The neglected tool in the Bayesian ecologist's shed: a case study testing informative priors' effect on model accuracy

Despite benefits for precision, ecologists rarely use informative priors. One reason that ecologists may prefer vague priors is the perception that informative priors reduce accuracy. To date, no ecological study has empirically evaluated data‐derived informative priors' effects on precision and accuracy. To determine the impacts of priors, we evaluated mortality models for tree species using data from a forest dynamics plot in Thailand. Half the models used vague priors, and the remaining half had informative priors. We found precision was greater when using informative priors, but effects on accuracy were more variable. In some cases, prior information improved accuracy, while in others, it was reduced. On average, models with informative priors were no more or less accurate than models without. Our analyses provide a detailed case study on the simultaneous effect of prior information on precision and accuracy and demonstrate that when priors are specified appropriately, they lead to greater precision without systematically reducing model accuracy.     

缺失数据和贝叶斯系统发育分析精确度之探索

The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that incomplete taxa can be accurately placed as long as the overall number of characters in the analysis is large. However, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.     

The influence of data shape acquisition process and geometric accuracy of the mandible for numerical simulation

Computer-aided technologies have allowed new 3D modelling capabilities and engineering analyses based on experimental and numerical simulation. It has enormous potential for product development, such as biomedical instrumentation and implants. However, due to the complex shapes of anatomical structures, the accuracy of these technologies plays an important key role for adequate and accurate finite element analysis (FEA).

The objective of this study was to determine the influence of the geometry variability between two digital models of a human model of the mandible. Two different shape acquisition techniques, CT scan and 3D laser scan, were assessed. A total of 130 points were controlled and the deviations between the measured points of the physical and 3D virtual models were assessed.

The results of the FEA study showed a relative difference of 20% for the maximum displacement and 10% for the maximum strain between the two geometries.     

Multiomics data reveals the influences of myasthenia gravis on thymoma and its precision treatment

Thymoma is a rare characterized by a unique association with autoimmune diseases, especially myasthenia gravis (MG). However, little is known about the molecular characteristics of MG‐associated thymoma individuals. We aim to examine the influences of MG on thymoma by analyzing multiomics data. A total of 105 samples with thymoma was analyzed from TCGA and these samples were divided into subgroups with MG (MGT) or without MG (MGF) according to clinical information. We then characterized the differential gene expression, pathway activity, somatic mutation frequency, and likelihood of responding to chemotherapies and immunotherapies of the two identified subgroups. MGT subgroup was characterized by elevated inflammatory responses and metabolically related pathways, whereas the MGF subgroup was predicted to be more sensitive to chemotherapy and presented with mesenchymal characteristics. More copy number amplifications and deletions were observed in MGT, whereas GTF2I mutations occur at significantly higher frequencies in MGF. Two molecular subtypes were further identified within MGF samples by unsupervised clustering where one subtype was enriched in TGF‐β and WNT pathways with higher sensitivity to relevant targeted drugs but hardly respond to immunotherapy. For another subtype, a higher recurrence rate of thymoma and more likelihood of responding to immunotherapy were observed. Our findings presented a comprehensive molecular characterization of thymoma patients given the status of MG, and provided potential strategies to help individualized management and treatment.     

An approach to integrated data assessment in a proficiency test on the enumeration of Escherichia coli

Aims: To develop appropriate statistical approaches to plan and evaluate proficiency tests for the enumeration of Escherichia coli, addressing, in particular, a possible but frequently unavoidable lack of test sample homogeneity. Methods and Results: Each of 50 laboratories analysed two samples of a stabilized suspension of E. coli in duplicate, using various media, inoculation methods, and incubation times and conditions. In parallel, the E. coli suspension was tested by the organiser for homogeneity and stability. Escherichia coli counts followed a log‐normal distribution. After eliminating, by Youden analysis, two data sets that were considered outliers and eight data sets for underperformance of the laboratories (substantial lack of repeatability), the standard deviation of the mean was about 0·06 log₁₀ units. There was no evidence of bimodality of the data. Lack of homogeneity of distribution of bacteria had a strong effect on measurement uncertainty, in addition to laboratory bias and method repeatability. The homogeneity decreases during storage of the individual test vials; this effect could be modelled by the known kinetics of inactivation of micro‐organisms. The results were confirmed by Monte Carlo simulations. Conclusions: By a tailored analysis of proficiency testing data, it is possible to distinguish the effect of lack of homogeneity, laboratory bias and method repeatability, on the measurement uncertainty. Significance and Impact of the Study: A statistic tool is provided to solve problems related to lack of stability of microbiological test material and to separate the effects of sample inhomogeneity from the performance of the individual laboratory.     

Use of two formulations and two application techniques to deliver Bacillus thuringiensis var. israelensis for the control of Musca domestica (Diptera: Muscidae) larvae and adults in poultry houses

A field study was carried out for 6 wks to assess, from both an efficiency and economic perspective, the effect of individual and integrated success of feeding and topical applications of two formulations of Bacillus thuringiensis var. israelensis (Bti) in controlling house fly (Musca domestica L.) larvae and adults in poultry houses. There was no significant difference between the 1 g and 2 g L^?1 spray applications of Bti. In the absence of spray applications, no significant differences in larval mortalities were observed between the 250 mg and 500 mg kg^?1 feed applications. The percentage mortality of larvae accomplished as a result of using a combination of 250 mg kg^?1Bti feed and 2 g L^?1 spray applications was equivalent to that obtained as a result of combining 500 mg kg^?1Bti and 1g L^?1 spray applications. Treatment with Bti caused significant reductions in the emergence (up to 74%) of house fly adults compared to the control. The fact that the emergence of adult house flies was affected by Bti treatments implies that Bti has sublethal effects on house fly larvae. The cost–benefit analysis (expressed in terms of mortality of larvae growing) indicated that the most effective combination for house fly larvae and adult house fly emergence control was the 500 mg kg^?1 of feed and 2 g L^?1 spray application combination that resulted in 67% larval mortality and a 74% decrease in adult house fly emergence. This study presents commercial users with various alternatives for possible combinations of the two Bti formulations.     

A method to assess the effects of pesticides on the predatory mite Phytoseiulus persimilis (Acari Phytoseiidae) in the laboratory

Phytoseiulus persimilis Athias-Henriot (Acari Phytoseiidae) is a major predator of Tetranychus urticae (Acari Tetranychidae). The performance of P. persimilis in controlling T. urticae may be altered by pesticides used to manage other pests. Therefore, knowledge of the side-effects of pesticides is essential for IPM. A number of laboratory methods were suggested to evaluate pesticide side-effects on predatory mites. Most methods assess residual effects only, and a number of them are characterised by high predator escape rates from experimental units. A method aimed at evaluating the topical and residual effects of pesticides on P. persimilis is herein described. Mites were treated by microimmersion and then reared in holding cells, on bean leaves previously dipped in a pesticide solution. Three insecticides (pyrethrins, spinosad and thiamethoxam), an insecticide-acaricide (abamectin), and two fungicides (azoxystrobin and tolylfluanide) were evaluated. The strain of P. persimilis used for evaluation was collected from unsprayed vegetable plants. All the pesticides affected the survival and fecundity of P. persimilis. Pesticides did not affect the egg-hatching of P. persimilis females exposed to pesticides. Pyrethrins and abamectin proved to be more toxic than other pesticides, and thiamethoxam was more toxic than spinosad, azoxystrobin and tolylfluanide. The escape rate from experimental units was lower than 5% in all trials. Additional experiments were performed on P. persimilis eggs by dipping leaves with eggs in the pesticide solution. None of the pesticides affected egg survival. Semi-field trials conducted on potted bean plants obtained results similar to those reported in laboratory trials.     

GMO生物安全评价研究进展

讨论了GMO生物安全评价的主要内容、常用的检测方法和近年来国内外有关生物安全问题的研究进展。本文还介绍了我国生物安全管理的现状、法律法规和运行机制,并就我国今后如何加强生物安全管理提出了相应的对策。     

Physical Limits on the Precision of Mitotic Spindle Positioning by Microtubule Pushing forces

Tissues are shaped and patterned by mechanical and chemical processes. A key mechanical process is the positioning of the mitotic spindle, which determines the size and location of the daughter cells within the tissue. Recent force and position‐fluctuation measurements indicate that pushing forces, mediated by the polymerization of astral microtubules against­ the cell cortex, maintain the mitotic spindle at the cell center in Caenorhabditis elegans embryos. The magnitude of the centering forces suggests that the physical limit on the accuracy and precision of this centering mechanism is determined by the number of pushing microtubules rather than by thermally driven fluctuations. In cells that divide asymmetrically, anti‐centering, pulling forces generated by cortically located dyneins, in conjunction with microtubule depolymerization, oppose the pushing forces to drive spindle displacements away from the center. Thus, a balance of centering pushing forces and anti‐centering pulling forces localize the mitotic spindles within dividing C. elegans cells.     

The effects of environmental heterogeneity on root growth and root/shoot partitioning

AIMS: The purpose of this Botanical Briefing is to stimulate reappraisal of root growth, root/shoot partitioning, and analysis of other aspects of plant growth under heterogeneous conditions. SCOPE: Until recently, most knowledge of plant growth was based upon experimental studies carried out under homogeneous conditions. Natural environments are heterogeneous at scales relevant to plants and in forms to which they can respond. Responses to environmental heterogeneity are often localized rather than plant-wide, and not always predictable from traditional optimization arguments or from knowledge of the ontogenetic trends of plants growing under homogeneous conditions. These responses can have substantial impacts, both locally and plant-wide, on patterns of resource allocation, and significant effects on whole-plant growth. Results from recent studies are presented to illustrate responses of plants, plant populations and plant communities to nutritionally heterogeneous conditions. CONCLUSIONS: Environmental heterogeneity is a constant presence in the natural world that significantly influences plant behaviour at a variety of levels of complexity. Failure to understand its effects on plants prevents us from fully exploiting aspects of plant behaviour that are only revealed under patchy conditions. More effort should be invested into analysis of the behaviour of plants under heterogeneous conditions.     

基于性信息素诱捕的广东草地贪夜蛾发生动态及多生物防治因子组合对其控制效果评价

采用性信息素诱捕器对广东省佛山市、茂名市、韶关市和梅州市的草地贪夜蛾Spodoptera frugiperda发生动态进行监测;以清水作为空白对照,以20%氯虫苯甲酰胺为药剂对照,评价了螟黄赤眼蜂Trichogramma chilonis、螟黄赤眼蜂+苏云金杆菌、螟黄赤眼蜂+金龟子绿僵菌、螟黄赤眼蜂+莱氏绿僵菌、螟黄赤眼蜂+爪哇棒束孢菌、螟黄赤眼蜂+甘蓝夜蛾核型多角体病毒、螟黄赤眼蜂+蠋蝽、螟黄赤眼蜂+蠋蝽+甘蓝夜蛾核型多角体病毒这8种生防措施对玉米田草地贪夜蛾的防控效果。结果表明,草地贪夜蛾在所监测的4个地市全年均有发生,其中佛山监测点的草地贪夜蛾诱捕量高于其它3个监测点,并具有1个明显的发生高峰期（2019年10月中旬至11月中旬）,高峰期与玉米种植面积呈正相关。田间生防试验结果表明,单一释放螟黄赤眼蜂或与其他生防因子联合使用均对草地贪夜蛾有一定的控制作用,处理7 d后的防虫效果为54.87%~76.49%,其中以螟黄赤眼蜂+甘蓝夜蛾核型多角体病毒及螟黄赤眼蜂+蠋蝽+甘蓝夜蛾核型多角体病毒的防治效果最好,防效分别为76.49%及71.56%,但均低于氯虫苯甲酰胺的防虫效果（94.60%）;但14 d后,20%氯虫苯甲酰胺的防虫效果下降至78.51%,而螟黄赤眼蜂+甘蓝夜蛾核型多角体病毒及螟黄赤眼蜂+蠋蝽+甘蓝夜蛾核型多角体病毒的防效呈上升趋势,防效分别为81.31%与83.35%,具有较好的持续性与稳定性,是防治玉米草地贪夜蛾的理想生物防治组合。研究结果为了解广东草地贪夜蛾的发生规律及综合防控提供了相关科学依据与技术支撑。     

几种药剂及施药方式对稻纵卷叶螟的防治效果

对稻纵卷叶螟Cnaphalocrocis medinalis Guen e高龄幼虫防治药剂31%氟虫腈.三唑磷ME和当地几种常用药剂及不同施药方法对防治效果影响进行试验。结果表明:(1)毒死蜱(48%乐斯本EC)有较好速效性,药后1 d可达理想防效,三唑磷与氟出腈、氟铃脲复配的药剂(31%氟虫腈.三唑磷ME、21%氟虫腈.三唑磷EC、15%氟铃脲.三唑磷EC)药后3d才能达到理想防效;(2)药后3d,各处理均达到理想防效,防效依次为31%氟虫腈.三唑磷ME1.5L/hm2>31%氟虫腈.三唑磷ME1.05L/hm2>21%氟虫腈.三唑磷EC1.5L/hm2>48%毒死蜱EC1.5L/hm2>15%氟虫腈.三唑磷EC1.5L/hm2>15%阿维菌素.毒死蜱EC1.5L/hm2;(3)分虫龄防效统计,药后3d供试药剂对1龄以下(施药时虫龄,后同)幼虫防效均在91%以上,对2~3龄幼虫,31%氟虫腈.三唑磷ME保持90%以上的防效,其它处理防效明显下降,对4龄以上高龄幼虫,31%氟虫腈.三唑磷1.5L/hm2细喷雾处理防效仍达95.6%,其它处理防效很低。(4)细喷雾可提高31%氟虫腈.三唑磷ME对稻纵卷叶螟的防治效果,尤其是对高龄幼虫,与工农16型1.8mm孔径喷片的常规喷雾相比,1.2mm孔径喷片细喷雾处理药后3 d防效提高5.5%,东方红18型弥雾处理防效提高7.8%,其中,弥雾处理对1~2龄幼虫防效提高4.7%,对4~5龄幼虫防效提高了20.8%。     

The algae-lytic ability of bacterium DC10 and the influence of environmental factors on the ability

Nowadays, eutrophication and massive accumula-tions of microalgae have caused serious environmental problems. So it is very important to find an effective method for controlling the growth of the algae and the algal blooms. Measures for controlling the algae in-clude physical, chemical and biological means. Physi-cal means are limited and usually act as an assistant for controlling the algae, and include mechanical means, high frequent electromagnetic pulses and ul-trasonic processes[1]. Algae…     

基于ChIP-seq的差异组蛋白修饰区域的筛选

组蛋白修饰是在基因组水平上起到重要调控作用的表观遗传修饰,随着ChIP-Seq的广泛使用,高通量数据的积累,为从全基因组研究组蛋白修饰模式奠定了基础。但目前缺乏在多样本间筛选疾病相关的调控区域的方法,因而本文开发了一种多细胞系的差异筛选算法来识别差异组蛋白修饰区域。本文通过窗口移动法来估计组蛋白修饰水平,并根据信息熵理论定量各个细胞系之间的差异。基于随机背景来确定差异显著性阈值。利用此算法来筛选人类全基因组9个细胞系间H3K4me3差异的区域,结果显示这些区域显著富集在基因启动子上和其他重要的染色质状态上,且与先前人们发现的活性启动子染色质状态显著重叠。通过文献挖掘进一步证实了与白血病相关的基因组标记。这些结果表明基于熵的策略可有效地挖掘多细胞系间以及与疾病相关的差异组蛋白修饰。     

Effect of sex,dietary glycerol or dietary fat during late fattening,on fatty acid composition and positional distribution of fatty acids within the triglyceride in pigs

The effect of sex, source of saturated fat (lard v. palm oil) and glycerol inclusion in the fattening diet on composition and fatty acid positional distribution in the triglyceride molecule was studied in pigs from 78 to 110 kg BW. Average daily gain and carcass characteristics, including ham and loin weight, were not affected by dietary treatment but sex affected backfat depth (P<0.01). A significant interaction between sex and glycerol inclusion was observed; dietary glycerol increased lean content in gilts but not in barrows (P<0.05 for the interaction). Individual and total saturated fatty acid (SFA) concentrations were greater in barrows than in gilts. In contrast, the concentration of total polyunsaturated fatty acids (PUFA) and of C18:2n-6, C18:3n-3, C20:3n-9 and C20:4n-6 in the intramuscular fat (IMF) was higher (P<0.05) in gilts than in barrows. Sex did not affect total monounsaturated fatty acids (MUFA) concentration in the IMF. The proportion of SFA in the subcutaneous fat (SF) was higher in barrows than in gilts (P<0.001). Within the individual SFA, sex affected only the concentrations of C14:0 and C16:0 (P<0.001). Dietary fat did not affect total SFA or PUFA concentrations of the IMF but the subcutaneous total MUFA concentration tended to be higher (P=0.079) in pigs fed lard than in pigs fed palm oil. Dietary glycerol increased total MUFA and C18:1n-9 concentration in the IMF and increased total MUFA and decreased C18:2n-6, C18:3n-3 and total PUFA concentrations in the SF. The data indicate that altering the fatty acid composition of the triglyceride molecule at the 2-position, by dietary intervention during the fattening phase, is very limited.     

杨树粒肩天牛幼虫林间化学防治试验

选用3种化学药剂应用不同的施药方法对杨树粒肩天牛幼虫进行林间药效试验,结果表明,采用虫道注射与毒签两种施药方法林间防治粒肩天牛幼虫都具有良好的防治效果,15d后防治效果达71.44～97.54%,可在生产中推广应用。     

基于多模态生态治理数据构建生态管理知识图谱技术

我国新时代十年是生态环境保护认识最深、力度最大、举措最实、推进最快、成效最显著的十年。生态环境治理取得成效的同时,管理措施也逐步成熟和规范化,相关生态管理知识成果的文本、视频、照片等多模态数据也日益丰厚。采用先进的知识图谱理念创新我国生态环境保护工作,对未来助力打赢污染防治攻坚战,构建现代环境治理体系具有重要意义。聚焦我国美丽中国和生态文明建设工程领域,将典型污染防治攻坚战、生态恢复工程多模态素材作为数据源,通过数据整合、知识抽取、知识融合后形成标准知识表述,构建生态管理知识图谱体系。具体包括(1)定量分析深圳市"散乱污"企业整治成功案例数据,抽取管理主体、管理对象等实体,挖掘其空间特征、污染特征、治理效果关系;(2)关联分析企业驻点、污染物热点和城市空间相互关系;(3)通过我国典型生态环境损害赔偿案件中的"实施行为-破坏对象-损害功能"特定关系分析,抽取"生态治理行为--受影响环境要素--生态服务提升程度"生态环境管理知识图谱;(4)最终形成了整合"散乱污"治理、生态环境治理行为的综合性生态管理知识图谱,构建了包含12类本体、82个实体,4类、201条关系的图数据库。研究表明,通过污染防治攻坚战成功案例、生态恢复工程成效的多模态数据构建我国生态管理知识图谱,能够形成贴近现实需求的知识体系,有助于依法治污、科学治污和精准治污全过程;也有助于生态环境损害鉴定评估工作中的"多因一果"和"一因多果"分析。建议未来加大生态管理知识图谱的应用,精准识别管理对象、实现科学分析与智能决策,促进公众参与生态管理和加快生态产品价值实现。     

Bias in the effect of habitat structure on pitfall traps: An experimental evaluation

Habitat structure has been implicated as a source of bias for pitfall-trap data but most evidence is observational or anecdotal. This study used an experimental approach to quantify biases due to habitat structure. In a randomized block design, I manipulated native grassland to create three types of habitat structure and measured pitfall-trap catches of grassland ants. Small patches of modified habitat were surrounded by otherwise unmodified grassland with the assumption that population density remained unaffected by the modification and that the effects observed were due to changes in trappability. I assessed magnitude, direction, predictability, and consistency of bias for the following types of data: population abundance for single species, relative abundance among species, species composition of assemblages, and species richness. The magnitude of the bias in population abundance was large for most species. However, since the direction of the bias varied predictably with habitat structure, pitfall-trap data can be used to judge differences in population abundance in some situations. The magnitude of the bias in relative abundance was less than for abundance. However, there was inconsistency in the direction and magnitude of bias among species. Thus, interpretation of relative abundance data in pitfall-trap studies may be compromised. Species richness and species composition were biased by habitat structure but were affected significantly only when the groundcover was very dense, suggesting a threshold effect of habitat structure. To help to interpret survey data, pitfall-trap studies should routinely measure attributes of habitat structure and incorporate an experimental component to characterize the bias.