• Genomics & Informatics
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• v.18 no.3
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• pp.26.1-26.6
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• 2020

Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type-specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.169.2-170
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• 2003

Erythropietin (EPO), a hematopoietic factor is also required for normal brain development, and its receptor is localized in brain. Therefore, it is possible that EPO could act as a neurotropic factor inducing differentiation of neurons. The present study, we therefore investigated whether EPO can increase differentiation of undifferentiated cortical neuron isolated from postneonatal (Day 1) rat brains and PC12 cell, undifferentiated dopaminagic cell line. EPO dose (1-100 U/ml) dependently increased cell differentiation and expression of differentiation marker gene (neurofilament and tyrosine hydroxylase) in both cells. (omitted)

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.221.3-222
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• 2003

Adenophorae Radix, the roots of Adenophora triphylla var. japonica Hara (Campanulaceae) is known to be an anti-inflammatory and antitussive drug used for the treatment of lung disease. However quality control method is not established yet. This study is to establish the quality control method of Adenophorae Radix.From the roots of this plant, we isolated (6R,7R)-E,E-tetradeca-4,12-diene-8,10-diyne-1,6,7-triol (1) as a marker compound for the quality control and determined its content by HPLC-UV detector. (omitted)

• Journal of Veterinary Science
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• v.24 no.3
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• pp.36.1-36.7
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• 2023

Platelet to lymphocyte ratio (PLR) is a prognostic marker in human hepatocellular carcinoma (HCC) however, its utility in canine HCC has not been explored. The aim of the study was to determine if PLR could predict survival outcomes in 42 dogs with HCC. PLR was not a significant predictive factor (p = 0.15) but lymphopenia alone was significantly correlated with a reduced probability of survival (p = 0.024). Further studies are needed to evaluate if peripheral lymphocyte count mirrors that of the tumor microenvironment in canine HCC.

• Journal of Digestive Cancer Research
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• v.1 no.2
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• pp.95-99
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• 2013

MicroRNA (miRNA) dysregulations are associated with various types of human cancers, and miRNAs can function as tumor suppressors and oncogenes. Emerging evidence has shown that miRNA pathway is also altered during colorectal tumorigenesis. The detection of cancer-related miRNAs in stool samples may become useful diagnostic marker for colorectal cancer, because miRNAs in stool samples has high stability, and maintains a high portion of its original level. Recent studies reported that stool-based miRNAs can offer more sensitivity and specificity than currently used stool-based screening methods for CRC. In addition, unlike fecal occult blood test, sampling on consecutive dates and special dietary restrictions are not required. In this review, the authors discuss stool-based miRNA for the early diagnosis of CRC and perspectives on future application.

• Mycobiology
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• v.51 no.6
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• pp.463-467
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• 2023

Soybean is one of the world's most widely cultivated food crops, and soybean seeds are supplied from national seed resources in Korea. However, the transmission of seed-borne diseases through infected soybean seeds is problematic. Among these diseases, soybean seed decay is caused by Diaporthe spp. Infecting the pods, and the infected seeds show rotting symptoms. Most diseased seeds are removed during the selection process; however, it is difficult to distinguish infected seeds that do not display symptoms. Hence, a sequencebased method was devised to screen Diaporthe-infected seeds. Based on the nuclear ribosomal internal transcribe spacer (ITS) region of the pathogen, a primer was designed to distinguish the infection from other soybean seed pathogens. As a result of the comparison between healthy and Diaporthe-diseased seeds by using the primers, Diaporthe was detected only in the diseased seeds. Therefore, it is possible to distribute healthy soybean seeds by detecting Diaporthe-diseased seeds at the genetic level using the Diaporthe-specific primers.

• Asian review of World Histories
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• v.1 no.1
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• pp.5-44
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• 2013

This essay offers a historically based critique of the idea of "alternative modernities" that has acquired popularity in scholarly discussions over the last two decades. While significant in challenging Euro/American-centered conceptualizations of modernity, the idea of "alternative modernities" (or its twin, "multiple modernities") is open to criticism in the sense in which it has acquired currency in academic and political circles. The historical experience of Asian societies suggests that the search for "alternatives" long has been a feature of responses to the challenges of Euromodernity. But whereas "alternative" was conceived earlier in systemic terms, in its most recent version since the 1980s cultural difference has become its most important marker. Adding the adjective "alternative" to modernity has important counter-hegemonic cultural implications, calling for a new understanding of modernity. It also obscures in its fetishization of difference the entrapment of most of the "alternatives" claimed--products of the reconfigurations of global power--within the hegemonic spatial, temporal and developmentalist limits of the modernity they aspire to transcend. Culturally conceived notions of alternatives ignore the common structural context of a globalized capitalism which generates but also sets limits to difference. The seeming obsession with cultural difference, a defining feature of contemporary global modernity, distracts attention from urgent structural questions of social inequality and political injustice that have been globalized with the globalization of the regime of neoliberal capitalism. Interestingly, "the cultural turn" in the problematic of modernity since the 1980s has accompanied this turn in the global political economy during the same period. To be convincing in their claims to "alterity", arguments for "alternative modernities" need to re-articulate issues of cultural difference to their structural context of global capitalism. The goal of the discussion is to work out the implications of these political issues for "revisioning" the history and historiography of modernity.

• Korean Journal of Environment and Ecology
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• v.32 no.6
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• pp.566-574
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• 2018

The purpose of this study was to identify the phylogenetic relationships of the plants in the Korean genus Suaeda and to find out the molecular markers that could confirm the interspecies relationships in the family tree through molecular phylogenetic studies. We used the nuclear ribosomal DNA ITS and the chloroplast DNA matK, psbA-trnH, and trnL-trnF as the molecular markers. We could not distinguish between S. japonica and S. maritima and between S. maritima and S. australis in the ITS region and could not distinguish between S. japonica and S. australis with the base sequence in the psbA-trnH and trnL-trnF region. However, we analyzed the combinations of four molecular marker regions and confirmed that each of five plant species of the genus Suaeda formed the independent line. Therefore, it is considered that combinations of molecular markers would be useful for the analysis of phylogenetic relationships in the genus Suaeda. Further investigations of the ecological and morphological characteristics would be needed to understand the phylogenetic relationship and lineage diversification in the genus Suaeda.

• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.401-411
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• 2019

All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, $tRNA^{Ile(GAT)}$ and $tRNA^{Ala(TGC)}$, which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the $tRNA^{Ala}$ gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies.

• BMB Reports
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• v.54 no.10
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• pp.497-504
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• 2021

EGR1 (early growth response 1) is dysregulated in many cancers and exhibits both tumor suppressor and promoter activities, making it an appealing target for cancer therapy. Here, we used a systematic multi-omics analysis to review the expression of EGR1 and its role in regulating clinical outcomes in breast cancer (BC). EGR1 expression, its promoter methylation, and protein expression pattern were assessed using various publicly available tools. COSMIC-based somatic mutations and cBioPortal-based copy number alterations were analyzed, and the prognostic roles of EGR1 in BC were determined using Prognoscan and Kaplan-Meier Plotter. We also used bc-GenEx-Miner to investigate the EGR1 co-expression profile. EGR1 was more often downregulated in BC tissues than in normal breast tissue, and its knockdown was positively correlated with poor survival. Low EGR1 expression levels were also associated with increased risk of ER+, PR+, and HER2- BCs. High positive correlations were observed among EGR1, DUSP1, FOS, FOSB, CYR61, and JUN mRNA expression in BC tissue. This systematic review suggested that EGR1 expression may serve as a prognostic marker for BC patients and that clinicopathological parameters influence its prognostic utility. In addition to EGR1, DUSP1, FOS, FOSB, CYR61, and JUN can jointly be considered prognostic indicators for BC.