data science

数据科学
  • 文章类型: Journal Article
    目的:放疗指南的依从性对于维持治疗质量和一致性至关重要,特别是在大多数治疗发生的非试验患者环境中。该研究旨在评估指南更改对治疗计划实践的影响,并将手动注册数据的准确性与治疗计划数据进行比较。
    方法:这项研究利用了DBCGRTNation队列,丹麦的乳腺癌放射治疗数据集,评估2008年至2016年对指南的遵守情况。该队列包括7448例高危乳腺癌患者。国家准则的变化包括,分馏,引入呼吸门控,乳腺内淋巴结的照射,在描绘实践中使用同时集成的增强技术和左前下降冠状动脉的纳入。结构名称映射的方法,侧向性检测,检测人群平均肺容积的时间变化,和剂量评估进行了介绍和应用。从丹麦乳腺癌数据库获得手动登记的治疗特征数据用于比较。
    结果:研究发现,丹麦放疗中心立即且一致地遵守指南变更。指南实施之前的治疗实践已记录在案,并显示各中心之间存在差异。对于某些措施,手动注册数据与实际治疗计划数据之间的差异高达10%。
    结论:可以在常规治疗数据中检测到国家指南的变化,具有高度的合规性和较短的实施时间。与医疗登记数据相比,从治疗计划数据文件提取的数据提供了更准确和详细的治疗和指南依从性表征。
    Guideline adherence in radiotherapy is crucial for maintaining treatment quality and consistency, particularly in non-trial patient settings where most treatments occur. The study aimed to assess the impact of guideline changes on treatment planning practices and compare manual registry data accuracy with treatment planning data.
    This study utilised the DBCG RT Nation cohort, a collection of breast cancer radiotherapy data in Denmark, to evaluate adherence to guidelines from 2008 to 2016. The cohort included 7448 high-risk breast cancer patients. National guideline changes included, fractionation, introduction of respiratory gating, irradiation of the internal mammary lymph nodes, use of the simultaneous integrated boost technique and inclusion of the Left Anterior Descending coronary artery in delineation practice. Methods for structure name mapping, laterality detection, detection of temporal changes in population mean lung volume, and dose evaluation were presented and applied. Manually registered treatment characteristic data was obtained from the Danish Breast Cancer Database for comparison.
    The study found immediate and consistent adherence to guideline changes across Danish radiotherapy centres. Treatment practices before guideline implementation were documented and showed a variation among centres. Discrepancies between manual registry data and actual treatment planning data were as high as 10% for some measures.
    National guideline changes could be detected in the routine treatment data, with a high degree of compliance and short implementation time. Data extracted from treatment planning data files provides a more accurate and detailed characterisation of treatments and guideline adherence than medical register data.
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  • 文章类型: Journal Article
    科学出版的格局正在经历向开放获取(OA)的转型转变,一种要求提供数据等研究成果的范式,代码,材料,和出版物。OA提供增加的再现性并且允许这些资源的再利用。本文为科学研究的最佳出版实践提供了指导,数据,和相关资源,包括代码,在APS期刊上。关键领域,如诊断分析,实验设计,数据共享,和代码沉积进行了详细的探索。本指南与其他主要期刊观察到的指南一致。我们希望本文中收集的信息将提高人们对最佳实践的认识,并能够更好地评估生物学现象在植物病理学中的真实影响。
    The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.
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  • 文章类型: Editorial
    暂无摘要。
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  • 文章类型: Review
    目的:电子算法的使用,临床决策支持系统,和其他临床信息学干预措施在重症监护中正在增加。小儿急性呼吸窘迫综合征(PARDS)是一种复杂的,与大量临床数据和床边频繁决策相关的动态状况。新颖的数据驱动技术,可以帮助屏幕,提示,并支持临床医生的决策可能对患者预后产生重大影响.我们试图确定并总结与PARDS和成人呼吸窘迫综合征(ARDS)的临床信息学干预相关的证据。第二届小儿急性肺损伤共识会议。
    方法:MEDLINE(Ovid),Embase(Elsevier),和CINAHL完成(EBSCOhost)。
    方法:我们纳入了对患有ARDS或有ARDS风险的儿科或成人危重症患者的研究,这些研究检查了自动筛查工具,电子算法,或临床决策支持系统。
    方法:标题/摘要评论,全文回顾,和使用标准化的数据提取表单进行数据提取。
    结果:建议评估的分级,使用开发和评估方法来识别和总结证据并提出建议。确定了26项研究用于全文提取,以解决患者/干预/比较/结果问题。和14个用于建议/声明。产生了两个临床建议,与使用电子筛查工具和自动监控最佳实践指南的遵守情况有关。产生了两个研究陈述,与多中心数据协作的开发以及可通用算法和电子工具的设计有关。生成了一个政策声明,与医疗机构提供物质和人力资源有关,以授权临床医生开发临床信息学干预措施,以改善PARDS患者的护理。
    结论:我们在文献系统综述和专家共识的基础上,针对PARDS患者使用电子算法和临床信息学工具,提出了两项临床建议和三项声明(两项研究一项政策)。
    The use of electronic algorithms, clinical decision support systems, and other clinical informatics interventions is increasing in critical care. Pediatric acute respiratory distress syndrome (PARDS) is a complex, dynamic condition associated with large amounts of clinical data and frequent decisions at the bedside. Novel data-driven technologies that can help screen, prompt, and support clinician decision-making could have a significant impact on patient outcomes. We sought to identify and summarize relevant evidence related to clinical informatics interventions in both PARDS and adult respiratory distress syndrome (ARDS), for the second Pediatric Acute Lung Injury Consensus Conference.
    MEDLINE (Ovid), Embase (Elsevier), and CINAHL Complete (EBSCOhost).
    We included studies of pediatric or adult critically ill patients with or at risk of ARDS that examined automated screening tools, electronic algorithms, or clinical decision support systems.
    Title/abstract review, full text review, and data extraction using a standardized data extraction form.
    The Grading of Recommendations Assessment, Development and Evaluation approach was used to identify and summarize evidence and develop recommendations. Twenty-six studies were identified for full text extraction to address the Patient/Intervention/Comparator/Outcome questions, and 14 were used for the recommendations/statements. Two clinical recommendations were generated, related to the use of electronic screening tools and automated monitoring of compliance with best practice guidelines. Two research statements were generated, related to the development of multicenter data collaborations and the design of generalizable algorithms and electronic tools. One policy statement was generated, related to the provision of material and human resources by healthcare organizations to empower clinicians to develop clinical informatics interventions to improve the care of patients with PARDS.
    We present two clinical recommendations and three statements (two research one policy) for the use of electronic algorithms and clinical informatics tools for patients with PARDS based on a systematic review of the literature and expert consensus.
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  • 文章类型: Journal Article
    目的:本指南的目的是为手工制作和基于深度学习的方法提供可靠的影像组学分析最佳实践的全面信息。
    方法:在EANM和SNMMI之间的合作努力中,我们就目前的最佳实践和关于影像组学分析相关方面的建议达成一致,包括研究设计,质量保证,数据收集,收购和重建的影响,检测和分割,功能标准化和实施,以及适当的建模方案,模型评估,和解释。我们还对未来的前景进行了展望。
    结论:影像组学是一个发展非常迅速的研究领域。本指南侧重于既定的发现以及基于最新技术的建议。尽管本指南承认手工制作和基于深度学习的影像组学方法,它主要集中在前者,因为这个领域更加成熟。一旦更多的研究和结果有助于改善关于深度学习方法在放射组学中的应用的共识,该指南将被更新。尽管本文档中的方法学建议对大多数医学图像模式都有效,我们在这里专注于核医学,并在必要时对PET/CT提出具体建议,PET/MR,和定量SPECT。
    The purpose of this guideline is to provide comprehensive information on best practices for robust radiomics analyses for both hand-crafted and deep learning-based approaches.
    In a cooperative effort between the EANM and SNMMI, we agreed upon current best practices and recommendations for relevant aspects of radiomics analyses, including study design, quality assurance, data collection, impact of acquisition and reconstruction, detection and segmentation, feature standardization and implementation, as well as appropriate modelling schemes, model evaluation, and interpretation. We also offer an outlook for future perspectives.
    Radiomics is a very quickly evolving field of research. The present guideline focused on established findings as well as recommendations based on the state of the art. Though this guideline recognizes both hand-crafted and deep learning-based radiomics approaches, it primarily focuses on the former as this field is more mature. This guideline will be updated once more studies and results have contributed to improved consensus regarding the application of deep learning methods for radiomics. Although methodological recommendations in the present document are valid for most medical image modalities, we focus here on nuclear medicine, and specific recommendations when necessary are made for PET/CT, PET/MR, and quantitative SPECT.
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  • 文章类型: Journal Article
    生物治疗优化,无论是改进一般属性还是设计特定属性,是一个耗时的过程,结果不确定。相反,一致性蛋白质设计已被证明是增强蛋白质稳定性同时保持功能的可行方法。在将这种方法用于更有限数量的蛋白质序列时,我们研究了来自8个公开可获得的CD3结合序列的21个共有单点变体,这些序列具有高度相似性,但具有不同的生物物理和药理学特性.所有单点共有变体保留CD3结合并在基于细胞的功能测定中类似地进行。使用岭回归分析,我们鉴定了变体和序列位置,其对CD3结合剂的发育性属性具有总体有益影响。将这些取代组合到单个分子中的第二轮序列产生产生具有全局优化的可发育性属性的独特CD3结合剂。在治疗性抗体的首次应用中,适应性一致的蛋白质设计被发现在铅优化中是非常有益的,节约资源和最小化迭代。这种一般策略的未来实施可能有助于加速药物发现并提高将新型生物治疗剂推向市场的成功率。
    Biotherapeutic optimization, whether to improve general properties or to engineer specific attributes, is a time-consuming process with uncertain outcomes. Conversely, Consensus Protein Design has been shown to be a viable approach to enhance protein stability while retaining function. In adapting this method for a more limited number of protein sequences, we studied 21 consensus single-point variants from eight publicly available CD3 binding sequences with high similarity but diverse biophysical and pharmacological properties. All single-point consensus variants retained CD3 binding and performed similarly in cell-based functional assays. Using Ridge regression analysis, we identified the variants and sequence positions with overall beneficial effects on developability attributes of the CD3 binders. A second round of sequence generation that combined these substitutions into a single molecule yielded a unique CD3 binder with globally optimized developability attributes. In this first application to therapeutic antibodies, adapted Consensus Protein Design was found to be highly beneficial within lead optimization, conserving resources and minimizing iterations. Future implementations of this general strategy may help accelerate drug discovery and improve success rates in bringing novel biotherapeutics to market.
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