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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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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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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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Theoretical study on the stability of nanobubbles and its verification in molecular dynamics simulation

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Particuology 2024年第4期87卷 99-105页

作者： Sheng mi Chaofeng Hou Wei Ge School of Chemical Engineering and Technology Tianjin UniversityTianjin300072China State Key Laboratory of Multiphase Complex Systems Institute of Process EngineeringChinese Academy of SciencesBeijing.100190China School of Chemical Engineering University of Chinese Academy of SciencesBeijing100049China

The stability of vapor nanobubbles in bulk liquid was investigated theoretically and the critical bubble size was derived from macroscale thermodynamic equations,below which the system destabilizes with sharp drop in *** critical size was quantitatively verified in molecular dynamic simulation using the Lennard-Jones model of argon,where stronger attraction between the molecules at lower density is found to contribute most to the drop of system pressure and,as the Laplace pressure on the curved bubble interface fails to balance the pressure difference across the interface,the bubbles become *** theoretical model could be extended to other systems where reliable equations of state and interfacial tension are available.

关键词： Nanobubble Stability Phase diagram Critical size

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The SARS-CoV-2 spike protein induces lung cancer migration and invasion in a TLR2-dependent manner

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Cancer Communications 2024年第2期44卷 273-277页

作者： mi-Jeong Kim Ji young Kim Ji Hye Shin Juhee Son Yeeun Kang Soo-Kyung Jeong Duk-Hwan Kim Kyun-Hwan Kim Eunyoung Chun Ki-young Lee Department of Immunology Samsung Biomedical Research InstituteSungkyunkwan University School of MedicineSuwonRepublic of Korea Research and Development Center CHA Vaccine InstituteSeongnam-siRepublic of Korea Department of Molecular Cell Biology Sungkyunkwan University School of MedicineSuwonRepublic of Korea Department of Precision Medicine Sungkyunkwan University School of MedicineSuwonRepublic of Korea Department of Health Sciences and Technology Samsung Advanced Institute for Health Sciences&TechnologySamsung Medical CenterSungkyunkwan UniversitySeoulRepublic of Korea

Dear editor,Severe acute respiratory syndrome coronavirus2(SARS-CoV-2)infection can lead to severe outcomes in patients with cancer[1].It has been reported that patients with lung cancers disproportionately manifest severe COVID-19 with a high rate of hospitalization and death[2].Notably,the SARS-CoV-2 Spike(S)protein can induce hyper-inflammation in both epithelial cells and macrophages through toll-like receptor(TLR)1/TLR2 or TLR2/6-dependent nuclear factor-kappaB(NF-κB)path-way[3].However,molecular and cellular evidence on whether the SARS-CoV-2 virus affects the severity of lung cancer patients through TLR1/2 or TLR2/6 signaling remains unclear.

关键词： lung TLR2 invasion

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Systemic lupus erythematosus in a 15-year-old female with multiple splenic nodules:A case report

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World Journal of Clinical Cases 2024年第12期12卷 2128-2133页

作者： mi Il Kang Hyeok Chan Kwon Division of Rheumatology Department of Internal MedicineDankook University College of MedicineCheonan-si 31116South Korea Division of Rheumatology Department of Internal MedicineDankook University HospitalDankook University College of MedicineCheonan-si 31116South Korea

BACKGROUND Systemic lupus erythematosus(SLE)is a chronic inflammatory disease primarily affecting young *** can invade any organ,and various forms of splenic invasion have been *** include splenomegaly and splenic infarction,rupture,and *** study encountered a rare case of splenic involvement,with nodules of various sizes without calcifications or *** SUMMARY A 15-year-old girl presented with arthralgia,weight loss,fever,increased levels of inflammatory markers,and positive antinuclear antibody test *** patient was diagnosed with *** was asymptomatic while taking steroids and *** months after discharge,the patient developed a fever and abdominal *** enteritis was suspected,and abdominopelvic computed tomography(AP-CT)was *** were no specific findings in the gastrointestinal tract,but multiple splenic nodules were *** or hemangioma was considered;however,no specific radiological findings were observed.A biopsy of the spleen was performed to determine the possibility of *** histological findings of the spleen included extensive periarteriolar necrosis with hematoxylin bodies and numerous karyorrhectic *** on the biopsy results,the patient was diagnosed with an SLE flare-up and was maintained on high-dose steroids and *** As disease activity increased,multiple nodules in the spleen that were previously unseen were observed using AP-CT and histologically *** invasion by SLE can appear in multiple nodular forms and ***,physicians should consider these findings when differentiating these nodules from infections and malignancies.

关键词： Multiple nodules Spleen Splenectomy Systemic lupus erythematosus Differential diagnosis Case report

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Evidence for distortion-induced local electric polarization in α-RuCl_(3)

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Science China(Physics,Mechanics & Astronomy) 2024年第9期67卷 165-173页

作者： Xinrun mi De Hou Xiao Wang Sabreen Hammouda Caixing Liu Zijian Xiong Han Li Yan Liu Guiwen Wang Aifeng Wang Yisheng Chai Yang Qi Wei Li Xiaoyuan Zhou Yixi Su DIKhomskii mingquan He Zhigao Sheng young Sun College of Physics Center of Quantum Materials and DevicesChongqing UniversityChongqing 401331China Anhui Key Laboratory of Condensed Matter Physics at Extreme Conditions High Magnetic Field LaboratoryHefei Institutes of Physical ScienceAnhuiChinese Academy of SciencesHefei 230031 China University of Science and Technology of China Hefei 230026China Jülich Centre for Neutron Scienceat Heinz Maier-Leibnitz Zentrum(JCNS-MLZ) Forschungszentrum Jülich GmbHGarching D-85747Germany School of Physics Beihang UniversityBeijing 100191China Analytical and Testing Center Chongqing UniversityChongqing 401331China State Key Laboratory of Surface Physics Department of PhysicsFudan UniversityShanghai 200433China CAS Key Laboratory of Theoretical Physics Institute of Theoretical PhysicsChinese Academy of SciencesBeijing 100190China Ⅱ.Physikalisches Institut Universität zu KölnKöln D-50937Germany

The spin-orbit assisted Mott insulator α-RuCl_(3) is a prime candidate for material realization of the Kitaev quantum spin *** little attention has been paid to charge degrees of freedom,charge effects,such as electric polarization,may arise in this ***,we report distortion-induced local electric polarization in α-RuCl_(3) as evidenced by single-crystal X-ray diffraction,second harmonic generation(SHG)and dielectric *** SHG signal appears at room temperature and develops substantially in the Kitaev paramagnetic state when short-range spin correlations come into *** sizable pyroelectric currents in the Kitaev paramagnetic state,the absence of hysteresis in the polarization-electric field(P-E)points to the shortrange nature of electric *** localized electric polarization is likely the result of distortion-induced charge dimerization,achieved through virtual hopping-induced charge *** addition,the electric polarization is boosted by short-range spin correlations via spin-phonon coupling in the Kitaev paramagnetic *** results emphasize the importance of charge degrees of freedom in α-RuCl_(3),which establish a novel platform to investigate charge effects in Kitaev materials.

关键词： Mott insulator Kitaev quantum spin liquid electric polarization

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SARS-CoV-2 aberrantly elevates mitochondrial bioenergetics to induce robust virus propagation

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Signal Transduction and Targeted Therapy 2024年第6期9卷 2702-2715页

作者： Hye Jin Shin Wooseong Lee Keun Bon Ku Gun young Yoon Hyun-Woo Moon Chonsaeng Kim mi-Hwa Kim Yoon-Sun Yi Sangmi Jun Bum-Tae Kim Jong-Won Oh Aleem Siddiqui Seong-Jun Kim Department of Convergent Research of Emerging Virus Infection Korea Research Institute of Chemical TechnologyDaejeon 34114Republic of Korea Gyeongnam Biohealth Research Center Gyeongnam Branch InstituteKorea Institute of ToxicologyJinju 52834Republic of Korea Center for Research Equipment Korea Basic Science InstituteCheongjuChungcheongbuk-do 28119Republic of Korea Department of Biotechnology Yonsei UniversitySeoul 03722Republic of Korea Division of Infectious Diseases School of MedicineUniversity of CaliforniaSan DiegoLa JollaCA 92093USA Present address:Department of microbiology Chungnam National University School of MedicineDaejeon 35015Republic of Korea

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)is a‘highly transmissible respiratory pathogen,leading to severe multiorgan ***,knowledge regarding SARS-CoV-2-induced cellular alterations is *** this study,we report that SARSCoV-2 aberrantly elevates mitochondrial bioenergetics and activates the EGFR-mediated cell survival signal cascade during the early stage of viral ***-CoV-2 causes an increase in mitochondrial transmembrane potential via the SARS-CoV-2 RNAnucleocapsid cluster,thereby abnormally promoting mitochondrial elongation and the OXPHOS process,followed by enhancing ATP ***,SARS-CoV-2 activates the EGFR signal cascade and subsequently induces mitochondrial EGFR trafficking,contributing to abnormal OXPHOS process and viral *** EGFR inhibitors remarkably reduce SARS-CoV-2 propagation,among which vandetanib exhibits the highest antiviral *** of SARS-CoV-2-infected cells with vandetanib decreases SARS-CoV-2-induced EGFR trafficking to the mitochondria and restores SARS-CoV-2-induced aberrant elevation in OXPHOS process and ATP generation,thereby resulting in the reduction of SARS-CoV-2 ***,oral administration of vandetanib to SARS-CoV-2-infected hACE2 transgenic mice reduces SARS-CoV-2 propagation in lung tissue and mitigates SARS-CoV-2-induced lung *** also exhibits potent antiviral activity against various SARS-CoV-2 variants of concern,including alpha,beta,delta and omicron,in in vitro cell culture *** together,our findings provide novel insight into SARS-CoV-2-induced alterations in mitochondrial dynamics and EGFR trafficking during the early stage of viral infection and their roles in robust SARS-CoV-2 propagation,suggesting that EGFR is an attractive host target for combating COVID-19.

关键词： alterations aberrant thereby

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Uncovering hidden nodes and hidden links in complex dynamic networks

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Science China(Physics,Mechanics & Astronomy) 2024年第4期67卷 51-63页

作者： Zhaoyang Zhang Xinyu Wang Haihong Li Yang Chen Zhilin Qu Yuanyuan mi Gang Hu Department of Physics School of Physical Science and TechnologyNingbo UniversityNingbo 315211China School of Science Beijing University of Posts and TelecommunicationsBeijing 100876China Department of Medicine David Geffen School of MedicineUniversity of CaliforniaLos Angeles 90095USA Brainnetome Center and National Laboratory of Pattern Recognition Institute of AutomationChinese Academy of SciencesBeijing 100190China Department of Psychology Tsinghua UniversityBeijing 100084China Department of Physics Beijing Normal UniversityBeijing 100875China

Inferring network structures from available data has attracted much interest in network science;however,in many realistic networks,only some of the nodes are perceptible while others are hidden,making it a challenging *** this work,we develop a method for reconstructing the network with hidden nodes and links,taking account of fast-varying noise and time-delay *** calculating the correlations of available data with different derivative orders for multiple pairs of accessible nodes,analyzing and integrating the relationships between different correlations,and defining diverse hidden-node-related reconstruction motifs,we can effectively identify the hidden nodes and hidden links in the network.

关键词： networks and genealogical trees stochastic analysis methods time series analysis

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Full-Scale Isogeometric Topology Optimization of Cellular Structures Based on Kirchhoff-Love Shells

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Computer Modeling in Engineering & Sciences 2024年第6期139卷 2479-2505页

作者： mingzhe Huang mi Xiao Liang Gao mian Zhou Wei Sha Jinhao Zhang State Key Lab of Intelligent Manufacturing Equipment and Technology Huazhong University of Science and TechnologyWuhan430074China

Cellular thin-shell structures are widely applied in ultralightweight designs due to their high bearing capacity and strength-to-weight *** this paper,a full-scale isogeometric topology optimization(ITO)method based on Kirchhoff-Love shells for designing cellular tshin-shell structures with excellent damage tolerance ability is *** method utilizes high-order continuous nonuniform rational B-splines(NURBS)as basis functions for Kirchhoff-Love shell *** geometric and analysis models of thin shells are unified by isogeometric analysis(IGA)to avoid geometric approximation error and improve computational *** topological configurations of thin-shell structures are described by constructing the effective density field on the *** volume constraints are imposed in the proximity of each control point to obtain bone-like cellular *** facilitate numerical implementation,the p-norm function is used to aggregate local volume constraints into an equivalent global *** numerical examples are provided to demonstrate the effectiveness of the proposed *** simulation and comparative analysis,the results indicate that the cellular thin-shell structures optimized by the proposed method exhibit great load-carrying behavior and high damage robustness.

关键词： Cellular thin-shell structures isogeometric analysis full-scale topology optimization Kirchhoff–Love shells

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