Application of deep learning with bivariate models for genomic prediction of sow lifetime productivity-related traits.

OBJECTIVE: Pig breeders cannot obtain phenotypic information at the time of selection for sow lifetime productivity (SLP). They would benefit from obtaining genetic information of candidate sows. Genomic data interpreted using deep learning (DL) techniques could contribute to the genetic improvement of SLP to maximize farm profitability because DL models capture nonlinear genetic effects such as dominance and epistasis more efficiently than conventional genomic prediction methods based on linear models. This study aimed to investigate the usefulness of DL for the genomic prediction of two SLP-related traits; lifetime number of litters (LNL) and lifetime pig production (LPP). METHODS: Two bivariate DL models, convolutional neural network (CNN) and local convolutional neural network (LCNN), were compared with conventional bivariate linear models (i.e., genomic best linear unbiased prediction, Bayesian ridge regression, Bayes A, and Bayes B). Phenotype and pedigree data were collected from 40,011 sows that had husbandry records. Among these, 3,652 pigs were genotyped using the PorcineSNP60K BeadChip. RESULTS: The best predictive correlation for LNL was obtained with CNN (0.28), followed by LCNN (0.26) and conventional linear models (approximately 0.21). For LPP, the best predictive correlation was also obtained with CNN (0.29), followed by LCNN (0.27) and conventional linear models (approximately 0.25). A similar trend was observed with the mean squared error of prediction for the SLP traits. CONCLUSION: This study provides an example of a CNN that can outperform against the linear model-based genomic prediction approaches when the nonlinear interaction components are important because LNL and LPP exhibited strong epistatic interaction components. Additionally, our results suggest that applying bivariate DL models could also contribute to the prediction accuracy by utilizing the genetic correlation between LNL and LPP.

An intelligent method for pregnancy diagnosis in breeding sows according to ultrasonography algorithms.

Pig breeding management directly contributes to the profitability of pig farms, and pregnancy diagnosis is an important factor in breeding management. Therefore, the need to diagnose pregnancy in sows is emphasized, and various studies have been conducted in this area. We propose a computer-aided diagnosis system to assist livestock farmers to diagnose sow pregnancy through ultrasound. Methods for diagnosing pregnancy in sows through ultrasound include the Doppler method, which measures the heart rate and pulse status, and the echo method, which diagnoses by amplitude depth technique. We propose a method that uses deep learning algorithms on ultrasonography, which is part of the echo method. As deep learning-based classification algorithms, Inception-v4, Xception, and EfficientNetV2 were used and compared to find the optimal algorithm for pregnancy diagnosis in sows. Gaussian and speckle noises were added to the ultrasound images according to the characteristics of the ultrasonography, which is easily affected by noise from the surrounding environments. Both the original and noise added ultrasound images of sows were tested together to determine the suitability of the proposed method on farms. The pregnancy diagnosis performance on the original ultrasound images achieved 0.99 in accuracy in the highest case and on the ultrasound images with noises, the performance achieved 0.98 in accuracy. The diagnosis performance achieved 0.96 in accuracy even when the intensity of noise was strong, proving its robustness against noise.

Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations.

Sus scrofa is a globally distributed livestock species that still maintains two different ways of life: wild and domesticated. Herein, we detected copy number variation (CNV) of 328 animals using short read alignment on Sscrofa11.1. We compared CNV among five groups of porcine populations: Asian domesticated (AD), European domesticated (ED), Asian wild (AW), European wild (EW), and Near Eastern wild (NEW). In total, 21,673 genes were identified on 154,872 copy number variation region (CNVR). Differences in gene copy numbers between populations were measured by considering the variance-based value [Formula: see text] and the one-way ANOVA test followed by Scheffe test. As a result, 111 genes were suggested as copy number variable genes. Abnormally gained copy number on EEA1 in all populations was suggested the presence of minor CNV in the reference genome assembly, Sscrofa11.1. Copy number variable genes were related to meat quality, immune response, and reproduction traits. Hierarchical clustering of all individuals and mean pairwise [Formula: see text] in breed level were visualized genetic relationship of 328 individuals and 56 populations separately. Our findings have shown how the complex history of pig evolution appears in genome-wide CNV of various populations with different regions and lifestyles.

Genetic Parameter Estimation and Genome-Wide Association Analysis of Social Genetic Effects on Average Daily Gain in Purebreds and Crossbreds.

Average daily gain (ADG) is an important growth trait in the pig industry. The direct genetic effect (DGE) has been studied mainly to assess the association between genetic information and economic traits. The social genetic effect (SGE) has been shown to affect ADG simultaneously with the DGE because of group housing systems. We conducted this study to elucidate the genetic characteristics and relationships of the DGE and SGE of purebred Korean Duroc and crossbred pigs by single-step genomic best linear unbiased prediction and a genome-wide association study. We used the genotype, phenotype, and pedigree data of 1779, 6022, and 7904 animals, respectively. Total heritabilities on ADG were 0.19 ± 0.04 and 0.39 ± 0.08 for purebred and crossbred pigs, respectively. The genetic correlation was the greatest (0.77 ± 0.12) between the SGE of purebred and DGE of crossbred pigs. We found candidate genes located in the quantitative trait loci (QTLs) for the SGE that were associated with behavior and neurodegenerative diseases, and candidate genes in the QTLs for DGE that were related to body mass, size of muscle fiber, and muscle hypertrophy. These results suggest that the genomic selection of purebred animals could be applied for crossbred performance.

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon.

A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

Genetic relationship between purebred and synthetic pigs for growth performance using single step method.

OBJECTIVE: The objective of this study was to estimate the genetic correlation (rpc) of growth performance between purebred (Duroc and Korean native) and synthetic (WooriHeukDon) pigs using a single-step method. METHODS: Phenotypes of 15,902 pigs with genotyped data from 1,792 pigs from a nucleus farm were used for this study. We estimated the rpc of several performance traits between WooriHeukDon and purebred pigs: day of target weight (DAY), backfat thickness (BF), feed conversion rate (FCR), and residual feed intake (RFI). The variances and covariances of the studied traits were estimated by an animal multi-trait model that applied the Bayesian inference. RESULTS: rpc within traits was lower than 0.1 for DAY and BF, but high for FCR and RFI; in particular, rpc for RFI between Duroc and WooriHeukDon pigs was nearly 1. Comparison between different traits revealed that RFI in Duroc pigs was associated with different traits in WooriHeukDon pigs. However, the most of rpc between different traits were estimated with low or with high standard deviation. CONCLUSION: The results indicated that there were substantial differences in rpc of traits in the synthetic WooriHeukDon pigs, which could be caused by these pigs having a more complex origin than other crossbred pigs. RFI was strongly correlated between Duroc and WooriHeukDon pigs, and these breeds might have similar single nucleotide polymorphism effects that control RFI. RFI is more essential for metabolism than other growth traits and these metabolic characteristics in purebred pigs, such as nutrient utilization, could significantly affect those in synthetic pigs. The findings of this study can be used to elucidate the genetic architecture of crossbred pigs and help develop new breeds with target traits.

Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip.

BACKGROUND: Woori-Heukdon (KWH) is a Korean synthetic pig breed generated using Chookjin-Duroc (KCD), Chookjin-Chamdon (KCC), and their crossbreds. Currently, there is a severe lack of studies investigating the Korean breed populations including wild boars (KWB) throughout the genome. OBJECTIVE: This study was performed to investigate the genetic characteristics of Korean pig populations at the genome-wide level. METHODS: Using the SNP dataset derived from genotyped and downloaded datasets using the Illumina PorcineSNP60K BeadChip, we compared the genomes of 532 individuals derived from 23 pig breeds to assess the genetic diversity, inbreeding coefficient, genetic differentiation, and population structure. RESULTS: KWB showed the lowest average expected heterozygosity (HE = 0.1904), while KWH showed the highest genetic diversity (HE = 0.02859) among Korean populations. We verified that the genetic composition of KWH, showing USD of 74.8% and KCC of 25.2% in ADMIXTURE analysis. In population structure analyses, KCC was consistently shown to be separated from other pig populations. In addition, we observed gene flow from Western pigs to a part of Chinese populations. CONCLUSION: This study showed that Korean native pigs, KCC have genetic differences in comparison with Chinese and Western pigs; despite some historical records and recent genetic studies, we could not find any clear evidence that KCC was significantly influenced by Chinese or Western breeds in this study. We also verified the theoretical genomic composition of KWH at the molecular level in structure analyses. To our knowledge, this is the first genomic study to investigate the genomic characteristics of KWH and KCC.

Phe-140 Determines the Catalytic Efficiency of Arylacetonitrilase from Alcaligenes faecalis.

Arylacetonitrilase from Alcaligenes faecalis ATCC8750 (NitAF) hydrolyzes various arylacetonitriles to the corresponding carboxylic acids. A systematic strategy of amino acid residue screening through sequence alignment, followed by homology modeling and biochemical confirmation was employed to elucidate the determinant of NitAF catalytic efficiency. Substituting Phe-140 in NitAF (wild-type) to Trp did not change the catalytic efficiency toward phenylacetonitrile, an arylacetonitrile. The mutants with nonpolar aliphatic amino acids (Ala, Gly, Leu, or Val) at location 140 had lower activity, and those with charged amino acids (Asp, Glu, or Arg) exhibited nearly no activity for phenylacetonitrile. Molecular modeling showed that the hydrophobic benzene ring at position 140 supports a mechanism in which the thiol group of Cys-163 carries out a nucleophilic attack on a cyanocarbon of the substrate. Characterization of the role of the Phe-140 residue demonstrated the molecular determinant for the efficient formation of arylcarboxylic acids.

Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs.

In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.

The effects of breed and gender on meat quality of Duroc, Pietrain, and their crossbred.

This study evaluated the effects of breed and gender in Duroc (D), Pietrain (P), and crossbred (DP) pigs. Loin samples were collected from D (n = 79), P (n = 42), and DP (n = 45) pigs. Intramuscular fat content was significantly lower in P (p < 0.001), and pH was lowest in DP pigs (p < 0.001). Gilts had higher intramuscular fat (IMF) and pH values than did castrated males (p < 0.05). Water-holding capacity was lower in DP pigs than that in D and P pigs (p < 0.001). Shear force in DP pigs was higher than that in D and P pigs (p < 0.001). Lightness and yellowness of meat in DP pigs was increased compared with coloring of P pig meat (p < 0.01). Meat from DP pigs was redder compared with meat from in D and P pigs, and it was higher in gilts than in castrates (p < 0.001). The C16:0 content was lower in P and DP pigs than in D pigs (p < 0.01). C18:2 content was higher in P and DP pigs than in D pigs (p < 0.001). Unsaturated and saturated fatty acids increased in P pigs compared with levels in D pigs (p < 0.05). Our results suggest that meat quality can be controlled by crossbreeding to increase or reduce selected properties. This study provides the basic data on the meat characteristics of F1 DP pigs. Thus, further study should be conducted to estimate the meat quality of various crossbreeds.

CO2 -Reductive, Copper Oxide-Based Photobiocathode for Z-Scheme Semi-Artificial Leaf Structure.

Green plants convert sunlight into high-energy chemicals by coupling solar-driven water oxidation in the Z-scheme and CO2 fixation in the Calvin cycle. In this study, formate dehydrogenase from Clostridium ljungdahlii (ClFDH) is interfaced with a TiO2 -coated CuFeO2 and CuO mixed (ClFDH-TiO2 |CFO) electrode. In this biohybrid photocathode, the TiO2 layer enhances the photoelectrochemical (PEC) stability of the labile CFO photocathode and facilitates the transfer of photoexcited electrons from the CFO to ClFDH. Furthermore, inspired by the natural photosynthetic scheme, the photobiocathode is combined with a water-oxidizing, FeOOH-coated BiVO4 (FeOOH|BiVO4 ) photoanode to assemble a wireless Z-scheme biocatalytic PEC device as a semi-artificial leaf. The leaf-like structure effects a bias-free biocatalytic CO2 -to-formate conversion under visible light. Its rate of formate production is 2.45 times faster than that without ClFDH. This work is the first example of a wireless solar-driven semi-biological PEC system for CO2 reduction that uses water as an electron feedstock.

Tyr320 is a molecular determinant of the catalytic activity of ß-glucosidase from Neosartorya fischeri.

ß-Glucosidases (BGL) are key members of the cellulase enzyme complex that determine efficiency of lignocellulosic biomass degradation, which have shown great functional importance to many biotechnological systems. A previous reported BGL from Neosartorya fischeri (NfBGL) showed much higher activity than other BGLs. Screening the important residues based on sequence alignment, analyzing a homology model, and subsequent alteration of individually screened residues by site-directed mutagenesis were carried out to investigate the molecular determinants of the enzyme's high catalytic efficiency. Tyr320, located in the wild-type NfBGL substrate-binding pocket was identified as crucial to the catalytic function of NfBGL. The replacement of Tyr320 with aromatic amino acids did not significantly alter the catalytic efficiency towards p-nitrophenyl ß-d-glucopyranoside (pNPG). However, mutants with charged and hydrophilic amino acids showed almost no activity towards pNPG. Computational studies suggested that an aromatic acid is required at position 320 in NfBGL to stabilize the enzyme-substrate complex formation. This knowledge on the mechanism of action of the molecular determinants can also help rational protein engineering of BGLs.

Application of single-step genomic evaluation using social genetic effect model for growth in pig.

OBJECTIVE: Social genetic effects (SGE) are an important genetic component for growth, group productivity, and welfare in pigs. The present study was conducted to evaluate i) the feasibility of the single-step genomic best linear unbiased prediction (ssGBLUP) approach with the inclusion of SGE in the model in pigs, and ii) the changes in the contribution of heritable SGE to the phenotypic variance with different scaling ω constants for genomic relationships. METHODS: The dataset included performance tested growth rate records (average daily gain) from 13,166 and 21,762 pigs Landrace (LR) and Yorkshire (YS), respectively. A total of 1,041 (LR) and 964 (YS) pigs were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel. With the BLUPF90 software package, genetic parameters were estimated using a modified animal model for competitive traits. Giving a fixed weight to pedigree relationships (τ: 1), several weights (ωxx, 0.1 to 1.0; with a 0.1 interval) were scaled with the genomic relationship for best model fit with Akaike information criterion (AIC). RESULTS: The genetic variances and total heritability estimates (T2) were mostly higher with ssGBLUP than in the pedigree-based analysis. The model AIC value increased with any level of ω other than 0.6 and 0.5 in LR and YS, respectively, indicating the worse fit of those models. The theoretical accuracies of direct and social breeding value were increased by decreasing ω in both breeds, indicating the better accuracy of ω0.1 models. Therefore, the optimal values of ω to minimize AIC and to increase theoretical accuracy were 0.6 in LR and 0.5 in YS. CONCLUSION: In conclusion, single-step ssGBLUP model fitting SGE showed significant improvement in accuracy compared with the pedigree-based analysis method; therefore, it could be implemented in a pig population for genomic selection based on SGE, especially in South Korean populations, with appropriate further adjustment of tuning parameters for relationship matrices.

Clavicle fracture after reverse total shoulder arthroplasty: a case report with literature review.

In reverse total shoulder arthroplasty, retensioning of the deltoid muscle is essential for regaining active elevation. However, the procedure remains problematic, in that it may potentially produce complications not only because it is a complex procedure but also because it causes anatomical changes. We experienced a rare case of a 64-year-old woman presenting with non-traumatic clavicle fracture after reverse total shoulder arthroplasty via a deltopectoral approach. In our case, the patient presented with pain in the clavicle area, which worsened during joint movement. Therefore, surgeons should consider the possibility of clavicle fracture in patients presenting with pain in the clavicle area which worsens.

Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers.

Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

The effect of milrinone infusion on right ventricular function during coronary anastomosis and early outcomes in patients undergoing off-pump coronary artery bypass surgery.

BACKGROUND: During coronary anastomosis in off-pump coronary artery bypass surgery (OPCAB), hemodynamic alternations can be induced by impaired diastolic function of the right ventricle. This study was designed to examine the effect of milrinone on right ventricular function and early outcomes in patients undergoing OPCAB. METHODS: Forty patients undergoing OPCAB were randomly assigned in a double-blind manner to receive either milrinone (milrinone group, n = 20) or normal saline (control group, n = 20). Hemodynamic variables were measured after pericardiotomy (T1), 5 min after stabilizer application for anastomosis of the left anterior descending coronary artery (LAD, T2), the obtuse marginalis branch (OM, T3), the right coronary artery (RCA, T4), 5 min after sternal closure (T5), and after ICU arrival. The right ventricular ejection fraction (RVEF) and right ventricular volumetric parameters were also measured using the thermodilution technique. For evaluation of early outcomes, the 30-day operative mortality and morbidity risk models were used. RESULTS: There was no significant difference in hemodynamic variables, including mean arterial pressure, between the 2 groups, except for the cardiac index and RVEF. The cardiac index and RVEF were significantly greater at T3 in the milrinone group than in the control group. CONCLUSIONS: Continuous infusion of milrinone demonstrated a beneficial effect on cardiac output and right ventricular function in patients undergoing OPCAB, especially during anastomosis of the graft to the OM artery, and it had no adverse effect on early outcomes.

Update on Renin-Angiotensin-aldosterone blockade in heart failure.

There is convincing evidence that the renin-angiotensin-aldosterone system (RAAS) plays an important role in heart failure (HF), from the events that result in its inception through advanced disease. In particular, RAAS activation is one of the major pathways involved in maladaptive cardiac remodeling, a process that results in progressive cardiac dysfunction. Not surprisingly, strategies targeting the RAAS have substantial benefits in HF. These therapies, which include angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and aldosterone receptor antagonists, have emerged as cornerstones of HF therapy, particularly in patients with systolic dysfunction. Their role in HF with preserved ejection fraction, however, is less certain. New information and approaches targeting RAAS activation continue to emerge. Direct renin inhibitors are hypothesized to have beneficial effects in HF, but further studies are needed to evaluate their efficacy.

Low back pain in older adults: are we utilizing healthcare resources wisely?

OBJECTIVES: 1) To examine recent change in prevalence and Medicare-associated charges for non-invasive/minimally invasive evaluation and treatment of nonspecific low back pain (LBP); and 2) to examine magnetic resonance imaging (MRI) utilization appropriateness in older adults with chronic low back pain (CLBP). DESIGN: Two cross-sectional surveys of 1) national (1991-2002) and Pennsylvania (2000-2002) Medicare data; and 2) patients aged >or= 65 years with CLBP. SETTING: Outpatient data. PARTICIPANTS: Patients aged >or= 65 years with LBP. MEASUREMENTS: Study 1: Outpatient national and Pennsylvania Part A Medicare data were examined for number of patients and charges for all patients, and for those with nonspecific LBP. Total number of visits and charges for imaging studies, physical therapy (PT), and spinal injections was also examined for Pennsylvania. Study 2: 111 older adults with CLBP were interviewed regarding presence of red flags necessitating imaging and history of having a lumbar MRI, neurogenic claudication (NC), and back surgery. RESULTS: Study 1: Between 1991 and 2002, there was a 42.5% increase in total Medicare patients, 131.7% increase in LBP patients, 310% increase in total charges, and 387.2% increase in LBP charges. In Pennsylvania (2000-2002), there was a 5.5% increase in LBP patients and 33.2% increase in charges (0.2% for PT, 59.4% for injections, 41.9% for MRI/CT, and 19.3% for X rays). Study 2: None of the 111 participants had red flags and 61% had undergone MRIs (29% with NC, 24% with failed back surgery syndrome). CONCLUSION: LBP documentation and diagnostic studies are increasing in Medicare beneficiaries, and evidence suggests that MRIs may often be ordered unnecessarily. Injection procedures appear to account for a significant proportion of LBP-associated costs. More studies are needed to examine the appropriateness with which imaging procedures and non-invasive/minimally invasive treatments are utilized, and their effect on patient outcomes.