scholarly journals The accuracy and bias of single-step genomic prediction for populations under selection

2016 ◽  
Author(s):  
Wan-Ling Hsu ◽  
Dorian J. Garrick ◽  
Rohan L. Fernando
Keyword(s):  
Genomic Prediction ◽  
Single Step ◽  
Alternative Analysis ◽  
Genomic Analyses ◽  
Causal Variants ◽  
Entire Matrix ◽  
C And N ◽  
The Mean ◽  
Missing Genotypes ◽  
Improved Accuracy

ABSTRACTIn single-step analyses, missing genotypes are explicitly or implicitly imputed, and this requires centering the observed genotypes, ideally using the mean of the unselected founders. If genotypes are only available on selected individuals, centering on the unselected founder mean is impossible. Here, computer simulation is used to study an alternative analysis that does not require centering genotypes but fits the mean µg of unselected individuals as a fixed effect. To improve numerical properties of the analysis, centering the entire matrix of observed and imputed genotypes, using their sample means can be done in addition to fitting µg. Starting with observed diplotypes from 721 cattle, a 5 generation population was simulated with sire selection to produce 40,000 individuals with phenotypes of which the 1,000 sires had genotypes. The next generation of 8,000 genotyped individuals was used for validation. Evaluations were undertaken: with (J) or without (N) µg when marker covariates were not centered; and with (JC) or without (C) µg when all marker covariates were centered. A pedigree based evaluation was less accurate than genomic analyses. Centering did not influence accuracy of genomic prediction, but fitting µg did. Accuracies were improved when the panel comprised only QTL, models JC and J had accuracies of 99.2%; and models C and N had accuracies of 85.6%. When only markers were in the panel, the 4 models had accuracies of 63.9%. In panels that included causal variants, fitting µg in the model improved accuracy, but had little impact when the panel contained only markers.

scholarly journals Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 266
Author(s):  
Hossein Mehrban ◽  
Masoumeh Naserkheil ◽  
Deuk Hwan Lee ◽  
Chungil Cho ◽  
Taejeong Choi ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Beef Cattle ◽  
Genomic Prediction ◽  
Quantitative Trait ◽  
Carcass Traits ◽  
Best Linear Unbiased Prediction ◽  
Single Step ◽  
Linear Unbiased Prediction ◽  
Single Nucleotide ◽  
Best Linear Unbiased

The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.

An Electrophysiological Measure of Temporal Resolution in Normal Subjects Using Frequency Modulated Signals

2002 ◽  
Vol 11 (1) ◽  
pp. 42-49
Author(s):  
Devin L. McCaslin ◽  
Lawrence L. Feth ◽  
Gary P. Jacobson ◽  
Pamela J. Mishler
Keyword(s):  
Temporal Resolution ◽  
Mismatch Negativity ◽  
Normal Subjects ◽  
Single Step ◽  
Event Related Potential ◽  
Frequency Range ◽  
Temporal Properties ◽  
Step Duration ◽  
The Mean ◽  
Modulated Signals

This investigation was conducted to determine whether an exogenous event-related potential called the mismatch negativity (MMN) would change systematically in response to frequency-modulated signals with varying temporal properties. Both N1 and P2 waveforms were recorded for 50-ms frequency-modulated signals from normal hearing listeners. The standard stimuli for this investigation were continuous sweep tones with center frequencies of 1000 Hz that traversed a frequency range of 200 Hz in a single step. The rare stimuli were signals that traversed the same frequency range in two, four, six, or eight discrete steps. Results suggest that for the 10 participants, 1) the mean MMN peak-to-peak amplitude and mean area decreased significantly with decreases in step duration, 2) MMN area amplitude was the best indicator of psychophysical performance for the two magnitude measures, and 3) MMN onsets and peak latencies did not show either a significant increase or decrease in latency as step duration decreased.

scholarly journals Genomic prediction in a nuclear population of layers using single-step models

2018 ◽  
Vol 97 (2) ◽  
pp. 397-402 ◽  
Author(s):  
Yiyuan Yan ◽  
Guiqin Wu ◽  
Aiqiao Liu ◽  
Congjiao Sun ◽  
Wenpeng Han ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Single Step

scholarly journals Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information

2021 ◽  
Vol 12 ◽  
Author(s):  
Zigui Wang ◽  
Hao Cheng
Keyword(s):  
Molecular Markers ◽  
Genomic Prediction ◽  
Simulated Data ◽  
Software Tool ◽  
Biological Information ◽  
Superior Performance ◽  
Multiple Trait ◽  
Bayesian Lasso ◽  
Trait Analysis ◽  
Causal Variants

Genomic prediction has been widely used in multiple areas and various genomic prediction methods have been developed. The majority of these methods, however, focus on statistical properties and ignore the abundant useful biological information like genome annotation or previously discovered causal variants. Therefore, to improve prediction performance, several methods have been developed to incorporate biological information into genomic prediction, mostly in single-trait analysis. A commonly used method to incorporate biological information is allocating molecular markers into different classes based on the biological information and assigning separate priors to molecular markers in different classes. It has been shown that such methods can achieve higher prediction accuracy than conventional methods in some circumstances. However, these methods mainly focus on single-trait analysis, and available priors of these methods are limited. Thus, in both single-trait and multiple-trait analysis, we propose the multi-class Bayesian Alphabet methods, in which multiple Bayesian Alphabet priors, including RR-BLUP, BayesA, BayesB, BayesCΠ, and Bayesian LASSO, can be used for markers allocated to different classes. The superior performance of the multi-class Bayesian Alphabet in genomic prediction is demonstrated using both real and simulated data. The software tool JWAS offers open-source routines to perform these analyses.

scholarly journals 2-[Hydroxy(2-methoxyphenyl)methyl]acrylonitrile

2012 ◽  
Vol 68 (8) ◽  
pp. o2467-o2467
Author(s):  
M. Bakthadoss ◽  
R. Selvakumar ◽  
R. Madhanraj ◽  
S. Murugavel
Keyword(s):  
Hydrogen Bonds ◽  
Diffraction Pattern ◽  
Benzene Ring ◽  
Dihedral Angle ◽  
Title Compound ◽  
Acta Cryst ◽  
Compound C ◽  
C And N ◽  
The Mean ◽  
Solvent Molecules

In the title compound, C11H11NO2, the mean planes formed by the benzene ring and the C and N atoms of the acryl group are almost orthogonal to each other, with a dihedral angle of 85.7 (1)°. During the structure analysis, it was observed that the unit cell contains large accessible voids, with a volume of 186.9 Å3, which may host disordered solvent molecules. This affects the diffraction pattern, mostly at low scattering angles. Density identified in these solvent-accessible areas was calculated and corrected for using the SQUEEZE routine inPLATON[Spek (2009),Acta Cryst.D65, 148–155]. Despite the presence of the hydroxy group in the molecule, no classical or nonclassical hydrogen bonds are observed in the structure. This may reflect the fact that the O—H group points towards the solvent-accessible void.

scholarly journals Outcomes of a single-step endoscopic ultrasound-guided drainage of pancreatic-fluid collections using an electrocautery-enhanced coaxial lumen-apposing, self-expanding metal stent with and without fluoroscopy

2020 ◽  
Author(s):  
Babatunde Olaiya ◽  
Parit Mekaroonkamol ◽  
Bai-Wen Li ◽  
Julia Massaad ◽  
Cicily T Vachaparambil ◽  
...  
Keyword(s):  
Clinical Success ◽  
Stent Migration ◽  
Single Step ◽  
Success Rates ◽  
Metal Stent ◽  
Technical Success ◽  
Pancreatic Fluid Collections ◽  
Pancreatic Fluid ◽  
The Mean ◽  
Fluid Collections

Abstract Background Fluoroscopy is often used during the endoscopic drainage of pancreatic-fluid collections (PFCs). An electrocautery-enhanced coaxial lumen-apposing, self-expanding metal stent (ELAMS) facilitates a single-step procedure and may avoid the need for fluoroscopy. This study compares the treatment outcomes using ELAMS with and without fluoroscopy. Methods Patients with PFCs who had cystogastrostomy from January 2014 to February 2017 were enrolled. Two groups were studied based on fluoroscopy use. Technical success was defined as uneventful insertion of ELAMS at time of procedure. Clinical success was defined as (i) clinical resolution of symptoms after the procedure and (ii) >75% reduction in cyst size on computed tomography 8 weeks after stent placement. Adverse events including bleeding, stent migration, and infection were recorded. Results A total of 21 patients (13 males) had PFCs drainage with ELAMS in the study period. The mean age was 51.6 ± 14.2 years. Thirteen patients had walled-off necrosis while eight had a pancreatic pseudocyst. The mean size of the PFCs was 11.3 ± 3.3 cm. Fluoroscopy was used in seven cases (33%) and was associated with a longer procedure time compared to non-fluoroscopy (43.1 ± 10.4 vs 33.3 ± 10.5 min, P = 0.025). This association was independent of the size, location, or type of PFCs. Fluoroscopy had no effect on the technical success rates. In fluoroless procedures, the clinical resolution was 91% as compared to 71% in fluoroscopy procedures (P = 0.52) and the radiologic resolution was 57% as compared to 71% in fluoroscopy procedures (P = 0. 65). Three cases of stent migration/displacement occurred in the fluoroless procedures. Conclusions ELAMS may avoid the need for fluoroscopy during cystogastrostomy. Procedures without fluoroscopy were significantly shorter and fluoroscopy use had no impact on the technical or clinical success rates.

scholarly journals The Accuracy and Bias of Single-Step Genomic Prediction for Populations Under Selection

2017 ◽  
Vol 7 (8) ◽  
pp. 2685-2694 ◽  
Author(s):  
Wan-Ling Hsu ◽  
Dorian J. Garrick ◽  
Rohan L. Fernando
Keyword(s):  
Genomic Prediction ◽  
Single Step

Simplified radioimmunoassay of bradykinin in human plasma.

1980 ◽  
Vol 26 (3) ◽  
pp. 429-432
Author(s):  
P S Verma ◽  
P E Lorenz ◽  
G E Sander
Keyword(s):  
Molecular Mass ◽  
Human Plasma ◽  
Normal Values ◽  
Normal Subjects ◽  
Single Step ◽  
Relative Molecular Mass ◽  
Blood Samples ◽  
Analytical Recovery ◽  
Assay Tube ◽  
The Mean

Abstract A greatly simplified radioimmunoassay for bradykinin in human plasma is described. Current techniques require multiple chromatographic steps or extraction procedures with analytical recoveries of bradykinin of often less than 60%. We present a method in which bradykinin is separated from components of higher relative molecular mass (including kininogens) in a single step, by use of a column of Sephadex G-25 medium (PD-10). The mean analytical recovery of tritiated bradykinin added to plasma is 85.5% (SD, 3.5%). The sensitivity of this radioimmunoassay is 25 pg per assay tube, equivalent to 125 ng per liter of plasma. Twenty to 30 blood samples may be completely processed and assayed within 6 h. As determined with this technique, concentrations of bradykinin in plasma from apparently normal subjects ranged from 2.5 to 5.2 microgram/L (mean 4.2, SD 1.1 microgram/L); these values are consistent with previously reported normal values.

scholarly journals Palladium-Catalysed Construction of All-Carbon Quaternary Centres with Propargylic Electrophiles: Challenges in the Simultaneous Control of Regio-, Chemo- and Enantioselectivity

Synthesis ◽  
2018 ◽  
Vol 50 (09) ◽  
pp. 1796-1814 ◽  
Author(s):  
Vilius Franckevičius ◽  
Miles Kenny ◽  
Sybrin Schröder ◽  
Nicholas Taylor ◽  
Paula Jackson ◽  
...  
Keyword(s):  
Careful Analysis ◽  
Single Step ◽  
The Other ◽  
Allylic Alkylation ◽  
Dicarbonyl Compounds ◽  
Simultaneous Control ◽  
C And N ◽  
Coupling Partner ◽  
Three Component Coupling

This article describes the palladium-catalysed three-component coupling of 1,3-dicarbonyl compounds with nucleophiles and propargylic electrophiles for the generation of quaternary all-carbon centres in a single step, which necessitates the simultaneous control of regio-, chemo- and enantioselectivity. The use of propargyl enol carbonates, the source of two of the components, was found to be essential in maintaining high levels of regiocontrol and chemoselectivity, whereas a careful analysis of pK a trends of O-, C- and N-nucleophiles as the other coupling partner indicates that the highest levels of selectivity are likely to be obtained with relatively acidic species, such as phenols, 1,3-dicarbonyl compounds and aromatic N-heterocycles. Finally, studies towards the development of the catalytic enantioselective construction of quaternary all-carbon centres by means of alkenylation and allylic alkylation are disclosed.

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