p>(<b>A</b>) A375 cells were treated with <span class="html-italic">L-Shikonin</span> (0, 2.5, 5, and 10 μM) for 24 h followed by staining with propidium iodide for flow cytometric analysis. (<b>B</b>) The proportion of G0/G1, S, and G2/M phase in the cell cycle. Significant analysis of G2/M phase: * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01 vs. Con, n = 3.</p>
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<p>(<b>A</b>) SEM images of Fe<sub>3</sub>O<sub>4</sub>-SH magnetic particles, (<b>B</b>) SEM images of Fe<sub>3</sub>O<sub>4</sub>@<span class="html-italic">L-Shikonin</span> magnetic particles, (<b>C</b>) size statistics of Fe<sub>3</sub>O<sub>4</sub>-SH and Fe<sub>3</sub>O<sub>4</sub>@<span class="html-italic">L-Shikonin</span> in a Malvern particle sizer, (<b>D</b>) potential statistics of Fe<sub>3</sub>O<sub>4</sub>-SH and Fe<sub>3</sub>O<sub>4</sub>@<span class="html-italic">L-Shikonin</span>: * <span class="html-italic">p</span> &lt; 0.05, **** <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>(<b>A</b>) Comparison of UV absorption spectra of supernatants before and after coupling <span class="html-italic">L-Shikonin</span>. (<b>B</b>) UV spectra of base hydrolysis before and after coupling <span class="html-italic">L-Shikonin</span>. (<b>C</b>) IR spectra before and after coupling <span class="html-italic">L-Shikonin</span>.</p>
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<p>Differential protein screening. The yellow and red lines are the screening boundaries for differential proteins.</p>
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<p>(<b>A</b>) Venn diagram of Fe3O4@<span class="html-italic">L-Shikonin</span> hooked differential protein and melanoma-related targets. (<b>B</b>) Molecular docking diagram of <span class="html-italic">L-Shikonin</span> with CPEB4, RPN1, and HNRNPUL1.</p>
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<p>(<b>A</b>) Effect of <span class="html-italic">L-Shikonin</span> on the expression of protein CPEB4. (<b>B</b>) Effect of <span class="html-italic">L-Shikonin</span> on the expression of protein HNRNPUL1. (<b>C</b>) Effect of <span class="html-italic">L-Shikonin</span> on the expression of protein RPN1. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01 vs. Con, n = 3.</p>
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14 pages, 5273 KiB  
Article
Structure of Genes Encoding Oxidosqualene Cyclases—Key Enzymes of Triterpenoid Biosynthesis from Sea Cucumber Eupentacta fraudatrix
by Sergey N. Baldaev, Viktoria E. Chausova, Ksenia V. Isaeva, Alexey V. Boyko, Valentin A. Stonik and Marina P. Isaeva
Int. J. Mol. Sci. 2024, 25(23), 12881; https://doi.org/10.3390/ijms252312881 - 29 Nov 2024
Viewed by 360
Abstract
Oxidosqualene cyclases (OSCs) are enzymes responsible for converting linear triterpenes into tetracyclic ones, which are known as precursors of other important and bioactive metabolites. Two OSCs genes encoding parkeol synthase and lanostadienol synthase have been found in representatives of the genera Apostichopus and [...] Read more.
Oxidosqualene cyclases (OSCs) are enzymes responsible for converting linear triterpenes into tetracyclic ones, which are known as precursors of other important and bioactive metabolites. Two OSCs genes encoding parkeol synthase and lanostadienol synthase have been found in representatives of the genera Apostichopus and Stichopus (family Stichopodidae, order Synallactida). As a limited number of sea cucumber OSCs have been studied thus far, OSCs encoding gene(s) of the sea cucumber Eupentacta fraudatrix (family Sclerodactylidae, order Dendrochirotida) were investigated to fill this gap. Here, we employed RACEs, molecular cloning, and Oxford Nanopore Technologies to identify candidate OSC mRNAs and genes. The assembled cDNAs were 2409 bp (OSC1) and 3263 bp (OSC2), which shared the same CDS size of 2163 bp encoding a 721-amino-acid protein. The E. fraudatrix OSC1 and OSC2 had higher sequence identity similarity to each other (77.5%) than to other holothurian OSCs (64.7–71.0%). According to the sequence and molecular docking analyses, OSC1 with L436 is predicted to be parkeol synthase, while OSC2 with Q439 is predicted to be lanostadienol synthase. Based on the phylogenetic analysis, E. fraudatrix OSCs cDNAs clustered with other holothurian OSCs, forming the isolated branch. As a result of gene analysis, the high polymorphism and larger size of the OSC1 gene suggest that this gene may be an ancestor of the OSC2 gene. These results imply that the E. fraudatrix genome contains two OSC genes whose evolutionary pathways are different from those of the OSC genes in Stichopodidae. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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<p>Alignment of OSCs proteins from sea cucumbers, sea urchin, starfish, and human. <span class="html-italic">E. fraudatrix</span> OSC1 and OSC2 (OR725688 and OR711403 in this study); <span class="html-italic">A. japonicus</span> LAS1 (PS) and LAS2 (LDS) (ON478352.1 and ON478353.1, respectively); <span class="html-italic">A. parvimensis</span> PS and LDS (ON478351.1 and ON478350.1); <span class="html-italic">S. horrens</span> OSC1 and OSC2 [<a href="#B14-ijms-25-12881" class="html-bibr">14</a>]; LSS: <span class="html-italic">A. planci</span> (XM 022227483.1), <span class="html-italic">S. purpuratus</span> (ON478349.1), <span class="html-italic">H. sapiens</span> (NM 002340.6). Conservative residues are in red colors. Active site residues are indicated by black circles. QXXXW motifs are marked on a consensus sequence by black boxes. LWIHCR and DTTAE motifs are marked by red boxes. Key residues, which determine enzyme function, are labeled with the blue box.</p>
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<p>Molecular docking of triterpenoid in the active site of oxidosqualene cyclase. Functionally significant residues L436/L435 of <span class="html-italic">Ef</span>OSC1 (<b>a</b>) and <span class="html-italic">Aj</span>LAS1 (<b>b</b>) near the B and C rings of parkeol are shown in red. Functionally significant residues Q439/Q444 of <span class="html-italic">Ef</span>OSC2 (<b>c</b>) and <span class="html-italic">Aj</span>LAS2 (<b>d</b>) near the B ring of lanostadienol are shown by blue.</p>
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<p>Maximum likelihood (ML) phylogenetic trees based on amino acid sequences of OSCs with (<b>a</b>) and without (<b>b</b>) sea cucumbers: <span class="html-italic">H. sapiens</span> (NM 002340.6), <span class="html-italic">B. taurus</span> (NM 001046564.1), <span class="html-italic">M. musculus</span> (XM 036155651.1), <span class="html-italic">B. belcheri</span> (XM 019790446.1), <span class="html-italic">S. kowalevskii</span> (XM 006825036.1), <span class="html-italic">L. anatina</span> (XM 013562424.1), <span class="html-italic">L. gigantea</span> (XM 009046756.1), <span class="html-italic">P. canaliculata</span> (XM 025240299.1), <span class="html-italic">L. variegatus</span> (XM 041622296.1), <span class="html-italic">S. purpuratus</span> (ON478349.1), <span class="html-italic">P. miniata</span> (ON478348.1), <span class="html-italic">A. planci</span> (XM 022227483.1), <span class="html-italic">T. adhaerens</span> (XM 002110738.1), <span class="html-italic">A. queenslandica</span> (XM 003383129.3), <span class="html-italic">E. fraudatrix</span> OSC1 (OR725688, this study), <span class="html-italic">E. fraudatrix</span> OSC2 (OR711403, this study), <span class="html-italic">A. japonicus</span> LAS1 (ON478352.1), <span class="html-italic">A. japonicus</span> LAS2 (ON478353.1), <span class="html-italic">A. parvimensis</span> PS (ON478351.1), <span class="html-italic">A. parvimensis</span> LDS (ON478350.1), <span class="html-italic">S. horrens</span> OSC1 [<a href="#B14-ijms-25-12881" class="html-bibr">14</a>], <span class="html-italic">S. horrens</span> OSC2 [<a href="#B14-ijms-25-12881" class="html-bibr">14</a>], <span class="html-italic">D. discoideum</span> (XM 641154.1), and <span class="html-italic">S. cerevisiae</span> (NP 011939.2).</p>
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<p>Comparison of <span class="html-italic">E. fraudatrix</span> OSCs gene structures and their haplotypes. (<b>a</b>) Gene structure schemes. (<b>b</b>) Scatter plots of OSC1 and OSC2 transcripts (<b>1</b>), deduced amino acid sequences (<b>2</b>), and gene sequences (<b>3</b>) comparison. (<b>c</b>) Scatter plots of pairwise alignment through BLAST of four OSC1 gene haplotypes (comparison <b>1</b>—haplotypes 1 and 2; <b>2</b>—haplotypes 1 and 3; <b>3</b>—haplotypes 1 and 4; <b>4</b>—haplotypes 2 and 3; <b>5</b>—haplotypes 2 and 4; <b>6</b>—haplotypes 3 and 4). (<b>d</b>) Scatter plots of pairwise alignment through BLAST of four OSC2 gene haplotypes (comparison <b>1</b>—haplotypes 1 and 2; <b>2</b>—haplotypes 1 and 3; <b>3</b>—haplotypes 1 and 4; <b>4</b>—haplotypes 2 and 3; <b>5</b>—haplotypes 2 and 4; <b>6</b>—haplotypes 3 and 4).</p>
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21 pages, 11232 KiB  
Article
Deep Learning-Based Docking Scheme for Autonomous Underwater Vehicles with an Omnidirectional Rotating Optical Beacon
by Yiyang Li, Kai Sun, Zekai Han and Jichao Lang
Drones 2024, 8(12), 697; https://doi.org/10.3390/drones8120697 - 21 Nov 2024
Viewed by 514
Abstract
Visual recognition and localization of underwater optical beacons are critical for AUV docking, but traditional beacons are limited by fixed directionality and light attenuation in water. To extend the range of optical docking, this study designs a novel omnidirectional rotating optical beacon that [...] Read more.
Visual recognition and localization of underwater optical beacons are critical for AUV docking, but traditional beacons are limited by fixed directionality and light attenuation in water. To extend the range of optical docking, this study designs a novel omnidirectional rotating optical beacon that provides 360-degree light coverage over 45 m, improving beacon detection probability through synchronized scanning. Addressing the challenges of light centroid detection, we introduce a parallel deep learning detection algorithm based on an improved YOLOv8-pose model. Initially, an underwater optical beacon dataset encompassing various light patterns was constructed. Subsequently, the network was optimized by incorporating a small detection head, implementing dynamic convolution and receptive-field attention convolution for single-stage multi-scale localization. A post-processing method based on keypoint joint IoU matching was proposed to filter redundant detections. The algorithm achieved 93.9% AP at 36.5 FPS, with at least a 5.8% increase in detection accuracy over existing methods. Moreover, a light-source-based measurement method was developed to accurately detect the beacon’s orientation. Experimental results indicate that this scheme can achieve high-precision omnidirectional guidance with azimuth and pose estimation errors of -4.54° and 3.09°, respectively, providing a reliable solution for long-range and large-scale optical docking. Full article
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<p>Framework of the underwater omnidirectional rotating optical beacon docking system.</p>
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<p>Schematic of the underwater omnidirectional rotating optical beacon docking system.</p>
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<p>Structural diagram of the underwater omnidirectional rotating optical beacon.</p>
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<p>Underwater light source selection. (<b>a</b>) 10 W, 60°; (<b>b</b>) 30 W, 60°; (<b>c</b>) 30 W, 10°.</p>
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<p>Annotation information of the underwater optical beacon dataset. (<b>a</b>) Normalized positions of the bounding boxes; (<b>b</b>) Normalized sizes of the bounding boxes. Both panels are presented through histograms with 50 bins per dimension, with darker colours indicating more partitions.</p>
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<p>Improved network architecture of YOLOv8-pose.</p>
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<p>Structure of RFAConv.</p>
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<p>Example of redundant bounding boxes.</p>
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<p>Detection results of different methods. Each row from top to bottom corresponds to scenario 1, scenario 2, and scenario 3, respectively. (<b>a</b>) Ours; (<b>b</b>) YOLOv8n-pose; (<b>c</b>) YOLOv8n with centroid; (<b>d</b>) Tradition; (<b>e</b>) CNN.</p>
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<p>Error diagram.</p>
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<p>Experimental setup.</p>
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<p>Detection results of different methods. (<b>a</b>) Daylight, the beacon faces forward; (<b>b</b>) darkness, the beacon faces forward; (<b>c</b>) daylight, the beacon faces sideways; (<b>d</b>) darkness, the beacon faces sideways.</p>
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24 pages, 12109 KiB  
Article
Case Study of an Integrated Design and Technical Concept for a Scalable Hyperloop System
by Domenik Radeck, Florian Janke, Federico Gatta, João Nicolau, Gabriele Semino, Tim Hofmann, Nils König, Oliver Kleikemper, Felix He-Mao Hsu, Sebastian Rink, Felix Achenbach and Agnes Jocher
Appl. Syst. Innov. 2024, 7(6), 113; https://doi.org/10.3390/asi7060113 - 11 Nov 2024
Viewed by 1045
Abstract
This paper presents the design process and resulting technical concept for an integrated hyperloop system, aimed at realizing efficient high-speed ground transportation. This study integrates various functions into a coherent and technically feasible solution, with key design decisions that optimize performance and cost-efficiency. [...] Read more.
This paper presents the design process and resulting technical concept for an integrated hyperloop system, aimed at realizing efficient high-speed ground transportation. This study integrates various functions into a coherent and technically feasible solution, with key design decisions that optimize performance and cost-efficiency. An iterative design process with domain-specific experts, regular reviews, and a dataset with a single source of truth were employed to ensure continuous and collective progress. The proposed hyperloop system features a maximum speed of 600 kmh and a capacity of 21 passengers per pod (vehicle). It employs air docks for efficient boarding, electromagnetic suspension (EMS) combined with electrodynamic suspension (EDS) for high-speed lane switching, and short stator motor technology for propulsion. Cooling is managed through water evaporation at an operating pressure of 10 mbar, while a 300 kW inductive power supply (IPS) provides onboard power. The design includes a safety system that avoids emergency exits along the track and utilizes separated safety-critical and high-bandwidth communication. With prefabricated concrete parts used for the tube, construction costs can be reduced and scalability improved. A dimensioned cross-sectional drawing, as well as a preliminary pod mass budget and station layout, are provided, highlighting critical technical systems and their interactions. Calculations of energy consumption per passenger kilometer, accounting for all functions, demonstrate a distinct advantage over existing modes of transportation, achieving greater efficiency even at high speeds and with smaller vehicle sizes. This work demonstrates the potential of a well-integrated hyperloop system to significantly enhance transportation efficiency and sustainability, positioning it as a promising extension to existing modes of travel. The findings offer a solid framework for future hyperloop development, encouraging further research, standardization efforts, and public dissemination for continued advancements. Full article
(This article belongs to the Section Control and Systems Engineering)
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<p>Illustration of essential hyperloop functions in the design loop (outer circle), their dependencies and important system parameters (center).</p>
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<p>Illustration of the concept definition phase in the systems engineering life cycle adopted from [<a href="#B15-asi-07-00113" class="html-bibr">15</a>].</p>
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<p>Travel time and distance comparison of different modes of transportation based on the data presented in <a href="#asi-07-00113-t002" class="html-table">Table 2</a>. Between the black dots, the hyperloop offers the shortest average travel time compared to other modes of transport.</p>
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<p>Conceptual sketch of bogie arrangements. Blue arrows indicate translational movement, while red arrows indicate rotation. (<b>A</b>) Conventional train layout, (<b>B</b>) Maglev layout via “bending” (rotation + shifting of each bogie), and (<b>C</b>) via “parallel shifting” (shifting + geometric deviation compensation). Adapted from [<a href="#B13-asi-07-00113" class="html-bibr">13</a>].</p>
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<p>Conceptual sketches of different high-speed and high-frequency lane switching concepts for electromagnetic suspension. (<b>A</b>) Horizontal switching, hanging from the top. (<b>B</b>) Rail-like horizontal switching with a secondary electromagnetic system. (<b>C</b>) Vertical switching with a secondary electrodynamic system. (<b>D</b>) Vertical switching with a movable electromagnetic suspension.</p>
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<p>Schematic overview over the three major error procedures for safe handling of different hazard scenarios with their severity and probability.</p>
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<p>Conceptual sketch of the safety system, showcasing major elements.</p>
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<p>Cross-sectional sketch showcasing the interaction of the subsystems.</p>
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<p>True-to-scale sketch of the cross section for the inside surface of the low-speed (280<math display="inline"><semantics> <mfrac> <mi>km</mi> <mo>h</mo> </mfrac> </semantics></math>) tube with BR = <math display="inline"><semantics> <mrow> <mn>0.62</mn> </mrow> </semantics></math>, the nominal-speed (530<math display="inline"><semantics> <mfrac> <mi>km</mi> <mo>h</mo> </mfrac> </semantics></math>) tube with BR = <math display="inline"><semantics> <mrow> <mn>0.33</mn> </mrow> </semantics></math>, and the full-speed (600<math display="inline"><semantics> <mfrac> <mi>km</mi> <mo>h</mo> </mfrac> </semantics></math>) tube with BR = <math display="inline"><semantics> <mrow> <mn>0.26</mn> </mrow> </semantics></math>. The pod is colored in gray. Dimensions are given in millimeter.</p>
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<p>Rendering of a pod with maximum packaging for 21 passengers plus one person with reduced mobility in an isometric view (<b>A</b>) and front view (<b>B</b>).</p>
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<p>Schematic drawing of three different station layouts. (<b>A</b>) Lung design with moving rollers in the low-speed switch. (<b>B</b>) Autonomous crawler station. (<b>C</b>) Scissor lift design for small and compact stations.</p>
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18 pages, 7497 KiB  
Article
Cross-Docking Layout Optimization in FlexSim Software Based on Cold Chain 4PL Company
by Augustyn Lorenc
Sustainability 2024, 16(22), 9620; https://doi.org/10.3390/su16229620 - 5 Nov 2024
Viewed by 994
Abstract
The paper highlights the potential of cross-docking to reduce storage time and costs. The study addresses evolving market demands that push logistics providers to adopt new technologies for operational efficiency, emphasizing the often-overlooked importance of optimizing cross-docking layouts. The research, conducted in two [...] Read more.
The paper highlights the potential of cross-docking to reduce storage time and costs. The study addresses evolving market demands that push logistics providers to adopt new technologies for operational efficiency, emphasizing the often-overlooked importance of optimizing cross-docking layouts. The research, conducted in two phases, first analyzed the current warehouse layout (Variant I) to identify inefficiencies and then designed a new layout (Variant II) that was simulated using FlexSim 2022 software. The results showed significant improvements with the new layout, including a 35% increase in deliveries and a 3.23% reduction in forklift travel distances, leading to lower operational costs. Even minor adjustments in the warehouse design proved to enhance logistics efficiency, particularly during peak demand periods like holidays. The study demonstrates how FlexSim software can be applied in cold chain logistics to optimize warehouse operations, underscoring the benefits of cross-docking for cost-effective logistics management. Full article
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<p>Diagram of research methodology, blue—processes; green—result of the steps.</p>
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<p>Cross-docking zone layout divided into two longitudinal corridors.</p>
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<p>Reference distribution process diagram. Blue arrows—direction of movement; blue spots—empty spots for supports.</p>
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<p>Load of individual pallet places (DP), Variant I.</p>
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<p>Box and whisker plot for each client’s base on boxes/products per order; light green—quartile over the median; dark blue—quartile under the median.</p>
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<p>Plan of the discussed layout for the second variant. Blue arrows—direction of movement; blue spots—empty spots for supports.</p>
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<p>Product types per client.</p>
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<p>Forklift configuration window in FlexSim.</p>
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<p>Forklift route in Variant I.</p>
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<p>Cross-docking zone model mapped in FlexSim.</p>
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<p>Load of individual pallet places (DP), Variant II.</p>
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<p>Comparison of Variant I and Variant II in the 12-month period.</p>
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7 pages, 590 KiB  
Proceeding Paper
Exploring Algal Metabolism: Insights from Metabolomics and Computational Approaches
by Maria Carpena, Aurora Silva, Franklin Chamorro, Javier Echave, Ana Olivia S. Jorge, Maria Fátima Barroso and Miguel A. Prieto
Biol. Life Sci. Forum 2024, 35(1), 9; https://doi.org/10.3390/blsf2024035009 - 4 Nov 2024
Viewed by 546
Abstract
Algae, despite being labeled as an underexplored biological source of chemical constituents, remain inadequately studied in terms of their metabolism. Metabolomics has emerged as a high-throughput technology to investigate the full metabolic profile of samples that could aid in the understanding and characterization [...] Read more.
Algae, despite being labeled as an underexplored biological source of chemical constituents, remain inadequately studied in terms of their metabolism. Metabolomics has emerged as a high-throughput technology to investigate the full metabolic profile of samples that could aid in the understanding and characterization of algae. By delving into their primary composition, particularly polysaccharides and phycobiliproteins, alongside secondary metabolites like polyphenols and pigments, researchers can uncover not only their rheological and nutritional properties but also their diverse biological activities. Given the growing interest in algae in food and related industries, innovative approaches should be explored to enhance the value of their functional components. In this sense, in the context of contemporary in-silico studies, metabolomics should be paired with computational methodologies, to develop novel techniques for studying biomolecular interactions. Molecular docking has emerged, with the function of predicting the atomic-level interaction between small molecules (ligands) and target proteins (proteins). This synergistic approach integrating both technologies could allow us to characterize algal profiles, evaluate their potential for bioactive properties, and better understand their metabolism. This work explores the development of metabolomic and computational strategies targeted toward the functional characterization of algae. By harnessing these technologies, we can unlock new possibilities for using algae in various industrial applications, paving the way for sustainable and innovative solutions in the future. Full article
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<p>(<b>A</b>) Typical workflow analysis. (<b>B</b>) Representation of the molecular interaction between Fucoxanthin with gyrase acetylcholinesterase and butyrycholinesterase. Fucoxanthin integration (yellow), donor regions of hydrogen bonds (violet), and acceptors (green).</p>
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Article
Evaluation of Selected Plant Phenolics via Beta-Secretase-1 Inhibition, Molecular Docking, and Gene Expression Related to Alzheimer’s Disease
by Tugba Uçar Akyürek, Ilkay Erdogan Orhan, F. Sezer Şenol Deniz, Gokcen Eren, Busra Acar and Alaattin Sen
Pharmaceuticals 2024, 17(11), 1441; https://doi.org/10.3390/ph17111441 - 28 Oct 2024
Viewed by 865
Abstract
Background: The goal of the current study was to investigate the inhibitory activity of six phenolic compounds, i.e., rosmarinic acid, gallic acid, oleuropein, epigallocatechin gallate (EGCG), 3-hydroxytyrosol, and quercetin, against β-site amyloid precursor protein cleaving enzyme-1 (BACE1), also known as β-secretase or memapsin [...] Read more.
Background: The goal of the current study was to investigate the inhibitory activity of six phenolic compounds, i.e., rosmarinic acid, gallic acid, oleuropein, epigallocatechin gallate (EGCG), 3-hydroxytyrosol, and quercetin, against β-site amyloid precursor protein cleaving enzyme-1 (BACE1), also known as β-secretase or memapsin 2, which is implicated in the pathogenesis of Alzheimer’s disease (AD). Methods and Results: The inhibitory potential against BACE1, molecular docking simulations, as well as neurotoxicity and the effect on the AD-related gene expression of the selected phenolics were tested. BACE1 inhibitory activity was carried out using the ELISA microplate assay via fluorescence resonance energy transfer (FRET) technology. Molecular docking experiments were performed in the human BACE1 active site (PDB code: 2WJO). Neurotoxicity of the compounds was carried out in SH-SY5Y, a human neuroblastoma cell line, by the Alamar Blue method. A gene expression analysis of the compounds on fourteen genes linked to AD was conducted using the real-time polymerase chain reaction (RT-PCR) method. Rosmarinic acid, EGCG, oleuropein, and quercetin (also used as the reference) were able to inhibit BACE1 with their respective IC50 values 4.06 ± 0.68, 1.62 ± 0.12, 9.87 ± 1.01, and 3.16 ± 0.30 mM. The inhibitory compounds were observed to occupy the non-catalytic site of the BACE1. However, hydrogen bonds were found to be present between rosmarinic acid and EGCG and aspartic amino acid D228 in the catalytic site. Oleuropein and quercetin effectively suppressed the expression of PSEN, APOE, and CLU, which are recognized to be linked to the pathogenesis of AD. Conclusions: The outcomes of the work bring quercetin, EGCG, and rosmarinic acid to the forefront as promising BACE1 inhibitors. Full article
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<p>The predicted binding modes for rosmarinic acid (<b>A</b>), EGCG (<b>B</b>), oleuropein (<b>C</b>), and quercetin (<b>D</b>) in human BACE1 active site (PDB: 2WJO). The yellow dotted lines represent H-bonds, and the cyan-dotted line represents π-π interactions.</p>
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<p>Fold regulation values of rosmarinic acid, EGCG, oleuropein, quercetin, 3–hydroxytyrosol, and gallic acid on genes compared to the control group. Multiple groups were compared by ANOVA and Dunnet <span class="html-italic">post hoc</span> test. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01.</p>
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30 pages, 5760 KiB  
Article
Modulation of Albumin Esterase Activity by Warfarin and Diazepam
by Daria A. Belinskaia, Anastasia A. Batalova, Polina A. Voronina, Vladimir I. Shmurak, Mikhail A. Vovk, Alexander M. Polyanichko, Tomash S. Sych, Kamila V. Samodurova, Vasilisa K. Antonova, Anastasia A. Volkova, Bogdan A. Gerda, Richard O. Jenkins and Nikolay V. Goncharov
Int. J. Mol. Sci. 2024, 25(21), 11543; https://doi.org/10.3390/ijms252111543 - 27 Oct 2024
Cited by 1 | Viewed by 836
Abstract
Data are accumulating on the hydrolytic activity of serum albumin towards esters and organophosphates. Previously, with the help of the technology of proton nuclear magnetic resonance (1H NMR) spectroscopy, we observed the yield of acetate in the solution of bovine serum [...] Read more.
Data are accumulating on the hydrolytic activity of serum albumin towards esters and organophosphates. Previously, with the help of the technology of proton nuclear magnetic resonance (1H NMR) spectroscopy, we observed the yield of acetate in the solution of bovine serum albumin and p-nitrophenyl acetate (NPA). Thus, we showed that albumin possesses true esterase activity towards NPA. Then, using the methods of molecular docking and molecular dynamics, we established site Sudlow I as the catalytic center of true esterase activity of albumin. In the present work, to expand our understanding of the molecular mechanisms of albumin pseudoesterase and true esterase activity, we investigated—in experiments in vitro and in silico—the interaction of anticoagulant warfarin (WRF, specific ligand of site Sudlow I) and benzodiazepine diazepam (DIA, specific ligand of site Sudlow II) with albumins of different species, and determined how the binding of WRF and DIA affects the hydrolysis of NPA by albumin. It was found that the characteristics of the binding modes of WRF in site Sudlow I and DIA in site Sudlow II of human (HSA), bovine (BSA), and rat (RSA) albumins have species differences, which are more pronounced for site Sudlow I compared to site Sudlow II, and less pronounced between HSA and RSA compared to BSA. WRF competitively inhibits true esterase activity of site Sudlow I towards NPA and does not affect the functioning of site Sudlow II. Diazepam can slow down true esterase activity of site Sudlow I in noncompetitive manner. It was concluded that site Sudlow I is more receptive to allosteric modulation compared to site Sudlow II. Full article
(This article belongs to the Section Macromolecules)
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Figure 1
<p>Structure of human serum albumin (HSA). (<b>A</b>) HSA domain structure; ice-blue, pink, yellow, orange, purple, and black ribbons represent domains IA, IB, IIA, IIB, IIIA, and IIIB, respectively. (<b>B</b>) Binding sites of HSA; the backbone of the protein is shown with a gray ribbon; nonpolar residues of the binding sites are shown with a gray surface; polar residues of the binding sites are shown with colored surfaces (Tyr150, His242, and Arg257, located at the bottom of site Sudlow I, are marked in blue; Lys195, Lys199, Arg218 and Arg222, located at the entrance of site Sudlow I, are marked in purple; Tyr411 and Arg410, located at the entrance of site Sudlow II, are marked in green; Tyr138 and Tyr161, located at the entrance of site III, are marked in red; Arg117 and Arg186, located at the base of site III, are marked in orange; Ser193, located at the boundary between sites I and III, is marked in cyan).</p>
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<p>Binding modes of warfarin (WRF) in site Sudlow I of HSA obtained by molecular docking procedure (<b>A</b>) and 50 ns molecular dynamics (MD) simulation (<b>B</b>). Green shows the binding modes of WRF according to molecular modeling data, pink shows the binding mode of WRF according to X-ray diffraction analysis (PBD structures 2BXD [<a href="#B5-ijms-25-11543" class="html-bibr">5</a>]). Cyan, blue, red and white sticks represent carbon, nitrogen, oxygen and hydrogen atoms, respectively. The designations of atoms are given, the distances between which determine the pose of the ligand molecule inside the binding site. Water molecules located in the vicinity of WRF according to MD simulation are shown. Nonpolar hydrogens are omitted for clarity.</p>
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<p>Binding modes of diazepam (DIA) in site Sudlow II of HSA obtained by molecular docking procedure (<b>A</b>) and 50 ns MD simulation (<b>B</b>). Green shows the binding modes of DIA according to molecular modeling data, pink shows the binding mode of DIA according to X-ray diffraction analysis (PBD structures 2BXF [<a href="#B5-ijms-25-11543" class="html-bibr">5</a>]). Cyan, blue, red, yellow, violet and white sticks represent carbon, nitrogen, oxygen, sulfur, chlorine and hydrogen atoms, respectively. The designations of atoms are given, the distances between which determine the pose of the ligand molecule inside the binding site. Water molecules located in the vicinity of DIA according to MD simulation are shown. Nonpolar hydrogens are omitted for clarity.</p>
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<p>Emission spectrum of BSA when its fluorescence is quenched by WRF (<b>A</b>) and DIA (<b>B</b>). The arrow indicates the change in ligand concentration: 1 → 9 corresponds to concentrations of 0, 14.7, 24.9, 32.3, 42.0, 54.6, 71.0, 92.3, 120.0 µM. The BSA concentration was 15 μM. For each ligand concentration, the spectrum was recorded three times; the figure displays the average curves.</p>
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<p>Emission spectrum of BSA when its fluorescence is quenched by WRF (<b>A</b>) and DIA (<b>B</b>). The arrow indicates the change in ligand concentration: 1 → 9 corresponds to concentrations of 0, 14.7, 24.9, 32.3, 42.0, 54.6, 71.0, 92.3, 120.0 µM. The BSA concentration was 15 μM. For each ligand concentration, the spectrum was recorded three times; the figure displays the average curves.</p>
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<p>Binding modes of WRF in site Sudlow I of BSA obtained by molecular docking procedure (<b>A</b>) and 50 ns MD simulation (<b>B</b>). Cyan, blue, red and white sticks represent carbon, nitrogen, oxygen and hydrogen atoms, respectively. Carbon atoms of WRF are shown in green. The designations of atoms are given, the distances between which determine the pose of the ligand molecule inside the binding site. Water molecules located in the vicinity of WRF according to MD simulation are shown. Nonpolar hydrogens are omitted for clarity.</p>
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<p>Binding modes of DIA in site Sudlow II of BSA obtained by molecular docking procedure (<b>A</b>) and 50 ns MD simulation (<b>B</b>). Cyan, blue, red, yellow, violet and white sticks represent carbon, nitrogen, oxygen, sulfur, chlorine and hydrogen atoms, respectively. Carbon atoms of DIA are shown in green. The designations of atoms are given, the distances between which determine the pose of the ligand molecule inside the binding site. Water molecules located in the vicinity of DIA according to MD simulation are shown. Nonpolar hydrogens are omitted for clarity.</p>
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<p>Binding modes of WRF in site Sudlow I of RSA obtained by molecular docking procedure (<b>A</b>) and 50 ns MD simulation (<b>B</b>). Cyan, blue, red and white sticks represent carbon, nitrogen, oxygen and hydrogen atoms, respectively. Carbon atoms of WRF are shown in green. The designations of atoms are given, the distances between which determine the pose of the ligand molecule inside the binding site. Water molecules located in the vicinity of WRF according to MD simulation are shown. Nonpolar hydrogens are omitted for clarity.</p>
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<p>Binding modes of DIA in site Sudlow II of RSA obtained by molecular docking procedure (<b>A</b>) and 50 ns MD simulation (<b>B</b>). Cyan, blue, red, yellow, violet and white sticks represent carbon, nitrogen, oxygen, sulfur, chlorine and hydrogen atoms, respectively. Carbon atoms of DIA are shown in green. The designations of atoms are given, the distances between which determine the pose of the ligand molecule inside the binding site. Water molecules located in the vicinity of DIA according to MD simulation are shown. Nonpolar hydrogens are omitted for clarity.</p>
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<p>Time dependence of the relative integral intensity of the signal of acetate during the hydrolysis of NPA (3.6 mM) by BSA (180 μM) in the presence of WRF (360 μM, (<b>A</b>)) and DIA (360 μM, (<b>B</b>)). I<sub>rel</sub> was calculated as the ratio of the integral signal intensity of the acetate group (1.86–1.81 ppm) to the integral signal intensity of the internal standard trimethylsilylpropanesulfonate (DSS, 0.0–−0.3 ppm, in the experiment with WRF) or dimethyl sulfoxide (DMSO, 2.65–2.55 ppm, in the experiment with DIA) [<a href="#B14-ijms-25-11543" class="html-bibr">14</a>]. I<sub>rel</sub><sup>0</sup> was taken as zero intensity, which is the relative integral intensity of the range 1.86–1.81 ppm (corresponding to the acetate signal) of the spectrum of pure BSA (for control measurements without an inhibitor) or the spectrum of a mixture of BSA with an inhibitor without substrate (for measurements with inhibitors).</p>
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<p>Effect of WRF and DIA on the esterase activity (stationary phase of nitrophenol yield) of BSA at concentrations of 150 μM (<b>A</b>) and 360 μM (<b>B</b>) towards NPA. Phosphate buffered-saline (PBS), control sample without inhibitors; DMSO, sample with the addition of a volume of DMSO equivalent to the volume of inhibitor solutions (10% of the total volume of the mixture); WRF, sample with the addition of WRF in a 2:1 ratio; DIA, sample with the addition of DIA in a ratio of 2:1; *, significance of difference from the control <span class="html-italic">p</span> &lt; 0.05.</p>
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<p>Time dependence of the distance (distC-O) between the carboxyl carbon of NPA and the hydroxyl oxygen of catalytic tyrosine (Tyr149 in site Sudlow I or Tyr410 in site Sudlow II of BSA). (<b>A</b>) Complex of BSA with NPA in site Sudlow I and empty site Sudlow II; (<b>B</b>) complex of BSA with NPA in site Sudlow I and DIA in site Sudlow II; (<b>C</b>) complex of BSA with NPA in site Sudlow II and empty site Sudlow I; (<b>D</b>) complex of BSA with NPA in site Sudlow II and WRF in site Sudlow I.</p>
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<p>Root mean square fluctuation (RMSF) of the Cα-atoms of BSA complexes with ligands and inhibitors. (<b>A</b>) NPA is bound in site Sudlow I and site Sudlow II is empty or interacts with DIA; (<b>B</b>) NPA is bound in site Sudlow II and Sudlow I site is empty or interacts with WRF.</p>
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<p>Interaction between subdomains IB and IIIB of BSA in its complex with NPA and DIA according to MD simulation. The regions most affected by DIA binding are highlighted blue and red (Lys106–Pro119 in domain IB and Thr495–Glu519 in domain IIIB). Cyan, blue and red spheres represent carbon, nitrogen and oxygen atoms, respectively. Carbon atoms of DIA are shown in green.</p>
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<p>Interaction between albumin and <span class="html-italic">p</span>-nitrophenyl acetate (NPA). S—substrate, P1—p-nitrophenol, P2—acetate.</p>
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17 pages, 4394 KiB  
Article
Real-Time Semantic Segmentation of 3D LiDAR Point Clouds for Aircraft Engine Detection in Autonomous Jetbridge Operations
by Ihnsik Weon, Soongeul Lee and Juhan Yoo
Appl. Sci. 2024, 14(21), 9685; https://doi.org/10.3390/app14219685 - 23 Oct 2024
Viewed by 759
Abstract
This paper presents a study on aircraft engine identification using real-time 3D LiDAR point cloud segmentation technology, a key element for the development of automated docking systems in airport boarding facilities, known as jetbridges. To achieve this, 3D LiDAR sensors utilizing a spinning [...] Read more.
This paper presents a study on aircraft engine identification using real-time 3D LiDAR point cloud segmentation technology, a key element for the development of automated docking systems in airport boarding facilities, known as jetbridges. To achieve this, 3D LiDAR sensors utilizing a spinning method were employed to gather surrounding environmental 3D point cloud data. The raw 3D environmental data were then filtered using the 3D RANSAC technique, excluding ground data and irrelevant apron areas. Segmentation was subsequently conducted based on the filtered data, focusing on aircraft sections. For the segmented aircraft engine parts, the centroid of the grouped data was computed to determine the 3D position of the aircraft engine. Additionally, PointNet was applied to identify aircraft engines from the segmented data. Dynamic tests were conducted in various weather and environmental conditions, evaluating the detection performance across different jetbridge movement speeds and object-to-object distances. The study achieved a mean intersection over union (mIoU) of 81.25% in detecting aircraft engines, despite experiencing challenging conditions such as low-frequency vibrations and changes in the field of view during jetbridge maneuvers. This research provides a strong foundation for enhancing the robustness of jetbridge autonomous docking systems by reducing the sensor noise and distortion in real-time applications. Our future research will focus on optimizing sensor configurations, especially in environments where sea fog, snow, and rain are frequent, by combining RGB image data with 3D LiDAR information. The ultimate goal is to further improve the system’s reliability and efficiency, not only in jetbridge operations but also in broader autonomous vehicle and robotics applications, where precision and reliability are critical. The methodologies and findings of this study hold the potential to significantly advance the development of autonomous technologies across various industrial sectors. Full article
(This article belongs to the Section Mechanical Engineering)
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<p>Configuration of the jetbridge autonomous sensor system [<a href="#B18-applsci-14-09685" class="html-bibr">18</a>].</p>
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<p>Schematics of the jetbridge system used for automation [<a href="#B18-applsci-14-09685" class="html-bibr">18</a>].</p>
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<p>The 3D point cloud data for the aircraft and jetbridge on the apron (no ground filter).</p>
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<p>The 3D point cloud data for the aircraft and jetbridge on the apron (ground filtered).</p>
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<p>Real 3D point cloud data (.pcd) format (x, y, z, intensity).</p>
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<p>Aircraft engine detection model for the PointNet algorithm.</p>
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<p>The 3D LiDAR data of aircraft engines used for training process.</p>
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<p>Center of the jetbridge and distance between the jetbridge and engine.</p>
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<p>Result of the segmentation with the PointNet model (daytime). Jetbridge(blue box).</p>
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<p>Jetbridge cabin degree and distance error between the jetbridge and engine (daytime).</p>
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<p>Jetbridge cabin degree and distance error between the Jetbridge (blue box) and engine (nighttime).</p>
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22 pages, 1144 KiB  
Article
Digitization and Green Technology Innovation of Chinese Firms Under Government Subsidy Policies
by Hao Kong, Linhui Sun and Wei Zhang
Systems 2024, 12(11), 447; https://doi.org/10.3390/systems12110447 - 23 Oct 2024
Viewed by 1088
Abstract
In the context of the digital economy, digital technology is an important driving force to promote green development and achieve the “dual-carbon goal”. Taking 1746 Shanghai and Shenzhen A-share enterprises from 2015 to 2022 as research objects, we empirically examine the relationship between [...] Read more.
In the context of the digital economy, digital technology is an important driving force to promote green development and achieve the “dual-carbon goal”. Taking 1746 Shanghai and Shenzhen A-share enterprises from 2015 to 2022 as research objects, we empirically examine the relationship between government subsidies, digital transformation, and corporate green technology innovation. The study shows that (1) there is an inverted “U”-shaped relationship between government subsidies and corporate green technological innovation, while digital transformation plays a mediating role, and there is a difference between the quality and quantity of digital transformation in promoting green technological innovation. (2) Through the analysis of the moderating effect, it is found that market concentration has an obvious inhibitory effect between enterprise digital transformation and green technology innovation. (3) The study, by classifying the nature of enterprises, shows that the promotion effect of digital transformation on green technology innovation is weaker under heavily polluted enterprises than under non-heavily polluted enterprises, but the promotion interval of the relationship between government subsidies and green technology innovation is larger. Therefore, enterprises should make full use of digital technology to inject new impetus into their innovation activities, and the government should fully consider the appropriate space for enterprises to receive subsidies, make reasonable use of the incentive effect of government subsidies, and smooth the information docking channels for government and enterprise subsidies. Full article
(This article belongs to the Special Issue Business Model Innovation in the Context of Digital Transformation)
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<p>Financial subsidies and the green technology innovation nexus (Firm 1).</p>
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<p>Financial subsidies and the green technology innovation nexus (Firm 2).</p>
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<p>The effect of the placebo test.</p>
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30 pages, 5629 KiB  
Article
Ouabain Ameliorates Alzheimer’s Disease-Associated Neuropathology and Cognitive Impairment in FAD4T Mice
by Dan Wang, Jiajia Liu, Qizhi Zhu, Xin Wei, Xiang Zhang, Qi Chen, Yu Zhao, Heng Tang and Weiping Xu
Nutrients 2024, 16(20), 3558; https://doi.org/10.3390/nu16203558 - 20 Oct 2024
Viewed by 1613
Abstract
Background: Alzheimer’s disease (AD) is a common clinical neurodegenerative disorder, primarily characterized by progressive cognitive decline and behavioral abnormalities. The hallmark pathological changes of AD include widespread neuronal degeneration, plaques formed by the deposition of amyloid β-protein (Aβ), and neurofibrillary tangles (NFTs). With [...] Read more.
Background: Alzheimer’s disease (AD) is a common clinical neurodegenerative disorder, primarily characterized by progressive cognitive decline and behavioral abnormalities. The hallmark pathological changes of AD include widespread neuronal degeneration, plaques formed by the deposition of amyloid β-protein (Aβ), and neurofibrillary tangles (NFTs). With the acceleration of global aging, the incidence of AD is rising year by year, making it a major global public health concern. Due to the complex pathology of AD, finding effective interventions has become a key focus of research. Ouabain (OUA), a cardiac glycoside, is well-known for its efficacy in treating heart disease. Recent studies have also indicated its potential in AD therapy, although its exact mechanism of action remains unclear. Methods: This study integrates bioinformatics, multi-omics technologies, and in vivo and in vitro experiments to investigate the effects of OUA on the pathophysiological changes of AD and its underlying molecular mechanisms. Results: This study analyzed the expression of the triggering receptor expressed on myeloid cells 2 (TREM2) across different stages of AD using bioinformatics. Serum samples from patients were used to validate soluble TREM2 (sTREM2) levels. Using an Aβ1-42-induced microglial cell model, we confirmed that OUA enhances the PI3K/AKT signaling pathway activation by upregulating TREM2, which reduces neuroinflammation and promotes the transition of microglia from an M1 proinflammatory state to an M2 anti-inflammatory state. To evaluate the in vivo effects of OUA, we assessed the learning and memory capacity of FAD4T transgenic mice using the Morris water maze and contextual fear conditioning tests. We used real-time quantitative PCR, immunohistochemistry, and Western blotting to measure the expression of inflammation-associated cytokines and to assess microglia polarization. OUA enhances cognitive function in FAD4T mice and has been confirmed to modulate microglial M1/M2 phenotypes both in vitro and in vivo. Furthermore, through bioinformatics analysis, molecular docking, and experimental validation, TREM2 was identified as a potential target for OUA. It regulates PI3K/Akt signaling pathway activation, playing a crucial role in OUA-mediated M2 microglial polarization and its anti-inflammatory effects in models involving Aβ1-42-stimulated BV-2 cells and FAD4T mice. Conclusions: These findings indicate that OUA exerts anti-neuroinflammatory effects by regulating microglial polarization, reducing the production of inflammatory mediators, and activating the PI3K/Akt signaling pathway. Given its natural origin and dual effects on microglial polarization and neuroinflammation, OUA emerges as a promising therapeutic candidate for neuroinflammatory diseases such as AD. Full article
(This article belongs to the Section Geriatric Nutrition)
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<p>The <span class="html-italic">TREM2</span> gene is associated with AD progression. (<b>A</b>) Boxplot showing the expression level of <span class="html-italic">TREM2</span> in samples from patients with severe AD and non-severe AD (GSE28146). (<b>B</b>) Volcano plot of differentially expressed genes between samples with high and low <span class="html-italic">TREM2</span> expression levels (GSE5281). (<b>C</b>) GO and KEGG analyses of the differentially expression genes. (<b>D</b>) Lollipop plot of GSEA results for the differentially expressed genes. The PI3K-AKTsignaling pathway is marked in red. (<b>E</b>) Boxplot showing the relative abundance of <span class="html-italic">TREM2</span> in clinical AD and control samples.</p>
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<p>Ouabain network pharmacology and molecular docking. (<b>A</b>) Venn diagram showing the overlap of AD-related targets obtained from various databases. (<b>B</b>) Venn diagram of the overlap between AD-related targets and potential targets of OUA and the ouabain–AD target PPI network. (<b>C</b>) Predicted target signaling pathway enrichment diagram. (<b>D</b>) Results of the GO enrichment analysis. (<b>E</b>) Ouabain–target network. (<b>F</b>,<b>G</b>) Ouabain–AD target network. (<b>H</b>) Molecular docking model of ouabain–TREM2.</p>
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<p>Effect on BV2 cell viability with and without Aβ<sub>1-42</sub> induction. (<b>A</b>) Chemical structure of OUA. (<b>B</b>) Effects of different concentrations of OUA on cell viability. (<b>C</b>) Effects of different concentrations of Aβ<sub>1-42</sub> on cell viability. (<b>D</b>) Effect of OUA on Aβ<sub>1-42</sub>-induced cell viability. Cell morphology of the following groups observed under an optical microscope (200×): (<b>E</b>) control, (<b>F</b>) model group (Aβ<sub>1-42</sub>), and (<b>G</b>) OUA+Aβ<sub>1-42</sub> group. (<b>H</b>) Calcein–AM/PI staining of cells treated with Aβ<sub>1-42</sub> and OUA. The data are presented as the means ± S.E.M.s, n = 3. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001 and **** <span class="html-italic">p</span> &lt; 0.0001 compared to the control group; <sup>###</sup> <span class="html-italic">p</span> &lt; 0.001 compared to the model group. Scale bar = 50 μm.</p>
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<p>Effect of OUA on the expressions of TREM2, Arg-1, and iNOS in BV-2 cells. (<b>A</b>,<b>B</b>) Representative TREM2, Arg-1, and iNOS protein levels determined using Western blot analysis. (<b>C</b>) The levels of TREM2, Arg-1, and iNOS. (<b>D</b>) Immunofluorescence detection of iNOS expression (100×); scale bar = 100 μm. (<b>E</b>) Immunofluorescence detection of Arg-1 expression (100×). The blue fluorescence in the figure represents DAPI staining, while the red fluorescence indicates target protein staining. The data are presented as the means ± S.E.M.s, n = 3. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 compared to the control group; <sup>#</sup> <span class="html-italic">p</span> &lt; 0.05 compared to the model group. Scale bar = 100 μm.</p>
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<p>Effects of OUA on the expression of channel-associated proteins and inflammatory factors. (<b>A</b>) Representative Western blot analysis of the levels of the PI3K, p-PI3K, AKT, and p-AKT proteins. (<b>B</b>–<b>E</b>) The levels of PI3K, p-PI3K, AKT, and p-AKT. The expression of IL-1β (<b>H</b>,<b>I</b>) and IL-4 (<b>F</b>,<b>G</b>) was detected using qPCR. The data are presented as the means ± S.E.M.s, n = 3. ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001 and **** <span class="html-italic">p</span> &lt; 0.0001 compared to the corresponding control group; <sup>#</sup> <span class="html-italic">p</span> &lt; 0.05, <sup>##</sup> <span class="html-italic">p</span> &lt; 0.01 and <sup>###</sup> <span class="html-italic">p</span> &lt; 0.001 compared to the corresponding model group; <sup>a</sup> <span class="html-italic">p</span> &lt; 0.05, <sup>aa</sup> <span class="html-italic">p</span> &lt; 0.01, <sup>aaa</sup> <span class="html-italic">p</span> &lt; 0.001 and <sup>aaaa</sup> <span class="html-italic">p</span> &lt; 0.0001 compared to the NC group under the same experimental conditions.</p>
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<p>OUA improves spatial learning and memory abilities in FAD<sup>4T</sup> mice. (<b>A</b>) Representative trajectory plots in the spatial exploration test. The four colors in the figure represent different quadrants. (<b>B</b>) Escape latency in the place navigation test. (<b>C</b>) Escape latency in the spatial exploration test. (<b>D</b>) Frequency at which mice crossed the original platform location in the experiment. (<b>E</b>) Time spent in the target quadrant. (<b>F</b>) Swimming distance in the target quadrant. (<b>G</b>) Freezing time during the adaptation period and the contextual fear memory test. (<b>H</b>) Freezing time during the adaptation period and the cued fear memory test. (<b>I</b>) Freezing time during the contextual fear memory test. (<b>J</b>) Freezing time during the cued fear memory test. The data are presented as the means ± S.E.M.s, n = 6. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 compared to the WT group; <sup>#</sup> <span class="html-italic">p</span> &lt; 0.05 and <sup>##</sup> <span class="html-italic">p</span> &lt; 0.01 compared to the FAD<sup>4T</sup> group; <sup>&amp;&amp;</sup> <span class="html-italic">p</span> &lt; 0.01, and <sup>&amp;&amp;&amp;</sup> <span class="html-italic">p</span> &lt; 0.001 when comparing the contextual or cued fear memory test periods to the adaptation period.</p>
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<p>OUA attenuates neuronal and synaptic damage and pathological changes and effects on signaling pathways in FAD<sup>4T</sup> mice. (<b>A</b>) Schematic diagram of mouse hippocampal structure. (<b>B</b>) HE staining of the hippocampus (200×); scale bar = 100 μm. (<b>C</b>) Nissl staining of the hippocampus (200×); scale bar = 100 μm. (<b>D</b>) Immunofluorescence detection of SYN expression (400×); scale bar = 20 μm. The black boxes in the figure indicate areas of magnification or focus. (<b>E</b>) Immunofluorescence detection of PSD98 expression (400×); scale bar = 20 μm. (<b>F</b>) Quantitative analysis of SYN and PSD95 fluorescence intensity. (<b>G</b>) Representative Arg-1, iNOS, TREM2, PI3K, p-PI3K, AKT, and p-AKT protein levels determined using Western blot analysis. (<b>H</b>) The levels of Arg-1, iNOS, TREM2, PI3K, p-PI3K, AKT, and p-AKT. The data are presented as the means ± S.E.M.s, n = 3. ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001 and **** <span class="html-italic">p</span> &lt; 0.0001 compared with the corresponding control group; <sup>#</sup> <span class="html-italic">p</span> &lt; 0.05 and <sup>###</sup> <span class="html-italic">p</span> &lt; 0.001 compared with the corresponding model group.</p>
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<p>OUA attenuates the proliferation and activation of astrocytes and oligodendrocytes and the effects on inflammatory factors in the brains of FAD<sup>4T</sup> mice. (<b>A</b>) Immunohistochemical detection of GFAP expression in the hippocampus (200×). Scale bar = 50 μm. (<b>B</b>) Immunohistochemical detection of OLIG2 expression in the CC and CG (200×). Scale bar = 100 μm. (<b>C</b>,<b>D</b>) Statistical map of positive areas in the CA1 and CA3 regions of the hippocampus. (<b>E</b>,<b>F</b>) Statistical map of positive areas in the CC and CG regions. The expression of TNF-α (<b>G</b>), IL-1β (<b>H</b>), IL-4 (<b>I</b>), and IL-10 (<b>J</b>) was detected using qPCR. The data are presented as the means ± S.E.M.s, n = 3. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 compared with the corresponding control group; <sup>#</sup> <span class="html-italic">p</span> &lt; 0.05 and <sup>##</sup> <span class="html-italic">p</span> &lt; 0.001 compared with the corresponding model group.</p>
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14 pages, 4862 KiB  
Article
Improving Hydrolytic Activity and Enantioselectivity of Epoxide Hydrolase from Phanerochaete chrysosporium by Directed Evolution
by Huanhuan Shao, Pan Xu, Xiang Tao, Xinyi He, Chunyan Pu, Shaorong Liang, Yingxin Shi, Xiaoyan Wang, Hong Feng and Bin Yong
Molecules 2024, 29(20), 4864; https://doi.org/10.3390/molecules29204864 - 14 Oct 2024
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Abstract
Epoxide hydrolases (EHs) catalyze the conversion of epoxides into vicinal diols. The epoxide hydrolase gene from P. chrysosporium was previously cloned and subjected to site-directed mutation to study its enzyme activity, but the results were unsatisfactory. This study used error prone PCR and [...] Read more.
Epoxide hydrolases (EHs) catalyze the conversion of epoxides into vicinal diols. The epoxide hydrolase gene from P. chrysosporium was previously cloned and subjected to site-directed mutation to study its enzyme activity, but the results were unsatisfactory. This study used error prone PCR and DNA shuffling to construct a PchEHA mutation library. We performed mutation-site combinations on PchEHA based on enzyme activity measurement results combined with directed evolution technology. More than 15,000 mutants were randomly selected for the preliminary screening of PchEHA enzyme activity alongside 38 mutant strains with increased enzyme activity or enantioselectivity. Protein expression and purification were conducted to determine the hydrolytic activity of PchEHA, and three mutants increased their activity by more than 95% compared with that of the wt. After multiple rounds of screening and site-specific mutagenesis, we found that F3 offers the best enzyme activity and enantioselectivity; furthermore, the molecular docking results confirmed this result. Overall, this study uncovered novel mutants with potential value as industrial biocatalysts. Full article
(This article belongs to the Section Chemical Biology)
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Figure 1

Figure 1
<p>Schematic view of the 3D structure of the epoxide hydrolase from <span class="html-italic">Phanerochaete chrysosporium</span>. α-helices, β-strands, and coils are represented by helical ribbons, arrows, and ropes, respectively. The catalytic triad (D105 H308 D277) and tyrosine residue (Y159) are shown by sticks.</p>
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<p>The <span class="html-italic">PchEHA</span> gene mutation library constructed via random mutation. (<b>A</b>) Electrophoresis analysis of mutant PCR products; dNTP/dITP in A1 lane is 25/175, dNTP/dITP in A2 lane is 50/150, dNTP/dITP in A3 lane is 75/125, and dNTP/dITP in A4 lane is 200/0; (<b>B</b>) electrophoresis analysis of PCR products without primer assembly, and DNA fragments obtained by EndoV enzymatic digestion serve as mutual primers in assembly PCR to enhance the mutational diversity of the DNA fragments. M: λ-EcoT14 I digest DNA Marker.</p>
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<p>Labeling of the secondary structure of PchEHA amino acid and the mutation sites. The red font represents mutation sites, and the black background represents conserved sequences. <span class="html-fig-inline" id="molecules-29-04864-i001"><img alt="Molecules 29 04864 i001" src="/molecules/molecules-29-04864/article_deploy/html/images/molecules-29-04864-i001.png"/></span> denotes β-sheets, <span class="html-fig-inline" id="molecules-29-04864-i002"><img alt="Molecules 29 04864 i002" src="/molecules/molecules-29-04864/article_deploy/html/images/molecules-29-04864-i002.png"/></span> represents an α-helix.</p>
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<p>SDS-PAGE of purified wt PchEHA and 5 mutants. M: PageRuler<sup>TM</sup> Protein Ladder (3.4–100 kDa); lane 2 is wt, lane 3–7 is M1–M5, lane 8 is protein bovine serum albumin (BSA) at a concentration of 2 μg, lane 9 is BSA at a concentration of 1 μg.</p>
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<p>Hydrolytic activity of PchEHA wt and mutants to substrates. (<b>A</b>) The hydrolytic reactions were carried out in reaction volume containing (RS)/(R)/(S)-SO and purified enzymes; (<b>B</b>) the hydrolytic reactions were carried out in reaction volumes containing (R)/(S)-GT and purified enzymes; (<b>C</b>) the hydrolytic reactions were carried out in reaction volumes containing (R)/(S)-Ep and purified enzymes.</p>
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<p>Hydrolytic activity of PchEHA wt and 13 combined mutants to substrates. (<b>A</b>) The hydrolytic reactions were carried out in reaction volumes containing (RS)/(R)/(S)-SO and purified enzymes; (<b>B</b>) the hydrolytic reactions were carried out in reaction volumes containing (R)/(S)-GT and purified enzymes; (<b>C</b>) the hydrolytic reactions were carried out in reaction volumes containing (R)/(S)-Ep and purified enzymes.</p>
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<p>Molecular dynamics simulations carried out with the wt and F3 for (R)/(S)-SO. (<b>A</b>) 2D and 3D structural analysis of the interaction between the catalytic sites of the WT and (R)-SO; (<b>B</b>) 2D and 3D structural analysis of the interaction between the catalytic sites of F3 and (R)-SO; (<b>C</b>) 2D and 3D structural analysis of the interaction between the catalytic sites of the WT and (S)-SO; (<b>D</b>) 2D and 3D structural analysis of the interaction between the catalytic sites of F3 and (S)-SO.</p>
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