Spatial Analysis of Hemorrhagic Fever with Renal Syndrome in Zibo City,China, 2009–2012

Background

Hemorrhagic fever with renal syndrome (HFRS) is highly endemic in mainland China, where human cases account for 90% of the total global cases. Zibo City is one of the most serious affected areas in Shandong Province China with the HFRS incidence increasing sharply from 2009 to 2012. However, the hotspots of HFRS in Zibo remained unclear. Thus, a spatial analysis was conducted with the aim to explore the spatial, spatial-temporal and seasonal patterns of HFRS in Zibo from 2009 to 2012, and to provide guidance for formulating regional prevention and control strategies.

Methods

The study was based on the reported cases of HFRS from the National Notifiable Disease Surveillance System. Annualized incidence maps and seasonal incidence maps were produced to analyze the spatial and seasonal distribution of HFRS in Zibo City. Then spatial scan statistics and space-time scan statistics were conducted to identify clusters of HFRS.

Results

There were 200 cases reported in Zibo City during the 4-year study period. One most likely cluster and one secondary cluster for high incidence of HFRS were identified by the space-time analysis. And the most likely cluster was found to exist at Yiyuan County in October to December 2012. The human infections in the fall and winter reflected a seasonal characteristic pattern of Hantaan virus (HTNV) transmission. The secondary cluster was detected at the center of Zibo in May to June 2009, presenting a seasonal characteristic of Seoul virus (SEOV) transmission.

Conclusion

To control and prevent HFRS in Zibo city, the comprehensive preventive strategy should be implemented in the southern areas of Zibo in autumn and in the northern areas of Zibo in spring.     

Local multiplicity adjustment for the spatial scan statistic using the Gumbel distribution

The spatial scan statistic is an important and widely used tool for cluster detection. It is based on the simultaneous evaluation of the statistical significance of the maximum likelihood ratio test statistic over a large collection of potential clusters. In most cluster detection problems, there is variation in the extent of local multiplicity across the study region. For example, using a fixed maximum geographic radius for clusters, urban areas typically have many overlapping potential clusters, whereas rural areas have relatively few. The spatial scan statistic does not account for local multiplicity variation. We describe a previously proposed local multiplicity adjustment based on a nested Bonferroni correction and propose a novel adjustment based on a Gumbel distribution approximation to the distribution of a local scan statistic. We compare the performance of all three statistics in terms of power and a novel unbiased cluster detection criterion. These methods are then applied to the well-known New York leukemia dataset and a Wisconsin breast cancer incidence dataset.     

Detecting genomic clustering of risk variants from sequence data: cases versus controls

As the ability to measure dense genetic markers approaches the limit of the DNA sequence itself, taking advantage of possible clustering of genetic variants in, and around, a gene would benefit genetic association analyses, and likely provide biological insights. The greatest benefit might be realized when multiple rare variants cluster in a functional region. Several statistical tests have been developed, one of which is based on the popular Kulldorff scan statistic for spatial clustering of disease. We extended another popular spatial clustering method—Tango’s statistic—to genomic sequence data. An advantage of Tango’s method is that it is rapid to compute, and when single test statistic is computed, its distribution is well approximated by a scaled χ ² distribution, making computation of p values very rapid. We compared the Type-I error rates and power of several clustering statistics, as well as the omnibus sequence kernel association test. Although our version of Tango’s statistic, which we call “Kernel Distance” statistic, took approximately half the time to compute than the Kulldorff scan statistic, it had slightly less power than the scan statistic. Our results showed that the Ionita-Laza version of Kulldorff’s scan statistic had the greatest power over a range of clustering scenarios.     

Predatory role of Neoseiulus fallacis (Acari: Phytoseiidae): spatial and temporal dynamics in Washington red raspberry fields

The seasonal abundance of spider mites and their predator Neoseiulus fallacis (Garman) (Acari: Phytoseiidae) was determined during three consecutive years in Washington State red raspberry fields. Tetranychus urticae Koch (Acari: Tetranychidae), Eotetranychus carpini borealis (Ewing) (Acari: Tetranychidae), and N. fallacis were commonly found in Skagit and Whatcom Counties. E. carpini borealis colonized the fruiting canes earlier in the season than T. urticae. The two phytophages overlapped in midseason, but T. urticae entered diapause earlier than E. carpini borealis and N. fallacis. Densities of N. fallacis increased with increase in spider mite densities. However, the numerical response of the predator was more evident for T. urticae than for E. carpini borealis. Nevertheless, the predator was spatially associated with the two prey species. The spatial and seasonal distribution of N. fallacis in relationship to host plant phenology and prey distribution may influence the effectiveness of this predator as a biological control agent against spider mites in red raspberry. Densities of the predator increased too late to prevent spider mite damage. The predatory role of N. fallacis could be enhanced by introducing or conserving predators that are more tolerant to climatic factors that prevail in and around the cane canopy in the beginning of the season.     

Seasonal change in the opportunity for sexual selection

Environmental and population parameters that influence the strength of sexual selection may vary considerably over the course of the reproductive season. However, the potential for sexual selection frequently fails to translate into variation in reproductive success among individuals. We investigated seasonal changes in variation in reproductive success, measured as the opportunity for sexual selection, using parentage analysis in 20 experimental populations of the European bitterling (Rhodeus amarus, Cyprinidae), a small freshwater fish with a promiscuous, resource-based mating system. We showed that although the largest males sired most offspring over the entire reproductive season, variation in reproductive success and hence the opportunity for sexual selection was low at the start of the season but increased significantly at its end. This seasonal difference probably arose from the superior competitive endurance of large males and from a higher temporal clustering of reproductively active females at the start of the breeding season than later in the season. The spatial distribution of oviposition sites had a negligible effect on the variation in reproductive success. We discuss the potential implications of our results for the importance and strength of sexual selection in natural populations.     

不同时间尺度喀斯特小流域溪流水文水化学特征

通过野外定位监测和室内测试分析,研究了典型喀斯特峰丛洼地小流域2013年6月—2014年3月期间溪流不同时间尺度(昼夜、次降雨、季节)主要水文水化学指标的动态变化特征及其影响因素.结果表明: 日尺度无雨条件下,溪流水化学过程表现出明显的波动规律,植物光合作用和呼吸作用在昼夜间的相互转换是导致这种变化的主要原因;次降雨尺度下,溪流水文水化学过程的日尺度效应被掩盖,水文水化学过程主要受控于前期无雨天数和降雨强度;从季节尺度看,溪流对降雨表现出较快的响应,雨季响应快于旱季,降雨季节分配差异和温度是影响溪流水文水化学变化的主要因素.     

The accumulation of mutations in asexual populations and the structure of genealogical trees in the presence of selection

We study the accumulation of unfavourable mutations in asexual populations by the process of Muller's ratchet, and the consequent inevitable decrease in fitness of the population. Simulations show that it is mutations with only moderate unfavourable effect that lead to the most rapid decrease in fitness. We measure the number of fixations as a function of time and show that the fixation rate must be equal to the ratchet rate once a steady state is reached. Large bursts of fixations are observed to occur simultaneously. We relate this to the structure of the genealogical tree. We derive equations relating the rate of the ratchet to the moments of the distribution of the number of mutations k per individual. These equations interpolate between the deterministic limit (an infinite population with selection present) and the neutral limit (a finite size population with no selection). Both these limits are exactly soluble. In the neutral case, the distribution of k is shown to be non-self-averaging, i.e. the fluctuations remain very large even for very large populations. We also consider the strong-selection limit in which only individuals in the fittest surviving class have offspring. This limit is again exactly soluble. We investigate the structure of the genealogical tree relating individuals in the same population, and consider the probability (T) that two individuals had their latest common ancestor T generations in the past. The function (T) is exactly calculable in the neutral limit and the strong-selection limit, and we obtain an empirical solution for intermediate selection strengths.     

Nitrogen storage and seasonal nitrogen cycling in Populus: bridging molecular physiology and ecophysiology

While both annual and perennial plants store nitrogen resources during the growing season, seasonal N cycling is a hallmark of the perennial habit. In Populus the vegetative storage proteins BSP, WIN4 and PNI288 all play a role in N storage during active growth, whereas BSP is the major form of reduced N storage during winter dormancy. In this review we explore cellular and molecular events implicated in seasonal N cycling in Populus, as well as environmental cues that modulate both the phenology of seasonal N cycling, and the efficiency and proficiency of autumn N resorption. We highlight recent advances that have been made using Populus genomics resources to address processes germane to seasonal N cycling. Genetic and genetological studies are enabling us to connect our understanding of seasonal N cycling at molecular and cellular levels with that at ecophysiological levels. With the genomics resources and foundational knowledge that are now in place, Populus researchers are poised to build an integrative understanding of seasonal N cycling that spans from genomes to ecosystems.     

Comparing brain networks of different size and connectivity density using graph theory

Graph theory is a valuable framework to study the organization of functional and anatomical connections in the brain. Its use for comparing network topologies, however, is not without difficulties. Graph measures may be influenced by the number of nodes (N) and the average degree (k) of the network. The explicit form of that influence depends on the type of network topology, which is usually unknown for experimental data. Direct comparisons of graph measures between empirical networks with different N and/or k can therefore yield spurious results. We list benefits and pitfalls of various approaches that intend to overcome these difficulties. We discuss the initial graph definition of unweighted graphs via fixed thresholds, average degrees or edge densities, and the use of weighted graphs. For instance, choosing a threshold to fix N and k does eliminate size and density effects but may lead to modifications of the network by enforcing (ignoring) non-significant (significant) connections. Opposed to fixing N and k, graph measures are often normalized via random surrogates but, in fact, this may even increase the sensitivity to differences in N and k for the commonly used clustering coefficient and small-world index. To avoid such a bias we tried to estimate the N,k-dependence for empirical networks, which can serve to correct for size effects, if successful. We also add a number of methods used in social sciences that build on statistics of local network structures including exponential random graph models and motif counting. We show that none of the here-investigated methods allows for a reliable and fully unbiased comparison, but some perform better than others.     

Intra-annual variations in abundance and species composition of carabid beetles in a temperate forest in Northeast China

In most habitats in temperate zones, species show clear intra-annual shifts in abundance and species composition. Here we aimed to present a comprehensive picture of community composition and seasonal dynamics of carabid beetles (Coleoptera: Carabidae) in broad-leaved Korean pine mixed forest in Northeast China, which harbors a large diversity. We sampled 23,336 individuals from 14 genera and 39 species with pitfall traps over more than 1 year in a 25-ha plot. The six most abundant species accounted for 76.65 % of all individuals. Species estimations for the 25 ha plot ranged from 40 to 45 species. Overall abundance, species diversity, community composition, and abundance of individual species varied seasonally. Most of the abundant species showed an activity pattern of single peak, and were most active between July and early September. Few species showed a bimodal seasonal activity pattern. Both temperature and precipitation significantly influenced the carabid community within a year. Hierarchical clustering indicated that carabid communities of ten consecutive sampling periods could be partitioned into three time-windows, respectively, corresponding with warm temperature-high rainfall season, warm temperature-low rainfall season, and cool and cold season. By using the extended method of indicator species analysis, 11 indicator species were identified for the three time-groups and their combinations, suggesting the existence of temporal niche partitioning among carabid species. We suggest that intra-annual patterns of carabid abundance and species composition can be explained by species responses to seasonal changes in hydrothermal conditions. Cost-effective sampling effort to assess native carabid diversity and assemblage was also discussed in this study.     

Muller''s Ratchet, Epistasis and Mutation Effects

In this study, computer simulation is used to show that despite synergistic epistasis for fitness, Muller's ratchet can lead to lethal fitness loss in a population of asexuals through the accumulation of deleterious mutations. This result contradicts previous work that indicated that epistasis will halt the ratchet. The present results show that epistasis will not halt the ratchet provided that rather than a single deleterious mutation effect, there is a distribution of deleterious mutation effects with sufficient density near zero. In addition to epistasis and mutation distribution, the ability of Muller's ratchet to lead to the extinction of an asexual population under epistasis for fitness depends strongly on the expected number of offspring that survive to reproductive age. This strong dependence is not present in the nonepistatic model and suggests that interpreting the population growth parameter as fecundity is inadequate. Because a continuous distribution of mutation effects is used in this model, an emphasis is placed on the dynamics of the mutation effect distribution rather than on the dynamics of the number of least mutation loaded individuals. This perspective suggests that current models of gene interaction are too simple to apply directly to long-term prediction for populations undergoing the ratchet.     

The sensitivity of annual grassland carbon cycling to the quantity and timing of rainfall

Global climate models predict significant changes to the rainfall regimes of the grassland biome, where C cycling is particularly sensitive to the amount and timing of precipitation. We explored the effects of both natural interannual rainfall variability and experimental rainfall additions on net C storage and loss in annual grasslands. Soil respiration and net primary productivity (NPP) were measured in treatment and control plots over four growing seasons (water years, or WYs) that varied in wet‐season length and the quantity of rainfall. In treatment plots, we increased total rainfall by 50% above ambient levels and simulated one early‐ and one late‐season storm. The early‐ and late‐season rain events significantly increased soil respiration for 2–4 weeks after wetting, while augmentation of wet‐season rainfall had no significant effect. Interannual variability in precipitation had large and significant effects on C cycling. We observed a significant positive relationship between annual rainfall and aboveground NPP across the study (P=0.01, r²=0.69). Changes in the seasonal timing of rainfall significantly affected soil respiration. Abundant rainfall late in the wet season in WY 2004, a year with average total rainfall, led to greater net ecosystem C losses due to a ～50% increase in soil respiration relative to other years. Our results suggest that C cycling in annual grasslands will be less sensitive to changes in rainfall quantity and more affected by altered seasonal timing of rainfall, with a longer or later wet season resulting in significant C losses from annual grasslands.     

Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits

Reproductive seasonality is a trait that often differs between domestic animals and their wild ancestors, with domestic animals showing prolonged or even continuous breeding seasons. However, the genetic basis underlying this trait is still poorly understood for most species, and because environmental factors and resource availability are known to play an important role in determining breeding seasons, it is also not clear in most cases to what extent this phenotypic shift is determined by the more lenient captive conditions or by genetic factors. Here, using animals resulting from an initial cross between wild and domestic rabbits followed by two consecutive backcrosses (BC1 and BC2) to wild rabbits, we evaluated the yearly distribution of births for the different generations. Similar to domestic rabbits, F1 animals could be bred all year round but BC1 and BC2 animals showed a progressive and significant reduction in the span of the breeding season, providing experimental evidence that reduced seasonal breeding in domestic rabbits has a clear genetic component and is not a simple by‐product of rearing conditions. We then took advantage of a recently published genome‐wide scan of selection in the domesticated lineage and searched for candidate genes potentially associated with this phenotypic shift. Candidate genes located within regions targeted by selection include well‐known examples of genes controlling clock functions (CRY1 and NR3C1) and reproduction (PRLR).     

Size of Precipitation Pulses Controls Nitrogen Transformation and Losses in an Arid Patagonian Ecosystem

Arid ecosystems receive precipitation pulses of different sizes that may differentially affect nitrogen (N) losses and N turnover during the growing season. We designed a rainfall manipulation experiment in the Patagonian steppe, southern Argentina, where we simulated different precipitation patterns by adding the same amount of water in evenly spaced three-small rainfall events or in one-single large rainfall event, three times during a growing season. We measured the effect of the size of rainfall pulses on N mineralization and N losses by denitrification, ammonia volatilization, and nitrate and ammonia leaching. Irrigation pulses stimulated N mineralization (P < 0.05), with small and frequent pulses showing higher responses than large pulses (P < 0.10). Irrigation effects were transient and did not result in changes in seasonal net N mineralization suggesting a long-term substrate limitation. Water pulses stimulated gaseous N losses by denitrification, with large pulses showing higher responses than small pulses (P < 0.05), but did not stimulate ammonia volatilization. Nitrate leaching also was higher after large than after small precipitation events (P < 0.05). Small events produced higher N transformations and lower N losses by denitrification and nitrate leaching than large events, which would produce higher N availability for plant growth. Climate change is expected to increase the frequency of extreme precipitation events and the proportion of large to small rainfall events. Our results suggest that these changes would result in reduced N availability and a competitive advantage for deep-rooted species that prefer nitrate over ammonia. Similarly, the ammonium:nitrate ratio might decrease because large events foster nitrate losses but not ammonium losses.     

高山林线交错带高山杜鹃的凋落物分解

凋落物分解是维持生态系统生产力、养分循环、土壤有机质形成的关键生态过程。高山林线交错带是陆地生态系统中对气候变化响应的敏感区域。季节变化和海拔梯度上的植被类型差异可能会影响该区域凋落物的分解,进而对高山生态系统的碳氮循环产生重要影响。采用凋落物分解袋的方法,研究了川西高山林线交错带优势种高山杜鹃(Rhododendron lapponicum)凋落叶在雪被期和生长季的分解特征。结果显示:(1)季节变化和植被类型对高山杜鹃凋落物的分解均具有显著影响(P0.05),凋落叶的质量损失主要发生在生长季且在高山林线最大,暗针叶林中雪被期的质量损失略高于生长季,但差异不显著;(2)林线交错带上高山杜鹃凋落叶分解缓慢,一年干物质失重率为9.62%,拟合分解系数k为0.145;(3)高山杜鹃凋落叶的质量变化主要体现在纤维素降解显著且集中在雪被期,木质素无明显降解,在高山林线上C/N、C/P、木质素/N变化幅度较小且C、N、P的释放表现得稳定而持续。结果表明,季节性雪被对林线交错带内高山杜鹃分解的影响不仅局限在雪被期内,雪被融化期间频繁的冻融作用和雪融水淋洗作用可能会促进高山杜鹃凋落物在生长季初期的分解。总的来看,在气候变暖的情景下,雪被的缩减、生长季的延长和高山杜鹃群落的扩张可能加速高山林线交错带高山杜鹃凋落物的分解。     

Seasonal variation in the nutritional value of woody plants along a natural gradient in Eastern Africa

Several hypotheses relate a negative relationship between foliar concentration of phenolic compounds and nitrogen to physiological processes such as leaf development, seasonal variation in allocation priorities, nutrient, light and water related growth limitation, as well as herbivore attack. We sampled four common deciduous woody species of central Tanzania monthly during the growing season to assess changes in this relation and their nutritional value to ruminants. We found a negative relationship between leaf N and phenolic compounds within and among species and sites that weakens during the course of the growing season that was consistent for total phenolics, but not for condensed tannins. Leaf N concentration decreased throughout the season, its withdrawal being positively related with leaf N at first sampling date. Secondary compounds concentration showed no consistent seasonal trend. Concentrations of leaf N and phenolics were correlated with ¹³C discrimination in the two shrub species and with soil P in the two tree species. Digestibility was positively correlated with foliar N and negatively correlated with secondary compounds. We conclude that phenolic compounds may serve as reliable clues for selecting foliage rich in N at site and species level only during the first months of the growing season.     

Rainfall and labile carbon availability control litter nitrogen dynamics in a tropical dry forest

N cycling in tropical dry forests is driven by rainfall seasonality but the mechanisms involved are not well understood. We studied the seasonal variation in N dynamics and microbial biomass in the surface litter of a tropical dry forest ecosystem in Mexico over a 2-year period. Litter was collected at 4 different times of the year to determine changes in total, soluble, and microbial C and N concentrations. Additionally, litter from each sampling date was incubated under laboratory conditions to determine potential C mineralization rate, net N mineralization, net C and N microbial immobilization, and net nitrification. Litter C concentrations were highest in the early-dry season and lowest in the rainy season, while the seasonal changes in N concentrations varied between years. Litter P was higher in the rainy than in the early-dry season. Water-soluble organic C (WSOC) and water-soluble N concentrations were highest during the early- and late-dry seasons and represented up to 4.1 and 5.9% of the total C and N, respectively. NH₄⁺ and NO₃⁻ showed different seasonal and annual variations. They represented an average 23% of soluble N. Microbial C was generally higher in the dry than in the wet seasons, while microbial N was lowest in the late-dry and highest in the early-rainy seasons. Incubations showed that lowest potential C mineralization rates and C and N microbial immobilization occurred in rainy season litter, and were positively correlated to WSOC. Net nitrification was highest in rainy season litter. Our results showed that the seasonal pattern in N dynamics was influenced by rainfall seasonality and labile C availability, and not by microbial biomass. We propose a conceptual model to hypothesize how N dynamics in the litter layer of the Chamela tropical dry forest respond to the seasonal variation in rainfall.     

GONe: software for estimating effective population size in species with generational overlap

GONe is a user-friendly, Windows-based program for estimating effective size (N(e) ) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N(e) is estimated at each locus and over all loci. Furthermore, N(e) estimates are output for three different genetic drift estimators (F(s) , F(c) and F(k) ). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N(e) values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/.     

Diversity and seasonal variation of ground and understory spiders from a tropical mountain cloud forest

We made intensive samplings to study the seasonal response of spiders across different forest strata (ground and understory) in a tropical mountain cloud forest from Mexico. We sampled spiders from ten plots in six sampling events during the dry and rainy season, to analyze their abundance, structure (distribution of abundance among species), diversity and the response of the five dominant species at each stratum. Results demonstrated that seasonal patterns of spider communities differed among strata, revealing a complex spatiotemporal dynamic. Abundance, structure, diversity of ground spiders, as well as the responses of four dominant species at this stratum, showed low seasonal variations. In contrast, a strong seasonal variation was observed for the understory assemblage, with lowest abundance and highest diversity in the rainy season, and different assemblage structures for each season. Seasonal patterns of each assemblage seem linked to the responses of their dominant species. We found high co‐occurrence among most of the ground dominant species with similar habitat use and with multivoltine patterns, contrasting with low co‐occurrence among most of the understory dominant species with similar habitat use and univoltine patterns. Our results showed that the spiders’ assemblages of tropical mountain cloud forest (opposed to what is found in temperate and boreal forests) increase their species richness with the height, and that their responses to seasonal change differ between strata. Management programs of these habitats should consider the spatial and temporal variations found here, as a better understanding of their ecological dynamics is required to support their sustainable management.     

季节性流感病毒 H1N1 BALB / c 鼠肺适应株的建立及其分子机制简

目的 建立季节性流感病毒H1N1的鼠肺适应株,并对适应的分子机理进行研究.方法 以病毒滴鼻感染小鼠,通过在BALB/c小鼠肺组织中连续传代,观察小鼠存活情况及肺病理改变,来获得季节性流感病毒H1N1的鼠肺适应株.结果季节性流感H1N1 A/Brisbane/59/2007病毒野生型毒株,经过在小鼠体内进行8次传代后,毒力逐渐增强,从无致病力到致死率达到100%,对鼠肺适应株与野生型毒株进行基因比对,发现适应株HA基因发生了3个有义突变.结论 野生季节性低致病力H1N1流感病毒可经在小鼠中经过多次传代而获得高致病力H1N1鼠肺适应株,HA蛋白89位Thr至Ile的突变对毒力的增强起决定性作用.