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"Contagious distributions."
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Conservation of taxonomic and biological trait diversity of European stream macroinvertebrate communities: a case for a collective public database
The use of databases for the conservation of biodiversity is increasing. During the last decade, such a database has been created for European stream macroinvertebrates. Today, it includes 527 sites that are the least human-impacted representatives of many stream types across many European regions. It includes data on the abundance of 312 invertebrate genera, several environmental site characteristics, collection methods, bibliographic data sources, and 11 biological traits of the genera (e.g. size, life cycle, food and feeding habits, described in 61 categories). The database will be useful in addressing many topics that are potentially relevant to biodiversity conservation. To illustrate this potential, we provide examples of how the data could be exploited. First, we describe the frequency of some taxonomic and biological characteristics (e.g. richness and diversity of genera and traits) of the macroinvertebrate communities and assess how these characteristics are related (e.g. how trait richness increases with genus richness). Second, we describe the frequency of some characteristics of the genera and traits (e.g. occurrence frequency, abundance, dispersion index) and again assess how these characteristics are related (e.g. how occurrence increases with abundance). Finally, we suggest how the database could be developed into a collective, publicly accessible database that covers stream types and regions of Europe more comprehensively.
Journal Article
Models for zero-inflated count data using the Neyman type A distribution
We explore the possibility of modelling zero-inflated count data using the Neyman
type A distribution. We extend three parameterizations of the Neyman type A
distribution to allow their parameters to depend on covariates. We develop models
which relate counts of Leadbeater’s possum to various habitat variables to
illustrate the methodology. Half-normal plots are constructed for each model to
explore the quality of the fit. We then formally compare the Neyman type A models
using the method of Cox to test non-nested hypotheses. Finally, we compare each of
the Neyman type A models with a model from a competing family, the conditional
Poisson model.
Journal Article
Estimating the Parameters of a Convolution by Maximum Likelihood
In the present age of computer sophistication, computational difficulty is no longer a justification for seeking alternative and inefficient estimation procedures in place of maximum likelihood estimation, particularly when there are only two or three parameters to be estimated. Convolution densities are an example where this has occurred. It is shown that in a large class of such densities, the maximum likelihood equations can be reduced by one. Thus for a two-parameter family, only a single equation need be solved iteratively. The required formulas are derived. The problem of basing inferences on the resulting maximum likelihood estimates is briefly discussed.
Journal Article
Parameter Orthogonality for a Family of Discrete Distributions
The standard contagious distributions (see Douglas 1980) have been used in such varied fields as biology and automobile insurance, often to model various physical phenomena as well as provide a good fit to count data when other models are inadequate. Unfortunately, the parameterizations often used when working with these distributions normally lead to extremely high correlations of the maximum likelihood estimators (MLE's). This tends to lead to mathematical complexities, and causes difficulty or even errors in their interpretation. Furthermore, numerical difficulties may arise when using numerical procedures to locate the estimates. Some of these difficulties were discussed by Douglas (1980, pp. 171, 204-205), who suggested that a reparameterization to reduce or even eliminate such correlation is desirable. If the MLE's are asymptotically uncorrelated, the parameterization is orthogonal. Philpot (1964) derived an orthogonal parameterization for the Neyman Type A distribution; Stein, Zucchini, and Juritz (1987) derived for the Poisson mixture by the inverse Gaussian distribution. Parameter orthogonality has several attractive features in the present context. Since there is no correlation asymptotically, the estimates (with their standard errors) provide a simpler summary of the data than in the absence of such orthogonality. The use of a parameterization where the MLEs are highly correlated can lead to a misleading analysis, or at best a more complicated analysis that would be necessary if an orthogonal parameterization had been used. To the extent that a high correlation exists, the parameters involved tend to measure similar quantities, and orthogonality separates information about the parameters from each other. This article gives an orthogonal parameterization for a large family of discrete distributions, including many of the contagious distributions, some Poisson mixtures, and some other generalized distributions. The previously cited works are unified and extended, for example, to the Polya-Aeppli, Poisson-binomial, and Sichel's Poisson-generalized inverse Gaussian distribution. One of the orthogonal parameters is the mean, and in many applications it is of interest to express the mean as a function of relevant covariate information. For example, Hinde (1982) considered some of these distributions in a regression context. This article shows how the results may be extended to deal with the covariate case in a relatively straightforward manner. Consequently, a convenient parameterization exists for a large family of distributions in a wide variety of situations. Some numerical examples are given, and a simple algorithm is given to find the maximum likelihood estimates in the case of no covariates.
Journal Article
Orf virus infection in Alaskan mountain goats, Dall’s sheep, muskoxen, caribou and Sitka black-tailed deer
Background
The zoonotic Orf virus (ORFV; genus
Parapoxvirus
,
Poxviridae
family) occurs worldwide and is transmitted between sheep and goats, wildlife and man. Archived tissue samples from 16 Alaskan wildlife cases, representing mountain goat (
Oreamnos americanus
, n = 8), Dall’s sheep (
Ovis dalli dalli
, n = 3), muskox (
Ovibos moschatus
, n = 3), Sitka black-tailed deer (
Odocoileus hemionus sitkensis
, n = 1) and caribou (
Rangifer tarandus granti
, n = 1), were analyzed.
Results
Clinical signs and pathology were most severe in mountain goats, affecting most mucocutaneous regions, including palpebrae, nares, lips, anus, prepuce or vulva, as well as coronary bands. The proliferative masses were solid and nodular, covered by dark friable crusts. For Dall’s sheep lambs and juveniles, the gross lesions were similar to those of mountain goats, but not as extensive. The muskoxen displayed ulcerative lesions on the legs. The caribou had two ulcerative lesions on the upper lip, as well as lesions on the distal part of the legs, around the main and dew claws. A large hairless spherical mass, with the characteristics of a fibroma, was sampled from a Sitka black-tailed deer, which did not show proliferative lesions typical of an ORFV infection. Polymerase chain reaction analyses for
B2L
,
GIF
,
vIL
-
10
and
ATI
demonstrated ORFV specific DNA in all cases. Sequences from Dall’s sheep formed a separate cluster, comparable to ORFV from domestic sheep. Sequences from the other species were different from the Dall’s sheep sequences, but almost identical to each other.
Conclusions
This is the first major investigation of parapoxvirus infections in large Alaskan game species, and the first report of parapoxvirus infection in caribou and Sitka black-tailed deer. This study shows that most of the wild ruminant species in Alaska and from most parts of Alaska, can carry and be affected by ORFV. These findings call for attention to transmission of ORFV from wildlife to livestock and to hunters, subsistence harvesters, and wildlife biologists.
Journal Article
Molecular identification and investigations of contagious ecthyma (Orf virus) in small ruminants, North west Ethiopia
Background
Orf virus, the prototype of parapoxvirus, is the main causative agent of contagious ecthyma. Little is known about the status of the disease in Ethiopia and this study was aimed at determining its status using PCR as a confirmatory tool.
Methods
a total of 400 randomly selected sheep and goat was screened for the identification of the virus using amplification of B2L gene and transfection of mammalian cells (VERO cells).
Results
Out of 400 animals screened for infection of the virus, 48 animals were found positive to PCR and revealed an overall incidence of 12%. Different epidemiological parameters were considered to look at the association with incidence of the disease and of which, only species of the animal(sheep), non-vaccinated and non-treated animals, nursing animals, poor body condition animals, extensively managed animals, animals having mouth lesion, and study areas having outbreak history showed higher prevalence. A univariate logistic regression analysis showed statistically significant difference in all variables (
P
< 0.05). Whereas, age and sex of animals showed no significant difference (
P
< 0.05).
Conclusion
The result of the present finding showed high incidence of Orf virus in the region as confirmed through PCR.
Journal Article
Evolutionary History of Contagious Bovine Pleuropneumonia Using Next Generation Sequencing of Mycoplasma mycoides Subsp. mycoides “Small Colony”
Mycoplasma mycoides subsp. mycoides \"Small Colony\" (MmmSC) is responsible for contagious bovine pleuropneumonia (CBPP) in bovidae, a notifiable disease to the World Organization for Animal Health (OIE). Although its origin is not documented, the disease was known in Europe in 1773. It reached nearly world-wide distribution in the 19(th) century through the cattle trade and was eradicated from most continents by stamping-out policies. During the 20(th) century it persisted in Africa, and it reappeared sporadically in Southern Europe. Yet, classical epidemiology studies failed to explain the re-occurrence of the disease in Europe in the 1990s. The objectives of this study were to obtain a precise phylogeny of this pathogen, reconstruct its evolutionary history, estimate the date of its emergence, and determine the origin of the most recent European outbreaks. A large-scale genomic approach based on next-generation sequencing technologies was applied to construct a robust phylogeny of this extremely monomorphic pathogen by using 20 representative strains of various geographical origins. Sixty two polymorphic genes of the MmmSC core genome were selected, representing 83601 bp in total and resulting in 139 SNPs within the 20 strains. A robust phylogeny was obtained that identified a lineage specific to European strains; African strains were scattered in various branches. Bayesian analysis allowed dating the most recent common ancestor for MmmSC around 1700. The strains circulating in Sub-Saharan Africa today, however, were shown to descend from a strain that existed around 1810. MmmSC emerged recently, about 300 years ago, and was most probably exported from Europe to other continents, including Africa, during the 19(th) century. Its diversity is now greater in Africa, where CBPP is enzootic, than in Europe, where outbreaks occurred sporadically until 1999 and where CBPP may now be considered eradicated unless MmmSC remains undetected.
Journal Article
Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa
Peste des petits ruminants (PPR) is a deadly viral disease that mainly affects small domestic ruminants. This disease threaten global food security and rural economy but its control is complicated notably because of extensive, poorly monitored animal movements in infected regions. Here we combined the largest PPR virus genetic and animal mobility network data ever collected in a single region to improve our understanding of PPR endemic transmission dynamics in West African countries. Phylogenetic analyses identified the presence of multiple PPRV genetic clades that may be considered as part of different transmission networks evolving in parallel in West Africa. A strong correlation was found between virus genetic distance and network-related distances. Viruses sampled within the same mobility communities are significantly more likely to belong to the same genetic clade. These results provide evidence for the importance of animal mobility in PPR transmission in the region. Some nodes of the network were associated with PPRV sequences belonging to different clades, representing potential \"hotspots\" for PPR circulation. Our results suggest that combining genetic and mobility network data could help identifying sites that are key for virus entrance and spread in specific areas. Such information could enhance our capacity to develop locally adapted control and surveillance strategies, using among other risk factors, information on animal mobility. As animals move so do viruses. The viral disease peste des petits ruminants (PPR) has a major impact on the livelihood of sheep and goat farmers across Africa, Middle-East and Asia. A global PPR eradication campaign is underway, but extensive movements of infected animals impede control efforts in many regions, such as West Africa. Here we show for the first time that PPR virus genetic data can be combined with information on animal mobility to identify routes of PPR circulation in Senegal and neighbouring countries. Such information can be used to design more efficient disease surveillance and control strategies adapted to local livestock farming practices.
Journal Article
Multitype branching process with non-homogeneous Poisson and contagious Poisson immigration
In a multitype branching process, it is assumed that immigrants arrive according to a non-homogeneous Poisson or a contagious Poisson process (both processes are formulated as a non-homogeneous birth process with an appropriate choice of transition intensities). We show that the normalized numbers of objects of the various types alive at time t for supercritical, critical, and subcritical cases jointly converge in distribution under those two different arrival processes. Furthermore, we provide some transient expectation results when there are only two types of particles.
Journal Article