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First Constraints on the Epoch of Reionization Using the non-Gaussianity of the Kinematic Sunyaev-Zel’dovich Effect from the South Pole Telescope and Herschel-SPIRE Observations

arXiv

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arXiv 2024年

作者： Raghunathan, S. Ade, P.A.R. Anderson, A.J. Ansarinejad, B. Archipley, M. Austermann, J.E. Balkenhol, L. Beall, J.A. Benabed, K. Bender, A.N. Benson, B.A. Bianchini, F. Bleem, L.E. Bock, J. Bouchet, F.R. Bryant, L. Camphuis, E. Carlstrom, J.E. Cecil, T.W. Chang, C.L. Chaubal, P. Chiang, H.C. Chichura, P.M. Chou, T.-L. Citron, R. Coerver, A. Crawford, T.M. Crites, A.T. Cukierman, A. Daley, C. Dibert, K.R. Dobbs, M.A. Doussot, A. Dutcher, D. Everett, W. Feng, C. Ferguson, K.R. Fichman, K. Foster, A. Galli, S. Gallicchio, J. Gambrel, A.E. Gardner, R.W. Ge, F. George, E.M. Goeckner-Wald, N. Gualtieri, R. Guidi, F. Guns, S. Gupta, N. de Haan, T. Halverson, N.W. Hivon, E. Holder, G.P. Holzapfel, W.L. Hood, J.C. Hrubes, J.D. Hryciuk, A. Huang, N. Hubmayr, J. Irwin, K.D. Kéruzoré, F. Khalife, A.R. Knox, L. Korman, M. Kornoelje, K. Kuo, C.-L. Lee, A.T. Levy, K. Li, D. Lowitz, A.E. Lu, C. Maniyar, A. Martsen, E.S. McMahon, J.J. Menanteau, F. Millea, M. Montgomery, J. Moran, C. Corbett Nakato, Y. Natoli, T. Nibarger, J.P. Noble, G.I. Novosad, V. Omori, Y. Padin, S. Pan, Z. Paschos, P. Patil, S. Phadke, K.A. Prabhu, K. Pryke, C. Quan, W. Rahimi, M. Rahlin, A. Reichardt, C.L. Rouble, M. Ruhl, J.E. Saliwanchik, B.R. Schaffer, K.K. Schiappucci, E. Sievers, C. Smecher, G. Sobrin, J.A. Stark, A.A. Stephen, J. Suzuki, A. Tandoi, C. Thompson, K.L. Thorne, B. Trendafilova, C. Tucker, C. Umilta, C. Veach, T. Vieira, J.D. Viero, M.P. Wan, Y. Wang, G. Whitehorn, N. Wu, W.L.K. Yefremenko, V. Young, M.R. Zebrowski, J.A. Zemcov, M. Center for AstroPhysical Surveys National Center for Supercomputing Applications UrbanaIL61801 United States School of Physics and Astronomy Cardiff University CardiffCF24 3YB United Kingdom Fermi National Accelerator Laboratory MS209 P.O. Box 500 BataviaIL60510 United States Kavli Institute for Cosmological Physics University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States Department of Astronomy and Astrophysics University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States School of Physics University of Melbourne ParkvilleVIC3010 Australia Department of Astronomy University of Illinois Urbana-Champaign 1002 West Green Street UrbanaIL61801 United States NIST Quantum Devices Group 325 Broadway Mailcode 817.03 BoulderCO80305 United States Department of Physics University of Colorado BoulderCO80309 United States Institut d’Astrophysique de Paris UMR 7095 CNRS & Sorbonne Université 98 bis boulevard Arago Paris75014 France High-Energy Physics Division Argonne National Laboratory 9700 South Cass Avenue. LemontIL60439 United States Kavli Institute for Particle Astrophysics and Cosmology Stanford University 452 Lomita Mall StanfordCA94305 United States Department of Physics Stanford University 382 Via Pueblo Mall StanfordCA94305 United States SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo ParkCA94025 United States California Institute of Technology PasadenaCA91125 United States Jet Propulsion Laboratory California Institute of Technology PasadenaCA91109 United States Enrico Fermi Institute University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States Department of Physics University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States Department of Physics McGill Space Institute McGill University 3600 Rue University MontrealQCH3A 2T8 Canada School of Mathematics Statistics & Computer Science University of KwaZulu-Natal Durban South Africa Unive

We report results from an analysis aimed at detecting the trispectrum of the kinematic Sunyaev-Zel’dovich (kSZ) effect by combining data from the South Pole Telescope (SPT) and Herschel-SPIRE experiments over a 100 deg2 field. The SPT observations combine data from the previous and current surveys, namely SPTpol and SPT-3G, to achieve depths of 4.5, 3, and 16 µK-arcmin in bands centered at 95, 150, and 220 GHz. For SPIRE, we include data from the 600 and 857 GHz bands. We reconstruct the velocity-induced large-scale correlation of the small-scale kSZ signal with a quadratic estimator that uses two cosmic microwave background (CMB) temperature maps, constructed by optimally combining data from all the frequency bands. We reject the null hypothesis of a zero trispectrum at 10.3σ level. However, the measured trispectrum contains contributions from both the kSZ and other undesired components, such as CMB lensing and astrophysical foregrounds, with kSZ being sub-dominant. We use the Agora simulations to estimate the expected signal from CMB lensing and astrophysical foregrounds. After accounting for the contributions from CMB lensing and foreground signals, we do not detect an excess kSZ-only trispectrum and use this non-detection to set constraints on reionization. By applying a prior based on observations of the Gunn-Peterson trough, we obtain an upper limit on the duration of reionization of (formula presented). We find these constraints are fairly robust to foregrounds assumptions. This trispectrum measurement is independent of, but consistent with, Planck’s optical depth measurement. This result is the first constraint on the epoch of reionization using the non-Gaussian nature of the kSZ signal. © 2024, CC BY.

关键词： Kinematics

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Harmonized-Multinational qEEG norms (HarMNqEEG)

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NEUROIMAGE 2022年 256卷 119190-119190页

作者： Li, Min Wang, Ying Lopez-Naranjo, Carlos Hu, Shiang Reyes, Ronaldo Cesar Garcia Paz-Linares, Deirel Areces-Gonzalez, Ariosky Hamid, Aini Ismafairus Abd Evans, Alan C. Savostyanov, Alexander N. Calzada-Reyes, Ana Villringer, Arno Tobon-Quintero, Carlos A. Garcia-Agustin, Daysi Yao, Dezhong Dong, Li Aubert-Vazquez, Eduardo Reza, Faruque Razzaq, Fuleah Abdul Omar, Hazim Abdullah, Jafri Malin Galler, Janina R. Ochoa-Gomez, John F. Prichep, Leslie S. Galan-Garcia, Lidice Morales-Chacon, Lilia Valdes-Sosa, Mitchell J. Trondle, Marius Zulkifly, Mohd Faizal Mohd Rahman, Muhammad Riddha Bin Abdul Milakhina, Natalya S. Langer, Nicolas Rudych, Pavel Koenig, Thomas Virues-Alba, Trinidad A. Lei, Xu Bringas-Vega, Maria L. Bosch-Bayard, Jorge F. Valdes-Sosa, Pedro Antonio [a]The Clinical Hospital of Chengdu Brain Science Institute MOE Key Lab for Neuroinformation School of Life Science and Technology University of Electronic Science and Technology of China Chengdu China [b]Cuban Center for Neurocience La Habana Cuba [c]McGill Centre for Integrative Neuroscience Ludmer Centre for Neuroinformatics and Mental Health Montreal Neurological Institute Canada [d]Department of Neurosciences School of Medical Sciences Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [e]Brain and Behaviour Cluster School of Medical Sciences Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [f]Hospital Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [g]Humanitarian Institute Novosibirsk State University Novosibirsk 630090 Russia [h]Laboratory of Psychophysiology of Individual Differences Federal State Budgetary Scientific Institution Scientific Research Institute of Neurosciences and Medicine Novosibirsk 630117 Russia [i]Laboratory of Psychological Genetics at the Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russia [j]University of Pinar del Río “Hermanos Saiz Montes de Oca” Pinar del Río Cuba [k]Department of Neurology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany [l]Department of Cognitive Neurology University Hospital Leipzig Leipzig Germany [m]Center for Stroke Research Charité-Universitätsmedizin Berlin Berlin Germany [n]Grupo Neuropsicología y Conducta - GRUNECO Faculty of Medicine Universidad de Antioquia Colombia [o]Research Department Institución Prestadora de Servicios de Salud IPS Universitaria Colombia [p]The Cuban center aging longevity and health Havana Cuba [q]Research Unit of NeuroInformation Chinese Academy of Medical Sciences Chengdu 2019RU035 China [r]School of Electrical Engineering Zhengzhou University Zhengzhou 4500

This paper extends frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. (i) Create lifespan Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross spectral tensors were shared. After visual and automatic quality control, developmental equations for the mean and standard deviation of qEEG traditional and Riemannian DPs were calculated using additive mixed-effects models. We demonstrate qEEG "batch effects " and provide methods to calculate harmonized z-scores. (ii) We also show that harmonized Riemannian norms produce z-scores with increased diagnostic accuracy predicting brain dysfunction produced by malnutrition in the first year of life and detecting COVID induced brain dysfunction. (iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.

关键词： Quantitative EEG EEG cross-spectrum Riemannian geometry Batch effects Z-score Harmonization Malnutrition Covid induced brain dysfunction Developmental Brain Chart

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QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

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Current Protocols in Bioinformatics 2020年第1期70卷 e100页

作者： Estaki, Mehrbod Jiang, Lingjing Bokulich, Nicholas A. McDonald, Daniel González, Antonio Kosciolek, Tomasz Martino, Cameron Zhu, Qiyun Birmingham, Amanda Vázquez-Baeza, Yoshiki Dillon, Matthew R. Bolyen, Evan Caporaso, J. Gregory Knight, Rob Department of Pediatrics University of California San Diego La Jolla CA United States Division of Biostatistics University of California San Diego La Jolla CA United States Center for Applied Microbiome Science Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ United States Department of Biological Sciences Northern Arizona University Flagstaff AZ United States Małopolska Centre of Biotechnology Jagiellonian University Kraków Poland Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA United States Center for Microbiome Innovation University of California San Diego La Jolla CA United States Center for Computational Biology and Bioinformatics University of California San Diego La Jolla CA United States Jacobs School of Engineering University of California San Diego La Jolla CA United States Department of Computer Science and Engineering University of California San Diego La Jolla CA United States Department of Bioengineering University of California San Diego La Jolla CA United States

QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open-source web-based platform, to re-use available data for meta-analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug-ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses—e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta-analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://***. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://***. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data. Support Protocol: Further microbiome analyses. © 2020 The Authors.

关键词： bioinformatics metagenomics microbiome QIIME 2 Qiita

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Measurements of the Temperature and E-mode Polarization of the Cosmic Microwave Background from the Full 500-square-degree SPTpol Dataset

arXiv

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arXiv 2025年

作者： Chou, T.-L. Ade, P.A.R. Anderson, A.J. Austermann, J.E. Balkenhol, L. Beall, J.A. Bender, A.N. Benson, B.A. Bianchini, F. Bleem, L.E. Carlstrom, J.E. Chang, C.L. Chaubal, P. Chiang, H.C. Citron, R. Moran, C. Corbett Crawford, T.M. Crites, A.T. de Haan, T. Dobbs, M.A. Dutcher, D. Everett, W. Gallicchio, J. George, E.M. Gupta, N. Halverson, N.W. Holder, G.P. Holzapfel, W.L. Hrubes, J.D. Huang, N. Hubmayr, J. Irwin, K.D. Knox, L. Lee, A.T. Li, D. Lowitz, A. McMahon, J.J. Montgomery, J. Natoli, T. Nibarger, J.P. Noble, G.I. Novosad, V. Omori, Y. Padin, S. Patil, S. Pryke, C. Quan, W. Reichardt, C.L. Ruhl, J.E. Saliwanchik, B.R. Schaffer, K.K. Sievers, C. Smecher, G. Stark, A.A. Tucker, C. Veach, T. Vieira, J.D. Wang, G. Whitehorn, N. Wu, W.L.K. Yefremenko, V. Zebrowski, J.A. Department of Astronomy and Astrophysics University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States Kavli Institute for Cosmological Physics University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States Cardiff University CardiffCF10 3XQ United Kingdom Fermi National Accelerator Laboratory MS209 P.O. Box 500 BataviaIL60510 United States NIST Quantum Devices Group 325 Broadway Mailcode 817.03 BoulderCO80305 United States Department of Physics University of Colorado BoulderCO80309 United States Sorbonne Universit’e CNRS UMR 7095 Institut d’Astrophysique de Paris 98 bis bd Arago Paris75014 France High Energy Physics Division Argonne National Laboratory 9700 S. Cass Avenue ArgonneIL60439 United States SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo ParkCA94025 United States Department of Physics University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States Enrico Fermi Institute University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States School of Physics University of Melbourne ParkvilleVIC3010 Australia Department of Physics McGill University 3600 Rue University MontrealQCH3A 2T8 Canada School of Mathematics Statistics & Computer Science University of KwaZulu-Natal Durban South Africa University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States Jet Propulsion Laboratory PasadenaCA91109 United States Department of Physics Cornell University IthacaNY United States Department of Astronomy Cornell University IthacaNY United States Department of Physics University of California BerkeleyCA94720 United States Physics Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Ibaraki Tsukuba305-0801 Japan Canadian Institute for Advanced Research CIFAR Program in Gravity and the Extreme Universe TorontoONM5G 1Z8 Canada Joseph Henry Laboratories of Physics Jadwin Hall Princeton University PrincetonNJ08544

Using the full four-year SPTpol 500 deg2 dataset in both the 95 GHz and 150 GHz frequency bands, we present measurements of the temperature and E-mode polarization of the cosmic microwave background (CMB), as well as the E-mode polarization auto-power spectrum (EE) and temperature-E-mode cross-power spectrum (TE) in the angular multipole range 50 0 = 70.48 ± 2.16 km s−1 Mpc−1 and Ωm = 0.271 ± 0.026, when using only the SPTpol data and a Planck-based prior on the optical depth to reionization. The ΛCDM parameter constraints are consistent across the 95 GHz-only, 150 GHz-only, TE-only, and EE-only data splits. Between the 1000 data splits, the ΛCDM parameter constraints are borderline consistent at the ∼ 2σ level. This consistency improves when including a parameter AL, the degree of lensing of the CMB inferred from the smearing of acoustic peaks. When marginalized over AL, the ΛCDM parameter constraints from SPTpol are consistent with those from Planck. The power spectra presented here are the most sensitive measurements of the lensed CMB damping tail to date for roughly > 1700 in TE and > 2000 in EE. Copyright © 2025, The Authors. All rights reserved.

关键词： Cosmology

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Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation

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Nature biotechnology 2023年第11期41卷 1656页

作者： Julia M Gauglitz Kiana A West Wout Bittremieux Candace L Williams Kelly C Weldon Morgan Panitchpakdi Francesca Di Ottavio Christine M Aceves Elizabeth Brown Nicole C Sikora Alan K Jarmusch Cameron Martino Anupriya Tripathi Michael J Meehan Kathleen Dorrestein Justin P Shaffer Roxana Coras Fernando Vargas Lindsay DeRight Goldasich Tara Schwartz MacKenzie Bryant Gregory Humphrey Abigail J Johnson Katharina Spengler Pedro Belda-Ferre Edgar Diaz Daniel McDonald Qiyun Zhu Emmanuel O Elijah Mingxun Wang Clarisse Marotz Kate E Sprecher Daniela Vargas-Robles Dana Withrow Gail Ackermann Lourdes Herrera Barry J Bradford Lucas Maciel Mauriz Marques Juliano Geraldo Amaral Rodrigo Moreira Silva Flavio Protasio Veras Thiago Mattar Cunha Rene Donizeti Ribeiro Oliveira Paulo Louzada-Junior Robert H Mills Paulina K Piotrowski Stephanie L Servetas Sandra M Da Silva Christina M Jones Nancy J Lin Katrice A Lippa Scott A Jackson Rima Kaddurah Daouk Douglas Galasko Parambir S Dulai Tatyana I Kalashnikova Curt Wittenberg Robert Terkeltaub Megan M Doty Jae H Kim Kyung E Rhee Julia Beauchamp-Walters Kenneth P Wright Maria Gloria Dominguez-Bello Mark Manary Michelli F Oliveira Brigid S Boland Norberto Peporine Lopes Monica Guma Austin D Swafford Rachel J Dutton Rob Knight Pieter C Dorrestein Collaborative Mass Spectrometry Innovation Center University of California San Diego La Jolla CA USA. Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA. Beckman Center for Conservation Research San Diego Zoo Wildlife Alliance Escondido CA USA. Center for Microbiome Innovation Joan and Irwin Jacobs School of Engineering University of California San Diego La Jolla CA USA. Division of Biological Sciences University of California San Diego La Jolla CA USA. Department of Pediatrics School of Medicine University of California San Diego La Jolla CA USA. Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Division of Rheumatology Allergy & Immunology Department of Medicine University of California San Diego La Jolla CA USA. Division of Epidemiology and Community Health School of Public Health University of Minnesota Minneapolis MN USA. Department of Integrative Physiology University of Colorado Boulder Boulder CO USA. Department of Population Health Sciences University of Wisconsin-Madison Madison WI USA. Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar Puerto Ayacucho Amazonas Venezuela. Department of Pediatrics Billings Clinic Billings MT USA. Department of Animal Science Michigan State University East Lansing MI USA. Department of Pharmacology Ribeirão Preto Medicinal School Center of Research in Inflammatory Diseases University of São Paulo Ribeirão Preto Sao Paolo Brazil. Multidisciplinary Health Institute Federal University of Bahia Vitória da Conquista Bahia Brazil. NPPNS Department of Biomolecular Sciences School of Pharmaceutical Sciences of Ribeirão Preto University of São Paulo Ribeirão Preto Sao Paolo Brazil. Department of Internal Medicine Ribeirão Preto Medical School Center of Research in Inflammatory Diseases University of São Paulo Ribeirão Preto Sao Paolo Brazil. Department

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Combination of curcumin or chitosan with photodynamic therapy as an effective alternative therapy for overcoming wound infection associated with multidrug-resistant Acinetobacter baumannii

Microbe (Netherlands)

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Microbe (Netherlands) 2025年 7卷

作者： Yonpiam, Manta Wannigama, Dhammika Leshan Shein, Aye Mya Sithu Liao, Tingting Hurst, Cameron Monk, Peter N. Amarasiri, Mohan Phattharapornjaroen, Phatthranit Ounjai, Puey Saethang, Thammakorn Badavath, Vishnu Nayak Luk-in, Sirirat Nilgate, Sumanee Rirerm, Ubolrat Srisakul, Sukrit Ngamwongsatit, Natharin Leelahavanichkul, Asada Ragupathi, Naveen Kumar Devanga Kanjanabuch, Talerngsak Narkban, Phurin Miyanaga, Kazuhiko Cui, Longzhu Boontaveeyuwat, Einapak Higgins, Paul G. Kicic, Anthony Hamamoto, Hiroshi Abe, Shuichi Hongsing, Parichart Chatsuwan, Tanittha Department of Microbiology Faculty of Medicine Chulalongkorn University King Chulalongkorn Memorial Hospital Thai Red Cross Society Bangkok Thailand Center of Excellence in Antimicrobial Resistance and Stewardship Research Faculty of Medicine Chulalongkorn University Bangkok Thailand Dual degree Medical Science program Faculty of Medicine Chulalongkorn University Bangkok 10330 Thailand Department of Infectious Diseases and Infection Control Yamagata Prefectural Central Hospital Yamagata Japan School of Medicine Faculty of Health and Medical Sciences The University of Western Australia Nedlands WA Australia Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries The University of Sheffield Sheffield United Kingdom Pathogen Hunter's Research Team Department of Infectious Diseases and Infection Control Yamagata Prefectural Central Hospital Yamagata Japan Department of Infectious Diseases Faculty of Medicine Yamagata University Yamagata Japan Department of Clinical Epidemiology Faculty of Medicine Thammasat University Rangsit 10120 Thailand Center of Excellence in Applied Epidemiology Thammasat University Rangsit 10120 Thailand Department of Infection Immunity & Cardiovascular Disease University of Sheffield Medical School United Kingdom Department of Civil and Environmental Engineering Graduate School of Engineering Tohoku University Miyagi Japan Faculty of Health Science Technology Chulabhorn Royal Academy Bangkok 10210 Thailand HRH Princess Chulabhorn Disaster and Emergency Medicine Center Chulabhorn Royal Academy Bangkok 10210 Thailand Department of Biology Faculty of Science Mahidol University Bangkok Thailand Department of Computer Science Faculty of Science Kasetsart University Bangkok Thailand School of Pharmacy & Technology Management SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Hyderabad 509301 India Department of Clinical Microbiology and Applied Technology Faculty of Medical Technology Mahidol Unive

The increasing prevalence of multidrug-resistant Acinetobacter baumannii as an opportunistic pathogen in wound infections raises significant concerns due to its antibiotic resistance and biofilm-mediated antibiotic tolerance. This underscores the urgent need to explore an alternative approach to effectively managing wound infections caused by MDR A. baumannii. In this study, combining subinhibitory concentrations of curcumin (25 µg/ml) or chitosan (156 µg/ml) with photodynamic therapy-PDT (10 J/cm2) resulted in a significant reduction of planktonic viabilities and biofilm biovolume of MDR A. baumannii clinical isolates in vitro. In murine A. baumannii-associated wound infection, a combination of curcumin (25 µg/ml) or chitosan (156 µg/ml) with PDT (10 J/cm2) resulted in complete bacterial eradication with wound healing at Day 15 of post-treatments with these combination therapies. Our study demonstrated that combining curcumin or chitosan with PDT at their subinhibitory concentrations represents a promising alternative strategy as localized therapy for effectively managing A. baumannii-associated wound infection. © 2025 The Authors

关键词： Acinetobacter baumannii Alternative therapy Biofilm eradication Chitosan Curcumin Multidrug-resistant (MDR) Photodynamic therapy (PDT) Wound infection

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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