• Genomics & Informatics
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• v.18 no.4
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• pp.42.1-42.9
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• 2020

Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) is a powerful technology to profile the location of proteins of interest on a whole-genome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could accurately explain the binding features of target proteins detected by ChIP-Seq. Here, publicly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was compared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak prediction. There were no major differences among peak callers when analyzing point source histone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parameters, which indicates that their peak positions might not be located accurately. Our comparative results could provide a helpful guide to choose a suitable peak calling program for specific histone modifications.

• Mycobiology
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• v.46 no.4
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• pp.421-428
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• 2018

The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2016.10a
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• pp.401-404
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• 2016

This paper proposes entropy coding method of HEVC CABAC Encoder for efficient hardware architecture. The Binary Arithmetic Encoder requires data dependency at each step, which is difficult to be operated in a fast. Proposed Binary Arithmetic Encoder is designed 4 stage pipeline to quickly process the input value bin. According to bin approach, either MPS or LPS is selected and the binary arithmetic encoding is performed. Critical path caused by repeated operation is reduced by using the LUT and designed as a shift operation which decreases hardware size and not using memory. The proposed Binary Arithmetic Encoder of CABAC is designed using Verilog-HDL and it was implemented in 65nm technology. Its gate count is 3.17k and operating speed is 1.53GHz.

• Molecules and Cells
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• v.42 no.1
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• pp.87-95
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• 2019

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.23 no.4
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• pp.431-437
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• 2019

PLC(Power Line Communication) is being used in various ways in smart grid system because of the advantages of low cost and high data throughput. However, power line channel has many problems due to impulse noise and various studies have been conducted to solve the problem. Recently, ACDL(Adaptive Cannonical Differential Limiter) which is based on an adaptive clipping with analog nonlinear filter, has been proposed and performs better than the others. In this paper, we show that ACDL is similar to the detection of slew rate with oversampled digital signal by simplification and analysis. Through the simulation under the PRIME standard it is shown that the proposed performs equal to or better than that of ACDL, but significantly reduce the complexity to implement. The BER performance is equal but the complexity is reduced to less than 10%.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.23 no.5
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• pp.581-588
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• 2019

In this paper, I propose an modified back-off algorithm to improve the fairness for slotted ALOHA sensor networks. In hierarchical networks, the performance degradation of a specific node can cause degradation of the overall network performance in case the data transmitted by lower nodes is needed to be synthesized and processed by an upper node. Therefore it is important to ensure the fairness of transmission performance to all nodes. The proposed scheme choose a back-off time of a node considering the previous transmission results as well as the current transmission result. Moreover a node that failed to transmit consecutively is given gradually shorter back-off time but a node that is success to transmit consecutively is given gradually longer back-off time. Through simulations, I compare and analyze the performance of the proposed scheme with the binary exponential back-off algorithm(BEB). The results show that the proposed scheme reduces the throughput slightly compared to BEB but improves the fairness significantly.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.22 no.1
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• pp.294-298
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• 2021

Recently, many electronic devices have been integrated with various kinds of wireless sensor network technologies that have been enabled with wireless network connections. These wireless sensor network devices have adopted various kinds of wireless network technologies. On the other hand, because each wireless network technology has its advantages and disadvantages, the target and purposes should be considered carefully at the beginning of the development. In particular, the approach to the magnetic sensor should be considered carefully because it has its own characteristic compared to general sensors. The magnetic field generates nonlinear data. This paper introduces the design aspects to reflect low cost and wearable devices to use in a wireless sensor network. In addition, this paper addresses how to select proper sensor network technology. As a result, wireless sensor network devices were integrated using Zigbee and showed the performance of the throughput.

• Korean Journal of Agricultural Science
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• v.47 no.4
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• pp.995-1010
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• 2020

In this study, a multivariate analysis model of partial least square regression (PLSR) was developed to predict the moisture content of green peppers using hyperspectral imaging (HSI). In HSI, illumination is essential for high-quality image acquisition and directly affects the analytical performance of the visible near-infrared hyperspectral imaging (VIS/NIR-HSI) system. When green pepper images were acquired using a direct lighting system, the specular reflection from the surface of the objects and their intensities fluctuated with time. The images include artifacts on the surface of the materials, thereby increasing the variability of data and affecting the obtained accuracy by generating false-positive results. Therefore, images without glare on the surface of the green peppers were created using a polarization filter at the front of the camera lens and by exposing the polarizer sheet at the front of the lighting systems simultaneously. The results obtained from the PLSR analysis yielded a high determination coefficient of 0.89 value. The regression coefficients yielded by the best PLSR model were further developed for moisture content mapping in green peppers based on the selected wavelengths. Accordingly, the polarization filter helped achieve an uniform illumination and the removal of gloss and artifact glare from the green pepper images. These results demonstrate that the HSI technique with a polarized lighting system combined with chemometrics can be effectively used for high-throughput prediction of moisture content and image-based visualization.

• Plant Breeding and Biotechnology
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• v.5 no.2
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• pp.134-142
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• 2017

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

• Journal of Trauma and Injury
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• v.34 no.1
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• pp.31-38
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• 2021

Purpose: Traumatic vertebral injuries have a prevalence of 4-5% at level I centers. Studies have demonstrated that isolated thoracolumbar transverse process fractures (iTPF) rarely require brace or surgical interventions. We hypothesized that similarly isolated thoracolumbar spinous process fractures (iSPF) would have less need for bracing and operative interventions than SPFs with associated vertebral body (VB) fractures (SPF+VB). We performed a similar analysis for iTPF compared to transverse process fractures associated with VB injury (TPF+VB). Methods: In this single-center, retrospective study from 2012 to 2016, patients were classified into iSPF, SPF+VB, iTPF, and TPF+VB groups. Data including the fracture pattern, neurologic deficits, and operative intervention were obtained. The primary outcome studied was the need for bracing and/or surgery. A statistical analysis was conducted. Results: Of 98 patients with spinous process fractures, 21 had iSPF and 77 had SPF+VB. No iSPF patients underwent surgery, whereas 24 (31.17%) SPF+VB patients did undergo surgery (p=0.012). In the iSPF group, three patients (15%) received braces only for comfort, whereas 37 (48.68%) of the SPF+VB group required bracing (p=0.058). Of 474 patients with transverse process fractures, 335 had iTPF and 139 had TPF+VB. No iTPF patients underwent surgery, whereas 28 (20.14%) TPF+VB patients did (p≤0.001). Of the iTPF patients, six (1.86%) were recommended to receive braces only for comfort, while 68 (50.75%) of the TPF+VB patients required bracing (p<0.001). Conclusions: No patients with iSPF or iTPF required surgical intervention, and bracing was recommended to patients in these groups for comfort only. It appears that these injures may be safely managed without interventions, calling into question the need for spine consultation.