Global, Regional, and National Burden of Spine Pain, 1990-2019: A Systematic Analysis of the Global Burden of Disease Study 2019.

OBJECTIVE: To describe the global, regional, national, and temporal trends in neck pain (NP) and low back pain (LBP) from 1990 to 2019 and analyze associations with age, sex, and sociodemographic index (SDI). DESIGN: Temporal trends analyses of the Global Burden of Disease 2019 data for global, regional, and national prevalence, incidence, and years lived with disabilities (YLDs) of NP and LBP from 1990 to 2019. SETTING: Not applicable. PARTICIPANTS: Not applicable. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURE(S): The temporal trends in prevalence, incidence, and YLDs of NP and LBP, and associations with age, sex, and SDI. RESULTS: Globally, the prevalence, incidence, and YLDs of NP and LBP significantly increased; however, the age-standardized rates of NP showed a stable trend, and those of LBP slightly decreased from 1990 to 2019. The burden of NP and LBP was higher in women than in men. Both NP and LBP exhibited similar age-related trends, with the total numbers and rates increasing with age and reaching their highest points in the middle- and old-aged groups, respectively, in 2019. Overall, the prevalence, incidence, and YLDs of NP and LBP were higher in regions with higher SDI over the 3 decades. CONCLUSIONS: NP and LBP impose significant major public health burden globally. Although both conditions are more frequent in women and middle-aged groups and tend to be prevalent in countries with high SDI, they have distinct temporal and regional patterns. By comprehending temporospatial trends in the disease burden of NP and LBP, policymakers and health care professionals can make future interventions and policies to effectively manage these conditions worldwide as well as to achieve equity in prevention, diagnosis, and treatment.

Echo-aware room impulse response generation.

In real-time applications, like interactive virtual reality environments, there is a significant need for low-complexity simulation of room impulse responses in highly complex virtual scenes, but this remains a challenging issue. In particular, simulating late reverberation using physically based acoustic modeling requires much computational effort, contrary to the early reflections that can be modeled by simpler techniques, e.g., the image source method. To tackle this computational complexity issue, we propose a neural network-based hybrid artificial reverberation framework (Echo2Reverb) that generates late reverberation from given early reflections. The proposed model can control both temporal texture and frequency-dependent energy decay, i.e., echo density and spectral energy distribution, of the generated reverberations by extracting spectral and echo-related features and filtering sampled sparse sequences and Gaussian noises using estimated features. To support the end-to-end training with controlled echo density, a differentiable approximation of the normalized echo density profile is proposed. We train and test the model not only for nearly diffuse but also distinct echoes prominent in late reverberations, such as with flutter echoes in narrow corridors. Evaluation results demonstrate that the proposed model can accurately reproduce frequency-dependent energy decay and temporal texture of a room impulse response using only early reflections.

Optimal needle electromyography approach to the serratus anterior muscle.

INTRODUCTION/AIMS: There are two conventional needle electromyography (EMG) approaches to the serratus anterior (SA), both of which can result in erroneous insertion into adjacent structures such as the latissimus dorsi (LD), teres major, or external oblique abdominis muscles and pose a risk of long thoracic nerve (LTN) injury. Therefore, we identified a novel needle insertion point for the SA in cadavers that avoids other muscles and LTN injury. METHODS: This study included 17 cadavers: 12 to devise the new method and 5 to verify its accuracy. Novel landmarks were the inferior angle of the scapula (I), sternal notch (S), and xiphoid process (X). The relationships of the LD, pectoralis major (PM), SA, and LTN were determined relative to these landmarks. RESULTS: When inserting a needle into the proximal one third along the line connecting points I and X, there were adequate safety margins around the LD, PM, and LTN, and the new method had excellent accuracy. DISCUSSION: Compared to the conventional midaxillary method, our novel method improved the accuracy of needle EMG of the SA. Follow-up studies using clinical imaging techniques are needed to verify whether above findings are equally applicable in living subjects.

Gold single-atoms confined at the CeOx-TiO2interfaces with enhanced low-temperature activity toward CO oxidation.

We use CeOx-TiO2hetero-interfaces generated on the surface of CeOx-TiO2hybrid oxide supporting powders to stabilize Au single-atoms (SAs) with excellent low-temperature activity toward CO oxidation. Based on intriguing density functional theory calculation results on the preferential formation of Au-SAs at the CeOx-TiO2interfaces and the high activity of Au-SAs toward the Mars-van Krevelen type CO oxidation, we synthesized a Au/CeOx-TiO2(ACT) catalyst with 0.05 wt.% of Au content. The Au-SAs stabilized at the CeOx-TiO2interfaces by electronic coupling between Au and Ce showed improved low-temperature CO oxidation activity than the conventional Au/TiO2control group catalyst. However, the light-off profile of ACT showed that the early activated Au-SAs are not vigorously participating in CO oxidation. The large portion of the positive effect on the overall catalytic activity from the low activation energy barrier of ACT was retarded by the negative impact from the decreasing active site density at high temperatures. We anticipate that the low-temperature activity and high-temperature stability of Au-SAs that stand against each other can be optimized by controlling the electronic coupling strength between Au-SAs and oxide clusters at the Au-oxide-TiO2interfaces. Our results show that atomic-precision interface modulation could fine-tune the catalytic activity and stability of Au-SAs.

Impact of an anti-Salmonella. Typhimurium Bacteriophage on intestinal microbiota and immunity status of laying hens.

Typhoid is a distinct gastrointestinal disease that largely affects the public by consumption of inadequately or partially cooked eggs from contaminated laying hen farms. This has led the research on laying hens to focus on controlling the contamination by an effective anti-Salmonella spp. agent in the intestine. The treatments included, control, without challenge; PC, Salmonella typhimurium challenged (STC); BP5, 5 ppm bacteriophage/kg + STC; BP10, 10 ppm bacteriophage/kg + STC, on Salmonella shedding, body organs inflammatory reactions, and expression of toll-like receptor (TLR), pro-inflammatory cytokines, and heat shock protein (HSP) in the jejunum, liver,and thigh muscle in the STC laying hens. The RT-PCR method was used to enumerate the number of Salmonella typhimurium in the organs. The birds in the STC groups exhibited the increased population of Salmonella spp. in the excreta (p < .01). In the STC groups, the BP5 and BP10 laying hens exhibited a lower (p < .01) population of Salmonella spp. in the excreta at d 7 after STC. Supplementation of bacteriophage significantly decreased (p < .01) the colonization of S. Typhimurium in the spleen, oviduct, caecum and excreta. Among the STC treatments, the BP10 laying hens showed lower (p < .01) mRNA expression of interferon-γ (IFNγ) and TLR-4 in the jejunum compared with the PC treatment. After the STC, dietary supplementation with BP5 or BP10 decreased (p < .01) the mRNA expressions of IFNγ, HSP-27 and tumour necrosis factor-α in the liver compared with the PC treatment. These results suggest that bacteriophage can be used as an effective agent to decrease S. Typhimurium contamination in laying hens and possibly lower S. Typhimurium transfer to foods.

Personal audio system for neckband headset with low computational complexity.

Personal audio systems have been developed based on various approaches with the goal of synthesizing an isolated sound zone that avoids disturbing others in different locations. In this work, a near-field solution for a neckband headset using three loudspeakers positioned close to each ear is proposed. In particular, it is an attempt to derive a simple multichannel filter for reducing the computational cost in mobile devices. Unlike super-directive beamforming techniques, the controlled radiation pattern is not highly directional but can boost the near-field sound, thereby providing an extra sound level difference between the listener's ear locations and far-field surrounding areas. For this purpose, a multichannel filter is designed using a conventional pressure matching technique for reproducing a target signal at the ear location while suppressing sound radiation to a far-field. It is shown that the optimal filter weights can be successfully approximated in the form of a simple broadside differential array pattern. The simplified filter structure can be realized using only two second-order infinite impulse response filters for driving the middle and two side loudspeakers. Through various simulations and experiments, it is demonstrated that the proposed solution can effectively realize a personal audio system with a minimal loss of sound isolation performance.

Parametric direction-of-arrival estimation with three recurrence relations of spherical harmonics.

The eigenbeam estimation of signal parameters via the rotational invariance technique (EB-ESPRIT) is a well-known subspace-based beamforming algorithm for a spherical microphone array. EB-ESPRIT uses a recurrence relation to directly estimate directional parameters expressing directions-of-arrival (DOAs) of sound sources without an exhaustive grid-search. In the conventional EB-ESPRIT, the directional parameter along the elevational direction is given by a tangent function, which inevitably produces two shortcomings. First, the tangent function becomes singular for sources near the equator in spherical coordinates. Furthermore, two sources lying in exactly opposite directions in the spherical coordinates are indistinguishable and a strong ambiguity problem arises. In this work, an EB-ESPRIT technique based on generalized eigenvalue decomposition (GEVD) is proposed to resolve the singularity and ambiguity problems. The proposed technique uses three independent recurrence relations for spherical harmonics, thus the singularity problem due to the tangent function can be completely avoided. A common transformation matrix for extracting DOAs from recurrence relations are found from the GEVD, and the use of cosine and sine functions makes it possible to find DOAs without ambiguity and without extra transforms or angle-pairing processes. It is demonstrated that the proposed method not only overcomes the singularity and ambiguity problems, but also outperforms conventional techniques in terms of DOA accuracy.

Direction of arrival estimation using nonsingular spherical ESPRIT.

The eigenbeam-ESPRIT (EB-ESPRIT) is a parametric method that estimates the direction of arrival of source signals using a recurrence relation of spherical harmonics. In EB-ESPRIT, the sound-source elevation angle is estimated from an arctangent function, which diverges near the equator in the spherical coordinate system and inevitably induces an ill-conditioning problem. Here, a nonsingular spherical ESPRIT technique based on sine-based recurrence relations is proposed, in which the elevation angles are estimated from an arcsine function. It is shown that the proposed technique can estimate more sources than the conventional EB-ESPRIT technique while also avoiding ill-conditioning problems.

Multidimensional Anodized Titanium Foam Photoelectrode for Efficient Utilization of Photons in Mesoscopic Solar Cells.

Mesoscopic solar cells based on nanostructured oxide semiconductors are considered as a promising candidates to replace conventional photovoltaics employing costly materials. However, their overall performances are below the sufficient level required for practical usages. Herein, this study proposes an anodized Ti foam (ATF) with multidimensional and hierarchical architecture as a highly efficient photoelectrode for the generation of a large photocurrent. ATF photoelectrodes prepared by electrochemical anodization of freeze-cast Ti foams have three favorable characteristics: (i) large surface area for enhanced light harvesting, (ii) 1D semiconductor structure for facilitated charge collection, and (iii) 3D highly conductive metallic current collector that enables exclusion of transparent conducting oxide substrate. Based on these advantages, when ATF is utilized in dye-sensitized solar cells, short-circuit photocurrent density up to 22.0 mA cm-2 is achieved in the conventional N719 dye-I3- /I- redox electrolyte system even with an intrinsically inferior quasi-solid electrolyte.

An intracortical chondromyxoid fibroma in the diaphysis of the metatarsal.

Chondromyxoid fibromas (CMFs) are rare, benign, primary tumors of bones, and occur in the metaphyses of the medullary canals of the long bones. The occurrence of intracortical CMFs is extremely rare. Very few cases of intracortical CMFs located in the long tubular bones have been reported to date. Moreover, even though the feet are the second most common site for CMF (after the knees), intracortical metatarsal CMF has not been reported previously, to our knowledge. We report an intracortical CMF occurring in the diaphysis of the metatarsal in a 17-year-old man. It showed the same imaging findings as usual intramedullary CMFs, except for its cortical location. The development and serial increase in this tumor over time are also demonstrated in this report. Additionally, we present a review of current literature on intracortical CMFs.

Free-Standing Graphene Thermophone on a Polymer-Mesh Substrate.

A graphene thermoacoustic loudspeaker with a thin polymer mesh is fabricated using screen-printing. An experiment with substrates of various free-standing areas shows that a higher sound pressure level can be achieved as compared to previously reported graphene thermoacoustic loudspeakers. Moreover, a modified equation to predict the sound pressure level of the thermoacoustic loudspeaker with a thin and patterned substrate is proposed and verified by experimental results.

Reproduction of a higher-order circular harmonic field using a linear array of loudspeakers.

This paper presents a direct formula for reproducing a sound field consisting of higher-order circular harmonics with polar phase variation. Sound fields with phase variation can be used for synthesizing various spatial attributes, such as the perceived width or the location of a virtual sound source. To reproduce such a sound field using a linear loudspeaker array, the driving function of the array is derived in the format of an integral formula. The proposed function shows fewer reproduction errors than a conventional formula focused on magnitude variations. In addition, analysis of the sweet spot reveals that its shape can be asymmetric, depending on the order of harmonics.

Gene Expression Patterns Associated with Peroxisome Proliferator-activated Receptor (PPAR) Signaling in the Longissimus dorsi of Hanwoo (Korean Cattle).

Adipose tissue deposited within muscle fibers, known as intramuscular fat (IMF or marbling), is a major determinant of meat quality and thereby affects its economic value. The biological mechanisms that determine IMF content are therefore of interest. In this study, 48 genes involved in the bovine peroxisome proliferator-activated receptor signaling pathway, which is involved in lipid metabolism, were investigated to identify candidate genes associated with IMF in the longissimus dorsi of Hanwoo (Korean cattle). Ten genes, retinoid X receptor alpha, peroxisome proliferator-activated receptor gamma (PPARG), phospholipid transfer protein, stearoyl-CoA desaturase, nuclear receptor subfamily 1 group H member 3, fatty acid binding protein 3 (FABP3), carnitine palmitoyltransferase II, acyl-Coenzyme A dehydrogenase long chain (ACADL), acyl-Coenzyme A oxidase 2 branched chain, and fatty acid binding protein 4, showed significant effects with regard to IMF and were differentially expressed between the low- and high-marbled groups (p<0.05). Analysis of the gene co-expression network based on Pearson's correlation coefficients identified 10 up-regulated genes in the high-marbled group that formed a major cluster. Among these genes, the PPARG-FABP4 gene pair exhibited the strongest correlation in the network. Glycerol kinase was found to play a role in mediating activation of the differentially expressed genes. We categorized the 10 significantly differentially expressed genes into the corresponding downstream pathways and investigated the direct interactive relationships among these genes. We suggest that fatty acid oxidation is the major downstream pathway affecting IMF content. The PPARG/RXRA complex triggers activation of target genes involved in fatty acid oxidation resulting in increased triglyceride formation by ATP production. Our findings highlight candidate genes associated with the IMF content of the loin muscle of Korean cattle and provide insight into the biological mechanisms that determine adipose deposition within muscle.

Expression of ß-tubulin isotypes in urothelial carcinoma of the bladder.

PURPOSE: Our study aims to investigate the expressions of ß-tubulin isotypes and their significances in urothelial carcinoma of the bladder (UCB) as altered expression of a specific ß-tubulin isotype is associated with chemoresistance and poor prognosis in other malignancies. MATERIALS AND METHODS: Expression of ß-tubulin isotypes was retrospectively examined in 342 UCB samples obtained from 1995 to 2010 by immunohistochemistry. RESULTS: TUBB1 (307/342, 89.8 %) was most frequently overexpressed in the cytoplasm of UCB cases, followed by TUBB4 (101/342, 29.5 %), TUBB2 (85/342, 24.9 %), and TUBB3 (60/342, 17.5 %). TUBB1 overexpression was associated with older age (p = 0.032), high WHO grade (p = 0.001), and advanced TNM stage (p = 0.006). High levels of TUBB2 expression were associated with high WHO grade (p < 0.001), advanced TNM stage (p < 0.001), and non-papillary growth pattern (p = 0.007). TUBB3 overexpression was related to high WHO grade (p = 0.029). In univariate and multivariate survival analyses, TUBB1 overexpression was associated with poor recurrence-free survival (RFS) rates of all cases (hazard ratio 1.98, p = 0.031) and of the patients with transurethral and/or partial resection (hazard ratio 2.12, p = 0.031). TUBB2 overexpression was correlated with a short RFS of the patients with T2-T4 stages (hazard ratio 3.48, p = 0.007). TUBB3 overexpression was related to a poor RFS of the patients undergoing radical cystectomy (hazard ratio 5.90, p = 0.002). CONCLUSIONS: High TUBB1, TUBB2, and TUBB3 expressions are associated with unfavorable clinicopathologic factors and are independent prognostic factors for recurrence-free survival of UCB.

MAD2 and CDC20 are upregulated in high-grade squamous intraepithelial lesions and squamous cell carcinomas of the uterine cervix.

Abnormal expression of the spindle assembly checkpoint proteins causes tumor cell aneuploidy, which has been reported in various malignancies. The expression of mitotic arrest deficient 2 (MAD2) and cell-division cycle 20 homolog (CDC20), the key spindle assembly checkpoint proteins, has not been studied in cervical carcinogenesis. In this study, we compared the expression of MAD2 and CDC20 in 332 cases, including normal cervical tissues, low-grade squamous intraepithelial lesions, high-grade squamous intraepithelial lesions (HSILs), and invasive squamous cell carcinomas (SCCs). Both MAD2 and CDC20 were overexpressed in the nuclei or cytoplasm of dysplastic and malignant tumor cells. The frequency of MAD2 overexpression was markedly increased from undetectable (0/100) in normal cervical tissues and 2% (1/50) in low-grade squamous intraepithelial lesions to 67.1% (53/79) in HSILs and 52.4% (54/103) in SCCs. Similarly, CDC20 was overexpressed in 49.4% (39/79) of HSILs and 22.3% (23/103) of SCCs, whereas CDC20 was not detectable (0/100) in normal cervical tissues and overexpressed only in 8.0% (4/50) of low-grade squamous intraepithelial lesions. In SCC cases, MAD2 overexpression correlated with a patient age of less than 60 yr (P=0.043), nonkeratinizing histologic type (P=0.018), and a lesser degree of stromal invasion (P=0.026). In conclusion, MAD2 and CDC20 overexpression was increased in HSILs and SCCs, suggesting their involvement in the initiation of cervical cancers. Controlling CDC20 and MAD2 expression may be a therapeutic strategy for cervical cancer.

The sonographic "coffee bean" sign helps distinguish an axillary neurofibroma from a lymphadenopathy.

Axillary masses may represent various soft tissue tumors or lymphadenopathy. Neurofibromas are benign peripheral nerve sheath tumors and, while they are very uncommon, it is important to remember that neurogenic tumors arising from brachial plexus can develop in the axilla. We describe an axillary neurofibroma arising from the brachial plexus that presented with a "coffee bean sign" on sonography that distinguished it from axillary lymphadenopathy.

Surface anatomy and levator scapulae muscle injection: A cadaveric investigation.

Accurate detection of the levator scapulae muscle is critical for effective diagnostic and therapeutic interventions. The commonly used surface anatomy approach has not been validated and is less accurate than ultrasound-guided techniques. Therefore, we determined the needle insertion point for the levator scapulae using a new technique based on the anatomy of the scapula. This investigation used 15 fresh-frozen cadavers to explore the relationship between the acromial angle and medial tip of the scapular spine (O) of the scapular spine. Based on the x-axis (the distance [L] from Point O to point acromial angle) and the y-axis perpendicular to the x-axis passing through Point O, the barycentric coordinates were determined through the intersections of each axis and the superior angle of the scapula with the levator scapulae. Various ratios involving the established distance L) were ascertained, we compared the measurements and ratios between the male and female groups, and the accuracy of the new technique was compared with the conventional technique. The optimal site of the new technique was within 6 to 7% of distance L on the x-axis and 42 to 44% of distance L on the y-axis. This technique was significantly more accurate than the conventional technique (P = .006). Although ultrasound allows for accurate injections via real-time visualization, its unavailability in some cases highlights the importance of understanding surface anatomy landmarks. Our new technique, based on the anatomy of the scapula and relative measurements, is more accurate than the conventional technique. This should enable more precise detection of the levator scapulae for accurate and efficient diagnostic and therapeutic procedures.

Deep learning image reconstruction of diffusion-weighted imaging in evaluation of prostate cancer focusing on its clinical implications.

Background: Image-based assessment of prostate cancer (PCa) is increasingly emphasized in the diagnostic workflow for selecting biopsy targets and possibly predicting clinically significant prostate cancer (csPCa). Assessment is based on Prostate Imaging-Reporting and Data System (PI-RADS) which is largely dependent on T2-weighted image (T2WI) and diffusion weighted image (DWI). This study aims to determine whether deep learning reconstruction (DLR) can improve the image quality of DWI and affect the assessment of PI-RADS ≥4 in patients with PCa. Methods: In this retrospective study, 3.0T post-biopsy prostate magnetic resonance imaging (MRI) of 70 patients with PCa in Korea University Ansan Hospital from November 2021 to July 2022 was reconstructed with and without using DLR. Four DWI image sets were made: (I) conventional DWI (CDWI): DWI with acceleration factor 2 and conventional parallel imaging reconstruction, (II) DL1: DWI with acceleration factor 2 using DLR, (III) DL2: DWI with acceleration factor 3 using DLR, and (IV) DL3: DWI with acceleration factor 3 and half average b-value using DLR. Apparent diffusion coefficient (ADC) value, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) were measured by one reviewer, while two reviewers independently assessed overall image quality, noise, and lesion conspicuity using a four-point visual scoring system from each DWI image set. Two reviewers also performed PI-RADSv2.1 scoring on lesions suspected of malignancy. Results: A total of 70 patients (mean age, 70.8±9.7 years) were analyzed. The image acquisition time was 4:46 min for CDWI and DL1, 3:40 min for DL2, and 2:00 min for DL3. DL1 and DL2 images resulted in better lesion conspicuity compared to CDWI images assessed by both readers (P<0.05). DLR resulted in a significant increase in SNR, from 38.4±14.7 in CDWI to 56.9±21.0 in DL1. CNR increased from 25.1±11.5 in CDWI to 43.1±17.8 in DL1 (P<0.001). PI-RADS v2.1 scoring for PCa lesions was more agreeable with the DL1 reconstruction method than with CDWI (κ value CDWI, DL1; 0.40, 0.61, respectively). A statistically significant number of lesions were upgraded from PI-RADS <4 in CDWI image to PI-RADS ≥4 in DL1 images for both readers (P<0.05). Most of the PI-RADS upgraded lesions were from higher than unfavorable intermediate-risk groups according to the 2023 National Comprehensive Cancer Network guidelines with statistically significant difference of marginal probability in DL1 and DL2 for both readers (P<0.05). Conclusions: DLR in DWI for PCa can provide options for improving image quality with a significant impact on PI-RADS evaluation or about a 23% reduction in acquisition time without compromising image quality.

Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity.

BACKGROUND: Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes within regions of homozygosity were investigated to elucidate the genetic and genomic characteristics of Hanwoo. RESULTS: The Hanwoo bull genome was sequenced to 45.6-fold coverage using the ABI SOLiD system. In total, 4.7 million single-nucleotide polymorphisms and 0.4 million small indels were identified by comparison with the Btau4.0 reference assembly. Of the total number of SNPs and indels, 58% and 87%, respectively, were novel. The overall genotype concordance between the SNPs and BovineSNP50 BeadChip data was 96.4%. Of 1.6 million genetic differences in Hanwoo, approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Among 1,045 genes containing reliable specific NS/SS/Is in Hanwoo, 109 genes contained more than one novel damaging NS/SS/I. Of the genes containing NS/SS/Is, 610 genes were assigned as trait-associated genes. Moreover, 16, 78, and 51 regions of homozygosity (ROHs) were detected in Hanwoo, Black Angus, and Holstein, respectively. 'Regulation of actin filament length' was revealed as a significant gene ontology term and 25 trait-associated genes for meat quality and disease resistance were found in 753 genes that resided in the ROHs of Hanwoo. In Hanwoo, 43 genes were located in common ROHs between whole-genome resequencing and SNP chips in BTA2, 10, and 13 coincided with quantitative trait loci for meat fat traits. In addition, the common ROHs in BTA2 and 16 were in agreement between Hanwoo and Black Angus. CONCLUSIONS: We identified 4.7 million SNPs and 0.4 million small indels by whole-genome resequencing of a Hanwoo bull. Approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Additionally, we found 25 trait-associated genes for meat quality and disease resistance among 753 genes that resided in the ROHs of Hanwoo. These findings will provide useful genomic information for identifying genes or casual mutations associated with economically important traits in cattle.

Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle.

Hanwoo, Korean native cattle, is indigenous to the Korean peninsula. They have been used mainly as draft animals for about 5,000 years; however, in the last 30 years, their main role has been changed to meat production by selective breeding which has led to substantial increases in their productivity. Massively parallel sequencing technology has recently made possible the systematic identification of structural variations in cattle genomes. In particular, copy number variation (CNV) has been recognized as an important genetic variation complementary to single-nucleotide polymorphisms that can be used to account for variations of economically important traits in cattle. Here we report genome-wide copy number variation regions (CNVRs) in Hanwoo cattle obtained by comparing the whole genome sequence of Hanwoo with Black Angus and Holstein sequence datasets. We identified 1,173 and 963 putative CNVRs representing 16.7 and 7.8 Mbp from comparisons between Black Angus and Hanwoo and between Holstein and Hanwoo, respectively. The potential functional roles of the CNVRs were assessed by Gene Ontology enrichment analysis. The results showed that response to stimulus, immune system process, and cellular component organization were highly enriched in the genic-CNVRs that overlapped with annotated cattle genes. Of the 11 CNVRs that were selected for validation by quantitative real-time PCR, 9 exhibited the expected copy number differences. The results reported in this study show that genome-wide CNVs were detected successfully using massively parallel sequencing technology. The CNVs may be a valuable resource for further studies to correlate CNVs and economically important traits in cattle.