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Stellenangebote

Postdoctoral Researcher (f/m/n) Metagenomics & Soil Biodiversity

Project "Diversity and scenario modelling of molecular markers of plant pathogens in plant, litter and soil metagenomes" at theGerman  Centre  for  Integrative  Biodiversity  Research (Div)Halle-Jena-Leipzig: Soils  host  one  quarter  of  all species  on  Earth,  providing  critical  services  to  mankind. This  project asks how soil microorganism communities respond to global change and which changes in soil functions will occur. We will generate answers by mining metagenomics data covering large environmental gradients, available   in   our   consortium   and the   public   domain,   for molecular   markers   of   microbial plant pathogenicity.  On  this  basis  we  will model  global distribution of  microbial  plant  pathogens under climate  and land-use  change scenarios. We will integrate local experimental data to establish causality informing scenario modelling. The project is supervised by François Buscot at the Helmholtz-Centre for Environmental Research (UFZ) in Halle, together with Anna Heintz-Buschart (UFZ/iDiv), Nico Eisenhauer (iDiv), Carlos Guerra (iDiv), and Kirsten Küsel (Friedrich Schiller University of Jena).

Links: https://www.idiv.de/fileadmin/content/Vacancies_PDF/Vacancies_2021/Postdoc_flexpool_UFZ_04_Buscot_2021_final.pdf https://apply.idiv.de

Phd project in “Single cell genomic approaches to study mitochondrial genetics and disorders”

Project description

Mitochondria are central to numerous physiological processes and are unique organelles that carry their own genome, often in high copy number, encoding a subset of proteins, transfer RNAs, and ribosomal RNAs essential to their function. Germline inherited mitochondrial DNA (mtDNA) mutations are a major cause of human disease and hundreds of point mutations and deletions have been associated with a variety of overlapping phenotypes, estimated to affect ~1 in 4,300 individuals, placing them among the most common inherited metabolic disorders. Mitochondrial diseases are characterized by remarkable heterogeneity and while variable heteroplasmy (fraction of mitochondrial genomes carrying a variant) of associated pathogenic mutations/deletions may present a natural modulator of disease severity, many syndromes include cell-type specific phenotypes. Moreover, the accumulation of somatic mtDNA mutations has been associated with ageing phenotypes and malignancies. However, establishing genotype-phenotype correlations on a cellular and molecular level has been challenging due to the unique nature of mitochondrial genetics that include variant heteroplasmy as a dynamic variable, but also tissue-dependent differences in mtDNA copy number, its cell cycle-independent turnover and the uncertainty about rates and mechanisms underlying accumulation of somatic variants. To bridge this gap, we develop and apply single cell multi-omic technologies to enable the linkage of an individual cells’ mtDNA genotype to its phenotype, such as its gene expression, protein expression and/or chromatin accessibility profile to enhance our understanding of mitochondrial genetics and underlying human disease. In particular, we are interested to understand adaptive genomic and cellular responses to high levels of pathogenic mtDNA or an increased mutational burden in cellular and animal models, including primary patient specimens.

Keywords

Single cell multi-omics, mitochondrial genetics, mitochondrial disease, hematology, immunology

Entry requirements

Strong interest in life sciences, computational biology, method development and/or translational research. Master’s degree in computer science, bioinformatics, biotechnology, biochemistry, engineering, mathematics, physics, biology, (molecular) medicine or a related field. Expertise and interest to work computationally and/or experimentally, in particular with (single cell) sequencing data. Projects can be tailored accordingly. We in particular encourage applications from students with a computational background. Strong motivation to work independently as well as in an interdisciplinary research team. Very good language and communication skills in English.

Lab Location

Berlin Institute of Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin

Starting date

Between August and December 2021

Funding

Limited to 3 years

How to apply

Please apply via the HFA application portal. The Hector Research Career Development Awardees will arrange interviews (via skype or if feasible in-person) with the most promising applicants. The final candidates will be invited for a personal presentation on July 8, 2021 in Bremen (Germany). The final decisions will be announced by August 2021.

Application Deadline

31.03.2021

Enquiries

For questions related to making your application, please contact Hector Fellow Academy Office: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! or www.hector-fellow-academy.de

 

Carry out your own PhD project! - In Single Cell Genomics and Mitochondrial Genetics supervised by Dr. Dr. Leif S. Ludwig (Berlin Institute of Health, Charité, Berlin Institute of Medical Systems Biology)

The Hector Fellow Academy offers you the opportunity to realize a self-developed research project under supervision of Dr. Dr. Leif S. Ludwig. He is a Hector Research Career Development Awardee working at the interface of biology and medicine. He specializes in the development and application of single cell multi-omic applications to study stem cells in hematology, immunology and oncology and how genetic variation and mutations in our mitochondrial genomes contribute to human diseases.

Keywords

Single cell multi-omics, mitochondrial genetics, mitochondrial disease, hematology, immunology

Entry requirements

Strong interest in life sciences, computational biology, method development and/or translational research. Master degree in computer science, bioinformatics, biotechnology, biochemistry, engineering, mathematics, physics, biology, (molecular) medicine or a related field. Expertise and interest to work computationally and/or experimentally, in particular with (single cell) sequencing data. Projects can be tailored accordingly. We in particular encourage applications from students with a computational background. Strong motivation to work independently as well as in an interdisciplinary research team. Very good language and communication skills in English.

Lab Location

Berlin Institute of Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin

Starting date

Between August and December 2021

Funding

Limited to 3 years

How to apply

Please apply via the HFA application portal. The Hector Research Career Development Awardees will arrange interviews (via skype or if feasible in-person) with the most promising applicants. The final candidates will be invited for a personal presentation on July 8, 2021 in Bremen (Germany). The final decisions will be announced by August 2021.

Application Deadline

31.03.2021

Enquiries

For questions related to making your application, please contact Hector Fellow Academy Office: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! or www.hector-fellow-academy.de

PhD project in “Systems biology approach for elucidating bacterial revival after antibiotic treatment”

Project description

Resistance of bacterial pathogens to antibiotics is a serious threat to global health, with a predicted death toll of at least 2.4 billion people worldwide in the next 30 years, and costs up to $US3.5 billion per year. New solutions to fight antimicrobial resistance are imperative, both to rescue old antibiotics and also to undermine resistance development to newly discovered ones. Antibiotic tolerance – a transient physiological state where bacteria can tolerate antibiotics without being resistant – is increasingly associated with the raise of resistance. Tolerant bacteria survive antibiotic treatment, and once the antibiotic is removed they are able to resume growth, thus leading to relapsing infections. The aim of this project is to elucidate molecular mechanisms of bacterial revival of the enteric pathogen Salmonella Typhimurium after antibiotic treatment using systems biology approaches. This project is an excellent opportunity for students who want to develop their computational skills in tight combinabion with experiments in bacterial genetics and physiology. We are a dynamic, highly collaborative, multidisciplinary team with access to cutting-edge robotic platforms, thus our lab offers the perfect environment for such projects. We welcome applications from highly motivated students eager to explore exciting and innovative ideas. Your background can be from broad disciplines ranging from Biology to Computer Science. Don’t hesitate to get in touch if you want to find out more. In fact, you are encouraged to do so!

Keywords

Pathogenic Bacteria, Antibiotics, Genomics, Systems Biology, High-throughput Screening

Entry requirements

MSc. Degree in Biotechnology, Bioinformatics, Biology, Molecular Biology, Computer Science or similar

Location

Chair of Microbiology, University of Würzburg, Germany

Starting date

September 2021 (flexible)

Funding

Limited to 3 years

How to apply

Please apply via the HFA application portal.

The Hector Research Career Development Awardees will arrange interviews (via skype or if feasible in-person) with the most promising applicants. The final candidates will be invited for a personal presentation on July 8, 2021 in Bremen (Germany). The final decisions will be announced by August 2021.

Application Deadline

31.03.2021

Enquiries

For questions related to making your application, please contact Hector Fellow Academy Office: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! or www.hector-fellow-academy.de

Doctoral Position in Systems Immunology & Data Sciences

The start date is May 1st, 2021 or by agreement. The position is available until January 31, 2023 with the aim for extension towards the finalization of your doctoral degree.

The University of Konstanz is one of the eleven Excellence Universities in Germany. Since 2007 it has been successful in the German Excellence Initiative and its follow-up programme, the Excellence Strategy.

This position is an exciting opportunity for you, if you wish to develop strong data science skills and gain knowledge in molecular immunology by conducting bioinformatics research towards a better understanding of immune cell identity and function. The position is available within the newly established research group of Tenure Track Prof. Dr. Andreas Gruber, which has a focus on developing and applying data science approaches to study gene expression regulation in health and disease (further information: https://gruber-sciencelab.netlify.app).

Amongst others, you will be using computational tools to analyze bulk as well as single-cell RNA sequencing data of immune cells aiming to study the transcriptional programs that regulate isoform diversity observed across immune cell subpopulations. The results of your work will contribute to current efforts to better understand the molecular mechanisms underlying immune cell function as well as immune cell-associated diseases, such as auto-immune disorders, but also cancers. You will also have the opportunity to work on your own data science approaches / tools, as required, and contribute to research collaborations of the lab. If you have some experience in programming and/or analyzing data and you would like to conduct a doctoral thesis with a focus on data sciences and systems immunology, we are looking very much forward to your application!


Your Competencies

 - A Master or equivalent in a relevant field (e.g. Bioinformatics, Informatics, Molecular Biology, Biotechnology, Biology, Statistics, Data Sciences)

 - Ability to work independently and as part of a team (in English language)

 - Passion to analyse large high-throughput sequencing datasets

 - Some experience in programming and/or analysing data (e.g. using R or Python)


Your responsibilities

 - Analyze data from high-throughput sequencing experiments

 - Explore and select appropriate data analysis approaches

 - Implement and document sequencing data analysis workflows

 - Apply and develop your own data science tools and approaches

 - Interpret analysis results and contribute to publications, presentations and funding proposals of the lab


We Offer

 - Excellent development opportunities, extensive training and an attractive remuneration package

 - An exciting interdisciplinary working environment at the interface of data sciences and molecular cell biology

 - The opportunity to extend your data science and informatics skill set, while gaining knowledge in systems immunology and the molecular basis of health and disease


If you have any additional questions, please get directly in contact via e-mail: andreas.j.gruber [.at.] uni-konstanz [.dot.] de

Please submit your application (motivation letter, CV, degree certificates incl. grades) in one single pdf file until March 11, 2021 via the Online Application Portal of the University of Konstanz: https://stellen.uni-konstanz.de/jobposting/72c6d1f07934f09e58cee61cdb187690d678817a0

PhD Position: Modeling microbial interactions in marine ecosystems

We are offering a PhD position (E13 TV-L HU, 65%) at the Institute for Theoretical Biology (ITB) of the Humboldt-University of Berlin.

The project seeks to understand (the evolution of) metabolic interactions between phototrophic and heterotrophic microorganisms and the "self-organization" of ecosystems. The tasks for the PhD project are primarily computational and include reconstruction and constraint-based analysis of genome-scale metabolic models of microbial organisms, in particular cyanobacteria.

The project is inspired by recent works that provide novel insights into phototroph-heterotroph interactions and division of labour in marine ecosystems. In collaboration with experimental partners, our aim is to develop quantitative computational models that explain the trade-offs and metabolic prerequisites of such interactions. In particular, our hypothesis is that the concept of "cellular resource allocation" offers a unique and novel angle to understand the constraints and energetic trade-offs that govern the emergence of dependencies between photo- and heterotrophic microorganisms. The planned work directly builds upon our recent works to describe microbial/cyanobacterial resource allocation and growth:

- Sharma S and Steuer R (2019) Modeling microbial communities using biochemical resource allocation analysis. J. R. Soc. Interface 16: 20190474.
- Zavřel T et al. (2019) Quantitative insights into the cyanobacterial cell economy. eLife 2019;8:e42508
- Reimers AM et al. (2017) Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth. Proc Natl Acad Sci U S A. pii: 201617508.

In addition to the usual requirements (a passion for the topic, a university degree (typically M.Sc. in an appropriate field), very good programming skills in python or matlab, ...), the ideal candidate would have some experience with/strong interest in computational models of metabolism, constraint-based analysis of metabolism, biochemistry, comparative genomics and/or related concepts.  

The formal call and further instructions are available on the webpage of the HU (in german only, Reference: DR/012/21, the german text takes precedence):  https://www.personalabteilung.hu-berlin.de/de/stellenausschreibungen/wissenschaftliche-r-mitarbeiter-in-m-w-d-mit-65-v-h-d-regelm-arbeitszeit-e-13-tv-l-hu-drittmittelfinanzierung-befristet-bis-31-12-2023

The position will be embedded into the highly collaborative scientific environment here at the Institute for Theoretical Biology (ITB) in the center of Berlin, and offers further training opportunities, as well as the possibility to visit and work closely with our experimental partners.

Deadline for applications is March 2, 2021.

I am happy to also answer any questions or informal enquiries (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and would also encourage any students who are interested to send me an informal email.

Links: 

PostDoc Bioinformatik & Machine Learning für das Projekt „Glycosid Produktion“

An der Professur für Bioinformatik (https://bit.cs.tum.de) am TUM Campus Straubing für Biotechnologie und Nachhaltigkeit als kooperierende Forschungseinrichtung der Hochschule Weihenstephan-Triesdorf sowie der Technischen Universität München, ist vorbehaltlich der endgültigen Zuwendung seitens des Projektträgers, folgende Vollzeitstelle zu besetzen:

Wissenschaftliche Mitarbeiterin/Wissenschaftlicher Mitarbeiter (m/w/d) für das Projekt "Glycosid Produktion"

Die Stelle ist befristet bis zum 31.12.2022.

Ihr Aufgabengebiet:
Wir suchen einen hochmotivierten, exzellenten Bewerber (m/w/d) als Postdoktoranden (m/w/d) im Be- reich Bioinformatik und des maschinellen Lernens, um die kürzlich gegründete Synthetic Biology Foundry der TUM am Campus Straubing weiterzuentwickeln (SynBiofoundry@TUM). Hierfür sollen neuartige bioinformatische Methoden und Verfahren des maschinellen Lernens zur Analyse von komplexen biologischen Daten entwickelt werden:

  • Sie unterstützen die Weiterentwicklung der Infrastruktur der Synthetic Biology Foundry und helfen bei der Etablierung ein standardisiertes Setup zur Automatisierung eines Hochdurchsatz Design- Build-Test-Learn Zyklus
  • Sie arbeiten in enger Zusammenarbeit mit unseren Industriepartnern an projektrelevanten For- schungsfragen im Learn Cycle
  • Sie entwickeln neuartige bioinformatische Algorithmen und Machine Learning Methoden zur Analyse von unterschiedlichen biologischen Daten, insbesondere von OMICS Daten (z. B. DNAseq, RNAseq)
  • Sie entwickeln und erweitern Cloud-basierte Webanwendungen und Datenbanken zur Analyse biologischer Daten
  • Sie schreiben wissenschaftliche Veröffentlichungen und präsentieren wissenschaftliche Ergebnisse auf internationalen Konferenzen

Ihr Profil:
Sie haben Interesse an eigenständigem wissenschaftlichen Arbeiten. Darüber hinaus arbeiten Sie ziel- orientiert, verfügen über ein analytisches Denkvermögen sowie eine wissenschaftliche Neugier und sind teamfähig. Des Weiteren besitzen Sie fundierte Englischkenntnisse in Wort und Schrift sowie hervorra- gende Programmierkenntnisse, vorzugsweise in Python, C/C++. Exzellente Kenntnisse in den Berei- chen Bioinformatik, der Analyse von OMICS Daten (insbesondere von RNASeq Daten) und des ma- schinellen Lernens runden Ihr Profil ab.

Einstellungsvoraussetzungen:
Sie besitzen ein abgeschlossenes wissenschaftliches Hochschulstudium (Diplom [Uni] oder Master) und einen Doktor im Bereich der Bioinformatik, Biotechnologie, Informatik, Statistik oder in einem vergleich- baren Studiengang.

Wir bieten Ihnen:

  • Bezahlung nach dem Tarifvertrag für den öffentlichen Dienst der Länder (TV-L)
  • ein modernes Hochschulumfeld
  • ein spannendes, vielseitiges und verantwortungsvolles Tätigkeitsfeld
  • kollegiale Zusammenarbeit und vielfältige Austauschmöglichkeiten
  • die Möglichkeit zur Fort- und Weiterbildung
  • Sozialleistungen nach den Regelungen des Tarifvertrages für den öffentlichen Dienst der Länder (TV-L), insbesondere zusätzliche Altersversorgung sowie Jahressonderzahlungen
  • attraktive Nebenleistungen wie ein Jobticket für den öffentlichen Personenverkehr, vermögenswirksame Leistungen
  • ein wachsendes Angebot im Rahmen eines Behördlichen Gesundheitsmanagements
  • ein familienfreundliches Arbeitsumfeld mit flexiblen Arbeitszeiten

Hinweise:
Die Einstellung soll zum nächstmöglichen Zeitpunkt erfolgen. Die Bezahlung erfolgt nach den tarifrecht- lichen Bestimmungen, bei Vorliegen der persönlichen Voraussetzungen bis Entgeltgruppe 13 TV-L. Die Tätigkeit ist unter Berücksichtigung der dienstlichen Erfordernisse grundsätzlich auch für eine Teilzeit- beschäftigung geeignet. Bei ansonsten im Wesentlichen gleicher Eignung, Befähigung und fachlicher Leistung werden schwer- behinderte Menschen bevorzugt eingestellt. Die Bewerbung von Frauen wird ausdrücklich begrüßt.

Sie wollen Teil unseres Teams werden?
Wir freuen uns auf Ihre Bewerbung über unsere Homepage (http://www.hswt.de/stellenangebote.html?stelle=968) mit Anschreiben, Lebenslauf und Zeugnissen sowie Liste an Publikationen und Kontaktinformation von drei Referenzen bis zum 15.03.2021. Bitte bewerben Sie sich ausschließlich über den Button "Auf diese Stelle bewerben" (Online-Formular). Bewerbungen per Post oder per E-Mail werden nicht berücksichtigt.



Links:
Webseite der Forschungsgruppe: www.bit.cs.tum.de

Webseite der SynBiofoundry@TUM: https://www.cs.tum.de/forschung/synbiofoundry/

Online Stellenportal: http://www.hswt.de/stellenangebote.html?stelle=968

Bioinformatician within large metastasis research consortium

The Transregio TRR 305 is a DFG-funded collaborative research consortium between the Universities of Regensburg, Erlangen, and the Fraunhofer Society (https://www.experimentelle-medizin.de/verbundforschung). It focuses on the mechanisms of early metastasis formation with the goal to identify novel therapies to effectively treat systemic cancer. It will become one of the largest metastasis research consortia in Europe with an expected duration of 12 years. It comprises 18 research and three core projects. For the core project Z01, we are looking for a

 

Bioinformatician (m/f/d)

 

based in Erlangen to support project partners in the bioinformatics analysis of omics data.

 

Your tasks will include:

  • setting up and maintaining pipelines for sequencing data analyses (bulk and single-cell RNA-Seq, ATAC-Seq, ChIP-Seq);
  • closely interacting with CRC project partners to support post-processing analyses of omics data (e.g. functional enrichment, visualisation and interpretation of results, data integration with publicly available datasets, preparation of publication-ready figures);

Your qualifications:

  • academic degree (MSc/PhD) in bioinformatics, computational or life sciences. A PhD is preferred but not essential.
  • prior experience in the analysis of next-generation sequencing data is advantageous;
  • familiarity with working in a Linux/Unix environment;
  • strong programming skills (e.g. Python, Perl, R);
  • excellent communication skills and fluency in English.

 

Applications should be sent to Dr. Fulvia Ferrazzi, Institute of Pathology, FAU Erlangen-Nürnberg (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and Wencke Wallusch (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!), and include a letter of interest, a CV (containing a list of publications, if applicable), a brief description of research experience, as well as contact information of two references.

 

The position is available for 4 years, with the possibility of extension. The starting date is the earliest possible timepoint. Deadline for applications is 05.03.2021

ostDoc Position (m/f/d) in the project Nanopore sequencing for decentralized pathogen identification

 

Job offer ref. #11-21003

 

The Senckenberg Gesellschaft für Naturforschung (SGN) is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. SGN conducts natural history research with almost 800 employees and research institutions in six federal states. Within SGN, the Senckenberg Biodiversity and Climate Research Centre (BiK-F) explores the interactions between biodiversity, climate, and society.

 

Senckenberg BiK-F invites applications for a

 

 

 

PostDoc Position (m/f/d) in the project

 

Nanopore sequencing for decentralized pathogen identification

 

(100 %)

 

 

 

The position is in the research group of Professor Marco Thines at the Senckenberg Biodiversity and Climate Research Centre. The research conducted in this group spans a wide range of disciplines and topics including cell biology, ecology, evolutionary biology, genomics and plant-pathogen interactions of oomycetes. Their aim is to gain insights in the biodiversity of oomycetes and a deeper knowledge of the evolutionary processes that have shaped oomycete diversity and their biotic interaction.

 

You will initially work in the project: “Securing the future of agriculture through mobile, biopore-based, universal high-throughput sequencing for the detection of plant pathogens and parasites (AGRIFUTURE)”, funded by the BMEL. 

 

Your profile:

 

·       PhD in evolutionary biology, ecology, bioinformatics, microbiology, or related field

 

·       Strong publication record showing keen interest in nanopore sequencing

 

·       Excellent communication and writing skills in English

 

·       Bioinformatics skills, including NGS data analysis, e.g. de novo genome assembly, metabarcoding, metagenomics, transcriptomics

 

·       Laboratory experience, e.g. DNA extraction, library construction

 

·       Creativity, ambition, analytical and collaborative skills

 

 

 

Salary and benefits are according to a full-time public service position in Germany (TV-H E 13, 100 %). The contract should start as soon as possible - ideally on March 15th, 2021 - and will initially be limited until 14.02.2024.

 

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, Germany.

 

Please send your application, mentioning the reference of this job offer (ref. #11-21003) before February 28th, 2021 by e-mail (attachment in a single pdf document) and including a cover letter detailing research interests and experience, a detailed CV and a copy of your certification to:

 

Senckenberg Gesellschaft für Naturforschung

 

Senckenberganlage 25

 

60325 Frankfurt am Main

 

E-Mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

 

For more information contact Prof. Marco Thines (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).

Postdoctoral researcher (bioinformatician) [ITEM]

The Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM) in Hannover has an opening for a Postdoctoral researcher (bioinformatician) for managing research projects in different areas of biomedical data analysis. We are looking for a highly qualified person with a PhD degree in Computer Science or Bioinformatics with expertise in biomedical data management. You will become part of a dynamic team in an exciting and innovative research environment at the interface between biotechnology, medicine and computer science.  You will significantly shape our application-oriented technological solutions and further expand the data analysis capacities at the Fraunhofer ITEM. You will use the Fraunhofer Life Science infrastructure and up-to-date information technologies.
Positions are open to all qualified persons independent of gender, disabilities, religion, etc...
Please submit your application via the Fraunhofer Recruiting portal.

Links:
Job announcement: https://recruiting.fraunhofer.de/Vacancies/56703/Description/2

and ITEM homepage:
https://www.item.fraunhofer.de/en.html

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