Estimating equivalence with quantile regression.

Equivalence testing and corresponding confidence interval estimates are used to provide more enlightened statistical statements about parameter estimates by relating them to intervals of effect sizes deemed to be of scientific or practical importance rather than just to an effect size of zero. Equivalence tests and confidence interval estimates are based on a null hypothesis that a parameter estimate is either outside (inequivalence hypothesis) or inside (equivalence hypothesis) an equivalence region, depending on the question of interest and assignment of risk. The former approach, often referred to as bioequivalence testing, is often used in regulatory settings because it reverses the burden of proof compared to a standard test of significance, following a precautionary principle for environmental protection.

Potential misuse of avian density as a conservation metric.

Effective conservation metrics are needed to evaluate the success of management in a rapidly changing world. Reproductive rates and densities of breeding birds (as a surrogate for reproductive rate) have been used to indicate the quality of avian breeding habitat, but the underlying assumptions of these metrics rarely have been examined. When birds are attracted to breeding areas in part by the presence of conspecifics and when breeding in groups influences predation rates, the effectiveness of density and reproductive rate as indicators of habitat quality is reduced.

Comparing national and global data collection systems for reporting, outbreaks of H5N1 HPAI.

Determining if outbreak data collected by regional or international organizations can reflect patterns observed in more detailed data collected by national veterinary services is a necessary first step if global databases are to be used for making inference about determinants of disease maintenance and spread and for emergency planning and response. We compared two data sources that capture spatial and temporal information about H5N1 highly pathogenic avian influenza outbreaks reported since 2004 in four countries: Bangladesh, Egypt, Turkey, and Vietnam. One data source consisted of reports collected as part of each country's national veterinary services surveillance program, while the other data source included reports collected using the Emergency Prevention System for Priority Animal and Plant Pests and Diseases (EMPRES-i) global animal health information system.

Poisson sampling: a sampling strategy for concurrently establishing freedom from disease and estimating population characteristics.

Surveys of animal populations are often designed to either demonstrate freedom from disease or to estimate parameters that describe the population, such as disease prevalence, proportion of vaccinated animals, or average animal weight and value. Targeted surveillance is a sampling approach where animals are selected for testing based on the presence of characteristics that indicate a higher probability of disease. This approach can substantially reduce the sample size that is required to demonstrate freedom from disease, but inferences about other population parameters are generally not possible because the sample design often lacks the properties required for making inferences in a traditional survey sample.

Population inferences from targeted sampling with uncertain epidemiologic information.

Targeted sampling is an increasingly popular method of data collection in animal-based epidemiologic studies. This sampling approach allows the user to exclusively choose samples from subpopulations that have a higher likelihood of the disease of interest. This is achieved by selecting animals from a subpopulation that exhibits some characteristic that indicates a higher probability of the presence of the disease.

What is normal? A field approach to characterizing health and management of the nation's animal populations.

There is a growing demand for information about the health and well-being of animals on farms. Such information has many uses. In some instances such information is used locally by livestock owners and producers to gauge their position relative to their peers.

Fundamental limits to the accuracy of deuterium isotopes for identifying the spatial origin of migratory animals.

Deuterium isotope analyses have revolutionized the study of migratory connectivity because global gradients of deuterium in precipitation (deltaD(P)) are expressed on a continental scale. Several authors have constructed continental scale base maps of deltaD(P) to provide a spatial reference for studying the movement patterns of migratory species and, although they are very useful, these maps present a static, 40-year average view of the landscape that ignores much underlying inter-annual variation. To more fully understand the consequences of this underlying variation, we analyzed the GNIP deuterium data, the source for all current deltaD(P) maps, to estimate the minimum separation in deltaD(P) (and latitude) necessary to conclude with a given level of confidence that distinct deltaD(P) values represent different geographic sites.

Simulating the influence of vernalization, photoperiod and optimum temperature on wheat developmental rates.

Background And Aims: Accurately representing development is essential for applying crop simulations to investigate the effects of climate, genotypes or crop management. Development in wheat (Triticum aestivum, T. durum) is primarily driven by temperature, but affected by vernalization and photoperiod, and is often simulated by reducing thermal-time accumulation using vernalization or photoperiod factors or limiting accumulation when a lower optimum temperature (T(optl)) is exceeded.

Estimating herd prevalence of bovine brucellosis in 46 USA states using slaughter surveillance.

Making valid inferences about herd prevalence from data collected at slaughter is difficult because the observed sample is dependent on the number of animals sampled from each herd, which varies with herd size and culling practices, and the probability of a positive test result, which depends on variable within-herd prevalence levels as well as test sensitivity and specificity. In this study, brucellosis herd prevalence among beef cow-calf operations is estimated from slaughter surveillance data using a method that combines process modeling with Bayesian inference. Inferences are made for two populations; the first population comprises cow-calf beef herds in a typical U.

Effect of antimicrobial dosage regimen on Salmonella and Escherichia coli isolates from feeder swine.

A body of evidence exists that suggests that antimicrobial use in food animals leads to resistance in both pathogenic and commensal bacteria. This study focused on the impact of three different antimicrobial regimes (low-level continuous, pulse, and no antimicrobial) for two antimicrobials (chlortetracycline and tylosin) on the presence of Salmonella spp. and on the prevalence of antimicrobial resistance of both Salmonella spp.

A quantile count model of water depth constraints on Cape Sable seaside sparrows.

1. A quantile regression model for counts of breeding Cape Sable seaside sparrows Ammodramus maritimus mirabilis (L.) as a function of water depth and previous year abundance was developed based on extensive surveys, 1992-2005, in the Florida Everglades.

The evolution of internet-based map server applications in the United States Department of Agriculture, Veterinary Services.

The internet is used increasingly as an effective means of disseminating information. For the past five years, the United States Department of Agriculture (USDA) Veterinary Services (VS) has published animal health information in internet-based map server applications, each oriented to a specific surveillance or outbreak response need. Using internet-based technology allows users to create dynamic, customised maps and perform basic spatial analysis without the need to buy or learn desktop geographic information systems (GIS) software.

Geospatial analysis and modelling in the prevention and control of animal diseases in the United States.

Geospatial analysis of disease investigation data improves data standardisation and validation and enhances pathogen detection. Grid-based surveillance systems for Newcastle disease in southern California and for bovine tuberculosis on Molokai Island, Hawaii, demonstrate the importance of this approach to operational planning. In addition, as shown by a bovine tuberculosis study in wildlife on Molokai Island, a lattice grid can be used to develop zonal strategies for disease regulatory actions.

Geospatial field applications within United States Department of Agriculture, Veterinary Services.

Epidemiologists, veterinary medical officers and animal health technicians within Veterinary Services (VS) are actively utilising global positioning system (GPS) technology to obtain positional data on livestock and poultry operations throughout the United States. Geospatial data, if acquired for monitoring and surveillance purposes, are stored within the VS Generic Database (GDB). If the information is collected in response to an animal disease outbreak, the data are entered into the Emergency Management Response System (EMRS).

Molecular epidemiology of vesicular stomatitis New Jersey virus from the 2004-2005 US outbreak indicates a common origin with Mexican strains.

Vesicular stomatitis (VS) outbreaks of unknown origin occur at 8-10-year intervals in the south-western USA with the most recent outbreak beginning in 2004. A previous study has suggested that strains causing US outbreaks are closely related to strains causing outbreaks in Mexico [Rodriguez (2002) Virus Res 85, 211-219]. This study determined the phylogenetic relationships among 116 vesicular stomatitis New Jersey virus (VSNJV) strains obtained from the 2004 outbreak and from endemic areas in Mexico.

Projected ecosystem impact of the Prairie Heating and CO2 Enrichment experiment.

The Prairie Heating and CO2 Enrichment (PHACE) experiment has been initiated at a site in southern Wyoming (USA) to simulate the impact of warming and elevated atmospheric CO2 on ecosystem dynamics for semiarid grassland ecosystems. The DAYCENT ecosystem model was parametrized to simulate the impact of elevated CO2 at the open-top chamber (OTC) experiment in north-eastern Colorado (1996-2001), and was also used to simulate the projected ecosystem impact of the PHACE experiments during the next 10 yr. Model results suggest that soil water content, plant production, soil respiration, and nutrient mineralization will increase for the high-CO2 treatment.

A qualitative assessment tool for the potential of infectious disease emergence and spread.

Improved understanding and assessment of the complex factors associated with disease emergence and spread will lead to better management and thus reduction of risk for disease occurrence. Specific biological, ecologic, environmental, and societal factors have been identified that precede emerging infections. Based on these factors, a qualitative tool was developed to assess risk for disease emergence and spread.

Description of live poultry markets in the United States and factors associated with repeated presence of H5/H7 low-pathogenicity avian influenza virus.

In 2005 the National Animal Health Monitoring System conducted a survey in 183 live poultry markets throughout the United States. The objectives of this study were to describe characteristics of live poultry markets in the United States and to identify potential risk factors for markets to be repeatedly positive for low-pathogenicity avian influenza virus (LPAIV) H5/H7. A questionnaire was administered to market operators that included questions regarding types of birds and other animals in the market, biosecurity, and cleaning and disinfecting practices.

An evaluation of scrapie surveillance in the United States.

Animal health surveillance systems should reflect national disease control priorities and promote the best use of public resources by maximizing effectiveness and efficiency. A surveillance system should be routinely evaluated to assess the degree to which the system accomplishes these goals, fulfills its stated objectives, and meets accepted surveillance standards. In the United States, there are a number of disparate endemic disease surveillance and eradication programs.

The concept of compartmentalisation.

The rationale for establishing trade 'regions' and 'zones' is based on principles of epidemiological science and risk analysis that assess and manage animal disease risks so that the safety of trade can be ensured. However, the boundaries of geographical regions and zones may readily be breached through numerous epidemiological pathways. The concept of a 'compartment' extends the application of a 'risk boundary' beyond that of a geographical interface and considers all epidemiological factors that can contribute to the creation of an effective boundary.

Estimation of temporary emigration in male toads.

Male boreal toads (Bufo boreas) are thought to return to the breeding site every year but, if absent in a particular year, will be more likely to return the following year. Using Pollock's robust design we estimated temporary emigration (the probability a male toad is absent from a breeding site in a given year) at three locations in Colorado, USA: two in Rocky Mountain National Park and one in Chaffee County. We present data that suggest that not all male toads return to the breeding site every year.

Identifying ecoregion boundaries.

This article summarizes the rationale I used in identifying ecoregion boundaries on maps of the United States, North America, and the world's continents, published from 1976 to 1998. The geographic reasoning used in drawing boundaries involves 20 principles, which are presented to stimulate discussion and further understanding. Brief background and references are provided for the principles.

Predicting the thermal effects of dam removal on the Klamath River.

The Klamath River once supported large runs of anadromous salmonids. Water temperature associated with multiple mainstem hydropower facilities might be one of many factors responsible for depressing Klamath salmon stocks. We combined a water quantity model and a water quality model to predict how removing the series of dams below Upper Klamath Lake might affect water temperatures, and ultimately fish survival, in the spawning and rearing portions of the mainstem Klamath.

Strategies for two-stage sampling designs for estimating herd-level prevalence.

We propose a herd-level sample-size formula based on a common adjustment for prevalence estimates when diagnostic tests are imperfect. The formula depends on estimates of herd-level sensitivity and specificity. With Monte Carlo simulations, we explored the effects of different intracluster correlations on herd-level sensitivity and specificity.