揭示群落结构及其环境响应的联合物种分布模型的研究进展

物种分布模型通常用于基础生态和应用生态研究,用来确定影响生物分布和物种丰富度的因素,量化物种与非生物条件的关系,预测物种对土地利用和气候变化的反应,并确定潜在的保护区.在传统的物种分布模型中,生物的相互作用很少被纳入,而联合物种分布模型(JSDMs)作为近年提出的一种新的可行方法,可以同时考虑环境因素和生物交互作用,因而成为分析生物群落结构和种间相互作用过程的有力工具.JSDMs以物种分布模型(SDMs)为基础,通常采用广义线性回归模型建立物种对环境变量的多变量响应,以随机效应的形式获取物种间的关联,同时结合隐变量模型(LVMs),并基于Laplace近似和马尔科夫蒙脱卡罗模拟的最大似然估计或贝叶斯方法来估算模型参数.本文对JSDMs的产生及理论基础进行归纳总结,重点介绍了不同类型JSDMs的特点及其在现代生态学中的应用,阐述了JSDMs的应用前景、使用过程中存在的问题及发展方向.随着对环境因素与多物种种间关系研究的深入,JSDMs将是今后物种分布模型研究的重点.     

Evaluating the Predictive Value of Biomarkers with Stratified Case‐Cohort Design

Summary Identification of novel biomarkers for risk assessment is important for both effective disease prevention and optimal treatment recommendation. Discovery relies on the precious yet limited resource of stored biological samples from large prospective cohort studies. Case‐cohort sampling design provides a cost‐effective tool in the context of biomarker evaluation, especially when the clinical condition of interest is rare. Existing statistical methods focus on making efficient inference on relative hazard parameters from the Cox regression model. Drawing on recent theoretical development on the weighted likelihood for semiparametric models under two‐phase studies ( Breslow and Wellner, 2007 ), we propose statistical methods to evaluate accuracy and predictiveness of a risk prediction biomarker, with censored time‐to‐event outcome under stratified case‐cohort sampling. We consider nonparametric methods and a semiparametric method. We derive large sample properties of proposed estimators and evaluate their finite sample performance using numerical studies. We illustrate new procedures using data from Framingham Offspring Study to evaluate the accuracy of a recently developed risk score incorporating biomarker information for predicting cardiovascular disease.     

遗传修饰生物体(GMOs)生态风险的监测

遗传修饰生物体(GMOs)释放的生态学风险往往要在相当长的时期内才表现出来,因而必须对其进行长期监测。监测的内容和方法依对象的不同而有所不同。在短期和长期监测中,数学模型具有重要的作用。本文就监测的内容、原则和方法进行了全面的论述。     

Evaluation of Epstein-Barr Virus Salivary Shedding in HIV/AIDS Patients and HAART Use: A Retrospective Cohort Study

Little data is available on the evaluation of the occurrence rates of Epstein-Barr virus(EBV) in saliva and relationship with highly active antiretroviral therapy(HAART) use in HIV/AIDS patients in China. We conducted a retrospective cohort study of EBV serological tests for HIV/AIDS patients who were treated in the hospitals for infectious diseases in Wuxi and Shanghai, China from May 2016 to April 2017. The EBV-seropositive samples were identified by ELISA. EBV-specific primers and probes were used for the quantitative detection of viral DNA from saliva via quantitative real-time polymerase chain reaction. CD4 cell counts of the HIV/AIDS patients were detected by a flow cytometry. A total of 372 HIV/AIDS patients were ultimately selected and categorized for this retrospective cohort study. For EBV IgG and IgM, the HIV/AIDS HAART use(H) and non-HAART use(NH) groups had significantly higher seropositive rates than the HIV-negative control group. The HIV/AIDS(NH) group had the highest seropositive rate(IgG, 94.27%; IgM, 68.98%) and the highest incidence of EBV reactivation or infection. For salivary EBV DNA-positive rates and quantities, the HIV/AIDS(H)(73.69%) and the HIV/AIDS(NH)(100%) groups showed significantly higher values than the HIV-negative control group(35.79%,[ twofold). Further, the salivary EBV DNA-negative population had significantly higher CD4 cell counts than the EBV DNA-positive population in the HIV/AIDS(H) group and the HIV/AIDS(NH) groups. Thus, HAART use is beneficial in decreasing the EBV salivary shedding in HIV/AIDS patients and indirectly decreases EBV transmission risk.     

Methods for analysing cardiovascular studies with repeated measures

Background. Repeated measurements in a single subject are generally more similar than unrepeated measurements in different subjects. Unrepeated analyses of repeated data cause underestimation of the treatment effects. Objective. To review methods adequate for the analysis of cardiovascular studies with repeated measures. Results. (1) For between-subjects comparisons, summary measures and random-effects mixedlinear models are possible. Examples of summary measures include the area under the curve of drug time-concentration and time-efficacy curves, maximal values, mean values, and changes from baseline. A problem is that precision is lost because averages, rather than individual data, are applied. Random-effects mixed-linear models, available in SPSS statistical software and other software programmes, provide better precision for that purpose. (2) For within-subjects comparisons, repeated-measures ANOVAs are available in SPSS and other software programmes. Subgroup factors such as gender differences and age class can be included. Discussion. For non-Gaussian data, Wilcoxon's and Friedman's tests are available, for binary data McNemar's tests can be used in case of two repeated observations. No standard methods are available for repeated binary measures with more than two observations. The purpose of this review was not to present a complete report but, rather, to underline that ample efforts should be made to account for the special nature of repeated measures. (Neth Heart J 2009;17:429–33.)     

连翘醋营抗感染 、 解热作用研究

本文观察了连翘酯苷的抗感染作用及解热作用,探讨其与中药连翘清热解毒作用的关系。制备小鼠三种细菌（绿脓杆菌、大肠杆菌、金黄色葡菌球菌）感染模型,观察动物的死亡数,计算死亡率;复制酵母致大鼠发热模型与内毒素致家兔发热模型。观察不同时间动物体温的变化。结果表明连翘酯苷各剂量组均可显著降低细菌感染模型动物的死亡数和死亡率;均可显著降低发热模型动物的体温。提示连翘酯苷具有明显的抗感染和解热作用。     

Consensual predictions of potential distributional areas for invasive species: a case study of Argentine ants in the Iberian Peninsula

Invasive species are known to influence the structure and function of invaded ecological communities, and preventive measures appear to be the most efficient means of controlling these effects. However, management of biological invasions requires use of adequate tools to understand and predict invasion patterns in recently introduced areas. The present study: (1) estimates the potential geographic distribution and ecological requirements of the Argentine ant (Linepithema humile Mayr), one of the most conspicuous invasive species throughout the world, in the Iberian Peninsula using ecological niche modeling, and (2) provides new insights into the process of selection of consensual areas among predictions from several modeling methodologies. Ecological niche models were developed using 5 modeling techniques: generalized linear models (GLM), generalized additive models (GAM), generalized boosted models (GBM), Genetic Algorithm for Rule-Set Prediction (GARP), and Maximum Entropy (Maxent). Models for the eastern and western portions of the Iberian Peninsula were built using subsets of occurrence and environmental data to investigate the potential for ecological niche differences between the invading populations. Our results indicate geographic differences between predictions of different approaches, and the utility of ensemble predictions in identifying areas of uncertainty regarding the species’ invasive potential. More generally, our models predict coastal areas and major river corridors as highly suitable for Argentine ants, and indicate that western and eastern Iberian Peninsula populations occupy similar environmental conditions.

Predicting and mapping the spatial distribution of Chamaecyparis formosensis in central Taiwan in a GIS with species distribution models

Analyzing the relationship between species and environment is always a focal question of ecological research. In recent years species distribution models (SDMs) has been widely used to predict the spatial distribution of species. SDMs are numerical tools that combine observations and species occurrence or abundance with environmental variables to predict the spatial distribution of species across landscapes, sometimes requiring extrapolation in space and time. Chamaecyparis formosensis (Taiwan red cypress, TRCs) is a coniferous species endemic to Taiwan, where it natural grows in the central mountains at moderate to high altitudes of 800–2800 m, and most stands in the range of 1500–2150 m. It is threatened by habitat loss and over-cutting for its valuable timber. To preserve TRCs species and achieve sustainable use of biological resources, we choose TRCs as a target for the study to predict its distribution in central Taiwan.The pure forests of TRCs in the study area were mainly located in Pachsienshan (P), Shouchentashan (S) and Baigou Mountain (B) in central Taiwan, and the distribution data were originally obtained by The Third Survey of Forest Resources and Land Use in Taiwan. Elevation, slope, aspect, and three vegetation indices were derived from both SPOT-5 satellite images and DEM. GIS technique was used to overlay those factors. Discriminant analysis (DA), decision tree (DT) and maximum entropy (MAXENT), three commonly used SDMs, were applied based on above-mentioned six variables to predict the suitable habitat of TRCs, and to evaluate which the best model is in terms of accuracy and efficiency. Three experiment designs (ED1, ED2 and ED3) with different combinations of samples were used for model building and validation. The 200 target samples were collected from the site P–B, B–S and P–S for model building under ED1, ED2 and ED3 respectively, while the 100 samples were collected from the site S, P and B for model validation. All experiment designs had same 1350 background samples. The results showed that the overall accuracy and kappa coefficient of DT (96%, 0.88) was higher than that of MAXENT (91%, 0.70), and their accuracies were better than that of DA (84%, 0.58). All the three models were highly efficient in implementation of model construction and evaluation, while the DT model was difficult for generating the entire predicted map of potential habitat due to its complex conditional sentence. Vegetation indices derived from SPOT-5 satellite images could not improve model accuracy because of its insufficiency of spectral resolution and spatial resolution. High spatial resolution and spectral resolution remotely sensed imagery should be used in our future research to improve model performance and reliability.     

Factors affecting the metal ion-hydroxamate interactions II: effect of the length of the connecting chain on the Fe(III), Mo(VI) and V(V) complexation of some new desferrioxamine B (DFB) model dihydroxamic acids

Three new dihydroxamic acids (HO(CH₃)NCO-(CH₂)₂-CO-NH-(CH₂)_x-CON(CH₃)OH where the x values are 4; 3 and 2, and the compounds are abbreviated as 2,4-DIHA, 2,3-DIHA and 2,2-DIHA), containing the peptide group in a certain position to one of the two functional groups and in different distances to the other one, were synthesized and their complexation with Fe(III), Mo(VI) and V(V) was studied by pH-potentiometric, spectrophotometric and in some cases by CV methods to evaluate the redox behaviour of the Fe(III) complexes and assess their potential biological activity as siderophore models. All these compounds are structural models for the natural siderophore, desferrioxamine B (DFB). The results were compared to those of the complexes of 2,5-DIHA having the same connecting chain structure and length as DFB has, and the effects of the length of the connecting chain on the co-ordination mode and on the stability of the complexes formed were evaluated.Very similar stability of the mono-chelated complexes formed with all these dihydroxamic acids was found. All the results obtained suggest that one dihydroxamic acid (even the 2,2-DIHA) is able to complete the four coordination sites of a MoO₂ ²⁺ core forming simple mononuclear complexes. Favoured monomeric structures of the bis-chelated complexes of these dihydroxamic acids are also suggested with V(V) having the smallest ionic radius among the three metal ions studied. In the case of iron(III), however, clear indication was obtained for the slightly different complexation behaviour of 2,2-DIHA. Namely, the formation of the mononuclear bis-chelated complex with this shortest ligand seems to have sufficient strain to induce the formation of bimetallic species such as [Fe(2,2-DIHA)₂Fe)]²⁺.     

Potential impact of harvesting on the population dynamics of two epiphytic bromeliads

Large numbers of epiphytes are extracted from cloud forests for ornamental use and illegal trade in Latin America. We examined the potential effects of different harvesting regimes on the population dynamics of the epiphytic bromeliads Tillandsia multicaulis and Tillandsia punctulata. The population dynamics of these species were studied over a 2-year period in a tropical montane cloud forest in Veracruz, Mexico. Prospective and retrospective analyses were used to identify which demographic processes and life-cycle stages make the largest relative contribution to variation in population growth rate (λ). The effect of simulated harvesting levels on population growth rates was analysed for both species. λ of both populations was highly influenced by survival (stasis), to a lesser extent by growth, and only slightly by fecundity. Vegetative growth played a central role in the population dynamics of these organisms. The λ value of the studied populations did not differ significantly from unity: T. multicaulis λ (95% confidence interval) = 0.982 (0.897–1.060) and T. punctulata λ = 0.967 (0.815–1.051), suggesting population stability. However, numerical simulation of different levels of extraction showed that λ would drop substantially even under very low (2%) harvesting levels. Matrix analysis revealed that T. multicaulis and T. punctulata populations are likely to decline and therefore commercial harvesting would be unsustainable. Based on these findings, management recommendations are outlined.     

用列联表研究纬度和海拔高度对红杉分布的影响

 本文目的在于探讨列联表用于植物地理学研究。通过用列联表研究垂直高度与纬度对红杉(Larix potaninii)分布的影响,找出垂直高度、纬度及其交互作用等的效应,并且找出了红杉的分布中心。由于卡方检验,剩余分析,有序表连带测度,Log-线性模型拟合联合运用,Log-线性模型的运用有一些改进。本文初步证明,列联表用于植物地理学研究是可以成功的。     

A Theoretical Study of the Molecular Coupled Structures of Aristolochic Acids and Humic Acid,Potential Environmental Contaminants

An understanding of the fate of organic compounds originating from plants in soil is crucial for determining their persistence and concentrations in the environment. Aristolochic acids are believed to be the causal agents that induce Balkan endemic nephropathy by food contamination through soil adsorption of humic acids, major components of soil. Aristolochic acids are active chemicals in Aristolochia plant species found in endemic villages. In this article, molecular structure interactions between 18 structures of aristolochic acids with an inserted humic acid structure were studied. These structures were optimized in vacuo and by periodic box simulation with water solvate using the computational molecular mechanics MM+ method with HyperChem software. The QSPR models were used for correlation of the relationship between the hydrophobicity values of 18 AA structures coupled with a HA structure by MM+ and QSAR+ properties. Computational hydrophobicity values were considered dependent variables and were related to the structural features obtained by molecular and quantum mechanics calculations by multiple linear regression approaches. The obtained model was validated, and the results indicated differing hydrophobicity between the MM+ and QSAR+ properties.     

Sampling beetle communities: Trap design interacts with weather and species traits to bias capture rates

Globally, many insect populations are declining, prompting calls for action. Yet these findings have also prompted discussion about sampling methods and interpretation of long‐term datasets. As insect monitoring and research efforts increase, it is critical to quantify the effectiveness of sampling methods. This is especially true if sampling biases of different methods covary with climate, which is also changing over time. We assess the effectiveness of two types of flight intercept traps commonly used for beetles, a diverse insect group responsible for numerous ecosystem services, under different climatic conditions in Norwegian boreal forest. One of these trap designs includes a device to prevent rainwater from entering the collection vial, diluting preservatives and flushing out beetles. This design is compared to a standard trap. We ask how beetle capture rates vary between these traps, and how these differences vary based on precipitation levels and beetle body size, an important species trait. Bayesian mixed models reveal that the standard and modified traps differ in their beetle capture rates, but that the magnitude and direction of these differences change with precipitation levels and beetle body size. At low rainfall levels, standard traps catch more beetles, but as precipitation increases the catch rates of modified traps overtake those of standard traps. This effect is most pronounced for large‐bodied beetles. Sampling methods are known to differ in their effectiveness. Here, we present evidence for a less well‐known but likely common phenomenon—an interaction between climate and sampling, such that relative effectiveness of trap types for beetle sampling differs depending on precipitation levels and species traits. This highlights a challenge for long‐term monitoring programs, where both climate and insect populations are changing. Sampling methods should be sought that eliminate climate interactions, any biases should be quantified, and all insect datasets should include detailed methodological metadata.     

闽北地区四代三化螟发生动态Fuzzy预测模型研究

根据Fuzzy数学原理和三化螟生物学特性,组建了四代三化螟发生动态综合预测模型经对福建省将乐县16年四代三化螟发生期、发生量回报及1995年的预报,拟合率及正确率均达100％。     

Helix-helix transitions in DNA: fibre X-ray study of the particular cases poly(dG-dC) · poly(dG-dC) and poly(dA) · 2poly(dT)

The helix-helix transitions which occur in poly(dG-dC) · poly(dG-dC) and in poly (dG-m⁵dC) · poly(dG-m⁵dC) are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable, especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2′)-endo and C(3′)-endo sugar puckering like the “alternating B-DNA” put forward some years ago. Dihedral angles, sets of atomic coordinates and stereo views of the two S-DNA structures are given, together with curves of calculated diffracted intensities. Furthermore, we question the possibility of obtaining semicrystalline fibres with triple helices of poly(dA) · 2poly(dT) in a way which renders X-ray diffraction efficient. It is suggested that, up to now, only double helices of poly(dA) · poly(dT) can actually be observed by fibre X-ray diffraction measurements. Received: 30 March 1999 / Revised version: 30 June 1999 / Accepted: 30 June 1999     

Differential effects of abandonment on the demography of the grassland perennial Succisa pratensis

Abandonment of traditional land-use practices can have strong effects on the abundance of species occurring in agricultural landscapes. However, the precise mechanisms by which individual performance and population dynamics are affected are still poorly understood. To assess how abandonment affects population dynamics of Succisa pratensis we used data from a 4-year field study in both abandoned and traditionally grazed areas in moist and mesic habitats to parameterize integral projection models. Abandoned populations had a lower long-term stochastic population growth rate (λ _S = 0.90) than traditionally managed populations (λ _S = 1.08), while λ _S did not differ between habitat types. The effect of abandonment differed significantly between years and had opposed effects on different vital rates. Individuals in abandoned populations experienced higher mortality rates and lower seedling establishment, but had higher growth rates and produced more flower heads per plant. Population viability analyses, based on a population survey of the whole study area in combination with our demographic models, showed that 32 % of the populations face a high risk of extinction (>80 %) within 20 years. These results suggest that immediate changes in management are needed to avoid extinctions and further declines in population sizes. Stochastic elasticity analyses and stochastic life table response experiments indicated that management strategies would be most effective if they increase survival of small plants as well as seedling establishment, while maintaining a high seed production. This may be achieved by varying the grazing intensity between years or excluding grazers when plants are flowering.     

Cancer induction by restriction of oncogene expression to the stem cell compartment

In human cancers, all cancerous cells carry the oncogenic genetic lesions. However, to elucidate whether cancer is a stem cell-driven tissue, we have developed a strategy to limit oncogene expression to the stem cell compartment in a transgenic mouse setting. Here, we focus on the effects of the BCR-ABLp210 oncogene, associated with chronic myeloid leukaemia (CML) in humans. We show that CML phenotype and biology can be established in mice by restricting BCR-ABLp210 expression to stem cell antigen 1 (Sca1)⁺ cells. The course of the disease in Sca1-BCR-ABLp210 mice was not modified on STI571 treatment. However, BCR-ABLp210-induced CML is reversible through the unique elimination of the cancer stem cells (CSCs). Overall, our data show that oncogene expression in Sca1⁺ cells is all that is required to fully reprogramme it, giving rise to a full-blown, oncogene-specified tumour with all its mature cellular diversity, and that elimination of the CSCs is enough to eradicate the whole tumour.