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关键词： Aerobiology   DNA extraction   Cloning   Sanger-sequencing   trnL  

摘要： Metabarcoding is a promising DNA-based method for identifying airborne pollen from environmental samples with advantages over microscopic methods. Sample preparation and DNA extraction are of fundamental importance for obtaining an optimal DNA yield. Currently, there is no standard procedure for these steps, especially for gravimetric pollen samplers. Therefore, the aim of this study was to develop protocols for processing environmental samples for pollen DNA extraction and for metabarcoding analysis and to assess the efficacy of these protocols for the taxonomic assignment of airborne pollen collected by gravimetric (Tauber trap) and volumetric (Hirst-type trap) samplers. Protocols were tested across an increasing complexity of samples, from pure single-species pollen to environmental multi-species samples. A short fragment (about 150 base pairs) of the chloroplast trnL gene was amplified using universal primers for plants. After PCR amplification, amplicons were Sanger-sequenced and taxonomic assignment was accomplished by comparison with a custom-made reference database including chloroplast DNA sequences from most of the anemophilous taxa occurring in the study area (Trentino, northern Italy), representing 46 plant families. Using the classical morphological pollen analysis as a benchmark, we show that DNA metabarcoding is efficient and applicable even in complex samples, provided that protocols for sample preparation, DNA extraction, and metabarcoding analysis are carefully optimized.

关键词： Multi-label   active learning   image classification   sample noise   label correlation   mapping relation   automatic labeling  

摘要： Multi-label active learning for image classification has been a popular research topic. It faces several challenges, even though related work has made great progress. Existing studies on multi-label active learning do not pay attention to the cleanness of sample data. In reality, data are easily polluted by external influences that are likely to disturb the exploration of data space and have a negative effect on model training. Previous methods of label correlation mining, which are purely based on observed label distribution, are defective. Apart from neglecting noise influence, they also cannot acquire sufficient relevant information. In fact, they neglect inner relation mapping from example space to label space, which is an implicit way of modeling label relationships. To solve these issues, we develop a novel multi-label active learning with low-rank application (ENMAL) algorithm in this paper. A low-rank model is constructed to quantize noise level, and the example-label pairs that contain less noise are emphasized when sampling. A low-rank mapping matrix is learned to signify the mapping relation of a multi-label domain to capture a more comprehensive and reasonable label correlation. Integrating label correlation with uncertainty and considering sample noise, an efficient sampling strategy is developed. We extend ENMAL with automatic labeling (denoted as AL-ENMAL) to further reduce the annotation workload of active learning. Empirical research demonstrates the efficacy of our approaches.

关键词： Medical innovations   Diffusion   Healthcare disparities   Patient-centered care   Race/ethnicity   US   Human papillomavirus (HPV)   Vaccine  

摘要： Rationale: Studies of inequities in diffusion of medical innovations rarely consider the role of patient-centered care. Objective: We used uptake of the human papillomavirus (HPV) vaccine shortly after its licensing to explore the role of patient-centered care. Methods: Using a longitudinal multi-site survey of US parents and adolescents, we assessed whether patient-centered care ratings might shape racial/ethnic and socioeconomic gaps at two decision points in the HPV vaccination process: (1) Whether a medical provider recommends the vaccine and (2) whether a parent decides to vaccinate. Results: We did not find evidence that the association of patient-centeredness with vaccination varies by parent education. In contrast, parent ratings of providers' patient-centeredness were significantly associated with racial/ethnic disparities in parents' reports of receiving a HPV vaccine recommendation from a provider: Among parents who rate patient-centered care as low, white parents' odds of receiving such a recommendation are 2.6 times higher than black parents' odds, but the racial/ethnic gap nearly disappears when parents report high patient-centeredness. Moderated mediation analyses suggest that patient-centeredness is a major contributor underlying vaccination uptake disparities: Among parents who report low patient-centeredness, white parents' odds of vaccinating their child are 8.1 times higher than black parents' odds, while both groups are equally likely to vaccinate when patient-centeredness is high. Conclusion: The results indicate that patient-centered care, which has been a relatively understudied factor in the unequal diffusion of medical innovations, deserves more attention. Efforts to raise HPV vaccination rates should explore why certain patient groups may be less likely to receive recommendations and should support providers to consistently inform all patient groups about vaccination. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： classification   correlation   metagenomics   set cover   taxonomic annotation  

摘要： The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample.

关键词： amplicon metagenetics   biodiversity   diatoms   next-generation sequencing   protists  

摘要： Next-generation sequencing is a common method for analysing microbial community diversity and composition. Configuring an appropriate sequence processing strategy within the variety of tools and methods is a nontrivial task and can considerably influence the resulting community characteristics. We analysed the V4 region of 18S rRNA gene sequences of marine samples by 454-pyrosequencing. Along this process, we generated several data sets with QIIME, mothur, and a custom-made pipeline based on DNAStar and the phylogenetic tree-based PhyloAssigner. For all processing strategies, default parameter settings and punctual variations were used. Our results revealed strong differences in total number of operational taxonomic units (OTUs), indicating that sequence preprocessing and clustering had a major impact on protist diversity estimates. However, diversity estimates of the abundant biosphere (abundance of 1%) were reproducible for all conducted processing pipeline versions. A qualitative comparison of diatom genera emphasized strong differences between the pipelines in which phylogenetic placement of sequences came closest to light microscopy-based diatom identification. We conclude that diversity studies using different sequence processing strategies are comparable if the focus is on higher taxonomic levels, and if abundance thresholds are used to filter out OTUs of the rare biosphere.

关键词： 临床分析   弥漫性血管内凝血   凝血检验  

摘要： 目的:分析弥漫性血管内凝血采取凝血检验进行诊断的临床意义.方法:将我院2015年4月—2017年3月纳入的58例弥漫性血管内凝血患者作为研究组,另选择同一时间来我院进行体检的健康人员58例作为对照组,比较两组患者的凝血检验结果.结果:经过分析两组患者凝血检验的结果,可以看出研究组凝血酶原时间、活化部分凝血活酶时间、凝血酶时间以及国际标准化比值均比对照组水平高,其纤维蛋白原水平低于对照组,差别均有统计学意义(P<0.05).结论:弥漫性血管内凝血诊断中采取凝血检验,可有效判断患者止血功能情况,在手术前做好预防措施,为之后的手术治疗提供有力依据.

关键词： 包装   大数据   知识图谱   分类体系  

摘要： 阐述了中国包装产业大数据知识图谱分类体系构建的意义,分析了中国包装产业大数据知识图谱分类体系的特点,探究了中国包装产业大数据知识图谱分类体系的构建原则,提出了构建中国包装产业大数据知识图谱分类体系的策略。

关键词： 理化检验   质量控制   突发公共卫生事件   作用  

摘要： 目的分析理化检验质量控制在突发公共卫生事件中的作用。方法对理化检验质量控制实施前(2011—2013年)与实施后(2014—2016年)各50例模拟突发公共卫生事件进行收集,对比实施前后的检验误差率、民众满意度以及有效控制时间。结果相较于理化检验质量控制实施前,实施后的检验误差率更低,民众满意度更高,报告发出时间、有效控制时间更短(P<0.05)。结论理化检验质量控制在突发公共卫生事件中的作用显著,能够将风险性降低,促使民众满意度显著提高。