• Journal of Microbiology and Biotechnology
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• 제26권12호
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• pp.2206-2213
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• 2016

Recently, several studies have revealed that commercial microbial identification systems do not accurately identify the uncommon causative species of candidiasis, including Candida famata, Meyerozyma guilliermondii, and C. auris. We investigated the accuracy of species-level identification in a collection of clinical isolates previously identified as C. famata (N = 38), C. lusitaniae (N = 1 2), and M. guilliermondii (N = 5) by the Vitek 2 system. All 55 isolates were re-analyzed by the Phoenix system (Becton Dickinson Diagnostics), two matrix-assisted laser desorption ionization-time of flight mass spectrometry analyzers (a Vitek MS and a Bruker Biotyper), and by sequencing of internal transcribed spacer (ITS) regions or 26S rRNA gene D1/D2 domains. Among 38 isolates previously identified as C. famata by the Vitek 2 system, the majority (27/38 isolates, 71.1%) were identified as C. tropicalis (20 isolates) or C. albicans (7 isolates) by ITS sequencing, and none was identified as C. famata. Among 20 isolates that were identified as C. tropicalis, 17 (85%) were isolated from urine. The two isolates that were identified as C. auris by ITS sequencing originated from ear discharge. The Phoenix system did not accurately identify C. lusitaniae, C. krusei, or C. auris. The correct identification rate for 55 isolates was 92.7% (51/55 isolates) for the Vitek MS and 94.6% (52/55 isolates) for the Bruker Biotyper, as compared with results from ITS sequencing. These results suggest that C. famata is very rare in Korea, and that the possibility of misidentification should be noted when an uncommon Candida species is identified.

• 한국동물위생학회지
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• 제46권1호
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• pp.93-106
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• 2023

Emerging and re-emerging zoonotic viruses become critical public health, economic, societal, and cultural burdens. The Coronavirus disease-19 (COVID-19) pandemic reveals needs for effective preparedness and responsiveness against the emergence of variants and the next virus outbreak. The targeted next-generation sequencing (NGS) significantly contributes to the acquisition of viral genome sequences directly from clinical specimens. Using this advanced NGS technology, the genomic epidemiology and surveillance play a critical role in identifying of infectious source and origin, tracking of transmission chains and virus evolution, and characterizing the virulence and developing of vaccines during the outbreak. In this review, we highlight the platforms and preparation of targeted NGS for the viral genomics. We also demonstrate the application of this strategy to take advantage of the responsiveness and prevention of emerging zoonotic viruses. This article provides broad and deep insights into the preparedness and responsiveness for the next zoonotic virus outbreak.

• Parasites, Hosts and Diseases
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• 제40권3호
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• pp.157-162
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• 2002

Plasmodium vivax malaria re-emerged in South Korea in 1993, and epidemics continue since then. We examined genetic variation in the region encompassing the apical membrane antigen-1 (PvAMA-1) of the parasites by DNA sequencing of the 22 re-emerging p. vivax isolates. The genotype of the PvAMA-1, which was based on sequence data previously reported for the polymorphic regions, showed that two haplotypes were present at one polymorphic site. Compared with reported data, the two types, SKOR type I and type II, were similar to Chinese CH- l0A and CH-05A isolates, respectively. Thus, the present study showed that two genotypes of AMA-1 genes coexist in the re-emerging Korean P. vivax.

• 한국멀티미디어학회:학술대회논문집
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• 한국멀티미디어학회 2002년도 추계학술발표논문집
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• pp.644-648
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• 2002

멀티미디어 서비스를 제공하는 미래의 이동통신 시스템에서는 데이터의 신뢰성 있는 전송을 위해 데이터링크 계층에서 제공하는 프레임 에러율(FER: Frame Error Rates)을 감소시켜야 한다. 이를 위해 라디오링크 프로토콜(RLP: radio link protocol) 계층에서는 ARQ(Automatic Repeat request) 기법을 사용한다. 본 논문에서는 기지국에서 이동 호스트로 전송되는 국부적인 재전송 프레임(Frame)의 순서가 연속된 에러로 인하여 순서가 뒤바뀌고, 이로 인하여 기지국 데이터 링크계층에서 잦은 재전송으로 발생되는 높은 상호지연을 줄이기 위해 개선된 비순서적 재전송 기법을 제안하였다. 제안된 기법은 재전송방법 중 선택적 거절(selective-reject) ARQ의 비순서적 재전송에 수정한 빠른 재전승 기법을 적용하였으며, 기지국과 이동호스트 사이에서 데이터그램(Datagram)의 단편화(fragment)로 인한 링크계층의 Re-Sequencing을 하지 않기 때문에, 종단간 지연된 성능을 향상 시킬 수 있다.

• Molecules and Cells
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• 제43권7호
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• pp.591-599
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• 2020

Complex cell-to-cell communication underlies the basic processes essential for homeostasis in the given tissue architecture. Obtaining quantitative gene-expression of cells in their native context has significantly advanced through single-cell RNA sequencing technologies along with mechanical and enzymatic tissue manipulation. This approach, however, is largely reliant on the physical dissociation of individual cells from the tissue, thus, resulting in a library with unaccounted positional information. To overcome this, positional information can be obtained by integrating imaging and positional barcoding. Collectively, spatial transcriptomics strategies provide tissue architecture-dependent as well as position-dependent cellular functions. This review discusses the current technologies for spatial transcriptomics ranging from the methods combining mechanical dissociation and single-cell RNA sequencing to computational spatial re-mapping.

• Journal of Plant Biotechnology
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• 제46권2호
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• pp.71-78
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• 2019

The objective of this study was to use 'Danta PR', NGS (Next Generation Sequencing) technology for genome resequencing to develop polymorphic makers between Chinese oriental melon, 'Hyangseo 1' and Korean oriental melon. From the resequencing data that covered about 81 times of the genome size, 104,357 of SSR motifs and Indel, and 1,092,436 of SNPs were identified. 299 SSR and 307 Indel markers were chosen to cover each chromosome with 25 markers. These markers were subsequently used to identify genotypes of 'Danta PR' BC1 (F1 x 'Danta PR') population and a genetic linkage map was constructed. SSR, Indel, and SNPs identified in this study would be useful as a breeding tool to develop new oriental melon varieties.

• Molecules and Cells
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• 제45권10호
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• pp.673-684
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• 2022

The past two decades have witnessed an upsurge in the appreciation of adipose tissue (AT) as an immunometabolic hub harbouring heterogeneous cell populations that collectively fine-tune systemic metabolic homeostasis. Technological advancements, especially single-cell transcriptomics, have offered an unprecedented opportunity for dissecting the sophisticated cellular networks and compositional dynamics underpinning AT remodelling. The "re-discovery" of functional brown adipose tissue dissipating heat energy in human adults has aroused tremendous interest in exploiting the mechanisms underpinning the engagement of AT thermogenesis for combating human obesity. In this review, we aim to summarise and evaluate the use of single-cell transcriptomics that contribute to a better appreciation of the cellular plasticity and intercellular crosstalk in thermogenic AT.

• Design & Manufacturing
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• 제16권3호
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• pp.34-38
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• 2022

Regular expression pattern matching is widely used in applications such as computer virus vaccine, NIDS and DNA sequencing analysis. Hardware-based pattern matching is used when high-performance processing is required due to time constraints. ReCPU, SMPU, and REMP, which are processor-based regular expression matching processors, have been proposed to solve the problem of the hardware-based method that requires resynthesis whenever a pattern is updated. However, these processor-based regular expression matching processors inefficiently handle repetitive operations of regular expressions. In this paper, we propose a new instruction set to improve the inefficient repetitive operations of ReCPU and SMPU. We propose REMPi, a regular expression matching processor that enables efficient iterative operations based on the REMP instruction set. REMPi improves the inefficient method of processing a particularly short sub-pattern as a repeat operation OR, and enables processing with a single instruction. In addition, by using a down counter and a counter stack, nested iterative operations are also efficiently processed. REMPi was described with Verilog and synthesized on Intel Stratix IV FPGA.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2019년도 추계학술대회
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• pp.153-153
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• 2019

• Ocean and Polar Research
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• 제27권2호
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• pp.205-214
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• 2005

From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by $^{40}Ar/^{39}Ar$ analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria $({\alpha},\;{\beta},\;and\;{\gamma})$, Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.