The impact of truncating data on the predictive ability for single‐step genomic best linear unbiased prediction          下载免费PDF全文

Jeremy T. Howard  Tom A. Rathje  Caitlyn E. Bruns  Danielle F. Wilson‐Wells  Stephen D. Kachman  Matthew L. Spangler 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2018,135(4):251-262

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.  相似文献   

A comparison of single and multiple stressor protocols to assess acute stress in a coastal shark species,Rhizoprionodon terraenovae     

Eric R. Hoffmayer  Jill M. Hendon  Glenn R. Parsons  William B. Driggers III  Matthew D. Campbell 《Fish physiology and biochemistry》2015,41(5):1253-1260

  相似文献   

Historical patterns of fire severity and forest structure and composition in a landscape structured by frequent large fires: Pumice Plateau ecoregion,Oregon, USA     

Hagmann  R. Keala  Merschel  Andrew G.  Reilly  Matthew J. 《Landscape Ecology》2019,34(3):551-568

Context

Lack of quantitative observations of extent, frequency, and severity of large historical fires constrains awareness of departure of contemporary conditions from those that demonstrated resistance and resilience to frequent fire and recurring drought.

Objectives

Compare historical and contemporary fire and forest conditions for a dry forest landscape with few barriers to fire spread.

Methods

Quantify differences in (1) historical (1700–1918) and contemporary (1985–2015) fire extent, fire rotation, and stand-replacing fire and (2) historical (1914–1924) and contemporary (2012) forest structure and composition. Data include 85,750-ha tree-ring reconstruction of fire frequency and extent; >?375,000-ha timber inventory following >?78,900-ha fires in 1918; and remotely-sensed maps of contemporary fire effects and forest conditions.

Results

Historically, fires?>?20,000 ha occurred every 9.5 years; fire rotation was 14.9 years; seven fires?>?40,469 ha occurred during extreme drought (PDSI <?? 4.0); and stand-replacing fire occurred primarily in lodgepole (Pinus contorta var. murrayana). In contemporary fires, only 5% of the ecoregion burned in 30 years, and stand-replacing fire occurred primarily in ponderosa (Pinus ponderosa) and mixed-conifer. Historically, density of conifers?>?15 cm dbh exceeded 120 trees/ha on?<?5% of the area compared to 95% currently.

Conclusions

Frequent, large, low-severity fires historically maintained open-canopy ponderosa and mixed-conifer forests in which large fire- and drought-tolerant trees were prevalent. Stand-replacing patches in ponderosa and mixed-conifer were rare, even in fires >?40,469 ha (minimum size of contemporary “megafires”) during extreme drought. In this frequent-fire landscape, mixed-severity fire historically influenced lodgepole and adjacent forests. Lack of large, frequent, low-severity fires degrades contemporary forest ecosystems.

  相似文献   

Temperate zone coastal seascapes: seascape patterning and adjacent seagrass habitat shape the distribution of rocky reef fish assemblages     

Swadling  Daniel S.  Knott  Nathan A.  Rees  Matthew J.  Davis  Andrew R. 《Landscape Ecology》2019,34(10):2337-2352

Landscape Ecology - Whilst the composition and arrangement of habitats within landscape mosaics are known to be important determinants of biodiversity patterns, the influence of seascape patterning...  相似文献   

Amplification of the <Emphasis Type="Italic">Phytophthora infestans</Emphasis> RG57 loci Facilitates <Emphasis Type="Italic">in planta</Emphasis> T-RFLP Identification of Late Blight Genotypes     

Champa P. Wijekoon  Binod B. Pageni  Melanie L. Kalischuk  Newton Z. Lupwayi  Lawrence M. Kawchuk 《American Journal of Potato Research》2017,94(3):251-257

Late blight, caused by the oomycete Phytophthora infestans (Mont.) de Bary, is a devastating disease in potato and tomato and causes yield and quality losses worldwide. The disease first emerged in central America and has since spread in North America including the United States and Canada. Several new genotypes of P. infestans have recently emerged, including US-22, US-23 and US-24. Due to significant economic and environmental impacts, there has been an increasing interest in the rapid identification of P. infestans genotypes. In addition to providing details regarding the various phenotypic characteristics such as fungicide resistance, host preference, and pathogenicity associated with various P. infestans genotypes, information related to pathogen movement and potential recombination may also be determined from the genetic analyses. Restriction fragment length polymorphism (RFLP) analysis with the RG57 loci is one of the most reliable procedures used to genotype P. infestans. However, the RFLP procedure requires propagation and isolation of the pathogen and relatively large amounts of DNA. Isolation of the late blight pathogen is sometimes impossible due to the poor condition of the infected tissues or the presence of fungicide residues. In this study, we describe a procedure to identify P. infestans at the molecular level in planta using terminal restriction fragment length polymorphism (T-RFLP) of the RG57 loci. This T-RFLP assay is sufficiently sensitive to detect and differentiate P. infestans genotypes directly in planta without propagation and isolation of the pathogen, to facilitate the timely implementation of best management practices.  相似文献   

Changes in lipid class content and composition of Isochrysis sp. (T-Iso) grown in batch culture     

Tim D. Nalder  Matthew R. Miller  Michael A. Packer 《Aquaculture International》2015,23(5):1293-1312

  相似文献   

Turbidity‐induced changes in emergent effects of multiple predators with different foraging strategies     

Matthew M. VanLandeghem  David H. Wahl 《Ecology of Freshwater Fish》2011,20(2):279-286

Abstract – In natural systems, prey frequently interact with multiple predators and the outcome often cannot be predicted by summing the effects of individual predator species. Multiple predator interactions can create emergent effects for prey, but how those change across environmental gradients is poorly understood. Turbidity is an environmental factor in aquatic systems that may influence multiple predator effects on prey. Interactions between a cruising predator (largemouth bass Micropterus salmoides) and an ambush predator (muskellunge Esox masquinongy) and their combination foraging on a shared prey (bluegill Lepomis macrochirus) were examined across a turbidity gradient. Turbidity modified multiple predator effects on prey. In clear water, combined predators consumed in total more prey than expected from individual predator treatments, suggesting risk enhancement for prey. In moderately turbid water, the predators consumed fewer prey together than expected, suggesting a risk reduction for prey. At high turbidity, there were no apparent emergent effects; however, the cruising predator consumed more prey than the ambush predator, suggesting an advantage for this predator. Understanding multiple predator traits across a gradient of turbidity increases our understanding of how complex natural systems function.  相似文献   

Soil CO2 emission in sugarcane management systems     

Rose Luiza Moraes Tavares  Zigomar Menezes de Souza  Diego Silva Siqueira  Newton La Scala Júnior  Alan Rodrigo Panosso 《Acta Agriculturae Scandinavica, Section B - Plant Soil Science》2013,63(8):755-762

Sugarcane management systems affect soil attributes such as the carbon cycle. This fact has stimulated the sugar and alcohol industry to refine the sugarcane production systems by replacing the pre-harvest burning (PB) and manual harvest with mechanized harvesting followed by residue deposition. The aim of this study was to evaluate different management systems with respect to C cycling carbon dioxide and soil parameters (chemical, physical and biological) which were determined over the season. Three sugarcane cultivation systems were evaluated at the following periods: (a) PB, (b) 5-year green harvest and (c) 10-year green harvest. The results indicated that CO₂ emission was 36% greater in the 10-year sugarcane green harvest system than in the PB system. The bulk density and macroporosity were the factors that were most affected by the different sugarcane management systems and that significantly influenced soil CO₂ emissions. The principal component analysis showed that soil CO₂ emission was 18% influenced by base saturation (V%) and 14% by pH, especially in the PB area. Additionally, 19% was affected by carbon and macroporosity in the 5- and 10-year green harvest areas, respectively. From our results, it can be concluded that the most CO₂ emissions are in the areas of sugarcane green, this is due to the higher carbon concentration when compared with the area of burning sugarcane. The parameters that most influenced the CO₂ emissions were bulk density, porosity, macroporosity, pH and V%.  相似文献   

The effects of maternal nutrition during the first 50 d of gestation on the location and abundance of hexose and cationic amino acid transporters in beef heifer uteroplacental tissues     

Matthew S Crouse  Kyle J McLean  Josephine Dwamena  Tammi L Neville  Ana Clara B Menezes  Alison K Ward  Lawrence P Reynolds  Carl R Dahlen  Bryan W Neville  Pawel P Borowicz  Joel S Caton 《Journal of animal science》2021,99(1)

We hypothesized that maternal nutrition during the first 50 d of gestation would influence the abundance of hexose transporters, SLC2A1, SLC2A3, and SLC2A5, and cationic amino acid transporters, SLC7A1 and SLC7A2, in heifer uteroplacental tissues. Angus-cross heifers (n = 43) were estrus synchronized, bred via artificial insemination, and assigned at breeding to 1 of 2 dietary intake groups (CON = 100% of requirements to achieve 0.45 kg/d of BW gain or RES = 60% of CON intake) and ovariohysterectomized on day 16, 34, or 50 of gestation (n = 6 to 9/d) in a completely randomized design with a 2 × 3 factorial arrangement of treatments. Uterine cross-sections were collected from the horn ipsilateral to the corpus luteum, fixed in 10% neutral buffered formalin, sectioned at 5 µm, and stained via immunofluorescence for transporters. For each image, areas of fetal membrane (FM; chorioallantois), luminal epithelium (ENDO), superficial glands (SG), deep glands (DG), and myometrium (MYO) were analyzed separately for relative intensity of fluorescence as an indicator of transporter abundance. Analysis of FM was only conducted for days 34 and 50. No transporters in target areas were influenced by a day × treatment interaction (P ≥ 0.06). In ENDO, all transporters were differentially abundant from days 16 to 50 of gestation (P ≤ 0.04), and SLC7A2 was greater (P = 0.05) for RES vs. CON. In SG, SLC7A1 and SLC7A2 were greater (P ≤ 0.04) at day 34 vs. day 16. In DG, SLC2A3 and SLC7A1 were greater (P ≤ 0.05) for CON vs. RES heifers; furthermore, SLC7A1 was greater (P < 0.01) at day 50 vs. days 16 and 34 of gestation. In MYO, SLC7A1 was greater (P < 0.01) for CON vs. RES and was greater (P = 0.02) at days 34 and 50 vs. day 16. There were no differences in FM (P ≥ 0.06). Analysis of all uterine tissues at day 16 determined that SLC2A1, SLC2A3, and SLC7A2 were all differentially abundant across uterine tissue type (P < 0.01), and SLC7A1 was greater (P = 0.02) for CON vs. RES. Analysis of all uteroplacental tissues at days 34 and 50 demonstrated that all transporters differed (P < 0.01) across uteroplacental tissues, and SLC7A1 was greater (P < 0.01) for CON vs. RES. These data are interpreted to imply that transporters are differentially affected by day of gestation, and that hexose and cationic amino acid transporters are differentially abundant across utero-placental tissue types, and that SLC7A1 is responsive to maternal nutritional treatment.  相似文献   

Development and characterization of a technique for percutaneous radiologic gastrojejunostomy tube placement in the dog          下载免费PDF全文

Rebekah M. Mack DVM  DACVIM  Benjamin Staiger DVM  Daniel K. Langlois DVM  DACVIM  Stephen J. Mehler DVM  DACVS  Nathaniel Lam DVM  DACVS  Trevor Moore DVM  DACVIM  Andrew Brown DVM  DACVECC  DECVECC  Matthew W. Beal DVM  DACVECC 《Journal of Veterinary Emergency and Critical Care》2016,26(5):646-653

  相似文献