• Animal Bioscience
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• v.34 no.9
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• pp.1439-1450
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• 2021

Objective: With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects. Methods: Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3). Results: In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results. Conclusion: Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

• Communications of Mathematical Education
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• v.36 no.4
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• pp.487-509
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• 2022

The purpose of this study is to analyze classroom discourse in the math classroom of middle school in China, which has a unique math classroom background of entrance examination for high school. To this end, this study analyzed teacher question statistics and episodes by teacher question type as starting speech in mathematics classroom discourse, and five IRF subtypes were especially identified by class discourse structure analysis. The data were analyzed focusing on a total of 15 transcripts of math classes recorded by three math teachers at H School in Guiyang, Guizhou Province, China, and written interviews of teachers. According to the results of this study, an average of 20 teacher questions were observed for each class, and the teacher question type was classified into confirmation question (understanding confirmation question, explanation request question, and double check question) and information question (information presentation question). In addition, according to classroom discourse analysis, the IRF discourse structure was divided into fragmentary evaluation, evaluation+reason, evidence of explanation, evaluation+student response re-statement, guidance on other thoughts or solutions, and student answer correction or teacher opinion presentation.

• Journal of fish pathology
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• v.35 no.2
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• pp.141-155
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• 2022

Rock bream iridovirus (RBIV) causes high mortality and economic losses in the rock bream (Oplegnathus fasciatus) aquaculture industry in Korea. Viral open reading frames (ORFs) expression profiling at different RBIV infection stages was investigated using microarray approaches. Rock bream were exposed to the virus and held for 7 days at 23 ℃ before the water temperature was reduced to 17 ℃. Herein, 28% mortality was observed from 24 to 35 days post infection (dpi), after which no mortality was observed until 70 dpi (end of the experiment). A total of 27 ORFs were significantly up- or down-regulated after RBIV infection. In RBIV-infected rock bream, four viral genes were expressed after 2 dpi. Most RBIV ORFs (26 genes, 96.2%) were significantly elevated between 7 and 20 dpi. Among them, 12 ORF (44.4%) transcripts reached their peak expression intensity at 15 dpi, and 14 ORFs (51.8%) were at peak expression intensity at 20 dpi. Expression levels began to decrease after 25 dpi, and 92.6% of ORFs (25 genes) were expressed below 1-fold at 70 dpi. From the microarray data, in addition to the viral infection, viral gene expression profiles were categorized into three infection stages, namely, early (2 dpi), middle (7 to 20 dpi), and recovery (25 and 70 dpi). RBIV ORFs 009R, 023R, 032L, 049L, and 056L were remarkably expressed during RBIV infection. Furthermore, six ORFs (001L, 013R, 052L, 053L, 058L, and 061L) were significantly expressed only at 20 dpi. To verify the cDNA microarray data, we performed quantitative real-time PCR, and the results were similar to that of the microarray. Our results provide novel observations on broader RBIV gene expression at different stages of infection and the development of control strategies against RBIV infection.

• Molecules and Cells
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• v.45 no.9
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• pp.660-672
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• 2022

The target of rapamycin complex (TORC) plays a key role in plant cell growth and survival by regulating the gene expression and metabolism according to environmental information. TORC activates transcription, mRNA translation, and anabolic processes under favorable conditions, thereby promoting plant growth and development. Tomato fruit ripening is a complex developmental process promoted by ethylene and specific transcription factors. TORC is known to modulate leaf senescence in tomato. In this study, we investigated the function of TORC in tomato fruit ripening using virus-induced gene silencing (VIGS) of the TORC genes, TOR, lethal with SEC13 protein 8 (LST8), and regulatory-associated protein of TOR (RAPTOR). Quantitative reverse transcription-polymerase chain reaction showed that the expression levels of tomato TORC genes were the highest in the orange stage during fruit development in Micro-Tom tomato. VIGS of these TORC genes using stage 2 tomato accelerated fruit ripening with premature orange/red coloring and decreased fruit growth, when control tobacco rattle virus 2 (TRV2)-myc fruits reached the mature green stage. TORC-deficient fruits showed early accumulation of carotenoid lycopene and reduced cellulose deposition in pericarp cell walls. The early ripening fruits had higher levels of transcripts related to fruit ripening transcription factors, ethylene biosynthesis, carotenoid synthesis, and cell wall modification. Finally, the early ripening phenotype in Micro-Tom tomato was reproduced in the commercial cultivar Moneymaker tomato by VIGS of the TORC genes. Collectively, these results demonstrate that TORC plays an important role in tomato fruit ripening by modulating the transcription of various ripening-related genes.

• Molecules and Cells
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• v.44 no.11
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• pp.805-829
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• 2021

CCCTC-binding factor (CTCF) critically contributes to 3D chromatin organization by determining topologically associated domain (TAD) borders. Although CTCF primarily binds at TAD borders, there also exist putative CTCF-binding sites within TADs, which are spread throughout the genome by retrotransposition. However, the detailed mechanism responsible for masking the putative CTCF-binding sites remains largely elusive. Here, we show that the ATP-dependent chromatin remodeler, chromodomain helicase DNA-binding 4 (CHD4), regulates chromatin accessibility to conceal aberrant CTCF-binding sites embedded in H3K9me3-enriched heterochromatic B2 short interspersed nuclear elements (SINEs) in mouse embryonic stem cells (mESCs). Upon CHD4 depletion, these aberrant CTCF-binding sites become accessible and aberrant CTCF recruitment occurs within TADs, resulting in disorganization of local TADs. RNA-binding intrinsically disordered domains (IDRs) of CHD4 are required to prevent this aberrant CTCF binding, and CHD4 is critical for the repression of B2 SINE transcripts. These results collectively reveal that a CHD4-mediated mechanism ensures appropriate CTCF binding and associated TAD organization in mESCs.

• Mycobiology
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• v.50 no.5
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• pp.366-373
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• 2022

Regulation of proper gene expression is important for cellular and organismal survival, maintenance, and growth. Abnormal gene expression, even for a single critical gene, can thwart cellular integrity and normal physiology to cause diseases, aging, and death. Therefore, gene expression profiling serves as a powerful tool to understand the pathology of diseases and to cure them. In this study, the difference in gene expression in Flammulina velutipes was compared between the wild type (WT) mushroom and the mutant one with clogging phenomenon. Differentially expressed transcripts were screened to identify the candidate genes responsible for the mutant phenotype using the DNA microarray analysis. A total of 88 genes including 60 upregulated and 28 downregulated genes were validated using the real-time quantitative PCR analysis. In addition, proteomic differences between the WT and mutant mushroom were analyzed using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Interestingly, the genes identified by these genomic and proteomic analyses were involved in stress response, translation, and energy/sugar metabolism, including HSP70, elongation factor 2, and pyruvate kinase. Together, our data suggest that the aberrant expression of these genes attributes to the mutant clogging phenotype. We propose that these genes can be targeted to foster normal growth in F. velutipes.

• Communications of Mathematical Education
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• v.36 no.1
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• pp.39-57
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• 2022

This study aims to design an integral instruction method that follows the Abstraction in Context (AiC) framework proposed by Hershkowitz, Schwarz, and Dreyfus to help students in acquiring in-depth understanding of the relationship between indefinite integrals and definite integrals and to analyze how the students' understanding improved as a result. To this end, we implemented lessons according to the integral instruction method designed for eight 11th grade students in a science high school. We recorded and analyzed data from graded student worksheets and transcripts of classroom recordings. Results show that students comprehend three knowledge elements regarding relationship between indefinite integral and definite integral: the instantaneous rate of change of accumulation function, the calculation of a definite integral through an indefinite integral, and The determination of indefinite integral by the accumulation function. The findings suggest that the AiC framework is useful for designing didactical activities for conceptual learning, and the accumulation function can serve as a basis for teaching the three knowledge elements regarding relationship between indefinite integral and definite integral.

• Korean Journal of Otorhinolaryngology-Head and Neck Surgery
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• v.55 no.8
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• pp.498-507
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• 2012

Background and Objectives We aimed to develop a Korean version of the velopharyngeal insufficiency (VPI) speech corpus system. Subjects and Method After developing a 3-channel simultaneous speech recording device capable of recording nasal/oral and normal compound speech separately, voice data were collected from VPI patients aged more than 10 years with/without the history of operation or prior speech therapy. This was compared to a control group for which VPI was simulated by using a french-3 nelaton tube inserted via both nostril through nasopharynx and pulling the soft palate anteriorly in varying degrees. The study consisted of three transcriptors: a speech therapist transcribed the voice file into text, a second transcriptor graded speech intelligibility and severity and the third tagged the types and onset times of misarticulation. The database were composed of three main tables regarding (1) speaker's demographics, (2) condition of the recording system and (3) transcripts. All of these were interfaced with the Praat voice analysis program, which enables the user to extract exact transcribed phrases for analysis. Results In the simulated VPI group, the higher the severity of VPI, the higher the nasalance score was obtained. In addition, we could verify the vocal energy that characterizes hypernasality and compensation in nasal/oral and compound sounds spoken by VPI patients as opposed to that characgerizes the normal control group. Conclusion With the Korean version of VPI speech corpus system, patients' common difficulties and speech tendencies in articulation can be objectively evaluated. Comparing these data with those of the normal voice, mispronunciation and dysarticulation of patients with VPI can be corrected.

• Journal of Preventive Medicine and Public Health
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• v.55 no.3
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• pp.213-225
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• 2022

Objectives: The aim of this qualitative study was to investigate how members of the general public in Korea interpret the concept of health, and which dimensions of health are most important to them. We also explored their perceptions of the EuroQoL 5-Dimension (EQ-5D), including the EuroQoL visual analogue scale (EQ-VAS). Methods: We conducted face-to-face, in-depth interviews with 20 individuals from the general population, using a semi-structured interview guide. Content analysis was performed with verbatim transcripts and field notes to identify codes and categorize them according to their similarities and associations. Results: In total, 734 different codes were derived and classified into 4 categories. Participants cited the importance of both the mental and physical aspects of health, although they emphasized that the physical aspects appeared to play a larger role in their conceptualization of health. Participants noted that the EQ-5D has the advantage of being composed of 5 dimensions that are simple and contain both physical and mental areas necessary to describe health. However, some of them mentioned the need to add more dimensions of mental health and social health. Participants showed great satisfaction with the visually well-presented EQ-VAS. However, participants opined that the EQ-VAS scores might not be comparable across respondents because of different ways of responding to the scale. Conclusions: While physical health is a fundamental aspect of health, mental and social aspects are also important to Koreans. The content of the EQ-5D broadly matched the attributes of health considered important by Koreans.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2023.04a
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• pp.63-63
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• 2023

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops and provides up to 30% of the world's sugar production. In this study, we mainly performed RNA-sequencing to obtain identify putative genes involved in biosynthesis pathway of sucrose in sugar beet and comparative transcriptomic analyses in the four developmental stages (50, 90, 160 and 330 days after seedling). As a result of the sugar content analysis, it was increased significantly from 50 to 160 days after seedling (DAS), and then decreased at 330 DAS. On the other hand, the taproot weight, length, and width were increased during all the growth periods. Out of 21,451 genes with expressed value, 21,402 (99.77%) genes had functional descriptions. Among the three comparisons, S1 (50 DAS) vs. S2 (90 DAS), S1 vs. S3 (160 DAS), and S1 vs. S4 (330 DAS), expression profiling of the transcripts was identified 4,991 with differentially expressed genes (DEGs). By comparing the top 20 enriched gene ontology (GO) terms as three comparisons, the top GO terms were commonly confirmed with external encapsulating structure, cell wall, and extracellular regions. In addition, the 38 enriched candidate genes related to sucrose biosynthetic pathway were screened from the entire DEG pool, and the candidate genes might be providing a basic data for further sugar metabolism studies in development of sugar beet taproot.