Abstract
Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated ...using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H−1) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h2 = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G−1 and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.
Lay Summary
The estimation of variance components is computationally expensive under large-scale genetic evaluations due to several inversions of the coefficient matrix. Variance components are used as parameters for estimating breeding values in mixed model equations (MME). However, resulting breeding values are not Best Linear Unbiased Predictions (BLUP) unless the variance components approach the true parameters. The increasing availability of genomic data requires the development of new methods for improving the efficiency of variance component estimations. Therefore, this study aimed to reduce the costs of single-step genomic REML (ssGREML) with the Algorithm for Proven and Young (APY) for estimating variance components with truncated pedigree and phenotypes using simulated data. In addition, we investigated the influence of truncation on variance components and genetic parameter estimates. Under APY, the size of the core group influences the similarity of breeding values and their reliability compared to the full genomic matrix. In this study, we found that to ensure reliable variance component estimation, it is required to consider a core size that corresponds to the number of largest eigenvalues explaining around 98% of the total variation in G to avoid biased parameters. In terms of costs, the use of APY slightly decreased the time for ordering and symbolic factorization with no impact on estimations.
Estimation of variance components is becoming computationally challenging due to the increasing size of genomic information. We investigated the impacts of using the algorithm for proven and young (APY) in genetic evaluations. The use of APY has no impact on variance components and genetic parameters estimation.
Improvement in cognitive function after orthotopic liver transplantation (LT) has been demonstrated in the acute setting immediately after LT and in acute liver failure. However, the longterm changes ...in cerebral hemodynamics after LT remain unexplored. Therefore, we aimed to evaluate the longterm changes in cerebral hemodynamics of patients with cirrhosis after LT. In this prospective cohort study, we performed transcranial Doppler ultrasonography (TCD) measuring the pulsatility index (PI), resistance index (RI), and breath‐holding index (BHI) to evaluate cerebrovascular structural integrity and reactivity, respectively, in both middle cerebral arteries before and after LT. Neuropsychometric tests and West‐Haven criteria were used for hepatic encephalopathy (HE) characterization. Interleukin 6 and tumor necrosis factor α plasma levels were measured. Descriptive statistics and Wilcoxon’s test were used. There were 27 patients who were included. Median follow‐up after LT was 6 months, mean age before LT was 46.3 ± 10.3 years, the main etiology was hepatitis C virus (59%), and most of the patients were Child‐Pugh B (15/27). Model for End‐Stage Liver Disease (MELD) score was 16 ± 7.5, MELD‐Na was 19.3 ± 7.1, Psychometric Hepatic Encephalopathy Score was –3.48 ± 3.66, and critical flicker fusion (CFF) was 40.28 ± 5.70 Hz. Before LT, 17/27 patients had HE and 11/27 ascites. A decrease of 20.8% and 13.5% in PI and RI was observed after LT (P < 0.001, both), together with an increase in BHI (32.4%, P = 0.122). These changes in cerebral hemodynamics paralleled those in systemic inflammation. Clinical improvement in cognition was observed in all patients with overt HE after LT. In conclusion, these results show a significant improvement in cerebral hemodynamics after LT, obtained through TCD, indicating less arterial cerebral vasoconstriction together with a decrease in systemic inflammation. Changes in cerebral vasoconstriction can be the basis for the improvement in cognitive function after LT in the long term.
Abstract The objective of this work was to propose a new stopping criterion to shorten the computing time of the PampaPlus genetic improvement software, while maximizing the genetic qualification ...index (GQI) of the progeny, controlling inbreeding, and avoiding unintended culling. Data from two beef-cattle herds integrating PampaPlus were used. Five mating scenarios were built using different numbers of sires (9 to 37) and dams (142 to 568). The analyzed algorithm inputs were: expected progeny differences, pedigree information, maximum inbreeding, maximum and minimum number of matches for each sire, and penalty weights for poor performance. The analyzed response variables were computing time and the GQI of the progenies. Three stopping criteria were used: original stopping criterion fixed at 1,000 iterations; saturation stopping criterion (SSC), based on GQI variance; and Bhandari’s stopping criterion (BSC), which includes the generation interval parameter. SSC and BSC reduced processing time in 24.43-53.64% and in 14.32-50.87%, respectively. BSC reaches solution in less time, without losses in GQI quality. BSC is generalizable and effective to reduce the processing time of mating recommendations.
Resumo O objetivo deste trabalho foi propor um novo critério de parada para diminuir o tempo de processamento do programa de melhoramento genético PampaPlus, além de maximizar o índice de qualificação genética (GQI) da progênie, controlar a endogamia e evitar o descarte não intencional. Foram utilizados dados de dois rebanhos integrantes do PampaPlus. Cinco cenários de acasalamento foram elaborados com diferentes números de touros (9 a 37) e vacas (142 a 568). Os dados analisados foram: diferenças esperadas na progênie, informações de pedigree, máxima endogamia, número máximo e mínimo de acasalamentos por touro, e penalidades para desempenho inferior. As variáveis analisadas foram tempo de processamento e o GQI das progênies. Foram utilizados três critérios de parada: critério de parada original, fixado em 1.000 iterações; critério de parada por saturação (SSC), baseado na variância do GQI; e critério de parada de Bhandari (BSC), que inclui o parâmetro de intervalo de gerações. O SSC e o BSC reduziram o tempo de processamento em 24,43-53,64% e em 14,32-50,87%, respectivamente. O BSC atinge solução em menos tempo, sem perda da qualidade do GQI. O BSC é generalizável e efetivo em reduzir o tempo de processamento das recomendações de acasalamento.
Pedigree information is incomplete by nature and commonly not well-established because many of the genetic ties are not known
or can be wrong. The genomic era brought new opportunities to assess ...relationships between individuals. However, when pedigree and genomic information are used simultaneously, which is the case of single-step genomic BLUP (ssGBLUP), defining the genetic base is still a challenge. One alternative to overcome this challenge is to use metafounders, which are pseudo-individuals that describe the genetic relationship between the base population individuals. The purpose of this study was to evaluate the impact of metafounders on the estimation of breeding values for tick resistance under ssGBLUP for a multibreed population composed by Hereford, Braford, and Zebu animals. Three different scenarios were studied: pedigree-based model (BLUP), ssGBLUP, and ssGBLUP with metafounders (ssGBLUPm). In ssGBLUPm, a total of four different metafounders based on breed of origin (i.e., Hereford, Braford, Zebu, and unknown) were included for the animals with missing parents. The relationship coefficient between metafounders was in average 0.54 (ranging from 0.34 to 0.96) suggesting an overlap between ancestor populations. The estimates of metafounder relationships indicate that Hereford and Zebu breeds have a possible common ancestral relationship. Inbreeding coefficients calculated following the metafounder approach had less negative values, suggesting that ancestral populations were large enough and that gametes inherited from the historical population were not identical. Variance components were estimated based on ssGBLUPm, ssGBLUP, and BLUP, but the values from ssGBLUPm were scaled to provide a fair comparison with estimates from the other two models. In general, additive, residual, and phenotypic variance components in the Hereford population were smaller than in Braford across different models. The addition of genomic information increased heritability for Hereford, possibly because of improved genetic relationships. As expected, genomic models had greater predictive ability, with an additional gain for ssGBLUPm over ssGBLUP. The increase in predictive ability was greater for Herefords. Our results show the potential of using metafounders to increase accuracy of GEBV, and therefore, the rate of genetic gain in beef cattle populations with partial levels of missing pedigree information.
The aim of this study was to perform a Bayesian genomewide association study (GWAS) to identify genomic regions associated with growth traits in Hereford and Braford cattle, and to select Tag‐SNPs to ...represent these regions in low‐density panels useful for genomic predictions. In addition, we propose candidate genes through functional enrichment analysis associated with growth traits using Medical Subject Headings (MeSH). Phenotypic data from 126,290 animals and genotypes for 131 sires and 3,545 animals were used. The Tag‐SNPs were selected with BayesB (π = 0.995) method to compose low‐density panels. The number of Tag‐single nucleotide polymorphism (SNP) ranged between 79 and 103 SNP for the growth traits at weaning and between 78 and 100 SNP for the yearling growth traits. The average proportion of variance explained by Tag‐SNP with BayesA was 0.29, 0.23, 0.32 and 0.19 for birthweight (BW), weaning weight (WW205), yearling weight (YW550) and postweaning gain (PWG345), respectively. For Tag‐SNP with BayesA method accuracy values ranged from 0.13 to 0.30 for k‐means and from 0.30 to 0.65 for random clustering of animals to compose reference and validation groups. Although genomic prediction accuracies were higher with the full marker panel, predictions with low‐density panels retained on average 76% of the accuracy obtained with BayesB with full markers for growth traits. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene products related to the growth traits. The proposed Tag‐SNP panels may be useful for future fine mapping studies and for lower‐cost commercial genomic prediction applications.
The use of carotenoids in foods is limited due to their poor solubility in water-rich matrices, and the nanoencapsulation emerges as an alternative to allowing the solubilization and to protect the ...carotenoids against degradation. The aims of this study were to produce, by the interfacial deposition of the preformed polymer, to characterize, and evaluate the stability of nanocapsules obtained from a blend of β-carotene, α-carotene, and lutein (BALNs) and nanocapsules of synthetic β-carotene (BNs). The encapsulation efficiency, transmission electron microscopy, and the logarithm of the distribution of the coefficient of the BALNs and BNs, with 26 μg/mL of carotenoids, were performed after preparation. During 100 days of storage (4 °C) for the BALNs and BNs, the carotenoids retention, hydrogen potential, color, particle diameter, and the zeta potential were analyzed. The
z
-average and zeta potential after 100 days of storage for the BALNs and BNs were, respectively, 166.53 ± 4.71 nm/−18.37 ± 2.06 mV and 190.90 ± 7.87 nm/−9.08 ± 1.23 mV. At the end of storage, the β-carotene content was 67.62 ± 7.77 % (BALNs) and 11.69 ± 1.65 % (BNs). The β-carotene retention in the BALNs was higher than in the BNs probably due to the synergism that occurs among the compounds. Regardless of the decrease in the pH values and the b* coordinate, the formulations of the BALNs and BNs were considered physically stable during the storage. Nevertheless, beyond the physical stability, the BALNs presented a satisfactory carotenoid retention at end of storage.
Intracerebral hemorrhage (ICH) is associated with an ominous outcome influenced by the time to hospital presentation.
This study aims to identify the factors that influence an early hospital arrival ...after ICH and the relationship with outcome.
In this multicenter registry, patients with confirmed ICH on CT scan and well-known time of symptoms onset were studied. Clinical data, arrival conditions, and prognostic scores were analyzed. Multivariate models were built to find independent predictors of < 6 h arrival (logistic regression) and in-hospital death (Cox proportional-hazards model).
Among the 473 patients analyzed (51% women, median age 63 years), the median delay since onset to admission was 6.25 h (interquartile range: 2.5-24 h); 7.8% arrived in < 1 h, 26.3% in < 3 h, 45.3% in < 6 h, and 62.3% in < 12 h. The in-hospital, 30-day and 90-day case fatality rates were 28.8%, 30.0%, and 32.6%, respectively. Predictors of arrival in < 6 h were hypertension treatment (odds ratios OR: 1.675, 95% confidence intervals CI: 1.030-2.724), ≥ 3 years of schooling (OR: 1.804, 95% CI: 1.055-3.084), and seizures at ICH onset (OR: 2.416, 95% CI: 1.068-5.465). Predictors of death (56.9% neurological) were systolic blood pressure > 180 mmHg (hazards ratios HR: 1.839, 95% CI: 1.031-3.281), ICH score ≥ 3 (HR: 2.302, 95% CI: 1.300-4.074), and admission Glasgow Coma Scale < 8 (HR: 4.497, 95% CI: 2.466-8.199). Early arrival was not associated with outcome at discharge, 30 or 90 days.
In this study, less than half of patients with ICH arrived to the hospital in < 6 h. However, early arrival was not associated with the short-term outcome in this data set.
O uso de métodos estatísticos para avaliar o crescimento e produção das plantas é crucial para o avanço tecnológico do feijoeiro. A pesquisa teve por objetivo dimensionar a amostra para a estimação ...da média de caracteres avaliados em diferentes cultivares e condições hídricas. Os dados foram coletados quinzenalmente a partir de dois experimentos fatoriais 3 x 2 (3 cultivares: Triunfo, Garapiá e FC104; 2 regimes hídricos: irrigado, não irrigado). Foram coletados dezoito caracteres (estatura, diâmetro da haste, número de nós, comprimento da raiz, massa fresca e seca da parte aérea e raízes, temperatura foliar, área foliar, número de nódulos, massa fresca e seca dos nódulos, número de vagens, comprimento das vagens, grãos por vagem, grãos por planta e massa seca dos grãos). O tamanho da amostra foi determinado através do método de reamostragem boodstrap a partir de de 2.000 reamostragens, e foi definido pelo número de plantas a partir das quais o intervalo de confiança de 95% foi de 10% a 40% da estimativa média. Como resultado, o tamanho da amostra é diferente entre os caracteres e entre as cultivares e condições hídricas utilizadas. No intervalo de confiança de 95% com erro padrão de 40% da estimativa da média, para avaliar todos os caracteres analisados são necessárias 44 plantas dos caracteres de parte aérea, 132 plantas para os caracteres de raiz e 12 plantas nos caracteres produtivos. Para analisar os dezoito caracteres estudados são necessárias 132 plantas.
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