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PHD STUDENT (M/F/D) IN EXPERIMENTAL AND COMPUTATIONAL PEDIATRIC TUMOR RESEARCH (PART-TIME)

In the last years, single cell and epigenetic characterization techniques have gained tremendous attention in oncology and

broadened our understanding of the diseases. Our group specifically focuses on SMARCB1 deficient pediatric tumors.

To better understand these, we are applying various molecular genetic characterization techniques including ChIPsequencing,

whole genome and exome sequencing and single-cell sequencing.

Recently, we have performed integrative, large-scale multi-omic characterizations of pediatric rhabdoid tumors

(Johann et al. Cancer Cell 2016; Erkek, Johann et al, Cancer Cell 2019) and are now aiming to expand these techniques

to other SMARCB1-deficient tumors. Furthermore, to facilitate the translation of the results back to the clinic, we will

perform high-throughput drug screens which complement the multi-omics characterization of the tumors. To handle

both the experimental and the computational part of this project, we are looking for a highly-motivated PhD student,

who is able to work at the interface of molecular biology, epigenetics and computational biology.

 

Job description:

We are looking for a motivated PhD student with a background in computational biology (and ideally epigenetics) and an

interest in both wet and dry lab work. Our aim is to decipher the epigenetic landscape of various neoplasias that are characterized

by the loss of the tumor-suppressive SMARCB1 protein, including rhabdoid tumors and epithelioid sarcomas.

The successful applicant will

1) plan and perform drug treatment studies in cell lines of the aforementioned entities

2) apply methods for the epigenetic characterization of these tumors, including methylation analysis,

ChIP-Sequencing and RNA-sequencing

3) perform the integrative analysis of the generated datasets

 

Requirements:

• Graduation (Master of Science) in biology, cancer biology, genetics, bioinformatics or a related field

(with demonstrated experience in both bioinformatics and experimental work)

• Previous experience in the analysis of array and/or high throughput sequencing data is mandatory

(preferably in R and in a scripting language such as Python)

• Ability to collaborate and communicate within interdisciplinary teams (in German or English)

What we offer:

• Joint appointment at the University of Augsburg (Prof. Dr. M. Schlesner, Computational Biology) and the University

Hospital (PD Dr. P. Johann) and integration into both a clinical / experimental and a computational working group

• The possibility to work on your PhD thesis in a rapidly evolving community

• The opportunity to learn a wide variety of experimental and computational methods

• Support in generating an own, academic profile

 

Contact: PD Dr. Johann Pascal This email address is being protected from spambots. You need JavaScript enabled to view it. 

Predictive Medicine in Neurooncology

The Institute of Neuropathology at the University of Giessen, Germany, Director Prof. Till Acker, invites applications for

1 Postdoc or PhD position in

PREDICTIVE MEDICINE IN NEUROONCOLOGY

The position is available immediately.

Your Profile:

We are looking for enthusiastic and highly motivated applicants holding, or about to obtain, a Master or PhD degree in Bioinformatics, Computational Biology, Medical Informatics or related areas. The candidates should have strong expertise in Python, combined with Machine- and Deep-Learning techniques. Experience in Docker and Linux is helpful. Preference will be given to applicants with previous experience in one or more of the following areas: use of cBioPortal and DataSHIELD, analysis of Whole- Slide-Images, DNA methylation- and/or NGS-data.

Topic:

The aim of the project is the development of novel AI-based algorithms within a team of biomedical informaticians that generate synergistic results from different data sources in a clinical study system to assist predictive medicine in translational cancer research. The initiative for a “Comprehensive Cancer Center (CCC) Hessen” provides the framework with a recently established system for conducting multicenter clinical studies. In this framework medical – in particular neurooncology - patient data from morphomolecular analyses (digital histopathology and genomics) and clinical metadata data are combined to develop precision diagnostics and predictive medicine approaches. The development of novel interface and interaction tools will also be part of the project.

What we offer:

Our international team offers an open, supportive, dynamic and motivating academic environment with excellent training opportunities with the possibility to work on cutting edge research projects. We have won a number of external research grants and are involved in several national and international collaborative projects. We use a wide spectrum of methods including DNA methylation array analysis, next generation sequencing, bioinformatic analysis, animal models and in vivo tumor models as well as tumor biopsies, immunohistochemistry, in situ hybridization, light, epifluorescence and confocal microscopy, image analysis. Our group has a longstanding expertise in the molecular, cellular and functional characterization of brain, lung and breast cancer development, with a special emphasis on microenvironmentand hypoxia-induced mechanisms in tumor biology.

The activity of the successful candidate will be integrated into the framework of the initiative for a “Comprehensive Cancer Center (CCC) Hessen” and MIRACUMConsortium (Medical Informatics in Research and Care in University Medicine, Vice-

Speaker: Prof. Till Acker; see also: miracum.org). In addition, collaboration possibilities and advanced training at the de.NBI (German Network for Bioinformatics

Infrastructure) as well as the newly founded University Center of BioMedical Informatics are available.

Please send your application as a single PDF: cover letter, your CV, certificates of your qualifications, your publication list and the contact details of at least two referees until 15.04.2021 to our lead bioinformatician Daniel Amsel (Daniel.Amsel at patho.med.uni-giessen.de).

Applicants with disabilities but otherwise equal qualifications will be preferred.

Combinatorial Algorithms on Strings and Graphs

We are looking for a talented and motivated PhD student with a special interest in algorithms and data structures and their application in bioinformatics (sequence analysis). The PhD student will be positioned at CWI within the "Algorithms for PAngenome" (ALPACA) network

(https://alpaca-itn.eu/) funded by the European Commission through the Horizon 2020 Marie Sklodowska-Curie ITN Programme.

The move from sequence- to graph-based pan-genome data structures is unavoidable when seeking to exploit the wealth of genome data, instead of having devices massively congested. Putting the paradigm shift (from sequences to graphs) in effect requires new ways of thinking about genomes, as well as computer programs and mathematical models that reflect this. However, developing, maintaining and computationally exploiting graph-based pan-genomes requires skills that common-day education does not yet provide. The goal of ALPACA is to train a new class of researchers who are able to deal with the masses of genome data in terms of the progressive, graph-based approaches the research of this project deals with.

 

Objectives: Comparing pan-genomes amounts to comparing two graphs, generalizing the idea to align two genomes. We aim at developing algorithms for 'whole-pan-genome alignment'. Though for aligning two networks approaches already exist, they do not address the peculiarities of pan-genome graphs, in, for example, de Bruijn graph or variation graph based pan-genomic data structures. We will address these particular issues in full detail.

 

 Supervised by: Solon P. Pissis (https://homepages.cwi.nl/~solon/)

 

Co-supervised by: Leen Stougie (https://www.cwi.nl/people/leen-stougie)

  

**Requirements**

Candidates are required to have a Master’s degree in Computer Science, Mathematics or a related discipline, and a specialization in Algorithms, Combinatorics, Combinatorial Optimization or related fields. Preferable qualifications for candidates include proven research talent in a Master’s project, an excellent command of English, and good academic writing and presentation skills.

 

On the starting date of their employment with CWI, candidates must be in the first four years of their research career and have not (yet) been awarded a doctoral degree. Candidates also must not have resided and/nor have had their main activity (study, work, etc.) in the Netherlands for more than 12 months during the 3 years prior to the starting date of their employment with CWI.

 

More details and application instructions can be found here:

 

 https://www.cwi.nl/jobs/vacancies/866988

 

Application deadline: April 30, 2021

Bioinformatician [DKFZ, Division of Personalized Medical Oncology]

The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research.

 

The Division of Personalized Medical Oncology (Director: Prof. Dr. Dr. Sonja Loges) focusses on the identification of novel cancer-promoting mechanisms in the tumor microenvironment. Based on these functional insights we aim to derive novel targets for therapeutic intervention. Translation of research findings into the clinic will be possible at the newly founded „DKFZ-Hector Cancer Institute at the University Hospital Mannheim“, which is also directed by Prof. Sonja Loges and generously funded by the Hector Foundation II.

 

Job description:

 

Together with the Division of Applied Bioinformatics (Director: Prof. Dr. Benedikt Brors) we are looking for an enthusiastic individual to develop methods for integrative analysis of multi­level data on tumors, including whole-genome and/or whole-exome sequences of tumor and germline genomes, single-cell and spatial transcriptomics data, methylomes and corresponding clinical data. The position is placed in a dynamic and multinational, multidisciplinary team which works closely with national as well as international collaboration partners in academics as well as pharmaceutical companies. The workplace is located in Heidelberg.

 

Requirements:

 

The applicant should hold at least a master's degree in bioinformatics, computational biology or related fields, or a degree in biological sciences with demonstrated experience in computational biology / bioinformatics.

 

Previous experience in developing and applying computational methods applied to large datasets is expected. We especially seek candidates with prior experience in the analysis and the management of NGS data in the field of cancer biology.

 

Proficiency with relevant scripting languages and statistical data analysis tools such as Python and R (or equivalent) is required. Single-cell experience is a plus.

 

The ideal applicant should have demonstrated the ability to work independently and creatively. You should have excellent communications skills and be able to articulate clearly the scientific and technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners.

 

Full applications should include a curriculum vitae including any potential publications, a letter of motivation, certificates, expected availability date, and 2-3 references.

 

We offer:

 

  • Interesting, versatile workplace
  • International, attractive working environment
  • Campus with modern state-of-the-art infrastructure
  • Salary according to TV-L including social benefits
  • Possibility to work part-time
  • Flexible working hours
  • Comprehensive further training program

 

Earliest Possible Start Date: as soon as possible

 

Duration: The position is limited to 2 years with the possibility of prolongation.

 

The position can in principle be part-time.

 

Application Deadline: 17.04.2021

 

Contact:

 

Dr. Melanie Janning
Phone +49 (0)621/383-1757

 

Please note that we do not accept applications submitted via email. 

Links: https://jobs.dkfz.de/en/jobs/73328/bioinformatician

 

 

Professur (W 2) für Strukturelle Bioinformatik

In der Fakultät für Biologie und Vorklinische Medizin ist am Regensburg Center for Biochemistry eine Professur der Besoldungsgruppe W 2 für Strukturelle Bioinformatik im Beamtenverhältnis auf Lebenszeit zum nächstmöglichen Zeitpunkt zu besetzen. Die Professur soll den Schwerpunkt der Fakultät und des Regensburg Center for Biochemistry im Bereich der Strukturbiologie durch die bioinformatische Analyse zellulärer Makromoleküle ergänzen. Zudem ist eine Stärkung der bestehenden Sonderforschungsbereiche der Fakultät erwünscht, insbesondere des SFB 960. Die Ausschreibung richtet sich an hoch qualifizierte Persönlichkeiten, die durch exzellente Publikationsleistungen und Drittmitteleinwerbungen ausgewiesen sind. In der Lehre ist das Fachgebiet Bioinformatik im Rahmen der Bachelor- und Masterstudiengänge Biologie und Biochemie zu vertreten. Einstellungsvoraussetzungen sind neben den allgemeinen dienstrechtlichen Voraussetzungen ein abgeschlossenes Hochschulstudium, pädagogische Eignu
ng, besondere Befähigung zu wissenschaftlicher Arbeit, die in der Regel durch die Qualität einer Promotion nachgewiesen wird, sowie zusätzliche wissenschaftliche Leistungen, die durch eine Habilitation oder gleichwertige wissenschaftliche Leistungen, die auch außerhalb des Hochschulbereichs erbracht sein können, nachgewiesen oder im Rahmen einer Juniorprofessur erbracht werden. Die Vereinbarkeit von Familie und Beruf ist der Universität Regensburg ein besonderes Anliegen (nähere Infos unter www.uni-regensburg.de/chancengleichheit). Um den Gleichstellungsauftrag zu erfüllen und die Zahl ihrer Professorinnen zu erhöhen, fordert sie qualifizierte Wissenschaftlerinnen ausdrücklich zur Bewerbung auf. Schwerbehinderte werden bei im Wesentlichen gleicher Eignung bevorzugt berücksichtigt. Die beamtenrechtlichen Voraussetzungen für eine Ernennung richten sich nach den Bestimmungen des BayBG und des BayHSchPG. Die Altersgrenze des Art. 10 Abs. 3 BayHSchPG ist zu beachten. Bewerbungen 
mit den üblichen Unterlagen (Lebenslauf, Zeugnisse, Urkunden, Schriftenverzeichnis mit den wichtigsten Sonderdrucken, Forschungsplan, Lehrkonzept) sind elektronisch bis zum 3. Mai 2021 an den Dekan der Fakultät für Biologie und Vorklinische Medizin (This email address is being protected from spambots. You need JavaScript enabled to view it.) der Universität Regensburg, D-93040 Regensburg, zu richten. Hinweise zum Datenschutz finden Sie unter https://www.uni-regensburg.de/datenschutz/.

W1 Professorship for Biomedical Informatics

The Faculty of Medicine at Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) invites applications for a
 
W1 Professorship for Biomedical Informatics (Assistant Professor)
at the Institute of Medical Informatics, Biometry, and Epidemiology. The professorship is to be filled by the earliest possible starting date for an initial period of three years. Upon successful evaluation, the appointment will be extended for another three years. 
 
We seek to appoint a top early career scientist who will develop outstanding expertise in the field. The professorship is involved in the MIRACUM project, which unites ten university hospitals, two universities and a partner from the healthcare industry, with the aim of making clinical, image, molecular and genomic data available for use in innovative research projects via modular, scalable and federated data integration centres. Candidates should come from a biomedical informatics background and have experience in medical research data management (FAIR principles) to develop aspects of data engineering and data integration in a medical context in their own research. Experience of collaboration with clinical and pre-clinical working groups, international research and project and team management is an advantage. The successful candidate is expected to become actively involved in research networks at FAU and the Faculty of Medicine (Collaborative Research Centres, Research Training Groups, Interdisciplinary Centre for Clinical Research, leading-edge cluster Medical Valley, Graduate School in Advanced Optical Technologies [SAOT]) and collaborate with the Department of Artificial Intelligence in Biomedical Engineering (AIBE) at FAU, which is currently being established. The Faculty of Medicine offers degree programmes in medicine, dentistry, molecular medicine, medical process management and integrated immunology. The assistant professor will be expected to participate in teaching, which is mostly carried out in German, particularly in lectures for medicine and computer science (medical informatics as a minor subject).
 
Successful candidates demonstrate initial academic achievements and the capacity for independent research at the highest international standards. You have substantial research experience abroad and/or experience in managing research projects and in raising third-party funding. A university degree and an outstanding doctoral degree as well as a passion for education and pertinent teaching experience are also prerequisites. Candidates who are able and willing to teach in both English and German are desired.
 
FAU expects applicants to become actively involved in administering academic affairs and in developing strategic initiatives. FAU pursues a policy of intense student mentoring and therefore expects its teaching staff to be present during lecture periods.
 
FAU offers career development, mentoring and an attractive initial research budget. Based on international standards and transparent performance agreements, FAU ensures a fair evaluation process.
 
In its pursuit of academic excellence, FAU is committed to equality of opportunity and to a proactive and inclusive approach, which supports and encourages all under-represented groups, promotes an inclusive culture and values diversity. FAU is a family-friendly employer and is also responsive to the needs of dual career couples.
 
Please submit your complete application documents (CV, list of publications, list of lectures and courses taught, copies of certificates and degrees, list of third-party funding) online at https://berufungen.fau.de by 23. April 2021, addressed to the Dean of the Faculty of Medicine. Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. with any questions.): Titel: Text:

PhD student in precision cancer bioinformatics

Ref. no.: BIH-42.21

 

The Digital Health Center, headed by Prof. Roland Eils, develops and applies state-of-the-art and innovative technologies to healthcare research with a strong focus on machine learning, bioinformatics, imaging and genomics. The department has a strong standing within international consortium (e.g. Human Cell Atlas, ICGC, de.NBI, ELIXIR, EOSC), and have exceptional computational resources (in-house HPC, cloud, Nvidia DGX and FPGA technology).

 

We have recently established a precision medicine genomics platform, which aims to use whole genome and transcriptome sequencing for cancer patients. Building on top of an excellent existing pipeline, we aim to further develop the computational analytics part of the pipeline in the upcoming years.

 

Your area of responsibility:

 

- Undertake and publish excellent scientific research

- Interacting with other members of the clinical genomics program including management, pathology, genomics and clinical partners

- Analyzing genome sequencing data for prospective patients, working closely with clinicians to identify actionable mutations

- Analyzing genome sequencing data for retrospective studies

- Development of new genomics workflows (e.g. supporting new genome references and genomics lesions such as STRs and enhancer hijacking) and interacting with our Data Management Platform team for deployment in a production environment

- Development and implementation of novel computational methods that aid genomics based diagnostics and prognosis

- Interacting with other collaborative sites, in particular the DKFZ and NCT in Heidelberg

 

Your profile:

 

- A PhD candidate with a recent masters degree in bioinformatics, cancer genomics, computer science, medicine, physics or similar

- Ambitious, self-driven, a thirst for answering scientific questions and aim to build a scientific career in biomedical data science research

- Excellent programming proficiency especially in Python, R, Julia, bash or similar

- Experience in designing and implementing data analysis pipelines

- Experience with next generation sequencing data processing and analysis

- Experience with linux based HPC or cloud environments

- Fluent in English (written and spoken)

 

Qualifications – desirable:

 

- Prior research experience in liquid biopsies, cancer genomics data, single cell ‘omics data, or spatial transcriptomics

- Knowledge of transcriptional regulation and epigenomics

- Knowledge of cancer immunology

- Experience with machine learning methods (e. g. RF, NMF, VAE) and frameworks (e. g. PyTorch, TensorFlow, Keras, sklearn)

- Experience with workflow management systems and similar paradigs (e. g. ELIXIR-WES, snakemake, NextFlow)

 

Start: Immediately

 

Length of employment: 3 years

 

Working time: 25,35 hrs./week

 

Pay scale: E13 acc. to collective agreement TVöD VKA – K

 

Contact person: For further information please contact Dr. Naveed Ishaque, E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Research Associate (m/f/d)

To support the DFG-funded Specialised Information Service Biodiversity Research (BIOfid, www.biofid.de) at our location in Frankfurt am Main or optionally in Görlitz we are looking for a
 
Research Associate (m/f/d)
 
(full time)
 
at the earliest possible date.
 
We are an interdisciplinary team of natural scientists, text technologists and librarians developing new text mining tools for semantic indexing of 19th and 20th century Central European biodiversity literature (mainly in German language). Existing data on the systematics and ecology of various organisms, which have been difficult to access until now, can thus be mobilised and used by scientists for further studies. In our second project phase, we focus on ecosystem services in the sense of plant-pollinator interactions and soil invertebrates.
 
Your tasks
  • Extension, standardisation and structuring of existing vocabularies and thesauri on morphological and functional traits of soil fauna based on the data warehouse Edaphobase and in collaboration with an international team
  • Support for the ontology development on species traits of soil fauna and its linkage to taxonomic ontologies
  • Evaluation and consolidation of text mining technologies
  • Analysing and publishing project-related data
  • Project presentations at national and international conferences
  • Participation in the organisation of workshops for user groups
  • Reporting to the DFG and the scientific advisory board
     
 
Your profile
    • Successfully completed university studies (ideally a doctoral degree) in biology, bio(diversity)informatics or a related field
    • Good knowledge of terminologies and nomenclatures in biology, especially morphology, systematics and traits of soil fauna
    • Basic understanding of zoological-ecological interactions and functions
    • Knowledge of basic data standards for biodiversity data
    • Fluency in English both spoken and written
    • Excellent abilities in team work and communication as well as self-reliant service- and target-oriented operation
 
Salary and benefits are according to a full-time public service position in Germany (TV-H E 13). The contract should start as soon as possible and will initially be limited to one year (with option of extension).
 
The Senckenberg Research Institutes support equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. The place of employment is in Frankfurt am Main or optionally in Görlitz, Germany.
 
Please send your complete and meaningful application documents (letter of motivation, CV, educational and professional certificates and credentials, as well as professional references), mentioning the reference of this job announcement (ref. #01-21012) and if possible your preferred place of work (Frankfurt or Görlitz) before April 7th, 2021 by e-mail (attachment in a single pdf document) to This email address is being protected from spambots. You need JavaScript enabled to view it. or apply directly on our homepage using the online application form.
 
 

Postdoctoral position: Elucidating the gene regulatory network controlling oxidative phosphorylation (INSERM, CNRS, Marseille)

We are proposing a two-year Postdoctoral position in Bioinformatics to investigate the gene regulatory networks controlling OXPHOS gene expression in Drosophila. For this purpose, we will use a multiomics approach integrating DNA motifs, ChIPseq and RNAseq.

This Postdoctoral project is funded by the Turing Centre for Living Systems (CENTURI). Details of the project and host labs can be found here: https://centurilivingsystems.org/pdp202109/

- Application deadline: April 16, 2021 (CET)
- Information: https://centurilivingsystems.org/recruitment/
- Application form: https://centurilivingsystems.org/applicationformpdp202109/

Mitochondrial oxidative phosphorylation (OXPHOS) is an essential source of ATP for a cell's energy needs and is a highly dynamic and controlled process during cell differentiation and animal development and its dysfunction drives plethora human diseases and cancer. This project aims at identifying the gene regulatory network that underlies OXPHOS gene expression plasticity, an essential function of tissue development and stem cell differentiation. We have shown that the Drosophila transcription factor, M1BP, is responsible for basal level transcription of OXPHOS genes. The postdoc will integrate multiple "omics" datasets such as DNA motifs, interactomes, ChIPseq and transcriptomes to predict transcriptional cofactors of M1BP responsible for OXPHOS transcriptional plasticity. These predictions will be validated experimentally using RNAi and ChIPseq.

The postdoc candidate should have a PhD in bioinformatics, or related field, with interest in “omics” data analyses, genomics and gene regulation. Most of the projet work involves computational manipulation of large and highly multivariable datasets. Wet lab experience is a benefit, but not essential as these techniques are well established in the host lab.

Thank you for sharing this offer with motivated candidates.

- Andrew Saurin http://www.ibdm.univmrs.fr/equipe/mechanismsofgeneregulationbytranscriptionfactors
- Aitor González: https://tagc.univamu.fr/en/users/gonzalezaitor

Bioinformatician position available, Medical University of Vienna

We are looking for a bioinformatician in the fields of epigenetics, gene regulation & proteomics. This position is embedded in the special research program (SFB) “Histone deacetylases (HDACs) as regulators of T cell-mediated immunity in health and disease”. The ideal candidate has knowledge in the analysis of NGS dataset and pathway analysis. The candidate will be responsible for the computational analysis of NGS data and for basic pathway and network analysis. Throughout the project, the candidate will work in close collaboration with the whole research network.

 
ABOUT THE RESEARCH PROGRAM
The special research program (SFB) “Histone deacetylases (HDACs) as regulators of T cell-mediated immunity in health and disease” constitutes a major strategic grant, consortium and research network newly funded by the Austrian Science Fund (FWF). The overall aim of this 8-year SFB research program and consortium is to provide a mechanistic molecular rationale for the development and application of isoform-selective HDAC inhibitors for the treatment of T cell-mediated diseases, and to test essential regulatory roles of reversible lysine acetylation beyond histone modifications and epigenetic gene regulation in T helper cells. It comprises an interdisciplinary team of eight research groups, of which seven are located in Vienna and one in Salzburg, Austria. The project started in March 2019.
 
APPLICATION: Candidates have to demonstrate a strong motivation to engage in the SFB network. Previous research experience in Systems Biology, Bioinformatics, or another relevant discipline is desired. Electronic applications must include the following documents in a single PDF file:
1.   Academic Curriculum Vitae of no more than 2 -3 pages
2.   List of peer-reviewed publications (submitted papers must include the submission confirmation)
3.   Motivation letter explaining why you wish to start / continue a career in the field (1-page)

The job offer is open until March 31, 2021. The position will be filled as soon as suitable candidates have been identified and selected. Two reference letters must be e-mailed by mentors of applicants to This email address is being protected from spambots. You need JavaScript enabled to view it.. Short-listed candidates will be invited for Zoom interviews in April 2021. The position (initially for up to 2 years) is open immediately; the actual start date is flexible.
 
Links: www.meduniwien.ac.at/HIThttp://www.meduniwien.ac.at/HIT/contact.html,
 


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