zotero/translators/Nature Publishing Group.js

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{
"translatorID": "6614a99-479a-4524-8e30-686e4d66663e",
"translatorType": 4,
"label": "Nature Publishing Group",
"creator": "Aurimas Vinckevicius",
"target": "^https?://(www\\.)?nature\\.com/([^?/]+/)?(journal|archive|research|topten|search|full|abs|current_issue\\.htm|most\\.htm|articles/)",
"minVersion": "3.0",
"maxVersion": null,
"priority": 100,
"inRepository": true,
"browserSupport": "gcsibv",
"lastUpdated": "2024-02-29 20:30:00"
}
/**
Copyright (c) 2012 Aurimas Vinckevicius
This program is free software: you can redistribute it and/or
modify it under the terms of the GNU Affero General Public License
as published by the Free Software Foundation, either version 3 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public
License along with this program. If not, see
<http://www.gnu.org/licenses/>.
*/
// mimetype map for supplementary attachments
var suppTypeMap = {
pdf: 'application/pdf',
// 'zip': 'application/zip',
doc: 'application/msword',
xls: 'application/vnd.ms-excel',
excel: 'application/vnd.ms-excel'
};
function attachSupplementary(doc, item, next) {
// nature's new website
var attachAsLink = Z.getHiddenPref("supplementaryAsLink");
var suppDiv = doc.getElementById("supplementary-information");
if (suppDiv) {
var fileClasses = ZU.xpath(suppDiv, './/div[contains(@class, "supp-info")]/h2');
for (var i = 0, n = fileClasses.length; i < n; i++) {
var type = fileClasses[i].classList.item(0);
if (type) type = suppTypeMap[type];
if (!fileClasses[i].nextElementSibling) continue;
var dls = fileClasses[i].nextElementSibling.getElementsByTagName('dl');
for (var j = 0, m = dls.length; j < m; j++) {
var link = ZU.xpath(dls[j], './dt/a')[0];
if (!link) {
continue;
}
var title = dls[j].getElementsByTagName('dd')[0];
if (title) {
title = title.textContent.replace(
/^[\s\r\n]*(?:Th(?:is|e) )?file (?:contains|shows)\s+(\S+)/i,
function (m, firstWord) { // fix capitalization of first word
if (firstWord.toLowerCase() == firstWord) { // lower case word
return firstWord.charAt(0).toUpperCase() + firstWord.substr(1);
}
return firstWord;
}
).trim();
}
// add the heading from link
title = link.textContent.replace(/\s+\([^()]+\)\s*$/g, '').trim() // strip off the file size info
+ ". " + (title || '');
// fallback if we fail miserably
if (!title) title = "Supplementary file";
var attachment = {
title: title,
url: link.href
};
if (type) attachment.mimeType = type;
if (attachAsLink || !type) { // don't download unknown file types
attachment.snapshot = false;
}
item.attachments.push(attachment);
}
}
return;
}
// older websites, e.g. http://www.nature.com/onc/journal/v31/n6/full/onc2011282a.html
var suppLink = doc.getElementById('articlenav') || doc.getElementById('extranav');
if (suppLink) {
suppLink = ZU.xpath(suppLink, './ul/li//a[text()="Supplementary info"]')[0]; // unfortunately, this is the best we can do
if (!suppLink) return;
if (attachAsLink) { // we don't need to find links to individual files
item.attachments.push({
title: "Supplementary info",
url: suppLink.href,
mimeType: 'text/html',
snapshot: false
});
}
else {
ZU.processDocuments(suppLink.href, function (newDoc) {
var content = newDoc.getElementById('content');
if (content) {
var links = ZU.xpath(content, './div[@class="container-supplementary" or @id="general"]//a');
for (var i = 0, n = links.length; i < n; i++) {
var title = ZU.trimInternal(links[i].textContent);
var type = title.match(/\((\w+)\s+\d+[^)]+\)\s*$/);
if (type) type = suppTypeMap[type[1]];
if (!type) {
type = links[i].classList;
type = type.item(type.length - 1);
if (type) type = suppTypeMap[type.replace(/^(?:i|all)-/, '')];
}
// clean up title a bit
title = title.replace(/\s*\([^()]+\)$/, '')
.replace(/\s*-\s*download\b.*/i, '');
item.attachments.push({
title: title,
url: links[i].href,
mimeType: type,
snapshot: !!type // don't download unknown file types
});
}
}
next(doc, item);
});
return;
}
return;
}
// e.g. http://www.nature.com/ng/journal/v38/n11/full/ng1901.html
suppLink = ZU.xpath(doc, '(//a[text()="Supplementary info"])[last()]')[0];
if (suppLink) {
if (attachAsLink) { // we don't need to find links to individual files
item.attachments.push({
title: "Supplementary info",
url: suppLink.href,
mimeType: 'text/html',
snapshot: false
});
}
else {
Z.debug(suppLink.href);
ZU.processDocuments(suppLink.href, function (newDoc) {
var links = ZU.xpath(newDoc, './/p[@class="articletext"]');
Z.debug("Found " + links.length + " links");
for (var i = 0, n = links.length; i < n; i++) {
var link = links[i].getElementsByTagName('a')[0];
if (!link) continue;
var title = ZU.trimInternal(link.textContent);
var type = title.match(/\((\w+)\s+\d+[^)]+\)\s*$/);
if (type) type = suppTypeMap[type[1]];
// clean up title a bit
title = title.replace(/\s*\([^()]+\)$/, '')
.replace(/\s*-\s*download\b.*/i, '');
// maybe we can attach description to title
// can this be too long? I would probably make more sense to attach these as notes on the files
// how do we do that?
var desc = ZU.xpathText(links[i], './node()[last()][not(name())]'); // last text node
if (desc && (desc = ZU.trimInternal(desc))) {
title += '. ' + desc;
}
item.attachments.push({
title: title,
url: links[i].href,
mimeType: type,
snapshot: !!type // don't download unknown file types
});
}
next(doc, item);
});
}
}
}
// unescape Highwire's special html characters
function HWunescape(str) {
if (!str || !str.includes('[')) return str;
return str.replace(/\|?\[([^\]]+)\]\|?/g, function (s, p1) {
if (ISO8879CharMap[p1] !== undefined) {
return ISO8879CharMap[p1];
}
else {
return s;
}
});
}
// fix capitalization if all in upper case
function fixCaps(str) {
if (str && str == str.toUpperCase()) {
return ZU.capitalizeTitle(str.toLowerCase(), true);
}
else {
return str;
}
}
// get abstract
function getAbstract(doc) {
var abstractLocations = [
// e.g. https://www.nature.com/articles/onc2011282
'//*[@id="abstract-content"]',
// e.g. 'lead' http://www.nature.com/emboj/journal/v31/n1/full/emboj2011343a.html
// e.g. 'first_paragraph' http://www.nature.com/emboj/journal/vaop/ncurrent/full/emboj201239a.html
'//p[contains(@class,"lead") or contains(@class,"first_paragraph")]',
// e.g. http://www.nature.com/nprot/journal/v8/n11/full/nprot.2013.143.html
'//div[@id="abstract"]/div[@class="content"]/p',
// e.g.
'//div[@id="abs"]/*[self::div[not(contains(@class, "keyw-abbr"))] or self::p]',
// e.g. 'first-paragraph' http://www.nature.com/nature/journal/v481/n7381/full/nature10669.html
// e.g. 'standfirst' http://www.nature.com/nature/journal/v481/n7381/full/481237a.html
'//div[@id="first-paragraph" or @class="standfirst"]/p',
// e.g. http://www.nature.com/nature/journal/v481/n7381/full/nature10728.html
'//div[contains(@id,"abstract")]/div[contains(@class,"content")]/p',
// e.g. http://www.nature.com/ng/journal/v38/n8/abs/ng1845.html
'//span[@class="articletext" and ./preceding-sibling::*[1][name()="a" or name()="A"][@name="abstract"]]'
];
var paragraphs = [];
for (let i = 0, n = abstractLocations.length; i < n && !paragraphs.length; i++) {
paragraphs = Zotero.Utilities.xpath(doc, abstractLocations[i]);
}
if (!paragraphs.length) return null;
var textArr = [];
var p;
for (let i = 0, n = paragraphs.length; i < n; i++) {
// remove superscript references
p = ZU.xpathText(paragraphs[i], "./node()[not(self::sup and ./a)]", null, '');
if (p) p = ZU.trimInternal(p);
if (p) textArr.push(p);
}
return textArr.join("\n").trim() || null;
}
// some journals display keywords
function getKeywords(doc) {
var keywords = Zotero.Utilities.xpathText(doc, '//p[@class="keywords"]') // e.g. http://www.nature.com/onc/journal/v26/n6/full/1209842a.html
|| Zotero.Utilities.xpathText(doc, '//ul[@class="keywords"]//ul/li', null, '') // e.g. http://www.nature.com/emboj/journal/v31/n3/full/emboj2011459a.html
|| Zotero.Utilities.xpathText(doc, '//div[contains(@class,"article-keywords")]/ul/li/a', null, '; '); // e.g. http://www.nature.com/nature/journal/v481/n7382/full/481433a.html
if (!keywords) return null;
return keywords.split(/[;,]\s+/);
}
// get PDF url
function getPdfUrl(doc, url) {
var m = url.match(/(^[^#?]+\/)(?:full|abs)(\/[^#?]+?\.)[a-zA-Z]+(?=$|\?|#)/);
if (m && m.length) return m[1] + 'pdf' + m[2] + 'pdf';
else {
return attr(doc, 'a[data-track-action="download pdf"]', 'href');
}
}
// add using embedded metadata
function scrapeEM(doc, url, next) {
var translator = Zotero.loadTranslator("web");
// Embedded Metadata translator
translator.setTranslator("951c027d-74ac-47d4-a107-9c3069ab7b48");
translator.setDocument(doc);
translator.setHandler("itemDone", function (obj, item) {
// Replace HTML special characters with proper characters
// also remove all caps in Names and Titles
for (let i = 0; i < item.creators.length; i++) {
item.creators[i].lastName = HWunescape(item.creators[i].lastName);
item.creators[i].firstName = HWunescape(item.creators[i].firstName);
item.creators[i].lastName = fixCaps(item.creators[i].lastName);
item.creators[i].firstName = fixCaps(item.creators[i].firstName);
}
item.title = fixCaps(HWunescape(item.title));
if (item.abstractNote) item.abstractNote = ZU.cleanTags(item.abstractNote);
// the date in EM is usually online publication date
// If we can find a publication year, that's better
var year = ZU.xpathText(doc,
'//dd[preceding-sibling::dt[1][text()="Year published:" or text()="Date published:"]]');
if (year && (year = year.match(/\(\s*(.*?)\s*\)/))) {
item.date = year[1];
}
else if ((year = ZU.xpathText(doc, '//p[@id="cite"]'))
&& (year = year.match(/\((\d{4})\)/))) {
item.date = year[1];
}
else if (
(year = ZU.xpathText(doc, '//a[contains(@href,"publicationDate")]/@href'))
&& (year = year.match(/publicationDate=([^&]+)/))
// check that we at least have a year
&& year[1].match(/\d{4}/)) {
item.date = year[1];
}
// sometimes abstract from EM is description for the website.
// ours should always be better
var abstract = getAbstract(doc);
if (abstract
// maybe the abstract from meta tags is more complete
&& !(item.abstractNote
&& item.abstractNote.substr(0, 10) == abstract.substr(0, 10)
&& item.abstractNote.length > abstract.length)) {
item.abstractNote = abstract;
}
item.tags = getKeywords(doc) || item.tags;
if (item.notes) item.notes = [];
if (item.ISSN && ZU.cleanISSN) { // introduced in 3.0.12
var issn = ZU.cleanISSN(item.ISSN);
if (!issn) delete item.ISSN;
else item.ISSN = issn;
}
else if (item.ISSN === "ERROR! NO ISSN") {
delete item.ISSN;
}
next(item);
});
translator.getTranslatorObject(function (trans) {
// Make sure we always import as journal article (sometimes missing from EM)
// e.g. https://www.nature.com/articles/sdata201618
trans.itemType = "journalArticle";
trans.doWeb(doc, url);
});
}
function scrapeRIS(doc, url, next) {
var navBar = doc.getElementById('articlenav') || doc.getElementById('extranav');
var risURL;
if (navBar) {
risURL = doc.evaluate('//li[@class="export"]/a', navBar, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = doc.evaluate('//a[normalize-space(text())="Export citation" and not(@href="#")]', navBar, null, XPathResult.ANY_TYPE, null).iterateNext();
}
if (!risURL) risURL = doc.evaluate('//a[normalize-space(text())="RIS" and not(@href="#")]', doc, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = doc.evaluate('//li[@class="download-citation"]/a', doc, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = doc.evaluate('//a[normalize-space(text())="Export citation" and not(@href="#")]', doc, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = ZU.xpath(doc, '//ul[@data-component="article-info-list"]//a[@data-track-source="citation-download"]')[0];
if (!risURL) risURL = doc.querySelector('a[data-track-action="download article citation"]');
if (risURL) {
risURL = risURL.href;
ZU.doGet(risURL, function (text) {
if (text.search(/^TY /m) != -1) {
var translator = Zotero.loadTranslator('import');
translator.setTranslator('32d59d2d-b65a-4da4-b0a3-bdd3cfb979e7');
translator.setString(text);
translator.setHandler('itemDone', function (obj, newItem) {
newItem.notes = [];
next(newItem);
});
translator.setHandler('error', function () {
next();
});
translator.translate();
}
else {
next();
}
});
}
else {
Z.debug('Could not find RIS export');
next();
}
}
function getMultipleNodes(doc, url) {
var allHNodes = '*[self::h1 or self::h2 or self::h3 or self::h4 or self::h5]';
var nodex, titlex, linkx;
var nodes = [];
if (url.includes('/search/') || url.includes('/most.htm')) {
// search, "top" lists
nodex = '//ol[@class="results-list" or @id="content-list"]/li';
titlex = './' + allHNodes + '/node()[not(self::span)]';
linkx = './' + allHNodes + '/a';
nodes = Zotero.Utilities.xpath(doc, nodex);
}
else {
// Maybe there's a nice way to figure out which journal uses what style, but for now we'll just try one until it matches
// these seem to be listed in order of frequency
var styles = [
// ToC
{
nodex: '//tr[./td/span[@class="articletitle"]]',
titlex: './td/span[@class="articletitle"]',
linkx: './td/a[@class="contentslink" and substring(@href, string-length(@href)-3) != "pdf"][1]' // abstract or full text
},
// oncogene
{
nodex: '//div[child::*[@class="atl"]]',
titlex: './' + allHNodes + '[last()]/node()[not(self::span)]', // ignore "subheading"
linkx: './p[@class="links" or @class="articlelinks"]/a[contains(text(),"Full Text") or contains(text(),"Full text")]'
},
// embo journal
{
nodex: '//ul[@class="articles"]/li',
titlex: './' + allHNodes + '[@class="article-title"]/node()[not(self::span)]',
linkx: './ul[@class="article-links"]/li/a[contains(text(),"Full Text") or contains(text(),"Full text")]'
},
// nature
{
nodex: '//ul[contains(@class,"article-list") or contains(@class,"collapsed-list")]/li',
titlex: './/' + allHNodes + '/a',
linkx: './/' + allHNodes + '/a'
},
// archive (e.g. http://www.nature.com/bonekey/archive/type.html)
{
nodex: '//table[@class="archive"]/tbody/tr',
titlex: './td/' + allHNodes + '[last()]/a',
linkx: './td/' + allHNodes + '[last()]/a',
},
// some more ToC (e.g. http://www.nature.com/nrcardio/journal/v5/n1s/index.html)
{
nodex: '//div[@class="container"]/div[./h4[@class="norm"] and ./p[@class="journal"]/a[@title]]',
titlex: './h4[@class="norm"]',
linkx: './p[@class="journal"]/a[@title][1]'
},
// some new more ToC (e.g. https://www.nature.com/ng/volumes/38/issues/11)
{
nodex: '//article',
titlex: './div/h3',
linkx: './div/h3/a'
},
{
nodex: '//li[@itemtype="http://schema.org/Article"]',
titlex: './/h2',
linkx: './/h2/a'
}
];
for (var i = 0; i < styles.length && !nodes.length; i++) {
nodex = styles[i].nodex;
titlex = styles[i].titlex;
linkx = styles[i].linkx;
nodes = Zotero.Utilities.xpath(doc, nodex);
}
}
if (nodes.length) Z.debug("multiples found using: " + nodex);
return [nodes, titlex, linkx];
}
function isNature(url) {
return url.search(/^https?:\/\/(?:[^/]+\.)?nature.com/) != -1;
}
function detectWeb(doc, url) {
if (url.endsWith('.pdf')) return false;
if (url.search(/\/(full|abs)\/[^/]+($|\?|#)|\/fp\/.+?[?&]lang=ja(?:&|$)|\/articles\//) != -1) {
return 'journalArticle';
}
else if (doc.title.toLowerCase().includes('table of contents') // single issue ToC. e.g. http://www.nature.com/emboj/journal/v30/n1/index.html or http://www.nature.com/nature/journal/v481/n7381/index.html
|| doc.title.toLowerCase().includes('current issue')
|| url.includes('/research/') || url.includes('/topten/')
|| url.includes('/most.htm')
|| (url.includes('/vaop/') && url.includes('index.html')) // advanced online publication
|| url.includes('sp-q=') // search query
|| url.search(/journal\/v\d+\/n\d+\/index\.html/i) != -1 // more ToC
|| url.search(/volumes\/\d+\/issues\/\d+/i) != -1
|| url.includes('/search?')) { // new more ToC
return getMultipleNodes(doc, url)[0].length ? 'multiple' : null;
}
else if (url.includes('/archive/')) {
if (url.includes('index.htm')) return false; // list of issues
if (url.includes('subject.htm')) return false; // list of subjects
if (url.includes('category.htm') && !url.includes('code=')) return false; // list of categories
return getMultipleNodes(doc, url)[0].length ? 'multiple' : null; // all else should be ok
}
else {
return false;
}
}
function supplementItem(item, supp, prefer) {
for (var i in supp) {
if (!supp.hasOwnProperty(i)
|| (item.hasOwnProperty(i) && !prefer.includes(i))) {
continue; // this also skips creators, tags, notes, and related
}
Z.debug('Supplementing item.' + i);
item[i] = supp[i];
}
return item;
}
function runScrapers(scrapers, done) {
var items = [];
var args = Array.prototype.splice.call(arguments, 2); // remove scrapers and done handler
var run = function (item) {
items.push(item);
if (scrapers.length) {
(scrapers.shift())(...args);
}
};
args.push(run);
args.push(items);
scrapers.push(function () {
done(items);
});
(scrapers.shift())(...args);
}
function scrape(doc, url) {
runScrapers([scrapeEM, scrapeRIS], function (items) {
var item = items[0];
if (!item) { // EM failed (unlikely)
item = items[1];
}
else if (items[1]) {
var preferredRisFields = ['date', 'abstractNote'];
// palgrave-macmillan journals
if (!isNature(url)) {
preferredRisFields.push('publisher'); // all others are going to be dropped since we only handle journalArticle
if (item.rights.includes('Nature Publishing Group')) {
delete item.rights;
}
}
// for electronic only journals, EM just has 1-page#; we instead get article number from the extra field
var electronicOnly = ['Scientific Data', 'Nature Communications', 'Scientific Reports', 'npj Science of Food', 'Light: Science & Applications'];
if (electronicOnly.includes(item.publicationTitle)) {
preferredRisFields.push('pages');
}
item = supplementItem(item, items[1], preferredRisFields);
if (items[1].tags.length) item.tags = items[1].tags; // RIS doesn't seem to have tags, but we check just in case
if (!item.creators.length) {
// E.g. http://www.nature.com/nprot/journal/v1/n1/full/nprot.2006.52.html
item.creators = items[1].creators;
}
else {
// RIS can properly split first and last name
// but it does not (sometimes?) include accented letters
// We try to get best of both worlds by trying to re-split EM authors correctly
// hopefully the authors match up
for (var i = 0, j = 0, n = item.creators.length, m = items[1].creators.length; i < n && j < m; i++, j++) {
// check if last names match, then we don't need to worry
var risLName = ZU.removeDiacritics(items[1].creators[j].lastName.toUpperCase());
var emLName = ZU.removeDiacritics(item.creators[i].lastName.toUpperCase());
if (emLName == risLName) {
continue;
}
var fullName = item.creators[i].firstName + ' ' + item.creators[i].lastName;
emLName = fullName.substring(fullName.length - risLName.length);
if (ZU.removeDiacritics(emLName.toUpperCase()) != risLName) {
// corporate authors are sometimes skipped in RIS
if (i + 1 < n) {
var nextEMLName = item.creators[i + 1].firstName + ' '
+ item.creators[i + 1].lastName;
nextEMLName = ZU.removeDiacritics(
nextEMLName.substring(nextEMLName.length - risLName.length)
.toUpperCase()
);
if (nextEMLName == risLName) { // this is corporate author and it was skipped in RIS
item.creators[i].lastName = item.creators[i].firstName
+ ' ' + item.creators[i].lastName;
delete item.creators[i].firstName;
item.creators[i].fieldMode = 1;
j--;
Z.debug('It appears that "' + item.creators[i].lastName
+ '" is a corporate author and was skipped in the RIS output.');
continue;
}
}
// authors with same name are sometimes skipped in EM
if (j + 1 < m) {
var nextRisLName = ZU.removeDiacritics(items[1].creators[j + 1].lastName.toUpperCase());
var resplitEmLName = ZU.removeDiacritics(fullName.substring(fullName.length - nextRisLName.length).toUpperCase());
if (resplitEmLName == nextRisLName) {
item.creators.splice(i, 0, items[1].creators[j]); // insert missing author
Z.debug('It appears that "' + item.creators[i].lastName
+ '" was missing from EM.');
continue;
}
}
Z.debug(emLName + ' and ' + risLName + ' do not match');
continue; // we failed
}
if (items[1].creators[j].fieldMode !== 1) {
item.creators[i].firstName = fullName.substring(0, fullName.length - emLName.length).trim();
}
else {
delete item.creators[i].firstName;
item.creators[i].fieldMode = 1;
}
item.creators[i].lastName = emLName;
Z.debug(fullName + ' was split into '
+ item.creators[i].lastName + ', ' + item.creators[i].firstName);
}
}
}
if (!item) {
Z.debug('Could not retrieve metadata.');
return; // both translators failed
}
// small caps become lowercase in EM/RIS, so if the title contains a
// small-caps span, we'll use innerText.
if (doc.querySelector('h1.c-article-title .u-small-caps')) {
item.title = innerText('h1.c-article-title') || item.title;
}
// We prefer the publication date to some online first date
var pubdate = attr(doc, 'meta[name="citation_publication_date"]', 'content');
if (pubdate) {
item.date = ZU.strToISO(pubdate);
}
if (item.date) item.date = ZU.strToISO(item.date);
if (item.pages && !item.pages.includes('-')) {
var start = text(doc, 'span[itemprop="pageStart"]');
var end = text(doc, 'span[itemprop="pageEnd"]');
if (start && end) {
item.pages = start + '-' + end;
}
}
if (!item.pages) {
// For some online-only publications this should be the "Article number"
// but is not present in either EM or RIS. We grab it from page
var page = doc.querySelector('.citation .page');
if (page) {
item.pages = ZU.trimInternal(page.textContent);
}
}
// write 'en' instead of 'En'
if (item.language && item.language == 'En') item.language = 'en';
// journal abbreviations are now all wrong, i.e. the full title of the journal
if (item.journalAbbreviation && !item.publicationTitle) {
item.publicationTitle = 'Nature';// old articles mess this up
}
if (item.journalAbbreviation == item.publicationTitle) {
delete item.journalAbbreviation;
}
if (item.issue && item.number && item.issue == item.number) {
delete item.number;
}
var hasPDF = false;
for (let attach of item.attachments) {
if (attach.mimeType && attach.mimeType == "application/pdf") {
hasPDF = true;
}
}
if (!hasPDF) {
item.attachments = [{
document: doc,
title: 'Snapshot'
}];
var pdf = getPdfUrl(doc, url);
if (pdf) {
item.attachments.push({
url: pdf,
title: 'Full Text PDF',
mimeType: 'application/pdf'
});
}
}
// attach some useful links, like...
// GEO, GenBank, etc.
try { // this shouldn't really fail, but... just in case
var accessionDiv = doc.getElementById('accessions');
if (accessionDiv) {
var accessions = ZU.xpath(accessionDiv, './/div[@class="content"]//div[./h3]');
var repo, links;
for (let i = 0, n = accessions.length; i < n; i++) {
repo = accessions[i].getElementsByTagName('h3')[0].textContent;
if (repo) repo += ' entry ';
links = ZU.xpath(accessions[i], './ul[1]//a');
if (links.length) {
for (let j = 0, m = links.length; j < m; j++) {
item.attachments.push({
title: repo + '(' + links[j].textContent + ')',
url: links[j].href,
type: 'text/html',
snapshot: false
});
}
}
}
}
}
catch (e) {
Z.debug("Error attaching useful links.");
Z.debug(e);
}
// attach supplementary data
var async;
if (Z.getHiddenPref && Z.getHiddenPref("attachSupplementary")) {
try { // don't fail if we can't attach supplementary data
async = attachSupplementary(doc, item, function (doc, item) {
item.complete();
});
}
catch (e) {
Z.debug("Error attaching supplementary information.");
Z.debug(e);
if (async) item.complete();
}
if (!async) {
item.complete();
}
}
else {
item.complete();
}
}, doc, url);
}
function doWeb(doc, url) {
if (detectWeb(doc, url) == 'multiple') {
var nodes = getMultipleNodes(doc, url);
var titlex = nodes[1];
var linkx = nodes[2];
nodes = nodes[0];
if (nodes.length == 0) {
Z.debug("no multiples");
// return false; //keep going so we can report this to zotero.org instead of "silently" failing
}
var items = {};
for (var i = 0; i < nodes.length; i++) {
let title = Zotero.Utilities.xpathText(nodes[i], titlex, null, '');
let link = Zotero.Utilities.xpath(nodes[i], linkx);
if (title && link.length == 1) {
items[link[0].href] = title.trim();
}
}
var urls = [];
Zotero.selectItems(items, function (selectedItems) {
if (!selectedItems) return true;
for (var item in selectedItems) {
urls.push(item);
}
Zotero.Utilities.processDocuments(urls, scrape);
return true;
});
}
else {
scrape(doc, url);
}
}
// ISO8879 to unicode character map
var ISO8879CharMap = {
excl: "\u0021", quot: "\u0022", num: "\u0023", dollar: "\u0024",
percnt: "\u0025", amp: "\u0026", apos: "\u0027", lpar: "\u0028",
rpar: "\u0029", ast: "\u002A", plus: "\u002B", comma: "\u002C",
period: "\u002E", sol: "\u002F", colon: "\u003A", semi: "\u003B",
lt: "\u003C", equals: "\u003D", gt: "\u003E", quest: "\u003F",
commat: "\u0040", lsqb: "\u005B", lbrack: "\u005B", bsol: "\u005C",
rsqb: "\u005D", rbrack: "\u005D", lowbar: "\u005F", grave: "\u0060",
DiacriticalGrave: "\u0060", jnodot: "\u006A", lcub: "\u007B", lbrace: "\u007B",
verbar: "\u007C", vert: "\u007C", rcub: "\u007D", rbrace: "\u007D",
nbsp: "\u00A0", NonBreakingSpace: "\u00A0", iexcl: "\u00A1", cent: "\u00A2",
pound: "\u00A3", curren: "\u00A4", yen: "\u00A5", brvbar: "\u00A6",
sect: "\u00A7", die: "\u00A8", uml: "\u00A8",
copy: "\u00A9", ordf: "\u00AA", laquo: "\u00AB",
not: "\u00AC", shy: "\u00AD", reg: "\u00AE", circledR: "\u00AE",
macr: "\u00AF", deg: "\u00B0", plusmn: "\u00B1", pm: "\u00B1",
PlusMinus: "\u00B1", sup2: "\u00B2", sup3: "\u00B3", acute: "\u00B4",
DiacriticalAcute: "\u00B4", micro: "\u00B5", para: "\u00B6", middot: "\u00B7",
centerdot: "\u00B7", CenterDot: "\u00B7", cedil: "\u00B8", Cedilla: "\u00B8",
sup1: "\u00B9", ordm: "\u00BA", raquo: "\u00BB", frac14: "\u00BC",
frac12: "\u00BD", half: "\u00BD",
frac34: "\u00BE", iquest: "\u00BF", Agrave: "\u00C0", Aacute: "\u00C1",
Acirc: "\u00C2", Atilde: "\u00C3", Auml: "\u00C4", Aring: "\u00C5",
AElig: "\u00C6", Ccedil: "\u00C7", Egrave: "\u00C8", Eacute: "\u00C9",
Ecirc: "\u00CA", Euml: "\u00CB", Igrave: "\u00CC", Iacute: "\u00CD",
Icirc: "\u00CE", Iuml: "\u00CF", ETH: "\u00D0", Ntilde: "\u00D1",
Ograve: "\u00D2", Oacute: "\u00D3", Ocirc: "\u00D4", Otilde: "\u00D5",
Ouml: "\u00D6", times: "\u00D7", Oslash: "\u00D8", Ugrave: "\u00D9",
Uacute: "\u00DA", Ucirc: "\u00DB", Uuml: "\u00DC", Yacute: "\u00DD",
THORN: "\u00DE", szlig: "\u00DF", agrave: "\u00E0", aacute: "\u00E1",
acirc: "\u00E2", atilde: "\u00E3", auml: "\u00E4", aring: "\u00E5",
aelig: "\u00E6", ccedil: "\u00E7", egrave: "\u00E8", eacute: "\u00E9",
ecirc: "\u00EA", euml: "\u00EB", igrave: "\u00EC", iacute: "\u00ED",
icirc: "\u00EE", iuml: "\u00EF", eth: "\u00F0", ntilde: "\u00F1",
ograve: "\u00F2", oacute: "\u00F3", ocirc: "\u00F4", otilde: "\u00F5",
ouml: "\u00F6", divide: "\u00F7", div: "\u00F7", oslash: "\u00F8",
ugrave: "\u00F9", uacute: "\u00FA", ucirc: "\u00FB", uuml: "\u00FC",
yacute: "\u00FD", thorn: "\u00FE", yuml: "\u00FF", Amacr: "\u0100",
amacr: "\u0101", Abreve: "\u0102", abreve: "\u0103", Aogon: "\u0104",
aogon: "\u0105", Cacute: "\u0106", cacute: "\u0107", Ccirc: "\u0108",
ccirc: "\u0109", Cdot: "\u010A", cdot: "\u010B", Ccaron: "\u010C",
ccaron: "\u010D", Dcaron: "\u010E", dcaron: "\u010F", Dstrok: "\u0110",
dstrok: "\u0111", Emacr: "\u0112", emacr: "\u0113", Edot: "\u0116",
edot: "\u0117", Eogon: "\u0118", eogon: "\u0119", Ecaron: "\u011A",
ecaron: "\u011B", Gcirc: "\u011C", gcirc: "\u011D", Gbreve: "\u011E",
gbreve: "\u011F", Gdot: "\u0120", gdot: "\u0121", Gcedil: "\u0122",
Hcirc: "\u0124", hcirc: "\u0125", Hstrok: "\u0126", hstrok: "\u0127",
Itilde: "\u0128", itilde: "\u0129", Imacr: "\u012A", imacr: "\u012B",
Iogon: "\u012E", iogon: "\u012F", Idot: "\u0130", IJlig: "\u0132",
ijlig: "\u0133", Jcirc: "\u0134", jcirc: "\u0135", Kcedil: "\u0136",
kcedil: "\u0137", kgreen: "\u0138", Lacute: "\u0139", lacute: "\u013A",
Lcedil: "\u013B", lcedil: "\u013C", Lcaron: "\u013D", lcaron: "\u013E",
Lmidot: "\u013F", lmidot: "\u0140", Lstrok: "\u0141", lstrok: "\u0142",
Nacute: "\u0143", nacute: "\u0144", Ncedil: "\u0145", ncedil: "\u0146",
Ncaron: "\u0147", ncaron: "\u0148", napos: "\u0149", ENG: "\u014A",
eng: "\u014B", Omacr: "\u014C", omacr: "\u014D", Odblac: "\u0150",
odblac: "\u0151", OElig: "\u0152", oelig: "\u0153", Racute: "\u0154",
racute: "\u0155", Rcedil: "\u0156", rcedil: "\u0157", Rcaron: "\u0158",
rcaron: "\u0159", Sacute: "\u015A", sacute: "\u015B", Scirc: "\u015C",
scirc: "\u015D", Scedil: "\u015E", scedil: "\u015F", Scaron: "\u0160",
scaron: "\u0161", Tcedil: "\u0162", tcedil: "\u0163", Tcaron: "\u0164",
tcaron: "\u0165", Tstrok: "\u0166", tstrok: "\u0167", Utilde: "\u0168",
utilde: "\u0169", Umacr: "\u016A", umacr: "\u016B", Ubreve: "\u016C",
ubreve: "\u016D", Uring: "\u016E", uring: "\u016F", Udblac: "\u0170",
udblac: "\u0171", Uogon: "\u0172", uogon: "\u0173", Wcirc: "\u0174",
wcirc: "\u0175", Ycirc: "\u0176", ycirc: "\u0177", Yuml: "\u0178",
Zacute: "\u0179", zacute: "\u017A", Zdot: "\u017B", zdot: "\u017C",
Zcaron: "\u017D", zcaron: "\u017E", gacute: "\u01F5", circ: "\u02C6",
caron: "\u02C7", Hacek: "\u02C7", breve: "\u02D8", Breve: "\u02D8",
dot: "\u02D9", DiacriticalDot: "\u02D9", ring: "\u02DA", ogon: "\u02DB",
tilde: "\u02DC", DiacriticalTilde: "\u02DC", dblac: "\u02DD", DiacriticalDoubleAcute: "\u02DD",
Aacgr: "\u0386", Eacgr: "\u0388", EEacgr: "\u0389", Iacgr: "\u038A",
Oacgr: "\u038C", Uacgr: "\u038E", OHacgr: "\u038F", idiagr: "\u0390",
Agr: "\u0391", Bgr: "\u0392", Ggr: "\u0393", Gamma: "\u0393",
Dgr: "\u0394", Delta: "\u0394", Egr: "\u0395", Zgr: "\u0396",
EEgr: "\u0397", THgr: "\u0398", Theta: "\u0398", Igr: "\u0399",
Kgr: "\u039A", Lgr: "\u039B", Lambda: "\u039B", Mgr: "\u039C",
Ngr: "\u039D", Xgr: "\u039E", Xi: "\u039E", Ogr: "\u039F",
Pgr: "\u03A0", Pi: "\u03A0", Rgr: "\u03A1", Sgr: "\u03A3",
Sigma: "\u03A3", Tgr: "\u03A4", Ugr: "\u03A5", PHgr: "\u03A6",
Phi: "\u03A6", KHgr: "\u03A7", PSgr: "\u03A8", Psi: "\u03A8",
OHgr: "\u03A9", Omega: "\u03A9", Idigr: "\u03AA", Udigr: "\u03AB",
aacgr: "\u03AC", eacgr: "\u03AD", eeacgr: "\u03AE", iacgr: "\u03AF",
udiagr: "\u03B0", agr: "\u03B1", alpha: "\u03B1", bgr: "\u03B2",
beta: "\u03B2", ggr: "\u03B3", gamma: "\u03B3", dgr: "\u03B4",
delta: "\u03B4", egr: "\u03B5", epsiv: "\u03B5", zgr: "\u03B6",
zeta: "\u03B6", eegr: "\u03B7", eta: "\u03B7", thgr: "\u03B8",
thetas: "\u03B8", igr: "\u03B9", iota: "\u03B9", kgr: "\u03BA",
kappa: "\u03BA", lgr: "\u03BB", lambda: "\u03BB", mgr: "\u03BC",
mu: "\u03BC", ngr: "\u03BD", nu: "\u03BD", xgr: "\u03BE",
xi: "\u03BE", ogr: "\u03BF", pgr: "\u03C0", pi: "\u03C0",
rgr: "\u03C1", rho: "\u03C1", sfgr: "\u03C2", sigmav: "\u03C2",
sgr: "\u03C3", sigma: "\u03C3", tgr: "\u03C4", tau: "\u03C4",
ugr: "\u03C5", upsi: "\u03C5", phgr: "\u03C6", phiv: "\u03C6",
khgr: "\u03C7", chi: "\u03C7", psgr: "\u03C8", psi: "\u03C8",
ohgr: "\u03C9", omega: "\u03C9", idigr: "\u03CA", udigr: "\u03CB",
oacgr: "\u03CC", uacgr: "\u03CD", ohacgr: "\u03CE", thetav: "\u03D1",
vartheta: "\u03D1", Upsi: "\u03D2", phis: "\u03D5", straightphi: "\u03D5",
piv: "\u03D6", varpi: "\u03D6", "b.Gammad": "\u03DC", gammad: "\u03DD",
"b.gammad": "\u03DD", kappav: "\u03F0", varkappa: "\u03F0", rhov: "\u03F1",
varrho: "\u03F1", epsi: "\u03F5", epsis: "\u03F5",
straightepsilon: "\u03F5", bepsi: "\u03F6",
backepsilon: "\u03F6", IOcy: "\u0401", DJcy: "\u0402", GJcy: "\u0403",
Jukcy: "\u0404", DScy: "\u0405", Iukcy: "\u0406", YIcy: "\u0407",
Jsercy: "\u0408", LJcy: "\u0409", NJcy: "\u040A", TSHcy: "\u040B",
KJcy: "\u040C", Ubrcy: "\u040E", DZcy: "\u040F", Acy: "\u0410",
Bcy: "\u0411", Vcy: "\u0412", Gcy: "\u0413", Dcy: "\u0414",
IEcy: "\u0415", ZHcy: "\u0416", Zcy: "\u0417", Icy: "\u0418",
Jcy: "\u0419", Kcy: "\u041A", Lcy: "\u041B", Mcy: "\u041C",
Ncy: "\u041D", Ocy: "\u041E", Pcy: "\u041F", Rcy: "\u0420",
Scy: "\u0421", Tcy: "\u0422", Ucy: "\u0423", Fcy: "\u0424",
KHcy: "\u0425", TScy: "\u0426", CHcy: "\u0427", SHcy: "\u0428",
SHCHcy: "\u0429", HARDcy: "\u042A", Ycy: "\u042B", SOFTcy: "\u042C",
Ecy: "\u042D", YUcy: "\u042E", YAcy: "\u042F", acy: "\u0430",
bcy: "\u0431", vcy: "\u0432", gcy: "\u0433", dcy: "\u0434",
iecy: "\u0435", zhcy: "\u0436", zcy: "\u0437", icy: "\u0438",
jcy: "\u0439", kcy: "\u043A", lcy: "\u043B", mcy: "\u043C",
ncy: "\u043D", ocy: "\u043E", pcy: "\u043F", rcy: "\u0440",
scy: "\u0441", tcy: "\u0442", ucy: "\u0443", fcy: "\u0444",
khcy: "\u0445", tscy: "\u0446", chcy: "\u0447", shcy: "\u0448",
shchcy: "\u0449", hardcy: "\u044A", ycy: "\u044B", softcy: "\u044C",
ecy: "\u044D", yucy: "\u044E", yacy: "\u044F", iocy: "\u0451",
djcy: "\u0452", gjcy: "\u0453", jukcy: "\u0454", dscy: "\u0455",
iukcy: "\u0456", yicy: "\u0457", jsercy: "\u0458", ljcy: "\u0459",
njcy: "\u045A", tshcy: "\u045B", kjcy: "\u045C", ubrcy: "\u045E",
dzcy: "\u045F", ensp: "\u2002", emsp: "\u2003", emsp13: "\u2004",
emsp14: "\u2005", numsp: "\u2007", puncsp: "\u2008", thinsp: "\u2009",
ThinSpace: "\u2009", hairsp: "\u200A", VeryThinSpace: "\u200A", hyphen: "\u2010",
dash: "\u2010", ndash: "\u2013", mdash: "\u2014", horbar: "\u2015",
lsquo: "\u2018", OpenCurlyQuote: "\u2018", rsquo: "\u2019", rsquor: "\u2019",
lsquor: "\u201A", ldquo: "\u201C", OpenCurlyDoubleQuote: "\u201C", rdquo: "\u201D",
rdquor: "\u201D", ldquor: "\u201E", dagger: "\u2020", Dagger: "\u2021",
ddagger: "\u2021", bull: "\u2022", bullet: "\u2022", nldr: "\u2025",
hellip: "\u2026", mldr: "\u2026",
vprime: "\u2032", bprime: "\u2035", backprime: "\u2035", caret: "\u2041",
hybull: "\u2043", incare: "\u2105", planck: "\u210F", hbar: "\u210F",
hslash: "\u210F", ell: "\u2113", numero: "\u2116", copysr: "\u2117",
weierp: "\u2118", wp: "\u2118", real: "\u211C", Re: "\u211C",
realpart: "\u211C", rx: "\u211E", trade: "\u2122", ohm: "\u2126",
beth: "\u2136", gimel: "\u2137", daleth: "\u2138", frac13: "\u2153",
frac23: "\u2154", frac15: "\u2155", frac25: "\u2156", frac35: "\u2157",
frac45: "\u2158", frac16: "\u2159", frac56: "\u215A", frac18: "\u215B",
frac38: "\u215C", frac58: "\u215D", frac78: "\u215E", larr: "\u2190",
leftarrow: "\u2190", LeftArrow: "\u2190", ShortLeftArrow: "\u2190", uarr: "\u2191",
uparrow: "\u2191", UpArrow: "\u2191", ShortUpArrow: "\u2191", rarr: "\u2192",
rightarrow: "\u2192", RightArrow: "\u2192", ShortRightArrow: "\u2192", darr: "\u2193",
downarrow: "\u2193", DownArrow: "\u2193", ShortDownArrow: "\u2193", harr: "\u2194",
leftrightarrow: "\u2194", LeftRightArrow: "\u2194", varr: "\u2195", updownarrow: "\u2195",
UpDownArrow: "\u2195", nwarr: "\u2196", UpperLeftArrow: "\u2196", nwarrow: "\u2196",
nearr: "\u2197", UpperRightArrow: "\u2197", nearrow: "\u2197", drarr: "\u2198",
searrow: "\u2198", LowerRightArrow: "\u2198", dlarr: "\u2199", swarrow: "\u2199",
LowerLeftArrow: "\u2199", nlarr: "\u219A", nleftarrow: "\u219A", nrarr: "\u219B",
nrightarrow: "\u219B", rarrw: "\u219D", rightsquigarrow: "\u219D", Larr: "\u219E",
twoheadleftarrow: "\u219E", Rarr: "\u21A0", twoheadrightarrow: "\u21A0", larrtl: "\u21A2",
leftarrowtail: "\u21A2", rarrtl: "\u21A3", rightarrowtail: "\u21A3", map: "\u21A6",
RightTeeArrow: "\u21A6", mapsto: "\u21A6", larrhk: "\u21A9", hookleftarrow: "\u21A9",
rarrhk: "\u21AA", hookrightarrow: "\u21AA", larrlp: "\u21AB", looparrowleft: "\u21AB",
rarrlp: "\u21AC", looparrowright: "\u21AC", harrw: "\u21AD", leftrightsquigarrow: "\u21AD",
nharr: "\u21AE", nleftrightarrow: "\u21AE", lsh: "\u21B0", Lsh: "\u21B0",
rsh: "\u21B1", Rsh: "\u21B1", cularr: "\u21B6", curvearrowleft: "\u21B6",
curarr: "\u21B7", curvearrowright: "\u21B7", olarr: "\u21BA", circlearrowleft: "\u21BA",
orarr: "\u21BB", circlearrowright: "\u21BB", lharu: "\u21BC", LeftVector: "\u21BC",
leftharpoonup: "\u21BC", lhard: "\u21BD", leftharpoondown: "\u21BD", DownLeftVector: "\u21BD",
uharr: "\u21BE", upharpoonright: "\u21BE", RightUpVector: "\u21BE", uharl: "\u21BF",
upharpoonleft: "\u21BF", LeftUpVector: "\u21BF", rharu: "\u21C0", RightVector: "\u21C0",
rightharpoonup: "\u21C0", rhard: "\u21C1", rightharpoondown: "\u21C1", DownRightVector: "\u21C1",
dharr: "\u21C2", RightDownVector: "\u21C2", downharpoonright: "\u21C2", dharl: "\u21C3",
LeftDownVector: "\u21C3", downharpoonleft: "\u21C3", rlarr2: "\u21C4", rightleftarrows: "\u21C4",
RightArrowLeftArrow: "\u21C4", lrarr2: "\u21C6", leftrightarrows: "\u21C6", LeftArrowRightArrow: "\u21C6",
larr2: "\u21C7", leftleftarrows: "\u21C7", uarr2: "\u21C8", upuparrows: "\u21C8",
rarr2: "\u21C9", rightrightarrows: "\u21C9", darr2: "\u21CA", downdownarrows: "\u21CA",
lrhar2: "\u21CB", ReverseEquilibrium: "\u21CB", leftrightharpoons: "\u21CB", rlhar2: "\u21CC",
rightleftharpoons: "\u21CC", Equilibrium: "\u21CC", nlArr: "\u21CD", nLeftarrow: "\u21CD",
nhArr: "\u21CE", nLeftrightarrow: "\u21CE", nrArr: "\u21CF", nRightarrow: "\u21CF",
uArr: "\u21D1", Uparrow: "\u21D1", DoubleUpArrow: "\u21D1", dArr: "\u21D3",
Downarrow: "\u21D3", DoubleDownArrow: "\u21D3", hArr: "\u21D4", Leftrightarrow: "\u21D4",
DoubleLeftRightArrow: "\u21D4", vArr: "\u21D5", Updownarrow: "\u21D5", DoubleUpDownArrow: "\u21D5",
lAarr: "\u21DA", Lleftarrow: "\u21DA", rAarr: "\u21DB", Rrightarrow: "\u21DB",
comp: "\u2201", complement: "\u2201", nexist: "\u2204", NotExists: "\u2204",
nexists: "\u2204", empty: "\u2205", emptyset: "\u2205", varnothing: "\u2205",
prod: "\u220F", coprod: "\u2210", samalg: "\u2210", sum: "\u2211",
Sum: "\u2211", plusdo: "\u2214", dotplus: "\u2214", setmn: "\u2216",
ssetmn: "\u2216", setminus: "\u2216", Backslash: "\u2216",
vprop: "\u221D",
propto: "\u221D", Proportional: "\u221D", varpropto: "\u221D", ang: "\u2220",
angle: "\u2220", angmsd: "\u2221", measuredangle: "\u2221", mid: "\u2223",
smid: "\u2223", VerticalBar: "\u2223",
nmid: "\u2224", nsmid: "\u2224",
spar: "\u2225", parallel: "\u2225", DoubleVerticalBar: "\u2225",
shortparallel: "\u2225", npar: "\u2226", nspar: "\u2226",
nparallel: "\u2226", NotDoubleVerticalBar: "\u2226",
thksim: "\u223C", Tilde: "\u223C", thicksim: "\u223C",
bsim: "\u223D", backsim: "\u223D", wreath: "\u2240", VerticalTilde: "\u2240",
wr: "\u2240", nsim: "\u2241", NotTilde: "\u2241", nsime: "\u2244",
nsimeq: "\u2244", NotTildeEqual: "\u2244", ncong: "\u2247", NotTildeFullEqual: "\u2247",
asymp: "\u2248", thkap: "\u2248", TildeTilde: "\u2248",
approx: "\u2248",
nap: "\u2249", NotTildeTilde: "\u2249", napprox: "\u2249", ape: "\u224A",
approxeq: "\u224A", bcong: "\u224C", backcong: "\u224C", bump: "\u224E",
HumpDownHump: "\u224E", Bumpeq: "\u224E", bumpe: "\u224F", HumpEqual: "\u224F",
bumpeq: "\u224F", esdot: "\u2250", DotEqual: "\u2250", doteq: "\u2250",
eDot: "\u2251", doteqdot: "\u2251", efDot: "\u2252", fallingdotseq: "\u2252",
erDot: "\u2253", risingdotseq: "\u2253", colone: "\u2254", coloneq: "\u2254",
Assign: "\u2254", ecolon: "\u2255", eqcolon: "\u2255", ecir: "\u2256",
eqcirc: "\u2256", cire: "\u2257", circeq: "\u2257", trie: "\u225C",
triangleq: "\u225C", nequiv: "\u2262", NotCongruent: "\u2262", lE: "\u2266",
LessFullEqual: "\u2266", leqq: "\u2266", nlE: "\u2266\u0338", NotGreaterFullEqual: "\u2266\u0338",
nleqq: "\u2266\u0338", gE: "\u2267", GreaterFullEqual: "\u2267", geqq: "\u2267",
ngE: "\u2267\u0338", ngeqq: "\u2267\u0338", lnE: "\u2268", lneqq: "\u2268",
lvnE: "\u2268\uFE00", lvertneqq: "\u2268\uFE00", gnE: "\u2269", gneqq: "\u2269",
gvnE: "\u2269\uFE00", gvertneqq: "\u2269\uFE00", Lt: "\u226A", NestedLessLess: "\u226A",
ll: "\u226A", Gt: "\u226B", NestedGreaterGreater: "\u226B", gg: "\u226B",
twixt: "\u226C", between: "\u226C", nlt: "\u226E", NotLess: "\u226E",
nless: "\u226E", ngt: "\u226F", NotGreater: "\u226F", ngtr: "\u226F",
nle: "\u2270", NotLessEqual: "\u2270", nleq: "\u2270", nge: "\u2271",
NotGreaterEqual: "\u2271", ngeq: "\u2271", lsim: "\u2272", LessTilde: "\u2272",
lesssim: "\u2272", gsim: "\u2273", gtrsim: "\u2273", GreaterTilde: "\u2273",
lg: "\u2276", lessgtr: "\u2276", LessGreater: "\u2276", gl: "\u2277",
gtrless: "\u2277", GreaterLess: "\u2277", pr: "\u227A", Precedes: "\u227A",
prec: "\u227A", sc: "\u227B", Succeeds: "\u227B", succ: "\u227B",
cupre: "\u227C", PrecedesSlantEqual: "\u227C", preccurlyeq: "\u227C", sccue: "\u227D",
SucceedsSlantEqual: "\u227D", succcurlyeq: "\u227D", prsim: "\u227E", precsim: "\u227E",
PrecedesTilde: "\u227E", scsim: "\u227F", succsim: "\u227F", SucceedsTilde: "\u227F",
npr: "\u2280", nprec: "\u2280", NotPrecedes: "\u2280", nsc: "\u2281",
nsucc: "\u2281", NotSucceeds: "\u2281", nsub: "\u2284", nsup: "\u2285",
nsube: "\u2288", nsubseteq: "\u2288", NotSubsetEqual: "\u2288", nsupe: "\u2289",
nsupseteq: "\u2289", NotSupersetEqual: "\u2289", subne: "\u228A", subsetneq: "\u228A",
vsubne: "\u228A\uFE00", varsubsetneq: "\u228A\uFE00", supne: "\u228B", supsetneq: "\u228B",
vsupne: "\u228B\uFE00", varsupsetneq: "\u228B\uFE00", uplus: "\u228E", UnionPlus: "\u228E",
sqsub: "\u228F", SquareSubset: "\u228F", sqsubset: "\u228F", sqsup: "\u2290",
SquareSuperset: "\u2290", sqsupset: "\u2290", sqsube: "\u2291", SquareSubsetEqual: "\u2291",
sqsubseteq: "\u2291", sqsupe: "\u2292", SquareSupersetEqual: "\u2292", sqsupseteq: "\u2292",
sqcap: "\u2293", SquareIntersection: "\u2293", sqcup: "\u2294", SquareUnion: "\u2294",
oplus: "\u2295", CirclePlus: "\u2295", ominus: "\u2296", CircleMinus: "\u2296",
otimes: "\u2297", CircleTimes: "\u2297", osol: "\u2298", odot: "\u2299",
CircleDot: "\u2299", ocir: "\u229A", circledcirc: "\u229A", oast: "\u229B",
circledast: "\u229B", odash: "\u229D", circleddash: "\u229D", plusb: "\u229E",
boxplus: "\u229E", minusb: "\u229F", boxminus: "\u229F", timesb: "\u22A0",
boxtimes: "\u22A0", sdotb: "\u22A1", dotsquare: "\u22A1", vdash: "\u22A2",
RightTee: "\u22A2", dashv: "\u22A3", LeftTee: "\u22A3", top: "\u22A4",
DownTee: "\u22A4", models: "\u22A7", vDash: "\u22A8", DoubleRightTee: "\u22A8",
Vdash: "\u22A9", Vvdash: "\u22AA", nvdash: "\u22AC", nvDash: "\u22AD",
nVdash: "\u22AE", nVDash: "\u22AF", vltri: "\u22B2", vartriangleleft: "\u22B2",
LeftTriangle: "\u22B2", vrtri: "\u22B3", vartriangleright: "\u22B3", RightTriangle: "\u22B3",
ltrie: "\u22B4", trianglelefteq: "\u22B4", LeftTriangleEqual: "\u22B4", rtrie: "\u22B5",
trianglerighteq: "\u22B5", RightTriangleEqual: "\u22B5", mumap: "\u22B8", multimap: "\u22B8",
intcal: "\u22BA", intercal: "\u22BA", veebar: "\u22BB", diam: "\u22C4",
diamond: "\u22C4", Diamond: "\u22C4", sdot: "\u22C5", sstarf: "\u22C6",
Star: "\u22C6", divonx: "\u22C7", divideontimes: "\u22C7", bowtie: "\u22C8",
ltimes: "\u22C9", rtimes: "\u22CA", lthree: "\u22CB", leftthreetimes: "\u22CB",
rthree: "\u22CC", rightthreetimes: "\u22CC", bsime: "\u22CD", backsimeq: "\u22CD",
cuvee: "\u22CE", curlyvee: "\u22CE", cuwed: "\u22CF", curlywedge: "\u22CF",
Sub: "\u22D0", Subset: "\u22D0", Sup: "\u22D1", Supset: "\u22D1",
Cap: "\u22D2", Cup: "\u22D3", fork: "\u22D4", pitchfork: "\u22D4",
ldot: "\u22D6", lessdot: "\u22D6", gsdot: "\u22D7", gtrdot: "\u22D7",
Ll: "\u22D8", Gg: "\u22D9", ggg: "\u22D9", leg: "\u22DA",
LessEqualGreater: "\u22DA", lesseqgtr: "\u22DA", gel: "\u22DB", gtreqless: "\u22DB",
GreaterEqualLess: "\u22DB", cuepr: "\u22DE", curlyeqprec: "\u22DE", cuesc: "\u22DF",
curlyeqsucc: "\u22DF", lnsim: "\u22E6", gnsim: "\u22E7", prnsim: "\u22E8",
precnsim: "\u22E8", scnsim: "\u22E9", succnsim: "\u22E9", nltri: "\u22EA",
ntriangleleft: "\u22EA", NotLeftTriangle: "\u22EA", nrtri: "\u22EB", ntriangleright: "\u22EB",
NotRightTriangle: "\u22EB", nltrie: "\u22EC", ntrianglelefteq: "\u22EC", NotLeftTriangleEqual: "\u22EC",
nrtrie: "\u22ED", ntrianglerighteq: "\u22ED", NotRightTriangleEqual: "\u22ED", vellip: "\u22EE",
barwed: "\u2305", barwedge: "\u2305", Barwed: "\u2306", doublebarwedge: "\u2306",
lceil: "\u2308", LeftCeiling: "\u2308", rceil: "\u2309", RightCeiling: "\u2309",
lfloor: "\u230A", LeftFloor: "\u230A", rfloor: "\u230B", RightFloor: "\u230B",
drcrop: "\u230C", dlcrop: "\u230D", urcrop: "\u230E", ulcrop: "\u230F",
telrec: "\u2315", target: "\u2316", ulcorn: "\u231C", ulcorner: "\u231C",
urcorn: "\u231D", urcorner: "\u231D", dlcorn: "\u231E", llcorner: "\u231E",
drcorn: "\u231F", lrcorner: "\u231F", frown: "\u2322", sfrown: "\u2322",
smile: "\u2323", ssmile: "\u2323",
blank: "\u2423", oS: "\u24C8",
circledS: "\u24C8", boxh: "\u2500", boxv: "\u2502", boxdr: "\u250C",
boxdl: "\u2510", boxur: "\u2514", boxul: "\u2518", boxvr: "\u251C",
boxvl: "\u2524", boxhd: "\u252C", boxhu: "\u2534", boxvh: "\u253C",
boxH: "\u2550", boxV: "\u2551", boxdR: "\u2552", boxDr: "\u2553",
boxDR: "\u2554", boxdL: "\u2555", boxDl: "\u2556", boxDL: "\u2557",
boxuR: "\u2558", boxUr: "\u2559", boxUR: "\u255A", boxuL: "\u255B",
boxUl: "\u255C", boxUL: "\u255D", boxvR: "\u255E", boxVr: "\u255F",
boxVR: "\u2560", boxvL: "\u2561", boxVl: "\u2562", boxVL: "\u2563",
boxHd: "\u2564", boxhD: "\u2565", boxHD: "\u2566", boxHu: "\u2567",
boxhU: "\u2568", boxHU: "\u2569", boxvH: "\u256A", boxVh: "\u256B",
boxVH: "\u256C", uhblk: "\u2580", lhblk: "\u2584", block: "\u2588",
blk14: "\u2591", blk12: "\u2592", blk34: "\u2593", squ: "\u25A1",
Square: "\u25A1", squf: "\u25AA", blacksquare: "\u25AA", rect: "\u25AD",
marker: "\u25AE", xutri: "\u25B3", bigtriangleup: "\u25B3", utrif: "\u25B4",
blacktriangle: "\u25B4", utri: "\u25B5", triangle: "\u25B5", rtrif: "\u25B8",
blacktriangleright: "\u25B8", rtri: "\u25B9", triangleright: "\u25B9", xdtri: "\u25BD",
bigtriangledown: "\u25BD", dtrif: "\u25BE", blacktriangledown: "\u25BE", dtri: "\u25BF",
triangledown: "\u25BF", ltrif: "\u25C2", blacktriangleleft: "\u25C2", ltri: "\u25C3",
triangleleft: "\u25C3", loz: "\u25CA", lozenge: "\u25CA", cir: "\u25CB",
xcirc: "\u25EF", bigcirc: "\u25EF", starf: "\u2605", bigstar: "\u2605",
star: "\u2606", phone: "\u260E", female: "\u2640", male: "\u2642",
spades: "\u2660", spadesuit: "\u2660", clubs: "\u2663", clubsuit: "\u2663",
hearts: "\u2665", heartsuit: "\u2665", diams: "\u2666", diamondsuit: "\u2666",
sung: "\u266A", flat: "\u266D", natur: "\u266E", natural: "\u266E",
sharp: "\u266F", check: "\u2713", checkmark: "\u2713", cross: "\u2717",
malt: "\u2720", maltese: "\u2720", sext: "\u2736", xharr: "\u27F7",
longleftrightarrow: "\u27F7", LongLeftRightArrow: "\u27F7", xlArr: "\u27F8", Longleftarrow: "\u27F8",
DoubleLongLeftArrow: "\u27F8", xrArr: "\u27F9", Longrightarrow: "\u27F9", DoubleLongRightArrow: "\u27F9",
xhArr: "\u27FA", Longleftrightarrow: "\u27FA", DoubleLongLeftRightArrow: "\u27FA", rpargt: "\u2994",
lpargt: "\u29A0", lozf: "\u29EB", blacklozenge: "\u29EB", amalg: "\u2A3F",
les: "\u2A7D", LessSlantEqual: "\u2A7D", leqslant: "\u2A7D", nles: "\u2A7D\u0338",
NotLessSlantEqual: "\u2A7D\u0338", nleqslant: "\u2A7D\u0338", ges: "\u2A7E", GreaterSlantEqual: "\u2A7E",
geqslant: "\u2A7E", nges: "\u2A7E\u0338", NotGreaterSlantEqual: "\u2A7E\u0338", ngeqslant: "\u2A7E\u0338",
lap: "\u2A85", lessapprox: "\u2A85", gap: "\u2A86", gtrapprox: "\u2A86",
lne: "\u2A87", lneq: "\u2A87", gne: "\u2A88", gneq: "\u2A88",
lnap: "\u2A89", lnapprox: "\u2A89", gnap: "\u2A8A", gnapprox: "\u2A8A",
lEg: "\u2A8B", lesseqqgtr: "\u2A8B", gEl: "\u2A8C", gtreqqless: "\u2A8C",
els: "\u2A95", eqslantless: "\u2A95", egs: "\u2A96", eqslantgtr: "\u2A96",
pre: "\u2AAF", preceq: "\u2AAF", PrecedesEqual: "\u2AAF", npre: "\u2AAF\u0338",
npreceq: "\u2AAF\u0338", NotPrecedesEqual: "\u2AAF\u0338", sce: "\u2AB0", succeq: "\u2AB0",
SucceedsEqual: "\u2AB0", nsce: "\u2AB0\u0338", nsucceq: "\u2AB0\u0338", NotSucceedsEqual: "\u2AB0\u0338",
prnE: "\u2AB5", precneqq: "\u2AB5", scnE: "\u2AB6", succneqq: "\u2AB6",
prap: "\u2AB7", precapprox: "\u2AB7", scap: "\u2AB8", succapprox: "\u2AB8",
prnap: "\u2AB9", precnapprox: "\u2AB9", scnap: "\u2ABA", succnapprox: "\u2ABA",
subE: "\u2AC5", subseteqq: "\u2AC5", nsubE: "\u2AC5\u0338", nsubseteqq: "\u2AC5\u0338",
supE: "\u2AC6", supseteqq: "\u2AC6", nsupE: "\u2AC6\u0338", nsupseteqq: "\u2AC6\u0338",
subnE: "\u2ACB", subsetneqq: "\u2ACB", vsubnE: "\u2ACB\uFE00", varsubsetneqq: "\u2ACB\uFE00",
supnE: "\u2ACC", supsetneqq: "\u2ACC", vsupnE: "\u2ACC\uFE00", varsupsetneqq: "\u2ACC\uFE00",
"b.Gamma": "\uD835\uDEAA", "b.Delta": "\uD835\uDEAA", "b.Theta": "\uD835\uDEAF", "b.Lambda": "\uD835\uDEB2",
"b.Xi": "\uD835\uDEB5", "b.Pi": "\uD835\uDEB7", "b.Sigma": "\uD835\uDEBA", "b.Upsi": "\uD835\uDEBC",
"b.Phi": "\uD835\uDEBD", "b.Psi": "\uD835\uDEBF", "b.Omega": "\uD835\uDEC0", "b.alpha": "\uD835\uDEC2",
"b.beta": "\uD835\uDEC3", "b.gamma": "\uD835\uDEC4", "b.delta": "\uD835\uDEC5", "b.epsi": "\uD835\uDEC6",
"b.zeta": "\uD835\uDEC7", "b.eta": "\uD835\uDEC8", "b.thetas": "\uD835\uDEC9", "b.iota": "\uD835\uDECA",
"b.kappa": "\uD835\uDECB", "b.lambda": "\uD835\uDECC", "b.mu": "\uD835\uDECD", "b.nu": "\uD835\uDECE",
"b.xi": "\uD835\uDECF", "b.pi": "\uD835\uDED1", "b.rho": "\uD835\uDED2", "b.sigmav": "\uD835\uDED3",
"b.sigma": "\uD835\uDED4", "b.tau": "\uD835\uDED5", "b.upsi": "\uD835\uDED6", "b.phi": "\uD835\uDED7",
"b.chi": "\uD835\uDED8", "b.psi": "\uD835\uDED9", "b.omega": "\uD835\uDEDA", "b.epsiv": "\uD835\uDEDC",
"b.thetav": "\uD835\uDEDD", "b.kappav": "\uD835\uDEDE", "b.phiv": "\uD835\uDEDF", "b.rhov": "\uD835\uDEE0",
"b.piv": "\uD835\uDEE1", fflig: "\uFB00", filig: "\uFB01", fllig: "\uFB02",
ffilig: "\uFB03", ffllig: "\uFB04", sbsol: "\uFE68"
};
// Some unofficial aliases
ISO8879CharMap.prime = "\u2032"; // same as vprime
/** BEGIN TEST CASES **/
var testCases = [
{
"type": "web",
"url": "https://www.nature.com/onc/volumes/31/issues/6",
"items": "multiple"
},
{
"type": "web",
"url": "https://www.nature.com/articles/onc2011282",
"items": [
{
"itemType": "journalArticle",
"title": "Trastuzumab (herceptin) targets gastric cancer stem cells characterized by CD90 phenotype",
"creators": [
{
"firstName": "J.",
"lastName": "Jiang",
"creatorType": "author"
},
{
"firstName": "Y.",
"lastName": "Zhang",
"creatorType": "author"
},
{
"firstName": "S.",
"lastName": "Chuai",
"creatorType": "author"
},
{
"firstName": "Z.",
"lastName": "Wang",
"creatorType": "author"
},
{
"firstName": "D.",
"lastName": "Zheng",
"creatorType": "author"
},
{
"firstName": "F.",
"lastName": "Xu",
"creatorType": "author"
},
{
"firstName": "Y.",
"lastName": "Zhang",
"creatorType": "author"
},
{
"firstName": "C.",
"lastName": "Li",
"creatorType": "author"
},
{
"firstName": "Y.",
"lastName": "Liang",
"creatorType": "author"
},
{
"firstName": "Z.",
"lastName": "Chen",
"creatorType": "author"
}
],
"date": "2012-02",
"DOI": "10.1038/onc.2011.282",
"ISSN": "1476-5594",
"abstractNote": "Identification and characterization of cancer stem cells (CSCs) in gastric cancer are difficult owing to the lack of specific markers and consensus methods. In this study, we show that cells with the CD90 surface marker in gastric tumors could be enriched under non-adherent, serum-free and sphere-forming conditions. These CD90+ cells possess a higher ability to initiate tumor in vivo and could re-establish the cellular hierarchy of tumors from single-cell implantation, demonstrating their self-renewal properties. Interestingly, higher proportion of CD90+ cells correlates with higher in vivo tumorigenicity of gastric primary tumor models. In addition, it was found that ERBB2 was overexpressed in about 25% of the gastric primary tumor models, which correlates with the higher level of CD90 expression in these tumors. Trastuzumab (humanized anti-ERBB2 antibody) treatment of high-tumorigenic gastric primary tumor models could reduce the CD90+ population in tumor mass and suppress tumor growth when combined with traditional chemotherapy. Moreover, tumorigenicity of tumor cells could also be suppressed when trastuzumab treatment starts at the same time as cell implantation. Therefore, we have identified a CSC population in gastric primary tumors characterized by their CD90 phenotype. The finding that trastuzumab targets the CSC population in gastric tumors suggests that ERBB2 signaling has a role in maintaining CSC populations, thus contributing to carcinogenesis and tumor invasion. In conclusion, the results from this study provide new insights into the gastric tumorigenic process and offer potential implications for the development of anticancer drugs as well as therapeutic treatment of gastric cancers.",
"issue": "6",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "671-682",
"publicationTitle": "Oncogene",
"rights": "2012 Macmillan Publishers Limited",
"url": "https://www.nature.com/articles/onc2011282",
"volume": "31",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Apoptosis"
},
{
"tag": "Cell Biology"
},
{
"tag": "Human Genetics"
},
{
"tag": "Internal Medicine"
},
{
"tag": "Medicine/Public Health"
},
{
"tag": "Oncology"
},
{
"tag": "general"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nature10669",
"items": [
{
"itemType": "journalArticle",
"title": "Gravitational detection of a low-mass dark satellite galaxy at cosmological distance",
"creators": [
{
"firstName": "S.",
"lastName": "Vegetti",
"creatorType": "author"
},
{
"firstName": "D. J.",
"lastName": "Lagattuta",
"creatorType": "author"
},
{
"firstName": "J. P.",
"lastName": "McKean",
"creatorType": "author"
},
{
"firstName": "M. W.",
"lastName": "Auger",
"creatorType": "author"
},
{
"firstName": "C. D.",
"lastName": "Fassnacht",
"creatorType": "author"
},
{
"firstName": "L. V. E.",
"lastName": "Koopmans",
"creatorType": "author"
}
],
"date": "2012-01",
"DOI": "10.1038/nature10669",
"ISSN": "1476-4687",
"abstractNote": "The discovery of a distant, low-mass satellite galaxy helps to constrain the mass function for substructure beyond the local Universe to a form that agrees at the 95 per cent confidence level with predictions based on cold dark matter.",
"issue": "7381",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "341-343",
"publicationTitle": "Nature",
"rights": "2012 Springer Nature Limited",
"url": "https://www.nature.com/articles/nature10669",
"volume": "481",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Cosmology"
},
{
"tag": "Galaxies and clusters"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/481237a",
"items": [
{
"itemType": "journalArticle",
"title": "Antarctic Treaty is cold comfort",
"creators": [],
"date": "2012-01",
"DOI": "10.1038/481237a",
"ISSN": "1476-4687",
"abstractNote": "Researchers need to cement the bond between science and the South Pole if the region is to remain one of peace and collaboration.",
"issue": "7381",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "237-237",
"publicationTitle": "Nature",
"rights": "2012 Springer Nature Limited",
"url": "https://www.nature.com/articles/481237a",
"volume": "481",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Policy"
},
{
"tag": "Politics"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nature10728",
"items": [
{
"itemType": "journalArticle",
"title": "Structure of HDAC3 bound to co-repressor and inositol tetraphosphate",
"creators": [
{
"firstName": "Peter J.",
"lastName": "Watson",
"creatorType": "author"
},
{
"firstName": "Louise",
"lastName": "Fairall",
"creatorType": "author"
},
{
"firstName": "Guilherme M.",
"lastName": "Santos",
"creatorType": "author"
},
{
"firstName": "John W. R.",
"lastName": "Schwabe",
"creatorType": "author"
}
],
"date": "2012-01",
"DOI": "10.1038/nature10728",
"ISSN": "1476-4687",
"abstractNote": "Histone deacetylase enzymes (HDACs) are emerging cancer drug targets. They regulate gene expression by removing acetyl groups from lysine residues in histone tails, resulting in chromatin condensation. The enzymatic activity of most class I HDACs requires recruitment into multi-subunit co-repressor complexes, which are in turn recruited to chromatin by repressive transcription factors. Here we report the structure of a complex between an HDAC and a co-repressor, namely, human HDAC3 with the deacetylase activation domain (DAD) from the human SMRT co-repressor (also known as NCOR2). The structure reveals two remarkable features. First, the SMRT-DAD undergoes a large structural rearrangement on forming the complex. Second, there is an essential inositol tetraphosphate molecule—d-myo-inositol-(1,4,5,6)-tetrakisphosphate (Ins(1,4,5,6)P4)—acting as an intermolecular glue between the two proteins. Assembly of the complex is clearly dependent on the Ins(1,4,5,6)P4, which may act as a regulator—potentially explaining why inositol phosphates and their kinases have been found to act as transcriptional regulators. This mechanism for the activation of HDAC3 appears to be conserved in class I HDACs from yeast to humans, and opens the way to novel therapeutic opportunities.",
"issue": "7381",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "335-340",
"publicationTitle": "Nature",
"rights": "2011 Springer Nature Limited",
"url": "https://www.nature.com/articles/nature10728",
"volume": "481",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Humanities and Social Sciences"
},
{
"tag": "Science"
},
{
"tag": "Science"
},
{
"tag": "multidisciplinary"
},
{
"tag": "multidisciplinary"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/ng1901",
"items": [
{
"itemType": "journalArticle",
"title": "Genome-wide analysis of estrogen receptor binding sites",
"creators": [
{
"firstName": "Jason S.",
"lastName": "Carroll",
"creatorType": "author"
},
{
"firstName": "Clifford A.",
"lastName": "Meyer",
"creatorType": "author"
},
{
"firstName": "Jun",
"lastName": "Song",
"creatorType": "author"
},
{
"firstName": "Wei",
"lastName": "Li",
"creatorType": "author"
},
{
"firstName": "Timothy R.",
"lastName": "Geistlinger",
"creatorType": "author"
},
{
"firstName": "Jérôme",
"lastName": "Eeckhoute",
"creatorType": "author"
},
{
"firstName": "Alexander S.",
"lastName": "Brodsky",
"creatorType": "author"
},
{
"firstName": "Erika Krasnickas",
"lastName": "Keeton",
"creatorType": "author"
},
{
"firstName": "Kirsten C.",
"lastName": "Fertuck",
"creatorType": "author"
},
{
"firstName": "Giles F.",
"lastName": "Hall",
"creatorType": "author"
},
{
"firstName": "Qianben",
"lastName": "Wang",
"creatorType": "author"
},
{
"firstName": "Stefan",
"lastName": "Bekiranov",
"creatorType": "author"
},
{
"firstName": "Victor",
"lastName": "Sementchenko",
"creatorType": "author"
},
{
"firstName": "Edward A.",
"lastName": "Fox",
"creatorType": "author"
},
{
"firstName": "Pamela A.",
"lastName": "Silver",
"creatorType": "author"
},
{
"firstName": "Thomas R.",
"lastName": "Gingeras",
"creatorType": "author"
},
{
"firstName": "X. Shirley",
"lastName": "Liu",
"creatorType": "author"
},
{
"firstName": "Myles",
"lastName": "Brown",
"creatorType": "author"
}
],
"date": "2006-11",
"DOI": "10.1038/ng1901",
"ISSN": "1546-1718",
"abstractNote": "The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and the archetype of a molecular therapeutic target. We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells. Combining this unique resource with gene expression data demonstrates distinct temporal mechanisms of estrogen-mediated gene regulation, particularly in the case of estrogen-suppressed genes. Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer.",
"issue": "11",
"journalAbbreviation": "Nat Genet",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "1289-1297",
"publicationTitle": "Nature Genetics",
"rights": "2006 Springer Nature America, Inc.",
"url": "https://www.nature.com/articles/ng1901",
"volume": "38",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Agriculture"
},
{
"tag": "Animal Genetics and Genomics"
},
{
"tag": "Biomedicine"
},
{
"tag": "Cancer Research"
},
{
"tag": "Gene Function"
},
{
"tag": "Human Genetics"
},
{
"tag": "general"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nature08497",
"items": [
{
"itemType": "journalArticle",
"title": "An oestrogen-receptor-α-bound human chromatin interactome",
"creators": [
{
"firstName": "Melissa J.",
"lastName": "Fullwood",
"creatorType": "author"
},
{
"firstName": "Mei Hui",
"lastName": "Liu",
"creatorType": "author"
},
{
"firstName": "You Fu",
"lastName": "Pan",
"creatorType": "author"
},
{
"firstName": "Jun",
"lastName": "Liu",
"creatorType": "author"
},
{
"firstName": "Han",
"lastName": "Xu",
"creatorType": "author"
},
{
"firstName": "Yusoff Bin",
"lastName": "Mohamed",
"creatorType": "author"
},
{
"firstName": "Yuriy L.",
"lastName": "Orlov",
"creatorType": "author"
},
{
"firstName": "Stoyan",
"lastName": "Velkov",
"creatorType": "author"
},
{
"firstName": "Andrea",
"lastName": "Ho",
"creatorType": "author"
},
{
"firstName": "Poh Huay",
"lastName": "Mei",
"creatorType": "author"
},
{
"firstName": "Elaine G. Y.",
"lastName": "Chew",
"creatorType": "author"
},
{
"firstName": "Phillips Yao Hui",
"lastName": "Huang",
"creatorType": "author"
},
{
"firstName": "Willem-Jan",
"lastName": "Welboren",
"creatorType": "author"
},
{
"firstName": "Yuyuan",
"lastName": "Han",
"creatorType": "author"
},
{
"firstName": "Hong Sain",
"lastName": "Ooi",
"creatorType": "author"
},
{
"firstName": "Pramila N.",
"lastName": "Ariyaratne",
"creatorType": "author"
},
{
"firstName": "Vinsensius B.",
"lastName": "Vega",
"creatorType": "author"
},
{
"firstName": "Yanquan",
"lastName": "Luo",
"creatorType": "author"
},
{
"firstName": "Peck Yean",
"lastName": "Tan",
"creatorType": "author"
},
{
"firstName": "Pei Ye",
"lastName": "Choy",
"creatorType": "author"
},
{
"firstName": "K. D. Senali Abayratna",
"lastName": "Wansa",
"creatorType": "author"
},
{
"firstName": "Bing",
"lastName": "Zhao",
"creatorType": "author"
},
{
"firstName": "Kar Sian",
"lastName": "Lim",
"creatorType": "author"
},
{
"firstName": "Shi Chi",
"lastName": "Leow",
"creatorType": "author"
},
{
"firstName": "Jit Sin",
"lastName": "Yow",
"creatorType": "author"
},
{
"firstName": "Roy",
"lastName": "Joseph",
"creatorType": "author"
},
{
"firstName": "Haixia",
"lastName": "Li",
"creatorType": "author"
},
{
"firstName": "Kartiki V.",
"lastName": "Desai",
"creatorType": "author"
},
{
"firstName": "Jane S.",
"lastName": "Thomsen",
"creatorType": "author"
},
{
"firstName": "Yew Kok",
"lastName": "Lee",
"creatorType": "author"
},
{
"firstName": "R. Krishna Murthy",
"lastName": "Karuturi",
"creatorType": "author"
},
{
"firstName": "Thoreau",
"lastName": "Herve",
"creatorType": "author"
},
{
"firstName": "Guillaume",
"lastName": "Bourque",
"creatorType": "author"
},
{
"firstName": "Hendrik G.",
"lastName": "Stunnenberg",
"creatorType": "author"
},
{
"firstName": "Xiaoan",
"lastName": "Ruan",
"creatorType": "author"
},
{
"firstName": "Valere",
"lastName": "Cacheux-Rataboul",
"creatorType": "author"
},
{
"firstName": "Wing-Kin",
"lastName": "Sung",
"creatorType": "author"
},
{
"firstName": "Edison T.",
"lastName": "Liu",
"creatorType": "author"
},
{
"firstName": "Chia-Lin",
"lastName": "Wei",
"creatorType": "author"
},
{
"firstName": "Edwin",
"lastName": "Cheung",
"creatorType": "author"
},
{
"firstName": "Yijun",
"lastName": "Ruan",
"creatorType": "author"
}
],
"date": "2009-11",
"DOI": "10.1038/nature08497",
"ISSN": "1476-4687",
"abstractNote": "Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor α (ER-α) in the human genome. We found that most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.",
"issue": "7269",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "58-64",
"publicationTitle": "Nature",
"rights": "2009 Macmillan Publishers Limited. All rights reserved",
"url": "https://www.nature.com/articles/nature08497",
"volume": "462",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Humanities and Social Sciences"
},
{
"tag": "Science"
},
{
"tag": "Science"
},
{
"tag": "multidisciplinary"
},
{
"tag": "multidisciplinary"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nsmb.1371",
"items": [
{
"itemType": "journalArticle",
"title": "Structure of the SAM-II riboswitch bound to S-adenosylmethionine",
"creators": [
{
"firstName": "Sunny D.",
"lastName": "Gilbert",
"creatorType": "author"
},
{
"firstName": "Robert P.",
"lastName": "Rambo",
"creatorType": "author"
},
{
"firstName": "Daria",
"lastName": "Van Tyne",
"creatorType": "author"
},
{
"firstName": "Robert T.",
"lastName": "Batey",
"creatorType": "author"
}
],
"date": "2008-02",
"DOI": "10.1038/nsmb.1371",
"ISSN": "1545-9985",
"abstractNote": "In bacteria, numerous genes harbor regulatory elements in the 5 untranslated regions of their mRNA, termed riboswitches, which control gene expression by binding small-molecule metabolites. These sequences influence the secondary and tertiary structure of the RNA in a ligand-dependent manner, thereby directing its transcription or translation. The crystal structure of an S-adenosylmethionineresponsive riboswitch found predominantly in proteobacteria, SAM-II, has been solved to reveal a second means by which RNA interacts with this important cellular metabolite. Notably, this is the first structure of a complete riboswitch containing all sequences associated with both the ligand binding aptamer domain and the regulatory expression platform. Chemical probing of this RNA in the absence and presence of ligand shows how the structure changes in response to S-adenosylmethionine to sequester the ribosomal binding site and affect translational gene regulation.",
"issue": "2",
"journalAbbreviation": "Nat Struct Mol Biol",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "177-182",
"publicationTitle": "Nature Structural & Molecular Biology",
"rights": "2008 Springer Nature America, Inc.",
"url": "https://www.nature.com/articles/nsmb.1371",
"volume": "15",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Biochemistry"
},
{
"tag": "Biological Microscopy"
},
{
"tag": "Life Sciences"
},
{
"tag": "Membrane Biology"
},
{
"tag": "Protein Structure"
},
{
"tag": "general"
},
{
"tag": "general"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/ng/volumes/38/issues/11",
"items": "multiple"
},
{
"type": "web",
"url": "https://www.nature.com/nbt/volumes/30/issues/3",
"items": "multiple"
},
{
"type": "web",
"url": "https://www.nature.com/articles/nature10669",
"items": [
{
"itemType": "journalArticle",
"title": "Gravitational detection of a low-mass dark satellite galaxy at cosmological distance",
"creators": [
{
"firstName": "S.",
"lastName": "Vegetti",
"creatorType": "author"
},
{
"firstName": "D. J.",
"lastName": "Lagattuta",
"creatorType": "author"
},
{
"firstName": "J. P.",
"lastName": "McKean",
"creatorType": "author"
},
{
"firstName": "M. W.",
"lastName": "Auger",
"creatorType": "author"
},
{
"firstName": "C. D.",
"lastName": "Fassnacht",
"creatorType": "author"
},
{
"firstName": "L. V. E.",
"lastName": "Koopmans",
"creatorType": "author"
}
],
"date": "2012-01",
"DOI": "10.1038/nature10669",
"ISSN": "1476-4687",
"abstractNote": "The discovery of a distant, low-mass satellite galaxy helps to constrain the mass function for substructure beyond the local Universe to a form that agrees at the 95 per cent confidence level with predictions based on cold dark matter.",
"issue": "7381",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "341-343",
"publicationTitle": "Nature",
"rights": "2012 Springer Nature Limited",
"url": "https://www.nature.com/articles/nature10669",
"volume": "481",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Cosmology"
},
{
"tag": "Galaxies and clusters"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nature11968",
"items": [
{
"itemType": "journalArticle",
"title": "Patterns of population epigenomic diversity",
"creators": [
{
"firstName": "Robert J.",
"lastName": "Schmitz",
"creatorType": "author"
},
{
"firstName": "Matthew D.",
"lastName": "Schultz",
"creatorType": "author"
},
{
"firstName": "Mark A.",
"lastName": "Urich",
"creatorType": "author"
},
{
"firstName": "Joseph R.",
"lastName": "Nery",
"creatorType": "author"
},
{
"firstName": "Mattia",
"lastName": "Pelizzola",
"creatorType": "author"
},
{
"firstName": "Ondrej",
"lastName": "Libiger",
"creatorType": "author"
},
{
"firstName": "Andrew",
"lastName": "Alix",
"creatorType": "author"
},
{
"firstName": "Richard B.",
"lastName": "McCosh",
"creatorType": "author"
},
{
"firstName": "Huaming",
"lastName": "Chen",
"creatorType": "author"
},
{
"firstName": "Nicholas J.",
"lastName": "Schork",
"creatorType": "author"
},
{
"firstName": "Joseph R.",
"lastName": "Ecker",
"creatorType": "author"
}
],
"date": "2013-03",
"DOI": "10.1038/nature11968",
"ISSN": "1476-4687",
"abstractNote": "Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.",
"issue": "7440",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "193-198",
"publicationTitle": "Nature",
"rights": "2013 The Author(s)",
"url": "https://www.nature.com/articles/nature11968",
"volume": "495",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Epigenomics"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nature11899",
"items": [
{
"itemType": "journalArticle",
"title": "Crystal structures of the calcium pump and sarcolipin in the Mg2+-bound E1 state",
"creators": [
{
"firstName": "Chikashi",
"lastName": "Toyoshima",
"creatorType": "author"
},
{
"firstName": "Shiho",
"lastName": "Iwasawa",
"creatorType": "author"
},
{
"firstName": "Haruo",
"lastName": "Ogawa",
"creatorType": "author"
},
{
"firstName": "Ayami",
"lastName": "Hirata",
"creatorType": "author"
},
{
"firstName": "Junko",
"lastName": "Tsueda",
"creatorType": "author"
},
{
"firstName": "Giuseppe",
"lastName": "Inesi",
"creatorType": "author"
}
],
"date": "2013-03",
"DOI": "10.1038/nature11899",
"ISSN": "1476-4687",
"abstractNote": "The X-ray crystal structures of SERCA1a, a Ca2+-ATPase from the sarcoplasmic reticulum, in the presence and absence of sarcolipin are reported; the structures indicate that sarcolipin stabilizes SERCA1a in an open state that has not been well characterised previously, in which SERCA1a has not yet accepted calcium into its two high-affinity binding sites.",
"issue": "7440",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "260-264",
"publicationTitle": "Nature",
"rights": "2013 Springer Nature Limited",
"url": "https://www.nature.com/articles/nature11899",
"volume": "495",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "X-ray crystallography"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nature09944",
"items": [
{
"itemType": "journalArticle",
"title": "Enterotypes of the human gut microbiome",
"creators": [
{
"firstName": "Manimozhiyan",
"lastName": "Arumugam",
"creatorType": "author"
},
{
"firstName": "Jeroen",
"lastName": "Raes",
"creatorType": "author"
},
{
"firstName": "Eric",
"lastName": "Pelletier",
"creatorType": "author"
},
{
"firstName": "Denis",
"lastName": "Le Paslier",
"creatorType": "author"
},
{
"firstName": "Takuji",
"lastName": "Yamada",
"creatorType": "author"
},
{
"firstName": "Daniel R.",
"lastName": "Mende",
"creatorType": "author"
},
{
"firstName": "Gabriel R.",
"lastName": "Fernandes",
"creatorType": "author"
},
{
"firstName": "Julien",
"lastName": "Tap",
"creatorType": "author"
},
{
"firstName": "Thomas",
"lastName": "Bruls",
"creatorType": "author"
},
{
"firstName": "Jean-Michel",
"lastName": "Batto",
"creatorType": "author"
},
{
"firstName": "Marcelo",
"lastName": "Bertalan",
"creatorType": "author"
},
{
"firstName": "Natalia",
"lastName": "Borruel",
"creatorType": "author"
},
{
"firstName": "Francesc",
"lastName": "Casellas",
"creatorType": "author"
},
{
"firstName": "Leyden",
"lastName": "Fernandez",
"creatorType": "author"
},
{
"firstName": "Laurent",
"lastName": "Gautier",
"creatorType": "author"
},
{
"firstName": "Torben",
"lastName": "Hansen",
"creatorType": "author"
},
{
"firstName": "Masahira",
"lastName": "Hattori",
"creatorType": "author"
},
{
"firstName": "Tetsuya",
"lastName": "Hayashi",
"creatorType": "author"
},
{
"firstName": "Michiel",
"lastName": "Kleerebezem",
"creatorType": "author"
},
{
"firstName": "Ken",
"lastName": "Kurokawa",
"creatorType": "author"
},
{
"firstName": "Marion",
"lastName": "Leclerc",
"creatorType": "author"
},
{
"firstName": "Florence",
"lastName": "Levenez",
"creatorType": "author"
},
{
"firstName": "Chaysavanh",
"lastName": "Manichanh",
"creatorType": "author"
},
{
"firstName": "H. Bjørn",
"lastName": "Nielsen",
"creatorType": "author"
},
{
"firstName": "Trine",
"lastName": "Nielsen",
"creatorType": "author"
},
{
"firstName": "Nicolas",
"lastName": "Pons",
"creatorType": "author"
},
{
"firstName": "Julie",
"lastName": "Poulain",
"creatorType": "author"
},
{
"firstName": "Junjie",
"lastName": "Qin",
"creatorType": "author"
},
{
"firstName": "Thomas",
"lastName": "Sicheritz-Ponten",
"creatorType": "author"
},
{
"firstName": "Sebastian",
"lastName": "Tims",
"creatorType": "author"
},
{
"firstName": "David",
"lastName": "Torrents",
"creatorType": "author"
},
{
"firstName": "Edgardo",
"lastName": "Ugarte",
"creatorType": "author"
},
{
"firstName": "Erwin G.",
"lastName": "Zoetendal",
"creatorType": "author"
},
{
"firstName": "Jun",
"lastName": "Wang",
"creatorType": "author"
},
{
"firstName": "Francisco",
"lastName": "Guarner",
"creatorType": "author"
},
{
"firstName": "Oluf",
"lastName": "Pedersen",
"creatorType": "author"
},
{
"firstName": "Willem M.",
"lastName": "de Vos",
"creatorType": "author"
},
{
"firstName": "Søren",
"lastName": "Brunak",
"creatorType": "author"
},
{
"firstName": "Joel",
"lastName": "Doré",
"creatorType": "author"
},
{
"firstName": "Jean",
"lastName": "Weissenbach",
"creatorType": "author"
},
{
"firstName": "S. Dusko",
"lastName": "Ehrlich",
"creatorType": "author"
},
{
"firstName": "Peer",
"lastName": "Bork",
"creatorType": "author"
}
],
"date": "2011-05",
"DOI": "10.1038/nature09944",
"ISSN": "1476-4687",
"abstractNote": "Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced hostmicrobial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.",
"issue": "7346",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "174-180",
"publicationTitle": "Nature",
"rights": "2011 Springer Nature Limited",
"url": "https://www.nature.com/articles/nature09944",
"volume": "473",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Metagenomics"
},
{
"tag": "Microbiota"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/nprot.2006.52",
"items": [
{
"itemType": "journalArticle",
"title": "Bioluminescence resonance energy transfer (BRET) for the real-time detection of protein-protein interactions",
"creators": [
{
"firstName": "Kevin D. G.",
"lastName": "Pfleger",
"creatorType": "author"
},
{
"firstName": "Ruth M.",
"lastName": "Seeber",
"creatorType": "author"
},
{
"firstName": "Karin A.",
"lastName": "Eidne",
"creatorType": "author"
}
],
"date": "2006-06",
"DOI": "10.1038/nprot.2006.52",
"ISSN": "1750-2799",
"abstractNote": "A substantial range of protein-protein interactions can be readily monitored in real time using bioluminescence resonance energy transfer (BRET). The procedure involves heterologous coexpression of fusion proteins, which link proteins of interest to a bioluminescent donor enzyme or acceptor fluorophore. Energy transfer between these proteins is then detected. This protocol encompasses BRET1, BRET2 and the recently described eBRET, including selection of the donor, acceptor and substrate combination, fusion construct generation and validation, cell culture, fluorescence and luminescence detection, BRET detection and data analysis. The protocol is particularly suited to studying protein-protein interactions in live cells (adherent or in suspension), but cell extracts and purified proteins can also be used. Furthermore, although the procedure is illustrated with references to mammalian cell culture conditions, this protocol can be readily used for bacterial or plant studies. Once fusion proteins are generated and validated, the procedure typically takes 4872 h depending on cell culture requirements.",
"issue": "1",
"journalAbbreviation": "Nat Protoc",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "337-345",
"publicationTitle": "Nature Protocols",
"rights": "2006 Springer Nature Limited",
"url": "https://www.nature.com/articles/nprot.2006.52",
"volume": "1",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Analytical Chemistry"
},
{
"tag": "Biological Techniques"
},
{
"tag": "Computational Biology/Bioinformatics"
},
{
"tag": "Life Sciences"
},
{
"tag": "Microarrays"
},
{
"tag": "Organic Chemistry"
},
{
"tag": "general"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/ncomms7186",
"items": [
{
"itemType": "journalArticle",
"title": "ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters",
"creators": [
{
"firstName": "Swneke D.",
"lastName": "Bailey",
"creatorType": "author"
},
{
"firstName": "Xiaoyang",
"lastName": "Zhang",
"creatorType": "author"
},
{
"firstName": "Kinjal",
"lastName": "Desai",
"creatorType": "author"
},
{
"firstName": "Malika",
"lastName": "Aid",
"creatorType": "author"
},
{
"firstName": "Olivia",
"lastName": "Corradin",
"creatorType": "author"
},
{
"firstName": "Richard",
"lastName": "Cowper-Sal·lari",
"creatorType": "author"
},
{
"firstName": "Batool",
"lastName": "Akhtar-Zaidi",
"creatorType": "author"
},
{
"firstName": "Peter C.",
"lastName": "Scacheri",
"creatorType": "author"
},
{
"firstName": "Benjamin",
"lastName": "Haibe-Kains",
"creatorType": "author"
},
{
"firstName": "Mathieu",
"lastName": "Lupien",
"creatorType": "author"
}
],
"date": "2015-02-03",
"DOI": "10.1038/ncomms7186",
"ISSN": "2041-1723",
"abstractNote": "Chromatin interactions connect distal regulatory elements to target gene promoters guiding stimulus- and lineage-specific transcription. Few factors securing chromatin interactions have so far been identified. Here, by integrating chromatin interaction maps with the large collection of transcription factor-binding profiles provided by the ENCODE project, we demonstrate that the zinc-finger protein ZNF143 preferentially occupies anchors of chromatin interactions connecting promoters with distal regulatory elements. It binds directly to promoters and associates with lineage-specific chromatin interactions and gene expression. Silencing ZNF143 or modulating its DNA-binding affinity using single-nucleotide polymorphisms (SNPs) as a surrogate of site-directed mutagenesis reveals the sequence dependency of chromatin interactions at gene promoters. We also find that chromatin interactions alone do not regulate gene expression. Together, our results identify ZNF143 as a novel chromatin-looping factor that contributes to the architectural foundation of the genome by providing sequence specificity at promoters connected with distal regulatory elements.",
"issue": "1",
"journalAbbreviation": "Nat Commun",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "6186",
"publicationTitle": "Nature Communications",
"rights": "2015 Springer Nature Limited",
"url": "https://www.nature.com/articles/ncomms7186",
"volume": "6",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
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],
"tags": [
{
"tag": "Chromatin"
},
{
"tag": "Transcription factors"
},
{
"tag": "Transcriptional regulatory elements"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/search?q=zotero",
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{
"type": "web",
"url": "https://www.nature.com/articles/sdata201618",
"items": [
{
"itemType": "journalArticle",
"title": "The FAIR Guiding Principles for scientific data management and stewardship",
"creators": [
{
"firstName": "Mark D.",
"lastName": "Wilkinson",
"creatorType": "author"
},
{
"firstName": "Michel",
"lastName": "Dumontier",
"creatorType": "author"
},
{
"firstName": "IJsbrand Jan",
"lastName": "Aalbersberg",
"creatorType": "author"
},
{
"firstName": "Gabrielle",
"lastName": "Appleton",
"creatorType": "author"
},
{
"firstName": "Myles",
"lastName": "Axton",
"creatorType": "author"
},
{
"firstName": "Arie",
"lastName": "Baak",
"creatorType": "author"
},
{
"firstName": "Niklas",
"lastName": "Blomberg",
"creatorType": "author"
},
{
"firstName": "Jan-Willem",
"lastName": "Boiten",
"creatorType": "author"
},
{
"firstName": "Luiz Bonino",
"lastName": "da Silva Santos",
"creatorType": "author"
},
{
"firstName": "Philip E.",
"lastName": "Bourne",
"creatorType": "author"
},
{
"firstName": "Jildau",
"lastName": "Bouwman",
"creatorType": "author"
},
{
"firstName": "Anthony J.",
"lastName": "Brookes",
"creatorType": "author"
},
{
"firstName": "Tim",
"lastName": "Clark",
"creatorType": "author"
},
{
"firstName": "Mercè",
"lastName": "Crosas",
"creatorType": "author"
},
{
"firstName": "Ingrid",
"lastName": "Dillo",
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},
{
"firstName": "Olivier",
"lastName": "Dumon",
"creatorType": "author"
},
{
"firstName": "Scott",
"lastName": "Edmunds",
"creatorType": "author"
},
{
"firstName": "Chris T.",
"lastName": "Evelo",
"creatorType": "author"
},
{
"firstName": "Richard",
"lastName": "Finkers",
"creatorType": "author"
},
{
"firstName": "Alejandra",
"lastName": "Gonzalez-Beltran",
"creatorType": "author"
},
{
"firstName": "Alasdair J. G.",
"lastName": "Gray",
"creatorType": "author"
},
{
"firstName": "Paul",
"lastName": "Groth",
"creatorType": "author"
},
{
"firstName": "Carole",
"lastName": "Goble",
"creatorType": "author"
},
{
"firstName": "Jeffrey S.",
"lastName": "Grethe",
"creatorType": "author"
},
{
"firstName": "Jaap",
"lastName": "Heringa",
"creatorType": "author"
},
{
"firstName": "Peter A. C.",
"lastName": "t Hoen",
"creatorType": "author"
},
{
"firstName": "Rob",
"lastName": "Hooft",
"creatorType": "author"
},
{
"firstName": "Tobias",
"lastName": "Kuhn",
"creatorType": "author"
},
{
"firstName": "Ruben",
"lastName": "Kok",
"creatorType": "author"
},
{
"firstName": "Joost",
"lastName": "Kok",
"creatorType": "author"
},
{
"firstName": "Scott J.",
"lastName": "Lusher",
"creatorType": "author"
},
{
"firstName": "Maryann E.",
"lastName": "Martone",
"creatorType": "author"
},
{
"firstName": "Albert",
"lastName": "Mons",
"creatorType": "author"
},
{
"firstName": "Abel L.",
"lastName": "Packer",
"creatorType": "author"
},
{
"firstName": "Bengt",
"lastName": "Persson",
"creatorType": "author"
},
{
"firstName": "Philippe",
"lastName": "Rocca-Serra",
"creatorType": "author"
},
{
"firstName": "Marco",
"lastName": "Roos",
"creatorType": "author"
},
{
"firstName": "Rene",
"lastName": "van Schaik",
"creatorType": "author"
},
{
"firstName": "Susanna-Assunta",
"lastName": "Sansone",
"creatorType": "author"
},
{
"firstName": "Erik",
"lastName": "Schultes",
"creatorType": "author"
},
{
"firstName": "Thierry",
"lastName": "Sengstag",
"creatorType": "author"
},
{
"firstName": "Ted",
"lastName": "Slater",
"creatorType": "author"
},
{
"firstName": "George",
"lastName": "Strawn",
"creatorType": "author"
},
{
"firstName": "Morris A.",
"lastName": "Swertz",
"creatorType": "author"
},
{
"firstName": "Mark",
"lastName": "Thompson",
"creatorType": "author"
},
{
"firstName": "Johan",
"lastName": "van der Lei",
"creatorType": "author"
},
{
"firstName": "Erik",
"lastName": "van Mulligen",
"creatorType": "author"
},
{
"firstName": "Jan",
"lastName": "Velterop",
"creatorType": "author"
},
{
"firstName": "Andra",
"lastName": "Waagmeester",
"creatorType": "author"
},
{
"firstName": "Peter",
"lastName": "Wittenburg",
"creatorType": "author"
},
{
"firstName": "Katherine",
"lastName": "Wolstencroft",
"creatorType": "author"
},
{
"firstName": "Jun",
"lastName": "Zhao",
"creatorType": "author"
},
{
"firstName": "Barend",
"lastName": "Mons",
"creatorType": "author"
}
],
"date": "2016-03-15",
"DOI": "10.1038/sdata.2016.18",
"ISSN": "2052-4463",
"abstractNote": "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.",
"issue": "1",
"journalAbbreviation": "Sci Data",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "160018",
"publicationTitle": "Scientific Data",
"rights": "2016 The Author(s)",
"url": "https://www.nature.com/articles/sdata201618",
"volume": "3",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Publication characteristics"
},
{
"tag": "Research data"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/s41563-020-00871-7",
"items": [
{
"itemType": "journalArticle",
"title": "Evidence for a higher-order topological insulator in a three-dimensional material built from van der Waals stacking of bismuth-halide chains",
"creators": [
{
"firstName": "Ryo",
"lastName": "Noguchi",
"creatorType": "author"
},
{
"firstName": "Masaru",
"lastName": "Kobayashi",
"creatorType": "author"
},
{
"firstName": "Zhanzhi",
"lastName": "Jiang",
"creatorType": "author"
},
{
"firstName": "Kenta",
"lastName": "Kuroda",
"creatorType": "author"
},
{
"firstName": "Takanari",
"lastName": "Takahashi",
"creatorType": "author"
},
{
"firstName": "Zifan",
"lastName": "Xu",
"creatorType": "author"
},
{
"firstName": "Daehun",
"lastName": "Lee",
"creatorType": "author"
},
{
"firstName": "Motoaki",
"lastName": "Hirayama",
"creatorType": "author"
},
{
"firstName": "Masayuki",
"lastName": "Ochi",
"creatorType": "author"
},
{
"firstName": "Tetsuroh",
"lastName": "Shirasawa",
"creatorType": "author"
},
{
"firstName": "Peng",
"lastName": "Zhang",
"creatorType": "author"
},
{
"firstName": "Chun",
"lastName": "Lin",
"creatorType": "author"
},
{
"firstName": "Cédric",
"lastName": "Bareille",
"creatorType": "author"
},
{
"firstName": "Shunsuke",
"lastName": "Sakuragi",
"creatorType": "author"
},
{
"firstName": "Hiroaki",
"lastName": "Tanaka",
"creatorType": "author"
},
{
"firstName": "So",
"lastName": "Kunisada",
"creatorType": "author"
},
{
"firstName": "Kifu",
"lastName": "Kurokawa",
"creatorType": "author"
},
{
"firstName": "Koichiro",
"lastName": "Yaji",
"creatorType": "author"
},
{
"firstName": "Ayumi",
"lastName": "Harasawa",
"creatorType": "author"
},
{
"firstName": "Viktor",
"lastName": "Kandyba",
"creatorType": "author"
},
{
"firstName": "Alessio",
"lastName": "Giampietri",
"creatorType": "author"
},
{
"firstName": "Alexei",
"lastName": "Barinov",
"creatorType": "author"
},
{
"firstName": "Timur K.",
"lastName": "Kim",
"creatorType": "author"
},
{
"firstName": "Cephise",
"lastName": "Cacho",
"creatorType": "author"
},
{
"firstName": "Makoto",
"lastName": "Hashimoto",
"creatorType": "author"
},
{
"firstName": "Donghui",
"lastName": "Lu",
"creatorType": "author"
},
{
"firstName": "Shik",
"lastName": "Shin",
"creatorType": "author"
},
{
"firstName": "Ryotaro",
"lastName": "Arita",
"creatorType": "author"
},
{
"firstName": "Keji",
"lastName": "Lai",
"creatorType": "author"
},
{
"firstName": "Takao",
"lastName": "Sasagawa",
"creatorType": "author"
},
{
"firstName": "Takeshi",
"lastName": "Kondo",
"creatorType": "author"
}
],
"date": "2021-04",
"DOI": "10.1038/s41563-020-00871-7",
"ISSN": "1476-4660",
"abstractNote": "Low-dimensional van der Waals materials have been extensively studied as a platform with which to generate quantum effects. Advancing this research, topological quantum materials with van der Waals structures are currently receiving a great deal of attention. Here, we use the concept of designing topological materials by the van der Waals stacking of quantum spin Hall insulators. Most interestingly, we find that a slight shift of inversion centre in the unit cell caused by a modification of stacking induces a transition from a trivial insulator to a higher-order topological insulator. Based on this, we present angle-resolved photoemission spectroscopy results showing that the real three-dimensional material Bi4Br4 is a higher-order topological insulator. Our demonstration that various topological states can be selected by stacking chains differently, combined with the advantages of van der Waals materials, offers a playground for engineering topologically non-trivial edge states towards future spintronics applications.",
"issue": "4",
"journalAbbreviation": "Nat. Mater.",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "473-479",
"publicationTitle": "Nature Materials",
"rights": "2021 The Author(s), under exclusive licence to Springer Nature Limited",
"url": "https://www.nature.com/articles/s41563-020-00871-7",
"volume": "20",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Electronic properties and materials"
},
{
"tag": "Topological insulators"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/s41586-021-03972-8",
"items": [
{
"itemType": "journalArticle",
"title": "Evidence for European presence in the Americas in AD 1021",
"creators": [
{
"firstName": "Margot",
"lastName": "Kuitems",
"creatorType": "author"
},
{
"firstName": "Birgitta L.",
"lastName": "Wallace",
"creatorType": "author"
},
{
"firstName": "Charles",
"lastName": "Lindsay",
"creatorType": "author"
},
{
"firstName": "Andrea",
"lastName": "Scifo",
"creatorType": "author"
},
{
"firstName": "Petra",
"lastName": "Doeve",
"creatorType": "author"
},
{
"firstName": "Kevin",
"lastName": "Jenkins",
"creatorType": "author"
},
{
"firstName": "Susanne",
"lastName": "Lindauer",
"creatorType": "author"
},
{
"firstName": "Pınar",
"lastName": "Erdil",
"creatorType": "author"
},
{
"firstName": "Paul M.",
"lastName": "Ledger",
"creatorType": "author"
},
{
"firstName": "Véronique",
"lastName": "Forbes",
"creatorType": "author"
},
{
"firstName": "Caroline",
"lastName": "Vermeeren",
"creatorType": "author"
},
{
"firstName": "Ronny",
"lastName": "Friedrich",
"creatorType": "author"
},
{
"firstName": "Michael W.",
"lastName": "Dee",
"creatorType": "author"
}
],
"date": "2022-01",
"DOI": "10.1038/s41586-021-03972-8",
"ISSN": "1476-4687",
"abstractNote": "Transatlantic exploration took place centuries before the crossing of Columbus. Physical evidence for early European presence in the Americas can be found in Newfoundland, Canada1,2. However, it has thus far not been possible to determine when this activity took place35. Here we provide evidence that the Vikings were present in Newfoundland in ad1021. We overcome the imprecision of previous age estimates by making use of the cosmic-ray-induced upsurge in atmospheric radiocarbon concentrations in ad993 (ref.6). Our new date lays down a marker for European cognisance of the Americas, and represents the first known point at which humans encircled the globe. It also provides a definitive tie point for future research into the initial consequences of transatlantic activity, such as the transference of knowledge, and the potential exchange of genetic information, biota and pathologies7,8.",
"issue": "7893",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "388-391",
"publicationTitle": "Nature",
"rights": "2021 The Author(s)",
"url": "https://www.nature.com/articles/s41586-021-03972-8",
"volume": "601",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Archaeology"
},
{
"tag": "Mass spectrometry"
},
{
"tag": "Plant physiology"
}
],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.nature.com/articles/s41586-023-05742-0",
"items": [
{
"itemType": "journalArticle",
"title": "RETRACTED ARTICLE: Evidence of near-ambient superconductivity in a N-doped lutetium hydride",
"creators": [
{
"firstName": "Nathan",
"lastName": "Dasenbrock-Gammon",
"creatorType": "author"
},
{
"firstName": "Elliot",
"lastName": "Snider",
"creatorType": "author"
},
{
"firstName": "Raymond",
"lastName": "McBride",
"creatorType": "author"
},
{
"firstName": "Hiranya",
"lastName": "Pasan",
"creatorType": "author"
},
{
"firstName": "Dylan",
"lastName": "Durkee",
"creatorType": "author"
},
{
"firstName": "Nugzari",
"lastName": "Khalvashi-Sutter",
"creatorType": "author"
},
{
"firstName": "Sasanka",
"lastName": "Munasinghe",
"creatorType": "author"
},
{
"firstName": "Sachith E.",
"lastName": "Dissanayake",
"creatorType": "author"
},
{
"firstName": "Keith V.",
"lastName": "Lawler",
"creatorType": "author"
},
{
"firstName": "Ashkan",
"lastName": "Salamat",
"creatorType": "author"
},
{
"firstName": "Ranga P.",
"lastName": "Dias",
"creatorType": "author"
}
],
"date": "2023-03",
"DOI": "10.1038/s41586-023-05742-0",
"ISSN": "1476-4687",
"abstractNote": "The absence of electrical resistance exhibited by superconducting materials would have enormous potential for applications if it existed at ambient temperature and pressure conditions. Despite decades of intense research efforts, such a state has yet to be realized1,2. At ambient pressures, cuprates are the material class exhibiting superconductivity to the highest critical superconducting transition temperatures (Tc), up to about 133K (refs.35). Over the past decade, high-pressure chemical precompression6,7 of hydrogen-dominant alloys has led the search for high-temperature superconductivity, with demonstrated Tc approaching the freezing point of water in binary hydrides at megabar pressures813. Ternary hydrogen-rich compounds, such as carbonaceous sulfur hydride, offer an even larger chemical space to potentially improve the properties of superconducting hydrides1421. Here we report evidence of superconductivity on a nitrogen-doped lutetium hydride with a maximum Tc of 294K at 10kbar, that is, superconductivity at room temperature and near-ambient pressures. The compound was synthesized under high-pressure high-temperature conditions and then—after full recoverability—its material and superconducting properties were examined along compression pathways. These include temperature-dependent resistance with and without an applied magnetic field, the magnetization (M) versus magnetic field (H) curve, a.c. and d.c. magnetic susceptibility, as well as heat-capacity measurements. X-ray diffraction (XRD), energy-dispersive X-ray (EDX) and theoretical simulations provide some insight into the stoichiometry of the synthesized material. Nevertheless, further experiments and simulations are needed to determine the exact stoichiometry of hydrogen and nitrogen, and their respective atomistic positions, in a greater effort to further understand the superconducting state of the material.",
"issue": "7951",
"language": "en",
"libraryCatalog": "www.nature.com",
"pages": "244-250",
"publicationTitle": "Nature",
"rights": "2023 The Author(s), under exclusive licence to Springer Nature Limited",
"shortTitle": "RETRACTED ARTICLE",
"url": "https://www.nature.com/articles/s41586-023-05742-0",
"volume": "615",
"attachments": [
{
"title": "Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [
{
"tag": "Superconducting properties and materials"
}
],
"notes": [],
"seeAlso": []
}
]
}
]
/** END TEST CASES **/