Handling missingness when modeling the force of infection from clustered seroprevalence data     

Niel Hens  Christel Faes  Marc Aerts  Ziv Shkedy  Koen Mintiens  Hans Laevens  Frank Boelaert 《Journal of Agricultural, Biological & Environmental Statistics》2007,12(4):498-513

Modeling infectious diseases data is a relatively young research area in which clustering and stratification are key features. It is not unlikely for these data to have missing values. If values are missing completely at random, the analysis on the complete cases is valid. However, in practice this assumption is usually not fulfilled. This article shows the effect of ignoring missing data in modeling the force of infection of the bovine herpesvirus-1 in Belgian cattle and proposes the use of weighted generalized estimating equations with constrained fractional polynomials as a flexible modeling tool.  相似文献   

Activation of the Ah receptor by extracts of dietary herbal supplements,vegetables, and fruits     

Jeuken A  Keser BJ  Khan E  Brouwer A  Koeman J  Denison MS 《Journal of agricultural and food chemistry》2003,51(18):5478-5487

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Incorporating parameter uncertainty into prediction intervals for spatial data modeled via a parametric variogram     

Fujun Wang  Melanie M. Wall 《Journal of Agricultural, Biological & Environmental Statistics》2003,8(3):296-309

In spatial predictions, researchers usually treat the estimated theoretical variogram parameters as known without error and ignore the variability of the parameter estimators. Although the prediction is still unbiased, the prediction error is usually underestimated. Therefore, the coverage probability of the prediction interval usually is lower than the nominal probability. A simulation study is performed to show how the coverage probability for prediction relates to the true range and sill of an exponential variogram. This article proposes two parametric bootstrap methods to incorporate the variability of the corresponding parameter estimators. A simulation study is performed to evaluate the coverage probability of these proposed methods. Finally, we apply the parametric bootstrap methods to a real dataset and compare the results with those from naive (i.e., treating estimated parameters as known) and Bayesian methods.  相似文献   

Nitrogen fixation in biological soil crusts from southeast Utah,USA   总被引：20，自引：0，他引：20  

Jayne Belnap 《Biology and Fertility of Soils》2002,35(2):128-135

Biological soil crusts can be the dominant source of N for arid land ecosystems. We measured potential N fixation rates biweekly for 2 years, using three types of soil crusts: (1) crusts whose directly counted cells were >98% Microcoleus vaginatus (light crusts); (2) crusts dominated by M. vaginatus, but with 20% or more of the directly counted cells represented by Nostoc commune and Scytonema myochrous (dark crusts); and (3) the soil lichen Collema sp. At all observation times, Collema had higher nitrogenase activity (NA) than dark crusts, which had higher NA than light crusts, indicating that species composition is critical when estimating N inputs. In addition, all three types of crusts generally responded in a similar fashion to climate conditions. Without precipitation within a week of collection, no NA was recorded, regardless of other conditions being favorable. Low (<1°C) and high (>26°C) temperatures precluded NA, even if soils were moist. If rain or snow melt had occurred 3 or less days before collection, NA levels were highly correlated with daily average temperatures of the previous 3 days (r²=0.93 for Collema crusts; r²=0.86 for dark crusts and r²=0.83 for light crusts) for temperatures between 1°C and 26°C. If a precipitation event followed a long dry period, NA levels were lower than if collection followed a time when soils were wet for extended periods (e.g., winter). Using a combination of data from a recording weather datalogger, time-domain reflectometry, manual dry-down curves, and N fixation rates at different temperatures, annual N input from the different crust types was estimated. Annual N input from dark crusts found at relatively undisturbed sites was estimated at 9 kg ha^-1 year^-1. With 20% cover of the N-fixing soil lichen Collema, inputs are estimated at 13 kg ha^-1 year^-1. N input from light crusts, generally indicating soil surface disturbance, was estimated at 1.4 kg ha^-1 year^-1. The rates in light crusts are expected to be highly variable, as disturbance history will determine cyanobacterial biomass and therefore N fixation rates.  相似文献   

Interaction of Metallic Cations with the Humic Acids Extracted from a Solonetz-Solod-Black Soil Sequenze in Alberta     

S. U. Khan 《植物养料与土壤学杂志》1970,127(2):121-126

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QTL mapping of sheath blight resistance in a deep-water rice cultivar   总被引：2，自引：0，他引：2  

Dong Fu  Liang Chen  Guohui Yu  Yi Liu  Qiaojun Lou  Hanwei Mei  Liang Xiong  Mingshou Li  Xiaoyan Xu  Lijun Luo 《Euphytica》2011,180(2):209-218

Sheath blight, caused by the pathogen Rhizoctonia solani Kühn, is one of the most serious diseases of rice and leads to severe yield loss worldwide. A recombinant inbred line (RIL) population consisting of 121 lines was constructed from a cross between HH1B and RSB03, the latter of which is a deep-water rice variety. Five traits were used to evaluate sheath blight resistance, namely disease rating (DR), lesion length (LL), lesion height (LH), relative lesion length [RLL, the ratio of LL to plant height (PH)], and relative LH (RLH, the ratio of LH to PH). Using the RIL population and 123 molecular markers, we identified 28 quantitative trait loci (QTLs) for the five traits in two environments. These QTLs are located on nine chromosomes and most of them are environment specific. A major QTL for DR (qSBR1) on chromosome 1 was identified with contributions of 12.7% at Shanghai and 42.6% at Hainan, and it collocated with a QTL for PH. The allele at this locus from RSB03 enhances sheath blight resistance and increases PH. Another QTL for DR on chromosome 7 was adjacent to QTLs for heading date (HD) and four other disease traits. RSB03 also carries the resistant allele at this locus and shortens HD. The susceptible parent, HH1B, provides the resistance allele at the locus qSBR8, where QTLs for four other disease traits were identified. QTL mapping results showed that most QTLs for LL, LH, RLL, and RLH are collocated with QTLs for DR. Three QTLs for DR are independent from HD, PH, and four other disease traits, while four QTLs are closely related to HD and PH. Four QTLs for LL, LH, RLL, and RLH are independent from DR, HD, and PH, while there is only one region harboring QTLs for these four traits and HD. Correlation analysis and QTL mapping results indicated that LL, LH, RLL, and RLH might be important indices, like DR, for evaluating the level of resistance to rice sheath blight.  相似文献   

Allele mining and haplotype discovery in barley candidate genes for drought tolerance     

András Cseri  Mátyás Cserháti  Maria von Korff  Bettina Nagy  Gábor V. Horváth  András Palágyi  János Pauk  Dénes Dudits  Ottó Törjék 《Euphytica》2011,181(3):341-356

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.  相似文献   

Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamental traits and disease resistances     

Arwa Shahin  Paul Arens  Adriaan W. Van Heusden  Gerard Van Der Linden  Martijn Van Kaauwen  Nadeem Khan  Henk J. Schouten  W. Eric Van De Weg  Richard G. F. Visser  Jaap M. Van Tuyl 《Plant Breeding》2011,130(3):372-382

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Impact of epistasis and QTL × environmental interaction on the oil filling rate of soybean seed at different developmental stages     

Zhenfeng Jiang  Binbin Zhang  Weili Teng  Yingpeng Han  Xue Zhao  Desheng Sun  Zhongchen Zhang  Wenbin Li 《Euphytica》2011,177(3):431-442

The oil accumulation in the developing soybean seed has been shown to be a dynamic process with different rates and activities at different phases affected by both genotype and environment. The objective of the present study was to investigate additive, epistatic and quantitative trait loci (QTL) × environment interaction (QE) effects of the QTL controlling oil filling rate in soybean seed. A total of 143 recombinant inbred lines (RILs) derived from the cross of Charleston and Dongnong 594 were used in this study to obtain 2 years of field data (2004 and 2005). A total of 26 QTL with significantly unconditional and conditional additive (a) effect and/or additive × environment interaction (ae) effect at different filling stages were identified on 14 linkage groups. Among the QTL with significant a effects, 18 QTL showed positive effects and 6 QTL had negative effects on seed filling rate of oil content during seed development. A total of 29 epistatic pairwise QTL underlying seed filling rate were identified at different filling stages. About 28 pairs of the QTL showed additive × additive epistatic (aa) effects and 14 pairs of the QTL showed aa × environment interaction (aae) effects at different filling stages. QTL with aa and aae (additive × additive × environment) effects appeared to vary at different filling stages. Our results demonstrated that oil filling rate in soybean seed were under genetic, developmental and environmental control.  相似文献   

Molecular genetics of race non-specific rust resistance in wheat   总被引：1，自引：0，他引：1  

Evans S. Lagudah 《Euphytica》2011,179(1):81-91

Over 150 resistance genes that confer resistance to either leaf rust, stripe rust or stem rust have been catalogued in wheat or introgressed into wheat from related species. A few of these genes from the ‘slow-rusting’ adult plant resistance (APR) class confer partial resistance in a race non-specific manner to one or multiple rust diseases. The recent cloning of two of these genes, Lr34/Yr18, a dual APR for leaf rust and stripe rust, and Yr36, a stripe rust APR gene, showed that they differ from other classes of plant resistance genes. Currently, seven Lr34/Yr18 haplotypes have been identified from sequencing the encoding ATP Binding Cassette transporter gene from diverse wheat germplasm of which one haplotype is commonly associated with the resistance phenotype. The paucity of well characterised APR genes, particularly for stem rust, calls for a focused effort in developing critical genetic stocks to delineate quantitative trait loci, construct specific BAC libraries for targeted APR genes to facilitate robust marker development for breeding applications, and the eventual cloning of the encoding genes.  相似文献