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15 pages, 663 KiB  
Systematic Review
Graphene-Based Materials for Bone Regeneration in Dentistry: A Systematic Review of In Vitro Applications and Material Comparisons
by Azahara María Narváez-Romero, Francisco Javier Rodríguez-Lozano and María Pilar Pecci-Lloret
Nanomaterials 2025, 15(2), 88; https://doi.org/10.3390/nano15020088 - 8 Jan 2025
Viewed by 419
Abstract
Introduction: Graphene, a two-dimensional arrangement of carbon atoms, has drawn significant interest in medical research due to its unique properties. In the context of bone regeneration, graphene has shown several promising applications. Its robust structure, electrical conductivity, and biocompatibility make it an ideal [...] Read more.
Introduction: Graphene, a two-dimensional arrangement of carbon atoms, has drawn significant interest in medical research due to its unique properties. In the context of bone regeneration, graphene has shown several promising applications. Its robust structure, electrical conductivity, and biocompatibility make it an ideal candidate for enhancing bone tissue regeneration and repair processes. Studies have revealed that the presence of graphene can stimulate the proliferation and differentiation of bone cells, thereby promoting the formation of new bone tissue. Additionally, its ability to act as an effective carrier for growth factors and drugs allows controlled release, facilitating the engineering of specific tissues for bone regeneration. Aim: To assess the efficacy of graphene in enhancing bone regeneration through in vitro studies, identify key safety concerns, and propose directions for future research to optimize its clinical applicability. Materials and methods: The present systematic review was carried out using the PRISMA 2020 guideline. A first search was carried out on 20 November 2023 and was later updated on 14 February and 15 April 2024 in the databases of PubMed, Scopus, and Web of Science. Those in vitro studies published in English that evaluated the potential for bone regeneration with graphene in dentistry and also those which met the search terms were selected. Furthermore, the quality of the studies was assessed following the modified CONSORT checklist of in vitro studies on dental materials. Results: A total of 17 in vitro studies met the inclusion criteria. Among these, 12 showed increased osteoblast adhesion, proliferation, and differentiation, along with notable enhancements in mineralized matrix formation. Additionally, they exhibited a significant upregulation of osteogenic markers such as RUNX and COL1 (p < 0.05). However, the variability in methodologies and a lack of long-term assessments were noted as critical gaps. Conclusions: The evaluation of the efficacy and safety of graphene in bone regeneration in dentistry revealed significant potential. However, it is recognized that clinical implementation should be approached with caution, considering identified areas of improvement and suggestions for future research. Future studies should focus on standardized experimental designs, including in vivo studies to evaluate long-term safety, immune responses, and vascularization processes in realistic biological environments. Full article
(This article belongs to the Section Biology and Medicines)
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<p>PRISMA 2020 flow diagram. Identification of studies via databases and registers.</p>
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12 pages, 1743 KiB  
Article
Standard Cell Sizing for Worst-Case Performance Optimization Considering Process Variation in Subthreshold Region
by Peng Cao and Jingjing Guo
Electronics 2024, 13(22), 4477; https://doi.org/10.3390/electronics13224477 - 14 Nov 2024
Viewed by 496
Abstract
Ultra-low-voltage design brings considerable outcomes in power reduction and energy efficiency improvement at the cost of performance degradation and uncertainty. Conventional standard cell design methodology cannot guarantee optimal performance for subthreshold operations due to the lack of consideration of process variation. In this [...] Read more.
Ultra-low-voltage design brings considerable outcomes in power reduction and energy efficiency improvement at the cost of performance degradation and uncertainty. Conventional standard cell design methodology cannot guarantee optimal performance for subthreshold operations due to the lack of consideration of process variation. In this paper, an effective subthreshold cell sizing method is proposed to minimize the worst-case propagation delay by deriving the optimal pMOS-to-nMOS width ratio (β) analytically, which reveals the relation between the minimal worst-case delay and the process parameters and provides distinct guidance for standard cell library design. The proposed method demonstrated good agreement with the Monte Carlo SPICE simulation results and was validated at the cell level and the circuit level. At the cell level, the logic cells designed with the proposed method show at least 8.6% and 7.4% improvement, on average, for worst-case delay and energy-delay product (EDP), respectively, with an additional 3.2% energy overhead compared to the prior approaches. At the circuit level, the proposed method improves the worst-case performance and worst-case EDP of the ring oscillator by at least 15.5% and 15.0%, respectively, with a 0.9% energy penalty. Moreover, the ISCAS’89 and OpenCores circuits synthesized with the optimized cells achieve at least 6.6% worst-case performance enhancement, 6.9% power reduction, and 9.4% area saving. Full article
(This article belongs to the Section Microelectronics)
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<p>SPICE simulation results of the nominal and worst-case propagation delay for inverter under TSMC 28 nm (<b>a</b>) super-threshold region (1.1 V) and (<b>b</b>) subthreshold region (0.35 V).</p>
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<p>Inverter driving an identical inverter.</p>
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<p>Derivation of the signs of <span class="html-italic">S<sub>μ</sub></span> and <span class="html-italic">S<sub>σ</sub></span> by the relation of <span class="html-italic">h<sub>σ</sub></span>(<span class="html-italic">β</span>) and <span class="html-italic">g<sub>σ</sub></span>(<span class="html-italic">β</span>).</p>
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15 pages, 1134 KiB  
Review
Precision Medicine for Gastric Cancer: Current State of Organoid Drug Testing
by Tharindie N. Silva, Josephine A. Wright, Daniel L. Worthley and Susan L. Woods
Organoids 2024, 3(4), 266-280; https://doi.org/10.3390/organoids3040016 - 31 Oct 2024
Viewed by 1103
Abstract
Gastric cancer (GC) presents a significant health challenge and ranks as the fifth most common cancer in the world. Unfortunately, most patients with GC exhaust standard care treatment options due to late diagnosis and tumour heterogeneity that leads to drug resistance, resulting in [...] Read more.
Gastric cancer (GC) presents a significant health challenge and ranks as the fifth most common cancer in the world. Unfortunately, most patients with GC exhaust standard care treatment options due to late diagnosis and tumour heterogeneity that leads to drug resistance, resulting in poor survival outcomes. Potentially, this situation can be improved by personalising treatment choice. Organoids are an emerging cell model system that recapitulates tumour heterogeneity and drug responses. Coupled with genomic analysis, organoid culture can be used to guide personalised medicine. The GC organoid field, however, lacks standardised methodologies for assessing organoid drug sensitivities. Comparing results across different GC organoid studies and correlating organoid drug responses with patient outcomes is challenging. Hence, we aim to summarise the methodologies used in GC organoid drug testing and correlation with clinical outcomes and discuss design considerations and limitations to enhance the robustness of such studies in the future. Full article
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<p>Schematic representation of personalised cancer treatment using GC organoids. The flow chart depicts the establishment of GC organoids from human cancer tissue, the creation of a GC organoid biobank, and the analysis performed (genomic sequencing and drug assays). These patient-derived organoid drug responses can be directly compared to patient clinical responses to assess the clinical utility of this approach and guide personalised treatment in the future.</p>
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<p>Summary of patient to organoid drug response correlation in GC studies. Patient-derived organoids were treated using various chemotherapeutic and targeted drugs, and responses were evaluated by their cellular responses (cell viability, proliferation, and death percentage) and morphological changes. In contrast, patient clinical responses were evaluated using pathological assessments, imaging, and tumour-specific markers. Patient clinical responses and organoid responses to drug treatment were compared to evaluate the utility of using organoids as a pre-clinical model to guide personalised chemotherapy in GC studies [<a href="#B29-organoids-03-00016" class="html-bibr">29</a>,<a href="#B39-organoids-03-00016" class="html-bibr">39</a>,<a href="#B49-organoids-03-00016" class="html-bibr">49</a>,<a href="#B50-organoids-03-00016" class="html-bibr">50</a>,<a href="#B53-organoids-03-00016" class="html-bibr">53</a>,<a href="#B55-organoids-03-00016" class="html-bibr">55</a>,<a href="#B56-organoids-03-00016" class="html-bibr">56</a>,<a href="#B57-organoids-03-00016" class="html-bibr">57</a>,<a href="#B58-organoids-03-00016" class="html-bibr">58</a>]. N.R. not reported.</p>
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19 pages, 3031 KiB  
Review
How Far Is the Nanocellulose Chip and Its Production in Reach? A Literature Survey
by Elena Bencurova, André Chinazzo, Bipasa Kar, Matthias Jung and Thomas Dandekar
Nanomaterials 2024, 14(18), 1536; https://doi.org/10.3390/nano14181536 - 22 Sep 2024
Viewed by 1375
Abstract
The slowdown of Moore’s Law necessitates an exploration of novel computing methodologies, new materials, and advantages in chip design. Thus, carbon-based materials have promise for more energy-efficient computing systems in the future. Moreover, sustainability emerges as a new concern for the semiconductor industry. [...] Read more.
The slowdown of Moore’s Law necessitates an exploration of novel computing methodologies, new materials, and advantages in chip design. Thus, carbon-based materials have promise for more energy-efficient computing systems in the future. Moreover, sustainability emerges as a new concern for the semiconductor industry. The production and recycling processes associated with current chips present huge environmental challenges. Electronic waste is a major problem, and sustainable solutions in computing must be found. In this review, we examine an alternative chip design based on nanocellulose, which also features semiconductor properties and transistors. Our review highlights that nanocellulose (NC) is a versatile material and a high-potential composite, as it can be fabricated to gain suitable electronic and semiconducting properties. NC provides ideal support for ink-printed transistors and electronics, including green paper electronics. Here, we summarise various processing procedures for nanocellulose and describe the structure of exclusively nanocellulose-based transistors. Furthermore, we survey the recent scientific efforts in organic chip design and show how fully automated production of such a full NC chip could be achieved, including a Process Design Kit (PDK), expected variation models, and a standard cell library at the logic-gate level, where multiple transistors are connected to perform basic logic operations—for instance, the NOT-AND (NAND) gate. Taking all these attractive nanocellulose features into account, we envision how chips based on nanocellulose can be fabricated using Electronic Design Automation (EDA) tool chains. Full article
(This article belongs to the Special Issue Nanomaterials and Textiles)
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<p>Panel (<b>A</b>). Comparison of environmental impacts of various sources of electronic devices based on literature review and data synthesis. The categories on the x axis represent the impact areas, and the y axis shows the normalised impact levels on a scale from 1 to 10. Panel (<b>B</b>). Schematic overview of multi-layered paper-tronic circuits. Adapted from Rafiee et al. [<a href="#B39-nanomaterials-14-01536" class="html-bibr">39</a>].</p>
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<p>Schematic overview of the proposed transistor using non-treated nanocellulose as a dielectric layer, P- or N-type nanocellulose for the semiconductive channel [<a href="#B45-nanomaterials-14-01536" class="html-bibr">45</a>,<a href="#B50-nanomaterials-14-01536" class="html-bibr">50</a>], and GO-treated nanocellulose for the conducting parts.</p>
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<p>Production and functionalization of nanocellulose for enhanced conductivity. The flow chart illustrates the production and functionalization of NC from biological sources, including Scoby, cotton, trees, and agricultural residues. Extraction and purification can be performed through mechanical processing or chemical treatment, followed by a top-down approach (mechanical grinding) or a bottom-up approach (acid hydrolysis). Functionalization can be achieved by adding conductive materials like conductive polymers, metal nanoparticles, carbon-based agents, and ionic liquids to enhance the electrical properties of nanocellulose for advanced applications. References: 1: [<a href="#B21-nanomaterials-14-01536" class="html-bibr">21</a>], 2: [<a href="#B68-nanomaterials-14-01536" class="html-bibr">68</a>], 3: [<a href="#B59-nanomaterials-14-01536" class="html-bibr">59</a>], 4: [<a href="#B61-nanomaterials-14-01536" class="html-bibr">61</a>], 5: [<a href="#B69-nanomaterials-14-01536" class="html-bibr">69</a>], 6: [<a href="#B70-nanomaterials-14-01536" class="html-bibr">70</a>], 7: [<a href="#B64-nanomaterials-14-01536" class="html-bibr">64</a>], 8: [<a href="#B65-nanomaterials-14-01536" class="html-bibr">65</a>], 9: [<a href="#B71-nanomaterials-14-01536" class="html-bibr">71</a>], 9: [<a href="#B72-nanomaterials-14-01536" class="html-bibr">72</a>], 11: [<a href="#B73-nanomaterials-14-01536" class="html-bibr">73</a>], 12: [<a href="#B66-nanomaterials-14-01536" class="html-bibr">66</a>], 13: [<a href="#B74-nanomaterials-14-01536" class="html-bibr">74</a>], 14: [<a href="#B75-nanomaterials-14-01536" class="html-bibr">75</a>], 15: [<a href="#B76-nanomaterials-14-01536" class="html-bibr">76</a>], 16: [<a href="#B77-nanomaterials-14-01536" class="html-bibr">77</a>], 17: [<a href="#B58-nanomaterials-14-01536" class="html-bibr">58</a>], 18: [<a href="#B78-nanomaterials-14-01536" class="html-bibr">78</a>], 19: [<a href="#B79-nanomaterials-14-01536" class="html-bibr">79</a>], 20: [<a href="#B80-nanomaterials-14-01536" class="html-bibr">80</a>], 21: [<a href="#B81-nanomaterials-14-01536" class="html-bibr">81</a>], 22: [<a href="#B82-nanomaterials-14-01536" class="html-bibr">82</a>], 23: [<a href="#B83-nanomaterials-14-01536" class="html-bibr">83</a>].</p>
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<p>Schematic representation of nanocellulose-based transistor designs across different scales. The macroscopic design (<b>left</b>) shows a basic transistor structure with N- or P-doped nanocellulose integrated with graphene oxide nanocellulose (GO-NC) layers. At the microscopic level (<b>centre</b>), the diagram suggests replacing traditional wires with DNA strands to enhance sustainability at the molecular level in order to form gates (e.g., NAND). At the nanoscale (<b>right</b>), the image illustrates the potential for miniaturisation, showcasing a single-electron transistor (SET) configuration using nanocellulose, graphene oxide components, and a graphene back plate as a gate.</p>
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<p>Proposed process flow for the design and fabrication of complex digital circuits using nanocellulose-based transistors. Artifacts are indicated by parallelograms, and processes are indicated by rectangles. Processes are adapted to nanocellulose composites, including transistors made from nanocellulose.</p>
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16 pages, 533 KiB  
Review
Cell Therapy in the Treatment of Female Stress Urinary Incontinence: Current Status and Future Proposals
by Carmen González Enguita, María Garranzo García-Ibarrola, Jaime Jorge Tufet I Jaumont, Héctor Garde García, Raquel González López, Luis Miguel Quintana Franco, Gina Marcela Torres Zambrano and Mariano García-Arranz
Life 2024, 14(7), 861; https://doi.org/10.3390/life14070861 - 10 Jul 2024
Cited by 1 | Viewed by 1475
Abstract
Background: Stress urinary incontinence (SUI) is a common condition with a significant impact on the quality of life of female patients. The limitations of current treatment strategies have prompted the exploration of new effective and minimally invasive alternative approaches, including cell therapy. Methods: [...] Read more.
Background: Stress urinary incontinence (SUI) is a common condition with a significant impact on the quality of life of female patients. The limitations of current treatment strategies have prompted the exploration of new effective and minimally invasive alternative approaches, including cell therapy. Methods: A literature search was conducted to update the current clinical status of stem cell therapy in the management of female stress urinary incontinence. Results: Over thirty clinical studies have been designed to assess the feasibility, safety and efficacy of cell therapy for female SUI. Despite differences in cell types and protocols, the overall treatment procedures were similar. Standard subjective and objective assessment tools, and follow-up periods ranged from 6 weeks to 6 years have been used. Cell injection has shown to be a safe therapy in the treatment of female SUI. However, the results from more recent randomized trials have shown less promising results than expected in restoring continence. Heterogeneous research methodologies using different cell types and doses make it difficult to draw conclusions about effectiveness. Several key points remain that need to be further explored in future clinical trials. Conclusion: To advance in the development of cell therapy, it is essential to know the mechanisms involved to be able to direct it properly, its efficacy and the durability of the injected cells. Rigorous and homogenized preclinical and clinical studies that demonstrate its scope and improve its application are necessary for validation in the treatment of female SUI. Full article
(This article belongs to the Section Cell Biology and Tissue Engineering)
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<p>Stem cell injection therapy in female SUI.</p>
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13 pages, 618 KiB  
Review
A Review of the Paradigmatic Role of Adipose Tissue in Renal Cancer: Fat Measurement and Tumor Behavior Features
by Eliodoro Faiella, Elva Vergantino, Federica Vaccarino, Amalia Bruno, Gloria Perillo, Rosario Francesco Grasso, Bruno Beomonte Zobel and Domiziana Santucci
Cancers 2024, 16(9), 1697; https://doi.org/10.3390/cancers16091697 - 27 Apr 2024
Cited by 2 | Viewed by 1344
Abstract
(1) Background: Renal-cell carcinoma (RCC) incidence has been steadily rising, with obesity identified as a potential risk factor. However, the relationship between obesity and RCC prognosis remains unclear. This systematic review aims to investigate the impact of different adipose tissue measurements on RCC [...] Read more.
(1) Background: Renal-cell carcinoma (RCC) incidence has been steadily rising, with obesity identified as a potential risk factor. However, the relationship between obesity and RCC prognosis remains unclear. This systematic review aims to investigate the impact of different adipose tissue measurements on RCC behavior and prognosis. (2) Methods: A search of MEDLINE databases identified 20 eligible studies focusing on various fat measurements, including visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), perirenal adipose tissue (PRAT), and the Mayo adhesive probability (MAP) score. (3) Results: The review revealed conflicting findings regarding the association between adipose tissue measurements and RCC outcomes. While some studies suggested a protective role of certain fat deposits, particularly VAT, against disease progression and mortality, others reported contradictory results across different adipose metrics and RCC subtypes. (4) Conclusions: Methodological variations and limitations, such as retrospective designs and sample size constraints, pose challenges to standardization and generalizability. Further research is needed to understand these associations better and establish standardized approaches for adiposity assessment in RCC patients, which could inform clinical practice and therapeutic decision-making. Full article
(This article belongs to the Special Issue Cell Biology of Cancer Invasion)
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<p>PRISMA 2020 flow diagram for the selection of studies included in the review. * Consider, if feasible to do so, reporting the number of records identified from each database or register searched (rather than the total number across all databases/registers). ** If automation tools were used, indicate how many records were excluded by a human and how many were excluded by automation tools.</p>
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29 pages, 32996 KiB  
Review
Computational Modelling and Simulation of Scaffolds for Bone Tissue Engineering
by Haja-Sherief N. Musthafa, Jason Walker and Mariusz Domagala
Computation 2024, 12(4), 74; https://doi.org/10.3390/computation12040074 - 4 Apr 2024
Cited by 3 | Viewed by 4847
Abstract
Three-dimensional porous scaffolds are substitutes for traditional bone grafts in bone tissue engineering (BTE) applications to restore and treat bone injuries and defects. The use of computational modelling is gaining momentum to predict the parameters involved in tissue healing and cell seeding procedures [...] Read more.
Three-dimensional porous scaffolds are substitutes for traditional bone grafts in bone tissue engineering (BTE) applications to restore and treat bone injuries and defects. The use of computational modelling is gaining momentum to predict the parameters involved in tissue healing and cell seeding procedures in perfusion bioreactors to reach the final goal of optimal bone tissue growth. Computational modelling based on finite element method (FEM) and computational fluid dynamics (CFD) are two standard methodologies utilised to investigate the equivalent mechanical properties of tissue scaffolds, as well as the flow characteristics inside the scaffolds, respectively. The success of a computational modelling simulation hinges on the selection of a relevant mathematical model with proper initial and boundary conditions. This review paper aims to provide insights to researchers regarding the selection of appropriate finite element (FE) models for different materials and CFD models for different flow regimes inside perfusion bioreactors. Thus, these FEM/CFD computational models may help to create efficient designs of scaffolds by predicting their structural properties and their haemodynamic responses prior to in vitro and in vivo tissue engineering (TE) applications. Full article
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<p>Illustration of scaffolds-based BTE. TGF-β: Transforming Growth Factor-β, BMP: Bone Morphogenetic Proteins, IGF: Insulin-like Growth Factor, FGF: Fibroblast Growth Factor, MSCs: Mesenchymal Stem Cells, EPC: Endothelial Progenitor Cell, iPSC: Induced Pluripotent Stem Cells. Reproduced with permission from Ref. [<a href="#B12-computation-12-00074" class="html-bibr">12</a>] CC BY 4.0.</p>
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<p>(<b>A</b>–<b>D</b>) Implantation of a composite scaffold on a tibial bone defect region. (<b>E</b>) Bone remodelling in and out of the scaffold with white triangles denoting the external boundaries of the scaffold. Reproduced with permission from Ref. [<a href="#B13-computation-12-00074" class="html-bibr">13</a>] CC BY 4.0.</p>
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<p>The characteristics of a BTE scaffold and its related supportive functions [<a href="#B42-computation-12-00074" class="html-bibr">42</a>].</p>
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<p>Factors required for designing scaffolds. Reproduced with permission from Ref. [<a href="#B43-computation-12-00074" class="html-bibr">43</a>] CC BY 4.0.</p>
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<p>Types of scaffold designs based on their architectures. Their related structures can be viewed in <a href="#app1-computation-12-00074" class="html-app">Supplementary Materials Figures S1–S3</a>.</p>
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<p>Different stages of compressive behaviour of lattice structures. Reproduced with permission from Ref. [<a href="#B83-computation-12-00074" class="html-bibr">83</a>] CC BY-NC-ND 4.0.</p>
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<p>An image-based FEM computational workflow for BTE scaffolds using FEM and CFD modelling [<a href="#B82-computation-12-00074" class="html-bibr">82</a>].</p>
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<p>(<b>a</b>) An FE volume mesh for an FE model from an implicit body of a cuboid gyroid scaffold (conversion of the given implicit body to a surface mesh, to a volume mesh with tetrahedral elements and a FE volume mesh with quadratic order), (<b>b</b>) structural analysis of an FE model under compressive loading. (<b>c</b>) von Mises contour of PS550 (Pore size 500 µm and Strut size 300 µm) gyroid scaffold, and (<b>d</b>) displacement contour of PS550. Reproduced with permission from Ref. [<a href="#B84-computation-12-00074" class="html-bibr">84</a>] CC BY 4.0.</p>
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<p>Prediction of von Mises stress (S) and max principal strain (E) of scaffolds attached to dental implants using FEM-based linear isotropic models. Reproduced with permission from Ref. [<a href="#B86-computation-12-00074" class="html-bibr">86</a>] CC BY-NC-ND 4.0.</p>
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<p>FEA of solid and porous TPMS scaffolds based on segmental femur defect for BTE and its related stress contours (units are given in MPa): (<b>a</b>,<b>b</b>) Implantation of P-TPMS and solid scaffolds, (<b>c</b>,<b>d</b>) stress distribution contours on the bone, (<b>e</b>,<b>f</b>) von Mises stress contours of P and solid scaffolds, (<b>g</b>,<b>h</b>) stress distribution contours for P and solid scaffolds at 50 MPa. Reproduced with permission from Ref. [<a href="#B93-computation-12-00074" class="html-bibr">93</a>] CC BY 4.0.</p>
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<p>FEM-based BISO elastoplastic model prediction of scaffolds for tibial bone defect repair. Reproduced with permission from Ref. [<a href="#B94-computation-12-00074" class="html-bibr">94</a>] CC BY-NC-ND 4.0.</p>
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<p>Principal turbulent CFD methods (from top to bottom: lowest to highest computational cost) [<a href="#B131-computation-12-00074" class="html-bibr">131</a>].</p>
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<p>Steps in formulating a mathematical model in a CFD simulation [<a href="#B137-computation-12-00074" class="html-bibr">137</a>].</p>
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<p>An illustration (designed using nTopology software version 4.22.2) of creating a fluid domain for CFD by using Boolean subtraction of solid (bioreactor) by scaffold lattice; the top region of the fluid domain can be used as a velocity inlet of flow, and its bottom region can be used as a pressure outlet.</p>
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<p>(<b>A</b>) Pressure drops and (<b>B</b>) WSS contours of hexagonal honeycomb scaffolds based on (a) Simple Uniform structure, (b) Overlapping Simple Curved structure, (c) Simple Gradient structure, and (d) Simple Internal Curved structure. Reproduced with permission from Ref. [<a href="#B150-computation-12-00074" class="html-bibr">150</a>] CC BT-NC-ND 4.0.</p>
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<p>(<b>A</b>) Pressure drops, (<b>B</b>) WSS and (<b>C</b>) velocity contours of anatomically shaped BTE scaffolds for inlet blood velocities: (a) 1 mm/s, (b) 3 mm/s, (c) 5 mm/s, (d) 7 mm/s and (e) 9 mm/s. Reproduced with permission from Ref. [<a href="#B130-computation-12-00074" class="html-bibr">130</a>] CC BY 4.0.</p>
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<p>(<b>a</b>,<b>b</b>) Velocity contours and (<b>c</b>,<b>d</b>) WSS contours of Newtonian and non-Newtonian CFD models of gyroid scaffolds with relative density 0.1. Reproduced with permission from Ref. [<a href="#B156-computation-12-00074" class="html-bibr">156</a>] CC BY-NC-ND 4.0.</p>
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<p>CFD for permeability prediction of TPMS scaffolds to optimise innovative BTE implants. Reproduced with permission from Ref. [<a href="#B158-computation-12-00074" class="html-bibr">158</a>] CC BY-NC-ND 4.0.</p>
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17 pages, 1933 KiB  
Article
Influence of Wide-Bandgap Semiconductors in Interleaved Converters Sizing for a Fuel-Cell Power Architecture
by Victor Mercier, Toufik Azib, Adriano Ceschia and Cherif Larouci
World Electr. Veh. J. 2024, 15(4), 148; https://doi.org/10.3390/wevj15040148 - 3 Apr 2024
Viewed by 1374
Abstract
This study presents a decision-support methodology to design and optimize modular Boost converters in the context of fuel-cell electric vehicles. It involves the utilization of interleaved techniques to reduce fuel-cell current ripple, enhance system efficiency, tackle issues related to weight and size concerns, [...] Read more.
This study presents a decision-support methodology to design and optimize modular Boost converters in the context of fuel-cell electric vehicles. It involves the utilization of interleaved techniques to reduce fuel-cell current ripple, enhance system efficiency, tackle issues related to weight and size concerns, and offer better flexibility and modularity within the converter. The methodology incorporates emerging technologies by wide-bandgap semiconductors, providing better efficiency and higher temperature tolerance. It employs a multiphysical approach, considering electrical, thermal, and efficiency constraints to achieve an optimal power architecture for FCHEVs. Results demonstrate the advantages of wide-bandgap semiconductor utilization in terms of volume reduction and efficiency enhancements for different power levels. Results from one of the considered power levels highlight the feasibility of certain architectures through the utilization of WBG devices. These architectures reveal improvements in both efficiency and volume reduction as a result of incorporating WBG devices. Additionally, the analysis presents a comparison of manufacturing cost between standard and wide-bandgap semiconductors to demonstrate the market penetration potential. Full article
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<p>Schemes representation of a non-isolated and isolated converter: (<b>a</b>) Non-isolated Boost converter. (<b>b</b>) Isolated Flyback converter.</p>
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<p>Interleaving of a n-cell Boost converter.</p>
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<p>Current ripples waveforms of a two-phase interleaved boost converter.</p>
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<p>Parallel hybrid power source architecture.</p>
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<p>A diagram of the general principle of the developed approach.</p>
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<p>Particle Swarm Optimization principle.</p>
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<p>A global optimization methodology under multiphysical constraints.</p>
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<p>Thermal modeling of two semiconductors sharing the same heat sink: (<b>a</b>) Thermal dissipation setup scheme. (<b>b</b>) Equivalent thermal circuit of the adopted thermal management.</p>
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<p>Volume comparison of WBG and standard devices for a 2-kW load.</p>
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<p>Comparison of WBG and Si devices for a 2kW load: (<b>a</b>) Efficiency comparison. (<b>b</b>) Frequency comparison.</p>
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<p>Volume comparison of WBG and standard devices for a 40-kW load.</p>
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<p>Comparison of WBG and Si devices for a 40kW load: (<b>a</b>) Efficiency comparison. (<b>b</b>) Frequency comparison.</p>
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<p>Cost comparison of WBG and standard devices.</p>
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33 pages, 7079 KiB  
Article
Extracellular Vesicle Protein Expression in Doped Bioactive Glasses: Further Insights Applying Anomaly Detection
by Mauro Nascimben, Hugo Abreu, Marcello Manfredi, Giuseppe Cappellano, Annalisa Chiocchetti and Lia Rimondini
Int. J. Mol. Sci. 2024, 25(6), 3560; https://doi.org/10.3390/ijms25063560 - 21 Mar 2024
Viewed by 2179 | Correction
Abstract
Proteomic analysis of extracellular vesicles presents several challenges due to the unique nature of these small membrane-bound structures. Alternative analyses could reveal outcomes hidden from standard statistics to explore and develop potential new biological hypotheses that may have been overlooked during the initial [...] Read more.
Proteomic analysis of extracellular vesicles presents several challenges due to the unique nature of these small membrane-bound structures. Alternative analyses could reveal outcomes hidden from standard statistics to explore and develop potential new biological hypotheses that may have been overlooked during the initial evaluation of the data. An analysis sequence focusing on deviating protein expressions from donors’ primary cells was performed, leveraging machine-learning techniques to analyze small datasets, and it has been applied to evaluate extracellular vesicles’ protein content gathered from mesenchymal stem cells cultured on bioactive glass discs doped or not with metal ions. The goal was to provide additional opportunities for detecting details between experimental conditions that are not entirely revealed with classic statistical inference, offering further insights regarding the experimental design and assisting the researchers in interpreting the outcomes. The methodology extracted a set of EV-related proteins whose differences between conditions could be partially explainable with statistics, suggesting the presence of other factors involved in the bioactive glasses’ interactions with tissues. Outlier identification of extracellular vesicles’ protein expression levels related to biomaterial preparation was instrumental in improving the interpretation of the experimental outcomes. Full article
(This article belongs to the Special Issue Biomaterials for Dental and Orthopedic Applications)
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<p>Venn diagrams of extremely changing proteins as identified by Isolation Forest and Euclidean distances. On the (<b>left</b>), the Control versus Doped bioactive glass shows only one protein in common between “SBA3” and “ST”. On the (<b>right</b>), the Plastic versus Doped conditions sharing several proteins.</p>
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<p>The blue line is the quadratic fit of the log fold change and Euclidean distances (ctrl versus doped distances).</p>
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<p>The blue line is the quadratic fit of the log fold change and Euclidean distances (plast versus doped distances).</p>
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<p>Scheme of the proposed methodology.</p>
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<p>All data from the three donors and each experimental condition underwent automatic labeling to store only uniformly distributed values: the points in the blue cluster were retained in the next steps of the experimental sequence. The other colors represent the additional clusters identified by OPTICS.</p>
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<p>Values from the three donors marked as black dots were considered inliers, thus close to each other, in the three experimental conditions (Plast, Control, and Doped) by the Isolation Forest algorithm, whereas colored points were those showing more relevant changes (aka outliers).</p>
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<p>Retaining only the values considered outliers by Isolation Forest. The three axes represent the three donors.</p>
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<p>Euclidean distances between the Control and Doped conditions. The left panel is “SBA2” condition, the central image the “SBA3”, whereas the right one is “ST”. The statistical threshold is the red vertical line.</p>
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<p>Euclidean distances between the Plastic and Doped conditions. The left panel is “SBA2” condition, the central image the “SBA3”, whereas the right one is “ST”. The statistical threshold is the red vertical line.</p>
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<p>Distributions of the values from the three donors in <a href="#ijms-25-03560-t0A1" class="html-table">Table A1</a> (Protein GAMMA). There is a statistically significant difference between experimental conditions, exemplified by the distance between averages.</p>
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<p>Distributions of the values from the three donors in <a href="#ijms-25-03560-t0A2" class="html-table">Table A2</a> (Protein OMEGA). There is no significant difference between means in the two experimental conditions.</p>
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<p>Hypothetical (absolute) differential expression of the proteins GAMMA and OMEGA in the three donors “A”, “B”, and “C”.</p>
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<p>Example of the distance calculation between two points, each one representing an experimental condition in the 3D subjects’ space.</p>
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<p>Protein expression values from the three subjects belonging to the blue cluster retained for further analysis.</p>
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<p>Heatmap with Euclidean distances between the Control and Doped conditions. The left panel is “SBA2” condition, the central image the “SBA3”, whereas the right one is “ST”.</p>
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<p>Heatmap with Euclidean distances between the Plastic and Doped conditions. The left panel is “SBA2” condition, the central image the “SBA3”, whereas the right one is “ST”.</p>
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80 pages, 1834 KiB  
Review
A Drug Safety Briefing (II) in Transplantation from Real-World Individual Pharmacotherapy Management to Prevent Patient and Graft from Polypharmacy Risks at the Very Earliest Stage
by Ursula Wolf
Pharmaceuticals 2024, 17(3), 294; https://doi.org/10.3390/ph17030294 - 25 Feb 2024
Cited by 1 | Viewed by 2955
Abstract
For early and long-term patient and graft survival, drug therapy in solid organ and hematopoietic stem cell transplantation inevitably involves polypharmacy in patients with widely varying and even abruptly changing conditions. In this second part, relevant medication briefing is provided, in addition to [...] Read more.
For early and long-term patient and graft survival, drug therapy in solid organ and hematopoietic stem cell transplantation inevitably involves polypharmacy in patients with widely varying and even abruptly changing conditions. In this second part, relevant medication briefing is provided, in addition to the scores defined in the previously published first part on the design of the Individual Pharmacotherapy Management (IPM). The focus is on the growing spectrum of contemporary polypharmacy in transplant patients, including early and long-term follow-up medications. 1. Unlike the available drug–drug interaction (DDI) tables, for the first time, this methodological all-in-one device refers to the entire risks, including contraindications, special warnings, adverse drug reactions (ADRs), and DDIs. The selection of 65 common critical drugs results from 10 years of daily IPM with real-world evidence from more than 60,800 IPM inpatient and outpatient medication analyses. It includes immunosuppressants and typical critical antimicrobials, analgesics, antihypertensives, oral anticoagulants, antiarrhythmics, antilipids, antidepressants, antipsychotics, antipropulsives, antiemetics, propulsives, proton pump inhibitors (PPIs), sedatives, antineoplastics, and protein kinase inhibitors. As a guide for the attending physician, the drug-related risks are presented in an alphabetical overview based on the Summaries of Product Characteristics (SmPCs) and the literature. 2. Further briefing refers to own proven clinical measures to manage unavoidable drug-related high-risk situations. Drug-induced injuries to the vulnerable graft and the immunosuppressed comorbid patient require such standardized, intensive IPM and the comprehensive preventive briefing toolset to optimize the outcomes in the polypharmacy setting. Full article
(This article belongs to the Special Issue Therapeutic Drug Monitoring and Adverse Drug Reactions)
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<p>Comprehensive, reproducible IPM, based on the electronic patient record (adapted from [<a href="#B9-pharmaceuticals-17-00294" class="html-bibr">9</a>], Pharmaceutics, 2023). * IPM (applied patient and medication scores), based on the electronic hospital patient record at Halle University Hospital, conceptualized, implemented, and practiced by Wolf, MD, Head of Pharmacotherapy Management Department, Specialist in Internal Medicine, with expertise in Clinical Pharmacology and Transplantation, performed &gt; 60,800 individual medication reviews.</p>
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<p>The context of appropriate polypharmacy assessments and subsequent adjustments: (expanded version of [<a href="#B9-pharmaceuticals-17-00294" class="html-bibr">9</a>], Pharmaceutics, 2023) (<b>a</b>) The individual circuits affect each other. Therefore, interference monitoring is required. (<b>b</b>) The optimization of polypharmacy by continuous synoptic contribution and the adaptation to confounding risks from varying current patient condition and altering comedications through simultaneous IPM in real-time. An additional IPM toolset with tabulated medication scores for 65 commonly coadministered medications and a practice-oriented briefing on counteracting risk situations is provided. * IPM scores see <a href="#pharmaceuticals-17-00294-f001" class="html-fig">Figure 1</a>.</p>
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22 pages, 4336 KiB  
Article
Optimization, Metabolomic Analysis, Antioxidant Potential and Depigmenting Activity of Polyphenolic Compounds from Unmature Ajwa Date Seeds (Phoenix dactylifera L.) Using Ultrasonic-Assisted Extraction
by Fanar Alshammari, Md Badrul Alam, Marufa Naznin, Sunghwan Kim and Sang-Han Lee
Antioxidants 2024, 13(2), 238; https://doi.org/10.3390/antiox13020238 - 15 Feb 2024
Cited by 3 | Viewed by 2593
Abstract
This study sought to optimize the ultrasonic-assisted extraction of polyphenolic compounds from unmature Ajwa date seeds (UMS), conduct untargeted metabolite identification and assess antioxidant and depigmenting activities. Response surface methodology (RSM) utilizing the Box–Behnken design (BBD) and artificial neural network (ANN) modeling was [...] Read more.
This study sought to optimize the ultrasonic-assisted extraction of polyphenolic compounds from unmature Ajwa date seeds (UMS), conduct untargeted metabolite identification and assess antioxidant and depigmenting activities. Response surface methodology (RSM) utilizing the Box–Behnken design (BBD) and artificial neural network (ANN) modeling was applied to optimize extraction conditions, including the ethanol concentration, extraction temperature and time. The determined optimal conditions comprised the ethanol concentration (62.00%), extraction time (29.00 min), and extraction temperature (50 °C). Under these conditions, UMS exhibited total phenolic content (TPC) and total flavonoid content (TFC) values of 77.52 ± 1.55 mgGAE/g and 58.85 ± 1.12 mgCE/g, respectively, with low relative standard deviation (RSD%) and relative standard error (RSE%). High-resolution mass spectrometry analysis unveiled the presence of 104 secondary metabolites in UMS, encompassing phenols, flavonoids, sesquiterpenoids, lignans and fatty acids. Furthermore, UMS demonstrated robust antioxidant activities in various cell-free antioxidant assays, implicating engagement in both hydrogen atom transfer and single electron transfer mechanisms. Additionally, UMS effectively mitigated tert-butyl hydroperoxide (t-BHP)-induced cellular reactive oxygen species (ROS) generation in a concentration-dependent manner. Crucially, UMS showcased the ability to activate mitogen-activated protein kinases (MAPKs) and suppress key proteins including tyrosinase (Tyr), tyrosinase-related protein-1 and -2 (Trp-1 and -2) and microphthalmia-associated transcription factor (MITF), which associated melanin production in MNT-1 cell. In summary, this study not only optimized the extraction process for polyphenolic compounds from UMS but also elucidated its diverse secondary metabolite profile. The observed antioxidant and depigmenting activities underscore the promising applications of UMS in skincare formulations and pharmaceutical developments. Full article
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<p>Effect of (<b>A</b>) ethanol concentration; (<b>B</b>) extraction time; and (<b>C</b>) extraction temperature on UMS extraction on ethanol concentration, time and temperature single factor on the yield of TPC and TFC of UMS extract. Different letters represent statistical significance (<span class="html-italic">p</span> &lt; 0.05) between each group. (a, b, c and d for TPC; x, y and z for TFC).</p>
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<p>The three-dimensional (3D) response surface plots of UMS extraction on ethanol concentration, time and temperature for TPC (<b>A</b>) and TFC (<b>B</b>).</p>
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<p>Evaluation of ANN model performance. Assessing the validation of the constructed ANN model for (<b>A</b>) TPC and (<b>B</b>) TFC. Illustration of the optimal multilayer perceptron (MLP) architecture used in training, testing and validating the regression analysis to minimize errors for ANN model development for (<b>C</b>) TPC and (<b>D</b>) TFC.</p>
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<p>Model validation and comparative study of TPC and TFC of various extraction methods. (<b>A</b>) TPC and TFC value of optimized condition. (<b>B</b>) Relative standard deviation (RSD) and relative standard error (RSE) value of optimized condition. (<b>C</b>) Effect of various extraction techniques on the yield of TPC and TFC of UMS extract. (<b>D</b>) Effect of various extraction techniques on the DPPH and ABTS radical scavenging effects of UMS extract. Different letters represent statistical significance (<span class="html-italic">p</span> &lt; 0.05) between each group. (a, b, c and d for TPC; m, n, o, and p for TFC). U: ultrasonic assisted extraction; H: heat assisted extraction; M: maceration extract; OP: optimized condition; E: 100% EtOH; W: 100% aqueous; EW: 75% EtOH; AAE: ascorbic acid equivalent.</p>
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<p>Antioxidant effects of UMS. Cell-free (<b>A</b>) DPPH; (<b>B</b>) ABTS; (<b>C</b>) superoxide; (<b>D</b>) hydroxyl; and (<b>E</b>) NO radical scavenging activities of UMS. <span class="html-italic"><span class="html-small-caps">** </span>p</span> &lt; 0.01 vs. NT. (<b>F</b>) Reducing power activities of UMS in CUPRAC and FRAP assay. Different letters represent statistical significance (<span class="html-italic">p</span> &lt; 0.05) between each group. (a, b and c for CUPRAC; m, n and o for FRAP). (<b>G</b>) Cell viability of UMS in RAW 264.7 cells. <span class="html-italic">** p</span> &lt; 0.05 vs. NT, <sup>#</sup> <span class="html-italic">p</span> &lt; 0.01 vs. NT, ns: non-significant vs. NT, <sup>∇</sup> <span class="html-italic">p</span> &lt; 0.01 vs. UVB alone. (<b>H</b>) Effect of UMS on t-BHP induced cellular ROS generation. <sup>#</sup> <span class="html-italic">p</span> &lt; 0.001 vs. NT, <span class="html-italic">** p</span> &lt; 0.01 vs. UVB alone, ns: non-significant vs. UVB alone. ASC: ascorbic acid; GA: gallic acid; Q: quercetin and C: catechin. AAE: ascorbic acid equivalent.</p>
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<p>Effects of UMS on melanogenesis in MNT-1 cells. Cells were cultured with UMS (25–100 μg/mL) for 3 days. (<b>A</b>) Melanin content was determined. Western blot analysis of (<b>B</b>) melanogenesis factors such as Tyr, Trp-1, -2 and MITF, (<b>C</b>) MAPK proteins including p38, ERK and JNK. MNT-1 cells were co-treated with UMS and selective inhibitors of ERK (U0126) and p38 (SB239063). (<b>D</b>) MITF and Tyr levels were determined by western blot analysis, and (<b>E</b>) melanin content was also determined. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01 vs. NT, <sup>#</sup> <span class="html-italic">p</span> &lt; 0.01 vs. UMS alone, ns: non-significant vs. NT, ARB: arbutin.</p>
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14 pages, 2182 KiB  
Article
A Generic Approach for Miniaturized Unbiased High-Throughput Screens of Bispecific Antibodies and Biparatopic Antibody–Drug Conjugates
by Nadine Barron, Stephan Dickgiesser, Markus Fleischer, Angelika-Nicole Bachmann, Daniel Klewinghaus, Jens Hannewald, Elke Ciesielski, Ilja Kusters, Til Hammann, Volker Krause, Sebastian Winfried Fuchs, Vanessa Siegmund, Alec W. Gross, Dirk Mueller-Pompalla, Simon Krah, Stefan Zielonka and Achim Doerner
Int. J. Mol. Sci. 2024, 25(4), 2097; https://doi.org/10.3390/ijms25042097 - 8 Feb 2024
Cited by 4 | Viewed by 3090
Abstract
The toolbox of modern antibody engineering allows the design of versatile novel functionalities exceeding nature’s repertoire. Many bispecific antibodies comprise heterodimeric Fc portions recently validated through the approval of several bispecific biotherapeutics. While heterodimerization methodologies have been established for low-throughput large-scale production, few [...] Read more.
The toolbox of modern antibody engineering allows the design of versatile novel functionalities exceeding nature’s repertoire. Many bispecific antibodies comprise heterodimeric Fc portions recently validated through the approval of several bispecific biotherapeutics. While heterodimerization methodologies have been established for low-throughput large-scale production, few approaches exist to overcome the bottleneck of large combinatorial screening efforts that are essential for the identification of the best possible bispecific antibody. This report presents a novel, robust and miniaturized heterodimerization process based on controlled Fab-arm exchange (cFAE), which is applicable to a variety of heterodimeric formats and compatible with automated high-throughput screens. Proof of applicability was shown for two therapeutic molecule classes and two relevant functional screening read-outs. First, the miniaturized production of biparatopic anti-c-MET antibody–drug conjugates served as a proof of concept for their applicability in cytotoxic screenings on tumor cells with different target expression levels. Second, the automated workflow enabled a large unbiased combinatorial screening of biparatopic antibodies and the identification of hits mediating potent c-MET degradation. The presented workflow utilizes standard equipment and may serve as a facile, efficient and robust method for the discovery of innovative therapeutic agents in many laboratories worldwide. Full article
(This article belongs to the Section Molecular Pharmacology)
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<p>Optimization of miniaturized cFAE via TCEP and re-oxidation, applying dhAA or PEG-azide. (<b>a</b>) Scheme of the DuoBody reaction for heterodimerization. (<b>b</b>) Exemplary raw data set from SCX-HPLC monitoring cFAE over time, upon the addition of a 20-fold molar excess of TCEP at 1 mg/mL. Please refer to supplementary <a href="#app1-ijms-25-02097" class="html-app">Figure S1</a> indicating a negligible peak caused by PEG-azide. (<b>c</b>) cFAE kinetics for four TCEP concentrations applying a representative parental DuoBody pair to optimize TCEP concentration and incubation time. (<b>d</b>) Re-oxidation of interchain disulfide bonds using 10- or 20-fold dhAA or 20-fold PEG-azide (molar access over TCEP) compared to buffer exchange. PEG-azide yielded the formation of &gt;90% species of the size expected for the re-oxidized antibody similar to buffer exchange, confirmed by CE-SDS, as shown in <a href="#app1-ijms-25-02097" class="html-app">Figure S2</a>. Numerical data for sections (<b>b</b>,<b>c</b>) are listed in <a href="#app1-ijms-25-02097" class="html-app">Table S1</a>.</p>
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<p>Concentration and time dependency of the miniaturized reaction. (<b>a</b>) HIC HPLC analyses of the cFAE reaction with a 20-fold molar excess of TCEP for 4 h at 1 mg/mL, 0.3 mg/mL and 0.1 mg/mL, revealing a clear concentration dependency. (<b>b</b>) cFAE time course at 0.3 mg/mL and 0.1 mg/mL indicating slower reaction kinetics but completion at &gt;12 h incubation times. The working condition consisting of 0.7–1 mg/mL in 50–100 µL reaction volume and 4 h of cFAE reaction was found optimal. Numerical data for section (<b>b</b>) are listed in <a href="#app1-ijms-25-02097" class="html-app">Table S2</a>.</p>
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<p>Applicability for biparatopic ADC screening. (<b>a</b>) Scheme of the preparative steps including MTG-mediated linker–payload conjugation and heterodimerization to yield “half-ADC” candidates amendable for functional interrogation. (<b>b</b>) Representative CIEX-HPLC chromatograms indicating the successful generation of an REGN5093-based antibody–ADC heterodimer/biparatopic ADC (bpADC) applying the conditions optimized for bispecific antibody generation. (<b>c</b>) Triplicate analyses of biparatopic ADC formation at 1 mg/mL, 40 eq. TCEP and 6 h incubation time (please refer also to <a href="#app1-ijms-25-02097" class="html-app">Figure S3</a>). (<b>d</b>) Applicability of the generated half ADCs for functional screening such as for cytotoxic potency. Please note that the higher potency of the parental ADC is due to a higher DAR. (<b>e</b>) Potency determination of the samples shown in (<b>d</b>), demonstrating the option to screen for functionality with a DAR2 biparatopic ADC. * Indicates the calculated DAR values.</p>
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<p>Heterodimerization and c-MET degradation pilot study. (<b>a</b>) Scheme for automated matrix pipetting and heterodimerization followed by high-throughput functional interrogation and hit confirmation. (<b>b</b>) Representative HIC-HPLC chromatograms for 3 out of 624 c-MET biparatopic combinations. Marked peaks refer to bispecifics (Peak 2) and their respective parental antibodies (Peak 1, Peak 3) and indicate a high heterodimer content. Please, see also <a href="#app1-ijms-25-02097" class="html-app">Figure S3</a> for a broader data panel. (<b>c</b>) High-throughput screening for c-MET degradation yielded several potent combinations. Representative data indicate the nanomolar c-MET degradation potency (IC50 values: 0.91 nM, A03xB10v5; 0.80 nM, A03xE03; 1.47 nM, REGN5093) of two novel biparatopic antibodies comprising VHH A03 in combination with Fabs B10v5 or E03, similar to that of the re-produced REGN5093 reference, while the anti-DIG IgG isotype control did not degrade the antigen.</p>
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12 pages, 2324 KiB  
Article
Utility of an In-Vitro Micro-Neutralizing Test in Comparison to a Plaque Reduction Neutralization Test for Dengue Virus, Japanese Encephalitis Virus, and Zika Virus Serology and Drug Screening
by Kazumi Haga, Zhenying (Nancy) Chen, Misao Himeno, Ryuichi Majima and Meng Ling Moi
Pathogens 2024, 13(1), 8; https://doi.org/10.3390/pathogens13010008 - 20 Dec 2023
Cited by 1 | Viewed by 2438
Abstract
Flavivirus infections, including dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV), present significant global public health challenges. For successful vaccine design, the assessment of neutralizing antibody activity requires reliable and robust methodologies for determining antibody titers. Although the plaque reduction [...] Read more.
Flavivirus infections, including dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV), present significant global public health challenges. For successful vaccine design, the assessment of neutralizing antibody activity requires reliable and robust methodologies for determining antibody titers. Although the plaque reduction neutralization test (PRNT) is commonly acknowledged as the gold standard, it has limitations in terms of time and cost, and its usage may be limited in resource-limited settings. To address these challenges, we introduced the micro-neutralization test (MNT) as a simplified alternative to the PRNT. The MNT employs a 96-well plate format, conducts microscale neutralization assays, and assesses cell viability by dissolving cells to create a uniform color solution, which is measured with a spectrometer. In this study, we evaluated the utility of the MNT by contrasting the end-point titers of the MNT and PRNT using 4 monoclonal antibodies, 15 non-human primate serum samples, and 2 therapeutic drug candidates across flaviviruses. The results demonstrated a strong correlation between the MNT and PRNT titers, affirming the robustness and reproducibility of the MNT for evaluating control measures against flaviviruses. This research contributes valuable insights toward the development of a cost-effective antibody titer testing approach that is particularly suitable for resource-limited settings. Full article
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<p>The procedure for the PRNT is presented in this flowchart: (<b>A</b>) entails the cultivation of Vero-9013 cells on a 12-well plate, incubated at 37 °C for 24 h in a pre-prepared medium, while (<b>B</b>) corresponds to the neutralization phase. The virus and serially diluted testing samples are pre-incubated on ice for 30 min. The sample virus mixtures are then introduced to the pre-cultured cells. After 1 h of virus adsorption, overlay medium is added and the plate is incubated for 5 to 7 days. The cells then undergo fixation with methanol, staining with methylene blue, and the formed plaques are counted by the naked eye.</p>
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<p>The procedure for the MNT is presented in this flowchart: (<b>A</b>) entails the cultivation of Vero-9013 cells on a 96-well plate, incubated at 37 °C for 24 h in a pre-prepared medium, while (<b>B</b>) corresponds to the neutralization phase. The virus and serially diluted testing samples are pre-incubated under specified conditions (refer to the protocol for details). The sample virus mixtures are then introduced to the pre-cultured cells. Following 1 h of virus adsorption and 5–7 days of incubation, the cells undergo fixation with methanol, staining with crystal violet, dissolution with 1% SDS, and measurement of absorbance at 595 nm using a spectrometer.</p>
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<p>Vero-9013 cells were exposed to varying virus titers of DENV-1, JEV, and ZIKV, ranging from 10 pfu/well to 10<sup>5</sup> pfu/well using a 10-fold dilution series. OD<sub>595 nm</sub> measurements were performed for the experimental group and control group, from which the percentage of viable cells was subsequently calculated. Each data point represents the geometric mean derived from three replicate measurements, with the error bars denoting the standard deviation among these replicates.</p>
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<p>Ribavirin (<b>A</b>) and glycyrrhizin (<b>B</b>) were used to test the antiviral effects against DENV-1, JEV, and ZIKV through the MNT using Vero-9013 cells. Both ribavirin and glycyrrhizin were diluted in 2-folds ranging from 1000 <math display="inline"><semantics> <mrow> <mi mathvariant="sans-serif">μ</mi> <mi mathvariant="normal">g</mi> <mo>/</mo> <mi mathvariant="normal">m</mi> <mi mathvariant="normal">L</mi> </mrow> </semantics></math> to 0.975 <math display="inline"><semantics> <mrow> <mi mathvariant="sans-serif">μ</mi> <mi mathvariant="normal">g</mi> <mo>/</mo> <mi mathvariant="normal">m</mi> <mi mathvariant="normal">L</mi> </mrow> </semantics></math>. The percent reduction is calculated by the OD<sub>595 nm</sub> values of the experimental group, positive control group, negative group, and control group as shown in Equation (2). Each data point represents the geometric mean derived from six replicate measurements, with the error bars denoting the 95% confidence intervals among these replicates.</p>
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<p>Correlation between the neutralizing titers measured using the MNT and PRNT. MNT<sub>50</sub> and PRNT<sub>50</sub> of 4 anti-flavivirus mouse monoclonal antibodies and 15 serum samples are plotted in a logistic scale, and the correlation between the two is calculated (<math display="inline"><semantics> <mrow> <mi>r</mi> <mo>=</mo> <mn>0.916737</mn> </mrow> </semantics></math>), with a <span class="html-italic">p</span> value significantly smaller than 0.05. The 95% confidence interval of the linear regression is shown in the shaded area.</p>
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29 pages, 3090 KiB  
Review
Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems
by Roland Wohlgemuth
Metabolites 2023, 13(10), 1097; https://doi.org/10.3390/metabo13101097 - 19 Oct 2023
Cited by 1 | Viewed by 2273
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing [...] Read more.
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions. Full article
(This article belongs to the Section Thematic Reviews)
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<p>Selected reasons for the synthesis of metabolites and metabolite-like compounds. (<b>A</b>) For academic research applications in basic and applied sciences, where small quantities are usually needed, for example in biochemistry and other life sciences for the analysis of metabolic pathways, the discovery of unknown biological pathways, in preclinical research and development, and medical and diagnostic applications. (<b>B</b>) For applications in industry, where usually large quantities are needed of active ingredients and intermediates of pharmaceuticals, vitamins, flavors, fragrances, dyes, or agrochemicals. In clinical chemistry, standards are needed for blood and urine tests of biomarkers for diagnostic purposes and therapeutic drug monitoring or drug abuse. In medicinal chemistry, a diversity of test compounds and standards are needed for studying biological activity and efficacy, metabolism, and pharmacokinetics, and for determining the parameters of absorption, distribution, metabolism, excretion, and toxicity of novel molecular entities.</p>
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<p>Basic types of biocatalytic systems for the synthesis of metabolites and metabolite-like compounds.</p>
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<p>Selected naturally occurring metabolites with demonstrated total synthesis.</p>
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<p>Structures of vitamin B<sub>12</sub> and coenzyme B<sub>12</sub>.</p>
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<p>Complete stereochemistry and planar structure of palytoxin.</p>
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<p>Selected naturally occurring metabolites produced through bioprocesses at an industrial large scale.</p>
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<p>Plant cell fermentation for the industrial production of paclitaxel.</p>
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<p>Enzymatic process for the industrial production of the fragrance ingredient (-)-Ambrox.</p>
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<p>Biocatalytic synthesis of selected naturally occurring metabolites of the Emden–Meyerhof–Parnas, the Entner–Doudoroff, and the pentose phosphate pathways.</p>
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<p>Selected biocatalytic systems for the synthesis of metabolites labelled with <sup>2</sup>H-, <sup>13</sup>C-, or <sup>15</sup>N-stable isotopes.</p>
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<p>Selected biocatalytic systems for pharmaceutical drug metabolite synthesis.</p>
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<p>Biocatalytic synthesis of selected metabolite-like compounds.</p>
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28 pages, 827 KiB  
Review
Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation
by Jonathan Dao, Patrick J. Conway, Baskaran Subramani, Devi Meyyappan, Sammy Russell and Daruka Mahadevan
Int. J. Mol. Sci. 2023, 24(17), 13219; https://doi.org/10.3390/ijms241713219 - 25 Aug 2023
Cited by 27 | Viewed by 6083
Abstract
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, [...] Read more.
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management. Full article
(This article belongs to the Special Issue Liquid Biopsy in Cancers)
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Figure 1
<p>The cfDNA from liquid biopsy samples are analyzed in several ways: quantification of total cfDNA, qualitative and quantitative analysis of ctDNA mutations, and quantitative analysis of ctDNA methylation patterns. The analysis is then applied in the clinic at every step of patient management from screening to recurrence. Abbreviations: cntDNA: circulating non-tumor DNA; ctDNA: circulating tumor DNA; cfDNA: cell free DNA. Created with Biorender.com (accessed on 10 August 2023).</p>
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