DNA Methylation Patterns According to Fatty Liver Index and Longitudinal Changes from the Korean Genome and Epidemiology Study (KoGES).

The role of differentially methylated regions (DMRs) in nonalcoholic fatty liver disease (NAFLD) is unclear. This study aimed to identify the role of DMR in NAFLD development and progression using the Korean Genome and Epidemiology Study (KoGES) cohort. We used laboratory evaluations and Illumina Methylation 450 k DNA methylation microarray data from KoGES. The correlation between fatty liver index (FLI) and genomic CpG sites was analyzed in 322 subjects. Longitudinal changes over 8 years were confirmed in 33 subjects. To identify CpG sites and genes related to FLI, we obtained enrichment terms for 6765 genes. DMRs were identified for both high (n = 128) and low (n = 194) groups on the basis of FLI 30 in 142 men and 180 women. To confirm longitudinal changes in 33 subjects, the ratio of follow-up and baseline investigation values was obtained. Correlations and group comparisons were performed for the 8 year change values. PITPNM3, RXFP3, and THRB were hypermethylated in the increased FLI groups, whereas SLC9A2 and FOXI3 were hypermethylated in the decreased FLI groups. DMRs describing NAFLD were determined, and functions related to inflammation were identified. Factors related to longitudinal changes are suggested, and blood circulation-related functions appear to be important in the management of NAFLD.

Doppler-free three-photon coherence in Doppler-broadened diamond-type atomic system.

We investigated the relationship between three-photon electromagnetically induced absorption (TPEIA) and four-wave mixing (FWM) in the 5S1/2-5P3/2-5D5/2 transition of 87Rb atoms. When the driving field was additionally coupled to the ground and intermediate states of a lower V-type configuration in a typical ladder-type electromagnetically induced transparency (EIT) system, Doppler-free TPEIA and FWM spectra were simultaneously observed and then analyzed from the perspective of multi-photon atomic coherence. Comparing the TPEIA and FWM spectra according to the laser frequency detuning and laser intensity, we found that the enhanced TPEIA signal is strongly correlated with the generated FWM light. Analytical and numerical calculations for the analysis of the relationship are presented.

Trigger factor assisted soluble expression of recombinant spike protein of porcine epidemic diarrhea virus in Escherichia coli.

BACKGROUND: Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine. The spike glycoprotein (S) of PEDV is the major immunogenic determinant that plays a pivotal role in the induction of neutralizing antibodies against PEDV, which therefore is an ideal target for the development of subunit vaccine. In an attempt to develop a subunit vaccine for PEDV, we cloned two different fragments of S protein and expressed as glutathione S-transferase (GST)-tagged fusion proteins, namely rGST-COE and rGST-S1D, in E.coli. However, the expression of these recombinant protein antigens using a variety of expression vectors, strains, and induction conditions invariably resulted in inclusion bodies. To achieve the soluble expression of recombinant proteins, several chaperone co-expression systems were tested in this study. RESULTS: We firstly tested various chaperone co-expression systems and found that co-expression of trigger factor (TF) with recombinant proteins at 15 °C was most useful in soluble production of rGST-COE and rGST-S1D compared to GroEL-ES and DnaK-DnaJ-GrpE/GroEL-ES systems. The soluble rGST-COE and rGST-S1D were purified using glutathione Sepharose 4B with a yield of 7.5 mg/l and 5 mg/l, respectively. Purified proteins were detected by western blot using mouse anti-GST mAb and pig anti-PEDV immune sera. In an indirect ELISA, purified proteins showed immune reactivity with pig anti-PEDV immune sera. Finally, immunization of mice with 10 µg of purified proteins elicited highly potent serum IgG and serum neutralizing antibody titers. CONCLUSIONS: In this study, soluble production of recombinant spike protein of PEDV, rGST-COE and rGST-S1D, were achieved by using TF chaperone co-expression system. Our results suggest that soluble rGST-COE and rGST-S1D produced by co-expressing chaperones may have the potential to be used as subunit vaccine antigens.

Atomic coherence effects in four-wave mixing process of a ladder-type atomic system.

We investigate the effects of atomic coherence on four-wave mixing (FWM), with respect to the transition routes between the hyperfine states in the 5S1/2-5P3/2-5D5/2 transition of 87Rb atoms. By comparing the FWM spectra with the electromagnetically induced transparency (EIT) spectra of the hyperfine states, we confirm that the FWM process is significantly influenced by both ladder-type and V-type two-photon coherences. From the observed FWM signal of each hyperfine structure, we clarify the role of two-photon coherence in the FWM process under EIT, double-resonance optical pumping (DROP), and two-photon absorption (TPA) conditions in a ladder-type atomic system, which is dependent on the open degree of the hyperfine states, the laser intensity, and the laser frequency detuning.

Highly bright photon-pair generation in Doppler-broadened ladder-type atomic system.

We report a bright photon-pair source with a coincidence counting rate per input power (cps/mW) of tens of thousands, obtained via spontaneous four-wave mixing from a Doppler-broadened atomic ensemble of the 5S1/2-5P3/2-5D5/2 transition of 87Rb. The photon-pair generation rate is enhanced by the two-photon coherence contributions from almost all the atomic velocity groups in the Doppler-broadened ladder-type atomic system. We obtained the violation of the Cauchy-Schwarz inequality by a factor of 2370 ± 150. We believe that our scheme for highly bright paired photons is important as a useful quantum light source for quantum entanglement swapping between completely autonomous sources.

Production of soluble truncated spike protein of porcine epidemic diarrhea virus from inclusion bodies of Escherichia coli through refolding.

The emergence of highly pathogenic variant porcine epidemic diarrhea virus (PEDV) strains, from 2013 to 2014, in North American and Asian countries have greatly threatened global swine industry. Therefore, development of effective vaccines against PEDV variant strains is urgently needed. Recently, it has been reported that the N-terminal domain (NTD) of S1 domain of PEDV spike protein is responsible for binding to the 5-N-acetylneuraminic acid (Neu5Ac), a possible sugar co-receptor. Therefore, the NTD of S1 domain could be an attractive target for the development of subunit vaccines. In this study, the NTD spanning amino acid residues 25-229 (S25-229) of S1 domain of PEDV variant strain was expressed in Escherichia coli BL21 (DE3) in the form of inclusion bodies (IBs). S25-229 IBs were solubilized in 20 mM sodium acetate (pH 4.5) buffer containing 8 M urea and 1 mM dithiothreitol with 95% yield. Solubilized S25-229 IBs were refolded by 10-fold flash dilution and purified by one-step cation exchange chromatography with >95% purity and 20% yield. The CD spectrum of S25-229 showed the characteristic pattern of alpha helical structure. In an indirect ELISA, purified S25-229 showed strong reactivity with mouse anti-PEDV sera. In addition, immunization of mice with 20 µg of purified S25-229 elicited highly potent serum IgG titers. Finally, mouse antisera against S25-229 showed immune reactivity with native PEDV S protein in an immunofluorescence assay. These results suggest that purified S25-229 may have potential to be used as a subunit vaccine against PEDV variant strains.

Condition for Doppler-free three-photon resonance in a ladder-type atomic system.

We report the essential condition for three-photon electromagnetically induced absorption (TPEIA) in a Doppler-broadened ladder-type atomic system. When the two coupling lasers operate at different frequencies, we observed Doppler-free TPEIA resonance at a counterintuitive frequency, which is the almost half-frequency detuning of the frequency difference between the two coupling fields. Considering three-photon coherence in a Doppler-broadened ladder-type three-level atomic system, the TPEIA due to the atomic group of non-zero velocity was in good agreement with the calculated TPEIA spectrum under the one-photon resonance condition of all three optical fields. From the results, we found that an atomic group with a proper velocity for ladder-type TPEIA should satisfy the one-photon resonances of all three optical fields.

Relationship between two- and three-photon coherence in a ladder-type atomic system.

We investigated the relationship between two- and three-photon coherence in terms of the transition routes and coupling field intensities in a Doppler-broadened ladder-type atomic system for the 5S(1/2)-5P(3/2)-5D(5/2) transition in (87)Rb atoms. Three-photon electromagnetically induced absorption (TPEIA) due to three-photon coherence was observed in the only transition route that exhibited a dominant two-photon coherence effect. We showed that two-photon coherence is a necessary condition for three-photon coherence phenomena. A comparison of the relative magnitudes of the electromagnetically induced transparency and TPEIA as a function of the coupling field intensity revealed that the increase of three-photon coherence was faster than that of two-photon coherence. Considering three-photon coherence in a Doppler-broadened ladder-type three-level atomic system, the relation between two- and three-photon coherence was numerically calculated.

On a preference-based instrumental variable approach in reducing unmeasured confounding-by-indication.

Treatment preferences of groups (e.g., clinical centers) have often been proposed as instruments to control for unmeasured confounding-by-indication in instrumental variable (IV) analyses. However, formal evaluations of these group-preference-based instruments are lacking. Unique challenges include the following: (i) correlations between outcomes within groups; (ii) the multi-value nature of the instruments; (iii) unmeasured confounding occurring between and within groups. We introduce the framework of between-group and within-group confounding to assess assumptions required for the group-preference-based IV analyses. Our work illustrates that, when unmeasured confounding effects exist only within groups but not between groups, preference-based IVs can satisfy assumptions required for valid instruments. We then derive a closed-form expression of asymptotic bias of the two-stage generalized ordinary least squares estimator when the IVs are valid. Simulations demonstrate that the asymptotic bias formula approximates bias in finite samples quite well, particularly when the number of groups is moderate to large. The bias formula shows that when the cluster size is finite, the IV estimator is asymptotically biased; only when both the number of groups and cluster size go to infinity, the bias disappears. However, the IV estimator remains advantageous in reducing bias from confounding-by-indication. The bias assessment provides practical guidance for preference-based IV analyses. To increase their performance, one should adjust for as many measured confounders as possible, consider groups that have the most random variation in treatment assignment and increase cluster size. To minimize the likelihood for these IVs to be invalid, one should minimize unmeasured between-group confounding.

Spatial transport of atomic coherence in electromagnetically induced absorption with a paraffin-coated Rb vapor cell.

We report the spatial transport of spontaneously transferred atomic coherence (STAC) in electromagnetically induced absorption (EIA), which resulted from moving atoms with the STAC of the 5S(1/2) (F = 2)-5P(3/2) (F' = 3) transition of (87)Rb in a paraffin-coated vapor cell. In our experiment, two channels were spatially separate; the writing channel (WC) generated STAC in the EIA configuration, and the reading channel (RC) retrieved the optical field from the spatially transported STAC. Transported between the spatially separated positions, the fast light pulse of EIA in the WC and the delayed light pulse in the RC were observed. When the laser direction of the RC was counter-propagated in the direction of the WC, we observed direction reversal of the transported light pulse in the EIA medium. Furthermore, the delay time, the magnitude, and the width of the spatially transported light pulse were investigated with respect to the distance between the two channels.

Gene-gene interactions of fatty acid synthase (FASN) using multifactor-dimensionality reduction method in Korean cattle.

We examined the gene-gene interactions of five exonic single nucleotide polymorphisms (SNPs) in the gene encoding fatty acid synthase using 513 Korean cattle and using the model free and the non-parametrical multifactor dimensionality reduction method for the analysis. The five SNPs of g.12870 T>C, g.13126 T>C, g.15532 C>A, g.16907 T>C and g.17924 G>A associated with a variety of fatty acid compositions and marbling score were used in this study. The two-factor interaction between g.13126 T>C and g.15532 C>A had the highest training-balanced among the five-factor models and a testing-balanced accuracy at 70.18 % on C18:1 with a cross-validation consistency of 10 out of 10. Also, the two-factor interaction between g.13126 T>C and g.15532 C>A had the highest testing-balanced accuracy at 68.59 % with a 10 out of 10 cross-validation consistency, than any other models on MUFA. In MS, a single SNP g.15532 C>A had the best accuracy at 58.85 % and the two-factor interaction model g.12870 T>C and g.15532 C>A had the highest testing-balanced accuracy at 64.00 %. The three-factor interaction model g.12870 T>C, g.13126 T>C and g.15532 C>A was recorded as having a high testing-balanced accuracy of 63.24 %, but it was lower than the two-factor interaction model. We used likelihood ratio tests for interaction, and Chi square tests to validate our results, with all tests showing statistical significance. We also compared this with mean scores between the high-risk trait group and low-risk trait group. The genotypes of TTCA, TTAA and TCAA at g.15532 and g.13126 on C18:1, genotypes TTCC, TTCA, TTAA, TCAA CCAA at g.15532 and g.13126 on MUFA and genotypes CCCC, TCCA, CCCA, TTAA, TCAA and CCAA at g.15532 and g.12870 on MS were recommended for the genetic improvement of beef quality.

Detection of exonic variants within the melanocortin 1 receptor (MC1R) gene in Black Silky, White Leghorn and Golden duckwing Araucana chicken.

The melanocortin 1 receptor (MC1R) gene can be considered a candidate functional gene for the pigmentation of plumage color. The aim of this study was to investigate the association between the genotype frequencies of g.69 T>C, g.376 G>A and g.427 A>G SNPs within the MC1R gene in Black silky (O), Golden duckwing Araucana (GA) and White Leghorn (W). The CC and AA genotype frequencies of g.69 T>C and g.427 A>G SNPs in White Leghorn (W) were both 1.000, and the TT genotype frequency of the g.69 T>C SNP in Golden duckwing Araucana (GA) was also 1.000. The GG and AA genotype frequencies of g.376 G>A and g.427 A>G SNPs in Black silky (O) were both 0.100. When a haplotype is observed using a combination of markers, a Golden duckwing Araucana (GA) can especially be distinguished when it is a TAG, TGG and TAA type in the SNP combination of the MC1R gene. In case of the CAA types, only White Leghorn (W) could specifically be distinguished. Therefore, three SNPs in MC1R may provide identification in chicken breeds.

Characterization of ambrette seed oil and its mode of action in bacteria.

In the present study, chemical composition and the antibacterial mechanism of ambrette seed oil are investigated. Chemical composition of the oil was analysed by gas chromatography-mass spectrometry (GC-MS). Thirty-five compounds were identified and the major compounds were found to be farnesol acetate (51.45%) and ambrettolide (12.96%). The antibacterial activity was performed by well diffusion assay and the mechanisms were studied by measuring the alkaline phosphatase (ALP), lactate dehydrogenase (LDH) and protein leakage assays. The antibacterial effect of the ambrette seed oil showed inhibitory effect against Bacillus subtilis, Staphylococcus aureus and Enterococcus faecalis. The LDH activity was high in all tested bacteria compared with control, whereas the ALP and protein concentrations were also increased in E. faecalis. Molecular docking revealed the ligands farnesol acetate and ambrettolide had satisfactory binding energy towards the beta lactamase TEM-72 and dihydrofolate reductase (DHFR) protein. Due to its better antibacterial properties, the ambrette seed oil could be used as a source of antibacterial agents.

Identification of exonic nucleotide variants of the thyroid hormone responsive protein gene associated with carcass traits and Fatty Acid composition in korean cattle.

The thyroid hormone responsive protein (THRSP) gene is a functional gene that can be used to indicate the fatty acid compositions. This study investigates the relationships of exonic single nucleotide polymorphisms (SNPs) in the THRSP gene and fatty acid composition of muscle fat and marbling score in the 612 Korean cattle. The relationships between fatty acid composition and eight SNPs in the THRSP gene (g.78 G>A, g.173 C>T, g.184 C>T, g.190 C>A, g.194 C>T, g.277 C>G, g.283 T>G and g.290 T>G) were investigated, and according to the results, two SNPs (g.78 G>A and g.184 C>T) in exon 1 were associated with fatty acid composition. The GG and CC genotypes of g.78 G>A and g.184 C>T had higher unsaturated fatty acid (UFA) and monounsaturated fatty acid (MUFA) content (p<0.05). In addition, the ht1*ht1 group (Val/Ala haplotype) in a linkage disequilibrium increased MUFAs and marbling scores for carcass traits (p<0.05). As a result, g.78 G>A and g.184 C>T had significantly relationships with UFAs and MUFAs. Two SNPs in the THRSP gene affected fatty acid composition, suggesting that GG and CC genotypes and the ht1*ht1 group (Val/Ala haplotype) can be markers to genetically improve the quality and flavor of beef.

Development of a nucleic acid detection method based on the CRISPR-Cas13 for point-of-care testing of bovine viral diarrhea virus-1b.

Bovine viral diarrhea (BVD) is a single-stranded, positive-sense ribonucleic acid (RNA) virus belonging to the genus Pestivirus of the Flaviviridae family. BVD frequently causes economic losses to farmers. Among bovine viral diarrhea virus (BVDV) strains, BVDV-1b is predominant and widespread in Hanwoo calves. Reverse-transcription polymerase chain reaction (RT-PCR) is an essential method for diagnosing BVDV-1b and has become the gold standard for diagnosis in the Republic of Korea. However, this diagnostic method is time-consuming and requires expensive equipment. Therefore, Clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems have been used for point-of-care (POC) testing of viruses. Developing a sensitive and specific method for POC testing of BVDV-1b would be advantageous for controlling the spread of infection. Thus, this study aimed to develop a novel nucleic acid detection method using the CRISPR-Cas13 system for POC testing of BVDV-1b. The sequence of the BVD virus was extracted from National Center for Biotechnology Information (NC_001461.1), and the 5' untranslated region, commonly used for detection, was selected. CRISPR RNA (crRNA) was designed using the Cas13 design program and optimized for the expression and purification of the LwCas13a protein. Madin Darby bovine kidney (MDBK) cells were infected with BVDV-1b, incubated, and the viral RNA was extracted. To enable POC viral detection, the compatibility of the CRISPR-Cas13 system was verified with a paper-based strip through collateral cleavage activity. Finally, a colorimetric assay was used to evaluate the detection of BVDV-1b by combining the previously obtained crRNA and Cas13a protein on a paper strip. In conclusion, the CRISPR-Cas13 system is highly sensitive, specific, and capable of nucleic acid detection, making it an optimal system for the early point-of-care testing of BVDV-1b.

SNPs in microRNA seed region and impact of miR-375 in concurrent regulation of multiple lipid accumulation-related genes.

Bovine intramuscular fat (IMF), commonly referred to as marbling, is regulated by lipid metabolism, which includes adipogenesis, lipogenesis, glycerolipid synthesis, and lipolysis. In recent years, breeding researchers have identified single nucleotide polymorphisms (SNPs) as useful marker-assisted selection tools for improving marbling scores in national breeding programs. These included causal SNPs that induce phenotypic variation. MicroRNAs (miRNAs) are small highly conserved non-coding RNA molecules that bind to multiple non-coding regions. They are involved in post-transcriptional regulation. Multiple miRNAs may regulate a given target. Previously, three SNPs in the GPAM 3' UTR and four miRNAs were identified through in silico assays. The aim of this study is to verify the binding ability of the four miRNAs to the SNPs within the 3'UTR of GPAM, and to identify the regulatory function of miR-375 in the expression of genes related to lipid metabolism in mammalian adipocytes. It was verified that the four miRNAs bind to the GPAM 3'UTR, and identified that the miR-375 sequence is highly conserved. Furthermore, it was founded that miR-375 upregulated the GPAM gene, C/EBPα, PPARγ and lipid metabolism-related genes and promoted lipid droplet accumulation in 3T3-L1 cells. In conclusion, these results suggest that miR-375 is a multifunctional regulator of multiple lipid metabolism-related genes and may aid in obesity research as a biomarker.

Volatile and Nonvolatile Resistive Switching Coexistence in Conductive Point Hexagonal Boron Nitride Monolayer.

Recently, we demonstrated the nonvolatile resistive switching effects of metal-insulator-metal (MIM) atomristor structures based on two-dimensional (2D) monolayers. However, there are many remaining combinations between 2D monolayers and metal electrodes; hence, there is a need to further explore 2D resistance switching devices from material selections to future perspectives. This study investigated the volatile and nonvolatile switching coexistence of monolayer hexagonal boron nitride (h-BN) atomristors using top and bottom silver (Ag) metal electrodes. Utilizing an h-BN monolayer and Ag electrodes, we found that the transition between volatile and nonvolatile switching is attributed to the thickness/stiffness of chain-like conductive bridges between h-BN and Ag surfaces based on the current compliance and atomristor area. Computations indicate a "weak" bridge is responsible for volatile switching, while a "strong" bridge is formed for nonvolatile switching. The current compliance determines the number of Ag atoms that undergo dissociation at the electrode, while the atomristor area determines the degree of electric field localization that forms more stable conductive bridges. The findings of this study suggest that the h-BN atomristor using Ag electrodes shows promise as a potential solution to integrate both volatile neurons and nonvolatile synapses in a single neuromorphic crossbar array structure through electrical and dimensional designs.

Programmable Retention Characteristics in MoS2-Based Atomristors for Neuromorphic and Reservoir Computing Systems.

In this study, we investigate the coexistence of short- and long-term memory effects owing to the programmable retention characteristics of a two-dimensional Au/MoS2/Au atomristor device and determine the impact of these effects on synaptic properties. This device is constructed using bilayer MoS2 in a crossbar structure. The presence of both short- and long-term memory characteristics is proposed by using a filament model within the bilayer transition-metal dichalcogenide. Short- and long-term properties are validated based on programmable multilevel retention tests. Moreover, we confirm various synaptic characteristics of the device, demonstrating its potential use as a synaptic device in a neuromorphic system. Excitatory postsynaptic current, paired-pulse facilitation, spike-rate-dependent plasticity, and spike-number-dependent plasticity synaptic applications are implemented by operating the device at a low-conductance level. Furthermore, long-term potentiation and depression exhibit symmetrical properties at high-conductance levels. Synaptic learning and forgetting characteristics are emulated using programmable retention properties and composite synaptic plasticity. The learning process of artificial neural networks is used to achieve high pattern recognition accuracy, thereby demonstrating the suitability of the use of the device in a neuromorphic system. Finally, the device is used as a physical reservoir with time-dependent inputs to realize reservoir computing by using short-term memory properties. Our study reveals that the proposed device can be applied in artificial intelligence-based computing applications by utilizing its programmable retention properties.

Advances in Methane Emission Estimation in Livestock: A Review of Data Collection Methods, Model Development and the Role of AI Technologies.

This review examines the significant role of methane emissions in the livestock industry, with a focus on cattle and their substantial impact on climate change. It highlights the importance of accurate measurement and management techniques for methane, a potent greenhouse gas accounting for 14-16% of global emissions. The study evaluates both conventional and AI-driven methods for detecting methane emissions from livestock, particularly emphasizing cattle contributions, and the need for region-specific formulas. Sections cover livestock methane emissions, the potential of AI technology, data collection issues, methane's significance in carbon credit schemes, and current research and innovation. The review emphasizes the critical role of accurate measurement and estimation methods for effective climate change mitigation and reducing methane emissions from livestock operations. Overall, it provides a comprehensive overview of methane emissions in the livestock industry by synthesizing existing research and literature, aiming to improve knowledge and methods for mitigating climate change. Livestock-generated methane, especially from cattle, is highlighted as a crucial factor in climate change, and the review underscores the importance of integrating precise measurement and estimation techniques for effective mitigation.

Phase measurement of fast light pulse in electromagnetically induced absorption.

We report the phase measurement of a fast light pulse in electromagnetically induced absorption (EIA) of the 5S1/2 (F = 2)-5P3/2 (F' = 3) transition of 87Rb atoms. Using a beat-note interferometer method, a stable measurement without phase dithering of the phase of the probe pulse before and after it has passed through the EIA medium was achieved. Comparing the phases of the light pulse in air and that of the fast light pulse though the EIA medium, the phase of the fast light pulse at EIA resonance was not shifted and maintained to be the same as that of the free-space light pulse. The classical fidelity of the fast light pulse according to the advancement of the group velocity by adjusting the atomic density was estimated to be more than 97%.