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KoNA:Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 161-167页

作者： Gunhwan Ko Jae Ho Lee young Mi Sim Wangho Song Byung-Ha Yoon Iksu Byeon Bang Hyuck Lee Sang-Ok kim Jinhyuk Choi Insoo Jang Hyerin kim Jin Ok Yang Kiwon Jang Sora kim Jong-Hwan kim Jongbum Jeon Jaeeun Jung Seungwoo Hwang Ji-Hwan Park Pan-Gyu kim seon-young kim Byungwook Lee Korea Bioinformation Center Korea Research Institute of Bioscience&BiotechnologyDaejeon 34141Republic of Korea

During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enormous amounts of *** promote data-driven biological research,the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station(K-BDS),which consists of multiple databases for individual data ***,we introduce the Korean Nucleotide Archive(KoNA),a repository of nucleotide sequence *** of July 2022,the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome *** ensure data quality and prepare for international alignment,a standard operating procedure was adopted,which is similar to that of the International Nucleotide Sequence Database *** standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline,followed by manual *** ensure fast and stable data transfer,a high-speed transmission system called GBox is used in ***,the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called *** seamless coupling of KoNA,GBox,and Bio-Express enhances the data experience,including submission,access,and analysis of raw nucleotide *** not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in *** KoNA is available at https://***/kona/.

关键词： Korea BioData Station Nucleotide sequence Next-generation sequencing repository Genomics Deposition and access of big data

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Gene expression profiling:Canonical molecular changes and clinicopathological features in sporadic colorectal cancers

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World Journal of Gastroenterology 2008年第43期14卷 6662-6672页

作者： Jin Cheon kim seon young kim seon Ae Roh Dong-Hyung Cho Dae Dong kim Jeong Hyun kim Yong Sung kim Department of Surgery University of Ulsan College of Medicine and Asan Medical Centerand Laboratory of Cancer Biology & GeneticsAsan Institute for Life SciencesSeoul 138-736South Korea Medical Genomics Research Center Korea Research Institute of Bioscience & BiotechnologyDaejeon 305-806South Korea

AIM： To investigate alternative or subordinate pathways involved in colorectal tumorigenesis and tumor growth, possibly determining at-risk populations and predicting responses to treatment. METHODS： Using microarray gene-expression analysis, we analyzed patterns of gene expression relative to canonical molecular changes and clinicopathological features in 84 sporadic colorectal cancer patients, standardized by tumor location. Subsets of differentially expressed genes were confirmed by real-time reverse-transcript polymerase chain reaction （RT-PCR）. RESULTS： The largest number of genes identified as being differentially expressed was by tumor location, and the next largest number by lymphovascular or neural invasion of tumor cells and by mismatch repair （NMR） defects. Amongst biological processes, the immune response was significantly implicated in entire molecular changes observed during colorectal tumorigenesis （P 〈 0.001）. Amongst 47 differentially expressed genes, seven （PISD, NIBP, BAI2, STOML1, MRPL21, MRPL16, and MKKS） were newly found to correlate with tumorigenesis and tumor growth. Most location-associated molecular changes had distinct effects on gene expression, but the effects of the latter were sometimes contradictory. CONCLUSION： We show that several differentially expressed genes were associated with canonical molecular changes in sporadic colorectal cancers, possibly constituting alternative or subordinate pathways of tumorigenesis. As tumor location was the dominant factor influencing differential gene expression, location-specific analysis may identify location-associated pathways and enhance the accuracy of class prediction.

关键词： Colorectal adenocarcinomas Sporadic Gene expression Profiling Tumorigenesis

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Capsosiphon fulvescens suppresses LPS-stimulated inflammatory responses by suppressing TLR4/NF-κB activation in RAW264.7 murine macrophages

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Asian Pacific Journal of Tropical Biomedicine 2024年第3期14卷 115-126页

作者： seon Yeong Ji EunJin Bang Hyun Hwangbo Min Yeong kim Da Hye kim Su Hyun Hong Shin-Hyung Park Chang-young Kwon Gi-young kim You-Jin Jeon Suengmok Cho Yung Hyun Choi Department of Biochemistry Dong-eui University College of Korean MedicineBusan 47227Republic of Korea Basic Research Laboratory for the Regulation of Microplastic-Mediated Diseases and Anti-Aging Research Center Dong-eui UniversityBusan 47227Republic of Korea Department of Pathology Dong-eui University College of Korean MedicineBusan 47227Republic of Korea Department of Oriental Neuropsychiatry Dong-eui University College of Korean MedicineBusan 47227Republic of Korea Department of Marine Life Science Jeju National UniversityJeju 63243Republic of Korea Department of Food Science and Technology/Institute of Food Science Pukyong National UniversityBusan 48513Republic of Korea

Objective:To evaluate the effects of Capsosiphon fulvescens(***)ethanolic extract on inflammation in lipopolysaccharide(LPS)-induced RAW296.7 ***:The protective effects of *** ethanolic extract on LPS-induced inflammation in RAW264.7 macrophages were assessed using biochemical analysis,including enzyme-linked immunosorbent assay,quantitative reverse transcription-polymerase chain reaction,and Western blot *** examine reactive oxygen species(ROS)production,flow cytometry analysis,and immunofluorescence staining were ***,the modulatory effect of *** ethanolic extract on NF-κB activation was ***:*** ethanolic extract significantly attenuated LPS-induced levels of pro-inflammatory cytokines and notably reduced the secretion and mRNA levels of LPS-mediated matrix *** addition,*** ethanolic extract decreased ROS production and suppressed the TLR4/NF-κB signaling ***:*** ethanolic extract alleviates inflammation as well as oxidative stress by modulating the TLR4/NF-κB signaling in LPS-induced RAW264.7 *** can be used as a potential therapeutic agent to suppress inflammation and oxidative stress-associated diseases.

关键词： Capsosiphon fulvescens Inflammation Oxidative stress NF-κB Nrf2 TLR4

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RUFY4 deletion prevents pathological bone loss by blocking endo-lysosomal trafficking of osteoclasts

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Bone Research 2024年第2期12卷 407-420页

作者： Minhee kim Jin Hee Park Miyeon Go Nawon Lee Jeongin Seo Hana Lee Doyong kim Hyunil Ha Taesoo kim Myeong seon Jeong Suree kim Taesoo kim Han Sung kim Dongmin Kang Hyunbo Shim Soo young Lee Department of Life Science Ewha Womans UniversitySeoul 03760South Korea The Research Center for Cellular Homeostasis Ewha Womans UniversitySeoul 03760South Korea Department of Biomedical Engineering Yonsei UniversityWonju 26493South Korea KM Convergence Research Division Korea Institute of Oriental MedicineDaejeon 34054South Korea Chuncheon Center Korea Basic Science InstituteChuncheon 24341South Korea Fluorescence Core Imaging Center and Bioimaging Data Curation Center Ewha Womans UniversitySeoul 03760South Korea Multitasking Macrophage Research Center Ewha Womans UniversitySeoul 03760South Korea

Mature osteoclasts degrade bone matrix by exocytosis of active proteases from secretory lysosomes through a ruffled ***,the molecular mechanisms underlying lysosomal trafficking and secretion in osteoclasts remain largely ***,we show with GeneChip analysis that RUN and FYVE domain-containing protein 4(RUFY4)is strongly upregulated during *** lacking Rufy4 exhibited a high trabecular bone mass phenotype with abnormalities in osteoclast function in ***,deleting Rufy4 did not affect osteoclast differentiation,but inhibited bone-resorbing activity due to disruption in the acidic maturation of secondary lysosomes,their trafficking to the membrane,and their secretion of cathepsin K into the extracellular ***,RUFY4 promotes late endosome-lysosome fusion by acting as an adaptor protein between Rab7 on late endosomes and LAMP2 on primary ***,Rufy4-deficient mice were highly protected from lipopolysaccharide-and ovariectomy-induced bone ***,RUFY4 plays as a new regulator in osteoclast activity by mediating endo-lysosomal trafficking and have a potential to be specific target for therapies against bone-loss diseases such as osteoporosis.

关键词： osteoclast inhibited traffic

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Clinical assessment and identification of immuno-oncology markers concerning the 19-gene based risk classifier in stage Ⅳ colorectal cancer

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World Journal of Gastroenterology 2019年第11期25卷 1341-1354页

作者： Jong Lyul Lee seon Ae Roh Chan Wook kim Yi Hong Kwon Ye Jin Ha seon-Kyu kim seon-young kim Dong-Hyung Cho Yong Sung kim Jin Cheon kim Department of Surgery University of Ulsan College of Medicine Institute of Innovative Cancer Research Asan Medical Center Medical Genomics Research Center Korea Research Institute of Bioscience and Biotechnology School of Life Sciences Kyungpook National University

BACKGROUND Genomic profiling of tumors has contributed to the understanding of colorectal cancer(CRC), facilitating diagnosis, prognosis and selection of treatments,including targeted regimens. A report suggested that a 19-gene-based risk classifier(TCA19) was a prognostic tool for patients with stage III CRC. The survival outcomes in patients with stage IV CRC are still poor and appropriate selection of targeted therapies and immunotherapies is *** To assess clinical implication of TCA19 in patients with stage IV CRC, and to identify TCA19 with involvement in *** A retrospective review of the medical records of 60 patients with stage IV CRC was conducted, assessing clinicopathological variables and progression-free survival(PFS). TCA19 gene expression was determined by quantitative polymerase chain reaction(qPCR) in matched normal and tumor tissues taken from the study cohort. Expression of potential immune-oncology regulatory proteins and targets was examined by immunohistochemistry(IHC), western blot, immunofluorescence staining in tissues from a validation cohort of 10 patients, and in CRC cell lines co-cultured with monocyte in *** In the patients with TCA19 score higher than the median, the PFS rates of eight patients who received the targeted regimens were significantly higher than the PFS rates of four patients who received 5-fluorouracil-based regimen(P = 0.041).In multivariate analysis, expression of signaling lymphocytic activation molecule family, member 7(SLAMF7) and triggering receptor expressed on myeloid cells 1(TREM1) was associated with PFS in the 60-patient cohort. After checking another 10 validate set, the expression of the IHC, the level of real-time qPCR,and the level of western blot were lower for SLAMF7 and higher for TREM7 in primary and metastatic tumors than in normal tissues. In CRC cells expressing SLAMF7 that were co-cultured with a monocytic cell line, levels of CD 68 and CD73 were significant

关键词： Colorectal cancer Prognosis Immunotherapy Signaling lymphocytic activation molecule family,member 7 Triggering receptor expressed on myeloid cells 1

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Integration of earth-abundant cocatalysts for high-performance photoelectrochemical energy conversion

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Journal of Energy Chemistry 2024年第1期88卷 336-355,I0008页

作者： Joonhee Ma Sang Hyun Ahn Soo young kim Department of Materials Science and Engineering Korea UniversitySeoul 02841Republic of Korea School of Chemical Engineering and Materials Science Chung-Ang University84 Heukseok-roDongjak-guSeoul 06974Republic of Korea

Photoelectrochemical(PEC)energy conversion has emerged as a promising and efficient approach to sustainable energy harvesting and *** utilizing semiconductor photoelectrodes,PEC devices can harness solar energy and drive electrochemical reactions such as water splitting or carbon dioxide(CO_(2))reduction to generate clean fuels and value-added ***,PEC energy conversion faces several challenges such as high overpotential,sluggish reaction kinetics,charge carrier recombination,and stability issues,which limit its practical ***,significant research has been conducted to improve the overall conversion efficiency of PEC *** particularly promising approach is the use of cocatalysts,which involves introducing specific cocatalysts onto the photoelectrode surface to promote charge separation,improve reaction kinetics,and reduce the overpotential,thereby enhancing the overall performance of PEC energy *** review provides a comprehensive overview of the recent developments in the earth-abundant cocatalysts for PEC water splitting and CO_(2) *** main earth-abundant catalysts for the PEC water splitting include transition-metal dichalcogenide(TMD)-based materials,metal phosphides/carbides,and metal oxides/***,PEC-CO_(2)RR was divided into C_(1) and C_(2+)based on the final product since various products could be produced,focusing on diverse earth-abundant materials-based *** addition,we provide and highlight key advancements achieved in the very recent reports on novel PEC system design engineering with ***,the current problems associated with PEC systems are discussed along with a suggested direction to overcome these obstacles.

关键词： Solar energy Photo-electrochemical Water splitting CO_(2)reduction Cocatalysts

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Tailoring Classical Conditioning Behavior in TiO_(2) Nanowires:ZnO QDs-Based Optoelectronic Memristors for Neuromorphic Hardware

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Nano-Micro Letters 2024年第7期16卷 265-280页

作者： Wenxiao Wang Yaqi Wang Feifei Yin Hongsen Niu young-Kee Shin Yang Li Eun-seong kim Nam-young kim School of Information Science and Engineering University of JinanJinan 250022People’s Republic of China RFIC Centre NDAC CentreKwangwoon UniversityNowon-guSeoul 139-701South Korea Department of Electronics Engineering Kwangwoon UniversityNowon-GuSeoul 139-701South Korea School of Microelectronics Shandong UniversityJinan 250101People’s Republic of China Department of Molecular Medicine and Biopharmaceutical Sciences Seoul National UniversitySeoul 08826South Korea

Neuromorphic hardware equipped with associative learn-ing capabilities presents fascinating applications in the next generation of artificial ***,research into synaptic devices exhibiting complex associative learning behaviors is still ***,an optoelec-tronic memristor based on Ag/TiO_(2) Nanowires:ZnO Quantum dots/FTO was proposed and constructed to emulate the biological associative learning *** implementation of synaptic behaviors,including long and short-term plasticity,and learning-forgetting-relearning behaviors,were achieved in the device through the application of light and electrical *** the optoelectronic co-modulated characteristics,a simulation of neuromorphic computing was conducted,resulting in a handwriting digit recognition accuracy of 88.9%.Furthermore,a 3×7 memristor array was constructed,confirming its application in artificial visual *** importantly,complex biological associative learning behaviors were emulated by mapping the light and electrical stimuli into conditioned and unconditioned stimuli,*** training through associative pairs,reflexes could be triggered solely using light ***-sively,under specific optoelectronic signal applications,the four features of classical conditioning,namely acquisition,extinction,recovery,and generalization,were elegantly *** work provides an optoelectronic memristor with associative behavior capabilities,offering a pathway for advancing brain-machine interfaces,autonomous robots,and machine self-learning in the future.

关键词： Artificial intelligence Classical conditioning Neuromorphic computing Artificial visual memory Optoelectronic memristors ZnO Quantum dots

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Hydrangea serrata extract exerts tumor inhibitory activity against hepatocellular carcinoma HepG2 cells via inducing p27/CDK2-mediated cell cycle arrest and apoptosis

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Asian Pacific Journal of Tropical Biomedicine 2024年第2期14卷 65-72,I0002-I0005页

作者： Ye-eun kim Jeonghye Hwang Ki-young kim Graduate School of Biotechnology Kyung Hee UniversitySeocheonGiheungYonginGyeonggi-do 446-701Republic of Korea Department of Genetics and Biotechnology College of Life SciencesKyung Hee UniversitySeocheonGiheungYonginGyeonggi-do 446-701Republic of Korea

Objective:To examine the inhibitory effect of Hydrangea serrata extract against hepatocellular carcinoma HepG2 cells and its underlying ***:The effects of Hydrangea serrata extract on growth inhibition of tumor cells and spheroids were assessed using MTT and 3D culture *** real-time PCR and Western blot analyses were employed to investigate the changes in mRNA and protein expression levels of molecules related to cell cycle and ***:Hydrangea serrata extract effectively inhibited the growth of both tumor cells and *** extract also significantly upregulated p27 mRNA expression and downregulated CDK2 mRNA expression,leading to cell cycle ***,increased BAX/Bcl-2 ratio as well as caspase-9 and-3 were observed after treatment with Hydrangea serrata extract,indicating the induction of tumor cell ***:Hydrangea serrata extract has the potential to alleviate tumors by effectively modulating cell-cycle-related gene expressions and inducing apoptosis,thereby inhibiting tumor growth.

关键词： Hydrangea serrata Hepatocellular carcinoma Liver cancer Anticancer Cell cycle arrest Apoptosis

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Factors affecting length of stay according to bronchopulmonary dysplasia severity:a nationwide cohort study in Korea

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World Journal of Pediatrics 2024年第5期20卷 470-480页

作者： Hye Mi Lee Jeongmin Shin Sae Yun kim So young kim Department of Pediatrics College of MedicineThe Catholic University of KoreaSeoulRepublic of Korea Department of Pediatrics Yeouido St.Mary’s HospitalCollege of MedicineThe Catholic University of Korea1063-roYeongdeungpo-guSeoul07345Republic of Korea

Background Longer hospitalizations for preterm infants with bronchopulmonary dysplasia(BPD)delay developmental outcomes,increase the risk for hospital-acquired complications,and exert a substantial socioeconomic *** study aimed to identify factors associated with an extended length of stay(LOS)at different levels of severity of *** A cohort study was conducted using the Korean Neonatal Network registry of very low birth weight infants with BPD between 2013 and 2017 through retrospective *** A total of 4263 infants were diagnosed with *** mild BPD,infants requiring surgical treatment for patent ductus arteriosus needed a longer LOS[eadjustedβcoefficients(adjβ)1.041;95%confidence interval(CI):0.01–0.08]and hydrocephalus(eadjβ1.094;95%CI 0.01–0.17).In moderate BPD,infants administered steroids or with intraventricular hemorrhage required a longer LOS(eadjβ1.041;95%CI 0.00–0.07 and eadjβ1.271;95%CI 0.11–0.38,respectively).In severe BPD,infants with comorbidities required a longer LOS:pulmonary hypertension(eadjβ1.174;95%CI 0.09–0.23),administrated steroid for BPD(eadjβ1.116;95%CI 0.07–0.14),sepsis(eadjβ1.062;95%CI 0.01–0.11),patent ductus arteriosus requiring surgical ligation(eadjβ1.041;95%CI 0.00–0.08),and intraventricular hemorrhage(eadjβ1.016;95%CI 0.05–0.26).Additionally,the higher the clinical risk index score,the longer the LOS needed for infants in all *** The factors affecting LOS differed according to the severity of *** approaches to reducing LOS may be devised using knowledge of the various risk factors affecting LOS by BPD severity.

关键词： Bronchopulmonary dysplasia Length of stay Very low birth weight

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MXene-based hybrid materials for electrochemical and photoelectrochemical H_(2) generation

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Journal of Energy Chemistry 2024年第6期93卷 111-125,I0004页

作者： Jun young kim Seung Hun Roh Chengkai Xia Uk Sim Jung Kyu kim School of Material Science and Engineering North University of ChinaTaiyuan 030051China School of Chemical Engineering Sungkyunkwan University(SKKU)2066Seobu-roJangan-guSuwon 16419Republic of Korea Hydrogen Energy Technology Laboratory Korea Institute of Energy Technology(KENTECH)NajuJeollanamdo 58330Republic of Korea SKKU Advanced Institute of Nano Technology(SAINT) Sungkyunkwan University(SKKU)2066Seobu-roJangan-guSuwon 16419Republic of Korea

The conversion of solar energy to produce clean hydrogen fuel through water splitting is an emerging strategy for efficiently storing solar energy in the form of solar *** aligns with the increasing global demand for the development of an ideal energy alternative to fossil fuels that does not emit greenhouse ***(EC) and photoelectrochemical(PEC) water splitting technologies have garnered significant attention worldwide for advanced hydrogen solar fuel production in recent *** achieve sustainable green H_(2) production,it is essential to create efficient catalyst materials that are low-cost and can replace expensive noble metal-based *** characteristics make them an ideal catalyst material for the ***-dimensional MXenes with M_(n+1)X_(n) structure have been identified as a promising option for EC and PEC water splitting due to their superior hydrophilicity,metal-like conductivity,large surface area,and adjustable surface ***,we present a summary of recent advancements in the synthesis and performance enhancement methods for MXene hybrid materials in hydrogen production through EC and PEC water ***,we examine the challenges and insights associated with the rational design of MXene-based hybrid materials to facilitate efficient water splitting for sustainable solar fuel production.

关键词： MXene Hybrid materials EC PEC HER OER Water splitting

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