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Dual Catalysis of Gold Nanoclusters: Photocatalytic Cross-Dehydrogenative Coupling by Cooperation of Superatomic Core and Molecularly Modified Staples**

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Angewandte Chemie 2023年第2期136卷

作者： Dr. Katsuhiro Isozaki Kenta Iseri Ryohei Saito Kyosuke Ueda Prof. Dr. Masaharu Nakamura International Research Center for Elements Science Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan Department of Energy and Hydrocarbon Chemistry Graduate School of Engineering Kyoto University Nishikyo-ku Kyoto 615-8510 Japan Contribution: Conceptualization (lead) Data curation (lead) Formal analysis (lead) Funding acquisition (equal) Methodology (lead) Project administration (lead) Resources (lead) Software (lead) Supervision (lead) Validation (lead) Visualization (lead) Writing - original draft (lead) Writing - review & editing (equal) Contribution: Investigation (lead) Methodology (lead) Writing - original draft (supporting) Contribution: Investigation (supporting) Methodology (supporting) Contribution: Investigation (supporting) Contribution: Funding acquisition (equal) Supervision (equal) Writing - review & editing (equal)

Thiolate-protected gold nanoclusters (AuNCs) have attracted significant attention as nano-catalysts, revealing a superatomic core and gold-thiolate staples as distinct structural units. Here, we demonstrate the unprecedented dual catalytic activity of thiolate-protected [Au 25 (SR) 18 ] − nanoclusters, involving both photosensitized 1 O 2 generation by the Au 13 superatomic core and catalytic carbon-carbon bond formation facilitated by Au 2 (SR) 3 staples. This synergistic combination of two different catalytic units enables efficient cross-dehydrogenative coupling of terminal alkynes and tertiary aliphatic amines to afford propargylamines in high yields of up to 93 %. Mixed-ligand AuNCs bearing both thiolate and alkynyl ligands revealed the intermediacy of the alkynyl-exchanged AuNCs toward both photosensitization and C−C bond-forming catalytic cycles. Density functional theory calculations also supported the intermediacy of the alkynyl-exchanged AuNCs. Thus, the use of ligand-protected metal nanoclusters has enabled the development of an exceptional multifunctional catalyst, wherein distinct nanocluster components facilitate cooperative photo- and chemo-catalysis.

关键词： Cross-Dehydrogenative Coupling Dual Catalysis Gold Nanocluster Intermolecular Interaction Photocatalyst

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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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Deep learning for cardiac image segmentation: A review

arXiv

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arXiv 2019年

作者： Chen, Chen Qin, Chen Qiu, Huaqi Tarroni, Giacomo Duan, Jinming Bai, Wenjia Rueckert, Daniel Biomedical Image Analysis Group Department of Computing Imperial College London London United Kingdom Department of Computer Science City University of London London United Kingdom School of Computer Science University of Birmingham Birmingham United Kingdom Data Science Institute Imperial College London London United Kingdom Division of Brain Sciences Department of Medicine Imperial College London London United Kingdom

Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research. Copyright © 2019, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Monitoring system of agricultural performance based on multisensor data and cross-validation technique in merging temporal images

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Agronomy Journal 2022年第1期115卷

作者： N. P. G. Bhavani Prameeladevi Chillakuru Ramana Lakshmi Adusumilli Roobaea Alroobaea Saeed Rubaiee Abdulkader S. Hanbazazah Suman Mann Saveetha School of Engineering Chennai Tamil Nadu 602105 India Contribution: Data curation Formal analysis Rajalakshmi Engineering College Chennai Tamil Nadu 602105 India Contribution: Investigation Methodology Dep. of Computer Science and Engineering Prasad V Potluri Siddhartha Institute of Technology Kanuru Vijayawada Andhra Pradesh 520007 India Contribution: Resources Software Dep. of Computer Science College of Computers and Information Technology Taif Univ. P. O. Box 11099 Taif 21944 Saudi Arabia Contribution: Funding acquisition Supervision Dep. of Industrial and Systems Engineering College of Engineering Univ. of Jeddah Jeddah Saudi Arabia Contribution: Funding acquisition Visualization Contribution: Funding acquisition Writing - original draft Writing - review & editing Maharaja Surajmal Institute of Technology New Delhi 110058 India Contribution: Conceptualization Writing - original draft

Several approaches to forecasting agricultural production have been used across the country, but they have focused on information widely detected with technology that was not very successful. Unfortunately, because of many difficulties such as climate variables (50% global fog cover) with limited temporal accuracy, the remotely detected information necessary to predict crop production was often insufficient. As a result of these problems, existing methods of estimating agricultural production are ineffective or out of date. Several efforts have been made to overcome these challenges by combining images with high temporal accuracy but poor geographic detail. On the other hand, it is this kind of situation that is most suitable for extremely large and homogeneous agricultural areas. An innovative theoretical framework has developed that explains this absence of high-quality satellite images. This intelligent method was built around this new theoretical framework, which incorporates its use of something like the energy equation to improve the predictions of multiple cultures. Many producers were contacted and data regarding agricultural production were obtained to validate the results of the smart technology. The excellent reliability of this intelligent method has been shown by a comparative contrast between projected crop yields and actual output in various areas.

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The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)

arXiv

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arXiv 2024年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Gandhi, Deep Jiang, Zhifan Anwar, Syed Muhammed Albrecht, Jake Adewole, Maruf Anazodo, Udunna Anderson, Hannah Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Franson, Andrea Gottipati, Anurag Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Johansen, Elaine Jones, Blaise V. Khalili, Neda Kofler, Florian LaBella, Dominic Lai, Hollie Anne Van Leemput, Koen Li, Hongwei Bran Maleki, Nazanin McAllister, Aaron S. Meier, Zeke Menze, Bjoern Moawad, Ahmed W. Nandolia, Khanak K. Pavaine, Julija Piraud, Marie Poussaint, Tina Prabhu, Sanjay P. Reitman, Zachary Rudie, Jeffrey D. Sanchez-Montano, Mariana Shaikh, Ibraheem Salman Sheth, Nakul Tu, Wenxin Wang, Chunhao Ware, Jeffrey B. Wiestler, Benedikt Zapaishchykova, Anna Bornhorst, Miriam Deutsch, Michelle Fouladi, Maryam Lazow, Margot Mikael, Leonie Hummel, Trent Kann, Benjamin de Blank, Peter Hoffman, Lindsey Aboian, Mariam Nabavizadeh, Ali Packer, Roger Bakas, Spyridon Resnick, Adam Rood, Brian Vossough, Arastoo Linguraru, Marius George Children’s Hospital of Philadelphia PhiladelphiaPA United States Department of Neurosurgery University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Sage Bionetworks United States Lab Crestview Radiology Lagos Nigeria McGill University MontrealQC Canada Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center DurhamNC United States Mayo Clinic MN United States Center for Global Health Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States C. S. Mott Children’s Hospital University of Michigan MI United States Biomedical Engineering Rutgers University New BrunswickNJ United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Yale University New HavenCT United States PrecisionFDA U.S. Food and Drug Administration Silver SpringMD United States Cincinnati Children’s Hospital Medical Center OH United States Helmholtz AI Helmholtz Munich Germany Department of Radiation Oncology Duke University Medical Center DurhamNC United States Department of Radiology Children’s Health Orange County CA United States Department of Applied Mathematics and Computer Science Technical University of De

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge, focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors. © 2024, CC BY.

关键词： Deep learning

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BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023

arXiv

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arXiv 2024年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Haldar, Debanjan Jiang, Zhifan Zapaishchykova, Anna Pavaine, Julija Shah, Lubdha M. Jones, Blaise V. Sheth, Nakul Prabhu, Sanjay P. McAllister, Aaron S. Tu, Wenxin Nandolia, Khanak K. Rodriguez, Andres F. Shaikh, Ibraheem Salman Sanchez-Montano, Mariana Lai, Hollie Anne Adewole, Maruf Albrecht, Jake Anazodo, Udunna Anderson, Hannah Anwar, Syed Muhammed Aristizabal, Alejandro Bagheri, Sina Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Eddy, James Ezhov, Ivan Familiar, Ariana M. Farahani, Keyvan Gandhi, Deep Gottipati, Anurag Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Elaine, Elaine Karargyris, Alexandros Kassem, Hasan Khalili, Neda Kofler, Florian LaBella, Dominic Van Leemput, Koen Li, Hongwei B. Maleki, Nazanin Meier, Zeke Menze, Bjoern Moawad, Ahmed W. Pati, Sarthak Piraud, Marie Poussaint, Tina Reitman, Zachary J. Rudie, Jeffrey D. Saluja, Rachit Sheller, MIcah Shinohara, Russell Takeshi Viswanathan, Karthik Wang, Chunhao Wiestler, Benedikt Wiggins, Walter F. Davatzikos, Christos Storm, Phillip B. Bornhorst, Miriam Packer, Roger Hummel, Trent de Blank, Peter Hoffman, Lindsey Aboian, Mariam Nabavizadeh, Ali Ware, Jeffrey B. Kann, Benjamin H. Rood, Brian Resnick, Adam Bakas, Spyridon Vossough, Arastoo Linguraru, Marius George The Children’s Hospital of Philadelphia PA United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Neurosurgery Thomas Jefferson University Hospital PA United States Dana-Farber Brigham Cancer Center Boston Children’s Hospital BostonMA United States Department of Paediatric Radiology Royal Manchester Children’s Hospital Manchester University Hospitals NHS Foundation Trust University of Manchester Manchester United Kingdom University of Utah UT United States Cincinnati Children’s Hospital Medical Center OH United States Department of Radiology The Children’s Hospital of Philadelphia PA United States Division of Neuroradiology Department of Radiology Boston Children’s Hospital Harvard Medical School BostonMA United States Department of Radiology Nationwide Children’s Hospital OH United States College of Arts and Sciences University of Pennsylvania PA United States Department of Diagnostic and Interventional Radiology All India Institute of Medical Sciences Rishikesh India Department of Diagnostic & Interventional Imaging Neuroradiology Section The University of Texas Health HoustonTX United States Beth Israel Deaconess Medical Center Harvard Medical School MA United States Unidad de Patologia Clinica:Guadalajara Jalisco Mexico Department of Radiology Children’s Health Orange County CA United States Lab Crestview Radiology Lagos Nigeria Sage Bionetworks United States McGill University MontrealQC Canada Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States MLCommons United States Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center DurhamNC United States Mayo Clinic MN

Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children. The five-year survival rate for high-grade glioma in children is less than 20%. The development of new treatments is dependent upon multi-institutional collaborative clinical trials requiring reproducible and accurate centralized response assessment. We present the results of the BraTS-PEDs 2023 challenge, the first Brain Tumor Segmentation (BraTS) challenge focused on pediatric brain tumors. This challenge utilized data acquired from multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. BraTS-PEDs 2023 aimed to evaluate volumetric segmentation algorithms for pediatric brain gliomas from magnetic resonance imaging using standardized quantitative performance evaluation metrics employed across the BraTS 2023 challenges. The top-performing AI approaches for pediatric tumor analysis included ensembles of nnU-Net and Swin UNETR, Auto3DSeg, or nnU-Net with a self-supervised framework. The BraTS-PEDs 2023 challenge fostered collaboration between clinicians (neuro-oncologists, neuroradiologists) and AI/imaging scientists, promoting faster data sharing and the development of automated volumetric analysis techniques. These advancements could significantly benefit clinical trials and improve the care of children with brain tumors. © 2024, CC BY.

关键词： Pediatrics

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Search for the rare decay B^(0)→J/ψФ

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Chinese Physics C 2021年第4期45卷 47-60页

作者： R.Aaij C.Abellin Beteta T.Ackernley B.Adeva M.Adinolfi H.Afsharnial C.A.Aidala S.Aiola Z.Ajaltouni S.Akar J.Albrecht F.Alessio M.Alexander A.Alfonso Albero Z.Aliouche G.Alkhazov P.Alvarez Cartelle S.Amato Y.Amhis L.An L.Anderlini A.Andreianov M.Andreotti F.Archilli A.Artamonov M.Artuso K.Arzymatov E.Aslanides M.Atzeni B.Audurier S.Bachmann M.Bachmaver J.J.Back S.Baker P.Baladron Rodriguez V.Balagura W.Baldinit J.Baptista Leite R.J.Barlow S.Barsuk W.Barter M.Bartolini F.Baryshnikov J.M.Basels G.Bassi B.Batsukh A.Battig A.Bay M.Becker F.Bedeschis I.Bediaga A.Beiter V.Belavin S.Belin V.Bellee K.Belous I.Belov I.Belyaev G.Bencivenni E.Ben-Haim A.Berezhnoy *** D.Berninghoff H.C.Bernstein C.Bertella E.Bertholet A.Bertolin C.Betancourt F.Betti M.O.Bettler Ia.Bezshyiko S.Bhasin J.Bhom L.Bian M.S.Bieker S.Bifani P.Billoir M.Birch F.C.R.Bishop A.Bizzeti M.Biorn M.P.Blago T.Blake F.Blanc S.Blusk D.Bobulska J.A.Boelhauve O.Boente Garcia T.Boettcher A.Boldyrev A.Bondar N.Bondar S.Borghi M.Borisyak M.Borsato J.T.Borsuk S.A.Bouchiba T.J.V.Bowcock A.Boyer C.Bozzi M.J.Bradley S.Braun A.Brea Rodriguezs M.Brodski J.Brodzicka A.Brossa Gonzalo D.Brundu A.Buonaura C.Burr A.Burschee A.Butkevich J.S.Butter J.Buytaert W.Byczynski S.Cadeddu H.Cai R.Calabrese L.Calefice L.Calero Diaz S.Cali R.Calladine M.Calvi M.Calvo Gomez P.Camargo Magalhaes A.Camboni P.Campana D.H.Campora Perez A.F.Campoverde Quezada S.Capelli L.Capriotti A.Carbonel G.Carboni R.Cardinale A.Cardini I.Carli P.Carniti L.Carus K.Carvalho Akiba A.Casais Vidal G.Casse M.Cattaneo G.Cavallero S.Celani J.Cerasoli A.J.Chadwick M.G.Chapman M.Charles Ph.Charpentier G.Chatzikonstantinidis C.A.Chavez Barajas M.Chefdeville C.Chen S.Chen A.Chernov S.-G.Chitic V.Chobanova S.Cholak M.Chrzaszcz A.Chubykin V.Chulikov P.Ciambrone M.F.Cicala X.Cid Vidal G.Ciezarek P.E.L.Clarke M.Clemencic H.V.Cliff J.Closier J.L.Cobbledick V.Coco J.A.B.Coelho J.Cogan E.Cogneras L.Cojocariu P.Collins T.Colombo L.Congedo A.Contu N.Cooke G.Coombs G.Corti C.M.Costa Sobral B.Couturier D.C.Craik J.Crkovska M.Cruz Centro Brasileiro de Pesquisas Fisicas(CBPF) Riode JaneiroBrazil Universidade Federal do Riode Janeiro(UFRJ) Riode JaneiroBrazil Center for High Energy Physics Tsinghua UniversityBeijingChina School of Physics State Key Laboratory of Nuclear Physics and Technology Peking UniversityBeijingChina University of Chinese Academy of Sciences BeijingChina Institute Of High Energy Physics(IHEP) BejingChina Institute of Particle Physics Central China Normal UniversityWuhanHubeiChina Univ.Grenoble Alpes Univ.Savoie Mont BlancCNRSIN2P3-LAPPAnnecyFrance Universite Clermont Auvergne CNRS/IN2P3LPCClermont-FerrandFrance Aix Marseille Univ CNRS/IN2P3CPPMMarseilleFrance Universitq Paris-Saclay CNRS/IN2P3IJCLabOrsayFrance LPNHE Sorbonne UniversiteParis Diderot Sorbonne Paris CiteCNRS/IN2P3ParisFrance I.Physikalisches Institut RWTH Aachen UniversityAachenGermany Fakultat Physik Technische Universitat DortmundDortmundGermany Max-Planck-Institut fir Kernphysik(MPIK) HeidelbergGermany Physikalisches Institut Ruprecht-Karls-Universitat HeidelbergHeidelbergGermany School of Physics University College DublinDublinIreland INFN Sezione di Bari BariItaly INFN Sezione di Bologna BolognaItaly INFN Sezione di Ferrara FerraraItaly INFN Sezione di Firenze FirenzeItaly INFN Laboratori Nazionali di Frascati Frascatiltaly INFN Sezione di Genova GenovaItaly INFN Sezione di Milano Bicocca Milanolaly INFN Sezione di Milano MilanoItaly INFN Sezione di Cagliari Monserratoltaly Universita degli Studi di Padova Universita e INFNPadovaPadovaItaly INFN Sezione di Pisa PisaItaly INFN Sezione di Roma Tor Vergata RomaItaly INFN Sezione di Roma La Sapienza RomaItaly Nikhef National Institute for Subatomic Physics AmsterdamNetherlands Nikhef National Institute for Subatomic Physics and VU University Amsterdam AmsterdamNetherlands Henryk Niewodniczanski Institute of Nuclear Physics Polish Academy of Sciences KrakowPoland AGH-University of Science and Technology Faculty of Physics and Applied Computer Science

A search for the rare decay B^(0)→J/ψФis performed using Pp collision data collected with the LHCb dete-ctor at centre-of-mass energies of 7,8 and 13 TeV,corresponding to an integrated luminosity of9 *** significant signal of the decay is observed and an upper limitof 1.1x 10^(-7)at 90%confidence level is set on the branching fraction.

关键词： B physics flavour physics rare decay ω-Фmixing branching fraction

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The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

arXiv

引用

arXiv 2021年

作者： Baheti, Bhakti Chakrabarty, Satrajit Akbari, Hamed Bilello, Michel Wiestler, Benedikt Schwarting, Julian Calabrese, Evan Rudie, Jeffrey Abidi, Syed Mousa, Mina Villanueva-Meyer, Javier Fields, Brandon K.K. Kofler, Florian Shinohara, Russell Takeshi Iglesias, Juan Eugenio Mok, Tony C.W. Chung, Albert C.S. Wodzinski, Marek Jurgas, Artur Marini, Niccolò Atzori, Manfredo Müller, Henning Grosbröhmer, Christoph Siebert, Hanna Hansen, Lasse Heinrich, Mattias P. Canalini, Luca Klein, Jan Gerken, Annika Heldmann, Stefan Hering, Alessa Hahn, Horst K. Meng, Mingyuan Bi, Lei Feng, Dagan Kim, Jinman Zeineldinal, Ramy A. Karar, Mohamed E. Mathis-Ullrich, Franziska Burgert, Oliver Abderezaei, Javid Pionteck, Aymeric Chopra, Agamdeep Kurt, Mehmet Yan, Kewei Yan, Yonghong Tang, Zhe Ma, Jianqiang Nasser, Sahar Almahfouz Kurian, Nikhil Cherian Meena, Mohit Shamsi, Saqib Sethi, Amit Tustison, Nicholas J. Avants, Brian B. Cook, Philip Gee, James C. Tian, Lin Greer, Hastings Niethammer, Marc Hoopesar, Andrew Hoffmannas, Malte Dalcaar, Adrian V. Christodoulidis, Stergios Estiene, Théo Vakalopoulou, Maria Paragios, Nikos Marcus, Daniel S. Davatzikos, Christos Sotiras, Aristeidis Menze, Bjoern Bakas, Spyridon Waldmannstetter, Diana Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Electrical and Systems Engineering Washington University in St. Louis St. LouisMO United States GE HealthCare San RamonCA United States University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Mallinckrodt Institute of Radiology Washington University School of Medicine St. LouisMO United States Institute for Informatics Data Science & Biostatistics Washington University School of Medicine St. LouisMO United States Department of Bioengineering Santa Clara University Santa ClaraCA United States Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Computer Science TUM School of Computation Information and Technology Technical University of Munich Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Munich Germany Department of Nuclear Medicine University Hospital Regensburg Regensburg Germany University Hospital Regensburg Regensburg Germany Department of Radiology & Biomedical Imaging University of California San FranciscoCA United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Radiology University of California San DiegoCA United States Helmholtz AI Helmholtz Munich Neuherberg Germany Penn Statistics in Imaging and Visualization Center Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Philadelphia United States Massachusetts General Hospital Harvard Medical School United States Centre for Medical Imaging Computing University College London United Kingdom The Hong Kong University of Science and Technology Hong Kong University of Applied Sciences West

Registration of longitudinal brain Magnetic Resonance Imaging (MRI) scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been considerable progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The challenge was conducted in conjunction with both the IEEE International Symposium on Biomedical Imaging (ISBI) 2022 and the International Conference on Medical Image Computing and computer-Assisted Intervention (MICCAI) 2022. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. The training data with their GT annotations, were publicly released to enable the development of registration algorithms. The validation data, without their GT annotations, were also released to allow for algorithmic evaluation prior to the testing phase, which only allowed submission of containerized algorithms for evaluation on hidden hold-out testing data. Quantitative evaluation and ranking was based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency

关键词： Magnetic resonance imaging

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Biomedical image analysis competitions: The state of current participation practice

arXiv

引用

arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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Complementary time-frequency domain networks for dynamic parallel MR image reconstruction

arXiv

引用

arXiv 2020年

作者： Qin, Chen Duan, Jinming Hammernik, Kerstin Schlemper, Jo Küstner, Thomas Botnar, René Prieto, Claudia Price, Anthony N. Hajnal, Joseph V. Rueckert, Daniel Institute for Digital Communications School of Engineering University of Edinburgh Edinburgh United Kingdom Department of Computing Imperial College London London United Kingdom School of Computer Science University of Birmingham Birmingham United Kingdom Institute for AI and Informatics Klinikum Rechts der Isar Technical University of Munich Munich Germany Hyperfine Research Inc. GuilfordCT United States School of Biomedical Engineering and Imaging Sciences King's College London St. Thomas' Hospital London United Kingdom Department of Diagnostic and Interventional Radiology Medical Image and Data Analysis University Hospital of Tuebingen Tuebingen Germany

Purpose To introduce a novel deep learning based approach for fast and high-quality dynamic multi-coil MR reconstruction by learning a complementary time-frequency domain network that exploits spatio-temporal correlations simultaneously from complementary domains. Theory and Methods Dynamic parallel MR image reconstruction is formulated as a multi-variable minimisation problem, where the data is regularised in combined temporal Fourier and spatial (x-f ) domain as well as in spatio-temporal image (x-t) domain. An iterative algorithm based on variable splitting technique is derived, which alternates among signal de-aliasing steps in x-f and x-t spaces, a closed-form point-wise data consistency step and a weighted coupling step. The iterative model is embedded into a deep recurrent neural network which learns to recover the image via exploiting spatio-temporal redundancies in complementary domains. Results Experiments were performed on two datasets of highly undersampled multi-coil short-axis cardiac cine MRI scans. Results demonstrate that our proposed method outperforms the current state-of-the-art approaches both quantitatively and qualitatively. The proposed model can also generalise well to data acquired from a different scanner and data with pathologies that were not seen in the training set. Conclusion The work shows the benefit of reconstructing dynamic parallel MRI in complementary time-frequency domains with deep neural networks. The method can effectively and robustly reconstruct high-quality images from highly undersampled dynamic multi-coil data (16× and 24× yielding 15s and 10s scan times respectively) with fast reconstruction speed (2.8s). This could potentially facilitate achieving fast single-breath-hold clinical 2D cardiac cine imaging. © 2020, CC BY.

关键词： Magnetic resonance imaging

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