- BBClist - maillist.psb.ugent.be

vacancy post-doc/assistant professor Microbial Bioinformatics
by Schaik, W. van 23 Apr '15

23 Apr '15

Dear BeNeLux bioinformaticians I want to draw your attention to this exciting opportunity in microbial bioinformatics (on the post-doc/Assistant Professor-level, with possibility of tenure) in the University Medical Center Utrecht, The Netherlands: http://www.werkenbijumcutrecht.nl/vacatures/Paginas/postdoc-assistant-profe… Please feel free to contact me if you want to discuss this position informally. Sincerely Willem van Schaik Associate Professor | Department of Medical Microbiology | University Medical Center Utrecht Room G04.614 | Heidelberglaan 100 | 3584CX Utrecht | The Netherlands T +31 (0)88 75 565 35 | E w.vanschaik(a)umcutrecht.nl<mailto:w.vanschaik@umcutrecht.nl> | twitter: @WvSchaik ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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JOB: PhD candidate in Network Biology/Bioinformatics at Maastricht UMC+
by Arts Ilja (EPID) 21 Apr '15

21 Apr '15

PhD candidate in Network Biology/Bioinformatics for a multidisciplinary project at Maastricht UMC+, CARIM School for Cardiovascular Diseases and NUTRIM School of Nutrition and Translational Research in Metabolism (AT2015.64) The obesity epidemic is a rapidly growing health threat, but there is substantial heterogeneity in cardiometabolic risk among the obese. Current clinical practice uses metabolic syndrome diagnosis to establish cardiovascular disease (CVD) risk. This is an insensitive tool, and data suggest that a substantial proportion of individuals without metabolic syndrome are yet at high risk for CVD, and vice versa. In this project we will generate metabolomics multi-marker profiles that improve clinical decision-making by identifying obese individuals at high risk of CVD, and identify novel molecular descriptors for prevention and early diagnosis, and targets for treatment of obese individuals at high risk of CVD, independent of their metabolic syndrome status. We will use data from several large human studies, including The Maastricht Study (http://www.demaastrichtstudie.nl/research) and Diogenes (http://www.diogenes-eu.org) Details and application procedure: https://www.academictransfer.com/employer/UM/vacancy/27320/lang/en/

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Postdoc position in bioinformatics (Lyon, France)
by GABUT Mathieu 16 Apr '15

16 Apr '15

Dear all, A postdoctoral position in bioinformatics (transcriptome analysis) is available for 3 years in the Gabut laboratory at the Cancer Research Centre of Lyon, in Lyon (France). The lab is interested in deciphering the function of post-transcriptional mechanisms in the control of normal/cancer stem cell physiology and pluripotency. A detailed description of the position is provided in the attached PDF file. Thank you for advertising about this position to your students, postdocs and colleagues. Best regards, Sincerely, Mathieu Gabut -- Mathieu Gabut ATIP/AVENIR lab "Transcriptome diversity in stem cells" Cancer Research Centre of Lyon - CRCL INSERM U1052, CNRS UMR 5286 Cheney A - 4e é巘age Centre L帹n B帹ard 28 Rue Laennec 69008 Lyon (France) http://www.crcl.fr/ Tel: +33-(0)4 69 85 60 92 (new phone number!) Fax: +33-(0)4 78 78 27 20 E-mail: mathieu.gabut(a)inserm.fr mathieu.gabut(a)lyon.unicancer.fr

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NL course: Gene expression data analysis
by J.M. Boer 16 Apr '15

16 Apr '15

Dear genomics/bioinformatics researcher, In June we are organizing the next edition of our Gene expression data analysis course in Rotterdam. We are looking forward to your participation. Registration closes on May 25. Kind regards, Judith Boer * Gene expression data analysis using R: How to make sense out of your RNA-Seq/microarray data 22-26 June 2015 Five days hands-on computer course for biological and clinical researchers whose research involves experiments that generate gene expression data. The course focuses on microarray and next-generation sequencing gene expression data, but some concepts may be applicable to other types of genomics data. Most of the speakers (and therefore examples) have a biomedical background. Software packages used are freeware, including the statistical software R, Bioconductor, Cytoscape and web tools. The total number of participants is limited to 40. For more information and registration: www.molmed.nl<http://www.molmed.nl> ------------------------------------------------------- Judith M. Boer, PhD Erasmus MC - Sophia Children's Hospital Laboratory of Pediatric Oncology/ Hematology, room Ee 1575a Dr. Molewaterplein 50 3015 GE Rotterdam the Netherlands Phone: +31 10 70 38264 Fax: +31 10 70 44708 e-mail: j.m.boer(a)erasmusmc.nl

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[Gtpb] GTPB Bioinformatics Training Course Announcement ARANGS15
by Pedro Fernandes 15 Apr '15

15 Apr '15

Applications are now open for ARANGS15 Automated and reproducible analysis of NGS data IMPORTANT DATES for this Course Deadline for applications: May 3rd 2015 Latest notification of acceptance: May 4th 2015 Course date: May 11th - May 15th 2015 One of our most acclaimed courses "This course teaches best practices in NGS workflow development" (former participant statement) Details at: http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS15/index.html Diuration: 5 days Course fee: Euro 450.00 -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt

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[Gtpb] SMLMC15 Training Course - new deadline for applications
by Pedro Fernandes 14 Apr '15

14 Apr '15

Dear All, Some people have requested that we open a wider time window to apply for this course: "Structural Modelling for Large Macromolecular Complexes" IMPORTANT DATES for this Course Deadline for applications: April 18th 2015 <====== NEW! Latest notification of acceptance: April 20th 2015 Course date: April 27th - April 30th 2015 With Joanna Kasprzak and Mateusz Dobrychlop Description We will present a range of techniques to generate, analyse, and optimise models of proteins, RNA, and their complexes. We will talk about new approaches to structure determination of macromolecules and macromolecular complexes. During the practical sessions participants will learn how to use methods for modelling protein and RNA 3D structures such as Modeller and ModeRNA. Also we will focus on methods dedicated to protein-RNA complexes modelling, e.g. by combining data from low-resolution density maps, SAXS and biochemistry. In particular, we will present how to use PyRy3D, a computational tool to build models of macromolecular complexes based on data from various sources. Participants will be able to bring-in specific biological questions and/or their on data to work with during the course. Target Audience The course has been designed for molecular and structural biologists, bioinformaticians and biotechnologists and other scientists interested in modelling of biological complexes. The content is suitable for researchers, both at the graduate and post-graduate levels. SMLMC15 Course duration: 4 days SMLMC15 Course Fee: Euro 360.00 Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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BioSB Course Kick start R (3rd edition) , April 24 2015, Amsterdam
by Celia.vanGelder＠radboudumc.nl 13 Apr '15

13 Apr '15

BioSB Course Kick start R (3rd edition) Date: April 24, 2015 Location: Amsterdam Course Coordinator: Douwe Molenaar (VU) Website, including course programme: http://biosb.nl/education/course-portfolio/course-kick-start-r-3rd-edition/ Registration: http://biosb.nl/education/course-portfolio/enrollment-kick-start-r-course-3… On April 24, 2015, BioSB organises the third edition of the Kick Start R course in Amsterdam. This is a one-day introduction course for researchers about the possibilities of the statistical calculation environment R for those who would like to use it, or have already started using R for statistical data analysis but would like to obtain a bit more background. The main goal is to provide the participant with a kick-start in R. Clearly, good and practically applicable knowledge of R will only be gained by subsequent self-study. A kick start is achieved through the following sub-goals: 1. The participant will become acquainted with the structure and philosophy behind the R-language. The participant will thereby be able to gain a quicker understanding of the R-language compared to the "immediate problem solving" approach taken by most (online) manuals. 2. The participant will become acquainted with a number of tools specific to the R-language. This will help the participant to start using R quickly in a professional manner This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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PhD positions for EpiPredict
by A.H.C. van Kampen 10 Apr '15

10 Apr '15

12 PhD positions for EpiPredict project The EpiPredict EU Innovative Training Network focuses on epigenetic regulation of endocrine therapy resistance in breast cancer, an urgent clinical problem. EpiPredict includes 15 (academic and private) organisations from eight different countries, providing unique research training to 12 PhD students. The multidisciplinary fellows will master and apply urgently needed new approaches to address complex diseases taking personalized patient aspects and systems medicine into consideration being equipped to succeed in their careers. Strong involvement of the private sector ensures exploitation of EpiPredict achievements and exposure to an entrepreneurial mind-set. For more recruitment information visit: www.EpiPredict.eu | Prof dr Antoine H.C. van Kampen | (1) Bioinformatics Laboratory | Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB) | Academic Medical Center (AMC) | Visiting address: Meibergdreef 9, J1B-208 (J-building, floor 1B) | Postal address: PO Box 22700, 1100 DE Amsterdam, the Netherlands | www.bioinformaticslaboratory.nl<http://www.bioinformaticslaboratory.nl/> | (2) Biosystems Data Analysis | Swammerdam Institute for Life Sciences (SILS) | University of Amsterdam | Visiting address: Science Park 904, C2-205 | 1098 XH Amsterdam, The Netherlands | www.bdagroup.nl<http://www.bdagroup.nl/> |phone: ++31-20-5667096 (AMC) |Mobile: 06-41768067 | a.h.vankampen(a)amc.uva.nl<mailto:a.h.vankampen@amc.uva.nl> | Skype:antoine.van.kampen | ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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Fwd: [Aaa-ds] AAA DS postdoc joint advertisement
by Sanne Abeln 09 Apr '15

09 Apr '15

*We are hiring: 14 Postdoctoral researchers/PhD candidates for AAA Data Science* *3 positions available on the interface between Data Science & Life Science* Amsterdam Data Science <http://amsterdamdatascience.nl/>, an initiative of the University of Amsterdam (UvA) <http://www.uva.nl/en/home>, VU University Amsterdam (VU) <http://vu.nl/nl/index.asp>, Amsterdam University of Applied Sciences (HvA) <http://www.amsterdamuas.com/>, and Centrum Wiskunde & Informatica (CWI) <http://www.cwi.nl/> is looking for 14 researchers at the postdoctoral/PhD level. These positions are funded by the Amsterdam Academic Alliance (AAA), a joint initiative of the UvA and VU aimed at intensifying collaboration with each other and knowledge institutions in the region, to cement Amsterdam's position as a hub of academic excellence. These positions are partially co-funded by CWI, Faculty of Social and Behavioural Sciences of the UvA, HvA, ORTEC, Spinoza fund of Prof. Vossen, and VUmc. Amsterdam Data Science provides a network in which some 300 Amsterdam based scientists exchange Data Science knowledge and forge partnerships within and outside the academic community. This comprises the foundations of data science and data science for the life sciences, social analytics, business analytics, and digital humanities. *14 AAA Data Science positions in the following areas:* *Computer Science with Life Sciences affinity - Mapping high dimensional data on pathways: large scale machine learning of cancer networks * The postdoc will use large scale machine learning methods to gain an improved understanding of cancer biology by integrating pathway knowledge with molecular profiling data. Organizational units: with Prof. Jaap Heringa (Dept. of Informatics, Section Bioinformatics, VU University Amsterdam) and Prof. Max Welling (Informatics Institute, University of Amsterdam). Further information: Prof. Jaap Heringa, *j.heringa(a)vu.nl* <j.heringa(a)vu.nl>, Prof. Max Welling, *m.welling(a)uva.nl* <m.welling(a)uva.nl> · *Cheminformatics and Bioinformatics* The candidate will develop new computational tools and workflows that allow the integration and exploitation of chemogenomic and phenotypic data for the prediction of (synergistic) drug efficacy. Organizational units: with Prof. Iwan de Esch (Medicinal Chemistry, VU University Amsterdam) and Prof. Tom Wurdinger (VUmc Cancer Center Amsterdam). Further information: Dr. Chris de Graaf, *c.de.graaf(a)vu.nl* <c.de.graaf(a)vu.nl>, +31 20 598 75 53. · *Network-based data integration * The postdoc will develop methods for combining data fusion approaches with biological network information. Organizational units: with Prof. Bas Teusink (AIMMS, VU University Amsterdam) and Prof. Age Smilde (SILS, University of Amsterdam). Further information: Prof. Age Smilde, *a.k.smilde(a)uva.nl* <a.k.smilde(a)uva.nl>, +31 20 525 5062, or Prof. Bas Teusink, *b.teusink(a)vu.nl* <b.teusink(a)vu.nl>, +31 20 598 94 35. · *Citizen Data Science* Conduct computer science research, with a focus on social media analysis and analysis of sensory data. Organizational units: with Prof. Maarten de Rijke (Informatics Institute, University of Amsterdam) and Drs. Sabine Niederer (CREATE-IT applied research, Amsterdam University of Applied Sciences). Further information: Prof. Maarten de Rijke, derijke(a)uva.nl · *From Data to Semantics and Back Again* The postdoc researches methodologies to integrate large volumes of data into a coherent relational schema. Organizational units: with Prof. dr. Boncz (database architectures group of CWI - the Dutch national research institute for computer science and mathematics) and with dr. Urbani and Prof. dr. Bal (Dept. of Computer Science, VU University Amsterdam). Further Information: dr. Jacopo Urbani *<jacopo(a)cs.vu.nl>* <jacopo(a)cs.vu.nl>, Prof. Peter Boncz *<P.Boncz(a)cwi.nl>* <P.Boncz(a)cwi.nl>, Prof. Henri Bal *<bal(a)cs.vu.nl>* <bal(a)cs.vu.nl>. Telephone: +31 20 592 4309 (Peter Boncz) · *Bias and Engagement in Political Social Media* Conduct research at the interface of computer science and communication science, with a focus on social media analysis. Organizational units: with Prof. Claes de Vreese (Amsterdam School of Communication Research ASCoR, University of Amsterdam) and Prof. Maarten de Rijke (Informatics Institute, University of Amsterdam). Further information: Prof. Maarten de Rijke, *derijke(a)uva.nl* <derijke(a)uva.nl>, Prof. Claes De Vreese, *c.h.devreese(a)uva.nl* <c.h.devreese(a)uva.nl> · *Complex network theory on large knowledge graphs* Postdoc position for foundational studies on the nature of data objects, specifically aimed at graph-structured data. Organizational units: with Prof. Frank van Harmelen (Dept. of Computer Science, VU University Amsterdam) and Prof. Pieter Adriaans (group of Prof. Cees de Laat, Informatics Institute, University of Amsterdam). Further information: Prof. Frank van Harmelen, *Frank.van.Harmelen(a)vu.nl* <Frank.van.Harmelen(a)vu.nl>, +31 20 598 7731 · *Analysis of Images and Text in Social Media for Marketing Applications* The postdoc will investigate innovative computer vision techniques for analyzing images in their social context in order to do large scale quantitative marketing. Organizational units: with Prof. Marcel Worring (Informatics Institute and Amsterdam Business School, University of Amsterdam) and Prof. Willemijn van Dolen (Amsterdam Business School, University of Amsterdam). Further information: Prof. Marcel Worring, Informatics Institute and Amsterdam Business School, Tel 020 527521, e-mail: *m.worring(a)uva.nl* <m.worring(a)uva.nl> · *Advertisement & Sales Optimization Algorithms for the 21st century* The postdoc or PhD candidate will develop a cross-channel multi-device model to understand the relation between advertisement and sales. Organizational units: with Prof. Marc Salomon and Prof. Peter Boswijk (Faculty of Economics and Business, University of Amsterdam) and Prof. Ger Koole (Faculty of Sciences, VU University Amsterdam), and with the company ORTEC. Further information: Prof. Marc Salomon, *marc.salomon(a)uva.nl* <marc.salomon(a)uva.nl>. · *Data-driven decision support in complex markets* This project aims to understand decision behaviors in the emerging social commerce platforms and develop policy implications for the platform owners. Organizational units: with Prof. Marleen Huysman (Faculty of Economics and Business administration, VU University Amsterdam) and Prof. Henri Bal (Department of Computer Science, VU University Amsterdam). The postdoc will have its primary workspace at the Amsterdam Center for Business Analytics ( *www.acba.nl* <http://www.acba.nl/>). Further information: dr. Frans Feldberg (*f.feldberg(a)vu.nl* <f.feldberg(a)vu.nl>) · *Digital Humanities - Representation of Data Perspectives* The postdoc will investigate long-term changes of perspectives and perception in cultural texts through emotion anlysis, topic modeling, and genre analysis. Organizational units: with Prof. Rens Bod (Institute for Logic, Language and Computation, University of Amsterdam) and with Prof. Inger Leemans (Department of History, VU University Amsterdam). Further information: Prof. Rens Bod, *l.w.m.bod(a)uva.nl* <l.w.m.bod(a)uva.nl>, and Prof. Inger Leemans, *i.b.leemans(a)vu.nl* <i.b.leemans(a)vu.nl>. · *Quality, Trust and Reliability of Web Data for Scholarly Research* The postdoc will investigate the identification of factors that influence the quality and reliability of Web data for scholarly research. Organizational units: with dr. Lora Aroyo (Computer Science, Faculty of Science, VU University Amsterdam) and with Prof. Julia Noordegraaf (Media Studies, Faculty of Humanities, University of Amsterdam). Further information: Dr. Lora Aroyo, *lora.aroyo(a)vu.nl* <lora.aroyo(a)vu.nl>, +31 6 20329972, and Prof. Julia Noordegraaf *J.J.Noordegraaf(a)uva.nl* <J.J.Noordegraaf(a)uva.nl>*.* · *Computational Linguistics * The postdoc or PhD candidate will develop 1) a perspective model for representing the subjective relation between the source of information and the statements, and 2) software to detect such interpersonal communication layers and perspectives from text. Organizational units: with Prof. Piek Vossen (Computational Lexicology and Terminology Lab, Faculty of Humanities, VU University Amsterdam) and Dr. Lora Aroyo (Department of Computer Science, VU University Amsterdam). Further information: Prof. Piek Vossen (*piek.vossen(a)vu.nl* <piek.vossen(a)vu.nl>): +31 6-81773878 or +31 20-59 86457, and Dr. Lora Aroyo, *lora.aroyo(a)vu.nl* <lora.aroyo(a)vu.nl>, +31 6 20329972. · *Program Manager at postdoctoral level* The Program Manager will manage the AAA Data Science program, will coordinate the educational activities, and will coordinate the acquisition activities. Organizational units: with Prof. Maarten de Rijke (Informatics Institute, University of Amsterdam) and with Prof. Frank van Harmelen (Dept. of Computer Science, VU University Amsterdam). Further information: Prof. Maarten de Rijke, *derijke(a)uva.nl* <derijke(a)uva.nl> and Prof. Frank van Harmelen, *Frank.van.Harmelen(a)vu.nl* <Frank.van.Harmelen(a)vu.nl>, +31 20 598 7731 . *Job application * To apply, please have a look at the vacancy pages of the websites of the UvA and the VU. The full texts plus opportunity to apply will be on these websites (soon): vacancies University of Amsterdam <http://www.uva.nl/en/about-the-uva/working-at-the-uva/vacancies> and the vacancies VU University. <http://vu.nl/en/employment/vacancies/index.asp> ----- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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New Master in Science: Bioinformatics at Ghent University
by Katrijn Vannerum 08 Apr '15

08 Apr '15

Dear student, Dear colleague, We are happy to announce that our Master in Science: Bioinformatics is approved by the Flemish government and that the program will start next academic year! Embedded in the Bioinformatics Institute Ghent and the Ghent Biotech environment, this English master seeks a balance between generalization and specialization. In addition to a common package designed for the acquisition of interdisciplinary competences, we try to respect the individuality of the different students' backgrounds by offering numerous specific courses in each of the three specializations. Within the 'Systems Biology' track the biological problem is central. The specialization 'Bioscience Engineering' focuses on the application, combination and integration of existing (bio)-informatics tools and techniques for solving complex problems with industrial/practical finality. The third specialization, 'Engineering' is aimed at training bioinformaticians to develop on an independent basis new algorithms and complex software implementations. Students with a bio-engineering, biochemistry, biotechnology, molecular biology, engineering or computer scientist Bach. Sc. education can follow the M. Sc. in Bioinformatics. Preparatory programs are there for biologists, biomedical scientists and students from other study domains. The master bioinformatics at Ghent University prepares its students for a future full of challenges and job security in academics or life science companies, since bioinformatics has become a necessity for all life sciences! All information can be found on the website http://www.nucleotides2networks.be/master Thank you to spread this message within your network. Excuses for possible double postings. With kind regards, Katrijn Vannerum PhD Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01D0720A.0D3438B0] [cid:image002.png@01D0720C.86AE7AA0]

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