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Author Correction: O-GlcNAc modification of leucyl-tRNA synthetase 1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine

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Nature communications 2022年第1期13卷 6253页

作者： Kibum Kim Hee Chan Yoo Byung Gyu Kim Sulhee Kim Yulseung Sung Ina Yoon Ya Chun Yu Seung Joon Park Jong Hyun Kim Kyungjae Myung Kwang Yeon Hwang Sunghoon Kim Jung Min Han Interdisciplinary Program of Integrated OMICS for Biomedical Science Graduate School Yonsei University Seoul 03722 South Korea. Yonsei Institute of Pharmaceutical Sciences College of Pharmacy Yonsei University Incheon 21983 South Korea. Center for Genomic Integrity Institute for Basic Science Ulsan 44919 South Korea. Department of Biotechnology College of Life Sciences and Biotechnology Korea University Seoul 02841 South Korea. Institute for Artificial Intelligence and Biomedical Research Medicinal Bioconvergence Research Center Yonsei University Incheon 21983 South Korea. College of Medicine Gangnam Severance Hospital Yonsei University Seoul 06273 South Korea. Department of Biochemistry School of Medicine Catholic University of Daegu Daegu 42472 South Korea. Department of Biomedical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 South Korea. Interdisciplinary Program of Integrated OMICS for Biomedical Science Graduate School Yonsei University Seoul 03722 South Korea. jhan74@yonsei.ac.kr. Yonsei Institute of Pharmaceutical Sciences College of Pharmacy Yonsei University Incheon 21983 South Korea. jhan74@yonsei.ac.kr. POSTECH Biotech Center Pohang University of Science and Technology Pohang 37673 South Korea. jhan74@yonsei.ac.kr.

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A Reconfigurable DNA Accordion Rack

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Angewandte Chemie 2018年第11期130卷

作者： Yeongjae Choi Hansol Choi Amos C. Lee Hyunung Lee Sunghoon Kwon Department of Electrical and Computer Engineering Seoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea Interdisciplinary Program for Bioengineering Seoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea Institute of Entrepreneurial Bio Convergence Seoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea Seoul National University Hospital Biomedical Research Institute Seoul National University Hospital 101 Daehak-ro Jongno-gu Seoul 03080 Republic of Korea

DNA nanostructure‐based mechanical systems that control the distance between elements of interest have demonstrated great potential for various applications, including nanoplasmonic systems, molecular reactors, and other nanotechnology platforms. However, previously reported systems could not collectively manipulate a 2D or 3D nanoscale network of elements to various forms in multiple stages. A reconfigurable DNA accordion rack structure is introduced that is a DNA beam lattice that changes its conformation with a small amount of short‐length DNA locks as the controlling input. The lattice shape of the 2D DNA accordion rack and the diameter and the height of the 3D DNA nanotubular structure made of the DNA accordion rack could be controlled. Furthermore, by sequentially repeating the detachment and the attachment of the different DNA locks using strand displacement, the shape reconfiguration was repeatedly carried out.

关键词： DNA-Nanomaschinen DNA-Nanotechnologie DNA-Strukturen Nanoporen Selbstorganisation

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Comparison of spatial distribution characteristics of shock wave pressure field and cavitation bubble cloud

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Proceedings of Meetings on Acoustics 2017年第1期32卷

作者： Gwansuk Kang Ohbin Kwon Jung Sik Huh Min Joo Choi 1Interdisciplinary Postgraduate Program in Biomedical Engineering Jeju National University Jejusi Jeju Special Self-Governing Province 63243 REPUBLIC OF KOREA mjchoi@jejunu.ac.kr djin89@*** 2Department of Urology Jeju National University Hospital Jeju-si Jeju Special Self-Governing Province REPUBLIC OF KOREA urohjs@jejunu.ac.kr 3Department of Medicine Jeju National University Jeju-si Jeju Special Self-Governing Province REPUBLIC OF KOREA

This study aims to compare the spatial characteristics of the cavitation bubble cloud and shockwave pressure field. Cavitation bubble cloud images were acquired using micro pulsed light with 150us exposure time and CCD camera, and images were accumulated after repeated several acquisitions. The shockwave field was measured using an optical hydrophone to compare with the distribution of cavitation bubbles. After the shockwave device was triggered, cavitation bubbles were generated and visualized during 150us light exposure and were collapsed at the same position where they were generated. Most of the bubbles are concentrated in the focal region of the shockwave. The largest bubbles were observed at the peak negative pressure position in the focal area In the remaining focal area, it was formed as relatively small bubbles. Outside the focal area, very small bubbles were sparsely observed. Cavitation bubbles produced by a single shockwave pulse are highly correlated with the shockwave pressure at exposed location since there is no significant positional movement with time. Therefore, the distribution of cavitation bubble is similar to the spatial characteristics of the shockwave pressure field. It is possible to qualitatively analyze the shockwave pressure field by observing the cavitation bubbles which is difficult to measure.

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An Open-Source Knowledge Graph Ecosystem for the Life Sciences

arXiv

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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Neuroprosthetics: Durable and Fatigue-Resistant Soft Peripheral Neuroprosthetics for In Vivo Bidirectional Signaling (Adv. Mater. 20/2021)

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Advanced Materials 2021年第20期33卷

作者： Hyunseon Seo Sang Ihn Han Kang-Il Song Duhwan Seong Kyungwoo Lee Sun Hong Kim Taesung Park Ja Hoon Koo Mikyung Shin Hyoung Won Baac Ok Kyu Park Soong Ju Oh Hyung-Seop Han Hojeong Jeon Yu-Chan Kim Dae-Hyeong Kim Taeghwan Hyeon Donghee Son School of Medicine Sungkyunkwan University Suwon 16419 Republic of Korea Center for Biomaterials Biomedical Research Institute Korea Institute of Science and Technology Seoul 02792 Republic of Korea Center for Nanoparticle Research Institute of Basic Science (IBS) Seoul 08826 Republic of Korea School of Chemical and Biological Engineering Seoul National University Seoul 08826 Republic of Korea Medical Device Development Center Daegu-Gyeongbuk Medical Innovation Foundation Daegu 41061 Republic of Korea Department of Electrical and Computer Engineering Sungkyunkwan University Suwon 16419 Republic of Korea Department of Electrical and Computer Engineering Inter-University Semiconductor Research Center Seoul National University Seoul 08826 Republic of Korea Department of Materials Science and Engineering Korea University Seoul 02841 Republic of Korea Interdisciplinary Program for Bioengineering Seoul National University Seoul 08826 Republic of Korea Department of Biomedical Engineering SKKU Institute for Convergence Sungkyunkwan University Suwon 16419 Republic of Korea Center for Neuroscience Imaging Research Institute for Basic Science (IBS) Suwon 16419 Republic of Korea Department of Superintelligence Engineering Sungkyunkwan University Suwon 16419 Republic of Korea

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Abstracts and Workshops 7th National Spinal Cord Injury Conference November 9-11, 2017 Fallsview Casino Resort Niagara Falls, Ontario, Canada Abstracts

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JOURNAL OF SPINAL CORD MEDICINE 2017年第6期40卷 813-869页

作者： [Anonymous] a NET Team Toronto Rehabilitation Institute - University Health Network Toronto ON Canada. fo Neural Engineering and Therapeutic Team Lyndhurst Centre Toronto Rehabilitation Institute - University Health Network Toronto ON Canada. c Rick Hansen Institute Vancouver BC Canada. ev Rick Hansen Institute Vancouver BC Canada. fc Stan Cassidy Hospital University of New Brunswick Fredericton NB Canada. fd Dalhousie University Halifax NS Canada. e University of Saskatchewan Saskatoon SK Canada. aa University of Calgary Calgary AB Canada. y Dalhousie University Halifax NS Canada. fa Health Sciences Centre Winnipeg MB Canada. fb University of Manitoba Winnipeg MB Canada. h University of Alberta Edmonton AB Canada. i Universite Laval Quebe c City QC Canada. bd Rick Hansen Institute Vancouver BC Canada. fz Clinician Investigator Lyndhurst Centre Toronto Rehabilitation Institute University Health Network and Assistant Professor Department of Medicine Division of Physical Medicine and Rehabilitation University of Toronto. v University of Toront o Toronto ON Canada. n Institute of Biomaterials and Biomedical Engineering University of Toronto Toronto ON Canada. o Toronto Rehabilitation Institute - University Health Network Toronto ON Canada. ga Clinical Scientist Lyndhurst Centre Toronto Rehabilitation Institute University Health Network and Assistant Professor Department of Physical Therapy University of Toronto. dx Department of Electrical and Computer Engineering University of Toronto Toronto ON Canada. fm Lawson Health Research Institute London ON Canada. r Parkwood Institute London ON Canada. bi Parkwood Institute London ON Canada. s University of British Columbia Vancouver BC Canada. t Simon Fraser University Burnaby BC Canada. u DeltaQuest Foundation Concord MA USA. z Institut national d'excellence en santé et en services sociaux (INESSS) Quebec City QC Ca

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Photonic Crystals: Light‐Patterned Crystallographic Direction of a Self‐Organized 3D Soft Photonic Crystal (Adv. Mater. 42/2017)

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Advanced Materials 2017年第42期29卷

作者： Zhi‐Gang Zheng Cong‐Long Yuan Wei Hu Hari Krishna Bisoyi Ming‐Jie Tang Zhen Liu Pei‐Zhi Sun Wei‐Qiang Yang Xiao‐Qian Wang Dong Shen Yannian Li Fangfu Ye Yan‐Qing Lu Guoqiang Li Quan Li Department of Physics East China University of Science and Technology Shanghai 200237 China Liquid Crystal Institute and Chemical Physics Interdisciplinary Program Kent State University Kent OH 44242 USA National Laboratory of Solid State Microstructures Collaborative Innovation Center of Advanced Microstructures and College of Engineering and Applied Sciences Nanjing University Nanjing 210093 China Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China Visual and Biomedical Optics Lab Department of Ophthalmology and Visual Science and Department of Electrical and Computer Engineering Ohio State University Columbus OH 43212 USA

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Author Correction: Predicting the efficiency of prime editing guide RNAs in human cells

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Nature biotechnology 2024年第3期42卷 529页

作者： Hui Kwon Kim Goosang Yu Jinman Park Seonwoo Min Sungtae Lee Sungroh Yoon Hyongbum Henry Kim Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Graduate School of Data Science Seoul National University Seoul Republic of Korea. Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac. Severance Biomedical Science Institute Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of NanoScience and Technology Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac.

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Publisher Correction: Serotonin signals through a gut-liver axis to regulate hepatic steatosis

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Nature communications 2019年第1期10卷 158页

作者： Wonsuk Choi Jun Namkung Inseon Hwang Hyeongseok Kim Ajin Lim Hye Jung Park Hye Won Lee Kwang-Hyub Han Seongyeol Park Ji-Seon Jeong Geul Bang Young Hwan Kim Vijay K Yadav Gerard Karsenty Young Seok Ju Chan Choi Jae Myoung Suh Jun Yong Park Sangkyu Park Hail Kim Graduate School of Medical Science and Engineering KAIST Daejeon 34141 Republic of Korea. Department of Biochemistry Yonsei University Wonju College of Medicine Wonju 26426 Republic of Korea. Biomedical Science and Engineering Interdisciplinary Program KAIST Daejeon 34141 Republic of Korea. Department of Internal Medicine Yonsei University College of Medicine Yonsei Liver Center Severance Hospital Seoul 03722 Republic of Korea. Center for Bioanalysis Division of Metrology for Quality of Life Korea Research Institute of Standards and Science Daejeon 34113 Republic of Korea. Biomedical Omics Group Korea Basic Science Institute Chungbuk 28119 Republic of Korea. Department of Genetics and Development Columbia University Medical Center New York NY 10032 USA. Department of Pathology Chonnam National University Medical School Gwangju 61469 Republic of Korea. Department of Internal Medicine Yonsei University College of Medicine Yonsei Liver Center Severance Hospital Seoul 03722 Republic of Korea. drpjy@yuhs.ac. Graduate School of Medical Science and Engineering KAIST Daejeon 34141 Republic of Korea. 49park@cku.ac.kr. Department of Biochemistry College of Medicine Catholic Kwandong University Gangneung 25601 Republic of Korea. 49park@cku.ac.kr. Graduate School of Medical Science and Engineering KAIST Daejeon 34141 Republic of Korea. hailkim@kaist.edu. Biomedical Science and Engineering Interdisciplinary Program KAIST Daejeon 34141 Republic of Korea. hailkim@kaist.edu. KAIST Institute for the BioCentury KAIST Daejeon 34141 Republic of Korea. hailkim@kaist.edu.

The originally published version of this Article contained an error in Figure 2. In panel g, the image of brown adipose tissue from SCD-fed Tph1 GKO mice (top-right) was inadvertently replaced with the equivalent image of SCD-fed WT mice (top-left) during assembly of the figure. This error has now corrected in both the PDF and HTML versions of the Article.

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Cancer Informatics: Profiling Age-Related Epigenetic Markers of Stomach Adenocarcinoma in Young and Old Subjects

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Cancer Informatics 2015年 14卷

作者： Byoung-Chul Kim Hyoung Oh Jeong Daeui Park Chul-Hong Kim Eun Kyeong Lee Dae Hyun Kim Eunok Im Nam Deuk Kim Sunghoon Lee Byung Pal Yu Jong Bhak Hae Young Chung Molecular Inflammation Research Center for Aging Intervention Pusan National University Busan Republic of Korea.Interdisciplinary Research Program of Bioinformatics and Longevity Science Pusan National University Busan Republic of Korea. Genomictree Inc. Yuseong-gu Daejeon Republic of Korea. Molecular Inflammation Research Center for Aging Intervention Pusan National University Busan Republic of Korea. Personal Genomics Institute Genome Research Foundation Suwon Republic of Korea.BioMedical Engineering UNIST Ulsan Republic of Korea. Department of Physiology University of Texas Health Science Center at San Antonio San Antonio TX USA.

The purpose of our study is to identify epigenetic markers that are differently expressed in the stomach adenocarcinoma (STAD) condition. Based on data from The Cancer Genome Atlas (TCGA), we were able to detect an age-related difference in methylation patterns and changes in gene and miRNA expression levels in young (n = 14) and old (n = 70) STAD subjects. Our analysis identified 323 upregulated and 653 downregulated genes in old STAD subjects. We also found 76 miRNAs with age-related expression patterns and 113 differentially methylated genes (DMGs), respectively. Our further analysis revealed that significant upregulated genes (n = 35) were assigned to the cell cycle, while the muscle system process (n = 27) and cell adhesion-related genes (n = 57) were downregulated. In addition, by comparing gene and miRNA expression with methylation change, we identified that three upregulated genes (ELF3, IL1β, and MMP13) known to be involved in inflammatory responses and cell growth were significantly hypomethylated in the promoter region. We further detected target candidates for age-related, downregulated miRNAs (hsa-mir-124-3, hsa-mir-204, and hsa-mir-125b-2) in old STAD subjects. This is the first report of the results from a study exploring age-related epigenetic biomarkers of STAD using high-throughput data and provides evidence for a complex clinicopathological condition expressed by the age-related STAD progression.

关键词： stomach adenocarcinoma age TCGA RNAseq miRNA DNA methylation

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