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Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content 以语义Web格式提供来自AOP Wiki的不利结果路径,以提高内容的可用性和可访问性
Q2 Health Professions Pub Date : 2021-01-06 DOI: 10.1089/aivt.2021.0010
Marvin Martens, C. Evelo, Egon Willighagen
Introduction: The AOP-Wiki is the main platform for the development and storage of adverse outcome pathways (AOPs). These AOPs describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content, and to link it with chemical and biological resources. Together, this allows more detailed exploration, which can be automated. Materials and Methods: We converted the complete AOP-Wiki content into resource description framework (RDF) triples. We used >20 ontologies for the semantic annotation of property–object relations, including the Chemical Information Ontology, Dublin Core, and the AOP Ontology. Results: The resulting RDF contains >122,000 triples describing 158 unique properties of >15,000 unique subjects. Furthermore, >3500 link-outs were added to 12 chemical databases, and >7500 link-outs to 4 gene and protein databases. The AOP-Wiki RDF has been made available at https://aopwiki.rdf.bigcat-bioinformatics.org Discussion: SPARQL queries can be used to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries. Conclusion: Overall, the AOP-Wiki RDF allows new ways to explore the rapidly growing AOP knowledge and makes the integration of this database in automated workflows possible, making the AOP-Wiki more FAIR.
简介:AOP-Wiki是不良结果通路(adverse outcome pathways, AOPs)开发和存储的主要平台。这些aop描述了有关毒性动力学过程的机制信息,可用于制定有效的风险评估策略。然而,自动和系统地解析、过滤和使用其内容是一项挑战。我们探索了更好地构建AOP-Wiki内容的解决方案,并将其与化学和生物资源联系起来。总之,这允许更详细的探索,这可以自动化。材料和方法:我们将完整的AOP-Wiki内容转换为资源描述框架(RDF)三元组。我们使用bbb20本体对属性-对象关系进行语义标注,包括化学信息本体、都柏林核心和AOP本体。结果:得到的RDF包含>122,000个三元组,描述>15,000个独特主题的158个独特属性。此外,在12个化学数据库中添加了>3500个链接,在4个基因和蛋白质数据库中添加了>7500个链接。AOP-Wiki RDF已在https://aopwiki.rdf.bigcat-bioinformatics.org上提供:SPARQL查询可用于回答生物学和毒理学问题,例如列出导致相关不良结果的所有关键事件的测量方法。当使用联邦查询将内容与外部数据库结合在一起时,使用这个新资源所提供的全部功能就变得显而易见了。总结:总的来说,AOP- wiki RDF提供了探索快速增长的AOP知识的新方法,并使该数据库集成到自动化工作流中成为可能,使AOP- wiki更加公平。
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引用次数: 12
Correction to: Exosomal microRNAs Release as a Sensitive Marker for Drug-Induced Liver Injury In Vitro by Messner CJ, et al. Appl In Vitro Toxicol 2020:6;77–89. DOI: 10.1089/aivt.2020.0008 Messner CJ等人对外泌体microRNAs释放作为药物性肝损伤的敏感标志物的更正。苹果体外毒理学杂志,2016:6;77-89。DOI: 10.1089 / aivt.2020.0008
Q2 Health Professions Pub Date : 2020-12-01 DOI: 10.1089/aivt.2020.0008.correx
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引用次数: 0
Nitric Oxide Regulates Macrophage Fungicidal Activity via S-nitrosylation of Dectin-1. 一氧化氮通过Dectin-1的s -亚硝基化调节巨噬细胞的杀真菌活性。
Q2 Health Professions Pub Date : 2020-09-01 Epub Date: 2020-09-17 DOI: 10.1089/aivt.2020.0009
James Gow, Yujie Yang, Mohan Govindraj, Changjiang Guo

Introduction: Recognition of fungal surface β-glucan by pattern recognition receptor Dectin-1 is a critical process for fungal clearance in the lung. In humans, persistent fungal infection is observed in individuals with particular Dectin-1 polymorphism. We have identified that nitric oxide (NO) modifies critical cysteines in pattern recognition molecules to disassemble and alter protein function. There is a hydrophobic S-nitrosylation motif present in surfactant protein-D (SP-D) that is also present in Dectin-1. We hypothesized that Dectin-1 can be modified by nitrosative stress potentially leading to impairment of fungal clearance. Materials and Methods: Recombinant Dectin-1 was incubated with l-nitrosocysteine (L-SNOC) and S-nitrosylated Dectin-1 was detected by Biotin-switch assay. Cells of a murine macrophage line (Raw 264.7) were incubated with S-nitroso-glutathione (GSNO) and Dectin-1 shedding from the cell surface was determined by Western blot. Dectin-1 quaternary structure was determined by native gel electrophoresis. Dectin-1 function was assayed by NF-κB activity and IL-6 mRNA real-time polymerase chain reaction (PCR). Phagocytic activity was measured by fluorescence labeled zymosan beads. Results: Dectin-1 was S-nitrosylated by l-nitrosocysteine (L-SNOC) in vitro, as determined by Biotin-switch assay, resulting in structural disruption. We used Western blotting and flow cytometry to demonstrate that incubation of a murine macrophage cell line (Raw 264.7 cells) with GSNO reduced the surface Dectin-1 expression as a result of shedding to the media. The shedding of Dectin-1 is due to formation of S-nitrosothiol (SNO)-Dectin-1 and disruption of the Dectin-1 oligomeric complex. GSNO also induces Dectin-1 shedding from the cell surface. The functional significance of GSNO treatment of macrophages is shown by reduced β-glucan-mediated signaling in terms of NF-κB function and IL-6 expression. Finally, it was demonstrated that GSNO treatment reduces the capability of macrophages to phagocytose zymosan. Conclusions: These data provide mechanistic data to support the role of Dectin-1 nitrosylation as a mediator of reduced fungal clearance in the face of increased NO exposure.

模式识别受体Dectin-1对真菌表面β-葡聚糖的识别是肺部真菌清除的关键过程。在人类中,在具有特定Dectin-1多态性的个体中观察到持续的真菌感染。我们已经确定一氧化氮(NO)修饰模式识别分子中的关键半胱氨酸,以分解和改变蛋白质功能。表面活性剂蛋白d (SP-D)中存在疏水s -亚硝基化基序,Dectin-1中也存在。我们假设Dectin-1可以被亚硝化胁迫修饰,可能导致真菌清除功能受损。材料与方法:重组Dectin-1与l-亚硝基半胱氨酸(L-SNOC)孵育,生物素开关法检测s -亚硝基化Dectin-1。用s -亚硝基谷胱甘肽(GSNO)孵育小鼠巨噬细胞系(Raw 264.7), Western blot检测细胞表面Dectin-1脱落情况。采用天然凝胶电泳法测定了Dectin-1的四级结构。采用NF-κB活性和IL-6 mRNA实时聚合酶链反应(PCR)检测Dectin-1的功能。用荧光标记酶珠测定吞噬活性。结果:生物素开关法测定,Dectin-1在体外被l-亚硝基半胱氨酸(L-SNOC) s -亚硝基化,导致结构破坏。我们使用Western blotting和流式细胞术证明,小鼠巨噬细胞系(Raw 264.7细胞)与GSNO孵生后,由于脱落到培养基中,表面Dectin-1的表达降低。Dectin-1的脱落是由于s -亚硝基硫醇(SNO)-Dectin-1的形成和Dectin-1寡聚物的破坏。GSNO还能诱导Dectin-1从细胞表面脱落。从NF-κB功能和IL-6表达的角度来看,β-葡聚糖介导的信号通路减少,表明GSNO治疗巨噬细胞的功能意义。最后,研究表明GSNO处理降低了巨噬细胞吞噬酶酶san的能力。结论:这些数据提供了机制数据,支持Dectin-1亚硝基化在面对增加的NO暴露时降低真菌清除率的中介作用。
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引用次数: 2
Call for Papers: Applied In Vitro Toxicology 论文征集:应用体外毒理学
Q2 Health Professions Pub Date : 2020-06-01 DOI: 10.1089/AIVT.2020.29024.CFP2
Editor-in-Chief Andrew Gow
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引用次数: 0
Precision Cut Lung Slices as a Model for 3R Application in Toxicology 精确切割肺片作为3R在毒理学应用的模型
Q2 Health Professions Pub Date : 2020-06-01 DOI: 10.1089/aivt.2020.29025.com
J. Herbert, A. Gow
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引用次数: 4
Workshop Series to Identify, Discuss, and Develop Recommendations for the Optimal Generation and Use of In Vitro Assay Data for Tobacco Product Evaluation: Phase 1 Genotoxicity Assays 确定、讨论和制定烟草制品评价体外测定数据的最佳生成和使用建议系列研讨会:1期遗传毒性测定
Q2 Health Professions Pub Date : 2020-06-01 DOI: 10.1089/aivt.2020.0004
Martha M. Moore, J. Clements, P. Desai, U. Doshi, M. Gaca, Xiaoqing Guo, Tsuneo Hashizume, Kristen G. Jordan, K. Monica Lee, R. Leverette, D. McHugh, J. Miller-Holt, G. Phillips, H. Raabe, L. Recio, Shambhu K. Roy, Daniel J. Smart, Leon F. Stankowski, D. Thorne, Elisabeth Weber, R. Wieczorek, K. Yoshino, R. Curren
Introduction: The Institute for In Vitro Sciences is sponsoring a workshop series to identify, discuss, and develop recommendations for optimal scientific and technical approaches for conducting in...
简介:体外科学研究所正在赞助一个系列研讨会,以确定,讨论,并制定最佳的科学和技术方法的建议进行…
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引用次数: 6
Unveiling the Lack of Inotropic Response of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes to Isoproterenol by Chronic External Stimulation 揭示人诱导的多能干细胞来源的心肌细胞在慢性外部刺激下对异丙肾上腺素缺乏肌力反应
Q2 Health Professions Pub Date : 2020-06-01 DOI: 10.1089/aivt.2020.0002
Haoyu Zeng, Jixin Wang, Holly Clouse, A. Lagrutta
Introduction: The lack of positive inotropic response to isoproterenol has been a caveat in the utilization of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) for cardiac saf...
引言:缺乏对异丙肾上腺素的正性肌力反应是利用人类诱导多能干细胞衍生的心肌细胞(hiPSC CMs)进行心脏安全的一个警告。。。
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引用次数: 0
Call for Papers: Applied In Vitro Toxicology 论文征集:应用体外毒理学
Q2 Health Professions Pub Date : 2019-12-01 DOI: 10.1089/aivt.2019.29021.cfp
Editor-in-Chief James M. McKim
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引用次数: 0
Assessing the Safety of Nanomedicines: A Mini Review 评估纳米药物的安全性:一个小综述
Q2 Health Professions Pub Date : 2019-09-17 DOI: 10.1089/aivt.2019.0009
A. Dickinson, J. Godden, Kateryna Lanovyk, S. Ahmed
Abstract Over the past decade, there has been a significant increase in preclinical development and clinical use of approved nanomedicines. The nanomedicinal field represents a wide variety of prod...
在过去的十年中,纳米药物的临床前开发和临床应用有了显著的增加。纳米医学领域代表了各种各样的药物。
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引用次数: 18
In Vitro Skin Penetration of Dendrimer Nanoparticles 树状纳米颗粒的体外皮肤渗透
Q2 Health Professions Pub Date : 2019-09-17 DOI: 10.1089/aivt.2019.0004
E. K. KraelingMargaret, D. ToppingVanessa, R. BelgraveKathleen, SchlickKristian, SimanekEric, ManSonny, DadiboyenaSureshbabu, K. PatriAnil, L. SprandoRobert, J. YourickJeffrey
Abstract Introduction: Dendrimers are highly branched, stable polymeric nanoparticles with functional groups capable of binding other molecules and may increase delivery of chemicals into skin. Mat...
摘要:树状大分子是一种高度支化、稳定的聚合物纳米颗粒,其官能团能够结合其他分子,并可能增加化学物质进入皮肤的递送。垫……
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引用次数: 8
期刊
Applied In Vitro Toxicology
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