Insights Into the Latent Multinomial Model Through Mark-Resight Data on Female Grizzly Bears With Cubs-of-the-Year

Mark-resight designs for estimation of population abundance are common and attractive to researchers. However, inference from such designs is very limited when faced with sparse data, either from a low number of marked animals, a low probability of detection, or both. In the Greater Yellowstone Ecosystem, yearly mark-resight data are collected for female grizzly bears with cubs-of-the-year (FCOY), and inference suffers from both limitations. To overcome difficulties due to sparseness, we assume homogeneity in sighting probabilities over 16 years of bi-annual aerial surveys. We model counts of marked and unmarked animals as multinomial random variables, using the capture frequencies of marked animals for inference about the latent multinomial frequencies for unmarked animals. We discuss undesirable behavior of the commonly used discrete uniform prior distribution on the population size parameter and provide OpenBUGS code for fitting such models. The application provides valuable insights into subtleties of implementing Bayesian inference for latent multinomial models. We tie the discussion to our application, though the insights are broadly useful for applications of the latent multinomial model.     

空间环境诱导的红小豆高世代性状变异及选择策略

本文对空间环境诱发的雄县红小豆大粒突变后代高世代群体材料的遗传变异进行了分析 ,结果表明 :(1 )对大粒性性状进行定向选择有效 ;(2 )在对大粒性选择的同时 ,其它农艺性状也有所改善 ,并保持相当的遗传变异 ;(3 )不同群体材料其农艺性状之间的相关性也有一定的差异 ,在对百粒重、单株产量等目标性状进行间接选择时 ,应考虑被选择的群体是家系还是单株 ,不同的群体应采用相对应的策略。     

A Baseline Category Logit Model for Assessing Competing Strains of <Emphasis Type="Italic">Rhizobium</Emphasis> Bacteria

In this paper we describe novel methodology for evaluating competition among strains of Rhizobium bacteria which can be found naturally occurring in or can be introduced into soil. Rhizobia can occupy nodules on the roots of legume plants allowing the plant to ‘fix’ atmospheric nitrogen. Our model defines competitive outcomes for a community (the multinomial count of nodules occupied by each strain at the end of a time period) relative to the past state of the community (the proportion of each strain present at the beginning of the time period) and incorporates this prior information in the analysis. Our approach for assessing competition provides an analogy to multivariate methods for continuous responses in competition studies and an alternative to univariate methods for discrete responses that respects the multivariate nature of the data. It can also handle zero values in the multinomial response providing an alternative to compositional data analysis methods, which traditionally have not been able to facilitate zero values. The proposed experimental design is based on the simplex design and the model is an extension of multinomial baseline category logit models that includes multiple offsets and random terms to allow for correlation among clustered responses. Supplemental materials for this article are available from the journal website.     

Starch properties of mutant rice high in resistant starch

As the staple food of over half the world's population, hot cooked rice high in resistant starch (RS) is of particular interest, which will have greater impact in the dietary prevention of diabetes and hyperlipidemia. A mutant rice high in RS in hot cooked rice, described as RS111, was comparatively studied with the wild type and common rice. Despite obviously low RS content in the raw milled rice, the RS content in the hot cooked rice of mutant RS111 was significantly higher than that of the wild type and common rice and, correspondingly, in vitro starch hydrolysis by porcine pancreatic alpha-amylase tends to be incomplete with low hydrolysis extent for the cooked mutant rice high in RS. Obvious differences in physicochemical properties, starch granule morphology, pasting properties, thermal properties, and X-ray diffraction pattern were observed among the mutant RS111, wild type, and common indica rice. The high-RS mutant was characterized by significantly higher apparent amylose content and crude lipid content, higher percentage of oval-shaped granules and bigger oval size, reduced paste viscosity, and low onset temperature, peak temperature, final temperature, enthalpy of gelatinization, and crystallinity.     

采后果蔬损伤检测研究进展

简介了果蔬采后损伤检测的研究进展。其中视觉观察是最为简单而常用的手段,能直接了解果蔬表面损伤的情况,如挤伤、开裂等;但可靠性相对较低。由于仪器分析可减少人为误差;因而,在实验室和商业上使用常常优于感观评价,并且能为研究人员、产业部门和消费者所接收。虽然能量吸收和声音、超音振动技术可反映采后果蔬内部的损伤情况,但这两种技术仅用于对果蔬挤伤敏感性的分析。与荧光和延迟光发射的方法只适用于含叶绿素的果蔬材料相比,光谱分析可广泛用于所有的果蔬损伤的检测;但这些方法只能用于果蔬表面损伤的评价。对研究人员和产业部门来讲,最大希望能更好地了解果蔬采后处理和流通过程中内部损伤的情况。目前,X-射线分析、磁场共振图像和激光检查虽能检测果蔬内部不同的损伤程度,但由于成本高,使用范围十分有限,未能在商业上应用。同其它所有技术一样,上述技术的检测成本正迅速下降;同时检测能力迅速提高。另外,利用生理活性,如呼吸速率、乙烯释放率和渗透率检测果蔬内部损伤的技术正在研制过程中。随着仪器、设备灵敏度的提高,这些技术的应用将成为可能。由于果蔬内部损伤包括多个方面,而每一种检测方法又针对某一特定的特性进行;因此,需要采用数学分析,结合每一种测定方法,这样才能确切反映果蔬内部的损伤情况。在将来可望采用一组检测器元件,通过指纹图像了解采后果蔬内部损伤及严重情况     

水稻DNA损伤修复同源基因纯合突变系的鉴定

在长期的进化过程中,生物逐步形成了应对各种DNA损伤的修复机制,以保护基因组的完整性,减轻或消除DNA损伤的影响。本研究通过同源搜索找到了与DNA损伤修复相关水稻同源基因,在水稻插入突变体库中搜索出插入突变系,并成功引进了其中的26份T1代突变材料。通过对插入位点的分子鉴定和进一步培育,获得了14份涉及8个水稻DNA损伤修复同源基因的T3代纯合插入突变系,并对其进行了初步的遗传分析和表型考察。这些纯合突变系涉及的水稻基因可能在DNA错配修复(Os02g0592300、Os09g0407600、Os10g0509000)和碱基切除修复(Os02g0465112、Os06g0643600、Os05g0567500、Os04g0673400、Os09g0420300)中发挥重要作用。与亲本相比,除1份材料外,其他纯合突变体系及其野生型姐妹系的结实率均有显著降低;某些纯合突变系的千粒重与亲本相比有显著下降。这些水稻DNA损伤修复基因突变系的育成为开展水稻DNA修复的遗传学和分子生物学研究以及培育抗逆水稻提供了珍贵的实验材料。     

Small Area Estimation of Proportions with Constraint for National Resources Inventory Survey

Motivated by the need to produce small area estimates for the National Resources Inventory survey, we develop a spatial hierarchical model based on the generalized Dirichlet distribution to construct small area estimators of compositional proportions in several mutually exclusive and exhaustive landcover categories. At the observation level, the standard design-based estimators of the proportions are assumed to follow the generalized Dirichlet distribution. After proper transformation of the design-based estimators, beta regression is applicable. We consider a logit mixed model for the expectation of the beta distribution, which incorporates covariates through fixed effects and spatial effect through a conditionally autoregressive process. In a design-based evaluation study, the proposed model-based estimators are shown to have smaller root-mean-square error and relative root-mean-square error than design-based estimators and multinomial model-based estimators. Supplementary materials accompanying this paper appear online.     

A comparison of North American avian conservation priority ranking systems

The need to prioritize species based on their perceived endangerment has led to the development of systems for categorizing and assessing their degree of vulnerability. Systems with divergent biological and geographical scopes can result in conflicting lists of high-priority species, potentially confusing conservationists and hampering the efficient allocation of resources. To assess conservation priorities for North American birds, we compare three priority-setting systems; those of the International Union for the Conservation of Nature (IUCN), NatureServe, and Partners in Flight (PIF). We found highest correspondence among the three systems in the highest and lowest categories of the respective systems with lower levels of correspondence in intermediate categories. We suggest that this is because the systems, while using different formulations of criteria, are based on the major factors known to be correlated with extinction risk. The few examples of species listed as a high conservation priority by one group but not one or both of the others appear to be the result of differences in availability or interpretation of data. Better communication and collaboration among those responsible for compiling the priority lists for each system is needed.A primary difference among the systems was the total number of species identified as conservation priorities. IUCN identified the fewest species (47) and PIF the most (157). This difference is the result of differences in geographic and taxonomic scope of each system. However, when considered as the percent of the total number of taxa evaluated by each system, all systems identified approximately 20% of species as of conservation concern. To reconcile disparate lists, we urge that conservationists use a hierarchical approach that first considers species that meet thresholds for endangerment under global systems, followed by species considered most vulnerable relative to all continental biota.     

Atmospheric deposition and forest decline

This paper discusses the economic implications of alternative scientific explanations of observed forest decline. The various explanations can be grouped into two categories. One category posits direct damage to the forest canopy that is reversible. The other category posits indirect damage via soil quality changes that may be irreversible or slow to recover. The paper argues that the decision maker should take into account all of the explanations in designing a control strategy for acid deposition. It would be costly to wait until a single explanation has emerged victorious. If the irreversible decline explanation turns out to be correct, the forest damages will already have been sustained with no recovery possible. Assuming that the impact of acid deposition is to reduce forest productivity by 5% per annum then the annual losses to the commercial timber industry in Canada is estimated to be $197 million ( in 1981 dollars). To this an annual loss of $1.29 billion (in 1981 dollars) should be added for disruption to recreation and wildlife habitat values.     

Public Views on Family and Corporate Farms

ABSTRACT

Contemporary agricultural practices and the public's understanding of the same are not necessarily in synchrony. Beliefs about the economic contribution of agriculture, farming practices, and their impacts on the environment and community, and the motivations of farmers were explored via a mail survey of Illinois residents. Respondents were asked to consider farms by structure and describe what they perceive to be attributes or behaviors differentiating family or corporate farms. Respondents recognized the value of agriculture to the state. Overall, agriculture was ranked among the seven standard industry categories as that with the most important economic impact. However, this sector was ranked lower by residents in counties with or adjacent to population centers of a hundred thousand residents or more and by the non farm population. Although perceived distinctions between crop and livestock operations were not substantial, strong differences were perceived between corporate and family farms. Perceived factors differentiating the two farm types included ownership, operation size, business motivation, separation of management and labor, operator's concern for and participation with the local community and environment, heritage, source of labor, and locale of residence. Family farms were perceived in a much more favorable light than their corporate counterparts.     

构建县域早稻氮磷钾施肥的系统聚类方法研究

【目的】 为建立县域早稻氮磷钾施肥类别,探讨多点肥效试验资料的定量分类方法。 【方法】 以仙游县 26 个早稻“3414”设计的氮磷钾肥试验结果为例,探讨不同系统聚类分析方法的适用性及其类别间差异显著性。 【结果】 对生产条件和生产技术水平差异较小的县域肥效试验资料,以能使类别间距离空间扩展范围较大的欧氏距离–离差平方和法为最佳系统聚类分析方法,可将 26 个试验资料清晰地分成 3 类,分别对应于该县的高产、中产和低产稻田类型;两两类别间的空白区产量和平衡施肥产量均达到差异显著水平,且在 95% 置信区间下,稻谷产量水平在 3 个类别间几乎不出现交叉重叠。在此基础上,根据 3 种施肥类别对应的试验点资料,分别建立三元二次多项式类特征肥料效应方程,进而得到这 3 个施肥类别的推荐施肥量。 【结论】 欧氏距离–离差平方和法系统聚类分析是县域多点肥效试验资料的一种有效定量分类方法,可将仙游县早稻分为具有统计显著性差异的 3 个氮磷钾施肥类别。      

Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies

 Genetic interactions among bacteria are mediated by one of the three distinct gene-exchange mechanisms: conjugation, transformation or transduction. Conjugative gene exchange relies on mobile elements, such as plasmids, which transfer between donor and recipient cells. In natural transformation, competent cells take up DNA and incorporate it into their genome. Gene transfer via transduction is mediated by bacteriophages which accidentally package donor DNA in their phage head and transfer it to recipient cells. Driven mainly by biosafety research and research into the rapid dissemination of antibiotic resistance, the evaluation of gene flux among bacteria in their natural habitats has become a focus of scientific interest in recent years. Accordingly, gene transfer has been assessed in laboratory-based studies employing model ecosystems, as well as in field experiments. Conjugative gene exchange has been shown to occur under a wide range of environmental conditions. Factors identified as conducive for conjugation include the presence of nutrients provided by the rhizosphere of plants. Studies addressing gene transfer via transformation have demonstrated that naturally transformable bacteria develop competence and take up DNA under in situ conditions. Moreover, DNA has been shown to persist to some extent in the environment, and thus be available for uptake by naturally competent cells. Gene exchange via transduction has been demonstrated under conditions of nutrient depletion and low densities of host cells. Whereas gene transfer is readily observed in the laboratory, more importantly, field studies have provided direct evidence that all three gene transfer mechanisms also occur in nature. DNA transfer frequencies observed in the environment in some cases differed considerably from those obtained under laboratory conditions. Transfers of low frequency observed in laboratory-based experiments have been readily detected in the environment in the presence of selective forces. Received: 8 July 1998     

Multiple comparisons in resource selection using logistic regression

Resource selection by wildlife is often studied by observing if a particular resource category is used or not, or by observing and comparing quantitative at tributes of used and unused plots. That is, plots may be described as used or not used, as belonging to a particular resource category, and through an array of quantitative characteristics thought to be related to their use status. Of interest is the situation where different resource categories have experienced differing treatments, and one category is considered the control. A method of comparing selection of treatment categories to selection of the control is presented here when several quantitative characteristics are concurrently measured on each plot. The method is used to investigate the effect of grazing and vegetative characteristics on use of plots by pygmy rabbits.     

Sulphur in air and soil

Natural S supplies are insufficient for high crop yields. The S brought down by rain is limited, even in industrial areas, and much of it is lost in drainage. Additional supplies are needed either as fertilizers or as SO₂, which vegetation readily absorbs. The margin between the minimum SO₂ concentration for full growth and the concentration at which damage occurs is wide enough for distribution via the air, without deleterious effects, of such S as is available from the combustion of fuels.     

耐辐射球菌中priA类似基因突变对DNA修复和DNA转化的影响

DNA损伤很易阻断复制叉的前进。损伤DNA的修复以及接下来停止复制叉的重启动过程对细胞生存极为重要。依赖于PriA的复制重启动机制是细菌复制重启动的主要途径。为了解priA类似基因Dr2606在耐辐射球菌中的作用,并检测Dr2606在DNA修复中的作用,本研究用卡那霉素抗性基因代替Dr2606阅读框,构建了Dr2606缺失突变株,并对突变株进行UV和丝裂霉素处理,测定了Dr2606突变株的转化效率。Dr2606的突变导致菌体生长缓慢,细胞生存率急剧下降。意外的是,耐辐射球菌的DNA修复能力没有削弱。但突变株的转化效率大大削弱。这说明在耐辐射球菌中priA类似基因Dr2606对停止复制叉的重启动过程并不是必需的;耐辐射球菌不依赖于原点的复制重启动过程可能与其他细菌不同。     

The quest for cryptic creatures: Impacts of species-focused recreational diving on corals

Coral reefs are popular with ecotourists, but the impact of divers on reefs is cause for concern. In this study, we assessed the damage to corals caused by divers seeking cryptic but charismatic fish such as seahorses (family Syngnathidae) and frogfishes (Antennariidae), which are found on reefs around the world. These fish are closely associated with the reef substratum, thus bringing divers into close proximity to coral. We found that when in the vicinity of frogfish and seahorses, divers made unintentional contact with corals significantly more often and for longer periods than when these species were absent. This change in diver behaviour resulted in a greater frequency of coral breakage and scarring at seahorse/frogfish sites than at ecologically equivalent control sites. However, the spatial extent of damage appeared limited. Beyond 1-3 m from the seahorse or frogfish, coral breakage and scarring rate decreased to levels similar to those of control sites. None of the coral species, which suffered the most damage, was particularly rare, suggesting that the habitat conservation concern of these marked shifts in diver behaviour is limited. Nevertheless, the use of pre-dive briefings and smaller dive group sizes could minimise the damage caused by divers approaching cryptic species of interest near the reef.     

Bayesian multivariate process modeling for prediction of forest attributes

This article investigates multivariate spatial process models suitable for predicting multiple forest attributes using a multisource forest inventory approach. Such data settings involve several spatially dependent response variables arising in each location. Not only does each variable vary across space, they are likely to be correlated among themselves. Traditional approaches have attempted to model such data using simplifying assumptions, such as a common rate of decay in the spatial correlation or simplified cross-covariance structures among the response variables. Our current focus is to produce spatially explicit, tree species specific, prediction of forest biomass per hectare over a region of interest. Modeling such associations presents challenges in terms of validity of probability distributions as well as issues concerning identifiability and estimability of parameters. Our template encompasses several models with different correlation structures. These models represent different hypotheses whose tenability are assessed using formal model comparisons. We adopt a Bayesian hierarchical approach offering a sampling-based inferential framework using efficient Markov chain Monte Carlo methods for estimating model parameters.     

川中不同类型小流域土壤侵蚀特征分析

以川中小流域为研究对象,2004年第5期小流域竣工验收报告为基础数据,以流域土地利用方式面积比例为指标进行聚类,将小流域分为不同类型,然后分别建立以不同类型小流域的土壤侵蚀量为因变量,用地面积为自变量的多元线性回归方程。从而比较区域内部小流域之间的差异,分析不同类型小流域的土壤侵蚀特征,以期更有针对性地为小流域综合治理提供理论和实际依据。研究表明:（1）根据其主要土地利用方式,研究区小流域分为4类;（2）不同类型小流域,水土流失主要及最大来源、侵蚀模数等特征有显著差异。     

Adapting global biodiversity indicators to the national scale: A Red List Index for Australian birds

The Red List Index (RLI), which uses information from the IUCN Red List to track trends in the projected overall extinction risk of sets of species, is among the indicators adopted by the world’s governments to assess performance under the Convention on Biological Diversity and the United Nations Millennium Development Goals. For greatest impact, such indicators need to be measured and used at a national scale as well as globally. We present the first application of the RLI based on assessments of extinction risk at the national scale using IUCN’s recommended methods, evaluating trends in the status of Australian birds for 1990–2010. We calculated RLIs based on the number of taxa in each Red List category and the number that changed categories between assessments in 1990, 2000 and 2010 as a result of genuine improvement or deterioration in status. A novel comparison between trends at the species and ultrataxon (subspecies or monotypic species) level showed that these were remarkably similar, suggesting that current global RLI trends at the species level may also be a useful surrogate for tracking losses in genetic diversity at this scale, for which no global measures currently exist. The RLI for Australia is declining faster than global rates when migratory shorebirds and seabirds are included, but not when changes resulting from threats in Australia alone are considered. The RLI of oceanic island taxa has declined faster than those on the continent or on continental islands. There were also differences in the performance of different jurisdictions within Australia.     

我国富铝化土的分类探讨

当今国内外富铝化土的分类指标多,但系统不一.本文通过71个剖面对地带性分类、数值分类和系统分类的归类比较,得出初步结果如下:1.地带性分类、数值分类和系统分类的依据,标准不一,因此,剖面归类差异主要在土纲、土类两级.其实质是诊断特征、特性并不完全和按照热量风化的成土阶段与富铁铝化强度相吻合.2.地带性分类48个指标通过数值分析确定B层(简称B,下同)染红度(简称B_red)、粘粒SiO₂/Al₂O₃、B0.05-0.005/<0.005、B_ECEC、A层(简称A,下同)铝离子含量(简称A(Al))、AFe_o/Fe_d等六个有独立意义的分类指标.数值分类与系统分类尽管依据、方式不同,但指标的内在联系使类型归属相一致.这样,后者可从前者吸取诊断特征特性.前者可从后者提炼变量.3.当今土壤分类趋向于属性诊断定量化.地带性不明显的富铝化土更应从国内外分类指标中筛选、吸取有效分类指标,修正系统分类的已有指标,如砖红壤、砖黄壤的B_ECEC、B_CEC值偏低,71个剖面无一符合,这可能与我国季风湿润区砖红壤、砖黄壤有较多的多水高岭有关.对此,国外报道净电荷可能更适用.