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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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Unraveling the role of METTL14 in metabolic dysfunction-associated fatty liver disease:insights and therapeutic implications

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Signal Transduction and Targeted Therapy 2024年第5期9卷 1781-1783页

作者： So Jung kim Jeongeun Hyun Institute of Tissue Regeneration Engineering(ITREN) Dankook UniversityCheonanRepublic of Korea Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine Dankook UniversityCheonanRepublic of Korea Mechanobiology Dental Medicine Research Center College of DentistryDankook UniversityCheonanRepublic of Korea

The recent article published in Signal Transduction and Targeted Therapy sheds light on the significance of N6-methyladenosine(m6A)methyltransferase-like protein METTL14 in mitigating the progression of metabolic dysfunction-associated fatty liver disease(MAFLD).1 In this study,Wang et *** the downregulation of METTL14 in hepatocytes from both MAFLD patients and high-fat diet(HFD)-induced MAFLD mouse models,underscoring its pivotal role in maintaining hepatic lipid and redox homeostasis in normal livers.

关键词： liver homeostasis al.

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Jun12682,a potent SARS-CoV-2 papain-like protease inhibitor with exceptional antiviral efficacy in mice

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Acta Pharmaceutica Sinica B 2024年第9期14卷 4189-4192页

作者： Mianling Yang Meehyein kim Peng Zhan Department of Medicinal Chemistry Key Laboratory of Chemical Biology(Ministry of Education)School of Pharmaceutical SciencesShandong UniversityJi’nan 250012China Infectious Diseases Therapeutic Research Center Korea Research Institute of Chemical Technology(KRICT)Daejeon 34114Republic of Korea

Recently,a collaborative research study published in Science,led by Jun Wang,Xufang Deng,Eddy Arnold,and Francesc Xavier Ruiz1,identified a series of potent small molecule inhibitors that specifically target SARS-CoV-2 papain-like protease(PLpro).The study demonstrated nanomolar PLpro inhibitory potency with ki values ranging from 13.2 to 88.2 nmol/*** employing a structure-based drug design strategy,the researchers discovered an exceptionally promising compound,named Jun12682,that effectively targets both the newly discovered ubiquitin Val70(Val70Ub)-binding site and the known blocking loop(BL2)groove near the S4 subsite of ***,studies on the mechanism of action revealed that Jun12682 inhibits the deubiquitinating and deISGylating activities of PLpro,which are crucial for antagonizing the host’s innate immune response upon viral *** biology studies confirmed the“two-pronged”binding mode of Jun12682,aligning perfectly with their drug design ***,Jun12682 exhibited potent antiviral activity against SARS-CoV-2 and its variants,including nirmatrelvir-resistant mutants,in Caco-2 cells(EC50:0.44e2.02 mmol/L).It is noteworthy that its oral administration significantly improved survival rates and alleviated both lung virus loads and histopathological lesions in a lethal SARS-CoV-2 mouse *** conclusion。

关键词： SARS-CoV-2 Papain-like protease Broad-spectrum Anti-drug resistance Drug candidate

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Erythrocytes serve as a template to create nanozymes with uniform Fe single-atom sites for healing bacteria-infected wound

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Science China(Life Sciences) 2024年第9期67卷 2048-2050页

作者： Thinh Viet Dang Moon Il kim Department of BioNano Technology Gachon UniversitySeongnam 13120Republic of Korea

Bacterial infection is recognized as one of the biggest global health threats,causing millions of people's death every year(Wang et al.,2020).Traditional antibiotics-based therapies have been widely utilized to control this issue(Kohanski et al.,2010);however,their excessive use leads to the emergence of antibioticresistant bacteria,endangering to human health(Levy and Marshall,2004).

关键词： template healing utilized

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Image enhancement with intensity transformation on embedding space

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CAAI Transactions on Intelligence Technology 2024年第1期9卷 101-115页

作者： Hanul kim Yeji Jeon Yeong Jun Koh Department of Applied Artificial Intelligence Seoul National University of Science and TechnologySeoulSouth Korea Department of Computer Science and Engineering Chungnam National UniversityDaejeonSouth Korea

In recent times,an image enhancement approach,which learns the global transformation function using deep neural networks,has gained ***,many existing methods based on this approach have a limitation:their transformation functions are too simple to imitate complex colour transformations between low-quality images and manually retouched high-quality *** order to address this limitation,a simple yet effective approach for image enhancement is *** proposed algorithm based on the channel-wise intensity transformation is ***,this transformation is applied to the learnt embedding space instead of specific colour spaces and then return enhanced features to *** this end,the authors define the continuous intensity transformation(CIT)to describe the mapping between input and output intensities on the embedding ***,the enhancement network is developed,which produces multi-scale feature maps from input images,derives the set of transformation functions,and performs the CIT to obtain enhanced *** experiments on the MIT-Adobe 5K dataset demonstrate that the authors’approach improves the performance of conventional intensity transforms on colour space ***,the authors achieved a 3.8%improvement in peak signal-to-noise ratio,a 1.8%improvement in structual similarity index measure,and a 27.5%improvement in learned perceptual image patch ***,the authors’algorithm outperforms state-of-the-art alternatives on three image enhancement datasets:MIT-Adobe 5K,Low-Light,and Google HDRþ.

关键词： computer vision deep learning image enhancement image processing

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Nanocrystalline low-silica X zeolite as an efficient ion-exchanger enabling fast radioactive strontium capture

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Frontiers of Chemical Science and Engineering 2024年第9期18卷 15-23页

作者： Hyungmin Jeon Susung Lee Jeong-Chul kim Minkee Choi Department of Chemical and Biomolecular Engineering(BK21 Four) Korea Advanced Institute of Science and Technology(KAIST)Daejeon 34141Republic of Korea Center for Nanomaterials and Chemical Reactions Institute for Basic Science(IBS)Daejeon 34141Republic of Korea

NaA zeolite(Si/Al=1.00)has been commercially applied for capturing radioactive 90Sr^(2+)because of its high surface charge density,effectively stabilizing the multivalent ***,owing to its narrow micropore opening(4.0Å),large micron-sized crystallites,and bulkiness of hydrated Sr^(2+),the Sr^(2+)exchange over NaA has been limited by very slow *** this study,we synthesized nanocrystalline low-silica X by minimizing a water content in a synthesis gel and utilizing a methyl cellulose hydrogel as a crystal growth *** resulting zeolite exhibited high crystallinity and Al-rich framework(Si/Al of approximately 1.00)with the sole presence of tetrahedral Al sites,which are capable of high Sr^(2+)uptake and ion ***,the zeolite with a FAU topology has a much larger micropore opening size(7.4Å)and a much smaller crystallite size(~340 nm)than NaA,which enable significantly enhanced ion-exchange *** to conventional NaA,the nanocrystalline low-silica X exhibited remarkably increased Sr^(2+)-exchange kinetics(>18-fold larger rate constant)in batch *** both the nanocrystalline low-silica X and NaA exhibited comparable Sr^(2+)capacities under equilibrated conditions,the former demonstrated a 5.5-fold larger breakthrough volume than NaA under dynamic conditions,attributed to its significantly faster Sr^(2+)-exchange kinetics.

关键词： Sr^(2+)removal low-silica X zeolite nanocrystal hydrogel methyl cellulose

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Emission wavelength selection via anomalous polarized fluorescence in ZnO-C nanowires

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Nano Research 2024年第5期17卷 4489-4497页

作者： Joon kiat Kang kim Yong Lim Chorng Haur Sow Department of Physics National University of SingaporeSingapore 117542Singapore

Defect fluorescence from high aspect ratio semiconductor nanowires typically displays a weak polarization parallel to the nanowire’s long axis due to dielectric mismatch in high aspect ratio ***,anomalous 2.2 eV defect fluorescence distinctly polarized perpendicular to the nanowire is observed and measured from carbon-incorporated zinc oxide *** observations are significant because polarized defect emissions with consistent polarization on a mesoscopic scale are *** a systematic study and comparison of experimental results with density functional theory calculations,an oriented defect complex comprising carbon substituting on an oxygen site and an oxygen vacancy(CO-VO)is deduced to be responsible for the anomalous yellow fluorescence,demonstrating a method for relating atomic-scale defect geometry to mesoscopic *** anomalous emission can appear in both green-and red-fluorescing nanowires grown with different carbon concentrations,verifying the independence and uniqueness of the 2.2 eV *** allows for polarization-dependent emission wavelength selection from a single nanowire.

关键词： anomalous polarization defects fluorescence zinc oxide carbon

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Removal of intrahepatic bile duct stone could reduce the risk of cholangiocarcinoma: A single-center retrospective study in South Korea

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World Journal of Clinical Cases 2024年第5期12卷 913-921页

作者： Tae In kim Sung Yong Han Jonghyun Lee Dong Uk kim Division of Gastroenterology Biomedical Research InstitutePusan National University HospitalBusan 49241South Korea Department of Internal Medicine Pusan National UniversityCollege of MedicineYangsan 50612South Korea

BACKGROUND Intrahepatic duct(IHD)stones are among the most important risk factors for cholangiocarcinoma(CCC).Approximately 10%of patients with IHD stones develop CCC;however,there are limited studies regarding the effect of IHD stone removal on CCC *** To investigate the association between IHD stone removal and CCC *** We retrospectively analyzed 397 patients with IHD stones at a tertiary referral center between January 2011 and December *** CCC occurred in 36 of the 397 enrolled *** univariate analysis,chronic hepatitis B infection(11.1%vs 3.0%,P=0.03),carbohydrate antigen 19-9(CA19-9,176.00 vs 11.96 II/mL,P=0.010),stone located in left or both lobes(86.1%vs 70.1%,P=0.042),focal atrophy(52.8%vs 26.9%,P=0.001),duct stricture(47.2%vs 24.9%,P=0.004),and removal status of IHD stone(33.3%vs 63.2%,Pupper normal limit,carcinoembryonic antigen>upper normal limit,stones located in the left or both lobes,focal atrophy,and complete removal of IHD stones without recurrence were independent factors influencing CCC ***,the type of removal method was not associated with CCC *** Complete removal of IHD stones without recurrence could reduce CCC risk.

关键词： Intrahepatic bile duct stone Cholangiocarcinoma Percutaneous transhepatic cholangioscopy Endoscopic retrograde cholangiopancreatography Carbohydrate antigen 19-9

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Modeling asymmetric fracture mechanics of Mg alloy wire in drawing process

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Journal of Magnesium and Alloys 2024年第5期12卷 2057-2069页

作者： Sunghoon Choi Jongwon Shin Joung Sik Suh Dongchoul kim Department of Mechanical Engineering Sogang UniversitySeoul04107Republic of Korea Advanced Metals Division Korea Institute of Materials ScienceChangwon 51508Republic of Korea

In this study,a numerical analysis was conducted on the ductile fracture of a 2-mm diameter Mg-1Zn-0.5Mn-0.5Sr-0.1Ca alloy wire during *** hexagonally close-packed crystal structure of Mg alloys causes asymmetric fracture behavior,especially in the compression *** aim of this study is to develop a comprehensive damage model for Mg alloy wire that accurately predicts ductile fracture,with a focus on the compression region.A novel experimental method was introduced to measure the ductile fracture of Mg alloy wires under different stress *** wire drawing process was simulated using the Generalized Incremental Stress-State dependent damage(GISSMO)Model and the Semi-Analytical Model for Polymers(samP)*** damage model's prediction and the experimental results were found to be in excellent agreement,especially in determining crack *** analysis established a safe zone diagram for die angle and reduction ratio,and experimental validation confirmed the feasibility of this *** proposed damage model can provide a practical and reliable analysis for optimizing the drawing process of Mg alloy wire.

关键词： Mg alloy Wire drawing Finite element method Damage model Safe zone diagram

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α1-COP modulates plasmodesmata function through sphingolipid enzyme regulation

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Journal of Integrative Plant Biology 2024年第8期66卷 1639-1657页

作者： Arya Bagus Boedi Iswanto Minh Huy Vu Jong Cheol Shon Ritesh Kumar Shuwei Wu Hobin Kang Da-Ran kim Geon Hui Son Woe Yoen kim Youn-Sig Kwak Kwang Hyeon Liu Sang Hee kim Jae-Yean kim Division of Applied Life Science(BK21 FOUR Program) Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 52828Korea College of Pharmacy and Research Institute of Pharmaceutical Sciences Kyungpook National UniversityDaegu 702-701Korea Departement of Plant Medicine Gyeongsang National UniversityJinju 52828Korea Division of Life Science Gyeongsang National UniversityJinju 52828Korea

Callose,aβ-1,3-glucan plant cell wall polymer,regulates symplasmic channel size at plasmodesmata(PD)and plays a crucial role in a variety of plant ***,elucidating the molecular mechanism of PD callose homeostasis is *** screened and identified an Arabidopsis mutant plant with excessive callose deposition at PD and found that the mutated gene wasα1-COP,a member of the coat protein I(COPI)coatomer *** report that loss of function ofα1-COP elevates the callose accumulation at PD by affecting subcellular protein localization of callose degradation enzyme Pd *** process is linked to the functions of ERH1,an inositol phosphoryl ceramide synthase,and glucosylceramide synthase through physical interactions with theα1-COP ***,the loss of function ofα1-COP alters the subcellular localization of ERH1 and GCS proteins,resulting in a reduction of Glc Cers and Glc HCers molecules,which are key sphingolipid(SL)species for lipid raft *** findings suggest thatα1-COP protein,together with SL modifiers controlling lipid raft compositions,regulates the subcellular localization of GPI-anchored PDBG2 proteins,and hence the callose turnover at PD and symplasmic movement of *** findings provide the first key clue to link the COPI-mediated intracellular trafficking pathway to the callose-mediated intercellular signaling pathway through PD.

关键词： callose coatomer proteins membrane-bound vesicle plasmodesmata sphingolipid enzymes

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