Archive for the 'pubmed' Category

zotero, la première fois; installer zotero; lien avec Web Of Science

Zotero est une extension destinée au navigateur Mozilla Firefox qui propose un système de gestion bibliographique (collecte, gestion, export de références).

Zotero fonctionne dans votre navigateur Internet Firefox, qui doit être ouvert pour que vous puissiez accéder à vos bibliothèques de références. Vous n’avez pas besoin d’être en ligne, pour utiliser Zotero. Les fonctions telles que les notes, la recherche et l’organisation fonctionneront parfaitement bien hors ligne. Bien évidemment, vous ne serez pas en mesure de consulter les articles en ligne de votre collection ou d’acquérir d’autres documents en ligne.

Le seul besoin est Firefox 3.0 pour Windows, Mac, ou Linux et de télécharger puis installer zotero (www.zotero.org).

Pour installer zotero: télécharger sur (www.zotero.org) puis cliquer sur le fichier téléchargé (prenez la 2.0 dès octobre 2009), il s’installe. Puis redémarrer firefox puis aller dans le menu outils /modules complémentaires puis cliquez sur activer et redémarrer. Zotero affiche une fenêtre cliquez OK. Vous avez un joli « zotero » en bas à droite. Cliquez dessus.

La fenêtre Zotero contient l’intégralité de votre collection: les références bibliographiques et l’ensemble des documents et fichiers, notes, et autres éléments tels qu’images et captures de pages Internet.

http://www.zotero.org/support/fr/quick_start_guide

Intégrée au navigateur, cette extension repose sur un système de translators qui, associés à différents sites web, permettent d’extraire les métadonnées des pages consultées comme pubmed. Ces translators sont surtout disponibles pour des catalogues de bibliothèque, mais on en trouve aussi pour des librairies en ligne, Wikipédia ou Flickr.

Pour tester et faire sa première banque de données bibliographiques, aller sur pubmed puis lancer une recherche.

Un petit symbol apparait dans la barre en haut à droite (barre http:// de firefox), cliquez dessus et c’est magique: vos références sont incorporées dans votre banque!

C’est du « just one clic ».

——–english:

Zotero is, at the most basic level, a citation manager. It is designed to store, manage, and cite bibliographic references, such as books and articles. In Zotero, each of these references constitutes an item.

Every item contains different metadata, depending on what type it is. Items can be everything from books, articles, and documents to web pages, artwork, films, sound recordings, bills, cases, or statutes, among many others.

Try the following video:

http://www.zotero.org/static/videos/zotero_1_5_cast.flv

——

L’indexation des pdf nécessite deux autres outils: pdf2text pdfinfo…

Zotero vous les installe automatiquement:

aller dans le menu de zotero en cliquant sur le symbole d’une roue engrenage puis préférence puis recherche et cliquez sur installer.

Sinon en mode manuel:

sur PC: http://www.foolabs.com/xpdf/download.html

sur mac: http://users.phg-online.de/tk/MOSXS/

http://users.phg-online.de/tk/MOSXS/xpdf-tools-3.dmg

{Xpdf is an open source viewer for Portable Document Format (PDF) files. Xpdf should work on pretty much any system which runs X11 and has Unix-like (POSIX) libraries. You’ll need ANSI C++ and C compilers to compile it.}

Il contient ausi 2 fichiers pour extraire une ou des  images d’un pdf

(aussi dans  http://users.phg-online.de/tk/MOSXS/Extract_Images_From_PDF.dmg).

Extract_Images_From_PDF.dmg
A simple Droplet including source combining the capabilities of XPDF’ « pdfimages » tool, « convert » from ImageMagick and « sips » from MacOS X 10.3. It creates for each PDF dragged onto the application a single folder containing all placed images as PNG including a Macintosh thumbnail.
Très utile!!!!!!!!!!
——————-
pour ceux qui utilisent Web Of Science
sauvegarder au format bibtex sous web of science cela fait un fichier txt;
puis l’importer dans zotero.
——————-
http://wiki-urfist.unice.fr/wiki_urfist/index.php/Mémoriser/Zotero

Zotero va analyser le code source de la page HTML que vous lisez avec votre navigateur à la recherche de métadonnées standardisées de type Dublin Core ou des métadonnées spécifiques à un entrepôt d’information (Base de Données, Archive Ouvertes, Catalogues, …) pour lesquelles Zotero possède un filtre (Cf. fig A et B.)

Zotero affiche alors dans la barre d’URL une icône en fonction du type de documents ou de sources (plusieurs types : références bibliographiques multiples, référence unique, page web, vidéo, image, … cf fig C)

fig A

fig B

fig C

Image:IconZOTEO-75.jpg

En cliquant sur une de ces icônes vous insérez alors la référence au document en question dans la base zotero [2], qu’il s’agisse d’une (ou des) référence(s) bibliographique(s) issues de bases de données, de moteurs de recherche, de catalogues ou qu’il s’agisse encore d’une page web, d’une vidéo, d’une photo, … (cf fig D)

Selon les options souhaitées par le menu « préférences Image:Engrenage.jpg » une copie du fichier PDF de la référence bibliographique, une copie web de la page, de la photo, … pourra être téléchargée dans la base zotero et jointe à votre référence.

fig D

Quand zotero n’affiche pas d’icône dans la barre d’URL, il est possible d’ajouter une référence par les boutons Image:Chaine.jpgImage:Capture.jpgImage:Nouvel element.jpg.

  • le premier effectue une opération similaire à l’insertion de signet dans son navigateur. L’URl est insérée dans la base zotero, avec le titre de la page et la date de consultation (on voit là l’orientation bibliographique)
  • le deuxième réalise un enregistrement de la page web avec l’url et la date. On pourra ultérieurement l’annoter par le menuImage:Annotation.jpg
  • le troisième opère les deux actions précédentes en même temps.

[]… et après ?

Une fois les références (Bibliographiques ou signets) intégrées (et éventuellement les documents primaires joints), Zotero se comporte finalement comme d’autres outils de gestion de références bibliographiques :

  • possibilités de tri, de recherche, …
  • interaction avec des logiciels de traitement de texte pour une insertion facilitée des citations et gestion de la bibliographie (Cf. renvoi sur le texte adhoc dans le guide)
  • on notera une gestion des mots clés « à la mode 2.0 ». Possibilité de « taguer » les références par drag&drop.
  • on n’oubliera pas les possibilités d’exportation des références. Vous choisirez d’exporter votre bibliothèque (ou collection) en… (plusieurs exemples, non exhaustif) :
    • Zotero RDF pour échanger avec d’autres utilisateurs de zotero ou sauvegarder vos données (en attendant que Zotero Server et/ou Zotero commons soient opérationnels) en cochant par exemple « les notes » et « les fichiers ». Attention toutefois au poids de « l’export » (le dossier comprenant le fichier RDF + les répertoires de contenus)
    • BibteX, Refer-BibeX, pour échanger seulement vos références avec d’autres logiciels de gestion de références ( » en local » : Endnote, bibus, zotero, … ou « en ligne » CiteUlike, Bibsonomy, EndNoteWeb, …)
    • RIS, pour échanger vos références avec les notes avec d’autres logiciels de gestion de références qui acceptent ce format.

[]Développements

Pour connaître les développements à venir de Zotero vous pouvez

  • consulter en 1ere page le texte grisé.
  • plus précisément, vous rendre aussi sur la la roadmap
  • et puis n’oubliez pas l’actu de zotero

Ce qu’il convient de retenir, concernant les futurs développements, dans le contexte de cet article, c’est la possibilité de partager en ligne ses collections, notes et tags (motsclés) issus des bibliothèques zotero de plusieurs utilisateurs.

[modifier]Liens utiles

————

Compatible sites

Zotero will automatically work with many sites not listed here; the best way to find out if Zotero works is to give it a try!
If you find a site that works with Zotero but does not appear in the list below, please let us know by sending an email totranslators@zotero.org.

Fully Supported
ABC-CLIO tested 05 October 2006, 10:42pm
ABI-Inform tested 26 June 2007, 11:00am Supported through ProQuest
Academic Search Premier tested 19 February 2008, 3:21pm Through EBSCO
Agencia del ISBN tested 19 February 2008, 12:09pm
Agricola: National Agricultural Library tested 07 January 2008, 2:38pm
Aleph tested 12 January 2007, 12:00pm
Amazon.com tested 27 September 2006, 4:24pm Now supports international sites and retrieves data from Amazon’s API
American Chemical Society (ACS) Publications tested 12 January 2007, 11:15am
American Geophysical Union tested 19 February 2008, 5:09pm
American Geophysical Union’s Journals tested 03 August 2007, 3:39pm
American Institute of Aeronautics and Astronautics tested 07 April 2008, 12:00pm
American Mathematical Society Journals tested 22 February 2008, 9:48am
American Meteorological Society Journals Online tested 19 February 2008, 5:12pm
American Physical Society Journals tested 19 February 2008, 3:07pm Physical Review Letters, etc. through Scitation
American Social History Online tested 21 April 2008, 3:25pm
Ancestry.com tested 29 August 2007, 2:27pm
Answers.com tested 19 February 2008, 11:41am
Appalachian School of Law tested 27 September 2006, 2:29pm
Arizona State University Libraries tested 28 September 2006, 1:28pm
ARTFL Encyclopédie tested 29 August 2007, 2:14pm
arXiv – UK tested 26 February 2008, 10:34am
arXiv.org tested 27 November 2006, 11:05am
ASCE Research Library tested 20 February 2008, 11:18am
Association for Computing Machinery (ACM) tested 12 January 2007, 11:06am
ATLA Religion Database tested 26 June 2007, 10:56am Supported through EBSCO and OVIDSP
Auburn University Libraries tested 04 February 2008, 11:00am
Australasian and New Zealand Legal Information Institute tested 26 June 2007, 11:02am
BBC News tested 03 August 2007, 3:44pm
Bennington College Library Catalog tested 09 January 2007, 8:21pm
Berkeley Electronic Press Journals tested 20 February 2008, 10:39am
Biblio.com tested 26 February 2008, 10:32am
Biblioteca Nacional de Espana tested 19 February 2008, 3:53pm
Bibliothek der Berufsakademie Heidenheim tested 11 March 2008, 3:14pm
Bibliothek der Berufsakademie Karlsruhe tested 11 March 2008, 3:23pm
Bibliothek der Berufsakademie Lörrach tested 11 March 2008, 3:23pm
Bibliothek der Berufsakademie Mannheim tested 11 March 2008, 3:23pm
Bibliothek der Berufsakademie Ravensburg tested 11 March 2008, 3:23pm
Bibliothek der Berufsakademie Stuttgart tested 11 March 2008, 3:33pm
Bibliothek der Berufsakademie Villingen-Schwenningen tested 11 March 2008, 3:33pm
Bibliothek der Hochschule der Medien Stuttgart tested 11 March 2008, 3:33pm
Bibliothek der Hochschule für Gestaltung Schwäbisch Gmünd tested 11 March 2008, 3:33pm
Bibliothek der Hochschule für Musik Karlsruhe tested 11 March 2008, 3:23pm
Bibliothek der Hochschule für Polizei Villingen-Schwenningenv tested 11 March 2008, 3:35pm
Bibliothek der Hochschule für Technik Stuttgart tested 11 March 2008, 3:33pm
Bibliothek der Musikhochschule Stuttgart tested 11 March 2008, 3:33pm
Bibliothek der Pädagogischen Hochschule Schwäbisch Gmünd tested 11 March 2008, 3:33pm
Bibliothek der Staatlichen Akademie der Künste Stuttgart tested 11 March 2008, 3:33pm
Bibliothek der Staatlichen Hochschule für Musik und Darstellende Kunst Mannheim tested 11 March 2008, 3:23pm
Bibliothek der Zeppelin University Friedrichshafen tested 11 March 2008, 3:14pm
Bibliothek derBerufsakademie Suttgart, Aussenstelle Horb tested 11 March 2008, 3:14pm
Bibliothek des Badischen Landesmuseums Karlsruhe tested 11 March 2008, 3:23pm
Bibliothek des Landesmuseums für Technik und Arbeit Mannheim tested 11 March 2008, 3:33pm
Bibliothek des Mathematischen Forschungsinstituts Oberwolfach tested 11 March 2008, 3:23pm
Bibliothek des Staatlichen Seminars für Didaktik und Lehrerbildung (Gymnasien) Heilbronn tested 11 March 2008, 3:33pm
Bibliothek des Staatlichen Seminars für Didaktik und Lehrerbildung (Gymnasien) Rottweil tested 11 March 2008, 3:33pm
BIBSYS tested 03 August 2007, 3:44pm
Bioinfobank tested 22 February 2008, 9:45am
BioMed Central tested 03 August 2007, 3:39pm
BioOne tested 20 February 2008, 9:53am
BIUM tested 19 February 2008, 5:42pm
Blackwell Compass Journals tested 20 February 2008, 10:15am
Blackwell Synergy tested 12 January 2007, 10:56am
Bluefield College tested 27 September 2006, 2:33pm
Boston College Libraries tested 28 September 2006, 1:30pm
Boston University Libraries tested 28 September 2006, 1:30pm
Bridgewater College tested 27 September 2006, 2:33pm
Brigham Young University Library tested 28 September 2006, 1:43pm
British and Irish Legal Information Institute tested 26 June 2007, 11:03am
British Library Integrated Catalogue tested 11 December 2006, 10:45am
Brown University Library tested 28 September 2006, 1:54pm
Bryn Mawr Classical Review tested 20 February 2008, 10:11am
Bryn Mawr, Haverford, and Swarthmore Colleges Library Catalog tested 24 November 2006, 10:22am
BSZ – Südwestdeutscher Bibliothekskatalog tested 22 April 2008, 11:23am
CAB Abstracts tested 26 February 2008, 11:14am
Cambridge Scientific Abstracts tested 12 January 2007, 11:01am
Cambridge University Journals Online tested 19 February 2008, 1:15pm
Cambridge University Libraries tested 10 October 2006, 4:41pm
Canada Institute for Scientific & Technical Information (CISTI) tested 28 September 2006, 2:18pm
Canadian Legal Information Institute tested 26 June 2007, 11:03am
Carleton University Library tested 07 April 2008, 12:18pm
Case Western Reserve University Libraries tested 28 September 2006, 2:18pm
Catalogue of the Universiteit van Amsterdam tested 19 February 2008, 2:39pm
Center for Research Libraries Catalog tested 05 June 2007, 12:33pm
Chinese University of Hong Kong tested 29 October 2007, 1:18pm
Christopher Newport University tested 27 September 2006, 12:26pm
Chronicle of Higher Education tested 12 February 2008, 10:49am
CINAHL tested 26 June 2007, 10:56am Supported through EBSCO and OVID
CiNii (National Institute of Informatics – Japan) tested 21 February 2008, 4:59pm
CiteBase tested 12 January 2007, 11:45am
CiteSeer tested 05 October 2006, 10:45pm
CiteULike tested 18 January 2007, 10:34am
CiteULike tested 26 February 2008, 9:48am
City University of New York (CUNY) tested 06 November 2006, 9:59am
Cleveland State Libraries tested 26 October 2006, 4:18pm
Cleveland State University Libraries’ SCHOLAR tested 12 February 2008, 10:41am
COinS (ContextObjects in Spans) specification tested 12 January 2007, 12:07pm
College of William & Mary tested 24 May 2006, 12:26pm
Colorado State University Libraries tested 28 September 2006, 2:38pm
Columbia University Libraries tested 28 September 2006, 2:38pm
Concordia University, Montreal tested 03 March 2008, 2:13pm
Copac Academic and National Library Catalogue tested 30 April 2007, 12:00pm
Copernicus Publications tested 19 February 2008, 5:11pm
Cornell University Library tested 28 September 2006, 2:46pm
Cornell’s Legal Information Institute tested 26 June 2007, 11:06am
CrossRef tested 12 January 2007, 11:45am
CSA Illumina tested 19 February 2008, 1:07pm
CSIRO Publishing Journal tested 26 February 2008, 11:04am
Dartmouth College Library tested 28 September 2006, 2:52pm
Digital Humanities Quarterly tested 20 February 2008, 10:19am
Duke University Libraries tested 28 September 2006, 3:00pm
Eastern Connecticut State University Library tested 18 December 2007, 10:07am
Eastern Mennonite University tested 27 September 2006, 2:36pm
Eastern Virginia Medical School tested 27 September 2006, 2:39pm
EBSCOhost tested 05 October 2006, 10:40pm
École Normale Supérieure tested 03 July 2008, 2:47pm
Ecological Society Journals tested 20 February 2008, 10:41am
Education Week tested 03 August 2007, 3:46pm
Education Week tested 19 February 2008, 5:01pm
Edutopia tested 19 February 2008, 3:02pm
Edward Via Virginia College of Osteopathic Medicine tested 27 September 2006, 2:39pm
Embedded Resource Description Framework (RDF) tested 12 January 2007, 11:35am
Emerald tested 19 February 2008, 2:40pm
Emory & Henry College tested 27 September 2006, 2:45pm
Emory University Libraries tested 28 September 2006, 3:00pm
Engineering Village tested 26 July 2007, 11:17am
English Short Title Catalogue (ESTC) at the British Library tested 20 November 2006, 11:48am
Epicurious.com tested 29 August 2007, 2:27pm
ERIC: Education Resource Information Center tested 26 July 2007, 11:20am
European Educational Research Journal tested 21 February 2008, 4:51pm
Factiva tested 12 January 2007, 11:01am
Ferrum College tested 27 September 2006, 2:45pm
Florida State University Libraries tested 28 September 2006, 3:08pm
Folger Shakespeare Library tested 20 November 2006, 2:38pm
GBV: Gemeinsamer Verbundkatalog (Common Library Network) tested 03 August 2007, 3:41pm
George Mason University’s Library Catalog (all libraries) tested 26 September 2006, 11:18am
George Washington University Library tested 28 September 2006, 3:11pm
Georgetown University Library tested 28 September 2006, 3:11pm
Georgia Institute of Technology Library tested 28 September 2006, 3:17pm
Ghent University Catalogue tested 29 October 2007, 1:25pm
Glasgow Caledonian University: tested 27 November 2007, 11:25am
Google Books tested 27 September 2006, 4:31pm
Google Scholar tested 27 September 2006, 4:31pm
Grove Art Online tested 19 February 2008, 2:34pm
Grove Music Online tested 19 February 2008, 2:33pm
Hampden-Sydney College tested 27 September 2006, 2:48pm
Hampton University tested 27 September 2006, 2:48pm
Harvard University Library tested 27 September 2006, 4:18pm
Helsinki University Technology Library tested 26 February 2008, 11:16am
Highwire tested 12 January 2007, 11:10am
History Cooperative tested 05 October 2006, 10:44pm
Hochschulbibliothek Aalen tested 11 March 2008, 2:48pm
Hochschulbibliothek Albstadt-Sigmaringen tested 11 March 2008, 2:48pm
Hochschulbibliothek Biberach tested 11 March 2008, 3:14pm
Hochschulbibliothek der HTWG Konstanz tested 11 March 2008, 3:23pm
Hochschulbibliothek Esslingen tested 11 March 2008, 3:14pm
Hochschulbibliothek Kehl tested 11 March 2008, 3:23pm
Hochschulbibliothek Ludwigsburg tested 11 March 2008, 3:23pm
Hochschulbibliothek Mannheim tested 11 March 2008, 3:33pm
Hochschulbibliothek Nürtingen-Geislingen tested 11 March 2008, 3:33pm
Hochschulbibliothek Ulm tested 11 March 2008, 3:33pm
Hollins University tested 27 September 2006, 2:55pm
Hong Kong Academic Library Link tested 29 October 2007, 1:18pm
Hong Kong Institute of Education library tested 29 October 2007, 1:18pm
Houston Community College tested 11 January 2008, 8:34am
Howard University Libraries tested 28 September 2006, 4:21pm
HubMed tested 10 October 2006, 12:35pm
Hydrology and Earth System Sciences tested 20 February 2008, 9:52am
IDEAS: Economics and Finance Research tested 26 July 2007, 11:23am
IDS Zürich Universität tested 27 November 2007, 11:39am
IEEE Xplore tested 12 January 2007, 10:58am
Indiana University Libraries Bloomington and Indianapolis tested 12 June 2007, 5:31pm
Informationsverbund IDS Basel Bern tested 27 November 2007, 11:25am
Informaworld tested 22 February 2008, 9:44am
InfoTrac College Edition tested 05 October 2006, 10:39pm
InfoTrac OneFile tested 05 October 2006, 10:39pm
InnoPAC tested 12 January 2007, 11:35am
Institute of Physics tested 29 August 2007, 2:16pm
Inter Research Science Center tested 19 February 2008, 5:14pm
International Herald Tribune tested 26 July 2007, 11:26am
International Journal of Health Geographics tested 19 February 2008, 4:46pm
Iowa State University Library tested 28 September 2006, 4:35pm
James Madison University tested 27 September 2006, 12:30pm
Johns Hopkins University Libraries tested 28 September 2006, 4:35pm
Journal of Vision tested 26 February 2008, 11:02am
JSTOR tested 05 October 2006, 10:42pm
Kent State University Libraries tested 28 September 2006, 4:40pm
LA Times tested 03 August 2007, 3:46pm
Laurentian University library catalog tested 01 November 2007, 2:40pm
LexisNexis tested 05 October 2006, 10:40pm
Liberty University tested 27 September 2006, 3:04pm
Library of Congress tested 27 September 2006, 4:18pm
Library of Virginia tested 27 September 2006, 2:25pm
LibraryThing tested 19 February 2008, 12:12pm
LIBRIS: Swedish National Union Catalogue tested 21 April 2008, 3:25pm
Lincoln University library catalogue tested 31 October 2007, 9:08am
Longwood University tested 27 September 2006, 12:30pm
Los Angeles Times tested 19 February 2008, 3:28pm
Lund University Library tested 24 April 2007, 9:41am
Lyell Collection: Geological Society Publications Online tested 22 February 2008, 1:56pm
Lynchburg College tested 27 September 2006, 3:04pm
Marquette University Libraries tested 10 October 2006, 12:33pm
Marymount University tested 27 September 2006, 3:10pm
MathSciNet tested 12 January 2007, 11:10am
Max Planck Institute for the History of Science: Virtual Laboratory Library tested 19 February 2008, 12:05pm
McGill University tested 24 November 2006, 10:34am
MEDLINE tested 19 February 2008, 1:55pm Through EBSCO
Microfinance Gateway Library tested 20 February 2008, 10:01am
MLA International Bibliography tested 19 February 2008, 11:12am Through GALE InfoTrac
Nanyang Technological University Library tested 21 April 2008, 3:24pm
NASA ADS tested 26 July 2007, 11:17am
National Bureau of Economic Research: Working Papers tested 26 July 2007, 11:26am
National Chengchi University Library tested 24 November 2006, 10:46am English version
National Library of Medicine at NIH tested 02 April 2007, 11:54am
National Library of Scotland tested 20 February 2008, 10:13am
National Library of Sweden tested 13 February 2008, 11:52am
National Library of Turkey tested 03 July 2008, 2:45pm
National Taiwan University Library tested 26 June 2007, 10:30am
Nature tested 12 January 2007, 10:58am
NBER (National Bureau of Economic Research) tested 19 February 2008, 2:30pm
Netzwerk von Bibliotheken und Informationsstellen in der Schweiz tested 27 November 2007, 11:39am
New York Public Library tested 06 November 2006, 9:59am
New York Review of Books tested 27 September 2006, 4:33pm Saves separate articles but not full issues.
New York Times tested 27 September 2006, 4:24pm Including TimesSelect Content
New York University tested 07 October 2006, 2:57pm
New Zealand Herald tested 29 August 2007, 2:25pm
Norfolk State University tested 27 September 2006, 12:35pm
Northeastern University Libraries tested 02 April 2007, 11:54am
Northwestern University Libraries tested 06 November 2006, 10:01am
OAIster tested 19 February 2008, 5:16pm
OCLC WorldCat/FirstSearch tested 05 October 2006, 12:00am
Ohio Link Library Catalog tested 12 February 2008, 10:44am
Ohio State University tested 26 October 2006, 4:25pm
OhioLink tested 26 October 2006, 4:25pm
Old Dominion University tested 27 September 2006, 12:35pm
Optics InfoBase tested 19 February 2008, 1:18pm
OpticsInfoBase tested 29 August 2007, 2:14pm
Oregon State University tested 05 June 2007, 12:31pm
OvidSP tested 12 January 2007, 10:45am
Oxford University Libraries tested 10 October 2006, 4:41pm
Pacific Lutheran University tested 10 January 2008, 8:52am
Pädagogische Zentralbibliothek Stuttgart tested 11 March 2008, 3:33pm
Patent Lens tested 08 January 2008, 8:48am
Philosopher’s Imprint tested 19 February 2008, 5:05pm
Philosopher’s Index tested 19 February 2008, 11:15am Through OvidSP
Physical Review Online Archive tested 05 April 2007, 5:53pm
Pion Journals including Perception tested 26 February 2008, 10:58am
Portland State University Library tested 21 April 2008, 3:24pm
POSTECH Library Catalog tested 04 May 2007, 12:16pm
Project Muse tested 05 October 2006, 10:44pm
ProQuest Digital Dissertations & Theses tested 19 February 2008, 1:39pm
ProQuest Research Library tested 05 October 2006, 12:00am
PsycARTICLES tested 30 April 2008, 10:51am Supported through EBSCO
Public Library of Science Journals tested 19 February 2008, 5:07pm
PubMed tested 05 October 2006, 10:45pm
Purdue University Libraries Catalog tested 07 December 2006, 4:58pm
Radford University tested 27 September 2006, 12:40pm
Randolph-Macon College tested 27 September 2006, 3:14pm
Randolph-Macon Woman’s College tested 27 September 2006, 3:14pm
Regent University tested 27 September 2006, 3:19pm
ReliefWeb tested 20 February 2008, 10:00am
Rensselaer Polytechnic Institute tested 25 October 2006, 3:06pm
Revues.org tested 26 February 2008, 10:41am
RIS file format tested 12 January 2007, 11:28am Many web-based scholarly resources that allow you to export in RIS format, such as Scirus, a search engine for scientific content, should now be Zotero-compatible, provided you’ve checked « Use Zotero for downloaded RIS/Refer files » in the Zotero preferences.
Roanoke College tested 27 September 2006, 3:19pm
Roanoke Higher Education Center tested 27 September 2006, 2:25pm
Royal Historical Society Bibliography of British and Irish History tested 19 February 2008, 2:53pm
RSC Publishing tested 29 August 2007, 2:16pm
RSC Publishing tested 29 August 2007, 2:17pm
Rutgers University Libraries tested 19 January 2007, 2:32pm
Sage Journals Online tested 22 February 2008, 10:57am
SAO/NASA Astrophysics Data System tested 19 February 2008, 3:24pm
SciELO – Scientific Electronic Library Online tested 20 February 2008, 11:20am
Science tested 21 April 2008, 3:25pm
Science Links Japan tested 21 February 2008, 5:00pm
ScienceDirect tested 12 January 2007, 10:45am
Scitation database tested 05 April 2007, 5:53pm
Scopus tested 13 February 2008, 11:54am
Shenandoah University tested 27 September 2006, 3:26pm
SirsiDynix tested 12 January 2007, 11:28am
SlideShare tested 26 February 2008, 10:35am
SPIE Digital Library tested 26 July 2007, 11:20am
SPIRES tested 29 August 2007, 2:53pm
SpringerLink tested 12 January 2007, 10:56am
Staatliche Kunsthalle Karlsruhe tested 11 March 2008, 3:23pm
Stanford Encyclopedia of Philosophy tested 03 July 2008, 2:26pm
Stony Brook University, SUNY, Libraries tested 07 October 2006, 2:57pm
Summit: Orbis Cascade Academic Union Catalog tested 26 July 2007, 2:44pm
Sweet Briar College tested 27 September 2006, 3:40pm
Sydney Morning Herald tested 29 August 2007, 2:25pm
Syracuse University Library tested 19 November 2006, 4:20pm
Système universitaire de documentation (SUDOC) tested 23 May 2007, 9:08am
Tate Library and Hyman Kreitman Research Centre. tested 07 January 2008, 2:56pm
Texas A&M University tested 10 January 2008, 8:52am
Texas A&M University Medical Sciences Library tested 10 January 2008, 8:53am
The Age tested 29 August 2007, 2:24pm
The Australian tested 29 August 2007, 2:24pm
The Economist tested 29 August 2007, 2:20pm
The Free Dictionary tested 19 February 2008, 11:46am
Thomas Branigan Memorial Library tested 30 October 2006, 6:56am
Thomas Jefferson Portal Online Library Catalog tested 19 February 2008, 3:26pm
Time tested 29 August 2007, 2:20pm
Trinity College Dublin Library tested 29 January 2007, 4:43pm
U.S. Electronic Code of Federal Regulations (e-CFR) tested 26 June 2007, 11:02am
Union Theological Seminary & Presbyterian School of Christian Education tested 27 September 2006, 3:42pm
United States Patent Office tested 26 June 2007, 11:06am
Universidad Nacional Autónoma de México tested 30 August 2007, 9:10am
Universitätsbibliothek Heidelberg tested 21 April 2008, 3:25pm
Université d’Ottawa tested 27 November 2007, 12:05pm
Université de Montréal Librairies tested 19 December 2006, 11:21am
University at Albany, SUNY, Libraries tested 28 September 2006, 1:19pm
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PLoS et langues officielles et ce que doivent savoir les auteurs

http://www.plos.org/

plos biology

http://www.plosone.org/home.action

le projet plos est crucial pour la difusion des connaissances scientifiques

Les articles restent obligatoire en anglais (ou en « airport english »).

Certaines organisations internationales ont aussi des langues officielles et/ou des langues de travail. Ainsi l’ONU s’est dotée de six langues officielles — arabe, anglais, chinois, espagnol, français, russe — qui sont les langues les plus largement comprises dans le monde, même dans les régions où on ne les parle pas spontanément ; tous ses travaux et débats sont retranscrits dans ces six langues officielles.

La francophonie est intéressante car c’est la langue par excellence de la renaissance et de la révolution francaise si importantes en science (i.e. système SI). Elle reste une langue de base pour la diplomatie, les mathématiques…

———-traduit par reverso.net (du point n°5; voir ci-dessous):

PLoS- ON considère les manuscrits de n’importe quelle longueur; nous encourageons la soumission tant des corps(organismes) en pied substantiels de travail que de manuscrits plus courts basés sur une gamme plus limitée d’expériences. Il n’y a aucun mot explicite, figure(chiffre), ou le soutien de restrictions de l’information, bien que nous encouragions un style d’écriture concis et accessible. Les rédacteurs peuvent faire des suggestions pour la façon de le réaliser, aussi bien que des suggestions pour des coupes(diminutions) ou les compléments qui pourraient être faits à l’article pour renforcer les arguments faits. Les auteurs sont encouragés à utiliser leur voix propre et décider comment le mieux présenter leurs idées, résultats et des conclusions.

Bien que nous encouragions des soumissions d’autour du globe, nous exigeons que les manuscrits soient soumis en anglais. Comme un pas(une étape) vers le fait de surmonter de barrières linguistiques, nous encourageons des auteurs fluides(faciles) dans d’autres langues à fournir les copies de leurs articles pleins(complets) ou résumés dans d’autres langues; ceux-ci seront rendus disponible avec le papier(journal) publié. Les traductions devraient être soumises comme le soutien d’informations.

———-traduit par google

http://www.plosone.org/static/guidelines.action#preparation

PLoS ONE Lignes directrices pour les auteurs

  1. About PLoS ONE À propos de PLoS ONE
  2. Criteria for Publication Critères de publication
  3. Overview of the Editorial Process Vue d’ensemble de la rédaction des processus
  4. Presubmission Inquiries Presubmission Demandes de renseignements
  5. Preparation of Research Manuscripts Préparation des manuscrits de recherche
  6. Discipline-Specific Requirements Discipline-Specific Requirements
  7. Overview of the Production Process Vue d’ensemble du processus de production
  8. Post-Publication Process Post-publication

1. 1. About PLoS ONE À propos de PLoS ONE

Scientific progress requires the exchange and discussion of data and ideas. PLoS ONE is a unique publication dedicated to presenting the results of scientific research from any scientific discipline in an open-access environment. Le progrès scientifique exige l’échange et la discussion des données et des idées. PLoS ONE est une publication consacrée à la présentation des résultats de la recherche scientifique de toute discipline scientifique dans un environnement libre-accès. At the same time, it provides a forum in which to discuss that scientific research and so provide for each and every paper its maximum possible impact. Dans le même temps, il fournit un forum pour discuter que la recherche scientifique et de fournir pour chaque document de son maximum d’impact. To achieve this, PLoS ONE combines traditional peer review with ‘Web 2.0’ tools to facilitate community evaluation and discourse around the published article. Pour ce faire, PLoS ONE traditionnels d’évaluation par les pairs avec ‘Web 2.0’ outils pour faciliter l’évaluation et la communauté des discours autour de l’article publié.

The peer review of each article is rigorous and concentrates on objective and technical concerns to determine whether the research has been sufficiently well conceived, well executed, and well described to justify inclusion in the scientific record. L’évaluation par les pairs de chaque article est rigoureuse et se concentre sur les objectifs et les préoccupations techniques pour déterminer si la recherche a été suffisamment bien conçu, bien exécuté, et bien décrit, pour justifier l’inclusion dans le dossier scientifique. Then, after publication, all papers are opened up for interactive discussions and assessment in which the whole scientific community can be involved. Puis, après la publication, tous les documents sont ouverts pour des discussions interactives et d’évaluation dans laquelle l’ensemble de la communauté scientifique peuvent être impliqués.

Unlike many journals which attempt to use the peer review process to determine whether or not an article reaches the level of ‘importance’ required by a given journal, PLoS ONE uses peer review to determine whether a paper is technically sound and worthy of inclusion in the published scientific record. Contrairement à de nombreux journaux qui tentent d’utiliser le processus d’examen par les pairs afin de déterminer si un article a atteint le niveau de «l’importance» requise par une revue PLoS ONE utilise l’examen par les pairs afin de déterminer si un document est techniquement viable et digne de figurer dans le scientifique publiée record. Once the work is published in PLoS ONE , the broader community is then able to discuss and evaluate the significance of the article (through the number of citations it attracts; the downloads it achieves; the media and blog coverage it receives; and the post-publication Notes, Comments and Ratings that it receives on PLoS ONE etc). Une fois les travaux sont publiés dans PLoS ONE, l’ensemble de la collectivité est alors en mesure de discuter et d’évaluer l’importance de l’article (par le nombre de citations, il attire, il atteint les téléchargements, les médias et la couverture blog, il reçoit, et l’après – Notes de publication, commentaires et évaluations qu’il reçoit sur PLoS ONE, etc.)

To provide open access, PLoS journals use a business model in which our expenses—including those of peer review, journal production, and online hosting and archiving—are recovered in part by charging a publication fee to the authors or research sponsors for each article they publish. Pour fournir un accès ouvert, les revues PLoS utiliser un modèle d’affaires dans lesquelles nos dépenses, y compris ceux de l’examen par les pairs, journal de production et d’hébergement en ligne et l’archivage sont récupérés en partie par la perception d’une taxe de publication pour les auteurs ou les commanditaires de recherche pour chaque article, ils publier. For PLoS ONE the publication fee is US$1300. PLoS ONE de la taxe de publication est de US $ 1300. Authors who are affiliated with one of our Institutional Members are eligible for a discount on this fee. Les auteurs qui sont affiliés à l’un de nos membres institutionnels sont admissibles à une remise sur ces frais.

We offer a complete or partial fee waiver for authors who do not have funds to cover publication fees. Nous offrons une gamme complète ou partielle, dispense de frais pour les auteurs qui ne disposent pas de fonds pour couvrir les frais de publication. Editors and reviewers have no access to payment information, and hence inability to pay will not influence the decision to publish a paper. Rédacteurs en chef et les commentateurs n’ont pas accès aux informations de paiement, et donc l’incapacité de payer ne sera pas influencer la décision de publier un document. These policies ensure that the fee is never a barrier to publication. Ces politiques de veiller à ce que la taxe n’est jamais un obstacle à la publication.

2. 2. Criteria for Publication Critères de publication

To be accepted for publication in PLoS ONE , research articles must satisfy the following criteria: Pour être accepté pour publication dans PLoS ONE, des articles de recherche doivent répondre aux critères suivants:

  1. The study presents the results of primary scientific research. L’étude présente les résultats des primaires de la recherche scientifique.
  2. Results reported have not been published elsewhere. Les résultats rapportés n’ont pas été publiés ailleurs.
  3. Experiments, statistics, and other analyses are performed to a high technical standard and are described in sufficient detail. Expériences, statistiques, et d’autres analyses sont effectuées à un haut niveau technique et sont décrits avec suffisamment de précision.
  4. Conclusions are presented in an appropriate fashion and are supported by the data. Les conclusions sont présentées de façon appropriée et sont soutenus par les données.
  5. The article is presented in an intelligible fashion and is written in standard English. L’article est présenté dans une manière intelligible et est écrit en anglais standard.
  6. The research meets all applicable standards for the ethics of experimentation and research integrity. La recherche répond à toutes les normes de l’éthique de l’expérimentation et l’intégrité de la recherche.
  7. The article adheres to appropriate reporting guidelines (eg CONSORT, MIAME, STROBE, EQUATOR) and community standards for data availability. L’article se conforme aux lignes directrices appropriées (par exemple, CONSORT, MIAME, STROBE, Equateur) et de la communauté des normes pour la disponibilité des données.

The PLoS ONE board of Academic Editors , and any invited external peer reviewers, will evaluate submissions against these criteria. Le conseil d’administration de PLoS ONE Academic Editors, et de tout invité examinateurs externes, évaluera arguments à l’encontre de ces critères.

To expand on each of these criteria: Pour développer sur chacun de ces critères:

1. 1. Does the manuscript report on primary research? Est-ce que le rapport manuscrit sur la recherche primaire?

PLoS ONE is designed specifically as a medium for primary, scientific research. PLoS ONE est spécifiquement conçu comme un moyen pour l’enseignement primaire, de la recherche scientifique. As such, it is not suitable for the publication of reviews, mini-reviews, opinion pieces, commentaries, essays or other items of secondary literature (unless invited for a specific purpose by PLoS staff). En tant que telle, elle ne convient pas pour la publication des revues, des mini-revues, articles d’opinion, des commentaires, des essais ou d’autres éléments de la littérature secondaire (à moins d’invités pour un but précis par PLoS personnel).

Systematic reviews and meta-analyses can be considered for publication in PLoS ONE but must apply the utmost rigour in the comprehensive and unbiased sampling of existing literature and must describe the methods used for the selection, inclusion and exclusion of data (see below). Des examens systématiques et les méta-analyses peuvent être considérés pour publication dans PLoS ONE, mais doit appliquer la plus grande rigueur dans l’échantillonnage et impartiale de la littérature existante, et doit décrire les méthodes utilisées pour la sélection, l’inclusion et l’exclusion des données (voir ci-dessous).

Individual case reports are not considered for publication in PLoS ONE. However, papers describing the results of studies involving only one individual (ie, n-of-1 studies) can be considered for publication in PLoS ONE if evidence is provided that the paper describes the results of a preplanned research project, rather than a description of the clinical care received by an individual patient. Rapports de cas individuels ne sont pas considérées pour publication dans PLoS ONE. Toutefois, des documents décrivant les résultats des études impliquant une seule personne (c’est-à-dire, de n-1-études) peuvent être considérés pour publication dans PLoS ONE, si la preuve est apportée que le document décrit les résultats d’un projet de recherche planifiées, plutôt que d’une description de la clinique des soins reçus par un patient individuel.

2. 2. Have the results reported been published elsewhere? Les résultats publiés par ailleurs été signalés?

PLoS ONE does not accept for publication work that has already been published elsewhere. PLoS ONE ne doit pas accepter pour publication des travaux déjà publiés ailleurs. However, studies that replicate results that are already in the literature may be considered for publication in PLoS ONE , as the independent confirmation of results can often be valuable, as can the presentation of a new dataset (for example, a new clinical trial). Cependant, les études que reproduire les résultats qui sont déjà dans la littérature mai être considérés pour publication dans PLoS ONE, que la confirmation indépendante des résultats peuvent souvent être utiles, comme la présentation d’un nouvel ensemble de données (par exemple, un nouvel essai clinique).

3. 3. Are the experiments, statistics, and other analyses performed to a high technical standard and are described in sufficient detail? Les expériences, les statistiques et autres analyses effectuées à un haut niveau technique et sont décrits avec suffisamment de détails?

The research must have been performed to a technical standard high enough to allow robust conclusions to be drawn from the data. La recherche doit avoir été effectué à un niveau technique assez élevé pour permettre des conclusions solides à tirer de ces données. Methods and reagents must also be described in sufficient detail so that another researcher is able to reproduce the experiments described. Les méthodes et les réactifs doivent également être décrites avec suffisamment de détails pour qu’un autre chercheur est capable de reproduire les expériences décrites.

4. 4. Are the conclusions presented in an appropriate fashion with speculations and hypotheses identified as such? Les conclusions sont-elles présentées de façon appropriée à des spéculations et des hypothèses identifiées comme telles?

The results must be interpreted appropriately, such that all conclusions are justified. Les résultats doivent être interprétés de façon appropriée, de telle sorte que toutes les conclusions sont justifiées. However, authors may discuss possible explanations for their results as long as these are clearly identified as speculations or hypotheses, rather than as firm conclusions. Toutefois, les auteurs discutent mai explications possibles de leurs résultats, tant que ceux-ci sont clairement identifiées en tant que de spéculations ou d’hypothèses, plutôt que comme des conclusions fermes. Inappropriate interpretation of results is a justifiable reason for rejection. Peut offenser l’interprétation des résultats est un motif de rejet.

5. 5. Is the article presented in an intelligible fashion and written in English? Est-ce que l’article présenté dans une manière intelligible et écrite en anglais?

PLoS ONE staff do not copyedit the text of accepted manuscripts; it is therefore important for the work, as presented, to be intelligible. PLoS ONE personnel ne copyedit le texte des manuscrits acceptés, il est donc important pour le travail, tel que présenté, pour être intelligible. Perfect, stylish English is not essential but the language must be clear and unambiguous. Perfect, de style anglais n’est pas indispensable, mais la langue doit être claire et sans ambiguïté. If the language of a paper is poor, Academic Editors should recommend that authors seek independent editorial help before submission of a revision. Si la langue d’un document est pauvre, Academic Editors recommande que les auteurs cherchent éditoriale indépendante d’aide, avant de présenter une révision. A list of scientific editing services can be found in the PLoS ONE Guide to Authors . Une liste des services d’édition scientifique se trouve dans les PLoS ONE Guide aux auteurs. Poor presentation and language is a justifiable reason for rejection. Mauvaise présentation et la langue est un motif de rejet.

6. 6. Does the research meet all applicable standards with regard to the ethics of experimentation and research integrity? Est-ce que la recherche de répondre à toutes les normes en matière d’éthique de l’expérimentation et l’intégrité de la recherche?

Research published in PLoS ONE must have been conducted to the highest ethical standards. Les travaux de recherche publiés dans PLoS ONE doit avoir été effectuée pour les plus hauts standards éthiques. A brief description of the most common of these is described in our Editorial and Publishing Policies . Une brève description de la plus commune est décrit dans notre rédaction et l’édition des politiques. Please contact PLoS ONE staff ( plosone [at] plos.org ) if you have queries as to whether these standards have been met. S’il vous plaît contactez PLoS ONE personnel (plosone [at] plos.org) si vous avez des questions quant à savoir si ces normes ont été respectées.

7. 7. Does the article adhere to appropriate reporting guidelines (eg CONSORT, MIAME, STROBE, EQUATOR) and community standards for data availability? Est-ce que l’article se conformer à des directives (par exemple, CONSORT, MIAME, STROBE, Equateur) et de la communauté des normes pour la disponibilité des données?

PLoS ONE aims to promote openness in research and intends that all work published in PLoS ONE can be built on by future researchers. PLoS ONE vise à promouvoir la transparence dans la recherche et entend que tous les travaux publiés dans PLoS ONE peut être construit par les futurs chercheurs. We therefore demand conformity to standards for the public deposition of data (for example gene sequences, microarray expression data, and structural studies). Nous exigeons donc la conformité aux normes à l’intention du public des dépôts de données (par exemple des séquences de gènes, expression microarray données et des études structurales). Other similar standards that are applicable to specific communities should also be upheld. D’autres normes sont applicables à des communautés spécifiques doivent également être respectés. Failure to comply with community standards is a justifiable reason for rejection. Défaut de se conformer à des normes communautaires est un motif de rejet.

3. 3. Overview of the Editorial Process Vue d’ensemble de la rédaction des processus

PLoS ONE provides all authors with an efficient and ‘hassle-free’ editorial process. PLoS ONE fournit tous les auteurs avec un efficace et sans tracas « processus éditorial. Our aim is to identify those submissions that warrant inclusion in the scientific record and present them to the scientific community with as few hurdles as possible. Notre objectif est d’identifier les documents qui justifient l’inclusion dans le dossier scientifique et de les présenter à la communauté scientifique, avec aussi peu d’obstacles que possible.

The editorial process is run by the journal’s extensive board of Academic Editors (AEs) who work together to orchestrate the peer-review process. Le processus éditorial est géré par le journal de bord de la vaste Academic Editors (AE) qui travaillent ensemble pour orchestrer les processus d’examen par les pairs. AEs are invited to handle submitted manuscripts on the basis of the content of the manuscript and their own expertise. AE sont invités à traiter les manuscrits soumis sur la base du contenu du manuscrit et de leur propre expertise. The AE evaluates the paper and decides whether it describes a body of work that meets the editorial criteria of PLoS ONE . Le document évalue l’AE et décide si elle décrit un corps de travail qui répond aux critères de rédaction de PLoS ONE. AEs can employ a variety of methods alone or in combination, to reach a decision in which they are confident: EA peut employer une variété de méthodes, seuls ou en association, afin de parvenir à une décision dans laquelle ils sont confiants:

  • They can conduct the peer review themselves, based on their own knowledge and experience Ils peuvent procéder à l’examen par les pairs eux-mêmes, sur la base de leurs connaissances et leurs expériences
  • They can take further advice through discussion with other members of the editorial board Ils peuvent prendre d’autres conseils par le biais de discussions avec les autres membres du comité de rédaction
  • They can solicit reports from further referees Ils peuvent solliciter des rapports des arbitres de plus amples

After appropriate consideration by the AE, a decision letter to the author is drafted. Après examen par l’AE, une lettre de décision de l’auteur est rédigé. This letter may also be circulated to other members of the editorial board, who are given a short time to comment on the editorial decision. Cette lettre mai également être distribué aux autres membres du comité de rédaction, qui ont reçu un peu de temps à faire des observations sur la décision éditoriale.

There are several types of decisions possible: Il existe plusieurs types de décisions possibles:

  • Accept in principle Accepter, en principe,
  • Minor revision Révision mineure
  • Major revision Révision majeure
  • Reject Rejeter

If authors are unsatisfied by the decision they receive they can submit an appeal, in the first instance to the paper’s original Academic Editor. Si les auteurs ne sont pas satisfaits par la décision qu’ils reçoivent, ils peuvent faire appel, en première instance à l’original du document Academic Editor. However if the author is still unsatisfied they can request a second opinion. Toutefois, si l’auteur est toujours insatisfait, ils peuvent demander un deuxième avis. In such cases the appeal will be considered by at least one further member of the Editorial Board. Dans ce cas, le recours sera examiné par au moins un autre membre du Comité de rédaction. If this second opinion supports the original decision that decision is final. Si ce deuxième avis favorable à la décision initiale selon laquelle la décision est définitive. Appeal requests should be addressed to plosone [at] plos.org . Appel demandes doivent être adressées à plosone [at] plos.org.

Upon acceptance, the manuscript is checked by PLoS ONE staff to ensure that it is in a form that will allow it to be efficiently handled by our production system. Après acceptation, le manuscrit est vérifiée par le personnel PLoS ONE pour veiller à ce qu’il est dans une forme qui lui permettra d’être efficacement pris en charge par notre système de production. The authors will be queried and allowed to make any final minor revisions that are needed. Les auteurs seront interrogés et ont permis de faire d’ultimes révisions mineures qui sont nécessaires.

This is the final stage at which an author will see their manuscript before publication. C’est la dernière étape, à un auteur qui vont voir leur manuscrit avant publication. The authors’ files will be carefully tagged to generate XML and PDF files, but will not be subject to detailed copyediting (see Overview of the Production Process ). Les auteurs des dossiers seront soigneusement étiquetés pour générer des fichiers XML et PDF, mais ne sera pas soumis à la révision détaillée (voir Vue d’ensemble du processus de production). It is therefore essential that authors provide a thoroughly proofread and checked manuscript, following the manuscript checklist and any comments from PLoS staff. Il est donc essentiel que les auteurs donnent un soigneusement relus et vérifiés manuscrit, à la suite du manuscrit liste de contrôle et d’observations de PLoS personnel.

4. 4. Presubmission Inquiries Presubmission Demandes de renseignements

PLoS ONE does not consider presubmission inquiries. PLoS ONE ne considère pas presubmission enquêtes. Such inquiries essentially request that the editors of a journal assess whether the paper is of potential interest to that journal by virtue of its subject area, novelty, or anticipated impact. Ces enquêtes demande essentiellement que les éditeurs d’un journal de déterminer si le papier est de l’intérêt potentiel de ce journal en raison de son domaine, la nouveauté ou l’impact prévu. In general, such subjective opinion would have little bearing on whether a paper should be published in PLoS ONE . En général, ces opinion subjective aurait peu d’incidence sur l’opportunité d’un document devrait être publié dans PLoS ONE. First of all, all subject areas are of interest to PLoS ONE, and furthermore, to judge whether a study has been sufficiently well performed and well documented to permit publication in PLoS ONE requires submission of the full paper. Tout d’abord, tous les domaines d’intérêt pour PLoS ONE, et, en outre, de juger si une étude a été suffisamment bien exécutées et bien documentées pour permettre la publication dans PLoS ONE exige la soumission de la totalité du document.

5. 5. Preparation of Research Manuscripts Préparation des manuscrits de recherche

PLoS ONE considers manuscripts of any length; we encourage the submission of both substantial full-length bodies of work and shorter manuscripts based on a more limited range of experiments. PLoS ONE considère les manuscrits de n’importe quelle longueur, et nous encourageons la présentation de deux importants organes de longue durée de travail plus courtes et des manuscrits sur la base d’un éventail plus limité d’expériences. There are no explicit word, figure, or supporting information restrictions, although we encourage a concise and accessible writing style. Il n’y a pas de mot explicite, figure, ou de l’information à l’appui des restrictions, mais nous encourageons une écriture concise et accessible style. Editors may make suggestions for how to achieve this, as well as suggestions for cuts or additions that could be made to the article to strengthen the arguments made. Editors mai de faire des suggestions sur la manière de réaliser cet objectif, ainsi que des suggestions pour des coupures ou des additions qui pourraient être apportées à l’article de renforcer les arguments présentés. Authors are encouraged to use their own voice and to decide how best to present their ideas, results, and conclusions. Les auteurs sont encouragés à utiliser leur propre voix et de décider de la meilleure manière de présenter leurs idées, les résultats et les conclusions.

Although we encourage submissions from around the globe, we require that manuscripts be submitted in English. Bien que nous encourageons les soumissions de partout dans le monde, nous avons besoin que les manuscrits sont rédigés en anglais. As a step toward overcoming language barriers, we encourage authors fluent in other languages to provide copies of their full articles or abstracts in other languages; these will be made available along with the published paper. Comme une étape vers surmonter les barrières linguistiques, nous encourageons les auteurs parlent couramment dans d’autres langues de fournir des copies de leurs articles complets ou abrégés dans d’autres langues, qui seront mis à disposition avec l’article publié. Translations should be submitted as supporting information. Les traductions doivent être présentées comme des informations complémentaires.

Cover Letter Lettre de motivation

It is important that you include a cover letter with your manuscript. Il est important que vous inclure une lettre avec votre manuscrit. Please explain why this manuscript is suitable for publication in PLoS ONE . S’il vous plaît expliquer pourquoi ce manuscrit est adapté pour la publication dans PLoS ONE. How does your paper provide a worthwhile addition to the scientific literature? Comment votre document de fournir une plus utile à la littérature scientifique? How does your paper relate to previously published work? Comment votre papier précédemment se rapportent à la publication de l’ouvrage? Which types of scientists do you believe will be most interested in your study? Quels types de scientifiques, selon vous, sera la plus intéressée par votre étude?

Please ensure that your cover letter also includes suggestions for PLoS ONE Academic Editors who would be suitable to consider your submission ( view full list of academic editors ). S’il vous plaît vous assurer que votre lettre comprend également des suggestions pour PLoS ONE académique Editors qui serait approprié d’examiner votre soumission (voir la liste des éditeurs universitaires). Please suggest as many Academic Editors as you like, but note that we cannot guarantee that they will be used. S’il vous plaît penser que de nombreux éditeurs universitaires que vous le souhaitez, mais notez que nous ne pouvons pas garantir qu’ils seront utilisés.

Electronic Formats Formats électroniques

Our publication system supports a limited range of formats for text and graphics. Notre système de publication prend en charge un nombre limité de formats de texte et de graphiques. Text files can be submitted in only the following formats: Word or RTF. Les fichiers texte peuvent être présentées que dans les formats suivants: Word ou RTF. Please convert LaTeX files to Word or RTF format . S’il vous plaît de convertir des fichiers LaTeX en Word ou RTF. Graphics files can only be submitted in the following formats: EPS or TIFF. Les fichiers graphiques ne peuvent être soumis dans les formats suivants: EPS ou TIFF.

If you experience difficulties with the manuscript submission Web site or are concerned about the suitability of your files, please contact the journal ( plosone [at] plos.org ). Si vous rencontrez des difficultés avec le manuscrit soumis site Web ou qui sont préoccupés par la pertinence de vos fichiers, s’il vous plaît contacter le journal (plosone [at] plos.org).

Prior Publication Avant de publication

When submitting their article, all authors are asked to indicate that they have not submitted a related or duplicate manuscript for publication elsewhere. Lors de l’introduction de leur article, les auteurs sont priés d’indiquer qu’ils n’ont pas présenté un ou deux exemplaires de manuscrits relatifs à la publication ailleurs. If similar or related work has been submitted elsewhere, then a copy must be included with the article submitted to PLoS. Si similaires ou connexes travail a été présenté par ailleurs, un exemplaire doit être inclus dans l’article soumis à PLoS. Reviewers will be asked to comment on the overlap between related submissions. Les examinateurs seront invités à faire des observations sur le chevauchement entre les présentations.

Financial Disclosure Divulgation

This section should describe sources of funding that have supported the work. Cette section devrait décrire les sources de financement qui ont appuyé le travail. Please include relevant grant numbers and the URL of any funder’s website. S’il vous plaît inclure les numéros de subvention et l’adresse du bailleur de fonds du site. Please also include this sentence: « The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. » S’il vous plaît inclure cette phrase: « Les bailleurs de fonds n’a joué aucun rôle dans la conception des études, la collecte de données et d’analyse, la décision de publier, ou de la préparation du manuscrit. » If this statement is not correct, you must describe the role of any sponsors or funders, and amend the aforementioned sentence as needed. Si cette déclaration n’est pas correcte, vous devez décrire le rôle des commanditaires ou des bailleurs de fonds, et de modifier la phrase ci-dessus en cas de besoin.

Author Status Auteur Situation

The involvement of any professional medical writer in publication must be declared. La participation de tout professionnel de la santé l’écrivain dans la publication doivent être déclarées. We encourage authors to consult the European Medical Writers’ Association Guidelines on the role of medical writers. Nous encourageons les auteurs à consulter le European Medical Writers Association des Lignes directrices sur le rôle de rédacteurs médicaux. For all PLoS journals, the corresponding author must submit the manuscript, related files, and all required data and information. Pour tous les PLoS revues, l’auteur doit soumettre le manuscrit, des photos, et toutes les données et informations requises. From the point of submission through to publication, all communication related to that manuscript will be directed to and received from the corresponding author only. Du point de soumission à la publication, toutes les communications relatives à ce manuscrit sera dirigé vers et reçus de l’auteur uniquement.

PLoS ONE bases its criteria for authorship on those outlined in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals , which are summarized below. PLoS ONE fonde ses critères d’auteur sur celles énoncées dans le règlement uniforme des exigences pour les manuscrits soumis à Biomedical Journals, qui sont résumées ci-dessous. However, if you believe that a particular individual should be an author, you may include them, provided they are able to take responsibility for a given part of the study. Toutefois, si vous croyez qu’une personne devrait être un auteur, vous mai inclure, à condition qu’ils soient en mesure de prendre la responsabilité d’une partie de l’étude. The contributions of all authors must be described. Les contributions de tous les auteurs doivent être décrites. Contributions that fall short of authorship should be mentioned in the acknowledgements. Les contributions qui sont loin d’auteur doivent être mentionnés dans les remerciements.

« Authorship credit should be based on « Authorship de crédit devrait être fondée sur
1) substantial contribution to conception and design, or acquisition of data, or analysis and interpretation of data; 1) une contribution à la conception et le design, ou de l’acquisition de données, ou de l’analyse et l’interprétation des données;
2) drafting the article or revising it critically for important intellectual content; and 2) la rédaction de l’article ou révision critique de son contenu intellectuel important, et
3) final approval of the version to be published. 3) l’approbation finale de la version à être publiés.

Authors should meet conditions 1, 2, and 3. Les auteurs doivent remplir les conditions 1, 2 et 3.

When a large, multi-center group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript (3). Quand un grand groupe multi-centre a dirigé les travaux, le groupe doit identifier les personnes qui acceptent la responsabilité directe du manuscrit (3). These individuals should fully meet the criteria for authorship defined above and editors will ask these individuals to complete journal-specific author and competing interests disclosure forms. Ces personnes devraient pleinement respecter les critères définis ci-dessus pour les auteurs et les éditeurs vont demander à ces personnes de remplir journal auteur et les intérêts concurrents des formes de divulgation. When submitting a group author manuscript, the corresponding author should clearly indicate the preferred citation and should clearly identify all individual authors as well as the group name. Lors de la soumission d’un groupe auteur manuscrit, l’auteur correspondant doit indiquer clairement la meilleure citation et doit clairement identifier tous les auteurs ainsi que le nom du groupe.

Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship. Acquisition de financement, de collecte de données, ou de la surveillance générale du groupe de recherche, seul, ne justifie pas l’auteur. All persons designated as authors should qualify for authorship, and all those who qualify should be listed. Toutes les personnes désignées comme les auteurs devraient bénéficier d’auteur, et tous ceux qui sont admissibles doivent être énumérés. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content. » Chaque auteur doit avoir participé suffisamment aux travaux de prendre la responsabilité publique pour des portions du contenu. « 

Competing Interests Des intérêts concurrents

The submitting author is asked at submission to declare, on behalf of all authors, whether there are any financial, personal, or professional interests that could be construed to have influenced the paper. La présentation de l’auteur est invité à soumettre à déclarer, au nom de tous les auteurs, s’il existe des financiers, personnels ou professionnels qui pourraient être interprétées d’avoir influencé le papier. Reviewers are also asked to declare any interests that might interfere with their objective assessment of a manuscript. Les réviseurs sont également invités à déclarer tout intérêt qui pourrait interférer avec leur objectif d’évaluation d’un manuscrit. Any relevant competing interests of authors must be available to editors and reviewers during the review process and will be stated in published articles. Toute les intérêts concurrents des auteurs doivent être disponibles pour les éditeurs et les commentateurs pendant le processus de révision et sera indiqué dans des articles publiés. Read more about the policy of PLoS regarding competing interests . En savoir plus sur la politique de PLoS en ce qui concerne les intérêts concurrents.

Abbreviations Abréviations

Please keep abbreviations to a minimum and define them upon first use in the text. S’il vous plaît garder à un minimum d’abréviations et de les définir lors de la première utilisation dans le texte. Non-standard abbreviations should not be used unless they appear at least three times in the text. Non-standard abréviations ne devrait pas être utilisée, sauf si elles apparaissent au moins trois fois dans le texte.

Figures Chiffres

For the article to be accepted for publication, the author will need to supply high-resolution versions of the figures. Pour l’article d’être accepté pour publication, l’auteur aura besoin de fournir des versions haute résolution des chiffres. When preparing your figures, please ensure that the files conform to our Guidelines for Figure and Table Preparation . Lors de la préparation de vos chiffres, s’il vous plaît assurer que les fichiers conformes à nos Lignes directrices pour la préparation de la figure et le tableau. Please do not upload panels for a single figure separately (for example, Figure 1A, Figure 1B-1D, Figure 1E); each figure file should be a single montage of all panels. S’il vous plaît ne pas envoyer de panneaux pour un seul chiffre séparément (par exemple, la Figure 1A, Figure 1B-1D, figure 1E), chaque chiffre doit être un fichier unique de montage de tous les panneaux.

Please note that PLoS ONE can only accept figures submitted as either TIFF or EPS files. S’il vous plaît noter que PLoS ONE ne peut accepter que les chiffres présentés en tant que fichiers EPS ou TIFF.

All figures will be published under a Creative Commons Attribution License, which allows them to be freely used, distributed, and built upon as long as proper attribution is given. Tous les chiffres seront publiés sous une licence Creative Commons qui leur permet d’être librement utilisé, distribué, et repose sur une bonne aussi longtemps que l’attribution est donnée. Please do not submit any figures that have been previously copyrighted unless you have express written permission from the copyright holder to publish under the CCAL license. S’il vous plaît ne pas présenter des chiffres qui ont été préalablement protégée, sauf si vous avez une permission écrite expresse du titulaire des droits à publier dans le cadre de la CCAL licence.

Organization of the Manuscript Organisation du manuscrit

Most articles published in PLoS ONE are organized in one of three fashions: La plupart des articles publiés dans PLoS ONE sont organisées dans l’un des trois modes:

  • Title, Authors, Affiliations, Abstract, Introduction, Results, Discussion, Materials and Methods, Acknowledgments, References, Figure Legends, and Tables. Titre, auteurs, affiliations, Résumé, Introduction, Résultats, Discussion, matériaux et méthodes, Remerciements, Références, Figure Legends, et les tableaux.
  • Title, Authors, Affiliations, Abstract, Introduction, Methods, Results, Discussion, Acknowledgments, References, Figure Legends, and Tables. Titre, auteurs, affiliations, Résumé, Introduction, Méthodes, Résultats, Discussion, Remerciements, Références, Figure Legends, et les tableaux.
  • Title, Authors, Affiliations, Abstract, Introduction, Analysis, Discussion, Acknowledgments, References, Figure Legends, and Tables. Titre, auteurs, affiliations, Résumé, Introduction, Analyse, Discussion, Remerciements, Références, Figure Legends, et les tableaux.

We advise that abstracts should not exceed 250–300 words. Nous conseillons que les résumés ne doit pas dépasser 250-300 mots. There are no specific length restrictions for the remaining sections of the manuscript; however, we urge authors to present and discuss their findings concisely. Il n’y a pas de restrictions de longueur pour les autres sections du manuscrit, mais nous exhortons les auteurs de présenter et de discuter de leurs conclusions avec concision.

You should include continuous line numbering throughout your manuscript. Vous devez inclure la numérotation des lignes continues tout au long de votre manuscrit.

Standard Microsoft Word templates are available to help authors prepare their manuscripts. Standard modèles Microsoft Word sont disponibles pour aider les auteurs à préparer leurs manuscrits. The templates consist of a standard set of headings that make up research articles of various types, with guidance regarding what to include in each section. Les modèles se composent d’une série de rubriques qui constituent des articles de recherche de différents types, avec des orientations en ce qui concerne ce qu’il faut inclure dans chaque section.

Download templates: Télécharger des modèles:

Title (150 characters or fewer) Titre (150 caractères ou moins)

The title should be specific to the project, yet concise. Le titre doit être spécifique au projet, mais concis. It should be comprehensible to readers outside your field. Il devrait être compréhensible pour les lecteurs en dehors de votre domaine. Avoid specialist abbreviations, if possible. Évitez les abréviations spécialiste, si possible. Titles should be presented in title case, meaning that all words except for prepositions, articles, and conjunctions should be capitalized. Les titres doivent être présentés au titre de cas, ce qui signifie que tous les mots, sauf pour les prépositions, les articles, les conjonctions et devrait être capitalisée.

Example: Exemple:
Detection of Specific Sequences among DNA Fragments Separated by Gel Electrophoresis Détection de séquences spécifiques d’ADN entre les fragments séparés par électrophorèse en gel

During the online submission process, you will also provide a brief « running head » of fewer than 30 characters. Au cours de la procédure de soumission en ligne, vous devrez également fournir un bref « en-tête » de moins de 30 caractères.

Authors and Affiliations Auteurs et Affiliations

Provide the first names or initials (if used), middle names or initials (if used), surnames, and affiliations—department, university or organization, city, state/province (if applicable), and country—for all authors. Fournir les prénoms ou initiales (le cas échéant), prénoms ou initiales (le cas échéant), prénom, département et les affiliations, l’université ou de l’organisation, ville, état / province (si applicable), et des pays de tous les auteurs. One of the authors should be designated as the corresponding author. Un des auteurs doit être désigné comme l’auteur correspondant. It is the corresponding author’s responsibility to ensure that the author list, and the summary of the author contributions to the study are accurate and complete. Il est l’auteur de veiller à ce que l’auteur de la liste, et le résumé des contributions de l’auteur de l’étude sont exacts et complets. If the article has been submitted on behalf of a consortium, all author names and affiliations should be listed at the end of the article. Si l’article a été présenté au nom d’un consortium, tous les noms d’auteurs et les affiliations doivent être indiqués à la fin de l’article.

Abstract Résumé

The abstract succinctly introduces the paper. Le résumé succinctement introduit le document. We advise that it should not exceed 250 – 300 words. Nous conseillons de ne pas dépasser 250 – 300 mots. It should mention the techniques used without going into methodological detail and should summarize the most important results. Il convient de mentionner les techniques utilisées, sans entrer dans les détails méthodologiques et devrait résumer les résultats les plus importants. The abstract is conceptually divided into the following three sections: Background, Methodology/Principal Findings, and Conclusions/Significance. Le résumé est conceptuellement divisé en trois sections: Historique, la méthodologie / des principales constatations, conclusions et / valeur. Please do not include any citations in the abstract. S’il vous plaît ne comprennent pas les citations dans l’abstrait. Avoid specialist abbreviations if possible. Évitez les abréviations spécialiste si possible.

Registration Inscription

Registration details should be included when reporting results of a clinical trial (see  » Reporting Clinical Trials  » for details). Enregistrement des détails doivent être inclus dans la déclaration des résultats d’un essai clinique (voir «Rapport sur les essais cliniques » pour les détails). For each location that your trial is registered, please list: name of registry, registry number, and URL of your trial in the registry database. Pour chaque emplacement que votre jugement est enregistrée, la liste s’il vous plaît: le nom d’immatriculation, numéro de registre, et l’URL de votre procès dans la base de registre.

Introduction Introduction

The introduction should put the focus of the manuscript into a broader context. L’introduction doit mettre l’accent du manuscrit dans un contexte plus large. As you compose the introduction, think of readers who are not experts in this field. Comme vous composer l’introduction, penser à des lecteurs qui ne sont pas des experts dans ce domaine. Include a brief review of the key literature. Inclure une brève revue de la littérature de la clé. If there are relevant controversies or disagreements in the field, they should be mentioned so that a non-expert reader can delve into these issues further. Si il ya des controverses ou des désaccords dans le domaine, ils doivent être mentionnés afin qu’un lecteur non-expert peut se plonger dans ces questions. The introduction should conclude with a brief statement of the overall aim of the experiments and a comment about whether that aim was achieved. L’introduction devrait conclure avec un bref exposé de l’objectif global des expériences et un commentaire pour savoir si cet objectif a été atteint.

Results Résultats

The results section should provide details of all of the experiments that are required to support the conclusions of the paper. La section des résultats devrait fournir les détails de toutes les expériences qui sont nécessaires pour appuyer les conclusions du document. There is no specific word limit for this section. Il n’existe pas de limite de mots pour cette section. The section may be divided into subsections, each with a concise subheading. La section mai être divisé en sous-sections, chacune avec un sous-titre concis. Large datasets, including raw data, should be submitted as supporting information files; these are published online alongside the accepted article. Les grandes bases de données, y compris les données, devrait être présenté à l’appui des fichiers d’information, qui sont publiés en ligne à côté de l’article accepté. We advise that the results section be written in past tense. Nous conseillons que les résultats sont écrits dans la section passé.

Discussion Discussion

The discussion should spell out the major conclusions of the work along with some explanation or speculation on the significance of these conclusions. La discussion devrait énoncer les principales conclusions des travaux avec une explication ou de la spéculation sur l’importance de ces conclusions. How do the conclusions affect the existing assumptions and models in the field? Comment les conclusions d’affecter les hypothèses et les modèles dans le domaine? How can future research build on these observations? Comment la recherche peut venir s’appuyer sur ces observations? What are the key experiments that must be done? Quelles sont les principales expériences qui doit être fait? The discussion should be concise and tightly argued. La discussion devrait être concis et bien argumenté. Conclusions firmly established by the presented data, hypotheses supported by the presented data, and speculations suggested by the presented data should be clearly identified as such. Conclusions fermement établi par la présente des données, des hypothèses soutenues par les données présentées, et de spéculations proposées par la présente les données doivent être clairement identifiées comme telles. The results and discussion may be combined into one section, if desired. Les résultats et la discussion mai être combinés en un seul article, si vous le souhaitez.

Materials and Methods Matériels et méthodes

This section should provide enough detail to allow full replication of the study by suitably skilled investigators. Cette section devrait fournir suffisamment de détails pour permettre la réplication complète de l’étude réalisée par des enquêteurs dûment qualifiés. Protocols for new methods should be included, but well-established protocols may simply be referenced. Les protocoles de nouvelles méthodes devraient être inclus, mais bien des protocoles établis mai simplement être référencés. We encourage authors to submit, as separate supporting information files, detailed protocols for newer or less well-established methods. Nous encourageons les auteurs à présenter, comme des informations à l’appui de fichiers, des protocoles détaillés pour les plus nouveaux ou moins bien les méthodes établies. These are published online only, but are linked to the article and are fully searchable. Ces documents sont publiés uniquement en ligne, mais sont liés à l’article et qui sont entièrement consultables.

Acknowledgments Remerciements

Details of the funding sources that have supported the work should be confined to the funding statement provided in the online submission system. Détails des sources de financement qui ont appuyé le travail devrait être limitée à la déclaration de financement prévue dans le système de soumission en ligne. Do not include them in the acknowledgments. Ne pas les inclure dans les remerciements.

References Références

Only published or accepted manuscripts should be included in the reference list. Seuls publiés ou manuscrits acceptés doivent être inclus dans la liste de référence. Meetings abstracts, conference talks, or papers that have been submitted but not yet accepted should not be cited. Des résumés de réunions, de conférences entretiens, ou les documents qui ont été présentés mais pas encore accepté ne doit pas être cité. Limited citation of unpublished work should be included in the body of the text only. Limited citation des travaux non publiés devraient être inclus dans le corps du texte seulement. All personal communications should be supported by a letter from the relevant authors. Toutes les communications personnelles doivent être soutenues par une lettre de la part des auteurs.

Mac users, hold down « Option » key and click the link to download the file to your computer. Les utilisateurs de Mac, maintenez la touche « Option » enfoncée et cliquez sur le lien pour télécharger le fichier sur votre ordinateur.

PLoS uses the numbered citation (citation–sequence) method. PLoS utilise le numéro de référence (citation-séquence) méthode. References are listed and numbered in the order that they appear in the text. Les références sont inscrites et numérotées dans l’ordre où elles apparaissent dans le texte. In the text, citations should be indicated by the reference number in brackets. Dans le texte, les références doivent être indiquées par le numéro de référence entre parenthèses. Multiple citations within a single set of brackets should be separated by commas. Citations multiples au sein d’une même série de crochets doivent être séparés par des virgules. Where there are three or more sequential citations, they should be given as a range. Lorsqu’il ya trois ou séquentielle de plus de citations, on devrait leur donner un éventail. Example: « … has been shown previously [1,4–6,22]. » Exemple: «… a été montré précédemment [1,4-6,22]. » Make sure the parts of the manuscript are in the correct order before ordering the citations. Assurez-vous que les parties du manuscrit sont dans le bon ordre avant de commander les citations.

Because all references will be linked electronically as much as possible to the papers they cite, proper formatting of the references is crucial. Parce que toutes les références seront reliés par voie électronique, autant que possible aux documents, ils citent, une bonne mise en forme des références est essentielle. Please use the following style for the reference list: S’il vous plaît utiliser le style suivant pour la liste de référence:

Published Papers Papiers de publication
1 Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. 1 Sanger F, Nicklen S, Coulson AR (1977), le séquençage de l’ADN avec les inhibiteurs de la chaîne de résiliation. Proc Natl Acad Sci USA 74: 5463–5467. Proc Natl Acad Sci USA 74: 5463-5467.

Please list the first five authors and then add « et al. » S’il vous plaît la liste des cinq premiers auteurs, puis ajouter «et al. if there are additional authors. si il existe d’autres auteurs. Use of a DOI number to the full-text article is acceptable as an alternative to or in addition to traditional volume and page numbers. L’utilisation d’un numéro de DOI à l’article en texte intégral est acceptable comme solution de rechange ou en plus des traditionnels, et les numéros de page.

Accepted Papers Accepted Papers
Same as above, but « in press » appears instead of the page numbers. Idem que ci-dessus, mais «sous presse» apparaît au lieu de les numéros de page. Example: Adv Clin Path. Exemple: Adv Clin Path. In press. In press.

Electronic Journal Articles 1 Loker WM (1996) « Campesinos » and the crisis of modernization in Latin America. Electronic Journal Articles 1 Loker WM (1996) « campesinos » et la crise de la modernité en Amérique latine. Jour Pol Ecol 3. Jour 3 Pol Ecol. Available: http://www.library.arizona.edu/ej/jpe/volume_3/ascii-lokeriso.txt. Disponible: http://www.library.arizona.edu/ej/jpe/volume_3/ascii-lokeriso.txt. Accessed 2006 Aug 11. Consulté le 11 août 2006.

Books Livres en anglais
1 Bates B (1992) Bargaining for life: A social history of tuberculosis. 1 B Bates (1992) de négociation pour la vie: une histoire sociale de la tuberculose. Philadelphia: University of Pennsylvania Press. Philadelphia: University of Pennsylvania Press. 435 p. 435 p.

Book Chapters Chapitres de livres
Hansen B (1991) New York City epidemics and history for the public. Hansen B (1991) New York City les épidémies et l’histoire pour le public. In: Harden VA, Risse GB, editors. In: Harden VA, GB Risse, éditeurs. AIDS and the historian. Sida et de l’historien. Bethesda: National Institute of Health. Bethesda: National Institute of Health. pp. pp. 21–28. 21-28.

Figure Legends Figure Legends

The aim of the figure legend should be to describe the key messages of the figure, but the figure should also be discussed in the text. L’objectif de la légende de figure devrait être de décrire les principaux messages de la figure, mais le chiffre devrait également être discuté dans le texte. An enlarged version of the figure and its full legend will often be viewed in a separate window online, and it should be possible for a reader to understand the figure without switching back and forth between this window and the relevant parts of the text. Une version agrandie de la figure et de sa légende complète sera souvent considéré dans une fenêtre distincte en ligne, et il devrait être possible pour un lecteur à comprendre la figure sans avoir à basculer en arrière entre la fenêtre et les parties pertinentes du texte. Each legend should have a concise title of no more than 15 words. Chaque légende doit avoir un titre concis d’au plus 15 mots. The legend itself should be succinct, while still explaining all symbols and abbreviations. La légende elle-même doit être succinct, tout en expliquant tous les symboles et les abréviations. Avoid lengthy descriptions of methods. Évitez les longues descriptions de méthodes.

Tables Tables

Tables should be included in the text file, at the very end of the manuscript. Les tableaux doivent être inclus dans le fichier texte, à la fin du manuscrit. All tables should have a concise title. Tous les tableaux doivent avoir un titre concis. Footnotes can be used to explain abbreviations. Notes de bas de page peut être utilisée pour expliquer les abréviations. Citations should be indicated using the same style as outlined above. Citations doit être indiqué en utilisant le même style, comme indiqué ci-dessus. Tables occupying more than one printed page should be avoided, if possible. Tables d’occupation plus d’une page imprimée doit être évitée, si possible. Larger tables can be published as online supporting information. Agrandir les tables peuvent être publiés en ligne des renseignements à l’appui. Please ensure that table formatting conforms to our Guidelines for Figure and Table Preparation . S’il vous plaît faire en sorte que le tableau de mise en forme conforme à nos Lignes directrices pour la préparation de la figure et le tableau.

Multimedia Files and Supporting Information Les fichiers multimédia et l’appui

We encourage authors to submit essential supporting files and multimedia files along with their manuscripts. Nous encourageons les auteurs à soumettre des fichiers de support essentiel et de fichiers multimédia avec leurs manuscrits. All supporting material will be subject to peer review. Tous les documents seront soumis à l’examen par les pairs.

Multimedia files should be smaller than 10 MB in size because of the difficulties that some users will experience in loading or downloading files. Fichiers multimédia doit être inférieur à 10 Mo en taille en raison des difficultés que certains utilisateurs de l’expérience dans le chargement ou le téléchargement de fichiers. Preferred formats for PLoS ONE are: Preferred PLoS ONE pour les formats sont:

  • Audio: MP3 Audio: MP3
  • Video: MOV, progressive download, 320x240px frame size Vidéo: MOV, progressive download, 320x240px taille
  • Flash: SWF Flash: SWF

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DOT-NIRS-University College London-Delpy 1999-1988

Use of mitochondrial inhibitors to demonstrate that cytochrome oxidase near-infrared spectroscopy can measure mitochondrial dysfunction noninvasively in the brain.

Cooper CE, Cope M, Springett R, Amess PN, Penrice J, Tyszczuk L, Punwani S, Ordidge R, Wyatt J, Delpy DT.

Department of Biological Sciences, University of Essex, Colchester, UK.

The use of near-infrared spectroscopy to measure noninvasively changes in the redox state of cerebral cytochrome oxidase in vivo is controversial. We therefore tested these measurements using a multiwavelength detector in the neonatal pig brain. Exchange transfusion with perfluorocarbons revealed that the spectrum of cytochrome oxidase in the near-infrared was identical in the neonatal pig, the adult rat, and in the purified enzyme. Under normoxic conditions, the neonatal pig brain contained 15 micromol/L deoxyhemoglobin, 29 micromol/L oxyhemoglobin, and 1.2 micromol/L oxidized cytochrome oxidase. The mitochondrial inhibitor cyanide was used to determine whether redox changes in cytochrome oxidase could be detected in the presence of the larger cerebral hemoglobin concentration. Addition of cyanide induced full reduction of cytochrome oxidase in both blooded and bloodless animals. In the blooded animals, subsequent anoxia caused large changes in hemoglobin oxygenation and concentration but did not affect the cytochrome oxidase near-infrared signal. Simultaneous blood oxygenation level-dependent magnetic resonance imaging measurements showed a good correlation with near-infrared measurements of deoxyhemoglobin concentration. Possible interference in the near-infrared measurements from light scattering changes was discounted by simultaneous measurements of the optical pathlength using the cerebral water absorbance as a standard chromophore. We conclude that, under these conditions, near-infrared spectroscopy can accurately measure changes in the cerebral cytochrome oxidase redox state.

Publication Types:

PMID: 9886352 [PubMed – indexed for MEDLINE]


Experimental and theoretical comparison of NIR spectroscopy measurements of cerebral hemoglobin changes.

Firbank M, Elwell CE, Cooper CE, Delpy DT.

Department of Medical Physics and Bioengineering, University College London, London WC1E 6JA, United Kingdom CO4 3SQ.

Two near-infrared spectroscopy (NIRS) methods are available for measuring changes (Delta) in total cerebral hemoglobin concentration (CHC): 1) a continuous measurement of the changes in total hemoglobin concentration (Delta[Hb]tot) and 2) the difference between two absolute measurements of CHC, each derived from a small, controlled change in inspired O2 fraction. This paper investigates the internal consistency of these two methods by using an experimental and theoretical comparison. NIRS was used to measure [Hb]tot in five newborn piglets before and after a change in arterial PCO2. Delta[Hb]tot demonstrated a low coefficient of variation of 2.8 +/- 2.8 (SD) % which allowed changes in CO2-cerebral blood volume reactivity to be clearly discriminated. However, a high coefficient of variation of 22.8 +/- 3.5% on the DeltaCHC measurements obscured any CO2 reactivity changes. A theoretical analysis demonstrates the effects of optical pathlength, background absorption, scatter, and blood vessel diameter on both methods. For more accurate monitoring of CHC, individual measurements of optical pathlength and more accurate pulse oximetry are required.

Publication Types:

PMID: 9804599 [PubMed – indexed for MEDLINE]


A theoretical study of the signal contribution of regions of the adult head to near-infrared spectroscopy studies of visual evoked responses.

Firbank M, Okada E, Delpy DT.

University Department of Radiology, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom.

Near-infrared (NIR) spectroscopy has been used in studies of the cerebral hemodynamic response to visual processing. In this paper, we present theoretical results from finite element and Monte Carlo modeling in order to help understand the contribution to the NIR signal from different parts of the head. The results from the models show that at the typical optode spacings used in these studies, an infrared spectroscopy measurement of intensity is sensitive to the outer 1-2 mm of the cortical gray matter and the partial optical path length in the gray matter is approximately 10 mm, compared with a total optical path length of 400 mm. When the NIR measurement is of change in mean photon arrival time (or phase shift), the signal comes from the upper 2-4 mm of the cortical surface and there is an increased lateral spread of the contributing tissue. We predict that for a 4-cm separation of input and detection optodes at 800 nm, a 1 microM change in hemoglobin concentration in the cortex corresponds to an attenuation change of approximately 0.001 OD (optical density) or 1 ps mean time change. Movement of the brain caused by this increase in volume will cause an absorption change of approximately half this magnitude, but does not affect the photon arrival time at 4-cm spacing. A discrepancy between the predicted and the experimentally measured intensities may support the supposition that the NIR signal is actually very sensitive to changes occurring in the pial cerebral vessels lying on the brain surface.

Publication Types:

PMID: 9698577 [PubMed – indexed for MEDLINE]


The relationship of oxygen delivery to absolute haemoglobin oxygenation and mitochondrial cytochrome oxidase redox state in the adult brain: a near-infrared spectroscopy study.

Cooper CE, Delpy DT, Nemoto EM.

Department of Biological Sciences, Central Campus, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK. ccooper@essex.ac.uk

Near-infrared spectroscopy was used to determine the effect of changes in the rate of oxygen delivery to the adult rat brain on the absolute concentrations of oxyhaemoglobin, deoxyhaemoglobin and the redox state of the CuA centre in mitochondrial cytochrome oxidase. The cytochrome oxidase detection algorithm was determined to be robust to large changes in haemoglobin oxygenation and concentration. By assuming complete haemoglobin deoxygenation and CuA reduction following mechanical ventilation on 100% N2O, the absolute concentration of oxyhaemoglobin (35 microM), deoxyhaemoglobin (27 microM) and the redox state of CuA (82% oxidized) were calculated in the normal adult brain. The mean arterial blood pressure was decreased by exsanguination. When the pressure reached 100 mmHg, haemoglobin oxygenation started to fall, but the total haemoglobin concentration and oxidized CuA levels only fell when cerebral blood volume autoregulation mechanisms failed at 50 mmHg. Haemoglobin oxygenation fell linearly with decreases in the rate of oxygen delivery to the brain, but the oxidized CuA concentration did not start to fall until this rate was 50% of normal. The results suggest that the brain maintains more than adequate oxygen delivery to mitochondria and that near-infrared spectroscopy may be a good measure of oxygen insufficiency in vivo.

Publication Types:

PMID: 9620863 [PubMed – indexed for MEDLINE]

PMCID: PMC1219521


In vivo measurements of the wavelength dependence of tissue-scattering coefficients between 760 and 900 nm measured with time-resolved spectroscopy.

Matcher SJ, Cope M, Delpy DT.

We present in vivo values for the optical transport coefficients (mu(a), mu(s)?) of the adult human forearm, calf, and head from 760 to 900 nm measured with time-resolved spectroscopy. The accuracy of the method is tested with tissue-simulating phantoms. We obtain mu(s)?(lambda) approximately 1.1 – (5.1 x 10(-4) lambda) mm(-1) (forearm), 1.6 – (8.9 x 10(-4) lambda) mm(-1) (calf), and 1.45 – (6.5 x 10(-4) lambda) mm(-1) (head), where lambda is measured in nanometers. At 800 nm we obtain mu(a) = 0.023 +/- 0.004 mm(-1) (forearm), 0.017 +/- 0.005 mm(-1) (calf), and 0.016 +/- 0.001 mm(-1) (head). Our values differ substantially from published in vitro data. In particular, our transport coefficients for the adult head are substantially lower than previously reported values for adult human cerebral matter and pig skull cortical bone measured in vitro.

PMID: 18250686 [PubMed – in process]


Theoretical and experimental investigation of near-infrared light propagation in a model of the adult head.

Okada E, Firbank M, Schweiger M, Arridge SR, Cope M, Delpy DT.

Near-infrared light propagation in various models of the adult head is analyzed by both time-of-flight measurements and mathematical prediction. The models consist of three- or four-layered slabs, the latter incorporating a clear cerebrospinal fluid (CSF) layer. The most sophisticated model also incorporates slots that imitate sulci on the brain surface. For each model, the experimentally measured mean optical path length as a function of source-detector spacing agrees well with predictions from either a Monte Carlo model or a finite-element method based on diffusion theory or a hybrid radiosity-diffusion theory. Light propagation in the adult head is shown to be highly affected by the presence of the clear CSF layer, and both the optical path length and the spatial sensitivity profile of the models with a CSF layer are quite different from those without the CSF layer. However, the geometry of the sulci and the boundary between the gray and the white matter have little effect on the detected light distribution.

PMID: 18250644 [PubMed – in process]


The effect of scalp ischaemia on measurement of cerebral blood volume by near-infrared spectroscopy.

Owen-Reece H, Elwell CE, Wyatt JS, Delpy DT.

Department of Anaesthesia, National Hospital for Neurology and Neurosurgery, London, UK.

Near-infrared spectroscopy (NIRS) is a noninvasive method of quantifying changes in cerebral haemodynamics from changes in the absorption of near-infrared light by oxyhaemoglobin and deoxyhaemoglobin. Measurement of neonatal cerebral blood volume (CBV) by NIRS was described in 1990 but it has been suggested that, in adults, scalp and skull blood content contribute a significant amount to the cerebral haemodynamic variables quantifiable by NIRS. To investigate this, CBV was measured in nine adult subjects, in the frontal region of the head, before and after inflating a pneumatic tourniquet proximal to the measurement site. Because a change in scalp blood content could potentially alter the pathlength of light passing through the head and hence affect the measured CBV, the optical pathlength factor was therefore also measured before and after tourniquet inflation. Blood flow occlusion was confirmed by laser Doppler velocimetry. The results showed that tourniquet inflation had no effect on the estimated value of CBV or the differential pathlength factor. We conclude that, provided the distance between light entry and exit on the surface of the scalp is sufficiently large, changes in scalp blood flow have no effect on NIRS measurement of cerebral haemodynamics.

Publication Types:

PMID: 8953626 [PubMed – indexed for MEDLINE]


Comment on:

Near-infrared spectroscopy and cerebral hemodynamics.

Owen-Reece H, Smith M, Elwell CE, Goldstone JC, Delpy DT.

Publication Types:

PMID: 8706504 [PubMed – indexed for MEDLINE]


Near-infrared spectroscopy: theory and applications.

Wahr JA, Tremper KK, Samra S, Delpy DT.

Department of Anesthesiology, University of Michigan, Ann Arbor, USA.

In conclusion, NIRS appears to offer both a new monitoring modality and new information about cerebral oxygenation. Technical problems in the application of this technology persist, most notably determination of pathlength and the volume of tissue interrogated. Those familiar with the history of pulse oximetry will recall that although Millikan developed an ear oximeter in 1947, it was not until Aoyagi combined recognition of the pulse signal with spectroscopy in the 1970s that oximetry was transformed into a clinically applicable monitor. In much the same way, NIRS may find the same tremendous usefulness as a noninvasive monitor of cerebral oxygen utilization, pending resolution of the remaining technical problems.

Publication Types:

PMID: 8725427 [PubMed – indexed for MEDLINE]


The finite element method for the propagation of light in scattering media: boundary and source conditions.

Schweiger M, Arridge SR, Hiraoka M, Delpy DT.

Department of Medical Physics and Bioengineering, University College London, England.

This paper extends our work on applying the Finite Element Method (FEM) to the propagation of light in tissue. We address herein the topics of boundary conditions and source specification for this method. We demonstrate that a variety of boundary conditions stipulated on the Radiative Transfer Equation can be implemented in a FEM approach, as well as the specification of a light source by a Neumann condition rather than an isotropic point source. We compare results for a number of different combinations of boundary and source conditions under FEM, as well as the corresponding cases in a Monte Carlo model.

Publication Types:

PMID: 8587533 [PubMed – indexed for MEDLINE]


Performance comparison of several published tissue near-infrared spectroscopy algorithms.

Matcher SJ, Elwell CE, Cooper CE, Cope M, Delpy DT.

University College London Department of Medical Physics and Bioengineering, United Kingdom.

We have collected multiwavelength near-infrared (NIR) attenuation spectra on human forearm muscle, the adult rat head, and newborn piglet head to compare the changes in chromophore concentration derived from these data using published algorithms from four groups. We find differences between the results from the algorithms on each data set, particularly in their estimation of cytochrome oxidase (cyt-aa3) redox changes. We also find some differences when applying the same algorithm to the three data sets, suggesting possible difficulties in transferring algorithms between different physiological systems (e.g., Kurth, C. D., Steven, J. M., Benaron, D., and Chance, B. (1993) J. Clin. Monit. 9, 163-170). We have also compared the algorithms using simulated data generated using measured hemoglobin absorption spectra and a diffusion model for light transport in tissue. We find that while the algorithms from three groups are in broad agreement, that published by Piantadosi (Piantadosi, C. A. (1993) Methods Toxicol. 2, 107-126) produces significantly different results for cyt-aa3 and HbO2. Either the hemoglobin spectra used to produce the simulated data are inaccurate or the modeling is incorrect, or this algorithm is erroneous.

Publication Types:

PMID: 7668392 [PubMed – indexed for MEDLINE]


The spatial resolution performance of a time-resolved optical imaging system using temporal extrapolation.

Hebden JC, Hall DJ, Delpy DT.

Department of Medical Physics, University College London, England.

Optical imaging methods are being explored as a potential means of screening for breast cancer. Previous investigations of time-resolved imaging techniques have suggested that due to the lack of photons with sufficiently small pathlengths, the spatial resolution achievable through a human breast would be unlikely to be better than a centimeter. Experimental results presented here indicate, however, that higher resolution may be achieved by extrapolating the measured temporal distribution of transmitted photons. This is performed using a least-squares fit between data and an analytic model of photon transport. The spatial resolution of a time-resolved imaging system was evaluated by measuring the edge response produced by an opaque mask embedded in the center of a 51-mm-thick, very highly scattering medium. The limiting spatial resolution was improved from about 13 mm to about 5 mm.

Publication Types:

PMID: 7565351 [PubMed – indexed for MEDLINE]


Measurement of the optical properties of the skull in the wavelength range 650-950 nm.

Firbank M, Hiraoka M, Essenpreis M, Delpy DT.

Department of Medical Physics and Bioengineering, University College London, UK.

The optical properties of samples of bone from pig skull have been measured over the wavelength range 650-950 nm. The scattering phase function was measured on thin samples of the bone using a goniometer, and a value for the mean cosine g, of the scattering angle, was calculated. The scattering and absorption coefficients, mu s and mu a were then determined from measurements of diffuse reflectance and transmittance made with a pair of integrating spheres, by a step-wise search through a table of diffuse reflectance and transmittance versus mu a and mu s generated by a Monte Carlo model incorporating the measured scattering phase function. Values for g measured on six samples varied from 0.925 +/- 0.014 at 650 nm to 0.945 +/- 0.013 at 950 nm. Corresponding values for mu a and mu s measured on 18 samples were mu a = 0.04 +/- 0.002 mm-1, mu s = 35 +/- 0.7 mm-1 at 650 nm to mu a = 0.05 +/- 0.002 mm-1, mu s = 24 +/- 0.6 mm-1 at 950 nm.

Publication Types:

PMID: 8488176 [PubMed – indexed for MEDLINE]


Wavelength dependence of the differential pathlength factor and the log slope in time-resolved tissue spectroscopy.

Essenpreis M, Cope M, Elwell CE, Arridge SR, van der Zee P, Delpy DT.

Department of Medical Physics and Bioengineering, University College London, UK.

Publication Types:

PMID: 8362674 [PubMed – indexed for MEDLINE]

————–

Estimation of optical pathlength through tissue from direct time of flight measurement.

Delpy DT, Cope M, van der Zee P, Arridge S, Wray S, Wyatt J.

Department of Medical Physics, University College London, UK.

Quantitation of near infrared spectroscopic data in a scattering medium such as tissue requires knowledge of the optical pathlength in the medium. This can now be estimated directly from the time of flight of picosecond length light pulses. Monte Carlo modelling of light pulses in tissue has shown that the mean value of the time dispersed light pulse correlates with the pathlength used in quantitative spectroscopic calculations. This result has been verified in a phantom material. Time of flight measurements of pathlength across the rat head give a pathlength of 5.3 +/- 0.3 times the head diameter.

Publication Types:

DOT- Imperial College London- Delpy 2008/06–2005/06

Measuring circulating blood volume in newborn infants using pulse dye densitometry and indocyanine green.

Aladangady N, Leung T, Costeloe K, Delpy D.

Department of Child Health, Homerton University Hospital/Bart’s and the London School of Medicine and Dentistry, London, UK.

Background: Circulating blood volume (BV) is an important, but often unconsidered, variable in newborn infants undergoing intensive care. The data on validation and repeatability of BV measurement are limited. Aim: To validate and test the repeatability of measuring BV in newborn infants using indocyanine green (ICG) and pulse dye densitometry (PDD). Methods: Validation- Paired measurements of BV were made using the fetal hemoglobin (HbF) dilution and the PDD method. Repeatability- The BV was measured twice at an interval of 30-40 min in a second group of infants. Results: Validation- Data from three of 13 infants studied were excluded because of probe dislodgement or ICG injection error. The median (range) birth weight of the 10 infants whose data were analyzed was 1032 g (740-2384 g) and seven (70%) were receiving either mechanical ventilation or nasal CPAP. The median BV measured by HbF dilution was 66.2 ml.kg(-1) (43.7-81.0 ml.kg(-1)) and by the PDD method was 68.9 ml.kg(-1) (49.3-101.0 ml.kg(-1)). The mean difference was 5.92 ml.kg(-1) (sd 17.33 ml.kg(-1)). Repeatability- Twelve infants were studied and three excluded because of probe dislodgement/motion artifact or ICG injection error. The median weight of the nine infants whose data were analyzed was 1208 g (795-2600 g). The median (range) BV1 and BV2 were 70.5 ml.kg(-1) (53.1-160 ml.kg(-1)) and 87.5 ml.kg(-1) (38.0-248.0 ml.kg(-1)), respectively. Mean difference of the two BV estimates (BV1-BV2) was -24.6 ml.kg(-1) (sd 33.3 ml.kg(-1)) and coefficient of repeatability was 66.5 ml.kg(-1). Conclusion: Pulse dye densitometry can be used to measure BV in the newborn infant at the cotside but the repeatability measurements suggest that its use is limited.

PMID: 18544143 [PubMed – as supplied by publisher]


Changes in prefrontal cortical behaviour depend upon familiarity on a bimanual co-ordination task: an fNIRS study.

Leff DR, Elwell CE, Orihuela-Espina F, Atallah L, Delpy DT, Darzi AW, Yang GZ.

Royal Wolfson Image Computing Laboratory and Department of Biosurgery and Surgical Technology, Imperial College London, UK.

To investigate neurocognitive mechanisms associated with task-related expertise development, this paper investigates serial changes in prefrontal activation patterns using functional near infrared spectroscopy (fNIRS). We evaluate cortical function in 62 healthy subjects with varying experience during serial evaluations of a knot-tying task. All tasks were performed bimanually and self paced, with fixed episodes of motor rest for five repetitions. Improvements in technical skill were evaluated using dexterity indices to quantify time, total movements and pathlength required to complete trials. Significant improvements in technical skills were observed in novices between the 2nd and 3rd trials, associated with increasing task familiarity. In trained subjects, minimal fluctuation in task-related oxyhaemoglobin (HbO(2)) and deoxyhaemoglobin (HHb) changes were observed in association with more stable task performance. In contrast, two significant transitions in prefrontal haemodynamic change were observed in novices. Greater task-related increases in HbO(2) and decreases in HHb were identified on the second trial compared to the first. Relative decreases in HbO(2) and increases in HHb change were observed between the third and fourth, and fourth and fifth trials respectively. These data suggest that prefrontal processing across five knot-tying trials is influenced by the level of experience on a task. Modifications in prefrontal activation appear to confer technical performance adaptation in novices.

PMID: 17964187 [PubMed – indexed for MEDLINE]


Measurement of frontal lobe functional activation and related systemic effects: a near-infrared spectroscopy investigation.

Tachtsidis I, Leung TS, Devoto L, Delpy DT, Elwell CE.

Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, Gower Street, London WC1E 6BT. iliastac@medphys.ucl.ac.uk

Near-infrared spectroscopy (NIRS) has been used to measure changes in cerebral oxy- and deoxy- haemoglobin (delta[HbO2], delta[HHb]) in response to functional activation. It has been previously reported that during functional activation of the motor cortex heart rate increases. The aim of this study was to investigate systemic changes during functional activation of the frontal cortex. The responses to anagram presentations with varying difficulty (4-Letters and 7-Letters) over a 6 minute period were recorded. A Hamamatsu NIRO 200 NIRS system recorded delta[HbO2] and delta[HHb] using the modified Beer Lambert law (MBL) and tissue oxygenation index (TOI) employing spatial resolved spectroscopy (SRS) over the left and right frontal hemisphere. Mean blood pressure (MBP) and heart rate (HR) were measured continuously. Nine young healthy volunteers (mean age 23) were included in the analysis. Significant task related changes were observed in both the NIRS and systemic signals during the anagram solving with increases in [HbO2] and [HHb] accompanied by changes in MBP and HR. The [HbO2] and [HHb] signals measured over the frontal region were found to have a varying association with the MBP signal across different volunteers. The effect of these systemic changes on measured NIRS signals must be considered

Publication Types:

PMID: 18290351 [PubMed – indexed for MEDLINE]


Measurement of cerebral tissue oxygenation in young healthy volunteers during acetazolamide provocation: a transcranial Doppler and near-infrared spectroscopy investigation.

Tachtsidis I, Tisdall M, Delpy DT, Smith M, Elwell CE.

Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, Gower Street, London WCIE 6BT. iliastac@medphys.ucl.ac.uk

Recent advances in near-infrared spectroscopy (NIRS) allow measurements of absolute tissue oxygen saturation (TOI) using spatially resolved spectroscopy (SRS), while enabling better depth sensitivity. However concerns remain regarding the relative contribution of the extracranial circulation to the cerebral NIRS TOI signal. In this study we investigated this during a period of selective rise in cerebral blood flow (CBF) produced by the administration of acetazolamide (ACZ) in 10 healthy volunteers. A two channel spectrometer (NIRO 300, Hamamatsu Photonics KK) was used to measure absolute cerebral TOI over the frontal cortex using the SRS technique using an optode spacing of 5 cm and 1.5 cm for channel 1 and 2 respectively. After ACZ administration we were able to observe a significant increase in the velocity of middle cerebral artery (V(mca), measured with the transcranial Doppler (TCD)) which was accompanied by an increase in TOI as monitored by the NIRO 300 with an optode spacing of 5 cm but not with an optode spacing of 1.5 cm. Furthermore a direct relationship was seen between the V(mca) and the TOI measured at 5 cm optode spacing. This work suggests that using this commercial NIRS instrument with an optode spacing of 5 cm one is able to detect the intracranial changes.

Publication Types:

PMID: 18290350 [PubMed – indexed for MEDLINE]


Cerebral tissue oxygen saturation calculated using low frequency haemoglobin oscillations measured by near infrared spectroscopy in adult ventilated patients.

Leung TS, Tisdall MM, Tachtsidis I, Smith M, Delpy DT, Elwell CE.

Department of Medical Physics and Bioengineering, University College London, London, UK.

Oxy- (HbO2) and deoxy- (HHb) haemoglobin signals measured by near infrared (NIR) spectroscopy over the human frontal lobes frequently contain respiratory and low frequency oscillations (LFOs). It has been suggested previously that venous oxygen saturation (SvO2) can be calculated from these respiratory oscillations. In this paper, we investigated the use of a Fourier transform based algorithm to calculate an oxygen saturation measure known as S(osc)O2 which may be a close estimate of the underlying SvO2. S(osc)O2 was calculated using three different frequency ranges, (1) respiratory oscillations only, (2) LFOs only, and (3) both respiratory oscillations and LFOs. At each frequency range S(osc)O2 was calculated using either (1) the modified Beer-Lambert law (MBL) or (2) spatially resolved spectroscopy (SRS). In total six different measurements of S(osc)O2 were investigated here. Experiments were performed in six adult ventilated patients with traumatic brain injury. The patients’ inspired oxygen fraction (FiO2) was raised in two hyperoxic phases. The calculated S(osc)O2 values were compared with other cerebral oxygenation measures including an intraparenchymal catheter based brain tissue oxygen tension (PbrO2) and the NIR based tissue oxygenation index (TOI). It was found that the S(osc)O2 calculated using the combined respiratory and LFO frequency range and the SRS method resulted in the highest detection rates of hyperoxic changes. This measure of S(osc)O2 may provide a viable, continuous, non invasive, bedside measure of cerebral venous oxygen saturation.

Publication Types:

PMID: 18290334 [PubMed – indexed for MEDLINE]


Investigation of frontal cortex, motor cortex and systemic haemodynamic changes during anagram solving.

Tachtsidis I, Leung TS, Tisdall MM, Devendra P, Smith M, Delpy DT, Elwell CE.

Department of Medical Physics and Bioengineering, Malet Place Engineering Building, Gower Street, University College London, London, UK WC1E 6BT.

We have previously reported changes in the concentrations of oxy-(delta[HbO2]) deoxy- (delta[HHb]) and total haemoglobin (delta[HbT] = delta[HbO2] + delta[HHb]) measured using near infrared spectroscopy (NIRS) over the frontal cortex (FC) during an anagram solving task. These changes were associated with a significant increase in both mean blood pressure (MBP) and heart rate (HR). The aim of this study was to investigate whether the changes in MBP previously recorded during an anagram solving task produces associated changes in scalp blood flow (flux) measured by laser Doppler and whether any changes are seen in NIRS haemodynamic measurements over a control region of the brain (motor cortex: MC). During the 4-Letter anagram task significant changes were observed in the delta[HbO2], delta[HHb] and delta[HbT] in both the frontal and motor cortex (n = 11, FC p < 0.01, MC p < 0.01). These changes were accompanied by significant changes in both MBP (n = 11, p < 0.01) and scalp flux (n = 9, p = 0.01). During the 7-Letter anagram task significant changes were observed in the delta[HbO2] and delta[HbT] (n = 11, FC p < 0.01, MC p < 0.01), which were accompanied by significant changes in both MBP (n = 11, p = 0.05) and flux (n = 9, p = 0.05). The task-related changes seen in MBP and flux in this study appear to contribute to the changes in the NIRS signals over both the activated and control regions of the cortex.

Publication Types:

PMID: 18290310 [PubMed – indexed for MEDLINE]


Functional optical signal analysis: a software tool for near-infrared spectroscopy data processing incorporating statistical parametric mapping.

Koh PH, Glaser DE, Flandin G, Kiebel S, Butterworth B, Maki A, Delpy DT, Elwell CE.

University College London, Department of Medical Physics and Bioengineering, Biomedical Optics Research Laboratory, Gower Street, London WC1E 6BT United Kingdom. pkoha.medphys.ucl.ac.uk

Optical topography (OT) relies on the near infrared spectroscopy (NIRS) technique to provide noninvasively a spatial map of functional brain activity. OT has advantages over conventional fMRI in terms of its simple approach to measuring the hemodynamic response, its ability to distinguish between changes in oxy- and deoxy-hemoglobin and the range of human participants that can be readily investigated. We offer a new software tool, functional optical signal analysis (fOSA), for analyzing the spatially resolved optical signals that provides statistical inference capabilities about the distribution of brain activity in space and time and by experimental condition. It does this by mapping the signal into a standard functional neuroimaging analysis software, statistical parametric mapping (SPM), and forms, in effect, a new SPM toolbox specifically designed for NIRS in an OT configuration. The validity of the program has been tested using synthetic data, and its applicability is demonstrated with experimental data.

Publication Types:

PMID: 18163826 [PubMed – indexed for MEDLINE]


Pioneers in biomedical optics: special section honoring professor Frans F. Jobsis of Duke University.

Delpy DT, Ferrari M, Piantadosi CA, Tamura M.

Publication Types:

Personal Name as Subject:

PMID: 18163804 [PubMed – indexed for MEDLINE]


Theoretical investigation of measuring cerebral blood flow in the adult human head using bolus Indocyanine Green injection and near-infrared spectroscopy.

Leung TS, Tachtsidis I, Tisdall M, Smith M, Delpy DT, Elwell CE.

Department of Medical Physics, University College London, London, UK. tsl@medphys.ucl.ac.uk

To investigate the accuracy of measuring cerebral blood flow (CBF) using a bolus injection of Indocyanine Green (ICG) detected by near-infrared spectroscopy in adult human heads, simulations were performed using a two-layered model representing the extracerebral and intracerebral layers. Modeled optical data were converted into tissue ICG concentration using either the one-detector modified Beer-Lambert law (MBLL) method, or the two-detector partial path-length (PPL) method. The CBFs were estimated using deconvolution and blood flow index techniques. Using the MBLL method, the CBFs were significantly underestimated but the PPL method improved their accuracy and robustness, especially when used as relative measures. The dispersion of the arterial input function also affected the CBF estimates.

Publication Types:

PMID: 17356602 [PubMed – indexed for MEDLINE]


Investigation of in vivo measurement of cerebral cytochrome-c-oxidase redox changes using near-infrared spectroscopy in patients with orthostatic hypotension.

Tachtsidis I, Tisdall M, Leung TS, Cooper CE, Delpy DT, Smith M, Elwell CE.

Department of Medical Physics and Bioengineering, Malet Place Engineering Building, University College London, Gower Street, London, UK. iliastac@medphys.ucl.ac.uk

We have previously used a continuous four-wavelength near-infrared spectrometer to measure changes in the cerebral concentrations of oxy-haemoglobin (Delta[HbO(2)] and deoxy-haemoglobin (Delta[HHb]) during head-up tilt in patients with primary autonomic failure. The measured changes in light attenuation also allow calculation of changes in the concentration of oxidized cytochrome-c-oxidase (Delta[(ox)CCO]), and this paper analyses the Delta[(ox)CCO] during the severe episodes of orthostatic hypotension produced by this experimental protocol. We studied 12 patients during a passive change in position from supine to a 60 degrees head-up tilt. The challenge caused a reduction in mean blood pressure of 59.93 (+/-26.12) mmHg (Mean (+/-SD), p < 0.0001), which was associated with a reduction in the total concentration of haemoglobin (Delta[HbT] = Delta[HbO(2)] + Delta[HHb]) of 5.02 (+/-3.81) microM (p < 0.0001) and a reduction in the haemoglobin difference concentration (Delta[Hb(diff)] = Delta[HbO(2)] – Delta[HHb]) of 14.4 (+/-6.73) microM (p < 0.0001). We observed a wide range of responses in Delta[(ox)CCO]. Six patients demonstrated a drop in Delta[(ox)CCO] (0.17 +/- 0.15 microM); four patients demonstrated no change (0.01 +/- 0.12 microM) and two patients showed an increase in Delta[(ox)CCO] (0.21 +/- 0.01 microM). Investigation of the association between the changes in concentrations of haemoglobin species and the Delta[(ox)CCO] for each patient show a range of relationships. This suggests that a simple mechanism for crosstalk, which might produce artefactual changes in [(ox)CCO], is not present between the haemoglobin and the (ox)CCO NIRS signals. Further investigation is required to determine the clinical significance of the changes in [(ox)CCO].

Publication Types:

PMID: 17237591 [PubMed – indexed for MEDLINE]


Synchronization between arterial blood pressure and cerebral oxyhaemoglobin concentration investigated by wavelet cross-correlation.

Rowley AB, Payne SJ, Tachtsidis I, Ebden MJ, Whiteley JP, Gavaghan DJ, Tarassenko L, Smith M, Elwell CE, Delpy DT.

Department of Engineering Science, University of Oxford, Oxford, UK. abr@robots.ox.ac.uk

Wavelet cross-correlation (WCC) is used to analyse the relationship between low-frequency oscillations in near-infrared spectroscopy (NIRS) measured cerebral oxyhaemoglobin (O(2)Hb) and mean arterial blood pressure (MAP) in patients suffering from autonomic failure and age-matched controls. Statistically significant differences are found in the wavelet scale of maximum cross-correlation upon posture change in patients, but not in controls. We propose that WCC analysis of the relationship between O(2)Hb and MAP provides a useful method of investigating the dynamics of cerebral autoregulation using the spontaneous low-frequency oscillations that are typically observed in both variables without having to make the assumption of stationarity of the time series. It is suggested that for a short-duration clinical test previous transfer-function-based approaches to analyse this relationship may suffer due to the inherent nonstationarity of low-frequency oscillations that are observed in the resting brain.

Publication Types:

PMID: 17237588 [PubMed – indexed for MEDLINE]


Quantitative spatially resolved measurement of tissue chromophore concentrations using photoacoustic spectroscopy: application to the measurement of blood oxygenation and haemoglobin concentration.

Laufer J, Delpy D, Elwell C, Beard P.

Department of Medical Physics & Bioengineering, University College London, Malet Place Engineering Building, London WC1E 6BT, UK.

A new approach based on pulsed photoacoustic spectroscopy for non-invasively quantifying tissue chromophore concentrations with high spatial resolution has been developed. The technique is applicable to the quantification of tissue chromophores such as oxyhaemoglobin (HbO(2)) and deoxyhaemoglobin (HHb) for the measurement of physiological parameters such as blood oxygen saturation (SO(2)) and total haemoglobin concentration. It can also be used to quantify the local accumulation of targeted contrast agents used in photoacoustic molecular imaging. The technique employs a model-based inversion scheme to recover the chromophore concentrations from photoacoustic measurements. This comprises a numerical forward model of the detected time-dependent photoacoustic signal that incorporates a multiwavelength diffusion-based finite element light propagation model to describe the light transport and a time-domain acoustic model to describe the generation, propagation and detection of the photoacoustic wave. The forward model is then inverted by iteratively fitting it to measurements of photoacoustic signals acquired at different wavelengths to recover the chromophore concentrations. To validate this approach, photoacoustic signals were generated in a tissue phantom using nanosecond laser pulses between 740 nm and 1040 nm. The tissue phantom comprised a suspension of intralipid, blood and a near-infrared dye in which three tubes were immersed. Blood at physiological haemoglobin concentrations and oxygen saturation levels ranging from 2% to 100% was circulated through the tubes. The signal amplitude from different temporal sections of the detected photoacoustic waveforms was plotted as a function of wavelength and the forward model fitted to these data to recover the concentrations of HbO(2) and HHb, total haemoglobin concentration and SO(2). The performance was found to compare favourably to that of a laboratory CO-oximeter with measurement resolutions of +/-3.8 g l(-1) (+/-58 microM) and +/-4.4 g l(-1) (+/-68 microM) for the HbO(2) and HHb concentrations respectively and +/-4% for SO(2) with an accuracy in the latter in the range -6%-+7%.

PMID: 17183133 [PubMed – indexed for MEDLINE]


Comment on:

Comment on ‘the use of the Henyey-Greenstein phase function in Monte Carlo simulations in biomedical optics’.

Binzoni T, Leung TS, Gandjbakhche AH, Rüfenacht D, Delpy DT.

In this letter the authors highlight the presence of an error appearing in the discussion of the note ‘The use of the Henyey-Greenstein phase function in Monte Carlo simulations in biomedical optics’ previously published by them (Binzoni et al 2006 Phys. Med. Biol. 51 N313). In the light of this error, the discussion and conclusions in the original paper are revised in this letter and the role of the use of the phase functions in MC simulations, interpreted in probabilistic terms, is better clarified. The exact definition for the probability density function for the deflection angle, in the case of the Henyey-Greenstein model, is also given.

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Three dimensional optical imaging of blood volume and oxygenation in the neonatal brain.

Austin T, Gibson AP, Branco G, Yusof RM, Arridge SR, Meek JH, Wyatt JS, Delpy DT, Hebden JC.

Department of Paediatrics and Child Health, University College London, UK. topunaustin@doctors.org.uk

Optical methods provide a means of monitoring cerebral oxygenation in newborn infants at risk of brain injury. A 32-channel optical imaging system has been developed with the aim of reconstructing three-dimensional images of regional blood volume and oxygenation. Full image data sets were acquired from 14 out of 24 infants studied; successful images have been reconstructed in 8 of these infants. Regional variations in cerebral blood volume and tissue oxygen saturation are present in healthy preterm infants. In an infant with a large unilateral intraventricular haemorrhage, a corresponding region of low oxygen saturation was detected. These results suggest that optical tomography may provide an appropriate technique for investigating regional cerebral haemodynamics and oxygenation at the cotside.

Publication Types:

PMID: 16644237 [PubMed – indexed for MEDLINE]


Optimal determination of detector placement in cerebral NIR spectroscopy of neonates using chemometric techniques.

Leung TS, Elwell CE, Delpy DT.

This paper investigates the optimal placement of NIRS optodes in order to maximise the detection of haemoglobin changes in cortical grey matter resulting from an evoked response in neonates. The analysis is based upon predictions of optical signal at the surface of the head, using a Finite Element based model of light diffusion in tissue. Using the generated intensity data, the combination of optode positions, which maximise the signal from cortical grey matter whilst minimising that from surface tissue or cerebral white matter, is determined using a Chemometric statistical analysis. The neonatal head is modelled as a 2 dimensional circle with 3 layers corresponding to the skin/scalp, and grey and white matter. A wide range of absorption coefficients for each layer is simulated, based upon physiologically reasonable values for parameters. Surface intensity at 10 different optode positions have been generated for a total of 31,250 combinations of these variables for the 3 layers. It was found that with 3 optodes at 5, 15, and 50 mm apart from the source, the smallest root-mean-square error between the estimated and modelled values can be obtained. Increasing the number of optodes further does not improve the performance.

Publication Types:

PMID: 16594128 [PubMed – indexed for MEDLINE]


Anisotropic photon migration in human skeletal muscle.

Binzoni T, Courvoisier C, Giust R, Tribillon G, Gharbi T, Hebden JC, Leung TS, Roux J, Delpy DT.

Département de Neurosciences Fondamentales, University of Geneva, Switzerland. Tiziano.Binzoni@medecine.unige.ch

It is demonstrated in the short head of the human biceps brachii of 16 healthy subjects (12 males and 4 females) that near infrared photon migration is anisotropic. The probability for a photon to travel along the direction of the muscle fibres is higher (approximately 0.4) than that of travelling along a perpendicular axis (approximately 0.3) while in the adipose tissue the probability is the same (approximately 0.33) in all directions. Considering that the muscle fibre orientation is different depending on the type of muscle considered, and that inside a given skeletal muscle the orientation may change, the present findings in part might explain the intrasubject variability observed in the physiological parameters measured by near infrared spectroscopy techniques. In other words, the observed regional differences might not only be physiological differences but also optical artefacts.

PMID: 16481676 [PubMed – indexed for MEDLINE]


Measurement of the absolute optical properties and cerebral blood volume of the adult human head with hybrid differential and spatially resolved spectroscopy.

Leung TS, Tachtsidis I, Smith M, Delpy DT, Elwell CE.

Department of Medical Physics & Bioengineering, University College London, Gower Street, London WC1E 6BT, UK.

A hybrid differential and spatially resolved spectroscopy (SRS) technique has been developed to measure absolute absorption coefficient (mu(a)), reduced scattering coefficient (mu'(s)) and cerebral blood volume (CBV) in the adult human head. A spectrometer with both differential and SRS capabilities has been used to carry out measurements in 12 subjects. Two versions of the calculation have been considered using the hybrid technique, with one considering water as a chromophore as well as oxy- and deoxy-haemoglobin, and one ignoring water. The CBV has also been measured using a previously described technique based on changing the arterial saturation (SaO(2)) measured separately by a pulse oximeter, resulting in mean +/- SD CBV(a) (intra-individual coefficient of variation) = 2.22 +/- 1.06 ml/100 g (29.9%). (The superscript on CBV indicates the different calculation basis.) Using the hybrid technique with water ignored, CBV(0) = 3.18 +/- 0.73 ml/100 g (10.0%), mu(0)(a)(813 nm) = 0.010 +/- 0.003 mm(-1) and mu'(0)(s)(813 nm) = 1.19 +/- 0.55 mm(-1) (data quoted at 813 nm). With water considered, CBV(w) = 3.05 +/- 0.77 ml/100 g (10.5%), mu(w)(a)(813 nm) = 0.010 +/- 0.003 mm(-1) and mu'(w)(s)(813 nm) = 1.28 +/- 0.56 mm(-1). The mean biases between CBV(0)/CBV(w), CBV(0)/CBV(a) and CBV(w)/CBV(a) are 0.14 +/- 0.09, 0.79 +/- 1.22 and 0.65 +/- 1.24 ml/100 g. The mean biases between mu(0)(a)(813 nm)/mu(w)(a)(813 nm) and mu'(0)(s)(813 nm)/mu'(w)(s)(813 nm) are (5.9 +/- 10.0) x 10(-4) mm(-1) and -0.084 +/- 0.266 mm(-1), respectively. The method we describe extends the functionality of the current SRS instrumentation.

Publication Types:

PMID: 16424590 [PubMed – indexed for MEDLINE]


Absorption and scattering coefficient dependence of laser-Doppler flowmetry models for large tissue volumes.

Binzoni T, Leung TS, Rüfenacht D, Delpy DT.

Département de Neurosciences Fondamentales, Faculty of Medicine, University of Geneva, Switzerland. Tiziano.Binzoni@medecine.unige.ch

Based on quasi-elastic scattering theory (and random walk on a lattice approach), a model of laser-Doppler flowmetry (LDF) has been derived which can be applied to measurements in large tissue volumes (e.g. when the interoptode distance is >30 mm). The model holds for a semi-infinite medium and takes into account the transport-corrected scattering coefficient and the absorption coefficient of the tissue, and the scattering coefficient of the red blood cells. The model holds for anisotropic scattering and for multiple scattering of the photons by the moving scatterers of finite size. In particular, it has also been possible to take into account the simultaneous presence of both Brownian and pure translational movements. An analytical and simplified version of the model has also been derived and its validity investigated, for the case of measurements in human skeletal muscle tissue. It is shown that at large optode spacing it is possible to use the simplified model, taking into account only a ‘mean’ light pathlength, to predict the blood flow related parameters. It is also demonstrated that the ‘classical’ blood volume parameter, derived from LDF instruments, may not represent the actual blood volume variations when the investigated tissue volume is large. The simplified model does not need knowledge of the tissue optical parameters and thus should allow the development of very simple and cost-effective LDF hardware.

Publication Types:

PMID: 16394341 [PubMed – indexed for MEDLINE]


Estimation of cerebral oxy- and deoxy-haemoglobin concentration changes in a layered adult head model using near-infrared spectroscopy and multivariate statistical analysis.

Leung TS, Elwell CE, Delpy DT.

Department of Medical Physics and Bioengineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK.

The non-invasive measurement of cerebral oxy- (DeltaHbO(br)2) and deoxy-haemoglobin (DeltaHHb(br)) changes using near-infrared spectroscopy instruments is often affected by the absorption in the extracerebral layer. We have exploited the multivariate calibration (partial least squares, PLS) method to minimize the errors for a range of blood volume, oxygen saturation and extracerebral layer thicknesses. The changes in the mean time of flight of photons (Delta tau) and attenuation (DeltaA) on the surface of a 3D adult head model were simulated using a finite-element method based on the diffusion equation. The PLS was then performed to identify the optimal number of detectors, their positions and weightings, to optimize the estimation of DeltaHbO(br)2 and DeltaHHb(br). We define the ‘nominal accuracy’ as the accuracy of estimating DeltaHbO(br)2 and DeltaHHb(br) over a nominal range of extracerebral layer thicknesses and ‘robustness’ as the accuracy beyond the nominal range. The results showed that for one or two detectors, Delta tau performed better than DeltaA while using them together gave the best performance. When more detectors were used, the performances of using Delta tau, DeltaA or both together became comparable, showing that a larger number of detectors can compensate for the performance of a simple DeltaA measurement despite this measurement having a relatively lower sensitivity to intracerebral absorption changes.

Publication Types:

PMID: 16333155 [PubMed – indexed for MEDLINE]


Time-resolved optical mammography using a liquid coupled interface.

Yates TD, Hebden JC, Gibson AP, Enfield L, Everdell NL, Arridge SR, Delpy DT.

University College London, Department of Medical Physics & Bioengineering, London WC1E 6BT, United Kingdom.

A method has been devised for generating three-dimensional optical images of the breast using a 32-channel time-resolved system and a liquid-coupled interface. The breast is placed in a hemispherical cup surrounded by sources and detectors, and the remaining space is filled with a fluid with tissue-like optical properties. This approach has three significant benefits. First, cups can accommodate a large range of breast sizes, enabling the entire volume of the breast to be sampled. Second, the coupling of the source and detector optics at the surface is constant and independent of the subject, enabling intensity measurements to be employed in the image reconstruction. Third, the external geometry of the reconstructed volume is known exactly. Images of isolated targets with contrasting absorbing and scattering properties have been acquired, and the performance of the system has been evaluated in terms of the contrast, spatial resolution, and localization accuracy. These parameters were strongly dependent on the location of the targets within the imaged volume. Preliminary images of a healthy human subject are also presented, which reveal subtle heterogeneity, particularly in the distribution of scatter. The ability to detect an absorbing target adjacent to the breast is also demonstrated.

Publication Types:

PMID: 16292971 [PubMed – indexed for MEDLINE]


Three-dimensional whole-head optical tomography of passive motor evoked responses in the neonate.

Gibson AP, Austin T, Everdell NL, Schweiger M, Arridge SR, Meek JH, Wyatt JS, Delpy DT, Hebden JC.

Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London WC1E 6BT, UK. agibson@medphys.ucl.ac.uk

Optical tomography has been used to reconstruct three-dimensional images of the entire neonatal head during motor evoked responses. Data were successfully acquired during passive movement of each arm on four out of six infants examined, from which eight sets of bilateral images of hemodynamic parameters were reconstructed. Six out of the eight images showed the largest change in total hemoglobin in the region of the contralateral motor cortex. The mean distance between the peak response in the image and the estimated position of the contralateral motor cortex was 10.8 mm. These results suggest that optical tomography may provide an appropriate technique for non-invasive cot-side imaging of brain function.

Publication Types:

PMID: 16246586 [PubMed – indexed for MEDLINE]


In vitro measurements of absolute blood oxygen saturation using pulsed near-infrared photoacoustic spectroscopy: accuracy and resolution.

Laufer J, Elwell C, Delpy D, Beard P.

Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London WC1E 6BT, UK.

Pulsed photoacoustic spectroscopy was used to measure blood oxygen saturation in vitro. An optical parametric oscillator laser system provided nanosecond excitation pulses over the wavelength range 740-1040 nm which were used to generate photoacoustic signals in a cuvette through which a saline suspension of red blood cells was circulated. The signal amplitude and the effective attenuation coefficient were extracted from the photoacoustic signals as a function of wavelength to provide photoacoustic spectra of the blood. From these, the relative concentrations of oxy- and deoxyhaemoglobin, and therefore blood oxygen saturation (SO2), were determined using forward models of the absorbed energy distribution based on diffusion theory. A standard linear model of the dependence of absorbance on the concentration of chromophores was also used to calculate the blood oxygen saturation from the signal amplitude spectra. The diffusion approximation model was shown to produce the highest accuracy in blood SO2. The photoacoustically determined oxygen saturation was found to have an accuracy of +/-4% SO2 for signal amplitude data and +/-2.5% SO2 for effective attenuation spectra. The smallest change in oxygen saturation that can be measured using this technique was +/-1% SO2.

Publication Types:

PMID: 16148401 [PubMed – indexed for MEDLINE]


Linear and nonlinear reconstruction for optical tomography of phantoms with nonscattering regions.

Gibson AP, Hebden JC, Riley J, Everdell N, Schweiger M, Arridge SR, Delpy DT.

Department of Medical Physics and Bioengineering, University College London, London WC1E 6JA, United Kingdom. agibson@medphys.ucl.ac.uk

Most research in optical imaging incorrectly assumes that light transport in nonscattering regions in the head may be modeled by use of the diffusion approximation. The effect of this assumption is examined in a series of experiments on tissue-equivalent phantoms. Images from cylindrical and head-shaped phantoms with and without clear regions [simulating the cerebrospinal fluid (CSF) filled ventricles] and a clear layer (simulating the CSF layer surrounding the brain) are reconstructed with linear and nonlinear reconstruction techniques. The results suggest that absorbing and scattering perturbations can be identified reliably with nonlinear reconstruction methods when the clear regions are also present in the reference data but that the quality of the image degrades considerably if the reference data does not contain these features. Linear reconstruction performs similarly to nonlinear reconstruction, provided the clear regions are present in the reference data, but otherwise linear reconstruction fails. This study supports the use of linear reconstruction for dynamic imaging but suggests that, in all cases, image quality is likely to improve if the clear regions are modeled correctly.

Publication Types:

PMID: 16004037 [PubMed – indexed for MEDLINE]


A physiological model of cerebral blood flow control.

Banaji M, Tachtsidis I, Delpy D, Baigent S.

Department of Medical Physics and Bioengineering, University College London, Gower Street, London WC1E 6BT, UK. m.banaji@ucl.ac.uk

The construction of a computational model of the human brain circulation is described. We combine an existing model of the biophysics of the circulatory system, a basic model of brain metabolic biochemistry, and a model of the functioning of vascular smooth muscle (VSM) into a single model. This represents a first attempt to understand how the numerous different feedback pathways by which cerebral blood flow is controlled interact with each other. The present work comprises the following: Descriptions of the physiology underlying the model; general comments on the processes by which this physiology is translated into mathematics; comments on parameter setting; and some simulation results. The simulations presented are preliminary, but show qualitative agreement between model behaviour and experimental results.

Publication Types:

PMID: 15854674 [PubMed – indexed for MEDLINE]


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