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Advances in clinical genetics and genomics 临床遗传学和基因组学进展
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-09-01 DOI: 10.1016/j.imed.2021.03.005
Sen Zhao , Xi Cheng , Wen Wen , Guixing Qiu , Terry Jianguo Zhang , Zhihong Wu , Nan Wu

Developments in genetics and genomics are progressing at an unprecedented speed. Twenty years ago, the human genome project provided the first glimpses into the human genome sequence and launched a new era of human genetics. The emerging of next-generation sequencing (NGS) in 2005 then made possible comprehensive genetic testing such as exome sequencing and genome sequencing. Meanwhile, great efforts have been put into the optimization of bioinformatic pipelines to make increasingly speedy and accurate variant analyses based on NGS data. These advances in sequencing technologies and analytical methods have revolutionized the diagnostic odyssey of suspected hereditary diseases. More recently, the genotype-phenotype relationship and polygenic risk scores (PRSs) generated from genome-wide association studies have expanded our horizon from rare genetic mutations to a genomic landscape implicated by the combined effect of both rare variants and polymorphisms. At the same time, clinicians and genetic counselors are facing huge challenges conferred by overwhelming genomic knowledge and long sheets of testing reports for comprehensive genomic sequencing. The path toward the “next-generation” clinical genetics and genomics may underlie semiautomatic pipelines assisted by artificial intelligence techniques.

遗传学和基因组学的发展正以前所未有的速度发展。20年前,人类基因组计划首次提供了人类基因组序列的一瞥,并开启了人类遗传学的新时代。2005年新一代测序技术(NGS)的出现,使外显子组测序和基因组测序等综合基因检测成为可能。同时,生物信息学管道的优化也在不断努力,使基于NGS数据的变异分析越来越快速和准确。测序技术和分析方法的这些进步彻底改变了疑似遗传性疾病的诊断过程。最近,从全基因组关联研究中产生的基因型-表型关系和多基因风险评分(prs)将我们的视野从罕见基因突变扩展到罕见变异和多态性共同影响的基因组景观。与此同时,临床医生和遗传咨询师正面临着铺天盖地的基因组知识和冗长的全面基因组测序测试报告所带来的巨大挑战。通往“下一代”临床遗传学和基因组学的道路可能是由人工智能技术辅助的半自动管道的基础。
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引用次数: 3
Predicting the pathological status of mammographic microcalcifications through a radiomics approach 通过放射组学方法预测乳房x线微钙化的病理状态
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-09-01 DOI: 10.1016/j.imed.2021.05.003
Min Li , Liyu Zhu , Guangquan Zhou , Jianan He , Yanni Jiang , Yang Chen

Objective The study aimed to develop a machine learning (ML)-coupled interpretable radiomics signature to predict the pathological status of non-palpable suspicious breast microcalcifications (MCs).

Methods We enrolled 463 digital mammographical view images from 260 consecutive patients detected with non-palpable MCs and BI-RADS scored at 4 (training cohort, n = 428; independent testing cohort, n = 35) in the First Affiliated Hospital of Nanjing Medical University between September 2010 and January 2019. Subsequently, 837 textures and 9 shape features were subsequently extracted from each view and finally selected by an XGBoost-embedded recursive feature elimination technique (RFE), followed by four machine learning-based classifiers to build the radiomics signature.

Results Ten radiomic features constituted a malignancy-related signature for breast MCs as logistic regression (LR) and support vector machine (SVM) yielded better positive predictive value (PPV)/sensitivity (SE), 0.904 (95% CI, 0.865–0.949)/0.946 (95% CI, 0.929–0.977) and 0.891 (95% CI, 0.822–0.939)/0.939 (95% CI, 0.907–0.973) respectively, outperforming their negative predictive value (NPV)/specificity (SP) from 10-fold cross-validation (10FCV) of the training cohort. The optimal prognostic model was obtained by SVM with an area under the curve (AUC) of 0.906 (95% CI, 0.834–0.969) and accuracy (ACC) 0.787 (95% CI, 0.680–0.855) from 10FCV against AUC 0.810 (95% CI, 0.760–0.960) and ACC 0.800 from the testing cohort.

Conclusion The proposed radiomics signature dependens on a set of ML-based advanced computational algorithms and is expected to identify pathologically cancerous cases from mammographically undecipherable MCs and thus offer prospective clinical diagnostic guidance.

目的建立一种机器学习(ML)耦合的可解释放射组学特征来预测不可触及的可疑乳房微钙化(MCs)的病理状态。方法:我们收集了260例连续检测到不可触及MCs的患者的463张数字乳房x线摄影图像,BI-RADS评分为4(训练队列,n = 428;独立检测队列,n = 35),于2010年9月至2019年1月在南京医科大学第一附属医院进行。随后,从每个视图中提取837个纹理和9个形状特征,最后通过嵌入xgboost的递归特征消除技术(RFE)进行选择,然后使用4个基于机器学习的分类器构建放射组学签名。结果10个放射学特征构成乳腺MCs的恶性相关特征,logistic回归(LR)和支持向量机(SVM)的阳性预测值(PPV)/敏感性(SE)更高,分别为0.904 (95% CI, 0.865-0.949)/0.946 (95% CI, 0.929-0.977)和0.891 (95% CI, 0.822-0.939)/0.939 (95% CI, 0.907-0.973),优于训练队列10倍交叉验证(10FCV)的阴性预测值(NPV)/特异性(SP)。通过支持向量机获得最佳预后模型,曲线下面积(AUC)为0.906 (95% CI, 0.834-0.969),准确度(ACC)为0.787 (95% CI, 0.680-0.855),而测试队列的AUC为0.810 (95% CI, 0.760-0.960), ACC为0.800。结论提出的放射组学特征依赖于一套基于ml的先进计算算法,有望从乳房x线摄影无法识别的MCs中识别病理癌病例,从而提供前瞻性临床诊断指导。
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引用次数: 3
Guide for Authors 作者指南
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-09-01 DOI: 10.1016/S2667-1026(21)00103-0
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引用次数: 0
A survey on deep learning in medical image reconstruction 深度学习在医学图像重建中的研究进展
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-09-01 DOI: 10.1016/j.imed.2021.03.003
Emmanuel Ahishakiye , Martin Bastiaan Van Gijzen , Julius Tumwiine , Ruth Wario , Johnes Obungoloch

Medical image reconstruction aims to acquire high-quality medical images for clinical usage at minimal cost and risk to the patients. Deep learning and its applications in medical imaging, especially in image reconstruction have received considerable attention in the literature in recent years. This study reviews records obtained electronically through the leading scientific databases (Magnetic Resonance Imaging journal, Google Scholar, Scopus, Science Direct, Elsevier, and from other journal publications) searched using three sets of keywords: (1) Deep learning, image reconstruction, medical imaging; (2) Medical imaging, Deep learning, Image reconstruction; (3) Open science, Open imaging data, Open software. The articles reviewed revealed that deep learning-based reconstruction methods improve the quality of reconstructed images qualitatively and quantitatively. However, deep learning techniques are generally computationally expensive, require large amounts of training datasets, lack decent theory to explain why the algorithms work, and have issues of generalization and robustness. The challenge of lack of enough training datasets is currently being addressed by using transfer learning techniques.

医学图像重建旨在以最小的成本和风险获得高质量的医学图像供临床使用。近年来,深度学习及其在医学成像,特别是图像重建中的应用受到了文献的广泛关注。本研究回顾了通过主要科学数据库(磁共振成像期刊、Google Scholar、Scopus、Science Direct、Elsevier和其他期刊出版物)以电子方式获得的记录,使用三组关键词进行检索:(1)深度学习、图像重建、医学成像;(2)医学成像,深度学习,图像重建;(3)开放科学,开放影像数据,开放软件。综述表明,基于深度学习的重建方法从定性和定量上提高了重建图像的质量。然而,深度学习技术通常在计算上是昂贵的,需要大量的训练数据集,缺乏像样的理论来解释为什么算法工作,并且存在泛化和鲁棒性问题。目前,迁移学习技术正在解决缺乏足够训练数据集的问题。
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引用次数: 47
Digital inclusion of older people: harnessing digital technologies to promote healthy ageing in the Western Pacific Region 老年人的数字包容:在西太平洋区域利用数字技术促进健康老龄化
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-09-01 DOI: 10.1016/j.imed.2021.08.002
Shan Xu, Dong Min, Yiwen Cheng, Peng Wang, Yue Gao

Adapting systems and technology for an aging population has benefits for older people, the consumer market industry itself and all of society. To promote knowledge sharing on innovations for healthy ageing and digital inclusion of older people in the Western Pacific Region, a hybrid conference on “Digital inclusion of older people: harnessing digital technologies to promote healthy ageing in the Western Pacific Region” was held on 23 June 2021 by China Academy of Information and Communications Technology, a WHO Collaborating Centre for Digital Health. Barriers from demand side include: (1) unaffordability; (2) poor Information and Communication technology (ICT) knowledge and skills for navigation; and (3) low self-efficacy and motivation. Supply barriers include: (1) youth-centred design; (2) ageism; and (3) anti-facilitative environment including infrastructure and age-biased technology. Existing practices to overcome digital inclusion barriers were shared: (1) landmark initiatives related to the health and social welfare; (2) laws and policies to improve aged care services, strengthen social services, enrich spiritual and cultural life for older people; (3) ICT infrastructure and residential care facilities based on the philosophy of family care and supported by community care; (4) affordable digital application and adaptive feature design to better enable and motivate their desire to use digital technology; and (5) community activities such as trainings and tutorials to enhance digital capacity and literacy of older people. Main principles highlighted include market motivation, human-centered design, creating enabling environments, and multi-stakeholder collaborations to provide guidance to customize strategy under context of different regions and countries, instead of a one-size-fits-all solution, to avoid the risk of exacerbating inequalities experienced by older people, caused by accelerated ICT innovation, and advocate for more affordable products in the silver market.

适应人口老龄化的系统和技术对老年人、消费市场行业本身和整个社会都有好处。为促进西太平洋区域健康老龄化和老年人数字化融合创新方面的知识共享,中国信息通信技术研究院(世卫组织数字卫生合作中心)于2021年6月23日举办了“老年人数字化融合:利用数字技术促进西太平洋区域健康老龄化”混合会议。需求方的障碍包括:(1)负担不起;(2)缺乏信息和通信技术(ICT)导航知识和技能;(3)自我效能和动机低下。供应障碍包括:(1)以青年为中心的设计;(2)对老年人的歧视;(3)反便利环境,包括基础设施和年龄偏见技术。与会者分享了克服数字包容障碍的现有做法:(1)与健康和社会福利有关的里程碑式举措;(2)完善养老服务、加强社会服务、丰富老年人精神文化生活的法律政策;(3)以家庭护理为理念,以社区护理为支撑的ICT基础设施和居家护理设施;(4)负担得起的数字应用程序和自适应功能设计,以更好地实现和激发他们使用数字技术的愿望;(5)社区活动,如培训和教程,以提高老年人的数字能力和识字率。重点强调的主要原则包括市场激励、以人为本的设计、创造有利环境以及多方利益相关者合作,为不同地区和国家的定制战略提供指导,而不是一刀切的解决方案,以避免信息通信技术创新加速导致老年人经历的不平等加剧的风险,并倡导在白银市场提供更多负担得起的产品。
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引用次数: 0
The critical need to establish standards for data quality in intelligent medicine 建立智能医疗数据质量标准的迫切需要
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-08-01 DOI: 10.1016/j.imed.2021.04.004
Ruiyang Li , Yahan Yang , Haotian Lin

Medical artificial intelligence (AI) is an important technical asset to support medical supply-side reforms and national development in the big data era. Clinical data from multiple disciplines represent building blocks for the development and application of AI-aided diagnostic and treatment systems based on medical big data. However, the inconsistent quality of these data resources in AI research leads to waste and inefficiencies. Therefore, it is crucial that the field formulates the requirements and content related to data processing as part of the development of intelligent medicine. To promote medical AI research worldwide, the “Belt and Road” International Ophthalmic Artificial Intelligence Research and Development Alliance will establish a series of expert recommendations for data quality in intelligent medicine.

医疗人工智能是大数据时代支持医疗供给侧改革和国家发展的重要技术资产。多学科临床数据是基于医疗大数据的人工智能辅助诊疗系统开发和应用的基石。然而,人工智能研究中这些数据资源的质量不一致导致了浪费和效率低下。因此,作为智能医疗发展的一部分,该领域制定与数据处理相关的要求和内容至关重要。为推动全球范围内的医疗人工智能研究,“一带一路”国际眼科人工智能研发联盟将针对智能医疗数据质量建立一系列专家建议。
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引用次数: 2
The national multi-center artificial intelligent myopia prevention and control project 国家多中心人工智能近视防治项目
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-08-01 DOI: 10.1016/j.imed.2021.05.001
Xun Wang , Yahan Yang , Yuxuan Wu , Wenbin Wei , Li Dong , Yang Li , Xingping Tan , Hankun Cao , Hong Zhang , Xiaodan Ma , Qin Jiang , Yunfan Zhou , Weihua Yang , Chaoyu Li , Yu Gu , Lin Ding , Yanli Qin , Qi Chen , Lili Li , Mingyue Lian , Haotian Lin

In recent years, the incidence of myopia has increased at an alarming rate among children and adolescents in China. The exploration of an effective prevention and control method for myopia is in urgent need. With the development of information technology in the past decade, artificial intelligence with the Internet of Things technology (AIoT) is characterized by strong computing power, advanced algorithm, continuous monitoring, and accurate prediction of long-term progression. Therefore, big data and artificial intelligence technology have the potential to be applied to data mining of myopia etiology and prediction of myopia occurrence and development. More recently, there has been a growing recognition that myopia study involving AIoT needs to undergo a rigorous evaluation to demonstrate robust results.

近年来,中国儿童和青少年的近视发病率以惊人的速度增长。迫切需要探索一种有效的近视防治方法。近十年来,随着信息技术的发展,以物联网技术(AIoT)为代表的人工智能具有计算能力强、算法先进、持续监测、对长期进展进行准确预测等特点。因此,大数据和人工智能技术具有应用于近视病因数据挖掘和近视发生发展预测的潜力。最近,越来越多的人认识到,涉及AIoT的近视研究需要经过严格的评估才能证明可靠的结果。
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引用次数: 2
Guide for Authors 作者指南
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-08-01 DOI: 10.1016/S2667-1026(21)00081-4
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引用次数: 0
Investigation and evaluation of randomized controlled trials for interventions involving artificial intelligence 涉及人工智能干预的随机对照试验的调查与评价
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-08-01 DOI: 10.1016/j.imed.2021.04.006
Jianjian Wang , Shouyuan Wu , Qiangqiang Guo , Hui Lan , Estill Janne , Ling Wang , Juanjuan Zhang , Qi Wang , Yang Song , Nan Yang , Xufei Luo , Qi Zhou , Qianling Shi , Xuan Yu , Yanfang Ma , Joseph L. Mathew , Hyeong Sik Ahn , Myeong Soo Lee , Yaolong Chen

Objective Complete and transparent reporting is of critical importance for randomized controlled trials (RCTs). The present study aimed to determine the reporting quality and methodological quality of RCTs for interventions involving artificial intelligence (AI) and their protocols.

Methods We searched MEDLINE (via PubMed), Embase, Web of Science, CBMdisc, Wanfang Data, and CNKI from January 1, 2016, to November 11, 2020, to collect RCTs involving AI. We also extracted the protocol of each included RCT if it could be obtained. CONSORT-AI (Consolidated Standards of Reporting Trials–Artificial Intelligence) statement and Cochrane Collaboration's tool for assessing risk of bias (ROB) were used to evaluate the reporting quality and methodological quality, respectively, and SPIRIT-AI (The Standard Protocol Items: Recommendations for Interventional Trials–Artificial Intelligence) statement was used to evaluate the reporting quality of the protocols. The associations of the reporting rate of CONSORT-AI with the publication year, journal's impact factor (IF), number of authors, sample size, and first author's country were analyzed univariately using Pearson's chi-squared test, or Fisher's exact test if the expected values in any of the cells were below 5. The compliance of the retrieved protocols to SPIRIT-AI was presented descriptively.

Results Overall, 29 RCTs and three protocols were considered eligible. The CONSORT-AI items “title and abstract” and “interpretation of results” were reported by all RCTs, with the items with the lowest reporting rates being “funding” (0), “implementation” (3.5%), and “harms” (3.5%). The risk of bias was high in 13 (44.8%) RCTs and not clear in 15 (51.7%) RCTs. Only one RCT (3.5%) had a low risk of bias. The compliance was not significantly different in terms of the publication year, journal's IF, number of authors, sample size, or first author's country. Ten of the 35 SPIRIT-AI items (funding, participant timeline, allocation concealment mechanism, implementation, data management, auditing, declaration of interests, access to data, informed consent materials and biological specimens) were not reported by any of the three protocols.

Conclusions The reporting and methodological quality of RCTs involving AI need to be improved. Because of the limited availability of protocols, their quality could not be fully judged. Following the CONSORT-AI and SPIRIT-AI statements and with appropriate guidance on the risk of bias when designing and reporting AI-related RCTs can promote standardization and transparency.

目的完整、透明的报告对随机对照试验(RCTs)至关重要。本研究旨在确定涉及人工智能(AI)及其协议的干预措施的随机对照试验的报告质量和方法质量。方法从2016年1月1日至2020年11月11日检索MEDLINE (PubMed)、Embase、Web of Science、CBMdisc、万方数据、中国知网,收集涉及人工智能的随机对照试验。我们还提取了每个纳入的RCT的方案,如果可以得到的话。采用consortium - ai(综合试验报告标准-人工智能)声明和Cochrane协作的偏倚风险评估工具(ROB)分别评估报告质量和方法质量,采用SPIRIT-AI(标准方案项目:介入性试验建议-人工智能)声明评估方案的报告质量。concont - ai报告率与出版年份、期刊影响因子(IF)、作者数量、样本量和第一作者所在国家的关系采用单因素Pearson卡方检验,如果任何单元格中的预测值低于5,则使用Fisher精确检验。描述了检索到的协议对SPIRIT-AI的遵从性。总的来说,29项随机对照试验和3项方案被认为是合格的。所有rct均报告了congo - ai项目“标题和摘要”和“结果解释”,报告率最低的项目是“资助”(0)、“实施”(3.5%)和“危害”(3.5%)。13项(44.8%)rct偏倚风险高,15项(51.7%)rct偏倚风险不明确。只有一项RCT(3.5%)具有低偏倚风险。合规性在出版年份、期刊的影响因子、作者数量、样本量或第一作者的国家方面没有显著差异。在35个SPIRIT-AI项目中,有10个项目(经费、参与者时间表、拨款隐藏机制、实施、数据管理、审计、利益申报、数据获取、知情同意材料和生物标本)未被三个方案中的任何一个报告。结论人工智能随机对照试验的报告质量和方法学质量有待提高。由于方案的可得性有限,因此无法充分判断其质量。在设计和报告与人工智能相关的随机对照试验时,遵循consortium - ai和SPIRIT-AI声明,并对偏倚风险进行适当的指导,可以促进标准化和透明度。
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引用次数: 2
Annotation and quality control specifications for fundus color photograph 眼底彩色照片注释及质量控制规范
Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2021-08-01 DOI: 10.1016/j.imed.2021.05.006
China Association for Quality Inspection
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引用次数: 5
期刊
Intelligent medicine
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