Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies.

BACKGROUND: Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities. RESULTS: By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues. CONCLUSIONS: Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.

The association between long working hours and obstructive sleep apnea assessed by STOP-BANG score: a cross-sectional study.

PURPOSE: The relationship between night-shift work and obstructive sleep apnea (OSA) is well known, but that between OSA and long working hours is still unknown. This study explores the association between long working hours and OSA. METHODS: Using cross-sectional Korean National Health and Nutrition Examination Survey 2020 data, we made multiple logistic regression models to calculate odds ratios (ORs) between weekly working hours and STOP-BANG scores for OSA screening. Stratified regression models by night or rotating shift work were also made. RESULTS: In an adjusted model of STOP-BANG high-risk versus low-risk groups, the OR in the group exceeding 40 h/wk was higher but not statistically significant, 1.19 [95% confidence interval (CI) 0.66-2.15] compared to the group working 40 h/wk (standard working hours) or less. In the group exceeding 52 h/wk, the OR was 2.03 with statistical significance (95% CI 1.08-3.80). In the stratification analysis of daytime and night-shift work, the daytime worker results were similar to those in the non-stratified model. The point estimation values of ORs in the night-shift workers were higher than in the daytime workers; however, we did not observe a statistical significance. CONCLUSION: Long working hours can increase the risk of OSA assessed by STOP-BANG scores.

Synergistic interaction between long shifts and short rest periods on depression in shift workers: A cross-sectional study from Korea.

BACKGROUND: Long shifts and short rest periods (SRP) between shifts are important factors that greatly affect shift workers' health. However, reports on the psychological effects of shift work, such as depression, have been inconsistent. Therefore, this study aimed to investigate the combined effect of long shifts and SRP on depression in shift workers. METHODS: This cross-sectional study included 3295 shift workers in the sixth Korean Working Conditions Survey. The relative excess risk due to interaction (RERI) was computed to estimate the combined effect of long shifts and SRP on depression. RESULTS: Depression in shift workers was not significantly associated with long shifts or SRP after adjustment, but the risk was significantly increased when exposed to both factors simultaneously (odds ratio 1.36, 95% confidence interval 1.03-1.79). The RERI between the two factors was statistically significant (p = 0.020), indicating a synergistic interaction with depression. Sensitivity analysis by occupation showed a significant interaction in the combined group of office and service workers (p = 0.034). CONCLUSIONS: Simultaneous exposure to SRP and long shifts should be avoided when planning shift work schedules or devising health policies for shift workers. Special consideration is needed for healthcare and service workers, who may be particularly vulnerable to negative health impacts due to shift work.

Priority analysis of factors affecting family planning practices among Ethiopians using a decision tree analysis.

This study aimed to identify the priorities of the factors affecting family planning practices in Ethiopia, with the ultimate aim of providing evidence to the Ethiopian government and international organizations for establishing family planning policies or family planning-related project plans. Multi-stage, clustered, stratified random sampling was performed on a total of 35,479 men aged above 15 years and women of childbearing age (15-49 years) in two metropolitan cities and five regions of Ethiopia. The survey was conducted by face-to-face interview using Tablet PC, and 25,972 responses, excluding censored data were included in the final analysis. The collected data were first analyzed using the Pearson chi-square test, independent sample t-test, and F-test with the Tukey HSD method as a post-hoc. Second, a decision-making tree analysis was conducted to identify priority factors affecting the decision to implement family planning The primary factor affecting the family planning practice was 'spouse or sexual partner's support for family planning (P <.001)'. 'Region (p <.001)' was the second priority factor for both the group receiving 'support for family planning by spouse or partner' and the group not receiving it. The third priority factors appeared differed by region in both groups. It is necessary to establish family planning policy and program plans targeting both men and women, and participation of religious and community leaders is considered important in the establishment process. In addition, it is considered necessary to enhance the professionalism by dividing the education and evaluation process for HEW to provide high-quality counseling, education, and services on family planning at the community level.

Association of sedentary work with colon and rectal cancer: systematic review and meta-analysis.

OBJECTIVES: There has been no research on sedentary behaviour in the occupational domain that occupies a large portion of the daily life. METHODS: We conducted a meta-analysis to investigate the association between sedentary work and colorectal cancer. We searched PubMed, Embase and Cochrane databases up to 12 August 2020 for peer-reviewed journal articles that assessed the association between sedentary work and colon or rectal cancer. Pooled estimates of ORs were obtained using random effects models. Statistical tests for publication bias, heterogeneity and sensitivity analysis were applied. RESULTS: Of the 5 381 studies initially identified, 23 studies with 64 reports were eligible for inclusion. Sedentary work significantly increased the risk of colon cancer (pooled OR=1.21, 95% CI 1.11 to 1.31, p value ≤0.0001) and rectal cancer (pooled OR=1.08, 95% CI 1.00 to 1.16, p value=0.0395). The adjustment for leisure time physical activity attenuated the association and made the risk estimates non-significant for sedentary behaviour, but the association was independent of sex, control of body mass index and assessment of sedentary behaviour. CONCLUSIONS: We found evidence of association between sedentary work and the risk of colon or rectal cancer. Limiting excessive sedentary work could be an important means of preventing colon and rectal cancer.

Health Effects Associated With Humidifier Disinfectant Use: A Systematic Review for Exploration.

BACKGROUND: It has been 10 years since the outbreak of lung disease caused by humidifier disinfectants in Korea, but the health effects have not yet been summarized. Therefore, this study aims to systematically examine the health effects of humidifier disinfectants that have been discovered so far. METHODS: All literature with humidifier disinfectants and their representative components as the main words were collected based on the web, including PubMed, Research Information Sharing Service, and government publication reports. A total of 902 studies were searched, of which 196 were selected. They were divided into four groups: published human studies (group 1), published animal and cytotoxicology studies (group 2), technical reports (group 3), and gray literature (group 4). RESULTS: Out of the 196 studies, 97 (49.5%) were published in peer-reviewed journals as original research. Group 1 consisted of 49 articles (50.5%), while group 2 consisted of 48 articles (49.5%). Overall, respiratory diseases such as humidifier disinfectant associated lung injury, interstitial lung disease, and asthma have a clear correlation, but other effects such as liver, heart, thymus, thyroid, fetal growth, metabolic abnormalities, and eyes are observed in toxicological experimental studies, but have not yet been identified in epidemiologic studies. CONCLUSION: The current level of evidence does not completely rule out the effects of humidifier disinfectants on extrapulmonary disease. Based on the toxicological evidence so far, it is required to monitor the population of humidifier disinfectant exposure continuously to see if similar damage occurs.

Occupational physical activity, not leisure-time physical activity, is associated with increased high-sensitivity C reactive protein levels.

OBJECTIVE: This study aims to explore the association between physical activity and high-sensitivity C reactive protein, based on different types of physical activity-occupational and leisure time. METHODS: Using cross-sectional data from the Korea National Health and Nutrition Examination Survey 2015-2018, we explored the association between different types of self-reported physical activity and high levels of high-sensitivity C reactive protein (>3 mg/L). We estimated the ORs for high-level high-sensitivity C reactive protein using multiple logistic regression models after adjusting for covariates from 12 970 eligible subjects (mean age 44.8). RESULTS: Compared with subjects who did not engage in moderate-to-vigorous level of occupational physical activity (OPA), the group that engaged in moderate-to-vigorous level of OPA showed a significantly high OR (1.32, 95% CI (1.03 to 1.69)), whereas the group that engaged in moderate-to-vigorous level of leisure-time physical activity (LPA) yielded a low OR (0.84, 95% CI (0.69 to 1.01)). The group that engaged in moderate-to-vigorous level of OPA but not LPA showed a significantly high OR (1.76, 95% CI (1.27 to 2.45)) compared with subjects who engaged in moderate-to-vigorous level of LPA but not in OPA. CONCLUSIONS: OPA is directly associated with high C reactive protein levels, suggesting that it increases the risk of inflammation.

The Occupational Characteristics and Health Status of Workers in Geographically Isolated and Confined Areas in the Republic of Korea.

BACKGROUND: This study investigates the safety and health status of geographically isolated and confined workers. METHODS: This study was conducted in Baekryeong Island in Korea in 2020. The age-standardized prevalence ratios (aSPR) for occupational injury, unmet medical needs, psychological status, and lifestyle were estimated from the available data. Also, we compared the aSPRs of workers in Baekryeong Island with a reference study population who participated in a nationally representative survey in Korea. RESULTS: The study revealed that Baekryeong Island workers had an increased risk of acquiring health and safety problems compared to the general worker population. The island workers showed a significant increase in unmet medical care (aSPR, 5.319; 95% confidence interval [CI], 3.984-6.958) and occupational injury (aSPR, 8.371; 95% CI, 3.820-15.892). CONCLUSION: This study identified the safety and health problems of geographically isolated workers in Baekryeong Island. The risk of occupational injury and unmet medical care are simultaneously highlighted in the region's population, thereby underscoring the importance of prevention.

TAMA: improved metagenomic sequence classification through meta-analysis.

BACKGROUND: Microorganisms are important occupants of many different environments. Identifying the composition of microbes and estimating their abundance promote understanding of interactions of microbes in environmental samples. To understand their environments more deeply, the composition of microorganisms in environmental samples has been studied using metagenomes, which are the collections of genomes of the microorganisms. Although many tools have been developed for taxonomy analysis based on different algorithms, variability of analysis outputs of existing tools from the same input metagenome datasets is the main obstacle for many researchers in this field. RESULTS: Here, we present a novel meta-analysis tool for metagenome taxonomy analysis, called TAMA, by intelligently integrating outputs from three different taxonomy analysis tools. Using an integrated reference database, TAMA performs taxonomy assignment for input metagenome reads based on a meta-score by integrating scores of taxonomy assignment from different taxonomy classification tools. TAMA outperformed existing tools when evaluated using various benchmark datasets. It was also successfully applied to obtain relative species abundance profiles and difference in composition of microorganisms in two types of cheese metagenome and human gut metagenome. CONCLUSION: TAMA can be easily installed and used for metagenome read classification and the prediction of relative species abundance from multiple numbers and types of metagenome read samples. TAMA can be used to more accurately uncover the composition of microorganisms in metagenome samples collected from various environments, especially when the use of a single taxonomy analysis tool is unreliable. TAMA is an open source tool, and can be downloaded at https://github.com/jkimlab/TAMA.

Population analysis of the Korean native duck using whole-genome sequencing data.

BACKGROUND: Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. The objective of this study is to perform population and functional analyses of Korean native duck, which has a distinct meat flavor and texture phenotype, using whole-genome sequencing data. To study the distinct genomic features of Korean native duck, we conducted population-level genomic analysis of 20 Korean native ducks together with 15 other duck breeds. RESULTS: A total of 15.56 million single nucleotide polymorphisms were detected in Korean native duck. Based on the unique existence of non-synonymous single nucleotide polymorphisms in Korean native duck, a total of 103 genes related to the unique genomic characteristics of Korean native duck were identified in comparison with 15 other duck breeds, and their functions were investigated. The nucleotide diversity and population structures among the used duck breeds were then compared, and their phylogenetic relationship was analyzed. Finally, highly differentiated genomic regions among Korean native duck and other duck breeds were identified, and functions of genes in those regions were examined. CONCLUSIONS: This is the first study to compare the population of Korean native duck with those of other duck breeds by using whole-genome sequencing data. Our findings can be used to expand our knowledge of genomic characteristics of Korean native duck, and broaden our understanding of duck breeds.

Long work hours and decreased glomerular filtration rate in the Korean working population.

OBJECTIVES: We studied the association between long working hours and decreased kidney function, which was determined using estimated glomerular filtration rate (eGFR), among the working population in South Korea. METHODS: We analysed nationally representative cross-sectional data for 20 851 Korean workers ≥20 years of age. A negative binomial regression model was used to test differences in the prevalence of chronic kidney disease (eGFR <60 mL/min/1.73 m2) among workers divided into groups according to weekly working hours (<30, 30-40, 41-51 and ≥52 hours/week). Multivariate linear regression analysis was performed to investigate the association between weekly working hours and eGFR, with adjustments made for age, sex/gender, income, education, shift work, occupation, smoking, alcohol use, hypertension, diabetes mellitus, body mass index, systolic blood pressure, fasting blood glucose and total serum cholesterol. RESULTS: A 1-hour increase in weekly working hours was associated with 0.057 mL/min/1.73 m2 (95% CI 0.005 to 0.109) decrease in eGFR among participants who worked ≥52 hours/week. Among participants without hypertension or diabetes, a 1-hour increase in weekly working hours was significantly associated with 0.248 and 0.209 mL/min/1.73 m2 decrease in eGFR among participants who worked 30-40 hours/week and 41-51 hours/week, respectively. CONCLUSION: Long working hours are associated with decreased kidney function. We expect that our findings could call for more research regarding this association and provide policy-oriented perspectives.

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.

Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions. Although many algorithms, databases and websites have been developed to help the study of PPIs, most of them are limited to visualize the structure and features of PPIs in a chosen single species with limited functions in the visualization perspective. This leads to difficulties in the identification of different patterns of PPIs in different species and their functional consequences. To resolve these issues, we developed a web application, called INTER-Species Protein Interaction Analysis (INTERSPIA). Given a set of proteins of user's interest, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/.

GMASS: a novel measure for genome assembly structural similarity.

BACKGROUND: Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have been developed to generate high quality de novo assemblies using the NGS reads, but their output is very different because of algorithmic differences. However, there are not properly structured measures to show the similarity or difference in assemblies. RESULTS: We developed a new measure, called the GMASS score, for comparing two genome assemblies in terms of their structure. The GMASS score was developed based on the distribution pattern of the number and coverage of similar regions between a pair of assemblies. The new measure was able to show structural similarity between assemblies when evaluated by simulated assembly datasets. The application of the GMASS score to compare assemblies in recently published benchmark datasets showed the divergent performance of current assemblers as well as its ability to compare assemblies. CONCLUSION: The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.

mySyntenyPortal: an application package to construct websites for synteny block analysis.

BACKGROUND: Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. RESULTS: To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users' own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. CONCLUSIONS: mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user's own genome data.

Synteny Portal: a web-based application portal for synteny block analysis.

Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomic regions conserved among multiple species, is key to understanding genomic architecture and the evolutionary history of genomes. However, the construction and visualization of such synteny blocks from multiple species are very challenging, especially for biologists with a lack of computational skills. Here, we present Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

Prediction of Return-to-original-work after an Industrial Accident Using Machine Learning and Comparison of Techniques.

BACKGROUND: Many studies have tried to develop predictors for return-to-work (RTW). However, since complex factors have been demonstrated to predict RTW, it is difficult to use them practically. This study investigated whether factors used in previous studies could predict whether an individual had returned to his/her original work by four years after termination of the worker's recovery period. METHODS: An initial logistic regression analysis of 1,567 participants of the fourth Panel Study of Worker's Compensation Insurance yielded odds ratios. The participants were divided into two subsets, a training dataset and a test dataset. Using the training dataset, logistic regression, decision tree, random forest, and support vector machine models were established, and important variables of each model were identified. The predictive abilities of the different models were compared. RESULTS: The analysis showed that only earned income and company-related factors significantly affected return-to-original-work (RTOW). The random forest model showed the best accuracy among the tested machine learning models; however, the difference was not prominent. CONCLUSION: It is possible to predict a worker's probability of RTOW using machine learning techniques with moderate accuracy.

Experimental studies on wave interactions of partially perforated wall under obliquely incident waves.

This study presents wave height distribution in terms of stem wave evolution phenomena on partially perforated wall structures through three-dimensional laboratory experiments. The plain and partially perforated walls were tested to understand their effects on the stem wave evolution under the monochromatic and random wave cases with the various wave conditions, incident angle (from 10 to 40 degrees), and configurations of front and side walls. The partially perforated wall reduced the relative wave heights more effectively compared to the plain wall structure. Partially perforated walls with side walls showed a better performance in terms of wave height reduction compared to the structure without the side wall. Moreover, the relative wave heights along the wall were relatively small when the relative chamber width is large, within the range of the chamber width in this study. The wave spectra showed a frequency dependency of the wave energy dissipation. In most cases, the existence of side wall is a more important factor than the porosity of the front wall in terms of the wave height reduction even if the partially perforated wall was still effective compared to the plain wall.

Experimental and numerical studies on wave breaking characteristics over a fringing reef under monochromatic wave conditions.

Fringing reefs play an important role in protecting the coastal area by inducing wave breaking and wave energy dissipation. However, modeling of wave transformation and energy dissipation on this topography is still difficult due to the unique structure. In the present study, two-dimensional laboratory experiments were conducted to investigate the cross-shore variations of wave transformation, setup, and breaking phenomena over an idealized fringing reef with the 1/40 reef slope and to verify the Boussinesq model under monochromatic wave conditions. One-layer and two-layer model configurations of the Boussinesq model were used to figure out the model capability. Both models predicted well (r (2) > 0.8) the cross-shore variation of the wave heights, crests, troughs, and setups when the nonlinearity is not too high (A 0/h 0 < 0.07 in this study). However, as the wave nonlinearity and steepness increase, the one-layer model showed problems in prediction and stability due to the error on the vertical profile of fluid velocity. The results in this study revealed that one-layer model is not suitable in the highly nonlinear wave condition over a fringing reef bathymetry. This data set can contribute to the numerical model verification.

Pay-for-performance and low back pain with interaction of overwork: findings from the cross-sectional Korean working conditions survey.

Background: Pay-for-performance (PFP) is a type of incentive system where employees receive monetary rewards for meeting predefined standards. While previous research has investigated the relationship between PFP and health outcomes, the focus has primarily been on mental health. Few studies have explored the impact of PFP on specific physical symptoms like pain. Methods: Data from the Korean Working Conditions Survey (KWCS) was analyzed, encompassing 20,815 subjects with information on PFP and low back pain (LBP). The associations between types of base pay (BP) and PFP with LBP were examined using multivariate logistic regression models, taking into account a directed acyclic graph (DAG). The interaction of overtime work was further explored using stratified logistic regression models and the relative excess risk for interaction. Results: The odds ratio (OR) for individuals receiving both BP and PFP was statistically significant at 1.19 (95% CI 1.04-1.35) compared to those with BP only. However, when the DAG approach was applied and necessary correction variables were adjusted, the statistical significance indicating a relationship between PFP and LBP vanished. In scenarios without PFP and with overtime work, the OR related to LBP was significant at 1.54 (95% CI 1.35-1.75). With the presence of PFP, the OR increased to 2.02 (95% CI 1.66-2.45). Conclusion: Pay-for-performance may influence not just psychological symptoms but also LBP in workers, particularly in conjunction with overtime work. The impact of management practices related to overtime work on health outcomes warrants further emphasis in research.

Dextrose-containing fluids causing false-positive serum galactomannan: a case-control study and interrupted time series analysis.

OBJECTIVES: This study aimed to identify the cause of false-positive serum Aspergillus antigen galactomannan (GM) results in our centre. METHODS: We performed a case-control study aiming to elucidate the factors associated with false-positive GM results. Independent risk factors for false-positive GM were evaluated through a multivariable regression analysis. An interrupted time series analysis was used to evaluate the effectiveness of an intervention removing the identified factors. RESULTS: Among 568 patients tested, GM was positive in 130 patients of whom 97 had false-positive GM (cases). These were compared with 427 patients with true-negative GM (controls). Administration of dextrose-containing fluids within 6 days before GM testing was an independent predictor for false-positive GM results (adjusted odds ratio [aOR], 18.60; 95% CI, 8.95-38.66. An analysis of GM presence in different dextrose-containing fluids revealed positivity in 34.8% (8 of 23) (manufacturer A) and 33.3% (5 of 15) (manufacturer B) of the samples. Investigation of the manufacturing process revealed that the saccharification process employed enzymes derived from Aspergillus niger. After identifying the root cause of false positivity, GM-containing dextrose fluid use was restricted. Interrupted time series analysis showed an immediate reduction of GM false-positivity (-6.5% per week, p = 0.045) and a declining trend (-0.33% per week, p = 0.005) postintervention. CONCLUSIONS: Administering dextrose-containing fluids was the primary factor causing false-positive serum Aspergillus antigen GM assay results. Our investigation led to a modification of the manufacturing process of the dextrose-containing fluids.