基于国产微滴数字PCR的SNP快速检测技术研究

目的 在法医学领域,现有的SNP检测主要依赖进口,检测工作量大、耗时长且成本较高。微滴数字PCR (droplet digital PCR,ddPCR)作为新一代的PCR技术,可以快速检测低浓度样本DNA,且有较强的抗干扰能力。本研究旨在国产ddPCR平台建立SNP分型检测体系并对其性能进行评估,以探讨ddPCR技术在法医学检验领域的应用价值。方法 在ddPCR平台建立高原适应性EPAS1单倍型(rs115321619、rs73926263、rs73926264、rs73926265和rs55981512)检测体系,测试各位点引物探针特异性,对体系的准确性、稳定性、灵敏度、检材适应性进行评估,并比较了ddPCR和SNaPshot微测序检测体系的抗抑制性,最后对样本地区来源进行测试。结果 ddPCR在2.5 h内即可快速获取检测结果,体系准确性和稳定性好,检测灵敏度为0.312 5 ng,且抗抑制性能力突出。70份测试样本检测结果与背景信息一致。结论 基于ddPCR的SNP检测体系具有准确可靠、简便快速、抗抑制能力强等优势,在法医学快速检验领域有较强的应用潜力,适合法医现场检验需求。     

Phytoclimatic segregation of sub-Antarctic Nothofagus woodland types in Tierra del Fuego,southern South America

Background: Climatic variables determining the most suitable sites for the woodlands of Tierra del Fuego are not yet as well understood as those related to their geographical range.

Aim: The aim of this paper is to provide some insights into the relationships between climatic niche and current distribution of three Nothofagus species in Tierra del Fuego.

Methods: We have identified the climatic variables responsible for the most suitable sites for three sub-Antarctic Nothofagus woodland types within their climatic ranges by calculating suitability indices, using the CLIMPAIR niche-based phytoclimatic model.

Results: The distribution range of the major Nothofagus woodlands is mainly driven by variables related to water stress, whereas phytoclimatic suitability is mainly driven by thermal variables related to warm summer temperatures for Nothofagus betuloides and N. pumilio and to winter cold for N. antarctica that are also mainly responsible for the peculiarity of the Fueguian climate.

Conclusions: These findings introduce a new perspective in the study of the Nothofagus ecology, based on the climatic traits responsible for the high-suitability locations instead of the traditional focus on the overall geographical distribution.     

Detecting and identifying Schistosoma infections in snails and aquatic habitats: A systematic review

BackgroundWe were tasked by the World Health Organization (WHO) to address the following question: What techniques should be used to diagnose Schistosoma infections in snails and in the water in potential transmission sites? Our goal was to review and evaluate the available literature and provide recommendations and insights for the development of WHO’s Guidelines Development Group for schistosomiasis control and elimination.MethodologyWe searched several databases using strings of search terms, searched bibliographies of pertinent papers, and contacted investigators who have made contributions to this field. Our search covered from 1970 to Sept 2020. All papers were considered in a PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework, and retained papers were grouped by technique and subjected to our GRADE (Grading of Recommendations, Assessment, Development and Evaluations) evidence assessment profile determined in consultation with WHO. We also considered issues of sensitivity, specificity, coverage, cost, robustness, support needs, schistosome species discrimination, and relevant detection limits.Principal findingsOur PRISMA process began with the perusal of 949 articles, of which 158 were retained for data extraction and evaluation. We identified 25 different techniques and for each applied a GRADE assessment considering limitations, inconsistency, imprecision, indirectness, and publication bias. We also provide advantages and disadvantages for each category of techniques.ConclusionsOur GRADE analysis returned an assessment of moderate quality of evidence for environmental DNA (eDNA), qPCR and LAMP (Loop-mediated isothermal amplification). No single ideal diagnostic approach has yet been developed, but considerable recent progress has been made. We note a growing trend to use eDNA techniques to permit more efficient and replicable sampling. qPCR-based protocols for follow-up detection offer a versatile, mature, sensitive, and specific platform for diagnosis though centralized facilities will be required to favor standardization. Droplet digital PCR (ddPCR) can play a complementary role if inhibitors are a concern, or more sensitivity or quantification is needed. Snail collection, followed by shedding, is encouraged to provide specimens for sequence verifications of snails or schistosomes. LAMP or other isothermal detection techniques offer the prospect of less expensive and more distributed network of analysis but may face standardization and verification challenges related to actual sequences amplified.Ability to detect schistosome infections in snails or in the water is needed if control and elimination programs hope to succeed. Any diagnostic techniques used need to be regularly verified by the acquisition of DNA sequences to confirm that the detected targets are of the expected species. Further improvements may be necessary to identify the ideal schistosome or snail sequences to target for amplification. More field testing and standardization will be essential for long-term success.     

AI for COVID-19 Detection from Radiographs: Incisive Analysis of State of the Art Techniques,Key Challenges and Future Directions

Background and objectiveIn recent years, Artificial Intelligence has had an evident impact on the way research addresses challenges in different domains. It has proven to be a huge asset, especially in the medical field, allowing for time-efficient and reliable solutions. This research aims to spotlight the impact of deep learning and machine learning models in the detection of COVID-19 from medical images. This is achieved by conducting a review of the state-of-the-art approaches proposed by the recent works in this field.MethodsThe main focus of this study is the recent developments of classification and segmentation approaches to image-based COVID-19 detection. The study reviews 140 research papers published in different academic research databases. These papers have been screened and filtered based on specified criteria, to acquire insights prudent to image-based COVID-19 detection.ResultsThe methods discussed in this review include different types of imaging modality, predominantly X-rays and CT scans. These modalities are used for classification and segmentation tasks as well. This review seeks to categorize and discuss the different deep learning and machine learning architectures employed for these tasks, based on the imaging modality utilized. It also hints at other possible deep learning and machine learning architectures that can be proposed for better results towards COVID-19 detection. Along with that, a detailed overview of the emerging trends and breakthroughs in Artificial Intelligence-based COVID-19 detection has been discussed as well.ConclusionThis work concludes by stipulating the technical and non-technical challenges faced by researchers and illustrates the advantages of image-based COVID-19 detection with Artificial Intelligence techniques.     

Direct and plant‐mediated effects of climate on bird diversity in tropical mountains

AimAlthough patterns of biodiversity across the globe are well studied, there is still a controversial debate about the underlying mechanisms and their generality across biogeographic scales. In particular, it is unclear to what extent diversity patterns along environmental gradients are directly driven by abiotic factors, such as climate, or indirectly mediated through biotic factors, such as resource effects on consumers.LocationAndes, Southern Ecuador; Mt. Kilimanjaro, Tanzania.MethodsWe studied the diversity of fleshy‐fruited plants and avian frugivores at the taxonomic level, that is, species richness and abundance, as well as at the level of functional traits, that is, functional richness and functional dispersion. We compared two important biodiversity hotspots in mountain systems of the Neotropics and Afrotropics. We used field data of plant and bird communities, including trait measurements of 367 plant and bird species. Using structural equation modeling, we disentangled direct and indirect effects of climate and the diversity of plant communities on the diversity of bird communities.ResultsWe found significant bottom‐up effects of fruit diversity on frugivore diversity at the taxonomic level. In contrast, climate was more important for patterns of functional diversity, with plant communities being mostly related to precipitation, and bird communities being most strongly related to temperature.Main conclusionsOur results illustrate the general importance of bottom‐up mechanisms for the taxonomic diversity of consumers, suggesting the importance of active resource tracking. Our results also suggest that it might be difficult to identify signals of ecological fitting between functional plant and animal traits across biogeographic regions, since different species groups may respond to different climatic drivers. This decoupling between resource and consumer communities could increase under future climate change if plant and animal communities are consistently related to distinct climatic drivers.     

江苏常熟地区汉族人群47个微单倍型的遗传多态性及遗传结构分析

目的 探索江苏常熟地区汉族人群在47个常染色体微单倍型基因座的遗传多态性,评估应用效能及法庭科学参数。方法 采用MHSeqTyper47混合DNA鉴定试剂盒进行基因座复合扩增及文库构建,使用MiSeq FGx测序平台进行测序,测得的数据应用MHTyper数据分析软件进行分析,对获得的样本遗传信息进行评估,结合千人基因组数据（1000 Genomes Project phase 3,1KG）评估群体间遗传分化指数及遗传距离,并计算法庭科学参数。结果 江苏常熟地区汉族人群与1KG中的中国北京群体的遗传分化和遗传距离最小,并得到最接近的有效等位基因数（A_e）,累积随机匹配概率（combined matching probability,CMP）与1KG中东亚参考人群的5个群体均接近,为1.25×10^-36,累积非父排除概率达0.999 999 999 964 1。结论 本研究报告了47个微单倍型基因座在江苏常熟地区汉族人群中的等位基因频率及遗传多态性信息,为47个微单倍型在法医学应用中提供了数据基础。另外,比较了1KG参考人群与江苏常熟地区汉族人群的多态性差异,并揭示了47个微单倍型在江苏常熟地区汉族人群中的遗传结构。总的来说,1KG中的东亚人群参考数据更符合江苏常熟地区汉族人群的遗传特征。     

Mortality,Rehospitalisation and Violent Crime in Forensic Psychiatric Patients Discharged from Hospital: Rates and Risk Factors

ObjectivesTo determine rates and risk factors for adverse outcomes in patients discharged from forensic psychiatric services.MethodWe conducted a historical cohort study of all 6,520 psychiatric patients discharged from forensic psychiatric hospitals between 1973 and 2009 in Sweden. We calculated hazard ratios for mortality, rehospitalisation, and violent crime using Cox regression to investigate the effect of different psychiatric diagnoses and two comorbidities (personality or substance use disorder) on outcomes.ResultsOver mean follow-up of 15.6 years, 30% of patients died (n = 1,949) after discharge with an average age at death of 52 years. Over two-thirds were rehospitalised (n = 4,472, 69%), and 40% violently offended after discharge (n = 2,613) with a mean time to violent crime of 4.2 years. The association between psychiatric diagnosis and outcome varied—substance use disorder as a primary diagnosis was associated with highest risk of mortality and rehospitalisation, and personality disorder was linked with the highest risk of violent offending. Furthermore comorbid substance use disorder typically increased risk of adverse outcomes.ConclusionViolent offending, premature mortality and rehospitalisation are prevalent in patients discharged from forensic psychiatric hospitals. Individualised treatment plans for such patients should take into account primary and comorbid psychiatric diagnoses.     

Towards automatic insect monitoring on witloof chicory fields using sticky plate image analysis

ContextSticky trap catches of agricultural pests can be employed for early hotspot detection, identification, and estimation of pest presence in greenhouses or in the field. However, manual procedures to produce and analyze catch results require substantial time and effort. As a result, much research has gone into creating efficient techniques for remotely monitoring possible infestations. A considerable number of these studies use Artificial Intelligence (AI) to analyze the acquired data and focus on performance metrics for various model architectures. Less emphasis, however, was devoted to the testing of the trained models to investigate how well they would perform under practical, in-field conditions.ObjectiveIn this study, we showcase an automatic and reliable computational method for monitoring insects in witloof chicory fields, while shifting the focus to the challenges of compiling and using a realistic insect image dataset that contains insects with common taxonomy levels.MethodsTo achieve this, we collected, imaged, and annotated 731 sticky plates - containing 74,616 bounding boxes - to train a YOLOv5 object detection model, concentrating on two pest insects (chicory leaf-miners and wooly aphids) and their two predatory counterparts (ichneumon wasps and grass flies). To better understand the object detection model's actual field performance, it was validated in a practical manner by splitting our image data on the sticky plate level.Results and conclusionsAccording to experimental findings, the average mAP score for all dataset classes was 0.76. For both pest species and their corresponding predators, high mAP values of 0.73 and 0.86 were obtained. Additionally, the model accurately forecasted the presence of pests when presented with unseen sticky plate images from the test set.SignificanceThe findings of this research clarify the feasibility of AI-powered pest monitoring in the field for real-world applications and provide opportunities for implementing pest monitoring in witloof chicory fields with minimal human intervention.     

Comparison of dose distribution in IMRT and RapidArc technique in prostate radiotherapy

AimThe aim was to provide a dosimetric comparison between IMRT and RapidArc treatment plans with RPI index with simultaneous comparison of the treatment delivery time.BackgroundIMRT and RapidArc provide highly conformal dose distribution with good sparing of normal tissues. However, a complex spatial dosimetry of IMRT and RapidArc plans hampers the evaluation and comparison between plans calculated for the two modalities. RPI was used in this paper for treatment plan comparisons. The duration of the therapeutic session in RapidArc is reported to be shorter in comparison to therapeutic time of the other dynamic techniques. For this reasons, total treatment delivery time in both techniques was compared and discussed.Materials and methods15 patients with prostate carcinoma were randomly selected for the analysis. Two competitive treatment plans using respectively the IMRT and RapidArc techniques were computed for each patient in Eclipse planning system v. 8.6.15. RPIwin^® application was used for RPI calculations for each treatment plan.Additionally, total treatment time was compared between IMRT and RapidArc plans. Total treatment time was a sum of monitor units (MU) for each treated field.ResultsThe mean values of the RPI indices were insignificantly higher for IMRT plans in comparison to rotational therapy. Comparison of the mean numbers of monitor units confirmed that the use of rotational technique instead of conventional static field IMRT can significantly reduce the treatment time.ConclusionAnalysis presented in this paper, demonstrated that RapidArc can compete with the IMRT technique in the field of treatment plan dosimetry reducing the time required for dose delivery.     

基于深度学习的微藻自动检测系统研究

目的 微藻养殖产业规模巨大,在养殖过程中微藻易受杂菌和其他污染物的影响,因此需要定期对微藻进行检测,以确定其生长情况。现有的光学显微成像法和光谱分析法对实验人员、实验设备及场地的要求较高,无法做到实时快速检测。为了实现实时快速检测,需要一套检测要求低、速度快的实时微藻检测系统。方法 本文开发了一种基于深度学习的微藻检测系统,通过搭建一套基于明场成像的显微成像设备,使用采集的图像训练基于YOLOv3的神经网络,并将训练好的神经网络部署到微型计算机,从而实现了实时便携微藻检测。本文对特征提取网络进行改进,包括引入跨区域残差连接机制和注意力选择机制,另外还将优化器改为Adam优化器,使用多阶段多方法组合策略。结果 加载跨区域残差连接机制时最高平均精度（mAP）值为0.92。通过与人工结果进行对比,得到检测误差为2.47%。结论 该系统能够实现微藻实时便携检测,提供较为准确的检测结果,可以应用于微藻养殖中的定期检测。     

Information Gain of Psychophysiological Detection of Deception in Forensic and Screening Settings

We adapted and applied the Wells and Olson’s (2002) Information Gain Analyses to examine the relative usefulness of a common psycho-physiological deception detection (PDD) technique, the Comparison Question Test, in forensic and screening settings as compared to unassisted lay and professional persons. We found that in forensic settings PDD provided substantial improvements in information gain over unassisted laypersons across nearly the complete range of the base rate of guilt. This was true for accuracy estimates based on laboratory and field data. At p(guilt) = 0.9, a benchmark set by critics of PDD, PDD provided 27 times the information gain of credibility decisions made by unassisted lay persons. Analyses of a screening PDD indicated that only deceptive outcomes provide useful information gain at relevant low base rates of guilt. These results strongly support the use of PDD in forensic settings and have implications for how screening PDD results are used.     

Receptor Autoradiography: The Last Ten Years

Abstract

The development of techniques for the microscopic visualization of receptor binding and other binding sites using autoradiography is reviewed. The application of these techniques to a number of pharmacological problems, particularly in the field of neuropharmacology is illustrated. The limitations and future trends in the field of receptor visualization are commented upon.     

基于单分子量子相干调制的细胞温度成像技术

目的 细胞温度成像可以帮助科学家研究和理解细胞内部的温度分布,揭示细胞代谢和生物化学过程的关键信息。目前,基于荧光温度探针的细胞温度成像技术存在低温度分辨率和有限测量范围等限制。本文旨在利用单分子量子相干过程依赖温度的特性,开发一种单细胞温度成像和实时检测技术。方法 基于飞秒脉冲激光制备延时和相位可调的飞秒脉冲对,调制的脉冲对通过显微系统激发细胞内标记的荧光单分子,之后收集并记录每个荧光光子的到达时间。利用单分子相干过程与周围环境温度的关系,定义单分子量子相干可视度（V）,建立V与环境温度的对应关系。通过调制解调荧光光子的到达时间,获取单分子周围环境温度,结合扫描成像,实现细胞的温度成像和实时检测。结果 该方法可以实现高精度（温度分辨率<0.1℃）和大范围温度（10～50℃）的温度成像和测量,并观测到了单个细胞代谢相关的温度变化。结论 该研究有助于深入了解细胞代谢、蛋白质功能和疾病机制,为生物医学研究提供重要工具。     

Development of an Immunochromatographic Test for Diagnosis of Visceral Leishmaniasis Based on Detection of a Circulating Antigen

BackgroundVisceral leishmaniasis (VL) is a life-threatening disease caused by protozoan parasites of the Leishmania donovani complex. Early case detection followed by adequate treatment is essential to the control of VL. However, the available diagnostic tests are either invasive and require considerable expertise (parasitological demonstration of the parasite in tissue smears) or unable to distinguish between past and active infection (serological methods). Therefore, we aimed to develop a lateral flow assay in the form of an immunochromatographic test (ICT) device based on the detection of a circulating Leishmania antigen using monoclonal antibodies (mAbs).Conclusion/SignificanceThe newly developed ICT is an easy to use and more accurate diagnostic tool which fulfils the performance and operational characteristics required for VL case detection under field and laboratory conditions. As our ICT detects a circulating antigen, it will also be useful in monitoring treatment success and diagnosing VL in immunocompromised patients.     

Hunting and the fate of French breeding waterbirds

Capsule French breeding populations of hunted waterbirds have more negative long-term population trends than closely related non-hunted species.

Aims To assess the relative fate of breeding populations of hunted and non-hunted waterbird species in France.

Methods We compared long-term population growth rates of hunted versus non-hunted waterbirds using two large-scale and long-term national surveys.

Results Waterbirds globally displayed long-term increases in population sizes most likely driven by their positive response to the implementation of numerous protected areas over remnant wetlands across the country since the early 1970s. In contrast, hunted species revealed more negative trends compared to non-hunted species.

Conclusion A causal relationship between hunting and population dynamics is not demonstrated here, but the results are consistent with species' breeding populations being negatively affected, on average, if they are hunted.     

Assessing breeding success in common woodland birds using a novel method

Capsule Repeated counts of fledged broods can provide a useful estimate of breeding success for most common woodland birds.

Aims To assess the efficacy of comparing fledged-brood survey data with territory mapping using simple mark–recapture analysis techniques to provide an estimate of breeding success for common woodland birds that does not involve finding nests.

Methods Three observers undertook territory mapping surveys of adults, followed by counts of fledged broods four times a week during May–July 2007 in two 15 ha woods each, both in southern England. Using known fledging to maturity periods, these counts were used to calculate daily detection probabilities for broods of ubiquitous species. These enabled fledged brood territory occupancy probabilities (i.e. brood to territory ratios) to be estimated that take account of the possibility that broods were present but missed by surveys.

Results Of the 19 species found in all six woods, mean daily detection probability estimates for fledged broods of 17 species ranged from 0.17 to 0.50 with significant variation between woods for 12 species, but within region/observer for four species. The mean probability of detecting a brood at least once was over 75% using four visits per week and over 50% using two visits. Only for Great Spotted Woodpeckers Dendrocopos major and Garden Warblers Sylvia borin was the fledging period too short and the daily detection probability too low to provide a reasonable estimate of the territory occupancy probability.

Conclusion Daily detection probabilities for fledged broods of most common woodland birds were sufficiently high to enable useable estimates of fledged-brood territory occupancy probabilities to be made based on a survey programme involving two or three visits per week between late May and the end June. The method used may have application as a means of providing a relatively easily derived productivity index for woodland bird monitoring programmes or for research studies.     

Effectiveness of different accelerated partial breast irradiation techniques for the treatment of breast cancer patients: Systematic review using indirect comparisons of randomized clinical trials

AimThis systematic review was conducted to compare the effectiveness of different accelerated partial breast irradiation (APBI) techniques for the treatment of breast cancer patients.BackgroundNumerous (APBI) techniques are available for clinical practice.Methods and materialsSystematic review of randomized controlled trials of APBI versus whole breast irradiation (WBI). The data from APBI studies were extracted for the analyses. Indirect comparisons were used to compare different APBI techniques.ResultsTen studies fulfilled the inclusion criteria. A total of 4343 patients were included, most of them with tumor stage T1-T2 and N0. Regarding APBI techniques, six trials used external beam radiation therapy; one intraoperative electrons; one intraoperative low-energy photons; one brachytherapy; and one external beam radiation therapy or brachytherapy. The indirect comparisons related to 5-years local control and 5-years overall survival were not significantly different between APBI techniques.ConclusionsBased on indirect comparisons, no differences in clinical outcomes were observed among diverse APBI techniques in published clinical trials that formally compared WBI to APBI. However wide confidence intervals and high risk of inconsistency precluded a sound conclusion. Further head-to-head clinical trials comparing different APBI techniques are required to confirm our findings. Studies comparing different techniques using individual participant data and/or real-life data from population-based studies/registries could also provide more robust results.     

基于CiteSpace的全球炭疽研究演化及其热点可视化分析

最新研究估算全球约有18.3亿人生活在炭疽风险区域内。经过几十年的发展,全球炭疽研究成果数量丰硕且总量在增长。【目的】对全球炭疽研究文献进行探析,以获取其研究领域演化趋势及热点变化。【方法】基于WOS来源文献,运用科学计量方法,对1998–2018年全球炭疽研究进行可视化分析,综合运用CiteSpace可视化分析软件中文献共被引、文献突现、关键词共现等工具,探析全球炭疽研究领域演化趋势及其热点变化。【结果】全球炭疽研究可分为1998–2004年"多维暴发"、2005–2013年"持续探索"和2014–2018年"新兴热点"3个研究阶段。【结论】炭疽快速实时痕量检测和新型炭疽疫苗有可能成为未来全球炭疽研究热点。