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PDBe-KB: collaboratively defining the biological context of structural data

NUCLEIC ACIDS RESEARCH 2022年第D1期50卷 D534-D542页

作者： Varadi, Mihaly Anyango, Stephen Armstrong, David Berrisford, John Choudhary, Preeti Deshpande, Mandar Nadzirin, Nurul Nair, Sreenath S. Pravda, Lukas Tanweer, Ahsan Al-Lazikani, Bissan Andreini, Claudia Barton, Geoffrey J. Bednar, David Berka, Karel Blundell, Tom Brock, Kelly P. Carazo, Jose Maria Damborsky, Jiri David, Alessia Dey, Sucharita Dunbrack, Roland Recio, Juan Fernandez Fraternali, Franca Gibson, Toby Helmer-Citterich, Manuela Hoksza, David Hopf, Thomas Jakubec, David Kannan, Natarajan Krivak, Radoslav Kumar, Manjeet Levy, Emmanuel D. London, Nir Macias, Jose Ramon Srivatsan, Madhusudhan M. Marks, Debora S. Martens, Lennart McGowan, Stuart A. McGreig, Jake E. Modi, Vivek Parra, R. Gonzalo Pepe, Gerardo Piovesan, Damiano Prilusky, Jaime Putignano, Valeria Radusky, Leandro G. Ramasamy, Pathmanaban Rausch, Atilio O. Reuter, Nathalie Rodriguez, Luis A. Rollins, Nathan J. Rosato, Antonio Rubach, Pawel Serrano, Luis Singh, Gulzar Skoda, Petr Sorzano, Carlos Oscar S. Stourac, Jan Sulkowska, Joanna, I Svobodova, Radka Tichshenko, Natalia Tosatto, Silvio C. E. Vranken, Wim Wass, Mark N. Xue, Dandan Zaidman, Daniel Thornton, Janet Sternberg, Michael Orengo, Christine Velankar, Sameer European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton United Kingdom Cancer Research UK Cancer Therapeutics Unit Division of Cancer Therapeutics The Institute of Cancer Research London United Kingdom University of Florence C.I.R.M.M.P. Magnetic Resonance Center Sesto Fiorentino Italy School of Life Sciences University of Dundee Dundee United Kingdom Masaryk University International Centre for Clinical Research St. Anne’s University Hospital Brno Department of Experimental Biology and RECETOX Brno Czech Republic Palacky University Olomouc Department of Physical Chemistry Olomouc Czech Republic University of Cambridge Department of Biochemistry Cambridge United Kingdom Computational and Systems Biology Massachusetts Institute of Technology Cambridge MA United States CNB-CSIC Biocomputing Unit - Instruct Image Processing Center Madrid Spain Imperial College London London United Kingdom Weizmann Institute of Science Rehovot Israel Fox Chase Cancer Center Institute for Cancer Research Philadelphia PA United States Instituto de Ciencias de la Vid y del Vino (CSIC - Universidad de La Rioja - Gobierno de La Rioja) Oenology Barcelona Spain Randall Centre for Cell & Molecular Biophysics King’s College London London United Kingdom European Molecular Biology Laboratory Heidelberg Germany Centre for Molecular Bioinformatics Department of Biology University of Rome Tor Vergata Rome Italy Charles University Prague Czech Republic University of Georgia Department of Biochemistry and Molecular Biology Institute of Bioinformatics Athens United States Indian Institute of Science Education and Research Pune India Ghent University Department of Biomolecular Medicine Ghent Belgium VIB-UGent Center for Medical Biotechnology Ghent Belgium University of Kent Canterbury Kent United Kingdom Barcelona Supercomputing Center Life Sciences Department Barcelona Spain University of Padova Deptartment of Biomedical

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://***) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

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Planet Masses, Radii, and Orbits from NASA’s K2 Mission

arXiv

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arXiv 2025年

作者： Howard, Andrew W. Sinukoff, Evan Blunt, Sarah Petigura, Erik A. Crossfield, Ian J.M. Isaacson, Howard Kosiarek, Molly Rubenzahl, Ryan A. Brewer, John M. Fulton, Benjamin J. Dressing, Courtney D. Hirsch, Lea A. Knutson, Heather Livingston, John H. Mills, Sean M. Roy, Arpita Weiss, Lauren M. Benneke, Bjorn Ciardi, David R. Christiansen, Jessie L. Cochran, William D. Crepp, Justin R. Gonzales, Erica Hansen, Brad M.S. Hardegree-Ullman, Kevin Howell, Steve B. Lépine, Sébastien Martinez, Arturo O. Rogers, Leslie A. Schlieder, Joshua E. Werner, Michael Polanski, Alex S. Angelo, Isabel Beard, Corey Behmard, Aida Bouma, Luke G. Brinkman, Casey L. Chontos, Ashley Dai, Fei Dalba, Paul A. Giacalone, Steven Grunblatt, Samuel K. Hill, Michelle L. Kane, Stephen R. Lubin, Jack Mayo, Andrew W. Mocnik, Teo Akana Murphy, Joseph M. Rice, Malena Rosenthal, Lee J. Tyler, Dakotah Van Zandt, Judah Yee, Samuel W. Department of Astronomy California Institute of Technology PasadenaCA United States Institute for Astronomy University of Hawaii 2680 Woodlawn Drive HonoluluHI United States Department of Physics and Astronomy Northwestern University EvanstonIL60208 United States Department of Astronomy & Astrophysics University of California Santa CruzCA United States Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Department of Physics & Astronomy University of California Los Angeles Los AngelesCA United States Department of Physics and Astronomy University of Kansas LawrenceKS United States Astronomy Department University of California BerkeleyCA United States Department of Physics and Astronomy San Francisco State University 1600 Holloway Ave. San FranciscoCA94132 United States IPAC - NASA Exoplanet Science Institute California Institute of Technology 770 S. Wilson Ave PasadenaCA United States Department of Chemical & Physical Sciences University of Toronto Mississauga 3359 Mississauga Road MississaugaONL5L 1C6 Canada Geological and Planetary Sciences California Institute of Technology PasadenaCA United States Astrobiology Center 2-21-1 Osawa Mitaka Tokyo181-8588 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Astronomical Science Program The Graduate University for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Space Telescope Science Institute 3700 San Martin Drive BaltimoreMD21218 United States Astrophysics & Space Institute Schmidt Sciences New YorkNY10011 United States Department of Physics and Astronomy University of Notre Dame Notre DameIN46556 United States Institut de Recherche sur les Exoplanètes Université de Montréal MontréalQC Canada McDonald Observatory Center for Planetary Systems Habitability The University of Texas AustinTX United States Department of Physics and Astronomy University of Toledo ToledoOH4

We report the masses, sizes, and orbital properties of 86 planets orbiting 55 stars observed by NASA’s K2 Mission with follow-up Doppler measurements by the HIRES spectrometer at the W. M. Keck Observatory and the Automated Planet Finder at Lick Observatory. Eighty-one of the planets were discovered from their transits in the K2 photometry, while five were found based on subsequent Doppler measurements of transiting planet host stars. The sizes of the transiting planets range from Earth-size to larger than Jupiter (1–3 R is typical), while the orbital periods range from less than a day to a few months. For 32 of the planets, the Doppler signal was detected with significance greater than 5-σ (51 were detected with >3-σ significance). An important characteristic of this catalog is the use of uniform analysis procedures to determine stellar and planetary properties. This includes the transit search and fitting procedures applied to the K2 photometry, the Doppler fitting techniques applied to the radial velocities, and the spectral modeling to determine bulk stellar parameters. Such a uniform treatment will make the catalog useful for statistical studies of the masses, densities, and system architectures of exoplanetary systems. This work also serves as a data release for all previously unpublished RVs and associated stellar activity indicators obtained by our team for these systems, along with derived stellar and planet parameters. © 2025, CC BY.

关键词： NASA

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Commentaries on Viewpoint: A (Baker's) dozen tips for enhancing early-stage academic career development in biomedical research

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Journal of applied physiology (Bethesda, Md. : 1985) 2021年第5期131卷 1516-1519页

作者： Francesco Luciano Gaspare Pavei Luca Ruggiero Letizia Rasica Lucrezia Zuccarelli João Antônio Gesser Raimundo Rafael Alves de Aguiar Gopika SenthilKumar Michael J. Asmussen Nicholas D. J. Strzalkowski Sarah A. Hewitt Jared R. Fletcher Trevor A. Day Morten Hostrup Jørgen Jensen Steven J. Elmer Isaac J. Wedig Department of Pathophysiology and Transplantation University of Milan Milan Italy. Faculty of Kinesiology University of Calgary Calgary Alberta Canada. Department of Medicine University of Udine Udine Italy. Human Performance Research Group Center for Health and Sport Science Santa Catarina State University Florianópolis Brazil. Department of Physiology Department of Medical Scientist Training Program Medical College of Wisconsin Milwaukee Wisconsin. Department of Biology Faculty of Science and Technology Mount Royal University Calgary Alberta Canada. Department of Health and Physical Education Faculty of Health Community and Education Mount Royal University Calgary Alberta Canada. Section of Integrative Physiology Department of Nutrition Exercise and Sports University of Copenhagen Copenhagen Denmark. Department of Physical Performance Norwegian School of Sport Sciences Oslo Norway. Department of Kinesiology and Integrative Physiology Michigan Technological University Houghton Michigan. Health Research Institute Michigan Technological University Houghton Michigan.

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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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Erratum: Measurement of prompt and nonprompt charmonium suppression in PbPb collisions at 5.02 TeV

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The European physical Journal C 2023年第2期83卷 1-15页

作者： Sirunyan, A. M. Tumasyan, A. Adam, W. Ambrogi, F. Asilar, E. Bergauer, T. Brandstetter, J. Brondolin, E. Dragicevic, M. Erö, J. Valle, A. Escalante Del Flechl, M. Friedl, M. Frühwirth, R. Ghete, V. M. Grossmann, J. Hrubec, J. Jeitler, M. König, A. Krammer, N. Krätschmer, I. Liko, D. Madlener, T. Mikulec, I. Pree, E. Rad, N. Rohringer, H. Schieck, J. Schöfbeck, R. Spanring, M. Spitzbart, D. Waltenberger, W. Wittmann, J. Wulz, C.-E. Zarucki, M. Chekhovsky, V. Mossolov, V. Gonzalez, J. Suarez De Wolf, E. A. Croce, D. Di Janssen, X. Lauwers, J. De Klundert, M. Van Haevermaet, H. Van Mechelen, P. Van Remortel, N. Van Zeid, S. Abu Blekman, F. D’Hondt, J. De Bruyn, I. De Clercq, J. Deroover, K. Flouris, G. Lontkovskyi, D. Lowette, S. Marchesini, I. Moortgat, S. Moreels, L. Python, Q. Skovpen, K. Tavernier, S. Doninck, W. Van Mulders, P. Van Parijs, I. Van Beghin, D. Bilin, B. Brun, H. Clerbaux, B. De Lentdecker, G. Delannoy, H. Dorney, B. Fasanella, G. Favart, L. Goldouzian, R. Grebenyuk, A. Kalsi, A. K. Lenzi, T. Luetic, J. Maerschalk, T. Marinov, A. Seva, T. Starling, E. Velde, C. Vander Vanlaer, P. Vannerom, D. Yonamine, R. Zenoni, F. Cornelis, T. Dobur, D. Fagot, A. Gul, M. Khvastunov, I. Poyraz, D. Roskas, C. Salva, S. Tytgat, M. Verbeke, W. Zaganidis, N. Bakhshiansohi, H. Bondu, O. Brochet, S. Bruno, G. Caputo, C. Caudron, A. David, P. De Visscher, S. Delaere, C. Delcourt, M. Francois, B. Giammanco, A. Komm, M. Krintiras, G. Lemaitre, V. Magitteri, A. Mertens, A. Musich, M. Piotrzkowski, K. Quertenmont, L. Saggio, A. Marono, M. Vidal Wertz, S. Zobec, J. Júnior, W. L. Aldá Alves, F. L. Alves, G. A. Brito, L. Junior, M. Correa Martins Hensel, C. Moraes, A. Pol, M. E. Teles, P. Rebello Chagas, E. Belchior Batista Das Carvalho, W. Chinellato, J. Coelho, E. Da Costa, E. M. Da Silveira, G. G. De Jesus Damiao, D. De Souza, S. Fonseca Guativa, L. M. Huertas Malbouisson, H. De Almeida, M. Melo Herrera, C. Mora Mundim, L. Nogima, H. Rosas, L. J. Sanchez Santoro, A. Sznajder, A. Thiel, M. Manganote, E. J. Tonelli Da Silva De Yerevan Physics Institute Yerevan Armenia Institut für Hochenergiephysik Vienna Austria Vienna University of Technology Vienna Austria Institute for Nuclear Problems Minsk Belarus Universiteit Antwerpen Antwerpen Belgium Vrije Universiteit Brussel Brussels Belgium Université Libre de Bruxelles Brussels Belgium Ghent University Ghent Belgium IRFU CEA Université Paris-Saclay Gif-sur-Yvette France Université Catholique de Louvain Louvain-la-Neuve Belgium Centro Brasileiro de Pesquisas Fisicas Rio de Janeiro Brazil Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil Universidade Estadual de Campinas Campinas Brazil Universidade Federal de Pelotas Pelotas Brazil Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil Universidade Federal do ABC São Paulo Brazil Institute for Nuclear Research and Nuclear Energy Bulgarian Academy of Sciences Sofia Bulgaria University of Sofia Sofia Bulgaria Beihang University Beijing China Université Libre de Bruxelles Bruxelles Belgium Institute of High Energy Physics Beijing China State Key Laboratory of Nuclear Physics and Technology Peking University Beijing China Tsinghua University Beijing China Universidad de Los Andes Bogota Colombia Faculty of Electrical Engineering Mechanical Engineering and Naval Architecture University of Split Split Croatia Faculty of Science University of Split Split Croatia Institute Rudjer Boskovic Zagreb Croatia Institute for Theoretical and Experimental Physics Moscow Russia University of Cyprus Nicosia Cyprus Charles University Prague Czech Republic Joint Institute for Nuclear Research Dubna Russia Universidad San Francisco de Quito Quito Ecuador Academy of Scientific Research and Technology of the Arab Republic of Egypt Egyptian Network of High Energy Physics Cairo Egypt Fayoum University El-Fayoum Egypt Now at British University in Egypt Cairo Egypt Now at Ain Shams University Cairo Egypt National Institute of Chemical Physics and Biophysics Tallinn

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JCMT 850 µm continuum observations of density structures in the G35 molecular complex

arXiv

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arXiv 2024年

作者： Shen, Xianjin Liu, Hong-Li Ren, Zhiyuan Tej, Anandmayee Li, Di Liu, Hauyu Baobab Fuller, Gary A. Xie, Jinjin Jiao, Sihan Yang, Aiyuan Koch, Patrick M. Xu, Fengwei Sanhueza, Patricio Diep, Pham Ngoc Peretto, Nicolas Yadav, Ram K. Kramer, Busaba H. Sugiyama, Koichiro Rawlings, Mark G. Lee, Chang Won Tatematsu, Kenichi Harsono, Daniel Eden, David Kwon, Woojin Tsai, Chao-Wei White, Glenn J. Kim, Kee-Tae Liu, Tie Wang, Ke Zhang, Siju Jiao, Wenyu Yang, Dongting Swagat, R. Das Wu, Jingwen Wang, Chen School of Physics and Astronomy Yunnan University Kunming650091 China National Astronomical Observatories Chinese Academy of Sciences Datun Road A20 Beijing China CAS Key Laboratory of FAST NAOC Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China Indian Institute of Space Science and Technology Kerala Thiruvananthapuram695 547 India University of KwaZulu-Natal Durban4000 South Africa Department of Physics National Sun Yat-Sen University No. 70 Lien-Hai Road Kaohsiung City80424 Taiwan Center of Astronomy and Gravitation National Taiwan Normal University Taipei116 Taiwan Jodrell Bank Centre for Astrophysics School of Physics and Astronomy University of Manchester Oxford Road ManchesterM13 9PL United Kingdom Physikalisches Institut University of Cologne Zülpicher Str. 77 KölnD-50937 Germany Key Laboratory of Radio Astronomy and Technology Chinese Academy of Sciences A20 Datun Road Datun Road A20 Beijing China Max-Plank-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Academia Sinica Institute of Astronomy and Astrophysics No. 1 Sec. 4 Roosevelt Road Taipei10617 Taiwan Kavli Institute for Astronomy and Astrophysics Peking University 5 Yiheyuan Road Haidian District Beijing100871 China Department of Astronomy School of Physics Peking University Beijing100871 China National Astronomical Observatory of Japan National Institutes of Natural Sciences 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Astronomical Science Program The Graduate University for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Vietnam National Space Center Vietnam Academy of Science and Technology 18 Hoang Quoc Viet Hanoi Viet Nam Cardiff Hub for Astrophysics Research & Technology School of Physics & Astronomy Cardiff University Queens Buildings The Parade CardiffCF24 3AA United Kingdom Sirindhorn AstroPark 260 Moo 4 T. Donkaew A. Maerim Chiangmai50180 Thailand Gemini Observato

Filaments are believed to play a key role in high-mass star formation. We present a systematic study of the filaments and their hosting clumps in the G35 molecular complex using JCMT SCUBA-2 850 µm continuum data. We identified five clouds in the complex and 91 filaments within them, some of which form 10 hub-filament systems (HFSs), each with at least 3 hub-composing filaments. We also compiled a catalogue of 350 dense clumps, 183 of which are associated with the filaments. We investigated the physical properties of the filaments and clumps, such as mass, density, and size, and their relation to star formation. We find that the global mass-length trend of the filaments is consistent with a turbulent origin, while the hub-composing filaments of high line masses (ml > 230 M☉ pc−1) in HFSs deviate from this relation, possibly due to feedback from massive star formation. We also find that the most massive and densest clumps (R > 0.2 pc, M > 35 M☉, Σ > 0.05 g cm−2) are located in the filaments and in the hubs of HFS with the latter bearing a higher probability of occurrence of high-mass star-forming signatures, highlighting the preferential sites of HFSs for high-mass star formation. We do not find significant variation in the clump mass surface density across different evolutionary environments of the clouds, which may reflect the balance between mass accretion and stellar feedback. Copyright © 2024, The Authors. All rights reserved.

关键词： Giant stars

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Novel electrospun poly(ε-caprolactone)/type Ⅰ collagen nanofiber conduits for repair of peripheral nerve injury

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Neural Regeneration Research 2019年第9期14卷 1617-1625页

作者： Chun-Ming Yen Chiung-Chyi Shen Yi-Chin Yang Bai-Shuan Liu Hsu-Tung Lee Meei-Ling Sheu Meng-Hsiun Tsai Wen-Yu Cheng Department of Neurosurgery Neurological InstituteTaichung Veterans General HospitalTaichungTaiwanChina Ph.D.Program in Translational Medicine National Chung Hsing UniversityTaichungTaiwanChina Department of Physical Therapy Hungkuang UniversityTaichungTaiwanChina Basic Medical Education Center Central Taiwan University of Science and TechnologyTaichungTaiwanChina Department of Medical Imaging and Radiological Sciences Central Taiwan University of Science and TechnologyTaichungTaiwanChina Institute of Biomedical Sciences National Chung Hsing UniversityTaichungTaiwanChina Department of Medical Research Taichung Veterans General HospitalTaichungTaiwanChina Rong Hsing Research Center for Translational Medicine National Chung Hsing UniversityTaichungTaiwanChina Department of Management Information System National Chung Hsing UniversityTaichungTaiwanChina

Recent studies have shown the potential of artificially synthesized conduits in the repair of peripheral nerve injury. Natural biopolymers have received much attention because of their biocompatibility. To investigate the effects of novel electrospun absorbable poly(ε-caprolactone)/type Ⅰ collagen nanofiber conduits(biopolymer nanofiber conduits) on the repair of peripheral nerve injury, we bridged 10-mm-long sciatic nerve defects with electrospun absorbable biopolymer nanofiber conduits, poly(ε-caprolactone) or silicone conduits in Sprague-Dawley rats. Rat neurologica1 function was weekly evaluated using sciatic function index within8 weeks after repair. Eight weeks after repair, sciatic nerve myelin sheaths and axon morphology were observed by osmium tetroxide staining, hematoxylin-eosin staining, and transmission electron microscopy.S-100(Schwann cell marker) and CD4(inflammatory marker) immunoreactivities in sciatic nerve were detected by immunohistochemistry. In rats subjected to repair with electrospun absorbable biopolymer nanofiber conduits, no serious inflammatory reactions were observed in rat hind limbs, the morphology of myelin sheaths in the injured sciatic nerve was close to normal. CD4 immunoreactivity was obviously weaker in rats subjected to repair with electrospun absorbable biopolymer nanofiber conduits than in those subjected to repair with poly(ε-caprolactone) or silicone. Rats subjected to repair with electrospun absorbable biopolymer nanofiber conduits tended to have greater sciatic nerve function recovery than those receiving poly(ε-caprolactone) or silicone repair. These results suggest that electrospun absorbable poly(ε-caprolactone)/type Ⅰ collagen nanofiber conduits have the potential of repairing sciatic nerve defects and exhibit good biocompatibility. All experimental procedures were approved by Institutional Animal Care and Use Committee of Taichung Veteran General Hospital, Taiwan, China(La-1031218) on October 2, 2014.

关键词： poly(ε-caprolactone) type Ⅰ collagen electrospinning sciatic nerve nerve conduit immunohistostaining walking track analysis peripheral nerve injury

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Serum Arachidonic Acid Oxylipins Indicate Small Vessel Injury And the Related Executive Function Decline In Stroke Patients

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Alzheimer's & Dementia 2023年第S15期19卷

作者： Di Yu Nuanyi Liang Lisa Y. Xiong Qing Shen William Z. Lin Miracle Ozzoude Maged Goubran Jennifer S. Rabin Joel Ramirez Sean Symons Seyyed MH Haddad Brian Tan Nuwan D. Nanayakkara Allison Ann Dilliott Malcolm Binns Derek Beaton Stephen R. Arnott Jane M Lawrenece-Dewar Demetrios J. Sahlas Leanne Casaubon Yurika Otoki Krista L. Lanctôt Mario Masellis Richard H. Swartz Ameer Y. Taha Walter Swardfager The ONDRI Investigators Department of Pharmacology and Toxicology University of Toronto Toronto ON Canada Sandra Black Centre for Brain Resilience and Recovery Sunnybrook Research Institute Toronto ON Canada Correspondece University of California Davis Davis CA USA Physical Sciences Platform Sunnybrook Research Institute University of Toronto Toronto ON Canada Department of Medical Biophysics University of Toronto Toronto ON Canada Harquail Centre for Neuromodulation Sunnybrook Research Institute Toronto ON Canada Division of Neurology Department of Medicine University of Toronto Toronto ON Canada Rehabilitation Sciences Institute University of Toronto Toronto ON Canada Physical Sciences Sunnybrook Research Institute Toronto ON Canada Hurvitz Brain Sciences Program Sunnybrook Research Institute Toronto ON Canada University of Toronto Toronto ON Canada Robarts Research Institute London ON Canada Rotman Research Institute Toronto ON Canada University of Western Ontario London ON Canada Western University London ON Canada Data Science & Advanced Analytics St. Michael’s Hospital Unity Health Toronto Toronto ON Canada Baycrest Hospital Toronto ON Canada Thunder Bay Regional Health Research Institute Northern Ontario School of Medicine University Thunder Bay ON Canada Department of Medicine McMaster University Hamilton ON Canada Division of Agricultural Chemistry Graduate School of Agricultural Science Tohoku University Sendai Tohoku Japan Department of Psychiatry Temerty Faculty of Medicine University of Toronto Toronto ON Canada Toronto Rehabilitation Institute Toronto ON Canada

Background Cerebral small vessel disease (SVD) frequently co-occurs with other neurodegenerative pathologies and collectively lead to cognitive deficits. Previously, we found that the ratios of soluble epoxide hydrolase (sEH)- derived diols to the parent epoxides (generated by CYP2J/2Cs) linoleic acids were associated with greater white matter hyperintensities (WMH) and poorer executive function in patients with transient ischemic attack. However, the associations with the diol and epoxide species derived from arachidonic acid (AA) have not been explored. Methods The study cohort is comprised of 159 stroke patients (mean age = 69.2, 32.1% female) from the Ontario Neurodegenerative Degenerative Research Initiative. EpETrEs (AA epoxides) and DiHETrEs (AA diols) were quantified by a targeted ultrahigh pressure liquid chromatography mass spectrometry (UPLC-MS/MS). Executive function was assessed using a composite score that included Digit Symbol Substitution Test (DSST), Trial-Making Test Part B, Stroop Color-Word Interference Test, and FAS Verbal Fluency Test. WMHs were quantified from T2-Fluid-Attenuated-Inversion-Recovery MRI through Lesion Explorer (https://***/***).In linear models controlling for age, sex, education or age, sex, glucose, cholesterol, and waist circumferences were used for cognitive and imaging out comes, respectively. Results 11(12)-EpETrE was found to be associated with less WHM (ρ = -0.175, p = 0.040) and better executive function (ρ = 0.166, p = 0.039). In a sub-cohort of patients with small vessel stroke (n = 50), the relationship between WMH and 11(12)-EpETrE became stronger (ρ = -0.390, p = 0.014). 14(15)-EpETrE was also associated with less WMH (ρ = -0.416, p = 0.009). Similar relationships were not seen with the diols or diol to epoxide ratios. Conclusions Oxylipins derived from sEH activity may be potential biomarkers of vascular cognitive impairment and small vessel disease in stroke patients.

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Optical force-induced nonlinearity and self-guiding of light in human red blood cell suspensions

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Light(science & Applications) 2019年第1期8卷 927-935页

作者： Rekha Gautam Yinxiao Xiang Josh Lamstein Yi Liang Anna Bezryadina Guo Liang Tobias Hansson Benjamin Wetzel Daryl Preece Adam White Matthew Silverman Susan Kazarian Jingjun Xu Roberto Morandotti Zhigang Chen Department of Physics and Astronomy San Francisco State UniversitySan FranciscoCA 94132USA Department of Biomedical Engineering Vanderbilt UniversityNashvilleTN 37240USA MOE Key Lab of Weak-Light Nonlinear Photonics TEDA Applied Physics Institute and School of PhysicsNankai UniversityTianjin 300457China Guangxi Key Lab for Relativistic Astrophysics Guangxi Colleges and Universities Key Lab of Novel Energy Materials and Related TechnologySchool of Physical Science and TechnologyGuangxi UniversityNanningGuangxi 530004China Department of Physics and Astronomy California State University NorthridgeNorthridgeCA 91330USA Institut National de la Recherche Scientifique Universite du QuebecVarennesQC J3X 1S2Canada Department of Physics Chemistry and BiologyLinkoping UniversityLinkoping SE-58183Sweden School of Mathematical and Physical Sciences University of SussexSussex HouseFalmerBrighton BN19RHUK Department of Biomedical Engineering University of California IrvineIrvineCAUSA Clinical Laboratory Science Program San Francisco State UniversitySan FranciscoCA 94132USA Institute of Fundamental and Frontier Sciences University of Electronic Science and Tech.of ChinaChengdu 610054China ITMO University Saint Petersburg 197101Russia

Osmotic conditions play an important role in the cell properties of human red blood cells(RBCs),which are crucial for the pathological analysis of some blood diseases such as *** the past decades,numerous efforts have mainly focused on the study of the RBC biomechanical properties that arise from the unique deformability of ***,we demonstrate nonlinear optical effects from human RBCs suspended in different osmotic ***,we observe self-trapping and scattering-resistant nonlinear propagation of a laser beam through RBC suspensions under all three osmotic conditions,where the strength of the optical nonlinearity increases with osmotic pressure on the *** tunable nonlinearity is attributed to optical forces,particularly the forward-scattering and gradient ***,in aged blood samples(with lysed cells),a notably different nonlinear behavior is observed due to the presence of free *** use a theoretical model with an optical force-mediated nonlocal nonlinearity to explain the experimental *** work on light self-guiding through scattering biosoft-matter may introduce new photonic tools for noninvasive biomedical imaging and medical diagnosis.

关键词： nonlinearity suspensions nonlinear

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Enhanced Deuteron Coalescence Probability in Jets

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physical Review Letters 2023年第4期131卷 042301-042301页

作者： S. Acharya D. Adamová A. Adler G. Aglieri Rinella M. Agnello N. Agrawal Z. Ahammed S. Ahmad S. U. Ahn I. Ahuja A. Akindinov M. Al-Turany D. Aleksandrov B. Alessandro H. M. Alfanda R. Alfaro Molina B. Ali A. Alici N. Alizadehvandchali A. Alkin J. Alme G. Alocco T. Alt I. Altsybeev M. N. Anaam C. Andrei A. Andronic V. Anguelov F. Antinori P. Antonioli N. Apadula L. Aphecetche H. Appelshäuser C. Arata S. Arcelli M. Aresti R. Arnaldi J. G. M. C. A. Arneiro I. C. Arsene M. Arslandok A. Augustinus R. Averbeck M. D. Azmi A. Badalà J. Bae Y. W. Baek X. Bai R. Bailhache Y. Bailung A. Balbino A. Baldisseri B. Balis D. Banerjee Z. Banoo R. Barbera F. Barile L. Barioglio M. Barlou G. G. Barnaföldi L. S. Barnby V. Barret L. Barreto C. Bartels K. Barth E. Bartsch N. Bastid S. Basu G. Batigne D. Battistini B. Batyunya D. Bauri J. L. Bazo Alba I. G. Bearden C. Beattie P. Becht D. Behera I. Belikov A. D. C. Bell Hechavarria F. Bellini R. Bellwied S. Belokurova V. Belyaev G. Bencedi S. Beole A. Bercuci Y. Berdnikov A. Berdnikova L. Bergmann M. G. Besoiu L. Betev P. P. Bhaduri A. Bhasin M. A. Bhat B. Bhattacharjee L. Bianchi N. Bianchi J. Bielčík J. Bielčíková J. Biernat A. P. Bigot A. Bilandzic G. Biro S. Biswas N. Bize J. T. Blair D. Blau M. B. Blidaru N. Bluhme C. Blume G. Boca F. Bock T. Bodova A. Bogdanov S. Boi J. Bok L. Boldizsár A. Bolozdynya M. Bombara P. M. Bond G. Bonomi H. Borel A. Borissov A. G. Borquez Carcamo H. Bossi E. Botta Y. E. M. Bouziani L. Bratrud P. Braun-Munzinger M. Bregant M. Broz G. E. Bruno M. D. Buckland D. Budnikov H. Buesching S. Bufalino O. Bugnon P. Buhler Z. Buthelezi S. A. Bysiak M. Cai H. Caines A. Caliva E. Calvo Villar J. M. M. Camacho P. Camerini F. D. M. Canedo M. Carabas A. A. Carballo F. Carnesecchi R. Caron L. A. D. Carvalho J. Castillo Castellanos F. Catalano C. Ceballos Sanchez I. Chakaberia P. Chakraborty S. Chandra S. Chapeland M. Chartier S. Chattopadhyay T. G. Chavez T. Cheng C. Cheshkov B. Cheynis V. Chibante Barroso D. D. Chinellato E. S. Chizzali J. Cho S. Cho P. Chochula P. Chri Université Clermont Auvergne CNRS/IN2P3 LPC Clermont-Ferrand France Nuclear Physics Institute of the Czech Academy of Sciences Husinec-Řež Czech Republic Johann-Wolfgang-Goethe Universität Frankfurt Institut für Informatik Fachbereich Informatik und Mathematik Frankfurt Germany European Organization for Nuclear Research (CERN) Geneva Switzerland Dipartimento DISAT del Politecnico and Sezione INFN Turin Italy INFN Sezione di Bologna Bologna Italy Variable Energy Cyclotron Centre Homi Bhabha National Institute Kolkata India Department of Physics Aligarh Muslim University Aligarh India Korea Institute of Science and Technology Information Daejeon Republic of Korea Faculty of Science P.J. Šafárik University Košice Slovak Republic Affiliated with an institute covered by a cooperation agreement with CERN Research Division and ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH Darmstadt Germany INFN Sezione di Torino Turin Italy Central China Normal University Wuhan China Instituto de Física Universidad Nacional Autónoma de México Mexico City Mexico Dipartimento di Fisica e Astronomia dell’Università and Sezione INFN Bologna Italy University of Houston Houston Texas United States Department of Physics and Technology University of Bergen Bergen Norway INFN Sezione di Cagliari Cagliari Italy Institut für Kernphysik Johann Wolfgang Goethe-Universität Frankfurt Frankfurt Germany Horia Hulubei National Institute of Physics and Nuclear Engineering Bucharest Romania Westfälische Wilhelms-Universität Münster Institut für Kernphysik Munster Germany Physikalisches Institut Ruprecht-Karls-Universität Heidelberg Heidelberg Germany INFN Sezione di Padova Padova Italy Lawrence Berkeley National Laboratory Berkeley California United States SUBATECH IMT Atlantique Nantes Université CNRS-IN2P3 Nantes France Laboratoire de Physique Subatomique et de Cosmologie Université Grenoble-Alpes CNRS-IN2P3 Grenoble France Universidade de São Pa

The transverse-momentum (pT) spectra and coalescence parameters B2 of (anti)deuterons are measured in p-p collisions at s=13 TeV for the first time in and out of jets. In this measurement, the direction of the leading particle with the highest pT in the event (pTlead>5 GeV/c) is used as an approximation for the jet axis. The event is consequently divided into three azimuthal regions, and the jet signal is obtained as the difference between the toward region, that contains jet fragmentation products in addition to the underlying event (UE), and the transverse region, which is dominated by the UE. The coalescence parameter in the jet is found to be approximately a factor of 10 larger than that in the underlying event. This experimental observation is consistent with the coalescence picture and can be attributed to the smaller average phase-space distance between nucleons in the jet cone as compared with the underlying event. The results presented in this Letter are compared to predictions from a simple nucleon coalescence model, where the phase-space distributions of nucleons are generated using pythia8 with the Monash 2013 tuning, and to predictions from a deuteron production model based on ordinary nuclear reactions with parametrized energy-dependent cross sections tuned on data. The latter model is implemented in pythia8.3. Both models reproduce the observed large difference between in-jet and out-of-jet coalescence parameters, although the almost flat trend of the B2Jet is not reproduced by the models, which instead give a decreasing trend.

关键词： Hadron-hadron interactions

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