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Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines

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Horticultural Plant Journal 2021年第6期7卷 539-551页

作者： Sampath Perumal Nomar Espinosa Waminal Jonghoon Lee Hyun-Jin Koo boem-soon choi Jee Young Park Kyounggu Ahn Tae-Jin Yang Department of Agriculture Forestry and BioresourcesPlant Genomics and Breeding Instituteand Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Global Institute for Food Security University of Saskatchewan421 Downey RoadSaskatoonSK S7N 4L8Canada Agriculture and Agri-Food Canada 107 Science PlaceSaskatoon S7N 0X2Canada Chromosome Research Institute Department of Life ScienceSahmyook UniversitySeoul 01795Republic of Korea Joeun Seeds.Co. LtdGoesan-GunChungcheongbuk-Do 367-833Republic of Korea Phyzen Genomics Institute 13Seongnam-daero 331beon-gilBundang-guSeongnam-siGyeonggi-do 13558Republic of Korea

Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop *** produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 *** breeding *** then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major *** genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 ***,some SNPs showed subspecies enrichment at certain chromosomal *** assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and *** 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 *** phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another *** morphotypes diverged during the last 0.17 million *** Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process *** polymorphic Cp markers provide a classification system for the cytoplasm types in ***,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active ***,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse *** morphotypes.

关键词： Brassica oleracea subspecies Chloroplast genome Nuclear ribosomal DNA Genetic diversity Phylogeny

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ELK3-ID4 axis governs the metastatic features of triple negative breast cancer

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Oncology Research 2024年第1期32卷 127-138页

作者： JIN-HO choi JOO DONG PARK SEUNG HEE choi EUN-SU KO HYE JUNG JANG KYUNG-soon PARK Department of Biomedical Science CHA UniversitySeongnamKorea

Purpose:Cancer cell metastasis is a multistep process,and the mechanism underlying extravasation remains ***3 is a transcription factor that plays a crucial role in regulating various cellular processes,including cancer *** on the finding that ELK3 promotes the metastasis of triple-negative breast cancer(TNBC),we investigated whether ELK3 regulates the extravasation of TNBC by forming the ELK3-ID4 ***4 functions as a transcriptional regulator that interacts with other transcription factors,inhibiting their activity and subsequently influencing various biological processes associated with cell differentiation,survival,growth,and ***:We assessed the correlation between the expression of ELK3 and that of ID4 in TNBCs using bioinformatics analyses,QRT-PCR,western blot analysis,luciferase reporter assays,and chromatin ***,adhesion,invasion,and lung metastasis assays were employed to determine whether the ELK3-ID4 axis regulates the metastatic features of ***:We found that ELK3 binds directly to a binding motif close to the ID4 promoter to repress promoter *** expression of E-cadherin in TNBC was regulated by the ELK3-ID4 *** vitro and in vivo analyses showed that inhibiting ID4 expression in ELK3-knockdown MDA-MB-231(ELK3KD)cells restored the ability to extravasate and ***:The results indicate that the ELK3 regulates ID4 promoter activity,and that the ELK3-ID4 axis regulates the metastatic characteristics of TNBC ***,the data suggest that the ELK3-ID4 axis regulates metastasis of TNBCs by modulating expression of E-cadherin.

关键词： E-cadherin Extravasation Colonization

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Zircon U-Pb ages and O-Hf isotopes of Quaternary trachytes from the East Sea:Implications for the genesis of low-δ^(18)O magmas

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Geoscience Frontiers 2024年第2期15卷 41-54页

作者： Hyun-Ok choi Jihye Oh Chang Hwan Kim soon Young choi Won Hyuck Kim Chan Hong Park Dokdo Research Center East Sea Research InstituteKorea Institute of Ocean Science and TechnologyUljin 36315Republic of Korea Deep-Sea and Seabed Mineral Resources Research Center Korea Institute of Ocean Science and TechnologyBusan 49111Republic of Korea Division of Science Education Kangwon National University1 Gangwondaehak-gilChuncheon-siGangwon-do 24341Republic of Korea

Quaternary intraplate magmatism formed several volcanic islands and seamounts,including Dokdo(DD),Ulleungdo(UD),Simheungtack(ST),Anyongbok,and Isabu in the southwest of the East Sea back-arc *** this study,we present whole-rock geochemical,zircon U–Pb age,and in situ O–Hf isotope data for the submerged volcanic rocks from DD,UD,and ST to provide new insights into the eruption timing of these volcanoes and constrain the magma evolution *** samples used in this study were trachytes and exhibited ferroan,alkalic,and metaluminous to weakly peraluminous *** showed light rare earth element(REE)-enriched patterns with(La/Yb)N ratios of 25.3–31.7 and mostly negative Eu anomalies in a chondrite-normalized REE *** addition,they were enriched in large-ion lithophile elements and high field strength elements;they exhibited positive Pb anomalies and strongly negative Ba,Sr,P,and Ti *** zircons yielded a weighted-mean 206Pb/238U age of 2.61,0.348–0.704,and 2.76–2.94 Ma for the DD,UD,and ST trachytes,*** zircons exhibited lowerδ^(18)O values than normal depleted mantle values,regardless of the crystallization age and spatial distribution of ***δ^(18)O values showed no correlation with U contents or Th/U ratios,indicating that the lowδ^(18)O signatures were of primary magmatic *** Hf isotopic compositions of the zircons were relatively heterogeneous but predominately characterized by positive eHf *** O–Hf mixing modeling revealed that low-δ^(18)O rocks with positive eHf values from the UD and ST volcanoes were derived from a hybrid source of recycled juvenile crustal materials with low-δ^(18)O and positive eHf signatures and an enriched mantle source with normalδ^(18)O and negative eHf *** juvenile oceanic crust in the source was likely metasomatized by seawater at high temperatures prior to *** contrast,the felsic magma that formed the DD volcanoes may have assimilated with regional

关键词： Quaternary intraplate volcanism East Sea Zircon O-Hf isotopes Low-δ^(18)O magma Recycled juvenile oceanic crust

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Metasurface doublet-integrated bidirectional grating antenna enabling enhanced wavelength-tuned beam steering

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Photonics Research 2022年第1期10卷 248-255页

作者： WOO-BIN LEE CHUL-soon IM CHANGYI ZHOU BISHAL BHANDARI DUK-YONG choi SANG-SHIN LEE Department of Electronic Engineering Kwangwoon UniversitySeoul 01897Republic of Korea Nano Device Application Center Kwangwoon UniversitySeoul 01897Republic of Korea Laser Physics Centre Research School of PhysicsAustralian National UniversityCanberraACT 2601Australia

We propose and demonstrate an optical phased-array-based bidirectional grating antenna(BDGA) in silicon nitride *** BDGA is integrated with a miniaturized all-dielectric metasurface doublet(MD) formed on a glass *** BDGA device,which takes advantage of alternately feeding light to its ports in opposite directions,is presumed to effectively provide a doubled wavelength-tuned steering efficiency compared to its unidirectional *** MD,which is based on vertically cascaded convex and concave metalenses comprising circular hydrogenated amorphous silicon nanopillars,is meticulously placed atop the BDGA chip to accept and deflect a beam emanating from the emission area,thereby boosting the beam-steering *** manufactured BDGA could achieve an enhanced beam-steering efficiency of 0.148 deg/nm as well as a stable spectral emission response in the wavelength range of 1530–1600 *** deploying a fabricated MD atop the silicon photonic BDGA chip,the steering efficiency was confirmed to be boosted by a factor of ~3.1,reaching 0.461 deg/nm,as intended.

关键词： beam thereby directions

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Dietary sophorolipid accelerates growth by modulation of gut microbiota population and intestinal environments in broiler chickens

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Journal of Animal Science and Biotechnology 2022年第1期13卷 256-264页

作者： Min-Jin Kwak Min-Young Park Yong-soon choi Junghwan Cho Duleepa Pathiraja Jonggun Kim Hanbae Lee In-Geol choi Kwang-Youn Whang Department of Biotechnology Korea University145 Anam-roSeoul 02841Republic of Korea Pathway Intermediates Seoul 02841Republic of Korea

Background:Gut is a crucial organ for the host’s defense system due to its filtering action of the intestinal membrane from hazardous foreign *** strategy to strengthen the gut epithelial barrier function is to upregulate beneficial microflora populations and their ***(SPL),which is a glycolipid biosurfactant,could increase beneficial microflora and decrease pathogenic bacteria in the gastrointestinal ***,herein,we conducted an experiment with broiler chickens to investigate the fortifying effects of SPL on the host’s gut defense system by modulating the microbiota ***:A total of 5401-day-old chicks(Ross 308)were used,and they were immediately allotted into three treatment groups(6 replications with 30 chicks/pen)according to their initial body *** dietary treatments consisted of CON(basal diet),BAM(10 mg/kg bambermycin),and SPL(10 mg/kg SPL).During the experiment,birds freely accessed feed and water,and body weight and feed intake were measured at the end of each *** d 35,birds(one bird/pen)were sacrificed to collect jejunum and cecum ***:Dietary SPL and BAM supplementation significantly accelerated birds’growth and also significantly improved feed efficiency compared to *** microbial community was significantly separated by dietary SPL supplementation from that of CON,and dietary SPL supplementation significantly increased Lactobacillus *** Akkermansia ***,birds fed with dietary SPL also showed the highest concentration of cecal butyrate among all treatment *** morphological analysis showed that dietary SPL significantly increased villus height,ratio of villus height to crypt depth,goblet cell numbers,and the gene expression levels of claudin-1 and mucin ***,dietary SPL significantly decreased the mRNA expression level of pro-inflammatory cytokine,interleukin-6,and increased that of anti-inflammatory cytokine,interleukin-10,compared

关键词： Broilers Gut microbiota Gut morphology Local inflammation Mucus barrier Sophorolipids

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Probabilistic seismic performance assessment of lap-spliced RC columns retrofitted by steel wrapping jackets

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Earthquake Engineering and Engineering Vibration 2016年第2期15卷 223-238页

作者： Eunsoo choi Heejung Youn Baik-soon Cho Department of Civil Engineering Hongik University Department of Civil Engineering CTRCInje University

In this study, the seismic fragility curves of two reinforced concrete（RC） columns that were lap-spliced at the bottom and retrofitted with steel wrapping jackets were generated. Their seismic performance was probabilistically assessed in comparison to that of lap-spliced or continuous reinforcement RC columns. This study used two types of steel wrapping jackets, a full jacket and a split jacket. Analytical models of the four types of columns were developed based on the experimental results of the columns using Open SEES, which is effective in conducting nonlinear time history analyses. A suite of ten artificial ground motions, modified from recorded ground motions, was used to perform nonlinear time history analyses of the analytical models with scaling of the peak ground acceleration from 0.1 g to 1.0 g in increments of 0.1 g. The steel wrapping jackets did not increase the medians for yield（slight damage state） of the lap-spiced column and did not exceed the corresponding median of the continuous reinforcement column. However, the two steel jackets increased the medians for failure by 1.872 and 2.017 times, respectively, and exceeded the corresponding median of the continuous reinforcement column by 11.8% and 20.5%, respectively.

关键词： columns reinforcement reinforced exceed acceleration scaling median assessed split probabilistic

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Rapid determination of lithium-ion battery degradation: High C-rate LAM and calculated limiting LLI

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Journal of Energy Chemistry 2022年第4期31卷 663-671页

作者： Gyuwon Seo Jaeyun Ha Moonsu Kim Jihyeon Park Jaewon Lee Eunoak Park Sungyool Bong Kiyoung Lee soon Jong Kwon Seung-pil Moon Jinsub choi Jaeyoung Lee Electrochemical Reaction and Technology Laboratory School of Earth Sciences and Environmental EngineeringGwangju Institute of Science and Technology(GIST)Gwangju 61005South Korea Department of Chemistry and Chemical Engineering Inha UniversityIncheon 22212South Korea Ertl Center for Electrochemistry and Catalysis GISTGwangju 61005South Korea Korea Electric Power Corporation Research Institute Daejeon 34056South Korea International Future Research Center of Chemical Energy Storage and Conversion Processes(ifRC-CHESS) GISTGwangju 61005South Korea

Herein,incremental capacity-differential voltage (IC-DV) at a high C-rate (HC) is used as a non-invasive diagnostic tool in lithium-ion batteries,which inevitably exhibit capacity fading caused by multiple mechanisms during charge/discharge *** battery degradation modes are complex,the simple output of capacity fading does not yield any useful data in that *** IC and DV curves obtained under restricted conditions (<0.1C,25℃) were applied in non-invasive analysis for accurate observation of degradation symptoms,a facile,rapid diagnostic approach without intricate,complex calculations is critical in on-board ***,Li Ni_(0.5)Mn_(0.3)Co_(0.2)O_(2)(NMC532)/graphite pouch cells were cycled at 4 and 6C and the degradation characteristics,i.e.,loss of active materials (LAM) and loss of lithium inventory (LLI),were parameterized using the IC-DV *** the incremental current cycling,the initial steep LAM and LLI slopes underwent gradual transitions to gentle states and revealed the gap between low-and high-current measurements.A quantitative comparison of LAM at high and low C-rate showed that a IC;revealed the relative amount of available reaction region limited by cell ***,this did not provide a direct relationship for estimating the LAM at a low ***,the limiting LLI,which is calculated at a C-rate approaching 0,was obtained by extrapolating the LLI through more than two points measured at high C-rate,and therefore,the LLI at 0.1C was accurately determined using rapid cycling.

关键词： Battery degradation Rapid degradation diagnosis Loss of active materials(LAM) Loss of lithium inventory(LLI) Incremental capacity(IC) Differential voltage(DV)

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Adenosine monophosphate enhances callus regeneration competence for de novo plant organogenesis

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Molecular Plant 2023年第12期16卷 1867-1870页

作者： Hong Gil Lee Seo Young Jang Eun Yee Jie Seung Hee choi Ok-Sun Park soon Hyung Bae Hyun-soon Kim Suk Weon Kim Geum-Sook Hwang Pil Joon Seo Department of Chemistry Seoul National UniversitySeoul 08826Korea Plant Genomics and Breeding Institute Seoul National UniversitySeoul 08826Korea Integrated Metabolomics Research Group Western Seoul CenterKorea Basic Science InstituteSeoul 03759Korea Biological Resource Center Korea Research Institute of Bioscience and BiotechnologyJeongeup56212Korea Plant Systems Engineering Research Center Korea Research Institute of Bioscience and BiotechnologyDaejeon 34141Korea College of Pharmacy Chung-Ang UniversitySeoul 06974Korea

Dear Editor,Plant tissue culture involves callus formation and de novo shoot ***,explants from differentiated tissues are used to generate a pluripotent cell mass,called callus,on auxin-rich callus-inducing medium(CIM),followed by shoot regeneration on cytokinin-rich shoot-inducing medium(SiM).Callus results from division of pericycle-like cells(Atta et al.,2009;Sugimoto et al.,2010);its cellular identity resembles that of lateral root primordia(Atta et al.,2009;Sugimoto et al.,2010).Callus acquires cellular pluripotency by forming root stem cell niches on CIM(Sugimoto et al.,2010)。

关键词： Adenosine callus

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Clinical outcomes of endoscopic papillectomy of ampullary adenoma: A multi-center study

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World Journal of Gastroenterology 2022年第17期28卷 1845-1859页

作者： Seong Ji choi Hong Sik Lee Jiyeong Kim Jung Wan Choe Jae Min Lee Jong Jin Hyun Jai Hoon Yoon Hyo Jung Kim Jae Seon Kim Ho soon choi Department of Internal Medicine Hanyang University College of MedicineSeoul 04763South Korea Division of Gastroenterology and Hepatology Department of Internal MedicineKorea University College of MedicineSeoul 02841South Korea Lab of Biostatistical Consulting and Research Medical Research Collaborating CenterIndustry-University Cooperation FoundationHanyang UniversitySeoul 04763South Korea

BACKGROUND Ampullary adenoma is a rare premalignant lesion,but its incidence is *** papillectomy has become the first treatment of choice for ampullary adenomas due to its safety and effectiveness,thereby replacing surgical ***,recurrence rates and adverse events after endoscopic papillectomy were reported in up to 30%of *** To review the long-term outcomes of endoscopic papillectomy and investigate the factors that affect these *** We retrospectively analyzed the data of patients who underwent endoscopic papillectomy for ampullary adenoma at five tertiary hospitals between 2013 and *** evaluated clinical outcomes and their risk *** definitions of outcomes were as follow:(1)curative resection:complete endoscopic resection without recurrence;(2)endoscopic success:treatment of ampullary adenoma with endoscopy without surgical intervention;(3)early recurrence:reconfirmed adenoma at the first endoscopic surveillance;and(4)late recurrence:reconfirmed adenoma after the first endoscopic *** A total of 106 patients were included for *** the included patients,81(76.4%)underwent curative resection,99(93.4%)had endoscopic success,showing that most patients with noncurative resection were successfully managed with *** patients(15.1%)had piecemeal resection,22 patients(20.8%)had shown positive/uncertain resection margin,11 patients(16.1%)had an early recurrence,13 patients(10.4%)had a late recurrence,and 6 patients(5.7%)had a *** multivariate analysis,a positive/uncertain margin[Odds ratio(OR)=4.023,P=0.048]and piecemeal resection(OR=6.610,P=0.005)were significant risk factors for early and late recurrence,*** resection was also a significant risk factor for non-curative resection(OR=5.424,P=0.007).Twenty-six patients experienced adverse events(24.5%).CONCLUSION Endoscopic papillectomy is a safe and effective treatment for ampullary ***

关键词： Endoscopic papillectomy Ampullary adenoma Clinical outcome Recurrence Adverse event

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Submergence promotes auxin-induced callus formation through ethylene-mediated post-transcriptional control of auxin receptors

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Molecular Plant 2022年第12期15卷 1947-1961页

作者： Seung Yong Shin Yuri choi Sang-Gyu Kim Su-Jin Park Ji-Sun Park Ki-Beom Moon Hyun-soon Kim Jae Heung Jeon Hye Sun Cho Hyo-Jun Lee Plant Systems Engineering Research Center Korea Research Institute of Bioscience and BiotechnologyDaejeon 34141Korea Department of Functional Genomics KRIBB School of BioscienceUniversity of Science and TechnologyDaejeon 34113Korea Department of Biological Sciences Korea Advanced Institute of Science and TechnologyDaejeon 34141Korea Department of Biosystems and Bioengineering KRIBB School of BiotechnologyUniversity of Science and TechnologyDaejeon 34113Korea Department of Biological Sciences Sungkyunkwan UniversitySuwon 16419Korea

Plant cells in damaged tissue can be reprogrammed to acquire pluripotency and induce callus ***,in the aboveground organs of many species,somatic cells that are distal to the wound site become less sensitive to auxin-induced callus formation,suggesting the existence of repressive regulatory mechanisms that are largely *** we reveal that submergence-induced ethylene signals promote callus formation by releasing post-transcriptional silencing of auxin receptor transcripts in non-wounded *** determined that short-term submergence of intact seedlings induces auxin-mediated cell dedifferentiation across the entirety of Arabidopsis thaliana *** constitutive triple response 1-1(ctr1-1)mutation induced callus formation in explants without submergence,suggesting that ethylene facilitates cell *** show that ETHYLENE-INSENSITIVE 2(EIN2)post-transcriptionally regulates the abundance of transcripts for auxin receptor genes by facilitating microRNA393 ***-induced calli in non-wounded regions were suitable for shoot regeneration,similar to those near the wound *** also observed submergence-promoted callus formation in Chinese cabbage(Brassica rapa),indicating that this may be a conserved mechanism in other *** study identifies previously unknown regulatory mechanisms by which ethylene promotes cell dedifferentiation and provides a new approach for boosting callus induction efficiency in shoot explants.

关键词： cell dedifferentiation auxin signaling ethylene callus formation EIN2

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