• Journal of KIISE
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• v.42 no.7
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• pp.910-918
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• 2015

This paper presents a parameter visualization technique to overcome the limitation of the naked eye in contrast-enhanced ultrasonography. A method is also proposed to compensate for the distortion and noise in ultrasound image sequences. Meaningful parameters for diagnosing liver disease can be extracted from the dynamic patterns of the contrast enhancement in ultrasound images. The visualization technique can provide more accurate information by generating a parametric image from the dynamic data. Respiratory motions and noise from micro-bubble in ultrasound data may cause a degradation of the reliability of the diagnostic parameters. A multi-stage algorithm for respiratory motion tracking and an image enhancement technique based on the Markov Random Field are proposed. The usefulness of the proposed methods is empirically discussed through experiments by using a set of clinical data.

• Journal of Korean Neurosurgical Society
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• v.59 no.1
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• pp.26-36
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• 2016

Objective : This study investigated whether pyrosequencing can be used to determine the methylation status of the MGMT promoter as a clinical biomarker using relatively old archival tissue samples of glioblastoma. We also examined other prognostic factors for survival of glioblastoma patients. Methods : The available study set included formalin-fixed paraffin-embedded (FFPE) tissue from 104 patients at two institutes from 1997 to 2012, all of which were diagnosed histopathologically as glioblastoma. Clinicopathologic data were collected by review of medical records. For pyrosequencing analysis, the PyroMark Q96 CpG MGMT kit (Qiagen, Hilden, Germany) was used to detect the level of methylation at exon 1 positions 17-39 of the MGMT gene, which contains 5 CpGs. Results : Methylation of the MGMT promoter was detected in 43 (41.3%) of 104 samples. The average percentage methylation was $14.0{\pm}16.8%$ overall and $39.0{\pm}14.7%$ for methylated cases. There was no significant pattern of linear increase or decrease according to the age of the FFPE block (p=0.687). In multivariate analysis, age, performance status, extent of surgery, method of adjuvant therapy, and methylation status estimated by pyrosequencing were independently associated with overall survival. Additionally, patients with a high level of methylation survived longer than those with low methylation (p=0.016). Conclusion : In this study, the status and extent of methylation of the MGMT promoter analyzed by pyrosequencing were associated with overall survival in glioblastoma patients. Pyrosequencing is a quantitative method that overcomes the problems of MSP and a simple technique for accurate analysis of DNA sequences.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.337-353
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• 2018

We used Illumina/HiSeq sequencing for analysis of gene expression profiling among four maize seed types (dent, CM3 and CM6; waxy, CM5 and CM19) at 10 DAP (days after pollination). A total of 88,993,000 (CM3), 103,817,340 (CM6), 103,139,640 (CM5), and 66,978,958 (CM19) sequence reads were generated with read lengths of about 0.9, 1.0, 1.0, and 0.7 billion bp, respectively. We obtained 69.1 (CM3), 71.0 (CM6), 71.2 (CM5), and 71.8% (CM19) high quality reads from the raw data and compared them with reference RNA sequences in a public DB (NCBI). It was revealed that mapped reads were 58%, 63%, 62%, and 62% of the EST reference in CM3, CM6, CM5 and CM19, respectively; and more than 51,000 genes were expressed based on RPKM criteria (over 0.25 value) in each CM3, CM6, CM5, and CM19 inbred line. In differentially expressed gene (DEG) analysis, we found that 3,527 genes were differentially expressed by at least two-fold with 1,709 upregulated in the two waxy inbred lines and 1,818 upregulated in the two dent inbred lines. We also detected genes for the sucrose and starch biosynthesis pathways based on BINs, and different expression patterns between waxy and dent inbred lines were shown for the gene set for starch synthesis, such as sh2, bt2, du1, wx1, and ae1. Although some genes were more expressed in dent lines, most genes for starch synthesis were much expressed in waxy lines. Especially, there was greater expression of the sus2 gene in both waxy lines compared with the dent lines.

• Journal of Korean Society of Industrial and Systems Engineering
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• v.41 no.4
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• pp.238-247
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• 2018

This paper considers the problem of scheduling loading and unloading operations of a crane in a railway terminal motivated from rail-road container transshipment operations at Uiwang Inland Container Depot (ICD). Unlike previous studies only considering the total handling time of containers, this paper considers a bi-criteria objective of minimizing the weighted sum of the total handling time and tenant service time. The tenant service time is an important criterion in terms of terminal tenants who are private logistics companies in charge of moving containers from/to the terminal using their trucks. In the rail-road container shipment yard, the tenant service time of a tenant can be defined by a time difference between beginning and finishing loading and unloading operations of a crane. Thus, finding a set of sequences and time of the crane operations becomes a crucial decision issue in the problem. The problem is formulated as a nonlinear program which is improved by linearizing a nonlinear constraint in the model. This paper develops a genetic algorithm to solve the problem and performs a case study on the Uiwang ICD terminal. Computational experiment results show that the genetic algorithm shows better performance than commercial optimization solvers. Operational implications in terms of tenants are drawn through sensitivity analyses.

• Journal of applied mathematics & informatics
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• v.39 no.3_4
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• pp.381-403
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• 2021

Consider the three-dimensional system of difference equations $x_{n+1}=\frac{{\prod_{j=0}^{k}}z_n-3j}{{\prod_{j=1}^{k}}x_n-(3j-1)\;\(a_n+b_n{\prod_{j=0}^{k}}z_n-3j\)}$, $y_{n+1}=\frac{{\prod_{j=0}^{k}}x_n-3j}{{\prod_{j=1}^{k}}y_n-(3j-1)\;\(c_n+d_n{\prod_{j=0}^{k}}x_n-3j\)}$, $z_{n+1}=\frac{{\prod_{j=0}^{k}}y_n-3j}{{\prod_{j=1}^{k}}z_n-(3j-1)\;\(e_n+f_n{\prod_{j=0}^{k}}y_n-3j\)}$, n ∈ ℕ₀, where k ∈ ℕ₀, the sequences $(a_n)_{n{\in}{\mathbb{N}}_0$, $(b_n)_{n{\in}{\mathbb{N}}_0$, $(c_n)_{n{\in}{\mathbb{N}}_0$, $(d_n)_{n{\in}{\mathbb{N}}_0$, $(e_n)_{n{\in}{\mathbb{N}}_0$, $(f_n)_{n{\in}{\mathbb{N}}_0$ and the initial values x_-3k, x_-3k+1, …, x₀, y_-3k, y_-3k+1, …, y₀, z_-3k, z_-3k+1, …, z₀ are real numbers. In this work, we give explicit formulas for the well defined solutions of the above system. Also, the forbidden set of solution of the system is found. For the constant case, a result on the existence of periodic solutions is provided and the asymptotic behavior of the solutions is investigated in detail.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.24 no.2
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• pp.268-275
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• 2020

A lightweight hardware design of self-timed ring based true random number generator (TRNG) suitable for information security applications is described. To reduce hardware complexity of TRNG, an entropy extractor with feedback structure was proposed, which minimizes the number of ring stages. The number of ring stages of the FSTR-TRNG was determined to be a multiple of eleven, taking into account operating clock frequency and entropy extraction circuit, and the ratio of tokens to bubbles was determined to operate in evenly-spaced mode. The hardware operation of FSTR-TRNG was verified by FPGA implementation. A set of statistical randomness tests defined by NIST 800-22 were performed by extracting 20 million bits of binary sequences generated by FSTR-TRNG, and all of the fifteen test items were found to meet the criteria. The FSTR-TRNG occupied 46 slices of Spartan-6 FPGA device, and it was implemented with about 2,500 gate equivalents (GEs) when synthesized in 180 nm CMOS standard cell library.

• International Journal of Industrial Entomology and Biomaterials
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• v.44 no.2
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• pp.55-64
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• 2022

Bombyx shini Park & Sohn, 2002 (Lepidoptera: Bombycidae), which was listed as an endemic species in South Korea has recently been renamed as the East Asian silk moth Rotunda rotundapex Miyata & Kishida, 1990 (Lepidoptera: Bombycidae). In this study, we sequenced the complete mitochondrial genome (mitogenome) of the R. rotundapex to announce genomic characteristics and to clarify its validity with a new name. The 15,294-bp long complete mitogenome comprises a typical set of genes [13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes] and one major noncoding, A + T-rich region, with an arrangement identical to that observed in most lepidopteran mitogenomes. The A/T content of the whole mitogenome was 79.22%; however, it varied among the regions/genes as follows: A + T-rich region, 91.62%; srRNA, 84.67%; lrRNA, 83.01%; tRNAs, 81.43%; and PCGs, 77.46%. Phylogenetic analyses of 35 species in the Bombycoidea superfamily showed the sister relationship between the families Sphingidae and Bombycidae s. str., with the higher nodal support [bootstrap support (BS) = 78%]. The Saturniidae was placed as the sister to the two families, but the nodal support for this relationship was low (BS = 53%). Current R. rotundapex was placed together with previously reported con-species with the highest nodal support, forming a separate clade from Bombyx, validating that B. shini can have a new genus name, Rotunda. However, the Korean R. rotundapex showed a substantial sequence divergence at 5.28% to that originated from an individual of type locality Taiwan in 1,459-bp of COI sequences. Considering such a high sequence divergence an additional study, which includes morphological and DNA barcoding data from further extensive distributional range maybe is needed for further robust taxonomic conclusion.

• The Plant Pathology Journal
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• v.38 no.4
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• pp.272-286
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• 2022

Black root rot (BRR) caused by Lasiodiplodia theobromae is an alarming disease of mulberry that causes tremendous economic losses to sericulture farmers in India and China. Successful control of this disease can be attained by screening germplasm and identifying resistant sources. Seventy four diseased root samples were collected from farmer's fields belonging to four major mulberry growing states of South India. Based on morpho-cultural and scanning electron microscopy studies, 57 fungal isolates were characterized and identified as L. theobromae. Phylogenetic analysis of concatenated internal transcribed spacer and β-tubulin sequences revealed variation of the representative 20 isolates of L. theobromae. Following the root dip method of inoculation, pathogenicity studies on susceptible mulberry genotypes (Victory-1 and Thailand male) recognized the virulent isolate MRR-142. Accordingly, MRR-142 isolate was used to evaluate resistance on a set of 45 diverse mulberry accessions. In the repeated experiments, the mulberry accession ME-0168 which is an Indonesian origin belonging to Morus latifolia was found to be highly resistant consistently against BRR. Eight accessions (G2, ME-0006, ME-0011, ME-0093, MI-0006, MI-0291, MI-0489, and MI-0501) were found to be resistant. These promising resistant resources may be exploited in mulberry breeding for developing BRR resistant varieties and to develop mapping populations which successively helps in the identification of molecular markers associated with BRR.

• Journal of Microbiology and Biotechnology
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• v.32 no.10
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• pp.1292-1298
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• 2022

Soil autotrophic bacterial communities play a significant role in the soil carbon (C) cycle in paddy fields, but little is known about how rhizosphere soil microorganisms respond to different long-term (35 years) fertilization practices under double rice cropping ecosystems in southern China. Here, we investigated the variation characteristics of rhizosphere soil RubisCO gene cbbL in the double rice ecosystems of in southern China where such fertilization practices are used. For this experiment we set up the following fertilizer regime: without any fertilizer input as a control (CK), inorganic fertilizer (MF), straw returning (RF), and organic and inorganic fertilizer (OM). We found that abundances of cbbL, 16S rRNA genes and RubisCO activity in rhizosphere soil with OM, RF and MF treatments were significantly higher than that of CK treatment. The abundances of cbbL and 16S rRNA genes in rhizosphere soil with OM treatment were 5.46 and 3.64 times higher than that of CK treatment, respectively. Rhizosphere soil RubisCO activity with OM and RF treatments increased by 50.56 and 45.22%, compared to CK treatment. Shannon and Chao1 indices for rhizosphere soil cbbL libraries with RF and OM treatments increased by 44.28, 28.56, 29.60, and 23.13% compared to CK treatment. Rhizosphere soil cbbL sequences with MF, RF and OM treatments mainly belonged to Variovorax paradoxus, uncultured proteobacterium, Ralstonia pickettii, Thermononospora curvata, and Azoarcus sp.KH33C. Meanwhile, cbbL-carrying bacterial composition was obviously influenced by soil bulk density, rhizosphere soil dissolved organic C, soil organic C, and microbial biomass C contents. Fertilizer practices were the principal factor influencing rhizosphere soil cbbL-carrying bacterial communities. These results showed that rhizosphere soil autotrophic bacterial communities were significantly changed under conditions of different long-term fertilization practices Therefore, increasing rhizosphere soil autotrophic bacteria community with crop residue and organic manure practices was found to be beneficial for management of double rice ecosystems in southern China.

• Korean journal of applied entomology
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• v.61 no.3
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• pp.507-512
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• 2022

The Gypsy moth, Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) is a serious pest that attacks forest as well as fruit trees. We sequenced the 15,548 bp long complete mitochondrial genome (mitogenome) of this species. It consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding A + T-rich region. The orientation and gene order of the L. dispar mitogenome are identical to that of the ancestral type found in majority of the insects. Phylogenetic analyses using concatenated sequences of 13 PCGs and 2 rRNAs (13,568 bp including gaps) revealed that the L. dispar examined in our study, together with other geographical samples of L. dispar in a group forming the family Erebidae and consistently supported the monophyly of each family (Erebidae, Euteliidae, Noctuidae, Nolidae and Notodontidae), generally with the highest nodal supports.