Incorporating Telemetry Error into Hidden Markov Models of Animal Movement Using Multiple Imputation

When data streams are observed without error and at regular time intervals, discrete-time hidden Markov models (HMMs) have become immensely popular for the analysis of animal location and auxiliary biotelemetry data. However, measurement error and temporally irregular data are often pervasive in telemetry studies, particularly in marine systems. While relatively small amounts of missing data that are missing-completely-at-random are not typically problematic in HMMs, temporal irregularity can result in few (if any) observations aligning with the regular time steps required by HMMs. Fitting HMMs that explicitly account for uncertainty attributable to location measurement error, temporally irregular observations, or other forms of missing data typically requires computationally demanding techniques, such as Markov chain Monte Carlo (MCMC). Using simulation and a real-world bearded seal (Erignathus barbatus) example, I investigate a practical alternative to incorporating measurement error and temporally irregular observations into HMMs based on multiple imputation of the position process drawn from a single-state continuous-time movement model. This two-stage approach is relatively simple, performed with existing software using efficient maximum likelihood methods, and completely parallelizable. I generally found the approach to perform well across a broad range of simulated measurement error and irregular sampling rates, with latent states and locations reliably recovered in nearly all simulated scenarios. However, high measurement error coupled with low sampling rates often induced bias in both the estimated probability distributions of data streams derived from the imputed position process and the estimated effects of spatial covariates on state transition probabilities. Results from the two-stage analysis of the bearded seal data were similar to a more computationally intensive single-stage MCMC analysis, but the two-stage analysis required much less computation time and no custom model-fitting algorithms. I thus found the two-stage multiple-imputation approach to be promising in terms of its ease of implementation, computation time, and performance. Code for implementing the approach using the R package “momentuHMM” is provided.Supplementary materials accompanying this paper appear online.     

基于网络环境下高职院校英语教学改革的思考

作为高等教育的一个重要分支,我国高职教育突出的办学特色是培养实用型人才。在教育部提出的＂建设基于计算机和网络的大学英语教学模式＂号召下,高职院校的英语教学结合自身的办学宗旨,在教学理念、教学手段和教学方法等方面做出相应调整,以顺应时代潮流,谋求更好的发展。     

Metabolite Analysis Allows Insight into the Differences in Functionality of 25 Saccharomyces cerevisiae Strains in Bread Dough Fermentation

During dough fermentation, yeast (Saccharomyces cerevisiae) changes the physical properties of the dough matrix. In this study, we investigate if different yeast strains have an impact on dough rheology and on the gas holding capacity of fermenting dough. Furthermore, we analyze whether observed differences are linked to the metabolite profiles of the yeast strains. More specifically, the impact of 25 yeast strains on dough spread, dough fermentation properties, and dough metabolite profile was analyzed. Our results demonstrate large differences in the fermentation ability and metabolite profile of the 25 strains. Analysis of metabolites in fermented dough confirmed that acetic acid and succinic acid are likely responsible for the lowering of dough pH during fermentation and that the onset of CO₂ release from dough is related to dough pH rather than to the volume of CO₂ within the dough. Our results further suggest that the spread test is an inadequate tool to quantify rheological differences observed for strains with different fermentation profiles.     

利用"组学"技术检测转基因作物非期望效应的潜在性

检测由遗传修饰引起的非期望效应是进行转基因作物安全性评价的一项重要内容.以“实质等同性”概念为基础的评价方法,重点对转基因作物和非转基因亲本中的关键性成分进行定性、定量分析和比较难以充分考虑到一些不可预见因素的发生.“组学”技术通过对转基因作物的整个功能基因组、蛋白质组以及代谢组进行分析,将结果与非转基因亲本进行比较,完善了目前所广泛采用的以“实质等同性”概念为基础的定向方法.“组学”技术是很有潜力的.综述介绍了功能基因组学、蛋白质组学和代谢组学所用技术的原理和方法,重点讨论了这三大“组学”技术在评价转基因作物非期望效应中的应用和局限性,介绍了转基因食品食用安全性评价中非期望效应检测方面的最新进展.     

四川某滑坡成因机制分析及稳定性评价研究

所研究滑坡位于四川东部某市境内,滑坡变形分布较为零散,规律性相对较差。鉴于该滑坡紧邻市区,危害严重,对其进行了成因机制的分析及稳定性的评价研究,以期为该滑坡的防治与治理工程提供科学依据。该滑坡为一小型土质顺层古滑坡体,受下覆基岩面的控制和滑坡体西北侧开挖临空面的影响,滑坡发生沿S82°W方向的滑动,同时向临空面产生方向约为N37°W的局部次级滑动。稳定性分析结果表明,在暴雨工况下,该滑坡将沿主滑方向发生失稳。     

An Insight into Machine Learning Algorithms to Map the Occurrence of the Soil Mattic Horizon in the Northeastern Qinghai-Tibetan Plateau

Soil diagnostic horizons, which each have a set of quantified properties, play a key role in soil classification. However, they are difficult to predict, and few attempts have been made to map their spatial occurrence. We evaluated and compared four machine learning algorithms, namely, the classification and regression tree(CART), random forest(RF), boosted regression trees(BRT), and support vector machine(SVM), to map the occurrence of the soil mattic horizon in the northeastern Qinghai-Tibetan Plateau using readily available ancillary data. The mechanisms of resampling and ensemble techniques significantly improved prediction accuracies(measured based on area under the receiver operator characteristic curve score(AUC)) and produced more stable results for the BRT(AUC of 0.921 ± 0.012, mean ± standard deviation) and RF(0.908 ± 0.013) algorithms compared to the CART algorithm(0.784 ± 0.012), which is the most commonly used machine learning method. Although the SVM algorithm yielded a comparable AUC value(0.906 ± 0.006) to the RF and BRT algorithms, it is sensitive to parameter settings, which are extremely time-consuming.Therefore, we consider it inadequate for occurrence-distribution modeling. Considering the obvious advantages of high prediction accuracy, robustness to parameter settings, the ability to estimate uncertainty in prediction, and easy interpretation of predictor variables, BRT seems to be the most desirable method. These results provide an insight into the use of machine learning algorithms to map the mattic horizon and potentially other soil diagnostic horizons.     

Insight into the distribution of arabinoxylans, endoxylanases, and endoxylanase inhibitors in industrial wheat roller mill streams

To gain insight into the distribution of arabinoxylans (AX), endoxylanases, and endoxylanase inhibitors in industrial wheat roller milling, all streams, that is, 54 flour fractions, 4 bran fractions, and the germ, were analyzed for ash, starch, and protein contents, alpha-amylase activity levels, total (TOT-AX) and water-extractable arabinoxylan (WE-AX) contents, endoxylanase activity levels, and endoxylanase inhibitor (TAXI and XIP) contents. In general, bran fractions were significantly richer in TOT-AX and WE-AX contents, endoxylanase activity levels, and endoxylanase inhibitor contents than germ and, even more so, than flour fractions. In the 54 different flour fractions, minimal and maximal values for TOT-AX and WE-AX contents differed by ca. 2-fold, whereas they differed by ca. 15-fold for endoxylanase activity levels. The latter were positively correlated with ash and negatively correlated with starch content, suggesting that the endoxylanase activity in flour is strongly influenced by the level of bran contamination. TAXI contents in the flour fractions varied ca. 4-fold and were strongly correlated with bran-related parameters such as ash content and enzyme activity levels, whereas XIP contents varied ca. 3-fold and were not correlated with any of the parameters measured in this study. The results can be valuable in blending and optimizing wheat flour fractions to obtain flours with specific technological and nutritional benefits.     

Determination of Soil Aggregate Porosity Using the Modified Water Saturation Method

The need to find a simple method for measuring soil aggregate porosity(φ) is justified by the growing interest of researchers in this important parameter of soil physical status. The aim of this study was to present a simple method(AM) for estimating the totalφ of a single soil aggregate. In this case, soil aggregate φ was calculated as the quotient between the pore volume, estimated from the weight of the aggregate saturated with ethanol, and the total volume(V_T) of aggregate, calculated from the particle density and dry aggregate weight. The V_T estimated with AM was compared with the corresponding volume measured with the photogrammetry(PHM) technique using soil aggregates of 8–16 mm in diameter and collected from three different tillage systems: conventional tillage(CT), reduced tillage(RT), and no tillage(NT). Next, the AM was used to study the effects of the tillage system on soil aggregateφ. Although a strong relationship(R~2= 0.99, P 0.000 1) between aggregate V_T measured with PHM and that estimated with AM was obtained, AM tended to underestimate aggregate V_T with an average deviation of 2.85%. This difference may be due to ethanol evaporation during the first 10 s before the ethanol-saturated aggregate was weighed. The use of AM to determine the effects of different tillage systems on aggregate φ showed that this method was sensitive to detect significant differences among the tillage treatments.The results showed that AM could be an accurate, simple, and inexpensive alternative to estimate φ of a single soil aggregate.     

湖南省2008年雨雪冰冻灾害形成机理分析

2008年初,我国南方发生了近50 a来最大的冰灾,给各行各业造成了严重的影响,尤其是湖南省灾情最为惨重.因此,探讨灾情的形成机理对今后应对巨灾具有重要意义.文章从系统的角度,分析了孕灾环境、致灾因子及其衍生的灾害链以及承灾体脆弱性与应急管理系统等在雨雪冰冻灾害形成中的作用.     

植物根系对土壤团聚体形成作用机制研究回顾

土壤团聚体是土壤结构的基本单元,土壤水力侵蚀的微观描述即为土壤团聚体的破裂过程。研究表明:植物根系可以改变土壤的力学以及水文特征,促进土壤团聚体的形成和稳定。因此,对近20年国内外的相关研究成果进行较为系统的回顾,从根系对土壤团聚体的物理、生物、电化学作用3个研究视角,分析了植物根系对土壤团聚体形成的作用机制,提出了现有研究中存在的问题及研究趋势,这对深入认识植物根系对土壤团聚体的影响及其作用机制、发展根-土相互作用的土壤侵蚀过程模型具有重要的意义。     

西昌黄联土林的成因初探

西昌黄联土林位于安宁河左岸的谷坡地带，它是发育在一套冰水冻融泥石流堆积体之上的地貌景观。文中重点阐述了土林发育的自然地质背景：气候、地质构造、地形地貌、地层岩性、水文地质条件等，提出了土林是在特定的物质条件、地形地貌条件、内外动力地质条件、气候环境条件下形成的一种特殊地貌景观。具有一定规模的黄联土林拥有独特的观赏价值和一定的科学价值。     

三峡库区某滑坡体成因机制分析与稳定性评价

该滑坡地处长江左岸万州区,体积60×10⁴m³,目前滑体上存在局部拉裂,待三峡库区蓄水升高后,滑体前缘处于175m水位以下,滑体稳定性进一步下降,对坡体上的居民以及三峡库区都将造成极大危害,影响严重.在深入分析滑坡地质特征、结构特征和变形特征的基础上,对滑坡的成因机制和影响因素进行了深入研究,并结合定量计算评价其稳定性,最后提出相应治理措施.     

气候变化影响链的形成机制及其应对

目前气候变化的影响研究多集中在直接影响,间接影响考虑较少。对气候变化影响传递认识的不全面是应对气候变化的盲点之一,探讨气候变化影响链的形成机制对应对气候变化具有重要意义。本研究基于对气候变化影响特征的分析,探讨气候变化影响链的形成机制,界定了气候变化影响链的内涵,明确了气候变化的影响层级,并提出气候变化影响链的应对途径。研究表明,气候变化影响具有广泛性、差异性、持续性、突发性、传递性及可转化性等特征。气候变化及其带来的各种胁迫与干扰作用于受体系统之后,受体系统与其它系统联系,把这种胁迫与干扰传递到其它系统,导致气候变化的影响在时间上和空间上不断延伸,形成复杂的气候变化影响链。气候变化作用于直接受体后,其影响在生态系统中会沿着食物链传递,在经济系统中沿着产业链传递,在社会系统中沿着社会关系链传递;影响链的传递以物质流、能量流、信息流的形式进行。气候变化的影响总是从低层级到高层级,沿着资源禀赋的变化上升到自然生产系统、经济生产系统直至社会系统。研究认为,有效阻控或切断气候变化不利影响的传递,能够有效降低气候变化影响的风险与损失。气候变化影响链及其形成机制为全面应对气候变化提供了思路与途径。     

红壤恢复林地微团聚体形成与稳定的影响机制研究进展

微团聚体是土壤团粒结构的基本组成单元,较大团聚体具有更强的稳定性,其形成与稳定对于土壤有机碳的长期吸存起着决定性作用。目前关于微团聚体形成与稳定性的研究多专注于农业土壤,红壤侵蚀地植被恢复后土壤团聚体稳定性、有机碳分布及微生物群落特征研究也主要集中在大团聚体上,而土壤微团聚体的动态变化及其主要影响因素尚不明确,对于其内在机制更缺乏了解。通过总结土壤微团聚体的形成过程及稳定性,综述了凋落物、根系和菌根对土壤微团聚体形成与稳定的影响,阐述了土壤微团聚体内微生物群落、化学结合态有机碳及有机碳结构是土壤有机碳稳定的重要机制,并提出了未来微团聚体研究方向,以期揭示红壤侵蚀退化地森林恢复过程中微团聚体形成和稳定的生物化学机制,从而为深入阐明有机质—土壤团聚结构—微生物—化学耦合作用和森林土壤碳吸存机制提供参考。     

大渡河松坪滑坡形成机制及稳定性分析

松坪滑坡变形主要表现为滑坡后部蠕变拉裂和滑坡前缘的蠕滑,目前坡体局部已处于不稳定状态,因此对该坡体进行稳定性分析尤为重要。根据坡体的结构及形态特征详细分析了滑坡的形成机制,判定松坪滑坡的破坏模式为蠕滑拉裂。同时采用地质分析及量化评价方法对该滑坡的稳定性进行了分析。结果表明:在天然状态下稳定性良好;但在天然+暴雨的条件下,滑坡体处于不稳定状态。最后,根据以上分析提出合理的防治措施。     

Insight into the origin of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) grown in the state of Jammu and Kashmir of north-western Himalayas

Common bean (Phaseolus vulgaris L.) is considered as one of the principal grain legume crops grown in north-western Himalayan state of Jammu and Kashmir (J&K), India. Huge diversity has been observed for this crop in state Jammu and Kashmir. The hilly regions of the state J&K are famous for producing high quality, tasty and highly flavoured beans. In order to characterise this huge diversity and trace the origin of common bean, systematic efforts have been made for the first time in collection, evaluation and characterization of bean collection from Jammu & Kashmir. A set of 428 common bean lines were initially collected/procured and based on cluster analysis using few qualitative traits/site of collection, a diverse set of 96 lines was selected. The PCR assay for phaseolin locus led to the characterization of 96 lines into Meso-american and Andean types. Out of 96 lines tested, 45 possessed “S” type phaseolin and 51 possess “T” type phaseolin. The ITS region of selected local and exotic lines was Sanger sequenced and the sequence analysis of ~ 800 bp long region revealed the presence of 12 SNPs including one promising SNPs showing significant association with phaseolin patterns. The clustering based on ITS sequence data led to the clear cut separation of common bean lines into two distinct clusters based on their phaseolin types. The results of the present study helped to gain insights into the origin of common bean landraces grown in state of J&K, India.     

~7Be示踪法估算土壤侵蚀速率模型计算结果比较

在总结现有7Be示踪法估算土壤侵蚀速率模型的基础上,通过坡耕地径流小区野外模拟降雨实测侵蚀资料,比较了Walling、杨明义和Wilson等所建的利用7Be示踪法估算土壤侵蚀速率模型的计算结果,并验证各模型的准确度。结果表明,对于不发生细沟侵蚀的小区,3个模型的计算值都有较高的准确度,但Wilson模型相对其它两个模型计算结果误差较大;对于发生细沟侵蚀的小区,Walling模型和杨明义模型估算坡面细沟间侵蚀量的绝对差值较小,但大于不发生细沟侵蚀小区的绝对差值;Wilson模型能够比较准确计算坡面的总侵蚀量,与实测值相比较,相对误差为3.59%～14.47%,不发生细沟侵蚀的小区相对误差大于发生细沟侵蚀的小区。随着侵蚀强度的增大,3个模型计算结果的准确度呈降低趋势。     

Selecting the Number of States in Hidden Markov Models: Pragmatic Solutions Illustrated Using Animal Movement

We discuss the notorious problem of order selection in hidden Markov models, that is of selecting an adequate number of states, highlighting typical pitfalls and practical challenges arising when analyzing real data. Extensive simulations are used to demonstrate the reasons that render order selection particularly challenging in practice despite the conceptual simplicity of the task. In particular, we demonstrate why well-established formal procedures for model selection, such as those based on standard information criteria, tend to favor models with numbers of states that are undesirably large in situations where states shall be meaningful entities. We also offer a pragmatic step-by-step approach together with comprehensive advice for how practitioners can implement order selection. Our proposed strategy is illustrated with a real-data case study on muskox movement.Supplementary materials accompanying this paper appear online.     

文县郭家坡滑坡形成机理与稳定性研究

选择受地震影响的郭家坡滑坡作为研究对象,在滑坡孕灾背景条件调查、大比例尺平面测绘、工程地质勘查、岩土测试等基础上,对其发育特征和形成机制进行了研究,然后运用有限元模拟定量分析了滑坡现状稳定性。结果表明:地震是滑坡整体破坏的主要诱因,高陡斜坡和裂隙发育的地层是造成郭家坡滑坡发生多级滑动的内在因素,滑坡在降雨饱水工况和地震工况下局部处于不稳定状态。