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关键词： Foodborne outbreak investigation   Microbial typing   Food source   Data sharing   Harmonization   Virtual research environment  

摘要： The source of a foodborne disease outbreak (FBO) is often difficult to identify, especially in the early phase where interventions would be most efficient. In addition, data on FBOs are mostly scattered in different formats either in national databases and reports or within pathogen-specific or regional reporting networks, both of which are often only accessible to a selected number of individuals. Here, we developed an international, open, shared and searchable data catalogue of past FBOs - the Global Food-source Identifier (GFI). GFI was developed with two objectives: a) to create a collaborative online community of FBO investigators, encouraging the international sharing of data in a harmonized, detailed and comparable manner and b) to support foodborne outbreak investigation worldwide by providing access to detailed records of past outbreaks, which can convey valuable insight into potential 'risk foods' of a detected pathogen. GFI is hosted within a Virtual Research Environment (VRE), which offers additional features to facilitate the collaboration between the outbreak investigators. These features allow document exchange, communication and data visualization and analysis between the VRE members. Based on scientific literature on foodborne outbreaks and discussions within a working group, we selected a total of 46 attributes characterising the outbreak records to be included in the catalogue, aggregated under the four overarching categories causative agent, epidata, food source and report details. Detailed descriptions of the attributes in the catalogue and instructions for harmonized data reporting are available on a wiki page in the VRE. At the time of writing and public launch of GFI, the data catalogue was populated with records of 102 FBOs occurred in Denmark over a period of 12 years (2005-2016) and covering the most frequent pathogens and a broad range of typing methods. The VRE features that enable data analysis, document sharing and communication betwee

关键词： Obesity   Insulin resistance   Anthropometry   Sagittal abdominal diameter   Body mass index   Abdominal obesity  

摘要： Background and aims: Body mass index (BMI) and waist circumference (WC) are commonly used markers of cardiometabolic risk. However, sagittal abdominal diameter (SAD) has been proposed as a possibly more sensitive marker of intra-abdominal obesity. We investigated differences in how SAD, WC, and BMI were correlated with cardiometabolic risk markers. Methods and results: This cross-sectional study investigated anthropometric and metabolic baseline measurements of individuals from six trials. Multiple linear regression and (partial) correlation coefficients were used to investigate associations between SAD, WC, and BMI and cardiometabolic risk markers, including components of the metabolic syndrome as well as insulin resistance, blood lipids, and low-grade inflammation. In total 1516 mostly overweight or obese individuals were included in the study. SAD was significantly more correlated with TG than WC for all studies, and overall increase in correlation was 0.05 (95% CI (0.02;0.08). SAD was significantly more correlated with the markers TG and DBP 0.11 (95% CI (0.08, 0.14)) and 0.04 (95% CI (0.006, 0.07), respectively compared to BMI across all or most studies. Conclusion: This study showed that no single anthropometric indicator was consistently more strongly correlated across all markers of cardiometabolic risk. However, SAD was significantly more strongly correlated with TG than WC and significantly more strongly correlated with DBP and TG than BMI. (C) 2020 Published by Elsevier B.V. on behalf of The Italian Diabetes Society, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition and the Department of Clinical Medicine and Surgery, Federico II University.

关键词： Targeted RNAseq   Unique molecular identifiers   Assay development   Breast cancer  

摘要： BackgroundOur objective was to assess whether modifications to a customized targeted RNA sequencing (RNAseq) assay to include unique molecular identifiers (UMIs) that collapse read counts to their source mRNA counts would improve quantification of transcripts from formalin-fixed paraffin-embedded (FFPE) tumor tissue samples. The assay (SET4) includes signatures that measure hormone receptor and PI3-kinase related transcriptional activity (SETER/PR and PI3Kges), and measures expression of selected activating point mutations and key breast cancer *** included steps to introduce eight nucleotides-long UMIs during reverse transcription (RT) in bulk solution, followed by polymerase chain reaction (PCR) of labeled cDNA in droplets, with optimization of the polymerase enzyme and reaction conditions. We used Lin's concordance correlation coefficient (CCC) to measure concordance, including precision (Rho) and accuracy (Bias), and nonparametric tests (Wilcoxon, Levene's) to compare the modified (NEW) SET4 assay to the original (OLD) SET4 assay and to whole transcriptome RNAseq using RNA from matched fresh frozen (FF) and FFPE samples from 12 primary breast *** modified (NEW) SET4 assay measured single transcripts (p<0.001) and SETER/PR (p=0.002) more reproducibly in technical replicates from FFPE samples. The modified SET4 assay was more precise for measuring single transcripts (Rho 0.966 vs 0.888, p<0.01) but not multigene expression signatures SETER/PR (Rho 0.985 vs 0.968) or PI3Kges (Rho 0.985 vs 0.946) in FFPE, compared to FF samples. It was also more precise than wtRNAseq of FFPE for measuring transcripts (Rho 0.986 vs 0.934, p<0.001) and SETER/PR (Rho 0.993 vs 0.915, p=0.004), but not PI3Kges (Rho 0.988 vs 0.945, p=0.051). Accuracy (Bias) was comparable between protocols. Two samples carried a PIK3CA mutation, and measurements of transcribed mutant allele fraction was similar in FF and FFPE samples and appeared more precise with the

关键词： 数字对象唯一标识符   中华医学会系列杂志   数字信息   互联网信息   唯一标识   DOI   条形码   ISSN  

摘要： 数字对象唯一标识符(digital object identifier,DOI)是对包括互联网信息在内的数字信息进行标识的一种工具。在传统的出版物中,书刊、磁带、光盘都有国际标准编号(ISBN、ISSNJSCN)及其条形码,作为出版物的唯一标识。这些标识使出版物得到有效的管理,便于读者查找和利用。

关键词： Neural network   Unscented Kalman filter   High-order sliding mode observer   Induction motor  

摘要： This paper presents a method to identify an unknown discrete-time nonlinear system, using high-order neural networks and high-order sliding mode algorithms, which may be subject to internal and external disturbances. Based on the information obtained from available system states, a high-order neural network model is proposed to approximate the system dynamics. Neural network weights are trained by means of the unscented Kalman filter and high-order sliding mode observer. A simulation example is included to illustrate effectiveness of the proposed scheme. (c) 2019 Elsevier B.V. All rights reserved.

关键词： 条形码   物理地址   数字对象   数字信息   网址   互联网信息   识别码   DOI  

摘要： 数字对象唯一标识符(digital object identifier,DOI)是对包括互联网信息在内的数字信息进行标识的一种工具。在传统的出版物中,书刊、磁带、光盘都有国际标准编号(ISBN、ISSN、ISCN)及其条形码,作为出版物的唯一标识。这些标识使出版物得到有效的管理,便于读者查找和利用。而网上的文档一旦变更了网址便无从追索。数字信息标注DOI如同出版物的条形码,是一个永久和唯一的标识号。随着时间推移,数字对象的某些有关信息可能会有变化(包括存储的物理位置),而DOI可让使用者直接由此链接到出版商的数据库、文献、摘要甚至是全文,识别码可以直接指引到出版物的本身,使国内外各种来源、不同物理地址的各种类型的学术信息实现互链互通。

关键词： CAx integration   re-imported CAD model   revised neutral models   exchangeable persistent identifications   elements associativity   computer-aided design   computer-aided engineering   computer-aided manufacturing  

摘要： Computer-aided design, engineering, and manufacturing (CAx) have improved product design and development. The associativity of revised design in native files for downstream applications, assembly design, finite element analysis, and numerical control (NC) manufacturing has been supported by homogeneous CAx systems. However, heterogeneous CAx environments have issues when neutral models are revised and re-imported because the required identification information is missing. This results in a problem of the associativity of neutral models. In this study, different computer-aided design (CAD) applications have been analyzed with respect to their capabilities for import and export of neutral models with identification information. A tool has been selected to demonstrate the key findings. Moreover, future directions have been discussed to solve associativity issues in design re-import based on neutral models.

关键词： 标注规则   数字对象   杂志内容   网络链接   网络传播权   知识产权   资源数字化   标识符  

摘要： 根据中华医学会杂志社有关通知要求,为更好的提升杂志内容资源数字化传播效能,保护数字资源在网络链接中的知识产权和网络传播权,实现对数字对象的持续追踪和阅读数据的有效统计,自2020年(第38卷)3期,我刊DOI号标注规则进行修订。

关键词： Clinical search harmonization   Data Safe Havens   Clinical research  

摘要： Over the last decades clinical research has been driven by informatics changes nourished by distinct research endeavors. Inherent to this evolution, several issues have been the focus of a variety of studies: multi-location patient data access, interoperability between terminological and classification systems and clinical practice and records harmonization. Having these problems in mind, the Data Safe Haven paradigm emerged to promote a newborn architecture, better reasoning and safe and easy access to distinct Clinical Data Repositories. This study aim is to present a novel solution for clinical search harmonization within a safe environment, making use of a hybrid coding taxonomy that enables researchers to collect information from multiple repositories based on a clinical domain query definition. Results show that is possible to query multiple repositories using a single query definition based on clinical domains and the capabilities of the Unified Medical Language System, although it leads to deterioration of the framework response times. Participants of a Focus Group and a System Usability Scale questionnaire rated the framework with a median value of 72.5, indicating the hybrid coding taxonomy could be enriched with additional metadata to further improve the refinement of the results and enable the possibility of using this system as data quality tagging mechanism.

关键词： Biotechnology   DNA sequencing   Molecular biology  

摘要： High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, we report a high-throughput amplicon sequencing approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies (ONT) or Pacific Biosciences circular consensus sequencing, yielding high-accuracy single-molecule consensus sequences of large genomic regions. We applied our approach to sequence ribosomal RNA operon amplicons (similar to 4,500 bp) and genomic sequences (>10,000 bp) of reference microbial communities in which we observed a chimera rate <0.02%. To reach a mean UMI consensus error rate <0.01%, a UMI read coverage of 15x (ONT R10.3), 25x (ONT R9.4.1) and 3x (Pacific Biosciences circular consensus sequencing) is needed, which provides a mean error rate of 0.0042%, 0.0041% and 0.0007%, respectively.