Bioengineering最新文献

{"title":"Identification of Key Genes and Potential Therapeutic Targets in Sepsis-Associated Acute Kidney Injury Using Transformer and Machine Learning Approaches.","authors":"Zhendong Zhai, JunZhe Peng, Wenjun Zhong, Jun Tao, Yaqi Ao, Bailin Niu, Li Zhu","doi":"10.3390/bioengineering12050536","DOIUrl":"10.3390/bioengineering12050536","url":null,"abstract":"<p><p>Sepsis-associated acute kidney injury (SA-AKI) is a life-threatening complication of sepsis, characterized by high mortality and prolonged hospitalization. Early diagnosis and effective therapy remain difficult despite extensive investigation. To address this, we developed an AI-driven integrative framework that combines a Transformer-based deep learning model with established machine learning techniques (LASSO, SVM-RFE, Random Forest and neural networks) to uncover complex, nonlinear interactions among gene-expression biomarkers. Analysis of normalized microarray data from GEO (GSE95233 and GSE69063) identified differentially expressed genes (DEGs), and KEGG/GO enrichment via clusterProfiler revealed key pathways in immune response, protein synthesis, and antigen presentation. By integrating multiple transcriptomic cohorts, we pinpointed 617 SA-AKI-associated DEGs-21 of which overlapped between sepsis and AKI datasets. Our Transformer-based classifier ranked five genes (<i>MYL12B, RPL10</i>, <i>PTBP1</i>, <i>PPIA</i>, and <i>TOMM7</i>) as top diagnostic markers, with AUC values ranging from 0.9395 to 0.9996 (MYL12B yielding 0.9996). Drug-gene interaction mining using DGIdb (FDR < 0.05) nominated 19 candidate therapeutics for SA-AKI. Together, these findings demonstrate that melding deep learning with classical machine learning not only sharpens early SA-AKI detection but also systematically uncovers actionable drug targets, laying groundwork for precision intervention in critical care settings.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stabilization of the Bio-Oil Organic Phase via Solvent-Assisted Hydrotreating, Part 1: Investigating the Influence of Various Solvents.","authors":"Manqoba Shezi, Manish Sakhakarmy, Sushil Adhikari, Sammy Lewis Kiambi","doi":"10.3390/bioengineering12050537","DOIUrl":"10.3390/bioengineering12050537","url":null,"abstract":"<p><p>Conventional mild hydrotreatment processes of bio-oil present significant challenges of a high degree of polymerization, a low oil yield, high coke formation, and poor catalyst recovery. To address these challenges, the current study looked into investigating and enhancing the properties of raw bio-oil organic phase samples via a solvent-assisted stabilization approach using methanol (METH), ethanol (ETH), isopropyl alcohol (IPA), and ethyl ether (DME). Solvents like methanol (METH) and ethanol (ETH), which are highly polar, yielded higher oil fractions (64% and 62%, respectively) compared to less polar solvents like ethyl ether (DME) at 59%. Isopropyl alcohol (IPA), with intermediate polarity, achieved a balanced oil yield of 63%, indicating its ability to dissolve both polar and non-polar components. Moisture reduction in stabilized bio-oils followed the order IPA > ETH > METH > DME, with IPA showing the highest reduction due to its structural characteristics facilitating dehydration. Viscosity reduction varied, with IPA > ETH > DME > METH. Carbon recovery in stabilized bio-oils ranged from 65% to 75% for DME, ETH, and METH and was 71% for IPA. The heating values of stabilized bio-oils ranged from 28 to 29 MJ/kg, with IPA-stabilized bio-oil showing the highest value (29.05 ± 0.06 MJ/kg). METH demonstrated high efficiency (74.8%) in stabilizing bio-oil, attributed to its strong hydrogen-donating capability. ETH followed closely at 69.5%, indicating its comparable performance in bio-oil stabilization. With moderate efficiency (69.3%), IPA presents a balanced alternative considering its molecular structure and hydrogen solubility. In contrast, DME exhibited lower efficiency (63.6%) due to its weaker hydrogenation capability and propensity for undesired side reactions. The current study suggests that subcritical conditions up to 200 °C are adequate for METH, ETH, and IPA in bio-oil stabilization, comparable to results obtained under supercritical conditions.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12109086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporary Anchorage Devices in Clear Aligner Therapy: A Systematic Review.","authors":"Grazia Marinelli, Angelo Michele Inchingolo, Alessio Danilo Inchingolo, Laura Ferrante, Pasquale Avantario, Merigrazia Campanelli, Andrea Palermo, Francesco Inchingolo, Gianna Dipalma","doi":"10.3390/bioengineering12050531","DOIUrl":"10.3390/bioengineering12050531","url":null,"abstract":"<p><p>This systematic review analyzed the combined use of aligners and orthodontic temporary anchorage devices (TADs) in orthodontic treatment. The aim was to evaluate the effectiveness, benefits, and potential challenges of integrating the use of miniscrews with aligners. This review was conducted according to the PRISMA statement, and the protocol was registered at PROSPERO under the ID CRD42024576712. A comprehensive search on PubMed, Scopus, and Web of Science was conducted to identify relevant papers involving patients treated with aligners and TADs, dating from 1 January 2004 to 17 July 2024. The electronic database search identified a total of 458 articles. After eligibility, 14 records were selected for qualitative analysis. The findings suggest that the combination of aligners and miniscrews significantly enhances treatment precision and control, especially in cases requiring complex tooth movements, such as intrusion, extrusion, and distalization. The use of miniscrews allows greater control of movement and stability. The integration of these two techniques presents challenges, such as the need for precise miniscrew placement and potential discomfort during insertion. However, there was high satisfaction due to the aesthetic and comfort benefits of aligners. Further research is desirable to delve deeper into the topic to optimize clinical outcomes.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cross-Subject Emotion Recognition with CT-ELCAN: Leveraging Cross-Modal Transformer and Enhanced Learning-Classify Adversarial Network.","authors":"Ping Li, Ao Li, Xinhui Li, Zhao Lv","doi":"10.3390/bioengineering12050528","DOIUrl":"10.3390/bioengineering12050528","url":null,"abstract":"<p><p>Multimodal physiological emotion recognition is challenged by modality heterogeneity and inter-subject variability, which hinder model generalization and robustness. To address these issues, this paper proposes a new framework, Cross-modal Transformer with Enhanced Learning-Classifying Adversarial Network (CT-ELCAN). The core idea of CT-ELCAN is to shift the focus from conventional signal fusion to the alignment of modality- and subject-invariant emotional representations. By combining a cross-modal Transformer with ELCAN, a feature alignment module using adversarial training, CT-ELCAN learns modality- and subject-invariant emotional representations. Experimental results on the public datasets DEAP and WESAD demonstrate that CT-ELCAN achieves accuracy improvements of approximately 7% and 5%, respectively, compared to state-of-the-art models, while also exhibiting enhanced robustness.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12109479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EMG-Controlled Soft Robotic Bicep Enhancement.","authors":"Jiayue Zhang, Daniel Vanderbilt, Ethan Fitz, Janet Dong","doi":"10.3390/bioengineering12050526","DOIUrl":"10.3390/bioengineering12050526","url":null,"abstract":"<p><p>Industrial workers often engage in repetitive lifting tasks. This type of continual loading on their arms throughout the workday can lead to muscle or tendon injuries. A non-intrusive system designed to assist a worker's arms would help alleviate strain on their muscles, thereby preventing injury and minimizing productivity losses. The goal of this project is to develop a wearable soft robotic arm enhancement device that supports a worker's muscles by sharing the load during lifting tasks, thereby increasing their lifting capacity, reducing fatigue, and improving their endurance to help prevent injury. The device should be easy to use and wear, functioning in relative harmony with the user's own muscles. It should not restrict the user's range of motion or flexibility. The human arm consists of numerous muscles that work together to enable its movement. However, as a proof of concept, this project focuses on developing a prototype to enhance the biceps brachii muscle, the primary muscle involved in pulling movements during lifting. Key components of the prototype include a soft robotic muscle or actuator analogous to the biceps, a control system for the pneumatic muscle actuator, and a method for securing the soft muscle to the user's arm. The McKibben-inspired pneumatic muscle was chosen as the soft actuator for the prototype. A hybrid control algorithm, incorporating PID and model-based control methods, was developed. Electromyography (EMG) and pressure sensors were utilized as inputs for the control algorithms. This paper discusses the design strategies for the device and the preliminary results of the feasibility testing. Based on the results, a wearable EMG-controlled soft robotic arm augmentation could effectively enhance the endurance of industrial workers engaged in repetitive lifting tasks.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12109154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pioneering Soundscapes: Investigating Commercial Fused Deposition Modelling Filament's Potential for Ultrasound Technology in Bone Tissue Scaffolds.","authors":"Hatice Kübra Bilgili, Masahiro Todoh","doi":"10.3390/bioengineering12050529","DOIUrl":"10.3390/bioengineering12050529","url":null,"abstract":"<p><p>Daily exposure to various forces creates defects in the musculoskeletal system, leading to health issues, especially for bones. Bone tissue scaffolds and ultrasound technology are both utilized in research and in clinics to enhance bone tissue regeneration. This study aimed to investigate the potential of commercially available fused deposition modeling (FDM) filaments for ultrasound technology using X-ray diffraction (XRD), Raman spectroscopy, nanoindentation, three-point bending, and scanning electron microscopy (SEM) characterization methods. Customized FDM filaments were produced by combining polylactic acid (PLA) FDM filaments with medical-grade polycaprolactone (PCL). Using these, we observed the successful production of complex tissue scaffolds via PLAPCL4060 and PLAPCL5050 FDM filaments. Additionally, the presence of the contrast difference observed via SEM for PLAPCL4060 suggests phase segregation and a material that has both damping and activating characteristics under ultrasound propagation. Mechanical characterization provided hardness and elastic modulus values, while the three-point bending results proved the flexible nature of PLAPCL4060 and PLAPCL5050, which is important for their dynamicity and responsiveness under ultrasound propagation. Accelerated degradation experiments provided crucial information regarding the effect of the porosity and gradients of scaffolds under ultrasound stimulation. Future studies based on this approach will contribute to understanding the true potential of these filaments for bone tissue.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of Running Surface Differences on Physiological and Biomechanical Responses During Specific Sports Loading.","authors":"Zhiqiang Liang, Qi Shuo, Chuang Gao, Chang-Te Lin, Yufei Fang","doi":"10.3390/bioengineering12050534","DOIUrl":"10.3390/bioengineering12050534","url":null,"abstract":"<p><p>The surface properties of the running surface have an effect on physiological and biomechanical responses to exercise, but their influence on body composition, blood pressure, and knee joint kinetics during controlled sports loading is less researched. This study compared the effects of treadmill running (TR) and overground running (OR) on acute physiological and biomechanical adaptation in ten male athletes aged between 23 and 26 years old following a 30 min protocol at 75% VO₂max. Pre- and post-running body composition (fat volume, protein content, and fluid distribution), blood pressure, and knee joint kinetics (total work of muscle extensors-TWMEs) were assessed using bioelectrical impedance analysis, blood pressure monitor, and isokinetic dynamometry. The results indicated that TR led to highly significant reductions in protein content with a considerable accumulation of intracellular fluid. At the same time, TR reduced knee TWME by 27.4%, and OR elevated TWME by 5.6%. No significant differences in blood pressure were observed. These findings highlight surface-specific metabolic stress and biomechanical loading patterns and show that TR augments catabolic responses and knee joint strain despite equivalent external workloads.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12109356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Future of Anaerobic Digestion: Challenges and Opportunities.","authors":"Marcell Nikolausz, Peter Kornatz","doi":"10.3390/bioengineering12050524","DOIUrl":"10.3390/bioengineering12050524","url":null,"abstract":"<p><p>Research on anaerobic digestion (AD) is still booming in the first quarter of the 21st century [...].</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12109329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms.","authors":"Günter A Müller","doi":"10.3390/bioengineering12050532","DOIUrl":"10.3390/bioengineering12050532","url":null,"abstract":"<p><p>So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a \"fit\" between donor and acceptor proteomes and structures. \"Fitting\" of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor <i>Pneumococci</i> of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor <i>Pneumococci</i> from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) \"Blending\" or mixing and fusion of donor and acceptor <i>Pneumococci</i> may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin's \"gemmules\" to \"stirps\", cytoplasmic and \"plasmon\" inheritance, \"rhizene agency\", \"communicology\", \"transdisciplinary membranology\" to up to Kirschner's \"facilitated variation\".</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12109375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transforming Bone Tunnel Evaluation in Anterior Cruciate Ligament Reconstruction: Introducing a Novel Deep Learning System and the TB-Seg Dataset.","authors":"Ke Xie, Mingqian Yu, Jeremy Ho-Pak Liu, Qixiang Ma, Limin Zou, Gene Chi-Wai Man, Jiankun Xu, Patrick Shu-Hang Yung, Zheng Li, Michael Tim-Yun Ong","doi":"10.3390/bioengineering12050527","DOIUrl":"10.3390/bioengineering12050527","url":null,"abstract":"<p><p>Evaluating bone tunnels is crucial for assessing functional recovery after anterior cruciate ligament reconstruction. Conventional methods are imprecise, time-consuming, and labor-intensive. This study introduces a novel deep learning-based system for accurate bone tunnel segmentation and assessment. The system has two primary stages. Firstly, the ResNet50-Unet network is employed to capture the bone tunnel area in each slice. Subsequently, in the bone texture analysis, the open-source software 3D Slicer is leveraged to execute three-dimensional reconstruction based on the segmented outcomes from the previous stage. The ResNet50-Unet network was trained and validated using a newly developed dataset named tunnel bone segmentation (TB-Seg). The outcomes reveal commendable performance metrics, with mean intersection over union (mIoU), mean average precision (mAP), precision, and recall on the validation set reaching 76%, 85%, 88%, and 85%, respectively. To assess the robustness of our innovative bone texture system, we conducted tests on a cohort of 24 patients, successfully extracting bone volume/total volume, trabecular thickness, trabecular separation, trabecular number, and volumetric information. The system excels with substantial significance in facilitating the subsequent analysis of the intricate interplay between bone tunnel characteristics and the postoperative recovery trajectory after anterior cruciate ligament reconstruction. Furthermore, in our five randomly selected cases, clinicians utilizing our system completed the entire analytical workflow in a mere 357-429 s, representing a substantial improvement compared to the conventional duration exceeding one hour.</p>","PeriodicalId":8874,"journal":{"name":"Bioengineering","volume":"12 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}