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Workshop announcement: HBP CodeJam #10
by Luca Leonardo Bologna Oct. 23, 2019

Oct. 23, 2019

Dear colleagues, You are invited to participate in: ---------------------------- The HBP CodeJam #10 Workshop Nov. 26, 2019 at 09:00 - Nov. 28, 2019 at 18:00 - Heidelberg | Germany https://www.humanbrainproject.eu/en/education/participatecollaborate/infras… Early-bird registration ends *31st October!* ---------------------------- The goal of the CodeJam workshops is to catalyze open-source, collaborative software development in computational and systems neuroscience and neuroinformatics by bringing together researchers, students and engineers to share ideas, present their work, and write code together. While the mornings are dedicated to invited and contributed talks, the afternoons are free for discussions, tutorials and code sprints. This year's theme is "Integration". It is aimed to gather scientists, students and engineers from different disciplines collaborating to build a highly integrated research infrastructure for computation-based neuroscience, and to show how this infrastructure can be used to model brain circuits, behaviour and learning, develop novel bio-inspired computing systems, and help discover new drugs for neurological disorders. Confirmed speakers: Mihai Andrei, CODEMART, Cluj-Napoca, Romania Axel von Arnim, fortiss GmbH, Munich, Germany Luca L. Bologna, Italian National Research Council, Italy Claudia Casellato, University of Pavia, Italy Andrew Davison, French National Centre for Scientific Research, France Alexander Dietz, Swiss Federal Institute of Technology Lausanne, Switzerland Allan Francani, EPFL, Switzerland Alberto Antonietti, University of Pavia, Italy Thanasis Karabatsis, National and Kapodistrian University of Athens, Athens, Greece Kostis Karozos, Athens University of Economics and Business (AUEB). Athens, Greece Michael Hines, Yale University, USA Christian Mauch, Heidelberg University, Germany Johannes Schemmel, Heidelberg University, Germany Philipp Spilger, Heidelberg University, Germany Lorenzo Vannucci, Instituto di BioRobotica, SSSA, Pisa, Italy Jonathan Villemaire-Krajden, EPFL, Switzerland Programme Committee Andrew Davison, French National Centre for Scientific Research, France Luca L. Bologna, Italien National Research Council, Italy Alexander Dietz, Swiss Federal Institute of Technology Lausanne, Switzerland Bernd Schuller, Forschungszentrum Jülich, Germany Evita Mailli, National and Kapodistrian University of Athens, Greece Eric Müller, Heidelberg University, Germany Egidio Falotico, Sant'Anna School of Advanced Studies, Italy Martina Schmalholz, Heidelberg University, Germany Please visit the event website https://www.humanbrainproject.eu/en/education/participatecollaborate/infras… to learn more and register. Places are limited, so early registration is recommended. Best regards, Luca Leonardo Bologna

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Open position in Juelich: Scientific coordinator in Computational Neuroscience in Juelich, Germany
by Martina Reske Oct. 21, 2019

Oct. 21, 2019

Dear comp-neuro The Institute of Neuroscience and Medicine (INM) at Research Center Jülich, Germany, investigates the structure and function of the human brain on different spatial and temporal scales within the research program “Decoding the Human Brain”. The Supercomputing Centre is home of one of the most powerful machines and has a leading role in the European exascale strategy. Basic neuroscience connects the two research areas as it heavily relies on modeling and simulation, which are necessary to approach the brain’s immense complexity, manage the huge amount of resulting data, and develop reliable control techniques. The subinstitute INM-6, Computational and Systems Neuroscience ( https://www.fz-juelich.de/inm/inm-6/EN/Home/home_node_INM6.html ), develops mathematical models of neuronal dynamics and function. Model-driven analyses of brain activity and structure as well as simulation of biologically realistic models form the core of our work. Among others, the INM-6/IAS-6 is actively involved in the EU flagship project „Human Brain Project“ (HBP, https://www.humanbrainproject.eu ). Together with its partners, INM-6 develops analysis tools and the leading simulation code (NEST) for brain scale networks with cellular resolution in an open source approach ( http://www.nest-initiative.org ). NEST has been under continuous development for 20 years and is serving a worldwide community. We are looking to recruit a Scientific Coordinator Your Job: * Supervision and controlling of administrative aspects of third party funded projects, incl. monitoring of project milestones, collecting and providing material for scientific reports, among others in EU projects in close collaboration with scientists, for instance within the Human Brain Project * Supporting the heads of the subinstitute in all scientific and administrative matters, incl. the recruitment of staff members * Collection, processing and evaluation of information relevant for the research strategy * Support of drafting of research proposals and grants * Organisation as well as professional and content-related preparation and monitoring of project-relevant events/meetings (e.g. meetings with internal and external cooperation partners, guest visits, conferences, workshops, reviews and committee meetings) * Communication with international research partners * PR work and social media: Support in the production of PR material and the presentation of scientific content in social media channels Your Profile: * Completed study in natural sciences, ideally with PhD * Experience in neuroscience, physics or computer science * Experience in administration of third-party funded projects * Strong organizational skills and multitasking capability * Ability to approach tasks with an eye toward efficiency and reproducibility * High communication skills and ability to work in a team * Excellent verbal and written forms of expression in both, German and English, especially with regard to drafting scientific and administrative texts * Ability to work under pressure, assertiveness and empathy * Skilled in software on project planning, text processing (Latex, Word), presentations (Powerpoint), scheduling of dates and websites * Willingness to travel * High ability to work in interdisciplinary, international team Beneficial: * Work experience abroad * Expertise in Computational Neuroscience * Professional experience in above-mentioned areas of responsibility Our Offer: * Exciting working environment on an attractive research campus with excellent infrastructure, located between the cities of Cologne, Düsseldorf and Aachen * International and interdisciplinary working atmosphere * Responsibility in world-class science environment at the interface between neuroscience and technology on the most complex known systems * High visibility through participation in an Open Source community project and work on key technologies of the European Human Brain Project * Integration into a interdisciplinary and international institute * A comprehensive further training programme * Flexible working hours and various opportunities to reconcile work and private life * Possibility, to apply for the desired level of working hours from 50% to a full position * Limited for 2 years with possible longer-term prospects * Salary and social benefits in conformity with the provisions of the Collective Agreement for the Civil Service (TVöD) Forschungszentrum Jülich aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. We look forward to receiving your application until 12.11.2019 via our online recruiting system, https://www.hrecruiting.de/obf2/bewerbermanagement.php?kunden_nr=t5ChjatkIf… quoting the reference number 2019-374. Martina Reske -- Dr. Martina Reske Scientific Coordinator Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience Jülich Research Centre and JARA Jülich, Germany Work +49.2461.611916 Work Cell +49.151.26156918 Fax +49.2461.619460 www.csn.fz-juelich.de<http://www.csn.fz-juelich.de> Office hours: TU & FR 9.00-17, WE & TH 9.00-13 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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SCiNDU 2020 Conference Announcement
by Geoffrey Goodhill Oct. 19, 2019

Oct. 19, 2019

3rd SYSTEMS AND COMPUTATIONAL NEUROSCIENCE DOWNUNDER (SCiNDU) CONFERENCE January 29-31, 2020 Queensland Brain Institute, University of Queensland, Brisbane, Australia http://www.qbi.uq.edu.au/scindu Abstract submission deadline Nov 15th 2019 Invited speakers: Matilde Balbi (University of British Columbia / University of Queensland) Tony Burkitt (Melbourne University) Gwyneth Card (Janelia) Kai-Hsiang Chuang (University of Queensland) Barry Dickson (Janelia / University of Queensland) Alex Fornito (Monash University) Takao Hensch (Harvard University, TBC) Vinod Menon (Stanford University) Lucy Palmer (Florey Institute) Nicholas Price (Monash University) Linda Richards (University of Queensland) Tatyana Sharpee (Salk Institute) Bruno van Swinderen (University of Queensland) Stephen Williams (University of Queensland) For registration, accommodation and abstract submission information please see http://www.qbi.uq.edu.au/scindu Professor Geoffrey J Goodhill Queensland Brain Institute and School of Mathematics & Physics University of Queensland St Lucia, QLD 4072, Australia Email: g.goodhill(a)uq.edu.au<mailto:g.goodhill@uq.edu.au> http://www.qbi.uq.edu.au/professor-geoffrey-goodhill

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Postdoc openings in the Lefebvre lab at uOttawa
by J?r?mie Lefebvre Oct. 18, 2019

Oct. 18, 2019

The Lefebvre lab at uOttawa is recruiting two postdoctoral fellows for the Winter 2020. Candidates interested in computational neuroscience, brain imaging and applied mathematics are encouraged to apply. Selected candidates will be involved in the following projects: 1. In collaboration with the Griffiths Lab at the CAMH Krembil Center for Neuroinformatics (KCNI) and University of Toronto, the goal of the project is to develop, analyse and explore computational models of non-invasive brain stimulation (e.g. TMS, TES) and their impact on multi-scale neural activity. Specifically, we seek to better understand network-based mechanisms of neural control, oscillatory entrainment and/or stimulation-induced brain plasticity. This project involves a combination of computational and mathematical modelling, has strong potential for knowledge translation, and aims to help inspire new non-invasive treatments for Major Depressive Disorder (MDD). 1. In collaboration with the Hospital for Sick Children (SickKids) in Toronto, the goal of this project is to better understand mechanisms of white matter plasticity, neuron-glia interactions, myelination and its impact on brain function. Using a combination of modelling and simulations, interfacing rodent and human data, the role of the fellow will be to examine the influence of white matter plasticity on neural synchrony and memory. This project involves a combination of computational and mathematical modelling, and strong interactions with experimentalists. The research will take place in the Department of Biology, the Brain and Mind Institute and the Center for Neural Dynamics of the University of Ottawa, a vivid interdisciplinary research cluster set in the bilingual capital of Canada. Both projects are deployed in the Ottawa-Toronto axis, through close collaborations between uOttawa, uToronto, CAMH KCNI, The University Health Network and The Krembil Research Institute. Based on the research needs and resources, candidates will be required to travel between both cities often. Throughout, candidates will interact closely with clinicians, experimentalists and scholars in neuroimaging. Requisites: Candidates should have completed their PhD in physics, mathematics, neuroscience or related disciplines, and have an excellent publication track record. Expertise in programming is a necessity, as well as independence in research. Experience in brain imaging, signal processing and dynamical systems are considered strong assets. Contracts are for one year, with possibility of extension subject to sufficient progress. of one additional year. While the positions are fully funded, candidates are nonetheless expected to apply for external/competitive funding throughout their training. To apply, please send 1) a letter of interest, 2) a full CV and 3) two(2) letters of reference to jeremie.lefebvre(a)hotmail.com<mailto:jeremie.lefebvre@hotmail.com> before Dec 1st , 2019. Selected candidates will be contacted for an interview in December. Jeremie Lefebvre PhD Scientist | Krembil Research Institute, University Health Network Assistant Professor | Department of Mathematics, University of Toronto Assistant Professor (cross appointed)| Institute for Biomaterial and Biomedical Engineering, University of Toronto Krembil Discovery Tower, 60 Leonard Ave, Room 4KD509, Toronto, M5T2S8, Canada Phone: +1 (416) 507-6935 Fax: +1 (416) 603-6274

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Head of the "Machine Learning Transfer Center"
by Philipp Berens Oct. 17, 2019

Oct. 17, 2019

The Cluster of Excellence "Machine Learning: New Perspectives for Science" at the University of Tübingen offers a position as Scientific Head of the central Cluster Facility "Scientific Transfer Center" (100%) to be filled as soon as possible. The position is initially limited until December 31, 2025, with the option of a tenured position. The Transfer Center will be a new facility of the Cluster of Excellence, intended to act as an interface between the Cluster and the various Departments of the University. The Scientific Head is going to promote the transfer of knowledge from the field of machine learning within the Cluster of Excellence to other Departments of the University and to help establishing links between scientific application domains and the research in the area of machine learning. YOUR TASKS - To counsel scientific projects from a variety of disciplines on questions in the field of machine learning - To develop prototypes for standard use cases of machine learning - To initiate networking events between researchers in the field of machine learning and scientific application domains - To develop a (small number of) special courses that introduce machine learning to doctoral students and scientists from other disciplines - To supervise the other scientists employed at the Transfer Center If you enjoy supporting scientific projects at the interface between machine learning and other fields of science, then this is the place for you. The position offers quite a lot of creative freedom. The opportunity to participate in publications is given, but is not the primary goal of the position. The Transfer Center will concentrate on the transfer of machine learning methods to other fields of science. Target persons are doctoral students and scientists from other disciplines. Teaching in Bachelor's or Master's degree programs and transfer to industry will explicitly not be the scope of the Transfer Center. YOUR PROFILE - A doctorate in machine learning or data science and a background in computer science, physics, mathematics or a similar field - Good communication skills with different people - You enjoy working on machine learning problems in different contexts. You are curious about research in various scientific disciplines - Programming experience in the common languages (Python, R, C++) - Experience in project management Further information on the Cluster of Excellence can be found at www.ml-in-science.uni-tuebingen.de. Applications with the usual documents (cover letter, curriculum vitae, copies of certificates, list of publications) are requested by November 08, 2019 in electronic form (as a single PDF, not exceeding 5 MB) to the Central Office of the Cluster of Excellence (ml-in-science(a)uni-tuebingen.de) Please also direct any questions regarding this advertisement to the Central Office. ml-in-science(a)uni-tuebingen.de - www.ml-in-science.uni-tuebingen.de https://www.academics.de/jobs/preview/1015018?preview_id=_GfViDrGixL5dwP6Y5… -- Prof. Dr. Philipp Berens Institute for Ophthalmic Research, University of Tübingen Excellence Cluster "Machine Learning - New Perspectives for Science" http://www.berenslab.org phone: +49-7071-2988833

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PhD posittion in machine learning for closed-loop deep brain stimulation
by Sebastián Castaño C. Oct. 17, 2019

Oct. 17, 2019

Dear mailing-list members, We are looking for a motivated student to work with us at the Brain State Decoding lab, University of Freiburg, Germany! Specifically, we have an open PhD position for investigating machine learning methods for closed-loop deep brain stimulation systems in Parkinson's disease patients. Find the full proposal under https://www.bsdlab.uni-freiburg.de/jobs/phd-position-closed-loop-control-fo… and apply to work with us! Best on behalf of the lab, Sebastian Castaño-Candamil Doctorate student Brain state decoding lab University of Freiburg E // sebastian.castano(a)blbt.uni-freiburg.de (mailto:sebastian.castano@blbt.uni-freiburg.de)

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CFP: FOSDEM 2020 Open Research Tools & Technologies track
by Achilleas Koutsou Oct. 16, 2019

Oct. 16, 2019

This is a *Call for Proposals* for the *Open Research Tools & Technologies* devroom/track at FOSDEM 2020. Web version: https://research-fosdem.github.io/ For the first time at FOSDEM, we are organising a track for the tools and technologies being used in and developed for researchers and scientists and the unique challenges surrounding these topics. FOSDEM (Free and Open source Software Developers' European Meeting) is a non-commercial, volunteer-organised European event centred on free and open-source software development. It is aimed at developers and anyone interested in the free and open-source software movement. It aims to enable developers to meet and to promote the awareness and use of free and open-source software. More info: https://fosdem.org/2020/about/ https://en.wikipedia.org/wiki/FOSDEM The *Open Research Tools & Technologies* devroom is a track dedicated to bringing together developers of research tools with users, potential future contributors, and developers of the wider FLOSS community to discuss the unique challenges for these particular areas of software development. We aim to: - Allow knowledge-based tool developers to publicise their efforts and become aware of other FLOSS projects. - Facilitate the pooling of coding efforts on (often poorly funded) tools. - Create a network where otherwise isolated developers and research engineers can share common concerns. - Provide social recognition for people who work in fields where designing and developing tools does not produce the traditionally recognisable outcomes, e.g., research papers. We seek talks about: - New software releases of research tools or technologies. - Feedback on open technology stacks used in research contexts (e.g., scientific research, journalistic inquiry, archive creation or publication, etc.) which collect, analyse, document, visualise, and/or share data. - Tool design and implementation for specific research contexts, e.g., how to hold an algorithm accountable to social scientists, how to foster better replicability and interoperability thanks to FLOSS, how to cope with biases of a chart for a data journalist, etc. - Issues and opportunities about bridging tech culture with research environments (research labs, libraries, newsrooms, museums, etc.). Talks will be around 20-40 minutes long + 5-10 minutes Q&A, must be in English, will be video recorded by the amazing FOSDEM staff and will be available on the FOSDEM video recordings archive. *Time and place:* Saturday 1st February 2020 from 10:30 to 19:00 ULB, Brussels, Belgium *How to submit proposals* *By submitting a proposal you agree to being recorded and to have your talk made available.* *Deadline:* Sunday 1st December 2019 23:59 CET Submissions must include: - Abstract - Session type (Lecture or Lightning talk) - Session length (20-40 min, 10 min for a lightning talk) - Expected prior knowledge / intended audience - Speaker bio The following information may also be provided but is optional: - Links to code / slides / material for the talk - Links to previous talks by the speaker Submission process is managed in the Pentabarf system used by the FOSDEM conference. Apply for a talk: https://penta.fosdem.org/submission/FOSDEM20 When submitting your talk in Pentabarf, make sure to select the *Open Research Tools and Technologies Devroom* as the Track. If you already have a Pentabarf account from a previous FOSDEM event, please reuse it. Feel free to contact me directly for any questions or concerns: koutsou(a)biologie.uni-muenchen.de <koutsou(a)bio.lmu.de> *Other devrooms that might be of interest* Even if FOSDEM is not science-specific, you might be interested by many other talks. Some developer rooms (tracks) that may be relevant to the interests of this mailing list: - HPC, Big Data, and Data Science - Graph systems and algorithms - Open source design - Community *Developer room organisers* Achilleas Koutsou, G-Node, http://g-node.org https://github.com/achilleas-k Michael Sonntag, G-Node, http://g-node.org https://github.com/mpsonntag Paul Girard, Sciences Po médialab, https://medialab.sciencespo.fr/equipe/paul-girard https://github.com/paulgirard Mathieu Jacomy, Aalborg University TANT Lab, https://www.tantlab.aau.dk/ https://github.com/jacomyma

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Postdoctoral position on computational modelling: interfacing models with nanoarrays to drive cultured neurons
by Yiota Poirazi Oct. 16, 2019

Oct. 16, 2019

1-2 Postdoctoral positions are available in the lab of Panayiota Poirazi ( www.dendrites.gr) in Crete, starting on January 1st, 2020. The positions are for 2 years, with a possibility of renewal for another 2 years. Salary is commensurate with experience. The successful applicant will work on a multi-disciplinary project funded by the FET (Future and Emerging Technologies) Open Instrument of the European Innovation Council. The NEUREKA project aims to develop a new prototype technology that can be used for drug discovery for neurological diseases. In this new hybrid technology, computational neuronal networks that simulate dysfunction will drive cultured neurons to replicate neuropathologies. A proof-of-concept will be provided for Alzheimer’s disease, using human (iPSC)-derived neurons while testing the effects of novel drug candidates. The NEUREKA partners include the University of Padua (Prof. Vassanelli), CNRS (Prof. Larrieu), the University of Milano Bicocca (Prof. Fanciulli) and Maxwell Biosystems. Pharma advisors include Roche and Cognition Therapeutics Inc. For more information please visit: http://www.dendrites.gr/en/openings-11 Applications (full CV, statement of research interest and name and contact of 2-3 referees) should be sent by e-mail to poirazi(a)imbb.forth.gr, quoting “NEUREKA: Postdoctoral position” in the subject line. The deadline for applications is *November 30th, 2019*. Applications will be examined until the position is filled. Informal enquiries are welcome. -- Panayiota Poirazi, Ph.D. Research Director Institute of Molecular Biology and Biotechnology (IMBB) Foundation of Research and Technology-Hellas (FORTH) Vassilika Vouton, P.O.Box 1385, GR 70013, Heraklion, Crete GREECE Tel: +30 2810 391139 Fax: +30 2810 391101 Εmail: poirazi(a)imbb.forth.gr Lab site: www.dendrites.gr

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Post-doctoral Researcher in Computational modelling of hippocampal circuits (Blue Brain Porject, Switzerland)
by Armando Romani Oct. 16, 2019

Oct. 16, 2019

Blue Brain Porject (Campus Biotech, Geneva, Switzerland) is looking for a *Post-doctoral Researcher in Computational modelling of hippocampal circuits*. Improve the existing large-scale models of rodent hippocampus. The current network models are already the product of several iterations and their emergent behavior can reproduce many features of the hippocampus. The work on the models continues by expanding the region of interest from CA1 (the first region we considered) to the full hippocampus, and eventually by connecting the hippocampus to the rest of the brain. In parallel, the models will include more or more details. For example, we are working on including gap junctions, long-term plasticity, structural plasticity, neuromodulation, glia, vasculature, and so on. Exploit the models to answer outstanding questions in the field, such as information processing in the hippocampus, spatial navigation, memory processes, development of pathological conditions (Alzheimer’s disease, epilepsy). The models are designed not to answer one specific question, but for a general purpose. This ensures a larger validity of the models and allows us to potentially test many different hypotheses and make likewise predictions. Follow the link below to learn more about the position and how to apply. https://recruiting.epfl.ch/Vacancies/1005/Description/2 — Armando Romani, PhD Junior Group Leader - Simulation Neuroscience Division EPFL - Blue Brain Project Campus Biotech Chemin des Mines 9 CH-1202 Geneva, Switzerland Phone +41 (0)21 693 7190

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Post-doctoral Researcher in Computational modelling of thalamo-cortical circuits (Blue Brain Porject, Switzerland)
by Armando Romani Oct. 16, 2019

Oct. 16, 2019

Blue Brain Porject (Campus Biotech, Geneva, Switzerland) is looking for a* Post-doctoral Researcher in Computational modelling of thalamo-cortical circuits*. The goal of this project is to leverage the Blue Brain software and existing thalamic models to build and validate biologically-accurate models of thalamo-cortical circuitry. Modelling these circuits is a crucial step to investigate brain functions, such us sensory transmission, sleep rhythms, wakefulness, alertness. The successful candidate would be responsible for gathering data about thalamo-cortical circuits from the literature, open-access datasets and in vitro studies in collaboration with the experimental lab. Interactions with biology and experimental experts would be fundamental to validate and confirm model predictions. In addition, the candidate would provide guidance and scientific expertise to the technical teams and contribute to the on-going refinement of workflows and tools to build data-driven unifying brain tissue models. Furthermore, the candidate will work in collaboration with engineering teams on visualization, high performance computing, data integration and with project managers to define objectives and timelines to achieve overarching objectives and meet aggressive deadlines. Follow the link below to learn more about the position and how to apply. https://recruiting.epfl.ch/Vacancies/827/Description/2 — Armando Romani, PhD Junior Group Leader - Simulation Neuroscience Division EPFL - Blue Brain Project Campus Biotech Chemin des Mines 9 CH-1202 Geneva, Switzerland Phone +41 (0)21 693 7190

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