Computational and structural biotechnology journal最新文献

{"title":"A systematic review on the state-of-the-art and research gaps regarding inorganic and carbon-based multicomponent and high-aspect ratio nanomaterials","authors":"","doi":"10.1016/j.csbj.2024.10.020","DOIUrl":"10.1016/j.csbj.2024.10.020","url":null,"abstract":"<div><div>This review explores the state-of-the-art with respect to multicomponent nanomaterials (MCNMs) and high aspect ratio nanomaterials (HARNs), with a focus on their physicochemical characterisation, applications, and hazard, fate, and risk assessment. Utilising the PRISMA approach, this study investigates specific MCNMs including cerium-zirconium mixtures (Ce_xZr_yO₂) and ZnO nanomaterials doped with transition metals and rare earth elements, as well as Titanium Carbide (TiC) nanomaterials contained in Ti-6Al-4V alloy powders. HARNs of interest include graphene, carbon-derived nanotubes (CNTs), and metallic nanowires, specifically Ag-based nanowires. The review reveals a significant shift in research and innovation (R&amp;I) efforts towards these advanced nanomaterials due to their unique properties and functionalities that promise enhanced performance across various applications including photocatalysis, antibacterial and biomedical uses, and advanced manufacturing. Despite the commercial potential of MCNMs and HARNs, the review identifies critical gaps in our understanding of their environmental fate and transformations upon exposure to new environments, and their potential adverse effects on organisms and the environment. The findings underscore the necessity for further research focused on the environmental transformations and toxicological profiles of these nanomaterials to inform Safe and Sustainable by Design (SSbD) strategies. This review contributes to the body of knowledge by cataloguing current research, identifying research gaps, and highlighting future directions for the development of MCNMs and HARNs, facilitating their safe and effective integration into industry.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554384","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}

{"title":"An AI-driven multiscale methodology to develop transparent wood as sustainable functional material by using the SSbD concept","authors":"","doi":"10.1016/j.csbj.2024.10.022","DOIUrl":"10.1016/j.csbj.2024.10.022","url":null,"abstract":"<div><div>Efficient design, production, and optimization of new safe and sustainable by design materials for various industrial sectors is an on-going challenge for our society, poised to escalate in the future. Wood-based composite materials offer an attractive sustainable alternative to high impact materials such as glass and polymers and have been the focus of experimental research and development for years. Computational and AI-based materials design provides significant speed-up the development of these materials compared to traditional methods of development. However, reliable numerical models are essential for achieving this goal. The AI-TranspWood project, recently funded by the European Commission, has the ambition to develop such computational and AI-based tools in the context of transparent wood (TW), a promising composite with potential applications in various industrial fields. In this project we advance the development specifically by using an Artificial Intelligence (AI)-driven multiscale methodology.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554383","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}

{"title":"Using patient-generated health data more efficient and effectively to facilitate the implementation of value-based healthcare in the EU – Innovation report","authors":"","doi":"10.1016/j.csbj.2024.10.026","DOIUrl":"10.1016/j.csbj.2024.10.026","url":null,"abstract":"<div><div>Healthcare services and products are rapidly changing due to the development of new technologies, offering relevant solutions to improve patient outcomes. Patient-Generated Health Data and knowledge-sharing across the European Union (EU) has a great potential of making healthcare provision more effective and efficient by putting the patient at the centre of the healthcare process. While such initiatives have been taken before, a uniting and overarching approach is still missing. The EU-funded IMPROVE project will develop an evidence-based and actual framework to effectively leverage the added value of people-centred integrated healthcare solutions, using predominantly PROMs, PPI, PREMs, and other Patient-Generated Health Data (PGHD). As a result, the project facilitates the effective and efficient implementation of Value-Based Healthcare across the EU by putting the patient central in the healthcare process.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553026","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}

{"title":"Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform","authors":"","doi":"10.1016/j.csbj.2024.10.018","DOIUrl":"10.1016/j.csbj.2024.10.018","url":null,"abstract":"<div><div>Modelling Data (MODA) reporting guidelines have been proposed for common terminology and for recording metadata for physics-based materials modelling and simulations in a CEN Workshop Agreement (CWA 17284:2018). Their purpose is similar to that of the Quantitative Structure-Activity Relationship (QSAR) model report form (QMRF) that aims to increase industry and regulatory confidence in QSAR models, but for a wider range of model types. Recently, the WorldFAIR project’s nanomaterials case study suggested that both QMRF and MODA templates are an important means to enhance compliance of nanoinformatics models, and their underpinning datasets, with the FAIR principles (Findable, Accessible, Interoperable, Reusable). Despite the advances in computational modelling of materials properties and phenomena, regulatory uptake of predictive models has been slow. This is, in part, due to concerns about lack of validation of complex models and lack of documentation of scientific simulations. The models are often complex, output can be hardware- and software-dependent, and there is a lack of shared standards. Despite advocating for standardised and transparent documentation of simulation protocols through its templates, the MODA guidelines are rarely used in practice by modellers because of a lack of tools for automating their creation, sharing, and storage. They also suffer from a paucity of user guidance on their use to document different types of models and systems. Such tools exist for the more well-established QMRF and have aided widespread implementation of QMRFs. To address this gap, a simplified procedure and online tool, Easy-MODA, has been developed to guide users through MODA creation for physics-based and data-based models, and their various combinations. Easy-MODA is available as a web-tool on the Enalos Cloud Platform (<span><span>https://www.enaloscloud.novamechanics.com/insight/moda/</span><svg><path></path></svg></span>). The tool streamlines the creation of detailed MODA documentation, even for complex multi-model workflows, and facilitates the registration of MODA workflows and documentation in a database, thereby increasing their Findability and thus Re-usability. This enhances communication, interoperability, and reproducibility in multiscale materials modelling and improves trust in the models through improved documentation. The use of the Easy-MODA tool is exemplified by a case study for nanotoxicity evaluation, involving interlinked models and data transformation, to demonstrate the effectiveness of the tool in integrating complex computational methodologies and its significant role in improving the FAIRness of scientific simulations.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142561042","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}

{"title":"NanoBioAccumulate: Modelling the uptake and bioaccumulation of nanomaterials in soil and aquatic invertebrates via the Enalos DIAGONAL Cloud Platform","authors":"","doi":"10.1016/j.csbj.2024.09.028","DOIUrl":"10.1016/j.csbj.2024.09.028","url":null,"abstract":"<div><div><em>NanoBioAccumulate</em> is a free-to-use web-based tool hosted on the Enalos DIAGONAL Cloud Platform (<span><span>https://www.enaloscloud.novamechanics.com/diagonal/pbpk/</span><svg><path></path></svg></span>) that provides users with the capability to model and predict the uptake and bioaccumulation of nanomaterials (NMs) by soil and aquatic invertebrates using two common first-order one-compartment biokinetic models. <em>NanoBioAccumulate</em> offers an approach for comprehensively analyzing the kinetics of different forms of NMs via a nonlinear fitting feature, integrating them with environmental fate models, and considering important physiological processes. <em>NanoBioAccumulate</em> overcomes the constraint of requiring prior knowledge of kinetic rate constants associated with the biokinetic models and eliminates the need for external statistical analysis software as it quantifies the kinetic rate constants and other constants through the application of nonlinear regression, using user-provided experimental data. Furthermore, <em>NanoBioAccumulate</em> incorporates statistical analysis measures like the adjusted R-squared and the bias-corrected Akaike information criterion, allowing for assessment of the goodness-of-fit of the two different biokinetic models, assisting in the identification of the best-performing model for a specific nanoform and its uptake kinetics by a specific invertebrate. The tool also includes model scenarios, retrieved from literature, which involve examining the exposure of soil and aquatic invertebrates to various types of NMs such as TiO₂, SiO₂, C₆₀, graphene, graphene oxide (GO), Au, Ag and its ionic control AgNO₃. These model scenarios aim to enhance understanding of the uptake and elimination rates exhibited by different NM-species. <em>NanoBioAccumulate</em> features advanced integration capabilities, enabled by an extensive Application Programming Interface (API). This functionality promotes efficient data exchange and interoperability with other software and web applications, significantly expanding its utility in research, regulatory risk assessment and environmental surveillance and monitoring contexts. The inclusion of a user-friendly Graphical User Interface (GUI) in <em>NanoBioAccumulate</em> greatly improves the overall user experience by simplifying complex tasks and eliminating the need for programming proficiency, thereby expanding the tool's applicability to a diverse range of users across various fields such as environmental research, monitoring, and regulation.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554386","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}

{"title":"BioKGrapher: Initial evaluation of automated knowledge graph construction from biomedical literature","authors":"","doi":"10.1016/j.csbj.2024.10.017","DOIUrl":"10.1016/j.csbj.2024.10.017","url":null,"abstract":"<div><div><strong>Background</strong> The growth of biomedical literature presents challenges in extracting and structuring knowledge. Knowledge Graphs (KGs) offer a solution by representing relationships between biomedical entities. However, manual construction of KGs is labor-intensive and time-consuming, highlighting the need for automated methods. This work introduces BioKGrapher, a tool for automatic KG construction using large-scale publication data, with a focus on biomedical concepts related to specific medical conditions. BioKGrapher allows researchers to construct KGs from PubMed IDs.</div><div><strong>Methods</strong> The BioKGrapher pipeline begins with Named Entity Recognition and Linking (NER+NEL) to extract and normalize biomedical concepts from PubMed, mapping them to the Unified Medical Language System (UMLS). Extracted concepts are weighted and re-ranked using Kullback-Leibler divergence and local frequency balancing. These concepts are then integrated into hierarchical KGs, with relationships formed using terminologies like SNOMED CT and NCIt. Downstream applications include multi-label document classification using Adapter-infused Transformer models.</div><div><strong>Results</strong> BioKGrapher effectively aligns generated concepts with clinical practice guidelines from the German Guideline Program in Oncology (GGPO), achieving <span><math><msub><mrow><mi>F</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span>-Scores of up to 0.6. In multi-label classification, Adapter-infused models using a BioKGrapher cancer-specific KG improved micro <span><math><msub><mrow><mi>F</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span>-Scores by up to 0.89 percentage points over a non-specific KG and 2.16 points over base models across three BERT variants. The drug-disease extraction case study identified indications for Nivolumab and Rituximab.</div><div><strong>Conclusion</strong> BioKGrapher is a tool for automatic KG construction, aligning with the GGPO and enhancing downstream task performance. It offers a scalable solution for managing biomedical knowledge, with potential applications in literature recommendation, decision support, and drug repurposing.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142526863","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}

{"title":"Toxicogenomic assessment of in vitro macrophages exposed to profibrotic challenge reveals a sustained transcriptomic immune signature","authors":"","doi":"10.1016/j.csbj.2024.10.010","DOIUrl":"10.1016/j.csbj.2024.10.010","url":null,"abstract":"<div><div>Immune signalling is a crucial component in the progression of fibrosis. However, approaches for the safety assessment of potentially profibrotic substances, that provide information on mechanistic immune responses, are underdeveloped. This study aimed to develop a novel framework for assessing the immunotoxicity of fibrotic compounds. We exposed macrophages in vitro to multiple sublethal concentrations of the profibrotic agent bleomycin, over multiple timepoints, and generated RNA sequencing data. Using a toxicogenomic approach, we performed dose-dependent analysis to discover genes dysregulated by bleomycin exposure in a dose-responsive manner. A subset of immune genes displayed a sustained dose-dependent and differential expression response to profibrotic challenge. An immunoassay revealed cytokines and proteinases responding to bleomycin exposure that closely correlated to transcriptomic alterations, underscoring the integration between transcriptional immune response and external immune signalling activity. This study not only increases our understanding of the immunological mechanisms of fibrosis, but also offers an innovative framework for the toxicological evaluation of substances with potential fibrogenic effects on macrophage signalling. Our work brings a new immunotoxicogenomic direction for hazard assessment of fibrotic compounds, through the implementation of a time and resource efficient in vitro methodology.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142424849","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}

{"title":"Transforming in-clinic post-operative and intermediate care with cosinuss°","authors":"","doi":"10.1016/j.csbj.2024.10.002","DOIUrl":"10.1016/j.csbj.2024.10.002","url":null,"abstract":"<div><div>Continuous, mobile patient monitoring plays a critical role in healthcare, particularly for post-surgery, intermediate care in clinics. The implementation of vital signs monitoring technology enables healthcare professionals to triage patients effectively by maintaining real-time awareness of their health status and allowing for prompt intervention when necessary. This technology supports early mobilization and facilitates the detection of potential complications such as post-surgical sepsis. cosinuss° technology has been evaluated in various studies, in terms of its accuracy in capturing vital parameters and its usability, emphasizing its potential to enhance intermediate patient care and outcomes. This report outlines the design and implementation of cosinuss° Health patient monitoring solution for use in intermediate, postoperative clinic settings. It presents the results and insights from three recent, in-clinic applications, discussing both technical and practical aspects, clinical processes, and the reported satisfaction from both patients and medical caregivers. The findings highlight the promising potential of cosinuss° Health on improving patient monitoring and overall clinical outcomes.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142427953","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}

{"title":"Text mining approach for feature extraction and cartilage disease grade classification using knee MRI radiology reports","authors":"","doi":"10.1016/j.csbj.2024.10.003","DOIUrl":"10.1016/j.csbj.2024.10.003","url":null,"abstract":"<div><div>MRI radiology reporting processes can be improved by exploiting structured and semantically labelled data that can be fed to artificial intelligence (AI) tools. AI-based tools assisting radiology reporting can help to automatically individuate cartilage grading in textual magnetic resonance imaging (MRI) reports, thus supporting clinicians' decisions regarding medical imaging utilisation, diagnosis and treatment. In this study, we extracted information (clinical findings, observations, anatomical regions, etc.) and classified knee cartilage degradation from medical reports utilising transfer-learning techniques applied to the Bidirectional Encoder Representations from Transformers (BERT) model and its variants, pre-trained on an Italian-language corpus. To realise this objective, we used a dataset of 750 MRI knee reports written by three radiologists who contributed to a manual annotation process to perform text classification (TC) and named entity recognition (NER) tasks. The dataset was obtained from an internal database of the IRCCS SYNLAB SDN. Seventy percent of the dataset was used for training, 10% was used for validation and 20% was used for testing. The best-performing configurations for NER and TC tasks were based on the pre-trained BERT model. The macro F1-scores obtained with the NER and TC models are 0.89 and 0.81, respectively. The accuracies calculated on the test set for both tasks are 0.96 and 0.99, respectively.</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142427955","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}

{"title":"NanoTube Construct: A web tool for the digital construction of nanotubes of single-layer materials and the calculation of their atomistic descriptors powered by Enalos Cloud Platform","authors":"","doi":"10.1016/j.csbj.2024.09.023","DOIUrl":"10.1016/j.csbj.2024.09.023","url":null,"abstract":"<div><div>NanoTube Construct is a web tool for the digital construction of nanotubes based on real and hypothetical single-layer materials including carbon-based materials such as graphene, graphane, graphyne polymorphs, graphidiyene and non-carbon materials such as silicene, germanene, boron nitride, hexagonal bilayer silica, haeckelite silica, molybdene disulfide and tungsten disulfide. Contrary to other available tools, NanoTube Construct has the following features: a) it is not limited to zero thickness materials with specific symmetry, b) it applies energy minimisation to the geometrically constructed Nanotubes to generate realistic ones, c) it derives atomistic descriptors (e.g., the average potential energy per atom, the average coordination number, etc.), d) it provides the primitive unit cell of the constructed Nanotube which corresponds to the selected rolling vector (i.e., the direction in which the starting nanosheet is rolled to form a tube), e) it calculates whether the Nanotube or its corresponding nanosheet is more energetically stable and f) it allows negative chirality indexes. Application of NanoTube Construct for the construction of energy minimised graphane and molybdenum disulfide nanotubes are presented, showcasing the tool's capability. NanoTube Construct is freely accessible through the Enalos Cloud Platform (<span><span>https://enaloscloud.novamechanics.com/diagonal/nanotube/</span><svg><path></path></svg></span>).</div></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554385","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}