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A bridging multi-scale method is proposed for the analysis of a class of localization problems in which the micropolar-continuum model is used to describe the localized deformation and the dynamic failure occurs only in a small number of localized regions. It starts with a concurrent discretization of the entire domain with both coarse- and fine-scale finite-element meshes. The coarse-scale mesh is employed to capture the nonlinear response with long wavelength outside the localized regions, whereas the fine-scale mesh captures the detailed physics of the localized deformation. For both the coarse and fine-scale meshes to coexist, a bridging scale term is constructed so that the information common to both scales is correctly subtracted. To achieve computational efficiency, the localized regions are first identified by a preliminary calculation and the fine-scale degrees of freedom (DOFs) outside the localized regions are mathematically represented by the construction of dynamic interface conditions applied to the edges of these regions. Hence, a large portion of the fine-scale DOFs are eliminated and the fine-scale equations are reduced to a much smaller set with the added dynamic interface conditions. The two-way coupled coarse-scale and reduced fine-scale equations are then solved by a mixed time integration procedure. Applications to one-dimensional and two-dimensional dynamic shear localization problems are presented. [Copyright &y& Elsevier]

The proposed mathematical model of nanomechanics for rubbery materials provides seven parameters to characterize the stress-strain response of rubbery materials as a function of time and temperature. Especially, two parameters of an attractive energy, κ , and an internal variable, ξ , are newly introduced to describe the departures from the classical thermodynamics of rubber elasticity. The mathematical model can reproduce the entropy and energy components on stress with various conditions such as the degree of cross-links, the extent of swelling, the temperature dependence and the strain rate dependence. It also offers physical insights represented by the quantitative molecular structural parameters such as the number of non-bonding interactions and its potential energy. As a conclusion the energy component can be associated with the non-bonding potential energy of the dipole-dipole interaction (0.3–0.9 kJ/mol) and the steric interaction to rotation about the chain backbone (16–20 kJ/mol). [ABSTRACT FROM AUTHOR]

Closed‐pig line breeding could change the genetic structure at a genome‐wide scale because of the selection in a pig breeding population. We investigated the changes in population structure among generations at a genome‐wide scale and the selected loci across the genome by comparing the observed and expected allele frequency changes in mycoplasma pneumonia of swine (MPS)‐selected pigs. Eight hundred and seventy‐four Landrace pigs, selected for MPS resistance without reducing average daily gain over five generations, had 37,299 single nucleotide polymorphisms (SNPs) and were used for genomic analyses. Regarding population structure, individuals in the first generation were the most widely distributed and then converged into a specific group, as they were selected over five generations. For allele frequency changes, 96 and 14 SNPs had higher allele frequency changes than the 99.9% and 99.99% thresholds of the expected changes, respectively. These SNPs were evenly spread across the genome, and a few of these selected regions overlapped with previously detected quantitative trait loci for MPS and immune‐related traits. Our results indicated that the considerable changes in allele frequency were identified in many regions across the genome by closed‐pig line breeding based on estimated breeding value. [ABSTRACT FROM AUTHOR]

Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for the genetic improvement of disease resistance in pigs. The objective of this study was to detect a novel QTL for a total of 22 production, respiratory disease, and immune-related traits in Landrace pigs. A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip. We performed single nucleotide polymorphism (SNP)-based and haplotype-based genome-wide association studies (GWAS) to detect a novel QTL and to evaluate the possibility of a pleiotropic QTL for these traits. SNP-based GWAS detected a total of six significant regions in backfat thickness, ratio of granular leucocytes to lymphatic cells, plasma concentration of cortisol at different ages, and complement alternative pathway activity in serum. The significant region detected by haplotype-based GWAS was overlapped across the region detected by SNP-based GWAS. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic QTL among traits, only three of these detected QTL regions overlapped among traits, and many detected regions independently affected the traits. [ABSTRACT FROM AUTHOR]

Five generations of Landrace pigs selected for average daily gain, backfat thickness, Mycoplasmal pneumonia of swine (MPS) lesion score, and plasma cortisol levels, was executed to decrease the MPS lesion score. Genetic parameters and correlated genetic responses for respiratory disease and peripheral blood immune traits were estimated in 1395 Landrace pigs. We estimated the negative genetic correlation of MPS lesion score with phagocytic activity (PA) at 7 weeks of age (-0.67). The breeding values of PA at 7 weeks of age and 105 kg body weight and the correlated selection response of the ratio of granular leukocytes to lymphocytes at 105 kg body weight were significantly increased, and sheep red blood cell-specific antibody production (AP) was significantly decreased in a selection-dependent manner. Increasing of natural immunological indicators (e.g. PA) and decreasing of humoral immunological indicator (e.g. AP) were observed due to genetically decreasing MPS lesion score. [ABSTRACT FROM AUTHOR]

Mycoplasma pneumonia of swine (MPS) is responsible for significant economic losses in the swine industry. We selected Landrace pigs for reduced MPS pulmonary lesions over five generations, and measured concentrations of the following cytokines: interleukin (IL)-10, IL-13, IL-17, tumor necrosis factor (TNF)-α and interferon (IFN)-? to estimate their correlation with MPS lesions. Sheep red blood cells (SRBC) were injected twice intramuscularly at 70 and 95 kg body weight. Blood serum samples were collected after 1 week of secondary SRBC inoculation and cytokine concentrations were analyzed by ELISA. Genetic parameters and breeding values were estimated. The heritability estimates of IL-10, IL-13, IL-17, TNF-α and IFN-? were 0.20 ± 0.06, 0.12 ± 0.06, 0.27 ± 0.07, 0.20 ± 0.10 and 0.05 ± 0.03, respectively. Genetic correlations of IL-17 and TNF-α with pulmonary MPS lesions were high (-0.86 ± 0.13 and 0.69 ± 0.29, respectively) and those of IFN-? and IL-13 with MPS lesions were moderately negative (-0.45). Through selection, the breeding values of IL-17 and IFN-? increased substantially and those of TNF-α decreased. These results suggest that innate and cellular immunity are more important for the suppression of pulmonary lesions in MPS than humoral-mediated immunity, such as antibody response. [ABSTRACT FROM AUTHOR]

The thoracic vertebral number is associated with body length and carcass traits, and represents one of the most important traits in the pig industry. Recent studies have shown that vertnin ( VRTN) gene is associated with variations in the vertebral number in commercial European pigs. However, the genetic relationships and effect of this VRTN gene in pig production and carcass traits remain uncertain. Therefore, we investigated the genetic relationships among traits such as vertebral numbers, carcass weight and length-related traits, and meat production traits, and the effect of VRTN gene polymorphisms on these traits in a Duroc purebred population selected for its meat production traits. Highly positive genetic correlations were obtained between the thoracic vertebral numbers and length-related traits (0.56 to 0.84), whereas low correlations were obtained with production traits and carcass weight (−0.16 to 0.05). VRTN gene polymorphisms indicated that the number of thoracic vertebrae and length-related traits were significantly associated with the VRTN genotype, but had no significant effect on production traits and carcass weight. The results indicate that VRTN gene may be used as an effective selection marker to obtain pigs with high thoracic vertebral numbers and length-related traits, without adversely affecting meat production traits. [ABSTRACT FROM AUTHOR]

ABSTRACT The leptin receptor ( LEPR) gene is considered a candidate gene for fatness traits. It is located on SSC 6 in a region in which quantitative trait loci (QTLs) for backfat thickness (BF), fat area ratios, and serum leptin concentration (LEPC) have previously been detected in a Duroc purebred population. The objectives of the present study were to identify porcine LEPR polymorphisms and examine the effects of LEPR polymorphisms on fatness traits in this same population. The Duroc pigs (226 to 953 pigs) were evaluated for BF, fat area ratios using image analysis, and LEPC. A total of seven single nucleotide polymorphisms (SNPs) in the full-length LEPR coding region were identified in pigs from the base population. Four non-synonymous SNPs of the LEPR gene and 15 microsatellite markers on SSC 6 were then genotyped in all pigs. During candidate gene analysis, we detected significant effects of the non-synonymous SNP c.2002C>T in exon 14 on all traits. In fine mapping analysis, significant QTLs for BF, fat area ratios, and LEPC were detected near the LEPR gene in the same region. These results indicated that the c.2002C>T SNP of LEPR has a strong effect on BF, fat area ratios and LEPC. [ABSTRACT FROM AUTHOR]

ABSTRACT The reduction of extra subcutaneous, intermuscular and abdominal fat is important to increase the carcass lean percentage of pigs. Image analyses of fat area ratios were effective for estimation of separated fat in pig carcasses. Serum concentrations of leptin are useful as physiological predictors of fat accumulation in pigs. The objectives of the present study were to perform a quantitative trait locus (QTL) analysis for fat area ratios and serum leptin concentrations in a Duroc purebred population. Pigs ( n = 226 to 538) were measured for fat area ratios of carcass cross-sections at the fifth to sixth thoracic vertebrae, half body length and last thoracic vertebra using an image analysis system, and serum leptin concentration. In total, animals were genotyped for 129 markers and used for QTL analysis. For fat area ratios, four significant and 12 suggestive QTLs were detected on chromosomes 1, 6, 7, 8, 9, 12 and 13. Significant QTLs were detected on the same region of chromosome 6, which was located near a leptin receptor gene. For serum leptin concentrations, two significant and two suggestive QTLs were detected on chromosomes 6, 9, and 16, and the QTLs on chromosome 6 were also in the same region for fat area ratios. [ABSTRACT FROM AUTHOR]

Abstract: Nucleotide oligomerization domain 2 (NOD2) is a cytosolic pattern recognition receptor (PRR) that responds to muramyldipeptide (MDP), a component of peptidoglycans of Gram positive and negative bacteria. NOD2 is involved in the modulation of signaling pathways for other PRRs, such as Toll-like receptors. Polymorphisms in NOD2 may evoke bowel disorders, and human Crohn''s disease is significantly correlated with mis-sense insertion of the NOD2 gene. Such polymorphisms affecting ligand recognition in the NOD2 gene may also influence bowel flora in livestock, which is compromised by bowel diseases such as diarrhea. We investigated the functional variance of mis-sense polymorphisms in ligand recognition by porcine NOD2. The 1949T>C polymorphism, located in the region encoding the hinge domain of the molecule, notably diminished the functional response of porcine NOD2 to MDP. By comparison, the 2197A>C polymorphism, localized in the region corresponding to leucine-rich repeats, significantly augmented the response of porcine NOD2 to the ligand. The 1949C allele was rare among pig breeds, suggesting that this mutation is a disadvantage to pigs in their immune response to microbes. The 2197C allele, in contrast, was widely distributed among Western breeds and is most likely to be derived from wild boars in Asia. This is the first report of a causal relationship between molecular function and polymorphisms in PRRs in non-primate, non-rodent mammals. These findings suggest that the 2197C allele might confer an immune response advantage in modern pig breeds and may be a useful marker for breeding aimed at disease resistance in pigs. [Copyright &y& Elsevier]

Pathogens localized extracellularly or incorporated into endosomes are recognized mainly by Toll-like receptors, whereas pathogens and pathogen-derived molecules that invade into the cytoplasm of host cells typically are recognized by intracellular pattern recognition receptors (PRRs), such as retinoic acid-inducible gene (RIG)-like helicases (RLHs) and nucleotide-binding oligmerization domain (NOD)-like receptors (NLRs). RIG-I and melanoma differentiation-associated gene 5 (MDA5), which belong to the RLH family, recognize viral genomic RNA, whereas NOD2, a member of the NLR family, responds to microbial peptidoglycans. These receptors may play an important role in pig opportunistic infectious diseases, such as pneumonia and diarrhea, which markedly impair livestock productivity, such that polymorphisms of these receptor genes are potential targets of pig breeding to increase disease resistance. Here, we report single nucleotide polymorphisms (SNPs) in porcine DDX58, IFIH1, and NOD2, which encode RIG-I, MDA5, and NOD2, respectively. Interestingly, compared with DDX58 and IFIH1, NOD2 abounded in nonsynonymous SNPs both throughout the coding sequence and in sequences encoding domains important for ligand recognition, such as helicase domains for RIG-I and MDA5 and leucine-rich repeats in NOD2. These differences in the distribution of SNPs in intracellular PRRs may parallel the diversity of their ligands, which include nucleic acids and peptidoglycans. [ABSTRACT FROM AUTHOR]

Abstract: Inspired by the pioneering work of Professor T.J.R. Hughes on the variational multi-scale method, this document summarizes recent developments in multiple-scale modeling using a newly developed technique called the bridging scale. The bridging scale consists of a two-scale decomposition in which the coarse scale is simulated using continuum methods, while the fine scale is simulated using atomistic approaches. The bridging scale offers unique advantages in that the coarse and fine scales evolve on separate time scales, while the high frequency waves emitted from the fine scale are eliminated using lattice impedance techniques. Recent advances in extending the bridging scale to quantum mechanical/continuum coupling are briefly described. The method capabilities are demonstrated via quasistatic nanotube bending, dynamic crack propagation and dynamic shear banding. [Copyright &y& Elsevier]

In this paper, a computational procedure combining experimental data and interphase inverse modeling is presented to predict filled rubber compound properties. The Fast Fourier Transformation (FFT) based numerical homogenization scheme is applied on the high quality filled rubber 3D Transmission Electron Microscope (TEM) image to compute its complex shear moduli. The 3D TEM filled rubber image is then compressed into a material microstructure database using a novel Reduced Order Modeling (ROM) technique, namely Self-consistent Clustering Analysis (a two-stage offline database creation from training and learning, followed by data compression via unsupervised learning, and online prediction approach), for improved efficiency and accuracy. An inverse modeling approach is formulated for quantitatively computing interphase complex shear moduli in order to understand the interphase behaviors. The two-stage SCA and the inverse modeling approach formulate a three-step prediction scheme for studying filled rubber, whose loss tangent curve can be computed in agreement with test data. • A comprehensive computational framework for predicting filled rubber properties. • Detailed experimental characterization of the filled rubber microstructure. • Filled rubber interphase inverse modeling for accurate property prediction. • Filled rubber property prediction with order reduction (52,631 speed-ups than FEM). [ABSTRACT FROM AUTHOR]