FORMATION ON : PubMed

Prsentation PowerPoint

FORMATION ON :

PubMed Prepared by Diane Sauv, B. Sc., M. Bibl.April 20141

PUBMED Go to: sdis.inrs.caAt the left, click in: Bases de donnesIn the box Titre, write Pubmed and click on GoClick on Pubmed2

PUBMEDStarted in 1996 is covering over 23.6 million citations

Oldest citations in PubMed date in 1809

5 citations sources: free access to Medline, Pubmed, PubMed-in process, PubMed-as supplied by publisher and PubMed-OldMedline

Database of literature citations, primarily for articles from journals in the life sciences, but also for books and technical reports that are included in the NCBI bookshelf

Made 2.5 billion of searches for 2013 in Medline/Pubmed

Developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM)

PUBMED : MEDLINEPrimary component of PubMed with more than 21 million citations

Subject scope of MEDLINE is medicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences

Since 2005, between 2,000-4,000 completed references with Medical Subject Headings are added each day Tuesday to Saturday

+735,000 citations indexed in 2013

Citations from 1946

PUBMED : MEDLINESmall number of newspapers, magazines, newsletters and 5,652 worldwide journal titles (November 2013)

Journals in 39 languages (60 languages for older journals)

Citations added from 2010-2012: about 93% are published in englishabout 84% have english abstracts written by authors of the articles

PUBMED : ADVANCED RESEARCH

PUBMED : SEARCH FIELDS

PUBMED : SEARCH FIELDS

PUBMED : DISPLAY FIELDS

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Enter the authors last name followed by a space, plus the first 2 initials of the given name without punctuation followed by a space and all suffixes at the end (e.g. Vollmer Charles Jr)

PubMed automatically truncates a search for an author's name, e.g., o'brien [au] = o'brien ma, o'brien kr, o'brien d o'brien j [au] = o'brien ja, o'brien jb, o'brien jc jr, o'brien j

To turn off this automatic truncation : enclose the authors name in double quotes and tag with [au] in brackets

PUBMED : AUTHOR

PUBMED : AUTHOR

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PUBMED : AUTHOR

Estimation of more than 2880 author nameshttp://www.ncbi.nlm.nih.gov/pubmed/2447625815

J. Virol. 2012, 86 (8) : 4380-43933

PUBMED : AUTHOR

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PUBMED : AUTHORFull author name may be searched for references published from 2002 forward if the full author name is available in the article

PUBMED : AUTHOR AFFILIATIONAuthor, Corporate Author, and Collaborator Affiliation Display Changes 2013 December 24Effective December 16, NLM now includes Author Affiliations for all Authors, Corporate Authors and Collaborators in PubMed if the data are supplied by publishers in their XML submissions for MEDLINE indexed journals

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PUBMED : JOURNAL

Enter the journal name or abbreviation

J. Virol. 2012, 86 (8) : 4380-4393

J. Virol. 2012, 86 (8) : 4380-4393

PUBMED : SELECTED TERMSLatent membrane protein 1LMP 1

Epstein-Barr virus

Apoptosis

B cellsABCDANDANDAND

J. Virol. 2012, 86 (8) : 4380-4393


1234Make selection of desired expressions

PUBMED : HISTORY

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PUBMED : HISTORY

1 Clic the left button

PUBMED : HISTORY

PUBMED : HISTORYLatent membrane protein 1

Latent membrane proteins 1Latent membrane protein1Latent membrane proteins1No result

Latent membrane protein* AND 1

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Come from: Show index listIf you choose this strategy, you will not have the MeSH

PUBMED : MeSH - MAIN HEADINGSMeSH : Medical Subject Headings

MeSH is the controlled vocabulary used for indexing articles for the MEDLINE subset of PubMed

Published since 1954

MeSH terms are arranged hierarchically (tree structure) by subject categories with more specific terms arranged beneath broader terms

It is updated weekly and reviewed annually

MeSH in english-french, english-swedish and english-spanish-portuguese: HTTP://mesh.inserm.fr

PUBMED : MeSH

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PUBMED : MeSH HEADINGSGive more complete results because you have no more problem of spelling variations, synonyms and near-synonyms

Give greater accuracy using the major descriptor ( MeSH major topic)

Permit to specify particular aspects of a descriptor in using subheadings

However, the references bearing the PubMed-in process and PubMed- as supplied by publisher or Pubmed status are not found because they have not yet or they will not received descriptors

However, if the research focuses on a new topic or subject very sharp, it could be that you dont find a MeSH or you find a too generic MeSH

PUBMED : MeSHThe MeSH types included:

Main Headings

Subheadings

Publication types

Geographics

Supplementary concept records34

PUBMED : MeSH - MAIN HEADINGSThe MeSH 2014 included 27 149 MeSH Headings in 16 categories:

PUBMED : MeSH - MAIN HEADINGS

11 MeSHMeSH Heading : Subject analysts examine each article and assign the most specific MeSH terms applicable, with a related subheading; typically 10 to 12 headings per citation[mh] or [MeSH]

PUBMED : MeSH

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PUBMED : MeSH

PUBMED : MeSH

PUBMED : MeSH - SUPPLEMENTARY CONCEPTS Formely called Supplementary chemical records

219,266 headings

Used to index chemicals, drugs and other concepts such rare diseases for Medline

Searched by Substance name [NM]

No tree numbers

Updated weekly

PUBMED : HISTORY

J. Virol. 2012, 86 (8) : 4380-4393

PUBMED : HISTORY

#6#7#9#8#4#543

PUBMED : HISTORY

Try: Epstein Barr viruses

PUBMED : MeSH

PUBMED : MeSH

PUBMED : MeSH - SUBHEADINGS


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SubheadingsSubheadings : are used to help describe more completely a particular aspect of a subjectThe subheadings logically paired with the main heading2 letters may be used for subheadings

PUBMED : RESEARCH STRATEGY

Pathogenicity of Epstein-Barr virus= ( A AND B) OR CAPathogen*BEpstein-Barr virusEBVHerpesvirus 4, Human/PathogenicityC51

PUBMED : HISTORY

PUBMED : MeSH

PUBMED : MeSH - MAJOR TOPICS

MAJRMajor Topics : used [majr] to restrict a search to citations where the term is the major topic or focus of the article, in the display reference , its represented by an asterisk

PUBMED : MeSH

PUBMED : MeSH

Generic termsSpecific terms

PUBMED : MeSH - EXPLOSION

What you cannot see in Search details:The terms that are more specific under Herpesviridae in the MeSH they are also searched 57

PUBMED : MeSH - ENTRY TERMS

Many synonyms, near-synonyms, and closely related concepts are included as entry terms to help users find the most relevant MeSH descriptor for the concept they are seeking

J. Virol. 2012, 86 (8) : 4380-4393

PUBMED : HISTORY

Do we have to add cell death?

PUBMED : MeSH - ASSOCIATED TERMS

J. Virol. 2012, 86 (8) : 4380-4393

PUBMED : HISTORY

B cell

B cells

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PUBMED : HISTORY

The maximum number of searches available in History is 100History will be lost after 8 hours of inactivity64

Smallpox virushttp://www.flickr.com/photos/sanofi-pasteur/5280407684/in/photostream/

PUBMED : AUTOMATIC TERM MAPPINGUntagged terms that are entered in the search box are matched (in this order) against :MeSH translation tableJournals translation tableFull Author translation tableAuthor indexFull Investigator (Collaborator)translation tableInvestigator (Collaborator) index

PUBMED : AUTOMATIC TERM MAPPINGThe MeSH Translation Table contains:

MeSH TermsSee-reference mappings (also known as entry terms) for MeSH terms MeSH SubheadingsPublication TypesPharmacologic ActionsTerms derived from the Unified Medical Language System (UMLS) that have equivalent synonyms or lexical variants in EnglishSupplementary Concepts (chemical, protocol or disease terms) and their synonyms67

PUBMED : PUBLICATION TYPES

: 7368

PUBMED : PUBLICATION TYPES

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PUBMED : AUTOMATIC TERM MAPPINGWhen a match is found for a term or phrase in a translation table the mapping process is complete and does not continue on to the next translation table

When you enter your search terms as a phrase, PubMed will not perform automatic term mapping that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy

If no match is found, PubMed breaks apart the phrase and repeats the above automatic process untill a match is found. Pubmed ignores stopwords in searches

If there is no match, the individual terms will be combined with AND together and searched in all fields

PUBMED : STOPWORDS

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PUBMED : AUTOMATIC TERM MAPPING

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PUBMED : AUTOMATIC TERM MAPPINGTerms enclosed in double quotes will be searched in all fields and not processed using automatic term mapping"Herpesvirus 4, human"

Herpesvirus 4, human

Herpesvirus 4, human[MeSH Terms]

PUBMED : AUTOMATIC TERM MAPPINGTruncation, quotes, search tags turn off automatic term mapping and the process that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy

N.B. If a truncated term (e.g., tox* for toxic, toxicologic, toxicology, toxicological, toxicologist, toxicologists ) produces more than 600 variations, a warning message displays to lengthen the root word to search for all endings

Herpesvirus*

PUBMED : AUTOMATIC TERM MAPPINGTruncation turns off automatic term mapping and the process that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy

Herpesvirus

Herpesviruses75

PUBMED : RECIPE FOR AN OPTIMAL RESEARCHPut a word or phrase without quotes

Make a second search with the plural of the word or the phrase without quotes

Dont forget to also search with abbreviations

Use the Show search details for points 1-3 to correct the terms or expressions displayed within the Show search details

See if you can find a descriptor and if so, look in the MeSH database for additional information to modify the search

Put the phrase in double quotes or use the truncationPUBMED :

Pseudomonas aeruginosahttp://phil.cdc.gov/phil/home.asp77

PUBMED : TERM SUGGESTED

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PUBMED : AUTHOR KEYWORDSAuthor Keywords in PubMed (2013 February 07)PubMed now displays author keywords when supplied by publishers. NLM will not review author keywords for accuracy or add them to non-publisher supplied citations. Author keywords can be searched untagged or using the Other Term [OT] or Text Words [TW] tags

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PUBMED : DISPLAY SETTINGS

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PUBMED : DISPLAY SETTINGS - SUMMARY

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PUBMED : DISPLAY SETTINGS - SUMMARY

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PUBMED : DISPLAY SETTINGS - SUMMARY - TEXT

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PUBMED : DISPLAY SETTINGS - SUMMARY - TEXT

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PUBMED : DISPLAY SETTINGS - ABSTRACT

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Structured abstract87

PUBMED : DISPLAY SETTINGS - STRUCTURED ABSTRACTFormats were developed in the late 1980s and early 1990s

To assist health professionals in selecting clinically relevant and methodologically valid journal articles

To guide authors in summarizing the content of their article

To facilitate the peer-review process

To enhance computerized literature searching

Standardized formats for structured abstracts have been defined for original research studies, review articles and clinical practice guidelines88


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PUBMED : DISPLAY SETTINGS - ABSTRACT - TEXT

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92Date createdOrganization that supplied citation dataModification dateIssue

PUBMED : DISPLAY SETTINGS - MEDLINE

Pubmed unique identifierStatus tagCompletion dateISSNVolumePublication dateAbstractFull author nameAffiliationLanguagePaginationTitlePii or doi that serves the role of paginationAuthorGrant numberDate created93

PUBMED : DISPLAY SETTINGS - MEDLINEPublication typePlace of publicationFull journal titleEnzyme Commission or Registry number of CASMeSH termsOther identification numbersMeSH datePublication history status datePublication statusDate of electronic publicationJournal title abbreviationNLM unique IDSubsetDate the citation was added to PubMedCreate dateArticle identifierSource94

PUBMED : DISPLAY SETTINGS - XML

Xml (ExTENSIBLE Markup Language) is generally used for displaying and manipulating data in software applications95PUBMED :

Bacillus anthracishttp://phil.cdc.gov/phil/home.asp96

PUBMED : STATUS TAGS

PUBMED : STATUS TAG - PUBMED - AS SUPPLIED BY PUBLISHER

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PUBMED : STATUS TAG - PUBMED - IN PROCESS

Citations bibliographic data will be reviewed and indexed

PUBMED : STATUS TAG - PUBMED - INDEXED FOR MEDLINE

Citations have been indexed with MeSH terms, Publication Type, Substance Names, etcBibliographic data has been reviewed

PUBMED : STATUS TAG - PUBMED - OLDMEDLINEOver 2 million OLDMEDLINE citations, most without abstractsCitations originally printed in hardcopy indexes published from 1946 throught 1965 that have not yet had all of their original subject terms mapped to current MeSHPartially MeSH indexed Bibliographic data has been reviewedBibliographic data has been reviewed

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PUBMED : STATUS TAG - PUBMED

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PUBMED : STATUS TAG - PUBMED-BOOKS & DOCUMENTS

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PUBMED : STATUS TAG - PUBMED

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PUBMED : SAVE SEARCH




PUBMED :

Influenza virushttp://www.flickr.com/photos/sanofi-pasteur/5280410308/in/photostream/109

PUBMED : SIGN IN TO NCBI

PUBMED : SIGN IN TO NCBI

If you have an accountIf you need an accountPUBMED : PASSWORD

Most common passwords of 2013

http://splashdata.com/press/worstpasswords2013.htmPASSWORD112

How to select your password? by Burin Gerek

Take care of the lenght A good password must have at least 8 characters

Choose well your words Avoid words that can be found in a dictionary, the names of dogs, cats of fish or dates birth, to use the same code for your login or password

No note on your keyboard Avoid putting your password on a post-it and attach it to the keyboard or on the screen, or worse to store it in a computer filePASSWORDTranslation of : http://www.symantec.com/region/fr/resources/mots_passe.html113PUBMED : PASSWORD

How to select your password? by Burin Gerek

Use exotic characters It must be composed of at least 3 differents types of characters among the 4 existing types of characters (uppercase, lowercase, numbers and special characters) *

Choose a sentence, a poem or the title of a movie that you know and take the first letters to form the password, for example:: Gone with the Wind" = GwtW26#?

Change your passwords regularly

Translation of : http://www.symantec.com/region/fr/resources/mots_passe.html

* Translation of : http://www.cnil.fr/linstitution/actualite/article/article/securite-comment-construire-un-mot-de-passe-sur-et-gerer-la-liste-de-ses-codes-dacces/

PASSWORD114

PUBMED : NEW ACCOUNT TO NCBI

PUBMED : SEND TO FILE (ENDNOTE)

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PUBMED : SEND TO FILE (ENDNOTE)With Internet Explorer (test version: 11): see the slides 113, 115-118, 121

With Chrome (test version: 34.0.1847.116 m): see the slides 114-118, 121

With Firefox (test version 19.0): see slides 119-121117


With Internet Explorer (test version: 11)118


With Chrome (test version: 34.0.1847.116 m)119


With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)120






12With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)3123


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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)

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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)With Internet Explorer (test version: 11): see the slides 129, 132-133

With Chrome (test version: 34.0.1847.116 m): see the slides 130, 132-133

With Firefox (test version 19.0): see slides 131-133128

PUBMED : SEND TO CITATION MANAGER (ENDNOTE)With Internet Explorer (test version: 11)

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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)With Chrome (test version: 34.0.1847.116 m)

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12With Internet Explorer (test version: 11With Chrome (test version: 34.0.1847.116 m)With Firefox (test version 19.0)132


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PUBMED : SEND TO COLLECTIONS

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PUBMED : SEND TO COLLECTIONS

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PUBMED : SEND TO COLLECTIONS12

3Limit of 1,000 referencesLimit of 100 alphanumeric charactersNote that accounts that do not register any activity in 2 years will be deleted.136

PUBMED : SEND TO CLIPBOARD

To save references temporarily to selected citations from one or several searches. It will be lost after 8 hours of inactivity on PubMed or other NCBI databases. 231137


The maximum number of 500 references138

PUBMED : SEND TO CLIPBOARDReferences in the clipboard are representes by the search number #0

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12To remove all referencesTo remove selected references140

PUBMED : SEND BY E-MAIL

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PUBMED : SEND TO MY BIBLIOGRAPHY

PUBMED : SEND TO MY BIBLIOGRAPHY1234You need to identify yourself

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Limite: 500 rfrences tlcharges par bloc



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PUBMED :

Rabies virushttp://www.flickr.com/photos/sanofi-pasteur/5279807113/in/photostream/158

PUBMED : NCBI ACCOUNT SETTINGS

PUBMED : NCBI ACCOUNT SETTINGS

PUBMED : MY NCBI - CUSTOMIZE HOMEPAGE

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PUBMED : MY NCBI - CUSTOMIZE HOMEPAGE

PUBMED : MY NCBI - SITE PREFERENCES


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PUBMED : MY NCBI - SAVE SEARCH

Send to referencesEdit the strategy166

PUBMED : MY NCBI - MY BIBLIOGRAPHY

PUBMED : MY NCBI - RECENT ACTIVITY

Recent Activity is tracking your searches and records viewed for the last 6 months

PUBMED : MY NCBI - COLLECTIONS

PUBMED : MY NCBI - COLLECTIONS - FAVORITES

The Favorites collection which helps you keep a list of your preferred NCBI database records.


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PUBMED : MY NCBI - FILTERS

You can have up to 15 active filters using My NCBI 179


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The "Popular" category lists the most commonly requested filters according to each NCBI database.182


The "LinkOut" category groups records that have links to resources provided by outside organizations, such as full-text publications, biological databases, consumer health information, library holdings and research tools. These links provide supplemental information related to records in NCBI databases183

PUBMED : MY NCBI - FILTRES

The "Properties" category groups records according to specific criteria for each database184


The "Links" category groups records that have links to other NCBI databases185

PUBMED : FILTERSLinks to Web accessible full text articles (all available free of charge)Links to Web accessible full text articles (some may require subscription)186

PUBMED : FILTERS

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PUBMED : FILTERS

The "in process" and "supplied by publisher" citations may be excluded for some filter selections (article types, species, sex and ages) because they have not yet completed the MEDLINE indexing process188PUBMED :

Mycobacterium tuberculosishttp://phil.cdc.gov/phil/home.asp189OR

PUBMED : FIND RELATED DATA

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PUBMED : FIND RELATED DATA

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PUBMED : SINGLE CITATION MATCHER

The Single Citation Matcher searchs for a citation when you have some bibliographic information192


To find a specific reference193


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PUBMED : RELATED CITATIONS The Related citations See alllink will retrieve a pre-calculated set of PubMed citations that are closely related to the selected article. The related citations will be displayed in ranked order from most to least relevant, with the linked from citation displayed first

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RSS (Really Simple Syndication) is an XML-based format used to send new items or information to recipients who use RSS feed readersPUBMED: RSS196

PUBMED : RSS

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PUBMED : RSS

Drag and drop the XML icon onto the feed reader interface 1Click198

PUBMED : RSS

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PUBMED :SIGN OUTMost of the information in coming from the sites :

http://www.ncbi.nlm.nih.gov/pubmedhttp://www.ncbi.nlm.nih.gov/books/NBK3827/200

Web address to see again this presentation:

HTTP://SDIS.INRS.CA/

Under the heading :

Formations/Autoformations/Pubmed/Formation PowerPoint IAF : Anglais

EndNote formation

Michel Courcelles

# 4275

michel.courcelles @iaf.inrs.ca202

For comments:

Diane Sauv

# 4340

[email protected]

FORMATION ON : PubMed

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