Epidemiological consequences of an incursion of highly pathogenic H5N1 avian influenza into the British poultry flock

Highly pathogenic avian influenza and in particular the H5N1 strain has resulted in the culling of millions of birds and continues to pose a threat to poultry industries worldwide. The recent outbreak of H5N1 in the UK highlights the need for detailed assessment of the consequences of an incursion and of the efficacy of control strategies. Here, we present results from a model of H5N1 propagation within the British poultry industry. We find that although the majority of randomly seeded incursions do not spread beyond the initial infected premises, there is significant potential for widespread infection. The efficacy of the European Union strategy for disease control is evaluated and our simulations emphasize the pivotal role of duck farms in spreading H5N1.     

Contact structures in the poultry industry in Great Britain: Exploring transmission routes for a potential avian influenza virus epidemic

Background  

The commercial poultry industry in United Kingdom (UK) is worth an estimated ￡3.4 billion at retail value, producing over 174 million birds for consumption per year. An epidemic of any poultry disease with high mortality or which is zoonotic, such as avian influenza virus (AIV), would result in the culling of significant numbers of birds, as seen in the Netherlands in 2003 and Italy in 2000. Such an epidemic would cost the UK government millions of pounds in compensation costs, with further economic losses through reduction of international and UK consumption of British poultry. In order to better inform policy advisers and makers on the potential for a large epidemic in GB, we investigate the role that interactions amongst premises within the British commercial poultry industry could play in promoting an AIV epidemic, given an introduction of the virus in a specific part of poultry industry in Great Britain (GB).     

BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network

BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant sub-modules of regulatory networks with high confidence are reconstructed by using our extended sub-network mining algorithm of directed graphs. BNArray can handle microarray datasets with missing data. To evaluate the statistical features of generated Bayesian networks, re-sampling procedures are utilized to yield collections of candidate 1st-order network sets for mining dense coherent sub-networks. AVAILABILITY: The R package and the supplementary documentation are available at http://www.cls.zju.edu.cn/binfo/BNArray/.     

Variation in the analysis of positively selected sites using nonsynonymous/synonymous rate ratios: an example using influenza virus

Sites in a gene showing the nonsynonymous/synonymous rate ratio (ω) >1 have been frequently identified to be under positive selection. To examine the performance of such analysis, sites of the ω ratio >1 in the HA1 gene of H3N2 subtype human influenza viruses were identified from seven overlapping sequence data sets in this study. Our results showed that the sites of the ω ratio >1 were of significant variation among the data sets even though they targeted similar clusters, indicating that the analysis is likely to be either of low sensitivity or of low specificity in identifying sites under positive selection. Most (43/45) of the sites showing ω >1 calculated from at least one data set are involved in B-cell epitopes which cover less than a half sites in the protein, suggesting that the analysis is likely to be of low sensitivity rather than of low specificity. It was further found that the analysis sensitivity could not be enhanced by including more sequences or covering longer time intervals. Previously some reports also likely identified only a portion of the sites under positive selection in the viral gene using the ω ratio. Low sensitivity of the analysis may result from that some sites under positive selection in the gene are also under negative (purifying) selection simultaneously for functional constrains, and so their ω ratios could be <1. Theoretically, the sites under the two opposite selection forces at the same time favor only certain nonsynonymous changes, e.g. those changing the antigenicity of the gene and maintaining the gene function. This study also suggested that sometimes we can identify more sites under positive selection using the ω ratio by integrating the positively selected sites estimated from multiple data sets.     

Partitioning of variance in true metabolizable energy determinations: an example using wheat data

A variance statistic was used to partition the total variance into that attributable to each step of a TME_N assay procedure. Estimation of the TME_N of wheat was used as an example. The variance statistic can also be used to optimize the design of a TME_N experiment with respect to cost of the experiment and desired accuracy of the result. Experimental design optimization is accomplished by providing a functional relationship between the accuracy of the estimate and the number of replicates of feed, the number of birds used in the experiment, and the cost of each step. The variance statistic is also a useful tool for identifying and removing outliers and highly variable measurements. This feature was demonstrated with the chosen example data. Gross energy of the feed will explain approximately 50% of the variance of the TME_N estimate depending on how many replicates are evaluated. Nitrogen content of the feed sample will explain approximately 40% of the total variance. It is recommended to replicate this measurement as many times as possible. Ten replicates were recommended for the example data. The energy content of excreta from fed birds represented the next largest source of variance, at approximately 4% of the total variance, respectively. If within-bird variance is large, better homogenization of the sample and more replicates are recommended. If among-bird variance is significantly different, more birds should be used. Nitrogen content of excreta from fed birds represented less than 2.5% of the total variance. Energy and nitrogen content of excreta from unfed birds combined represented less than 2% of the total variance, suggesting that the number of unfed birds and the amount of excreta sub-samples may be reduced without adversely affecting the accuracy of the TME_N estimate. Variance due to the amount of excreta collected from the fed birds, and variance due to the amount of feed consumed by the birds, are expected to be small. This result suggested that force-feeding may not be necessary for accurate TME_N estimates.     

Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data

Understanding the evolution of gene function is a primary challenge of modern evolutionary biology. Despite an expanding database from genomic and developmental studies, we are lacking quantitative methods for analyzing the evolution of some important measures of gene function, such as gene-expression patterns. Here, we introduce phylogenetic comparative methods to compare different models of gene-expression evolution in a maximum-likelihood framework. We find that expression of duplicated genes has evolved according to a nonphylogenetic model, where closely related genes are no more likely than more distantly related genes to share common expression patterns. These results are consistent with previous studies that found rapid evolution of gene expression during the history of yeast. The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism.     

Eu-social science: the role of internet social networks in the collection of bee biodiversity data

Background

Monitoring change in species diversity, community composition and phenology is vital to assess the impacts of anthropogenic activity and natural change. However, monitoring by trained scientists is time consuming and expensive.

Methodology/Principal Findings

Using social networks, we assess whether it is possible to obtain accurate data on bee distribution across the UK from photographic records submitted by untrained members of the public, and if these data are in sufficient quantity for ecological studies. We used Flickr and Facebook as social networks and Flickr for the storage of photographs and associated data on date, time and location linked to them. Within six weeks, the number of pictures uploaded to the Flickr BeeID group exceeded 200. Geographic coverage was excellent; the distribution of photographs covered most of the British Isles, from the south coast of England to the Highlands of Scotland. However, only 59% of photographs were properly uploaded according to instructions, with vital information such as ‘tags’ or location information missing from the remainder. Nevertheless, this incorporation of information on location of photographs was much higher than general usage on Flickr (∼13%), indicating the need for dedicated projects to collect spatial ecological data. Furthermore, we found identification of bees is not possible from all photographs, especially those excluding lower abdomen detail. This suggests that giving details regarding specific anatomical features to include on photographs would be useful to maximise success.

Conclusions/Significance

The study demonstrates the power of social network sites to generate public interest in a project and details the advantages of using a group within an existing popular social network site over a traditional (specifically-designed) web-based or paper-based submission process. Some advantages include the ability to network with other individuals or groups with similar interests, and thus increasing the size of the dataset and participation in the project.     

Episodic electric discharges in the course of social interactions: an example of Asian clariid catfish

Function of weak electric discharges is conclusively proved only for two fish orders - Mormyriformes and Gymnotiformes. Every specimen of the two groups emits electric discharges continuously or quite regularly for location, orientation and communication. The function of weak episodic electric discharges in other groups of weakly electric fish - Rajiformes, Uranoscopidae and Siluriformes, remains the puzzle since Darwin. Recent experiments made it possible to expand the list of weakly electric fish with episodic discharges. The range of behavioral situations accompanied with electric emission has been expanded as well. For instance, Asian catfish, Clarias macrocephalus, emit episodic discharges while in aggressive and spawning behavior. Asian catfish females emit the special burst of electrical discharges as a part of mating ritual. This burst cannot serve as an invitation to spawning or synchronization of reproductive products release, because females emit it after the sperm ejection. If females would need males' help for eggs release, it could be suggested that discharges assist in their mutual efforts. Since the electric field strength near fish is higher than fish's non-specialized electrical sensitivity thresholds, other hypotheses are possible. For example, it could be suggested that electric fields would make sperm or eggs more active. To proceed in our conception about episodic discharges function, new hardware and software are needed.     

Data decisiveness,data quality,and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.     

Developing an index of wetland condition from ecological data: An example using HGM functional variables from the Nanticoke watershed,USA

Demand for data on the ecological condition of wetlands is increasing as state and federal management programs recognize its value in reporting on the ambient condition of the resource, targeting restoration and protection efforts, evaluating the effects of mitigation and restoration practices, supporting regulatory decisions, and tracking the impact of land use decisions. We developed an approach for generating a single measure of wetland condition from ecological variables used in hydrogeomorphic (HGM) assessment. An Index of Wetland Condition (IWC) was developed from HGM field data collected to assess freshwater, non-tidal flat, riverine, and depression wetlands in the Nanticoke River watershed. The HGM variables were screened and scored based on a range check, responsiveness, and metric redundancy, employing a method used to develop indices of biotic integrity. Weights of the individual variables were adjusted to reflect our understanding of wetland ecology and to include variables that represented the vegetation, hydrology, and buffer of a wetland. The final IWC score discriminated high, medium, and low site disturbance classes in flat and riverine wetlands and high and low disturbance classes in depressions, one-way ANOVA F-values ranged from 44.5 to 79.1 (all p <0.0001). The combination of the IWC and HGM assessments provides a comprehensive evaluation of the wetland resource. HGM produces information on specific wetland functions. The IWC concisely conveys the ecological condition of the resource and maximizes the utility of the data collected in an HGM assessment.     

“山水林田湖草生命共同体”要素关联性分析——以长白山地区为例

对“山水林田湖草生命共同体”各要素相互关系的深入理解是对其实行保护、系统治理的重要基础。本研究以长白山地区为研究对象,利用空间叠置分析法定量分析该地区“山水林田湖草生命共同体”各要素间的关联性,解构各要素的关系以及相互影响程度,并量化其依存关系。研究结果显示：研究区内各市人口数量、城镇面积与耕地面积呈显著正相关关系（人口数量：R²=0.789,P < 0.05; 城镇面积：R²=0.863,P < 0.05）;耕地的分布与地表水体的分布具有较高的空间相关性（r=0.812）,两者的数量关系也呈显著正相关（R²=0.96,P < 0.01）;区内河流分布、土壤类型与地形、地貌密切相关;区内各市水土流失面积与其森林覆盖率呈显著线性负相关关系（R²=0.824,P < 0.05）。由此可见,6个要素之间存在很明显的依存关系。因此,长白山地区“山水林田湖草生命共同体”的保护与修复应该重视各要素之间的联系,针对其系统性和整体性特征实施相应的保护和治理。     

An avian embryo culture system for embryogenesis using an artificial vessel: possible conservation benefits in the rescue and management of endangered avian species

The development of artificial means to conserve some endangered avian species seems urgently needed. We devised an eggshell‐less embryo culture system for embryogenesis using chicken or quail embryos as a model system. As a result, 41/56 (73%) chicken embryos and 52/62 (83%) quail embryos with their own thick albumen developed as usual for 72 and 55 hr, respectively, using a Teflon membrane (Milliwrap) and an egg‐shaped plastic vessel. Furthermore, this study revealed that the most suitable vessel for culture would have the same size as the intact original eggshell. This technique opens the way for the rescue of endangered avian species even if their eggshells are abnormal or cracked. This new procedure also facilitates investigation of developmental events in many unknown birds. We discuss various aspects of the embryological techniques applicable to endangered avian species. Zoo Biol 00:000–000, 2005. © 2005 Wiley‐Liss, Inc.     

Contact networks in a wild Tasmanian devil (Sarcophilus harrisii) population: using social network analysis to reveal seasonal variability in social behaviour and its implications for transmission of devil facial tumour disease

The structure of the contact network between individuals has a profound effect on the transmission of infectious disease. Using a novel technology – proximity sensing radio collars – we described the contact network in a population of Tasmanian devils. This largest surviving marsupial carnivore is threatened by a novel infectious cancer. All devils were connected in a single giant component, which would permit disease to spread throughout the network from any single infected individual. Unlike the contact networks for many human diseases, the degree distribution was not highly aggregated. Nevertheless, the empirically derived networks differed from random networks. Contact networks differed between the mating and non-mating seasons, with more extended male–female associations in the mating season and a greater frequency of female–female associations outside the mating season. Our results suggest that there is limited potential to control the disease by targeting highly connected age or sex classes.     

Comparison of CATs, CURB-65 and PMEWS as triage tools in pandemic influenza admissions to UK hospitals: case control analysis using retrospective data

Triage tools have an important role in pandemics to identify those most likely to benefit from higher levels of care. We compared Community Assessment Tools (CATs), the CURB-65 score, and the Pandemic Medical Early Warning Score (PMEWS); to predict higher levels of care (high dependency--Level 2 or intensive care--Level 3) and/or death in patients at or shortly after admission to hospital with A/H1N1 2009 pandemic influenza. This was a case-control analysis using retrospectively collected data from the FLU-CIN cohort (1040 adults, 480 children) with PCR-confirmed A/H1N1 2009 influenza. Area under receiver operator curves (AUROC), sensitivity, specificity, positive predictive values and negative predictive values were calculated. CATs best predicted Level 2/3 admissions in both adults [AUROC (95% CI): CATs 0.77 (0.73, 0.80); CURB-65 0.68 (0.64, 0.72); PMEWS 0.68 (0.64, 0.73), p<0.001] and children [AUROC: CATs 0.74 (0.68, 0.80); CURB-65 0.52 (0.46, 0.59); PMEWS 0.69 (0.62, 0.75), p<0.001]. CURB-65 and CATs were similar in predicting death in adults with both performing better than PMEWS; and CATs best predicted death in children. CATs were the best predictor of Level 2/3 care and/or death for both adults and children. CATs are potentially useful triage tools for predicting need for higher levels of care and/or mortality in patients of all ages.     

An in vitro network of intermolecular interactions between viral RNA segments of an avian H5N2 influenza A virus: comparison with a human H3N2 virus

The genome of influenza A viruses (IAV) is split into eight viral RNAs (vRNAs) that are encapsidated as viral ribonucleoproteins. The existence of a segment-specific packaging mechanism is well established, but the molecular basis of this mechanism remains to be deciphered. Selective packaging could be mediated by direct interaction between the vRNA packaging regions, but such interactions have never been demonstrated in virions. Recently, we showed that the eight vRNAs of a human H3N2 IAV form a single interaction network in vitro that involves regions of the vRNAs known to contain packaging signals in the case of H1N1 IAV strains. Here, we show that the eight vRNAs of an avian H5N2 IAV also form a single network of interactions in vitro, but, interestingly, the interactions and the regions of the vRNAs they involve differ from those described for the human H3N2 virus. We identified the vRNA sequences involved in five of these interactions at the nucleotide level, and in two cases, we validated the existence of the interaction using compensatory mutations in the interacting sequences. Electron tomography also revealed significant differences in the interactions taking place between viral ribonucleoproteins in H5N2 and H3N2 virions, despite their canonical ‘7 + 1’ arrangement.     

基于多源数据空间分析的国家公园管控分区研究——以钱江源国家公园体制试点区为例

《关于建立以国家公园为主体的自然保护地体系的指导意见》提出国家公园实行管控分区的要求,以便实现国家公园最严格保护目标。然而,国家公园管控分区评价的指标尚不明确,以浙江钱江源国家公园体制试点区（以下简称"钱江源国家公园"）为研究对象,采用层次分析法从基础环境（包括高程、植被指数、交通道路影响和基本农田）、重点野生动植物分布（野生动植物、黑麂生境适宜性和白颈长尾雉生境适宜性）、自然资源保护基础（古田山国家级自然保护区、钱江源国家森林公园、钱江源风景名胜区和生态公益林）和生态现状（生态功能适宜性评价、自然资源承载力、三区三线和土地利用现状）等指标构建多源数据空间分析指标体系,利用空间叠加分析技术获取钱江源国家公园的管控分区结果,并与管控分区最终结果进行对比分析。结果表明：（1）基于多源数据的方法能有效地识别钱江源国家公园内生态保护价值较高区域;（2）多源数据空间分析结果与最终管控分区结果对比显示,其总体精度为78.07%（197.70 km²）,在核心保护区精度为83.55%（127.99 km²）,一般控制区精度为69.67%（69.71 km²）;（3）影响精度主要原因是新调入区域基础数据不足,以及通过定性分析解决管控分区破碎化等。研究认为基于多源空间数据分析技术能够客观、高效地划分国家公园管控分区,具有一定普适性,但仍需通过增加数据数量或优化算法提高精度。     

Techniques for the objective detection of pattern in chlorophyll samples at different temporal scales: an example using data from Lough Hyne, a seasonally stratified inlet

Chlorophyll concentrations in coastal systems are frequently variable to the extent that identifying the scales where pattern occurs is very difficult. Judgements on the temporal structure of data sets are frequently rather subjective. By examining the temporal structure of chlorophyll variation in Lough Hyne with hierarchical techniques, it was possible to identify the important temporal scales objectively. Suggestions can also be made about appropriate sampling programmes for similar coastal systems. There was significant variation in measured chlorophyll concentrations between seasons and between months within seasons. High chlorophyll concentrations were more likely during spring and autumn, as would be predicted from the seasonal cycle of stratification in the lough. Seasonality could also be detected in the tidal inflow to the lough from adjacent coastal waters. More intensive sampling during the summer did not reveal any temporal structure in surface water samples. However, there were 14 day periodicities associated with measurements of depth integrated chlorophyll, oxygen, salinity, water column stability and attenuation coefficient. It is suggested that these periodicities are consistent with spring neap tidal forcing. No interannual variation in chlorophyll concentrations was detected. Examination of the power in the analysis of variance suggested that the monthly sampling frequency was unlikely to have detected differences of less than 145% between the means of pairs of years. A sampling interval of less than a week would be needed to have confidence in detecting differences of 50% between annual means.