Computational and structural biotechnology journal最新文献_第10页

Instance-level medical image classification for text-based retrieval in a medical data integration center 医疗数据集成中心基于文本检索的实例级医学影像分类

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-12 DOI: 10.1016/j.csbj.2024.06.006

Ka Yung Cheng , Markus Lange-Hegermann , Jan-Bernd Hövener , Björn Schreiweis

{"title":"Instance-level medical image classification for text-based retrieval in a medical data integration center","authors":"Ka Yung Cheng , Markus Lange-Hegermann , Jan-Bernd Hövener , Björn Schreiweis","doi":"10.1016/j.csbj.2024.06.006","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.06.006","url":null,"abstract":"<div><p>A medical data integration center integrates a large volume of medical images from clinical departments, including X-rays, CT scans, and MRI scans. Ideally, all images should be indexed appropriately with standard clinical terms. However, some images have incorrect or missing annotations, which creates challenges in searching and integrating data centrally. To address this issue, accurate and meaningful descriptors are needed for indexing fields, enabling users to efficiently search for desired images and integrate them with international standards.</p><p>This paper aims to provide concise annotation for missing or incorrectly indexed fields, incorporating essential instance-level information such as radiology modalities (e.g., X-rays), anatomical regions (e.g., chest), and body orientations (e.g., lateral) using a Deep Learning classification model - ResNet50. To demonstrate the capabilities of our algorithm in generating annotations for indexing fields, we conducted three experiments using two open-source datasets, the ROCO dataset, and the IRMA dataset, along with a custom dataset featuring SNOMED CT labels. While the outcomes of these experiments are satisfactory (Precision of >75%) for less critical tasks and serve as a valuable testing ground for image retrieval, they also underscore the need for further exploration of potential challenges. This essay elaborates on the identified issues and presents well-founded recommendations for refining and advancing our proposed approach.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024002034/pdfft?md5=bd1fa074436c095e9ca887e9e8641a81&pid=1-s2.0-S2001037024002034-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141323309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Numerical simulation study of nanoparticle diffusion in gray matter 灰质中纳米粒子扩散的数值模拟研究

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-10 DOI: 10.1016/j.csbj.2024.06.002

Peiqian Chen , Bing Dong , Weiwu Yao

{"title":"Numerical simulation study of nanoparticle diffusion in gray matter","authors":"Peiqian Chen , Bing Dong , Weiwu Yao","doi":"10.1016/j.csbj.2024.06.002","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.06.002","url":null,"abstract":"<div><h3>Purpose</h3><p>Nanomedicine-based approaches have shown great potential in the treatment of central nervous system diseases. However, the fate of nanoparticles (NPs) within the brain parenchyma has not received much attention. The complexity of the microstructure of the brain and the invisibility of NPs make it difficult to study NP transport within the grey matter. Moreover, regulation of NP delivery is not fully understood.</p></div><div><h3>Methods</h3><p>2D interstitial system (ISS) models reflecting actual extracellular space (ECS) were constructed. A particle tracing model was used to simulate the diffusion of the NPs. The effect of NP size on NP diffusion was studied using numerical simulations. The diffusion of charged NPs was explored by comparing experimental and numerical simulation data, and the effect of cell membrane potential on the diffusion of charged NPs was further studied.</p></div><div><h3>Results</h3><p>The model was verified using previously published experimental data. Small NPs could diffuse efficiently into the ISS. The diffusion of charged NPs was hindered in the ISS. Changes in cell membrane potential had little effect on NP diffusion.</p></div><div><h3>Conclusion</h3><p>This study constructed 2D brain ISS models that reflected the actual ECS and simulated the diffusion of NPs within it. The study found that uncharged small NPs could effectively diffuse within the ISS and that the cell membrane potential had a limited effect on the diffusion of charged NPs. The model and findings of this study can aid the design of nanomedicines and nanocarriers for the diagnosis and treatment of brain diseases.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001995/pdfft?md5=e0a2801bf26e2243ba4d4d7cda644491&pid=1-s2.0-S2001037024001995-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141313388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiling the impact of the SMARTCLAP project on habilitation 揭示 SMARTCLAP 项目对适应训练的影响

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-03 DOI: 10.1016/j.csbj.2024.06.001

Matthew Bonello, Nathalie Buhagiar, Philip Farrugia, Joseph Mercieca

{"title":"Unveiling the impact of the SMARTCLAP project on habilitation","authors":"Matthew Bonello, Nathalie Buhagiar, Philip Farrugia, Joseph Mercieca","doi":"10.1016/j.csbj.2024.06.001","DOIUrl":"10.1016/j.csbj.2024.06.001","url":null,"abstract":"<div><p>This report summarises the SMARTCLAP research project, which employs a user-centred design approach to develop a revolutionary smart product service system. The system offers personalised motivation to encourage children with cerebral palsy to actively participate more during their occupational therapy sessions, while providing paediatric occupational therapists with an optimal tool to monitor children’s progress from one session to another. The product service system developed includes of a smart wearable device called DigiClap used to interact with a serious game in an Augmented Reality environment. The report highlights the research methodology used to advance the technology readiness level from 4 to 6, acknowledging the contribution of the consortium team and funding source. As part of the technology’s maturity process, DigiClap and the respective serious game were evaluated with target users, to identify the system’s impact in supporting the children’s overall participation and hand function, and to gather feedback from occupational therapists and caregivers on this novel technology. The outcomes of this study are discussed, highlighting limitations and lessons learned. The report also outlines future work and further funding for the sustainability of the project and to reach other individuals who have upper limb limitations. Ultimately, the potential of DigiClap and the overall achievements of this project are discussed.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001983/pdfft?md5=11b063bec7e9ada9f093ebc6cd45f4a4&pid=1-s2.0-S2001037024001983-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141279507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030) 实现安全、可持续的先进材料和创新材料的路线图。(2024-2030 年展望）

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-02 DOI: 10.1016/j.csbj.2024.05.018

Flemming R. Cassee , Eric A.J. Bleeker , Cyrille Durand , Thomas Exner , Andreas Falk , Steffi Friedrichs , Elisabeth Heunisch , Martin Himly , Sabine Hofer , Norbert Hofstätter , Danail Hristozov , Penny Nymark , Anna Pohl , Lya G. Soeteman-Hernández , Blanca Suarez-Merino , Eugenia Valsami-Jones , Monique Groenewold

{"title":"Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030)","authors":"Flemming R. Cassee , Eric A.J. Bleeker , Cyrille Durand , Thomas Exner , Andreas Falk , Steffi Friedrichs , Elisabeth Heunisch , Martin Himly , Sabine Hofer , Norbert Hofstätter , Danail Hristozov , Penny Nymark , Anna Pohl , Lya G. Soeteman-Hernández , Blanca Suarez-Merino , Eugenia Valsami-Jones , Monique Groenewold","doi":"10.1016/j.csbj.2024.05.018","DOIUrl":"10.1016/j.csbj.2024.05.018","url":null,"abstract":"<div><p>The adoption of innovative advanced materials holds vast potential, contingent upon addressing safety and sustainability concerns. The European Commission advocates the integration of Safe and Sustainable by Design (SSbD) principles early in the innovation process to streamline market introduction and mitigate costs. Within this framework, encompassing ecological, social, and economic factors is paramount. The NanoSafety Cluster (NSC) delineates key safety and sustainability areas, pinpointing unresolved issues and research gaps to steer the development of safe(r) materials. Leveraging FAIR data management and integration, alongside the alignment of regulatory aspects, fosters informed decision-making and innovation. Integrating circularity and sustainability mandates clear guidance, ensuring responsible innovation at every stage. Collaboration among stakeholders, anticipation of regulatory demands, and a commitment to sustainability are pivotal for translating SSbD into tangible advancements. Harmonizing standards and test guidelines, along with regulatory preparedness through an exchange platform, is imperative for governance and market readiness. By adhering to these principles, the effective and sustainable deployment of innovative materials can be realized, propelling positive transformation and societal acceptance.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001612/pdfft?md5=3bfe4c5dc0d32dcf2dae7bb35bbf05cb&pid=1-s2.0-S2001037024001612-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141275626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform CYCLOPEp 生成器：通过用户友好型网络平台促进环肽和纳米管研究

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-02 DOI: 10.1016/j.csbj.2024.05.044

Alfonso Cabezón , Fabián Suárez-Lestón , Juan R. Granja , Ángel Piñeiro , Rebeca Garcia-Fandino

{"title":"CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform","authors":"Alfonso Cabezón , Fabián Suárez-Lestón , Juan R. Granja , Ángel Piñeiro , Rebeca Garcia-Fandino","doi":"10.1016/j.csbj.2024.05.044","DOIUrl":"10.1016/j.csbj.2024.05.044","url":null,"abstract":"<div><p>The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at <span>http://cyclopep.com/</span><svg><path></path></svg></p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001892/pdfft?md5=e402d6fd21dd2d604ec1bb1695841fa1&pid=1-s2.0-S2001037024001892-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141280471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acidic sphingomyelinase interactions with lysosomal membranes and cation amphiphilic drugs: A molecular dynamics investigation 酸性鞘磷脂酶与溶酶体膜和阳离子两亲药物的相互作用：分子动力学研究

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-02 DOI: 10.1016/j.csbj.2024.05.049

Simone Scrima, Matteo Lambrughi, Lorenzo Favaro, Kenji Maeda, Marja Jäättelä, Elena Papaleo

{"title":"Acidic sphingomyelinase interactions with lysosomal membranes and cation amphiphilic drugs: A molecular dynamics investigation","authors":"Simone Scrima, Matteo Lambrughi, Lorenzo Favaro, Kenji Maeda, Marja Jäättelä, Elena Papaleo","doi":"10.1016/j.csbj.2024.05.049","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.05.049","url":null,"abstract":"Lysosomes are pivotal in cellular functions and disease, influencing cancer progression and therapy resistance with Acid Sphingomyelinase (ASM) governing their membrane integrity. Moreover, cation amphiphilic drugs (CADs) are known as ASM inhibitors and have anti-cancer activity, but the structural mechanisms of their interactions with the lysosomal membrane and ASM are poorly explored. Our study, leveraging all-atom explicit solvent molecular dynamics simulations, delves into the interaction of glycosylated ASM with the lysosomal membrane and the effects of CAD representatives, i.e., ebastine, hydroxyebastine and loratadine, on the membrane and ASM. Our results confirm the ASM association to the membrane through the saposin domain, previously only shown with coarse-grained models. Furthermore, we elucidated the role of specific residues and ASM-induced membrane curvature in lipid recruitment and orientation. CADs also interfere with the association of ASM with the membrane at the level of a loop in the catalytic domain engaging in membrane interactions. Our computational approach, applicable to various CADs or membrane compositions, provides insights into ASM and CAD interaction with the membrane, offering a valuable tool for future studies.","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141528109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRCDB: A Comprehensive Database for Integrating and Analyzing Multi-omics Data of Early-onset and Late-onset Colorectal Cancer CRCDB：整合和分析早发和晚发结直肠癌多组学数据的综合数据库

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-01 DOI: 10.1016/j.csbj.2024.05.051

Danyi Zou, Wanshan Ning, Luming Xu, Shijun Lei, Lin Wang, Zheng Wang

引用次数: 0

Antibody Glycan Quality Predicted from CHO Cell Culture Media Markers and Machine Learning 通过 CHO 细胞培养基标记物和机器学习预测抗体聚糖质量

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-06-01 DOI: 10.1016/j.csbj.2024.05.046

Meiyappan Lakshmanan, Sean Chia, K. Pang, L. C. Sim, Gavin Teo, S. Mak, Shuwen Chen, Hsueh Lee Lim, Alison P. Lee, Farouq Bin Mahfut, Say Kong Ng, Yuansheng Yang, Annie Soh, Andy Hee-Meng Tan, Andre Choo, Ying Swan Ho, Terry Nguyen-Khuong, Ian Walsh

引用次数: 0

Transcriptomic investigations of polymyxins and colistin/sulbactam combination against carbapenem-resistant Acinetobacter baumannii 针对耐碳青霉烯类鲍曼不动杆菌的多粘菌素和可乐定/舒巴坦联合疗法的转录组学研究

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-05-31 DOI: 10.1016/j.csbj.2024.05.043

Xingchen Bian, Mengyao Li, Xiaofen Liu, Yan Zhu, Jian Li, Phillip J. Bergen, Wanzhen Li, Xin Li, Meiqing Feng, Jing Zhang

{"title":"Transcriptomic investigations of polymyxins and colistin/sulbactam combination against carbapenem-resistant Acinetobacter baumannii","authors":"Xingchen Bian, Mengyao Li, Xiaofen Liu, Yan Zhu, Jian Li, Phillip J. Bergen, Wanzhen Li, Xin Li, Meiqing Feng, Jing Zhang","doi":"10.1016/j.csbj.2024.05.043","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.05.043","url":null,"abstract":"Carbapenem-resistant (CRAB) is a Priority 1 (Critical) pathogen urgently requiring new antibiotics. Polymyxins are a last-line option against CRAB-associated infections. This transcriptomic study utilized a CRAB strain to investigate mechanisms of bacterial killing with polymyxin B, colistin, colistin B, and colistin/sulbactam combination therapy. After 4 h of 2 mg/L polymyxin monotherapy, all polymyxins exhibited common transcriptomic responses which primarily involved disruption to amino acid and fatty acid metabolism. Of the three monotherapies, polymyxin B induced the greatest number of differentially expressed genes (DEGs), including for genes involved with fatty acid metabolism. Gene disturbances with colistin and colistin B were highly similar (89 % common genes for colistin B), though effects on gene expression were generally lower (0–1.5-fold in most cases) with colistin B. Colistin alone (2 mg/L) or combined with sulbactam (64 mg/L) resulted in rapid membrane disruption as early as 1 h. Transcriptomic analysis of this combination revealed that the effects were driven by colistin, which included disturbances in fatty acid synthesis and catabolism, and inhibition of nutrient uptake. Combination therapy produced substantially higher fold changes in 72 % of DEGs shared with monotherapy, leading to substantially greater reductions in fatty acid biosynthesis and increases in biofilm, cell wall, and phospholipid synthesis. This indicates synergistic bacterial killing with the colistin/sulbactam combination results from a systematic increase in perturbation of many genes associated with bacterial metabolism. These mechanistic insights enhance our understanding of bacterial responses to polymyxin mono- and combination therapy and will assist to optimize polymyxin use in patients.","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141528110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability 生物相互作用和环境变化决定共生微生物的多样性和稳定性

IF 6 2区生物学

Computational and structural biotechnology journal Pub Date : 2024-05-29 DOI: 10.1016/j.csbj.2024.05.047

Zhidong Liu, Zeguang Guo, Jin Zhou, Xuecheng Guo, Youhua Chen

{"title":"Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability","authors":"Zhidong Liu, Zeguang Guo, Jin Zhou, Xuecheng Guo, Youhua Chen","doi":"10.1016/j.csbj.2024.05.047","DOIUrl":"https://doi.org/10.1016/j.csbj.2024.05.047","url":null,"abstract":"Taking amphibians as island models, we examined the effects of interspecific interaction on the diversity and stability of microbial ecological. As skin area increased, the diversity and stability of skin microbes decreased, but the strength of negative interactions increased significantly. In contrast, as gut area increased, the diversity and stability of gut microbes increased, but the strength of interactions remained constant. These results indicate that microbial interactions are affected by habitat properties. When living in fluctuating environments without strong filtering, microorganisms can enhance their negative interactions with other taxa by changing the pH of their surroundings. In contrast, the pH of the gut is relatively stable, and colonized microorganisms cannot alter the gut pH and inhibit other colonizers. This study demonstrates that in the field of microbiology, diversity and stability are predominantly influenced by the intensity of interspecies interactions. The findings in this study deepen our understanding of microbial diversity and stability and provide a mechanistic link between species interactions, biodiversity, and stability in microbial ecosystems.","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141528111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0