Design standards for experimental and field studies to evaluate diagnostic accuracy of tests for infectious diseases in aquatic animals          下载免费PDF全文

E Laurin  K K Thakur  I A Gardner  P Hick  N J G Moody  M S J Crane  I Ernst 《Journal of fish diseases》2018,41(5):729-749

Design and reporting quality of diagnostic accuracy studies (DAS) are important metrics for assessing utility of tests used in animal and human health. Following standards for designing DAS will assist in appropriate test selection for specific testing purposes and minimize the risk of reporting biased sensitivity and specificity estimates. To examine the benefits of recommending standards, design information from published DAS literature was assessed for 10 finfish, seven mollusc, nine crustacean and two amphibian diseases listed in the 2017 OIE Manual of Diagnostic Tests for Aquatic Animals. Of the 56 DAS identified, 41 were based on field testing, eight on experimental challenge studies and seven on both. Also, we adapted human and terrestrial‐animal standards and guidelines for DAS structure for use in aquatic animal diagnostic research. Through this process, we identified and addressed important metrics for consideration at the design phase: study purpose, targeted disease state, selection of appropriate samples and specimens, laboratory analytical methods, statistical methods and data interpretation. These recommended design standards for DAS are presented as a checklist including risk‐of‐failure points and actions to mitigate bias at each critical step. Adherence to standards when designing DAS will also facilitate future systematic review and meta‐analyses of DAS research literature.  相似文献   

<Superscript>1</Superscript>H-NMR metabolite profiling of abalone digestive gland in response to short-term starvation     

John R. Sheedy  Sébastien Lachambre  David K. Gardner  Robert W. Day 《Aquaculture International》2016,24(2):503-521

The effect of a short-term feeding and starvation experiment on juvenile abalone (Haliotis rubra × H. laevigata) was investigated (average length = 67 mm; average weight = 48 g). All aquaculture experiments were conducted at The University of Melbourne, Australia. Artificial feed was supplied ad libitum to the fed group, and no feed was supplied to the starved group. A modified metabolite extraction protocol using deuterated solvents was developed for ¹H-NMR-based metabolite profiling of digestive gland in response to the short-term feeding/starvation experiment, to avoid lyophilisation prior to biochemical analysis. PLS-DA revealed that fed and starved abalone are metabolically distinct from each other after 28 and 56 days. After 28 days, the fed group was defined by an increase in arginine, glucose, glutamate, glycine, inosine and uracil (P < 0.05), and the starved group was defined by an increase in N,N-dimethylglycine. After 56 days, the fed group still displayed increased glucose (P < 0.05), while N,N-dimethylglycine remained elevated in the starved group (P < 0.05). Arginine and glycogen were all higher at 28 days compared to 56 days, suggesting decreased anaerobic energy production at the later time point. Only glucose and N,N-dimethylglycine were significantly different between the fed and starved groups after 56 days, suggesting that abalone had not acclimatised to the starvation treatment after 28 days. These results infer N,N-dimethylglycine is a robust marker for short-term starvation in abalone. ¹H-NMR was also conducted on the artificial feed and starved abalone faecal matter, revealing the biochemical differences between them and digestive gland tissue. These methodology and results will facilitate a deeper understanding of the nutritional and physiological requirements of abalone in an aquaculture setting.  相似文献   

Does ‘race to fish’ behaviour emerge in an individual transferable quota fishery when the total allowable catch becomes non‐binding?     

Timothy J Emery  Klaas Hartmann  Bridget S Green  Caleb Gardner  John Tisdell 《Fish and Fisheries》2014,15(1):151-169

Successful individual transferable quota (ITQ) management requires a binding (constraining) total allowable catch (TAC). A non‐binding TAC may result in a shift back towards open access conditions, where fishers increasingly compete (‘race’) to catch their share of the total harvest. This process was examined by comparing fishing fleet behaviour and profitability in the Tasmanian southern rock lobster (Jasus edwardsii) fishery (TSRLF), Australia. Between 2008 and 2010, the TSRLF had a non‐binding TAC and effectively reverted to a regulated, limited‐entry fishery. Fishers' uncertainty about future profitability and their ability to take their allocated catch weakened the security characteristic of the ITQ allocation. The low quota lease price contributed to an increase in fleet capacity, while the more limited reduction in quota asset value proved an investment barrier, hindering the autonomous adjustment of quota towards the most efficient fishers. In the TSRLF, catch rates vary more than beach price and are therefore more important for determining daily revenue (i.e., price x catch rate) than market price. Consequently, fishers concentrated effort during times of higher catch rates rather than high market demand. This increased rent dissipation as fishers engaged in competitive race to fish to be the first to exploit the stock and obtain higher catch rates. The history of this fishery emphasizes the need for a constraining TAC in all ITQ fisheries, not only for stock management, but also to manage the security of the ITQ allocation and prevent unanticipated and undesirable changes in fisher behaviour and fishery profitability.  相似文献   

Bayesian estimation of variance partition coefficients adjusted for imperfect test sensitivity and specificity     

Polychronis Kostoulas  Leonidas Leontides  William J. Browne  Ian A. Gardner 《Preventive veterinary medicine》2009,89(3-4):155-162

The variance partition coefficient (VPC) measures the clustering of infection/disease among individuals with a specific covariate pattern. Covariate-pattern-specific VPCs provide insight to the groups of individuals that exhibit great heterogeneity and should be targeted for intervention. VPCs should be taken into consideration when planning study designs, modeling data and estimating sample sizes. We present a Bayesian discrete mixed model for the estimation of covariate-pattern-specific VPCs when measurement of the infection/disease is based on an imperfect test. The utility of the presented model is demonstrated with three applications. In all cases, imperfect tests biased VPC estimates towards the null but corrected estimates could be obtained by modeling the sensitivity and specificity of the test procedure with beta distributions. The comparison of adjusted VPCs between the intercept only and the fitted models with higher level covariates explained the portion of heterogeneity in the data that was accounted for by the covariates.  相似文献   

Feasibility of near infrared spectroscopy for analyzing corn kernel damage and viability of soybean and corn kernels   总被引：1，自引：0，他引：1  

Lidia Esteve Agelet  David D. Ellis  Susan Duvick  A. Susana Goggi  Charles R. Hurburgh  Candice A. Gardner 《Journal of Cereal Science》2012

The current US corn grading system accounts for the portion of damaged kernels, measured by time-consuming and inaccurate visual inspection. Near infrared spectroscopy (NIRS), a non-destructive and fast analytical method, was tested as a tool for discriminating corn kernels with heat and frost damage. Four classification algorithms were utilized: Partial least squares discriminant analysis (PLS-DA), soft independent modeling of class analogy (SIMCA), k-nearest neighbors (K-NN), and least-squares support vector machines (LS-SVM). The feasibility of NIRS for discriminating normal or viable-germinating corn kernels and soybean seeds from abnormal or dead seeds was also tested. This application could be highly valuable for seed breeders and germplasm-preservation managers because current viability tests are based on a destructive method where the seed is germinated. Heat-damaged corn kernels were best discriminated by PLS-DA, with 99% accuracy. The discrimination of frost-damaged corn kernels was not possible. Discrimination of non-viable seeds from viable also was not possible. Since previous results in the literature contradict the current damage-discrimination results, the threshold of seed damage necessary for NIRS detection should be analyzed in the future. NIRS may accurately classify seeds based on changes due to damage, without any correlation with germination.  相似文献   

The REFLECT Statement: Methods and Processes of Creating Reporting Guidelines for Randomized Controlled Trials for Livestock and Food Safety     

A.M. O'Connor  J.M. Sargeant  I.A. Gardner  J.S. Dickson  M.E. Torrence  consensus meeting participants: C.E. Dewey  I.R. Dohoo  R.B. Evans  J.T. Gray  M. Greiner  G. Keefe  S.L. Lefebvre  P.S. Morley  A. Ramirez  W. Sischo  D.R. Smith  K. Snedeker  J. Sofos  M.P. Ward  R. Wills 《Journal of veterinary internal medicine / American College of Veterinary Internal Medicine》2010,24(1):57-64

The conduct of randomized controlled trials in livestock with production, health, and food-safety outcomes presents unique challenges that might not be adequately reported in trial reports. The objective of this project was to modify the CONSORT (Consolidated Standards of Reporting Trials) statement to reflect the unique aspects of reporting these livestock trials. A 2-day consensus meeting was held on November 18–19, 2008 in Chicago, IL, to achieve the objective. Before the meeting, a Web-based survey was conducted to identify issues for discussion. The 24 attendees were biostatisticians, epidemiologists, food-safety researchers, livestock production specialists, journal editors, assistant editors, and associate editors. Before the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items would need to be modified to address unique issues for livestock trials. The consensus meeting resulted in the production of the REFLECT (Reporting Guidelines for Randomized Control Trials) statement for livestock and food safety and 22-item checklist. Fourteen items were modified from the CONSORT checklist, and an additional subitem was proposed to address challenge trials. The REFLECT statement proposes new terminology, more consistent with common usage in livestock production, to describe study subjects. Evidence was not always available to support modification to or inclusion of an item. The use of the REFLECT statement, which addresses issues unique to livestock trials, should improve the quality of reporting and design for trials reporting production, health, and food-safety outcomes.  相似文献   

Differences in Ponderosa Pine Isocupressic Acid Concentrations Across Space and Time     

Daniel Cook  Dale R. Gardner  James A. Pfister  Kip E. Panter  Bryan L. Stegelmeier  Stephen T. Lee  Kevin D. Welch  Benedict T. Green  T. Zane Davis 《Herpetological Monographs》2010,32(2):14-17

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Consumption of Low Larkspur (Delphinium nuttallianum) by Grazing Sheep     

J.A. Pfister  D.R. Gardner  K.E. Panter 《Strength and Conditioning Journal》2010,63(2):263-266

Low larkspur (Delphinium nuttallianum Pritz.) poisoning causes serious economic loss to livestock producers that graze cattle on foothill and mountain ranges in western North America. In general, all Delphinium spp. are five times less toxic to sheep than to cattle. Because low larkspurs are less toxic to sheep than cattle, grazing sheep before cattle on rangelands with dense populations of low larkspur can reduce larkspur density and risk of poisoning to grazing cattle. All previous published work on sheep and larkspur interactions has involved tall larkspurs. This series of studies was conducted to determine if sheep would consume sufficient low larkspur to reduce subsequent risk to cattle. Four summer trials were conducted in Collbran, Colorado, and Soda Springs, Idaho on pastures with dense (> 9 plants · m^?2) low larkspur populations. In all trials, sheep ate very little low larkspur (< 0.5% of bites). During one final trial using high sheep density (two sheep · 0.015 ha^?1 for 9 d), sheep consumed little low larkspur, but animals appeared to trample much of the low larkspur. Toxic alkaloid concentrations in low larkspur ranged from 1.1 mg · g^?1 to 1.6 mg · g^?1 in all trials. The use of sheep to graze low larkspurs to reduce subsequent consumption by grazing cattle does not appear to be a viable option.  相似文献   

Influence of seed endophyte amounts on swainsonine concentrations in astragalus and oxytropis locoweeds     

DS Grum  D Cook  DR Gardner  JM Roper  JA Pfister  MH Ralphs 《Journal of agricultural and food chemistry》2012,60(33):8083-8089

Locoism is a toxic syndrome of livestock caused by the ingestion of a subset of legumes known as locoweeds endemic to arid and semiarid regions of the western United States. Locoweeds contain the toxic alkaloid swainsonine, which is produced by the endophytic fungi Undifilum species. Two chemotypes of plants can coexist within toxic populations of locoweeds: chemotype 1 plants are defined as individuals containing swainsonine concentrations greater than 0.01% and quantitatively greater amounts of Undifilum, while chemotype 2 plants are defined as individuals containing less than 0.01% swainsonine and quantitatively smaller amounts of Undifilum. To elucidate the mechanisms that govern chemotypes, the amount of Undifilum in seeds/embryos was manipulated, thus altering subsequent swainsonine concentrations in three locoweed species: Astragalus mollissimus, Astragalus lentiginosus, and Oxytropis sericea. Chemotype 1 seeds that were fungicide-treated or had the seed coat removed resulted in plants with swainsonine concentrations comparable to those in chemotype 2 plants. Conversely, embryos from seeds of chemotypes 1 and 2 that were inoculated with the endophyte resulted in plants with swainsonine concentrations comparable to those of chemotype 1 plants. This reproducible interconversion between the two swainsonine chemotypes suggests that the quantity of endophyte present in the seed at the time of germination is a key determinant of the eventual chemotype. Additionally, this is the first report of the inoculation of locoweeds with the endophyte Undifilum species.  相似文献   

How pristine are tropical forests? An ecological perspective on the pre-Columbian human footprint in Amazonia and implications for contemporary conservation     

Jos Barlow  Toby A. Gardner  Alexander C. Lees  Luke Parry  Carlos A. Peres 《Biological conservation》2012,151(1):45-49

Archeologists, paleoecologists and anthropologists argue that ecologists need to give greater consideration to the pre-historical influence of humans in shaping the current structure and composition of tropical forests. We examine these arguments within the context of Amazonia, and assess the extent to which (i) the concepts of “pristine forests” and “cultural parklands” are mutually exclusive, (ii) the aggregated distribution of some plants necessarily indicates enrichment planting, (iii) pre-Columbian human disturbance has increased forest biodiversity, (iv) pre-Columbian indigenous practices were always sustainable, and (v) if indeed, the ecological impacts of pre-Columbian peoples are relevant for modern biodiversity conservation. Overall, we reject the notion that “the pristine myth has been thoroughly debunked” by archeological evidence, and suggest that the environmental impacts of historical peoples occurred along gradients, with high-impacts in settlements and patches of Amazonian Dark Earth (ADE), lesser impacts where occasional enrichment planting took place in forests surrounding agricultural plots, and a very low influence (in terms of light hunting pressure and other types of resource extraction) across vast areas of Amazonia that may always have been far from permanent settlements and navigable rivers. We suggest that the spatial distribution of pre-Columbian finds is given more attention, and urge caution before case studies are extrapolated to the entire Basin. Above all, we feel that debates over “naturalness” and environmental impacts of pre-Columbian humans are of limited relevance to present and future biodiversity conservation, and can detract from the major challenges facing Amazonia and other tropical forest regions today.  相似文献