Browsing by Author "Liu H"

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    Comparison of linkage disequilibrium estimated from genotypes versus haplotypes for crossbred populations
    (BioMed Central Ltd, 2022-02-08) Alemu SW; Bijma P; Calus MPL; Liu H; Fernando RL; Dekkers JCM
    Background Linkage disequilibrium (LD) is commonly measured based on the squared coefficient of correlation (r²) between the alleles at two loci that are carried by haplotypes. LD can also be estimated as the r² between unphased genotype dosage at two loci when the allele frequencies and inbreeding coefficients at both loci are identical for the parental lines. Here, we investigated whether r² for a crossbred population (F1) can be estimated using genotype data. The parental lines of the crossbred (F1) can be purebred or crossbred. Methods We approached this by first showing that inbreeding coefficients for an F1 crossbred population are negative, and typically differ in size between loci. Then, we proved that the expected r² computed from unphased genotype data is expected to be identical to the r² computed from haplotype data for an F1 crossbred population, regardless of the inbreeding coefficients at the two loci. Finally, we investigated the bias and precision of the r² estimated using unphased genotype versus haplotype data in stochastic simulation. Results Our findings show that estimates of r² based on haplotype and unphased genotype data are both unbiased for different combinations of allele frequencies, sample sizes (900, 1800, and 2700), and levels of LD. In general, for any allele frequency combination and r² value scenarios considered, and for both methods to estimate r², the precision of the estimates increased, and the bias of the estimates decreased as sample size increased, indicating that both estimators are consistent. For a given scenario, the r² estimates using haplotype data were more precise and less biased using haplotype data than using unphased genotype data. As sample size increased, the difference in precision and biasedness between the r² estimates using haplotype data and unphased genotype data decreased. Conclusions Our theoretical derivations showed that estimates of LD between loci based on unphased genotypes and haplotypes in F1 crossbreds have identical expectations. Based on our simulation results, we conclude that the LD for an F1 crossbred population can be accurately estimated from unphased genotype data. The results also apply for other crosses (F2, F3, Fn, BC1, BC2, and BCn), as long as (selected) individuals from the two parental lines mate randomly.
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    Effect of Heat Treatment on Protein Self-Digestion in Ruminants' Milk
    (MDPI (Basel, Switzerland), 2023-09-21) Leite JAS; Montoya CA; Maes E; Hefer C; Cruz RAPA; Roy NC; McNabb WC; Liu Q; Liu H; Zhang J
    This study investigated whether heat treatments (raw, 63 °C for 30 min, and 85 °C for 5 min) affect protein hydrolysis by endogenous enzymes in the milk of ruminants (bovine, ovine, and caprine) using a self-digestion model. Self-digestion consisted of the incubation for six hours at 37 °C of the ruminants' milk. Free amino group concentration was measured by the o-phthaldialdehyde method, and peptide sequences were identified by chromatography-mass spectrometry. Results showed that heat treatments prior to self-digestion decreased the free NH2 by 59% in bovine milk heated at 85 °C/5 min, and by 44 and 53% in caprine milk heated at 63 °C/30 min and 85 °C/5 min, respectively. However, after self-digestion, only new free amino groups were observed for the raw and heated at 63 °C/30 min milk. β-Casein was the most cleaved protein in the raw and heated at 63 °C/30 min bovine milk. A similar trend was observed in raw ovine and caprine milk. Self-digestion increased 6.8-fold the potential antithrombin peptides in the bovine milk heated at 63 °C/30 min. Enhancing bioactive peptide abundance through self-digestion has potential applications in the industry for functional products. Overall, heat treatments affected the free amino groups according to the species and heat treatment applied, which was reflected in the varying degrees of cleaved peptide bonds and peptides released during self-digestion.
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    Immobilization of Horseradish Peroxidase and Myoglobin Using Sodium Alginate for Treating Organic Pollutants
    (MDPI (Basel, Switzerland), 2024-03-15) Wang X; Ghanizadeh H; Khan S; Wu X; Li H; Sadiq S; Liu J; Liu H; Yue Q; Hung Y-T
    Removing organic pollutants from wastewater is crucial to prevent environmental contamination and protect human health. Immobilized enzymes are increasingly being explored for wastewater treatment due to their specific catalytic activities, reusability, and stability under various environmental conditions. Peroxidases, such as horseradish peroxidase (HRP) and myoglobin (Mb), are promising candidates for immobilized enzymes utilized in wastewater treatment due to their ability to facilitate the oxidation process of a wide range of organic molecules. However, the properties of the carrier and support materials greatly influence the stability and activity of immobilized HRP and Mb. In this research, we developed immobilized HRP and Mb using support material composed of sodium alginate and CaCl2 as carriers and glutaraldehyde as a crosslinking agent. Following this, the efficacy of immobilized HRP and Mb in removing aniline, phenol, and p-nitrophenol was assessed. Both immobilized enzymes removed all three organic pollutants from an aqueous solution, but Mb was more effective than HRP. After being immobilized, both enzymes became more resilient to changes in temperature and pH. Both immobilized enzymes retained their ability to eliminate organic pollutants through eight treatment cycles. Our study uncovered novel immobilized enzyme microspheres and demonstrated their successful application in wastewater treatment, paving the way for future research.
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    Recent Advances in Pulse-Coupled Neural Networks with Applications in Image Processing
    (MDPI (Basel, Switzerland), 2022-10-11) Liu H; Liu M; Li D; Zheng W; Yin L; Wang R; Song BC
    This paper surveys recent advances in pulse-coupled neural networks (PCNNs) and their applications in image processing. The PCNN is a neurology-inspired neural network model that aims to imitate the information analysis process of the biological cortex. In recent years, many PCNN-derived models have been developed. Research aims with respect to these models can be divided into three categories: (1) to reduce the number of manual parameters, (2) to achieve better real cortex imitation performance, and (3) to combine them with other methodologies. We provide a comprehensive and schematic review of these novel PCNN-derived models. Moreover, the PCNN has been widely used in the image processing field due to its outstanding information extraction ability. We review the recent applications of PCNN-derived models in image processing, providing a general framework for the state of the art and a better understanding of PCNNs with applications in image processing. In conclusion, PCNN models are developing rapidly, and it is projected that more applications of these novel emerging models will be seen in future.
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    Transverse-momentum and pseudorapidity distributions of charged hadrons in pp collisions at square root of s = 7 TeV.
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CMS Collaboration
    Charged-hadron transverse-momentum and pseudorapidity distributions in proton-proton collisions at square root of s = 7  TeV are measured with the inner tracking system of the CMS detector at the LHC. The charged-hadron yield is obtained by counting the number of reconstructed hits, hit pairs, and fully reconstructed charged-particle tracks. The combination of the three methods gives a charged-particle multiplicity per unit of pseudorapidity dN(ch)/dη|(|η|<0.5) = 5.78 ± 0.01(stat) ± 0.23(syst) for non-single-diffractive events, higher than predicted by commonly used models. The relative increase in charged-particle multiplicity from square root of s = 0.9 to 7 TeV is [66.1 ± 1.0(stat) ± 4.2(syst)]%. The mean transverse momentum is measured to be 0.545 ± 0.005(stat) ± 0.015(syst)  GeV/c. The results are compared with similar measurements at lower energies.