The impact of truncating data on the predictive ability for single‐step genomic best linear unbiased prediction

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single‐step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively removed 1 year at a time based on the year an animal was born. For the swine data sets, correlations between corrected phenotypes (Cp) and EBV were used to evaluate the predictive ability on young animals born in 2016–2017. In the simulated data set, keeping data two generations back or greater resulted in no statistical difference (p‐value > 0.05) in the reduction in the true breeding value at generation 15 compared to utilizing all available data. Across swine data sets, removing phenotypes from animals born prior to 2011 resulted in a negligible or a slight numerical increase in the correlation between Cp and EBV. Truncating data is a method to alleviate computational issues without negatively impacting the predictive ability of selection candidate EBV.     

Spatiotemporal Distribution of Two Euschistus spp. Stink Bugs (Hemiptera: Pentatomidae) in Southeastern Farmscapes

Stink bugs (Hemiptera: Pentatomidae) are ubiquitous, cryptic, phytophagous pests that are found in many crops. In agroecosystems, individuals disperse from adjacent noncrop hosts and tend to aggregate or cluster within fields. In this study, we characterized the distribution of Euschistus servus (Say) and Euschistus tristigmus (Say) (Hemiptera: Pentatomidae) over 2 yr at three southeastern United States farmscapes. Stink bugs were captured in pheromone-baited traps, and Spatial Analysis by Distance Indices (SADIE) used to identify the location of significant aggregations by habitat type and season. Euschistus servus adults were more likely to be captured in pecan orchards, cotton, other crops, or unmanaged habitats than in woodland habitats. Significant aggregations of E. servus were detected in a variety of habitats including pecan, corn, cotton, peanut, and tobacco, as well as fallow and hay fields, pastures, and hedgerows. Fewer adult E. tristigmus were captured than E. servus adults, and E. tristigmus adults were typically trapped and aggregated in woodland habitats. The resulting data provide an important understanding regarding the seasonal movement and relative abundance levels of stink bug populations, which are critical to the development of integrated pest management strategies.     

Evidence from tag recapture experiments that fish learn to avoid fishing gear

We found evidence that tagging induced trap shyness in snapper (Pagrus auratus), i.e., tagged fish had a reduced probability of recapture by the method by which they had originally been caught. Tagging experiments in 1985 and 1994 involving single release over a short period and single recapture were conducted on a closed population (SNA 1: East Northland-Hauraki Gulf-Bay of Plenty). Initial capture was by trawling and by line fishing, while recapture over an extended period included other methods. A test for trap shyness that removed the possible effects of spatial and fish size heterogeneity gave a significant result for both years. The data suggested that the trap shyness effect might have been smaller for trawl-released fish than for line-released fish. However, we estimated a single trap shyness factor (0.71). There was also some evidence for attenuation of trap shyness over time.     

Chesapeake bay anoxia: origin, development, and significance

Anoxia occurs annually in deeper waters of the central portion of the Chesapeake Bay and presently extends from Baltimore to the mouth of the Potomac estuary. This condition, which encompasses some 5 billion cubic meters of water and lasts from May to September, is the result of increased stratification of the water column in early spring, with consequent curtailment of reoxygenation of the bottom waters across the halocline, and benthic decay of organic detritus accumulated from plankton blooms of the previous summer and fall. The Chesapeake Bay anoxia appears to have had significant ecological effects on many marine species, including several of economic importance.     

A new framework of spatial targeting for single-species conservation planning

Context

Organisations acting to conserve and protect species across large spatial scales prioritise to optimise use of resources. Spatial conservation prioritization tools typically focus on identifying areas containing species groups of interest, with few tools used to identify the best areas for single-species conservation, in particular, to conserve currently widespread but declining species.

Objective

A single-species prioritization framework, based on temporal and spatial patterns of occupancy and abundance, was developed to spatially prioritize conservation action for widespread species by identifying smaller areas to work within to achieve predefined conservation objectives.

Methods

We demonstrate our approach for 29 widespread bird species in the UK, using breeding bird atlas data from two periods to define distribution, relative abundance and change in relative abundance. We selected occupied 10-km squares with abundance trends that matched species conservation objectives relating to maintaining or increasing population size or range, and then identified spatial clusters of squares for each objective using a Getis-Ord-Gi* or near neighbour analysis.

Results

For each species, the framework identified clusters of 20-km squares that enabled us to identify small areas in which species recovery action could be prioritized.

Conclusions

Our approach identified a proportion of species’ ranges to prioritize for species recovery. This approach is a relatively quick process that can be used to inform single-species conservation for any taxa if sufficiently fine-scale occupancy and abundance information is available for two or more time periods. This is a relatively simple first step for planning single-species focussed conservation to help optimise resource use.

     

基于稳健统计学确定高潜在污染土壤Cu、Pb基线值

土壤重金属基线值的确定对于评价重金属积累现状具有重要意义。在存在人为污染的情况下,土壤重金属数据经常强烈地偏离正态分布和对数正态分布,影响统计分析结果的可信度,而稳健统计方法可以降低离群值对统计分析结果的影响。本研究以张家港为研究区域,采用稳健回归方法,建立表层和底层土壤Cu、Pb的回归关系,通过底层土壤Cu、Pb含量计算表层土壤Cu、Pb基线值,并对土壤Cu、Pb积累状况进行评价。结果表明,稳健回归方法确定的表层土壤Cu、Pb基线值可以反映出不同样点间,土壤Cu、Pb背景含量的自然变异。与稳健统计学方法相比,使用国家土壤环境质量标准值,或大区域（江苏省）的土壤背景值,评价自然背景本身存在变异区域的土壤重金属积累状况时,可能会产生较大的误差。     

基于稳健统计学确定高潜在污染土壤Cu、Pb基线值

土壤重金属基线值的确定对于评价重金属积累现状具有重要意义。在存在人为污染的情况下,土壤重金属数据经常强烈地偏离正态分布和对数正态分布,影响统计分析结果的可信度,而稳健统计方法可以降低离群值对统计分析结果的影响。本研究以张家港为研究区域,采用稳健回归方法,建立表层和底层土壤Cu、Pb的回归关系,通过底层土壤Cu、Pb含量计算表层土壤Cu、Pb基线值,并对土壤Cu、Pb积累状况进行评价。结果表明,稳健回归方法确定的表层土壤Cu、Pb基线值可以反映出不同样点间,土壤Cu、Pb背景含量的自然变异。与稳健统计学方法相比,使用国家土壤环境质量标准值,或大区域(江苏省)的土壤背景值,评价自然背景本身存在变异区域的土壤重金属积累状况时,可能会产生较大的误差。     

EFFECTS OF ACEPROMAZINE ON THREE-PHASE 99mTc-MDP BONE IMAGING IN 11 HORSES

Horses undergoing skeletal scintigraphy can have decreased radiopharmaceutical bone uptake in the limbs. This reduces the diagnostic value of the scan. The aim of the present study was to measure the changes in count density caused by vasodilatation and increased blood flow associated with intravenous injection of acepromazine during bone scintigraphy in normal horses. A three-phase bone scan was performed twice in 11 adult horses to study the effects of acepromazine on the count density of the resultant scintigrams. With acepromazine, there was a statistically significant mean difference of 12 s for initial blood flow and 21 s for peak flow. The time to initial blood flow and time to peak flow occurred earlier for the scans in which acepromazine was used. There were no significant differences in the bone to soft tissue ratios during the soft tissue and bone phases of the scan between procedures. Intravenous administration of acepromazine increases peripheral blood flow causing an earlier onset of the vascular phase during the three-phase bone scan. Acepromazine did not increase the count density of the bone phase scintigrams. As expected, the vasodilatation and increased blood flow associated with intravenous injection of acepromazine affected the count density of the vascular phase of the bone scan.     

Use of clinical information to predict the characteristics of bacteria isolated from clinical cases of bovine mastitis

Farmers recorded the clinical signs of cows with clinical mastitis and submitted milk samples for bacteriological examination, so that the clinical signs could be correlated with the bacteriological findings. Odds ratios for the demeanour of the cow, the appearance of the milk, milk yield, udder texture, and the administration of parenteral antibiotics were calculated for mastitis cases classified in terms of their microbiology as either enterobacteriaceae, major Gram-positive pathogens, minor pathogens, 'no growths' or 'all other pathogens'. Animals infected with enterobacteriaceae had the highest odds of being reported as having a reduced milk yield, swollen or hard udders, watery milk and/or being systemically sick. A logistic regression model was used to predict the Gram-staining characteristics of the bacteria causing clinical mastitis. The clinical findings found to be significant predictors in the model were the demeanour of the cow and its milk yield. The regression model was used as a basis for a predictive test. Using a test data set, the sensitivity of the test was 28 per cent, its specificity was 96 per cent, the positive predictive value was 74 per cent and the negative predictive value was 80 per cent. The overall accuracy of these predictions was 79 per cent.