Sampling

取样
  • 文章类型: Journal Article
    生物多样性保护面临方法论难题:生物多样性测量通常依赖于物种,其中大多数在各种尺度上都很罕见,特别是在全球变化下容易灭绝,但也是最具挑战性的样本和模型。使用常规物种分布模型预测稀有物种的分布变化具有挑战性,因为大多数调查系统几乎无法捕获稀有物种。当足够的数据可用时,预测通常在空间上偏向于物种最有可能出现的位置,违反了许多建模框架的假设。预测和最终绘制稀有物种分布的工作流程意味着数据量之间的重要权衡,质量,在调查和分析之前需要考虑的代表性和模型复杂性。我们的观点是,研究设计需要仔细整合不同的步骤,从物种取样到建模,根据不同类型的稀有和可用数据,以提高我们对稀有物种分布进行合理评估和预测的能力。在这篇文章中,我们总结并评论了不同类别的物种稀有性如何根据调查过程中做出的选择导致不同类型的发生和分布数据,即样本的空间分布(在哪里取样)和每个选定位置的取样协议(如何取样)。然后,我们根据不同类型的分布数据(如何建模)来阐明哪些物种分布模型是合适的。其中,对于大多数稀有形式,我们重点介绍了系统的以物种为目标的抽样以及分层模型的见解,这些模型可以纠正过度分散以及空间和抽样偏差的来源。我们的文章为科学家和从业者提供了一个急需的指南,通过不断增加的方法发展的多样性,根据稀有类型和可用数据改善稀有物种分布的预测。
    Biodiversity conservation faces a methodological conundrum: Biodiversity measurement often relies on species, most of which are rare at various scales, especially prone to extinction under global change, but also the most challenging to sample and model. Predicting the distribution change of rare species using conventional species distribution models is challenging because rare species are hardly captured by most survey systems. When enough data are available, predictions are usually spatially biased towards locations where the species is most likely to occur, violating the assumptions of many modelling frameworks. Workflows to predict and eventually map rare species distributions imply important trade-offs between data quantity, quality, representativeness and model complexity that need to be considered prior to survey and analysis. Our opinion is that study designs need to carefully integrate the different steps, from species sampling to modelling, in accordance with the different types of rarity and available data in order to improve our capacity for sound assessment and prediction of rare species distribution. In this article, we summarize and comment on how different categories of species rarity lead to different types of occurrence and distribution data depending on choices made during the survey process, namely the spatial distribution of samples (where to sample) and the sampling protocol in each selected location (how to sample). We then clarify which species distribution models are suitable depending on the different types of distribution data (how to model). Among others, for most rarity forms, we highlight the insights from systematic species-targeted sampling coupled with hierarchical models that allow correcting for overdispersion and spatial and sampling sources of bias. Our article provides scientists and practitioners with a much-needed guide through the ever-increasing diversity of methodological developments to improve the prediction of rare species distribution depending on rarity type and available data.
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  • 文章类型: Journal Article
    Infection with 2019 Novel Coronavirus (2019-nCoV) is mainly transmitted by respiratory droplets, airborne transmission and direct contact. However, conducting bronchoscopy on patients with 2019-nCoV is a high-risk procedure in which health care workers are directly exposed to the virus, and the protection and operation procedures need to be strictly regulated. According to the characteristics of bronchoscopy, it is necessary to formulate the procedure, requirements and precautions when conducting bronchoscopy in the current epidemic situation. Relevant standards for preventing from infections should be strictly implemented in the operation of bronchoscopy. It needs to emphasize that bronchoscopy should not be used as a routine means for the diagnosis of 2019-nCoV infection sampling. The indications for bronchoscopy for other diseases should be strictly mastered, and it is suggested that bronchoscopy should be postponed for those patients who is not in urgent situation.
    2019新型冠状病毒(2019 novel coronavirus,2019-nCoV)感染主要通过呼吸道飞沫传播、空气传播及接触传播,结合支气管镜操作的特点,制订了当前疫情下支气管镜诊疗操作的流程、要求及注意事项。进行支气管镜诊疗操作时须严格执行传染病防控相关标准,强调支气管镜检查不作为诊断新型冠状病毒感染采样的常规手段,在按要求做好防护的基础上,严格掌握支气管镜诊疗适应证,如非病情急需,建议暂缓检查。.
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  • 文章类型: Journal Article
    Telomere length has been used as a proxy of fitness, aging and lifespan in vertebrates. In the last decade, dozens of articles reporting on telomere dynamics in the fields of ecology and evolution have been published for a wide range of taxa. With this growing interest, it is necessary to ensure the accuracy and reproducibility of telomere length measurement techniques. Real-time quantitative PCR (qPCR) is routinely applied to measure relative telomere length. However, this technique is highly sensitive to several methodological variables and the optimization of qPCR telomere assays remains highly variable between studies. Therefore, standardized guidelines are required to enable the optimization of robust protocols, and to help in judging the validity of the presented results. This review provides an overview of preanalytical and analytical factors that can lead to qPCR inconsistencies and biases, including: (a) sample type, collection and storage; (b) DNA extraction, storage and quality; (c) qPCR primers, laboratory reagents, and assay conditions; and (d) data analysis. We propose a minimum level of information for publication of qPCR telomere assays in evolutionary ecology considering the methodological pitfalls and sources of error. This review highlights the complexity of the optimization and validation of qPCR for telomere measurement per se, demonstrating the importance of transparency and clarity of reporting methodological details required for reliable, reproducible and comparable qPCR telomere assays. We encourage efforts to implement standardized protocols that ensure the rigour and quality of telomere dynamics studies.
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  • 文章类型: English Abstract
    Infection with 2019 Novel Coronavirus (2019-nCoV) is mainly transmitted by respiratory droplets, airborne transmission and direct contact. However, conducting bronchoscopy on patients with 2019-nCoV is a high-risk procedure in which health care workers are directly exposed to the virus, and the protection and operation procedures need to be strictly regulated. According to the characteristics of bronchoscopy, it is necessary to formulate the procedure, requirements and precautions when conducting bronchoscopy in the current epidemic situation. Relevant standards for preventing from infections should be strictly implemented in the operation of bronchoscopy. It needs to emphasize that bronchoscopy should not be used as a routine means for the diagnosis of 2019-nCoV infection sampling. The indications for bronchoscopy for other diseases should be strictly mastered, and it is suggested that bronchoscopy should be postponed for those patients who is not in urgent situation.
    2019新型冠状病毒(2019 novel coronavirus,2019-nCoV)感染感染主要通过呼吸道飞沫传播、空气传播及接触传播,结合支气管镜操作的特点,制订了当前疫情下支气管镜诊疗操作的流程、要求及注意事项。进行支气管镜诊疗操作时须严格执行传染病防控相关标准,强调了支气管镜检查不作为诊断新冠感染采样的常规手段,在按要求做好防护的基础上,严格掌握支气管镜诊疗适应证,如非病情急需,建议暂缓检查。.
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  • 文章类型: Journal Article
    Ovarian carcinomas represent a heterogeneous group of lesions with specific therapeutic management for each histological subtype. Thus, the correct histological diagnosis is mandatory.
    References were searched by PubMed from January 2000 to January 2018 and original articles in French and English literature were selected.
    In case of ovarian mass suspicious for cancer, a frozen section analysis may be proposed, if it could impact the surgical management. A positive histological diagnosis of ovarian carcinoma (type and grade) has to be rendered on histological (and not cytological) material before any chemotherapy with multiples and large sized biopsies. In case of needle biopsy, at least three fragments with needles>16G are needed. Histological biopsies need to be formalin-fixed (4% formaldehyde) less than 1h after resection and at least 6hours fixation is mandatory for small size biopsies. Tissue transfer to pathological labs up to 48hours under vacuum and at +4°C (in case of large surgical specimens) may be an alternative. Gross examination should include the description of all specimens and their integrity, the site of the tumor and the dimension of all specimens and nodules. Multiples sampling is needed, including the capsule, the solid areas, at least 1 to 2 blocks per cm of tumor for mucinous lesions, the Fallopian tube in toto, at least 3 blocks on grossly normal omentum and one block on the largest omental nodule. WHO classification should be used to classify the carcinoma (type and grade), with the use of a panel of immunohistochemical markers. High-grade ovarian carcinomas (serous and endometrioid) should be tested for BRCA mutation and in case of a detectable tumor mutation, the patient should be referred to an oncogenetic consultation.
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  • 文章类型: Journal Article
    用于计算基于单个动物样本的调查的样本量的公式和软件是现成的。然而,样品尺寸公式不适用于生产环境中越来越多使用的口腔液和其他聚集样品。因此,这项研究的目的是为商业猪场中基于口腔液体的猪繁殖与呼吸综合征病毒(PRRSV)调查制定采样指南.在放置断奶猪后不久,从一个生产地点的3个谷仓中的所有围栏中每周9次采样收集口腔液样品。通过实时逆转录PCR(RT-rtPCR)测试样品(n=972),并使用分段指数生存模型对二元结果进行间隔删失分析,错误分类的时间到事件数据。此后,模拟研究被用来研究PRRSV检测的谷仓级概率作为样本大小的函数,样本分配(简单随机抽样与固定空间抽样),分析诊断灵敏度和特异性,和笔级患病率。这些研究通过样本量和谷仓内患病率提供了检测概率的估计。使用固定空间采样的检测效果与,或者比,简单随机抽样。在一个站点上采样多个谷仓会随着采样谷仓的数量而增加检测概率。这些结果与牛群的PRRSV控制或消除项目有关,区域,或国家层面,但是该结果也广泛适用于猪的传染性病原体,可以对其进行同等性能的口腔液测试。
    Formulas and software for calculating sample size for surveys based on individual animal samples are readily available. However, sample size formulas are not available for oral fluids and other aggregate samples that are increasingly used in production settings. Therefore, the objective of this study was to develop sampling guidelines for oral fluid-based porcine reproductive and respiratory syndrome virus (PRRSV) surveys in commercial swine farms. Oral fluid samples were collected in 9 weekly samplings from all pens in 3 barns on one production site beginning shortly after placement of weaned pigs. Samples (n=972) were tested by real-time reverse-transcription PCR (RT-rtPCR) and the binary results analyzed using a piecewise exponential survival model for interval-censored, time-to-event data with misclassification. Thereafter, simulation studies were used to study the barn-level probability of PRRSV detection as a function of sample size, sample allocation (simple random sampling vs fixed spatial sampling), assay diagnostic sensitivity and specificity, and pen-level prevalence. These studies provided estimates of the probability of detection by sample size and within-barn prevalence. Detection using fixed spatial sampling was as good as, or better than, simple random sampling. Sampling multiple barns on a site increased the probability of detection with the number of barns sampled. These results are relevant to PRRSV control or elimination projects at the herd, regional, or national levels, but the results are also broadly applicable to contagious pathogens of swine for which oral fluid tests of equivalent performance are available.
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