A new microtitration method for the enumeration of contagious bovine pleuropneumonia (CBPP) vaccines.

A new method is proposed for the microtitration of CBPP vaccines by performing eight parallel endpoint two-fold dilutions. When performed on a 96-well plate, it gives a titre with a precision of +/- 0.2 log10. By comparison, the established method, performed in tubes, gives a precision of only +/- 0.6 log10. The adaptation to microtitre plates allows much more economical culture of larger numbers of samples. Statistical analysis permits determination of vial-to-vial homogeneity of a batch and calculation of a titre with a precision of +/- 0.09 log10. The new method may be applied for the titration of mycoplasmas.     

A lateral flow protein microarray for rapid determination of contagious bovine pleuropneumonia status in bovine serum

Novel analytical methods for a next generation of diagnostic devices combine attributes from sensitive, accurate, fast, simple and multiplexed analysis methods. Here, we describe a possible contribution to these by the application of a lateral flow microarray where a panel of recombinant protein antigens was used to differentiate bovine serum samples in the context of the lung disease contagious bovine pleuropneumonia (CBPP). Lateral flow arrays were produced by attaching nitrocellulose onto microscopic slides and spotting of the recombinant proteins onto the membranes. The developed assay included evaluations of substrate matrix and detection reagents to allow for short assay times and convenient read-out options, and to yield a total assay time from sample application to data acquisition of less than ten minutes. It was found that healthy and disease-affected animals could be discriminated (AUC = 97%), and we suggest that the use of an antigen panel in combination with the lateral flow device offers an emerging analytical tool towards a simplified but accurate on-site diagnosis.     

Projected population persistence of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) using a stage-structured life-history model and population viability analysis

The population of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) in the Blue River, Indiana has undergone a dramatic decline over the last decade. Recruitment in these declining populations has been negligible, and populations are now composed almost entirely of older age classes (upwards of 20 years old). Given this dramatic decline, it is imperative to assess the impacts of these demographic patterns on population growth and long-term stability. Therefore, we developed a stage-structured, life-history model to examine the effects of varying levels of egg, juvenile, and adult survivorship on abundance, recruitment, and long-term population projections. We performed a sensitivity analysis of the model and determine which life-history parameters have the greatest potential to increase/stabilise hellbender population growth. Finally, we conducted a population viability analysis to determine the probability of extinction associated with varying management strategies. For eastern hellbender populations in Indiana, adults (especially females) are the most important component of long-term population viability. Sensitivity and elasticity analyses of the Lefkovitch matrix revealed that survival of adult and egg/larvae life-history stages are the most important for focused management efforts. Indeed, adults had the highest elasticity and reproductive value in the matrix model. Increasing survival by as little as 20% corresponded to the turning point at which the population ceased to decline and increased abundance (28% survival of egg/larvae). The importance of the transition from subadult to adult (transitional matrix element) was identified as an additional factor in maintaining abundance based on the relatively long period spent in this life-history stage (seven years for females). A population viability analysis was conducted to assess the likelihood and projected time frame of extinction for this population under no management (～25 years to complete extirpation; probability of extinction = 1) and if management efforts such as captive rearing and headstarting are undertaken (probability of extinction <0.2 at 25–30% survival of egg/larvae). Adult females had the greatest effect in reducing growth rate and population abundance when removed in exploitation simulations (91.3% versus 51.8% reduction in population growth rate), indicating translocation efforts should be designed to maintain females in the breeding pool. These models indicated that conservation management strategies aimed at ensuring the presence of adult females while concomitantly ameliorating survival at early life stages (population augmentation, translocations, introduction of artificial nest structures) are needed to stabilise the Indiana population of eastern hellbenders. This stage-structured model is the first to model eastern hellbenders and has broad implications for use across the geographic range where populations of eastern hellbenders are monitored and vital rates can be estimated.     

A two-part joint model for the analysis of survival and longitudinal binary data with excess zeros

Summary .   Many longitudinal studies generate both the time to some event of interest and repeated measures data. This article is motivated by a study on patients with a renal allograft, in which interest lies in the association between longitudinal proteinuria (a dichotomous variable) measurements and the time to renal graft failure. An interesting feature of the sample at hand is that nearly half of the patients were never tested positive for proteinuria (≥1g/day) during follow-up, which introduces a degenerate part in the random-effects density for the longitudinal process. In this article we propose a two-part shared parameter model framework that effectively takes this feature into account, and we investigate sensitivity to the various dependence structures used to describe the association between the longitudinal measurements of proteinuria and the time to renal graft failure.     

Habitat persistence for sedentary organisms in managed rivers: the case for the federally endangered dwarf wedgemussel (Alasmidonta heterodon) in the Delaware River

1. To manage the environmental flow requirements of sedentary taxa, such as mussels and aquatic insects with fixed retreats, we need a measure of habitat availability over a variety of flows (i.e. a measure of persistent habitat). Habitat suitability measures in current environmental flow assessments are measured on a ‘flow by flow’ basis and thus are not appropriate for these taxa. Here, we present a novel measure of persistent habitat suitability for the dwarf wedgemussel (Alasmidonta heterodon), listed as federally endangered in the U.S.A., in three reaches of the Delaware River. 2. We used a two‐dimensional hydrodynamic model to quantify suitable habitat over a range of flows based on modelled depth, velocity, Froude number, shear velocity and shear stress at three scales (individual mussel, mussel bed and reach). Baseline potentially persistent habitat was quantified as the sum of pixels that met all thresholds identified for these variables for flows ≥40 m³ s^?1, and we calculated the loss of persistently suitable habitat by sequentially summing suitable habitat estimates at lower flows. We estimated the proportion of mussel beds exposed at each flow and the amount of change in the size of the mussel bed for one reach. 3. For two reaches, mussel beds occupied areas with lower velocity, shear velocity, shear stress and Froude number than the reach average at all flows. In the third reach, this was true only at higher flows. Together, these results indicate that beds were possible refuge areas from the effects of these hydrological parameters. Two reaches showed an increase in the amount of exposed mussel beds with decreasing flow. 4. Baseline potentially persistent habitat was less than half the areal extent of potentially suitable habitat, and it decreased with decreasing flow. Actually identified beds and modelled persistent habitat showed good spatial overlap, but identified beds occupied only a portion of the total modelled persistent habitat, indicating either that additional suitable habitat is available or the need to improve habitat criteria. At one site, persistent beds (beds where mussels were routinely collected) were located at sites with stable substratum, whereas marginal beds (beds where mussels were infrequently collected or that were lost following a large flood event) were located in scoured areas. 5. Taken together, these model results support a multifaceted approach, which incorporates the effects of low and high flow stressors, to quantify habitat suitability for mussels and other sedentary taxa. Models of persistent habitat can provide a more holistic environmental flow assessment of rivers.     

Input data needed for a risk model for the entry,establishment and spread of a pathogen (Phomopsis vaccinii) of blueberries and cranberries in the EU

International trade in live plant materials has increased worldwide over the last four decades. This has led to a dramatic increase in the introduction, establishment and spread of non‐native plant pathogens. Regulatory authorities need advice on measures that may mitigate these adverse consequences of trade. Risk models may be used to underpin such advice. In this review, we give a systematic overview of the data needed for a quantitative risk model for Phomopsis vaccinii, which causes stem and fruit infections on Vaccinium species, and sometimes death, potentially also on native wild Vaccinium species in the EU. P. vaccinii is a quarantine organism worldwide, except for North America, where it is endemic. Despite extensive knowledge of the aetiology of the diseases caused by this pathogen and its taxonomy, quantitative data on transportation and detection of infected plants for planting and berries are scarce, and quantitative assessment of the future introduction, establishment and spread of P. vaccinii is difficult. Estimation of the potential impact of this pathogen in production fields and wild Vaccinium stands is even more difficult. P. vaccinii is not unique in this respect, and this review indicates the need for more and better quantitative data for assessment of the risks posed by newly introduced plant pathogens in areas where they are not endemic.     

A model of Taura syndrome virus (TSV) epidemics in Litopenaeus vannamei

Taura syndrome virus (TSV) is a highly virulent pathogen of Litopenaeus vannamei, has affected shrimp aquaculture throughout the world, and threatens wild populations. Despite its importance, little work has been done on the pathogen's formal epidemiology. Therefore we developed a compartment model for epidemics of TSV in closed populations of L. vannamei. The model includes five compartments, uninfected susceptible, prepatently infected, acutely infected, chronically infected, and dead infected shrimp. The transmission coefficients, patency coefficient, virulence coefficients, and removal coefficient (disappearance of dead infected shrimp) control the dynamics of the model. We estimated the coefficients in laboratory studies and inserted the estimates in the model to characterize TSV epidemics and to estimate the basic reproduction ratio R(0) and threshold density for TSV epidemics in L. vannamei. Further we examined through computer simulation the effect of varying the coefficients on R(0). Decreases in transmission decrease R(0), decreases in virulence increase R(0), increases in patency do not affect R(0), and increases in recovery most likely increase R(0) but under some conditions might decrease it.     

Key issues for the development and application of the species sensitivity distribution (SSD) model for ecological risk assessment

The species sensitivity distribution (SSD) model is one of the most commonly used methods for ecological risk assessment based on the potentially affected fraction (PAF) of and the combined PAF (msPAF) as quantitative indicators. There are usually four steps for the development of SSD models and their applications: (1) obtain the toxicity data of the pollutants; (2) fit the SSD curves; (3) calculate the potentially affected fractions (PAFs) of the individual pollutants for the ecological risk assessment of an individual pollutant; and (4) calculate the accumulated multi-substance potentially affected fractions (msPAFs) for the joint ecological risk assessment of multiple pollutants. Among the above mentioned four steps, the first two steps are paramount. In the present study, the following six key issues are discussed: (1) how to select the appropriate species, (2) how to preprocess the toxicity data collected from the ecotoxicity database, (3) how to transform the acute toxicity data into chronic data, (4) how to best fit the toxicity data, (5) how to calculate the msPAF of multiple pollutants, and (6) how to determine the uncertainty of the SSD model”. In response to these questions, several principles were proposed to select appropriate species; three data processing methods, including the geometric mean, weight assigning and using all raw data without processing, were compared to determine the appropriate method for the DDT (dichloro diphenyl trichloroethane) toxicity data preprocessing. The method of acute to chronic ratio (ACR) and binary correlation analysis were contrasted using the zinc toxicity data for the transformation of the acute toxicity data into chronic data. The Burr III, Loglogistic and Lognormal models were compared to determine the best fit model using the DDT toxicity data for invertebrates. The concentration addition or response addition were discussed to calculate msPAF according to the toxic model of action (TMoA). The uncertainties of the SSD models for five heavy metals and for eight polycyclic aromatic hydrocarbons (PAHs) were performed. The comparison of the coefficients of variation (CVs) for the toxicity data and exposure levels in Lake Chaohu for eight polycyclic aromatic hydrocarbons (PAHs) were also presented to demonstrate the uncertainties of the ecological risks assessed by the SSD model based on 5000 Monte Carlo simulations.     

A model for the explanation of vegetation stripes (tiger bush)

Abstract. Regular vegetation patterns appear on aerial views of plateaux in SW Niger where densely and sparsely populated zones alternate with each other. This spatial organization of the vegetation is an endogenous phenomenon which is not limited to specific plants or soils; it is a characteristic landscape of many arid regions throughout the world. The phenomenon is interpreted as the result of a spatial range difference between two biologically distinct interactions operating at the plant population level. The proposed mechanism is independent of external heterogeneities deriving from soil geomorphology or meteorology. We present a model to simulate the genesis of vegetation stripes. In addition, the model predicts the occurrence of vegetation hexagons corresponding to higher or lower density spots arranged in a hexagonal lattice. The distinction between the two spatial symmetries is discussed in terms of their Fourier transforms.     

Numerical model (switchable/dual model) of the human head for rigid body and finite elements applications

In this paper, a methodology for the development and validation of a numerical model of the human head using generic procedures is presented. All steps required, starting with the model generation, model validation and applications will be discussed. The proposed model may be considered as a dual one due to its capabilities to switch from deformable to a rigid body according to the application's requirements. The first step is to generate the numerical model of the human head using geometry files or medical images. The required stiffness and damping for the elastic connection used for the rigid body model are identified by performing a natural frequency analysis. The presented applications for model validation are related to impact analysis. The first case is related to Nahum's (Nahum and Smith 1970) experiments pressure data being evaluated and a pressure map generated using the results from discrete elements. For the second case, the relative displacement between the brain and the skull is evaluated according to Hardy's (Hardy WH, Foster CD, Mason, MJ, Yang KH, King A, Tashman S. 2001.Investigation of head injury mechanisms using neutral density technology and high-speed biplanar X-ray. Stapp Car Crash J. 45:337–368, SAE Paper 2001-22-0016) experiments. The main objective is to validate the rigid model as a quick and versatile tool for acquiring the input data for specific brain analyses.     

A model predicting the seasonal dynamics of intake and production for suckler cows and their calves fed indoors or at pasture

To investigate the dynamics of animal intake and production in grassland-based suckler systems, we constructed a model for suckling cows with their calves. The model calculates on a day-to-day basis the selective intake at pasture and the animal production (weight, condition, milk production) in response to energy intake. The model dynamically applies the feed evaluation systems developed by the INRA: the “cattle fill unit” system to predict forage intake, and the “feed unit” system to predict net energy requirements and supply. To predict intake at pasture, we adapted the cattle fill unit system by adding effects of herbage availability and sward structural composition on the amount and quality of intake.At pasture, the grazeable herbage is divided into structural components characterized by their biomass and digestibility. The model predicts the composition of the diet, assuming that the most digestible and abundant components of herbage are preferred. The amount of herbage ingested depends on the animal profile, the digestibility of the diet and the amount of herbage available. Sward depletion by animal intake at pasture has feedback effects on herbage growth and quality, which can be calculated by a vegetation model. Animal production is calculated based on net energy balance, which is the difference between net energy intake and net energy requirements for maintenance (for cow and calf), gestation and lactation (for the cow). The net energy balance determines weight and condition gain or loss, and – after 3 months of lactation – influences milk production the following day. Changes in weight and condition have feedback effects on energy requirements and intake capacity.Sensitivity analysis on the input values highlighted the importance of forage digestibility for the production of cows and calves. Calf growth was also driven over 3 months old by calf live weight, and under 3 months old by the milk production of the cow. The model's response to stocking rate during the grazing down of a paddock was consistent with current knowledge. The model was validated against experimental data for cows fed indoors or at pasture, at different feed allowances. Model predictions were precise for the digestibility of intake and for live weight (error represents 2–3% of the average observed value), satisfactory for dry matter intake, body condition score and milk production at the beginning of lactation (error represents 10% of the average observed value), and very imprecise for milk production after the third month of lactation (error represents 23% of the average observed value), but the latter had small consequences on calf live weight.     

A mixed model for the effects of single gene,polygenes and their interaction on quantitative traits

Summary A model for the effects of single gene (SG), polygenes (PG) and their interaction on quantitative traits was developed. It is a mixed model where the SG is a fixed effect and the PG is a random effect. A two-way factorial experiment, in which the SG and the PG are the main effects, is proposed. The experimental material is comprised of F₃ families derived from F₂ plants heterozygous for the SG. For this experiment an ANOVA table with expected mean square is proposed, which facilitates estimation of the components of the model and testing of their significance. A detailed method for the interpretation of results from such an experiment is proposed, with emphasis on the analysis of the SG × PG interaction. Theoretical and applied aspects of SG × PG interaction is discussed.This paper is part of a Ph.D. Thesis of the senior author to be submitted to the Hebrew University of Jerusalem     

A Bayesian multi-risks survival (MRS) model in the presence of double censorings

Semi-competing risks data include the time to a nonterminating event and the time to a terminating event, while competing risks data include the time to more than one terminating event. Our work is motivated by a prostate cancer study, which has one nonterminating event and two terminating events with both semi-competing risks and competing risks present as well as two censoring times. In this paper, we propose a new multi-risks survival (MRS) model for this type of data. In addition, the proposed MRS model can accommodate noninformative right-censoring times for nonterminating and terminating events. Properties of the proposed MRS model are examined in detail. Theoretical and empirical results show that the estimates of the cumulative incidence function for a nonterminating event may be biased if the information on a terminating event is ignored. A Markov chain Monte Carlo sampling algorithm is also developed. Our methodology is further assessed using simulations and also an analysis of the real data from a prostate cancer study. As a result, a prostate-specific antigen velocity greater than 2.0 ng/mL per year and higher biopsy Gleason scores are positively associated with a shorter time to death due to prostate cancer.     

First record of the freshwater snail Pseudosuccinea columella (Gastropoda: Lymnaeidae) in southern Pampas (Argentina) and assessment of future spread

ABSTRACT

The freshwater snail Pseudosuccinea columella was recorded for the first time in Argentina more than 60 years ago. Since then its distribution in the wild has been restricted to the northeastern provinces. Here we record the presence of P. columella in southern Pampas for the first time, extending its distribution more than 500?km southwards. The climatic suitability of this and other areas of South America for its establishment and spread was analysed using habitat modelling software. Hitherto its spread within and between watercourses in southern Pampas has been very limited, probably through a combination of low climatic suitability, recent introduction and low connectivity of the drainage basins. The suitability of other areas where it has been recently recorded indicates a moderate risk of further spread in central and northwestern Argentina and in coastal areas of the Pacific rim of South America (southern Perú and northern Chile). The recent spread of P. columella in the wild in Argentina may be the result of an increase in the trade in aquarium plants or of the evolution of a new lineage with different ecological capabilities.     

白背飞虱种群动态关联分析及预测模型的研究

根据灰色系统关联分析的基本原理,提出了白背飞虱种群动态的加权关联度预测法。衢县早稻后期白背飞虱发生量与历年6月25～30日平均百丛虫量X_1（t）、同期若虫比例X_2（t）、迟熟品种比例X_3（t）、6月下旬水分积分指数X_4（t）和平均气温X_5（t）等因素的关联序为：X_2（t）＞X_1（t）＞X_3（t）＞X_5（t）＞X_4（t）。据此建立的加权关联度预测模型,经12年资料回测和试报验证,结果令人满意。     

A review towards finding a simplified approach for modelling the kinetics of the soluble microbial products (SMP) in an integrated mathematical model of membrane bioreactor (MBR)

Soluble microbial products (SMPs) tend to accumulate in the membrane bioreactor (MBR) systems as a consequence of high membrane rejection and apparently low biodegradability within the wastewater treatment system. The extension of the activated sludge models (ASMs) with SMPs, therefore, has received crucial importance in recent days, particularly considering their potential use as indicators of the membrane fouling propensity. This paper presents a critical review of the formation and degradation kinetics of SMP subdivisions that have so far been used for the mathematical modelling of MBR. The paper identified a simplified approach to incorporate the kinetics of the SMP formation and degradation in the general mathematical models of MBR. It suggested that the inclusion of only four additional linear differential equations in the ASM1-SMP integrated mathematical model could simulate well the effluent quality and membrane fouling prediction. The model would also serve as a useful tool in optimizing operation conditions for better treatability and fouling control.     

A semi-stochastic model of the transmission of Escherichia coli O157 in a typical UK dairy herd: dynamics, sensitivity analysis and intervention/prevention strategies

When modelling the transmission of infection within small populations, it is necessary to consider the possibility of stochastic fade-out of infection. We present a semi-stochastic model for the transmission of a microparasite, in this case Escherichia coli O157, within a multigroup system, namely a typical UK dairy herd. The model includes birth, death, maturation, the dry/lactating cycle and various types of transmission (i.e. direct, pseudovertical (representing direct faecal-oral transmission between dam and calf within the first 48 h) and indirect (via free-living infectious units in the environment)). We present the results of our simulation study alongside data from empirical studies and also compare simulation results with those for the corresponding deterministic model. We then examine the effects of reducing shedding in the food-producing groups on outbreak size and prevalence of infection. A sensitivity analysis of herd prevalence reveals that, for both the deterministic and the semi-stochastic model, the prevalence within the herd is most sensitive to two parameters relating to the weaned group. This supports our previously reported conclusions for the deterministic model, which were based on an analysis of the next-generation matrix. The sensitivity analysis also indicates that herd prevalence is greatly affected by two other parameters relating to the lactating group. We conclude by discussing the possible efficacy of suggested intervention strategies.     

A simple sandwich ELISA (WELYSSA) for the detection of lyssavirus nucleocapsid in rabies suspected specimens using mouse monoclonal antibodies

Monoclonal antibody (MAb)-based capture enzyme-linked immunosorbent assays (ELISA) were developed for the diagnosis of rabies-suspect specimens. A combination of four mouse monoclonal antibodies directed against the rabies virus nucleocapsid was selected and used for the detection. The test was optimized and standardized so that maximum concordance could be maintained with the standard procedures of rabies diagnosis recommended by the WHO expert committee. Using prototype viruses from the different genotypes of lyssavirus and from various geographic origins and phylogenetic lineages, this paper presents a reliable, rapid and transferable diagnostic method, named WELYSSA that readily permits the detection of lyssaviruses belonging to the 7 genotypes of lyssavirus circulating in Europe, Africa, Asia and Oceania. The threshold of detection of lyssavirus nucleocapsids is low (0.8 ng/ml). With a panel of 1030 specimens received for rabies diagnostic testing, this test was found to be highly specific (0.999) and sensitive (0.970) when compared to other recommended rabies diagnostic methods.