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Commit 8e17a524 authored by Liliana Sanfilippo's avatar Liliana Sanfilippo
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"noImplicitAny": false

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......@@ -215,7 +215,7 @@ def bookHTML(dictio, x, out):
out.write("<li typeof=\"schema:Book\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x) + "\">"+ "\n")
# out.write("\t" + "<span property=\"schema:author\" typeof=\"schema:Organisation\">"+ "\n")
print("Just a sec, separating authors...")
if 'authors' in dictio:
if 'author' in dictio:
authors = dictio['author']
elif 'editor' in dictio:
authors = dictio['editor']
......
......@@ -152,43 +152,20 @@ New5.
language = {en}
}
new7.
@article{Bulcaen_Kortleven_Liu_Maule_Dreano_Kelly_Ensinck_Thierie_Smits_Ciciani_e,
title = {
Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in
human organoids and airway epithelial cells
},
author = {
Bulcaen, Mattijs and Kortleven, Phéline and Liu, Ronald B. and Maule, Giulia
and Dreano, Elise and Kelly, Mairead and Ensinck, Marjolein M. and Thierie,
Sam and Smits, Maxime and Ciciani, Matteo and Hatton, Aurelie and Chevalier,
Benoit and Ramalho, Anabela S. and Casadevall i Solvas, Xavier and Debyser,
Zeger and Vermeulen, François and Gijsbers, Rik and Sermet-Gaudelus, Isabelle
and Cereseto, Anna and Carlon, Marianne S.
},
year = 2024,
month = may,
journal = {Cell Reports Medicine},
pages = 101544,
doi = {10.1016/j.xcrm.2024.101544},
issn = {2666-3791},
abstractnote = {
Prime editing is a recent, CRISPR-derived genome editing technology capable
of introducing precise nucleotide substitutions, insertions, and deletions.
Here, we present prime editing approaches to correct L227R- and N1303K-CFTR,
two mutations that cause cystic fibrosis and are not eligible for current
market-approved modulator therapies. We show that, upon DNA correction of the
CFTR gene, the complex glycosylation, localization, and, most importantly,
function of the CFTR protein are restored in HEK293T and 16HBE cell lines.
These findings were subsequently validated in patient-derived rectal
organoids and human nasal epithelial cells. Through analysis of predicted and
experimentally identified candidate off-target sites in primary stem cells,
we confirm previous reports on the high prime editor (PE) specificity and its
potential for a curative CF gene editing therapy. To facilitate future
screening of genetic strategies in a translational CF model, a machine
learning algorithm was developed for dynamic quantification of CFTR function
in organoids (DETECTOR: “detection of targeted editing of CFTR in
organoids”).
}
@article{BULCAEN2024101544,
title = {Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells},
journal = {Cell Reports Medicine},
volume = {5},
number = {5},
pages = {101544},
year = {2024},
issn = {2666-3791},
doi = {https://doi.org/10.1016/j.xcrm.2024.101544},
url = {https://www.sciencedirect.com/science/article/pii/S2666379124002349},
author = {Mattijs Bulcaen and Phéline Kortleven and Ronald B. Liu and Giulia Maule and Elise Dreano and Mairead Kelly and Marjolein M. Ensinck and Sam Thierie and Maxime Smits and Matteo Ciciani and Aurelie Hatton and Benoit Chevalier and Anabela S. Ramalho and Xavier {Casadevall i Solvas} and Zeger Debyser and François Vermeulen and Rik Gijsbers and Isabelle Sermet-Gaudelus and Anna Cereseto and Marianne S. Carlon},
keywords = {cystic fibrosis, prime editing, patient-derived organoids, human nasal epithelial cells, gene editing, machine learning, DETEOR, CRISPR},
abstract = {Summary
Prime editing is a recent, CRISPR-derived genome editing technology capable of introducing precise nucleotide substitutions, insertions, and deletions. Here, we present prime editing approaches to correct L227R- and N1303K-CFTR, two mutations that cause cystic fibrosis and are not eligible for current market-approved modulator therapies. We show that, upon DNA correction of the CFTR gene, the complex glycosylation, localization, and, most importantly, function of the CFTR protein are restored in HEK293T and 16HBE cell lines. These findings were subsequently validated in patient-derived rectal organoids and human nasal epithelial cells. Through analysis of predicted and experimentally identified candidate off-target sites in primary stem cells, we confirm previous reports on the high prime editor (PE) specificity and its potential for a curative CF gene editing therapy. To facilitate future screening of genetic strategies in a translational CF model, a machine learning algorithm was developed for dynamic quantification of CFTR function in organoids (DETECTOR: “detection of targeted editing of CFTR in organoids”).}
}
new8.
@article{Ensinck_Deeersmaecker_Heylen_Ramalho_Gijsbers_Far,
......@@ -232,20 +209,19 @@ new8.
}
[new9]
@misc{ignatova2023,
title = {
Research Group Ignatova at the Institute of Biochemistry and Molecular
Biology
},
author = {Zoya Ignatova},
year = 2023,
url = {https://www.chemie.uni-hamburg.de/institute/bc/arbeitsgruppen/ignatova.html},
note = {Accessed: 20 August 2024},
institution = {University of Hamburg}
author = {Zoya Ignatova},
title = {Research Group Ignatova at the Institute of Biochemistry and Molecular Biology},
year = {2023},
howpublished = {\url{https://www.chemie.uni-hamburg.de/institute/bc/arbeitsgruppen/ignatova.html}},
note = {Accessed: 28 September 2024},
institution = {University of Hamburg},
}
new10.
@book{Mennella_2024,
title = {Cilia: methods and protocols},
year = 2024,
author = {Mennella, Vito},
publisher = {Humana Press},
address = {New York, NY},
isbn = {978-1-07-163507-0},
......
......@@ -14,3 +14,154 @@
{/*<!-- Citation num 2--> */}
<li typeof="schema:Book" role="doc-biblioentry" property="schema:citation" id="desc-2">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Dallas, M.</span>
<span property="schema:Name"> Bell, D.</span>
</span>
<span property="schema:name">&nbsp;Patch clamp electrophysiology: methods and protocols.</span>
<i property="schema:publisher" typeof="schema:Organization">&nbsp;Humana Press</i>
&nbsp;(<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2021">2021</time>).
</li>
{/*<!-- Citation num 3--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-3">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Priel, A.</span>
<span property="schema:Name"> Gil, Z.</span>
<span property="schema:Name"> Moy, V. T.</span>
<span property="schema:Name"> Magleby, K. L.</span>
<span property="schema:Name"> Silberberg, S. D.</span>
</span>
<span property="schema:name">&nbsp;
Ionic Requirements for Membrane-Glass Adhesion and Giga Seal Formation in
Patch-Clamp Recording
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Biophysical Journal</i>
<b property="issueNumber" typeof="PublicationIssue"> 92</b>
,&nbsp;<span property="schema:pageBegin"> 3893</span>-<span property="schema:pageEnd">3900</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2007">2007</time>).
<a className="doi" href="https://doi.org/10.1529/biophysj.106.099119"> doi: 10.1529/biophysj.106.099119</a>
</li>
{/*<!-- Citation num 4--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-4">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Billet, A.</span>
<span property="schema:Name"> Froux, L.</span>
<span property="schema:Name"> Hanrahan, J. W.</span>
<span property="schema:Name"> Becq, F.</span>
</span>
<span property="schema:name">&nbsp;
Development of Automated Patch Clamp Technique to Investigate CFTR Chloride
Channel Function
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Frontiers in Pharmacology</i>
<b property="issueNumber" typeof="PublicationIssue"> 8</b>
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2017">2017</time>).
<a className="doi" href="https://doi.org/10.3389/fphar.2017.00195"> doi: 10.3389/fphar.2017.00195</a>
</li>
{/*<!-- Citation num 5--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-5">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> DuBridge, R. B.</span>
<span property="schema:Name"> Tang, P.</span>
<span property="schema:Name"> Hsia, H. C.</span>
<span property="schema:Name"> Leong, P. M.</span>
<span property="schema:Name"> Miller, J. H.</span>
<span property="schema:Name"> Calos, M. P.</span>
</span>
<span property="schema:name">&nbsp;
Analysis of mutation in human cells by using an Epstein-Barr virus shuttle
system.
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Molecular and Cellular Biology</i>
<b property="issueNumber" typeof="PublicationIssue"> 7</b>
,&nbsp;<span property="schema:pageBegin"> 379</span>-<span property="schema:pageEnd">387</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 1987">1987</time>).
</li>
{/*<!-- Citation num 6--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-6">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Qin, J. Y.</span>
<span property="schema:Name"> Zhang, L.</span>
<span property="schema:Name"> Clift, K. L.</span>
<span property="schema:Name"> Hulur, I.</span>
<span property="schema:Name"> Xiang, A. P.</span>
<span property="schema:Name"> Ren, B.</span>
<span property="schema:Name"> Lahn, B. T.</span>
</span>
<span property="schema:name">&nbsp;
Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible
Promoter
</span>.
<i property="schema:publisher" typeof="schema:Organization"> PLOS ONE</i>
<b property="issueNumber" typeof="PublicationIssue"> 5</b>
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2010">2010</time>).
<a className="doi" href="https://doi.org/10.1371/journal.pone.0010611"> doi: 10.1371/journal.pone.0010611</a>
</li>
{/*<!-- Citation num 7--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-7">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Bulcaen, M.</span>
<span property="schema:Name"> Kortleven, P.</span>
<span property="schema:Name"> Liu, R. B.</span>
<span property="schema:Name"> Maule, G.</span>
<span property="schema:Name"> Dreano, E.</span>
<span property="schema:Name"> Kelly, M.</span>
<span property="schema:Name"> Ensinck, M. M.</span>
<span property="schema:Name"> et al.</span>
</span>
<span property="schema:name">&nbsp;Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells</span>.
<i property="schema:publisher" typeof="schema:Organization"> Cell Reports Medicine</i>
<b property="issueNumber" typeof="PublicationIssue"> 5</b>
<span property="schema:pageBegin">101544</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2024">2024</time>).
<a className="doi" href="https://doi.org/https://doi.org/10.1016/j.xcrm.2024.101544"> doi: https://doi.org/10.1016/j.xcrm.2024.101544</a>
</li>
{/*<!-- Citation num 8--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-8">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Ensinck, M.</span>
<span property="schema:Name"> De Keersmaecker, L.</span>
<span property="schema:Name"> Heylen, L.</span>
<span property="schema:Name"> Ramalho, A. S.</span>
<span property="schema:Name"> Gijsbers, R.</span>
<span property="schema:Name"> Farré, R.</span>
<span property="schema:Name"> De Boeck, K.</span>
<span property="schema:Name"> et al.</span>
</span>
<span property="schema:name">&nbsp;
Phenotyping of Rare CFTR Mutations Reveals Distinct Trafficking and
Functional Defects
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Cells</i>
<b property="issueNumber" typeof="PublicationIssue"> 9</b>
<span property="schema:pageBegin">754</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2020">2020</time>).
<a className="doi" href="https://doi.org/10.3390/cells9030754"> doi: 10.3390/cells9030754</a>
</li>
{/*<!-- Citation num 9--> */}
<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-9">
<span property="schema:author" typeof="schema:Organisation">
<span property="schema:Name"> Zoya Ignatova</span>.
</span>
<span property="schema:name">Research Group Ignatova at the Institute of Biochemistry and Molecular Biology.</span>
<i property="schema:publisher" typeof="schema:Organization">\url{https://www.chemie.uni-hamburg.de/institute/bc/arbeitsgruppen/ignatova.html}</i>
&nbsp;(<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2023">2023</time>).
</li>
{/*<!-- Citation num 10--> */}
<li typeof="schema:Book" role="doc-biblioentry" property="schema:citation" id="desc-10">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Mennella, V.</span>
</span>
<span property="schema:name">&nbsp;Cilia: methods and protocols.</span>
<i property="schema:publisher" typeof="schema:Organization">&nbsp;Humana Press</i>
&nbsp;(<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2024">2024</time>).
</li>
import * as BibtexParser from 'bibtex-parser-js';
interface BibTexEntry {
author: string;
title: string;
year: string;
url?: string;
note?: string;
institution?: string;
howpublished?: string;
}
export function Sources{
}
......@@ -96,7 +96,174 @@ export function Methods() {
</Section>
<Section title="References" id="References">
<ol>
{/*<!-- Citation num 1--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-1">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Roth, F. C.</span>
<span property="schema:Name"> Draguhn, A.</span>
</span>
<span property="schema:name">&nbsp;Die Entwicklung der Patch-Clamp-Technik</span>.
<i property="schema:publisher" typeof="schema:Organization"> Springer eBooks</i>
<b property="issueNumber" typeof="PublicationIssue"> </b>
,&nbsp;<span property="schema:pageBegin"> 1</span>-<span property="schema:pageEnd">14</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2023">2023</time>).
<a className="doi" href="https://doi.org/10.1007/978-3-662-66053-9"> doi: 10.1007/978-3-662-66053-9</a>
</li>
{/*<!-- Citation num 2--> */}
<li typeof="schema:Book" role="doc-biblioentry" property="schema:citation" id="desc-2">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Dallas, M.</span>
<span property="schema:Name"> Bell, D.</span>
</span>
<span property="schema:name">&nbsp;Patch clamp electrophysiology: methods and protocols.</span>
<i property="schema:publisher" typeof="schema:Organization">&nbsp;Humana Press</i>
&nbsp;(<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2021">2021</time>).
</li>
{/*<!-- Citation num 3--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-3">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Priel, A.</span>
<span property="schema:Name"> Gil, Z.</span>
<span property="schema:Name"> Moy, V. T.</span>
<span property="schema:Name"> Magleby, K. L.</span>
<span property="schema:Name"> Silberberg, S. D.</span>
</span>
<span property="schema:name">&nbsp;
Ionic Requirements for Membrane-Glass Adhesion and Giga Seal Formation in
Patch-Clamp Recording
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Biophysical Journal</i>
<b property="issueNumber" typeof="PublicationIssue"> 92</b>
,&nbsp;<span property="schema:pageBegin"> 3893</span>-<span property="schema:pageEnd">3900</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2007">2007</time>).
<a className="doi" href="https://doi.org/10.1529/biophysj.106.099119"> doi: 10.1529/biophysj.106.099119</a>
</li>
{/*<!-- Citation num 4--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-4">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Billet, A.</span>
<span property="schema:Name"> Froux, L.</span>
<span property="schema:Name"> Hanrahan, J. W.</span>
<span property="schema:Name"> Becq, F.</span>
</span>
<span property="schema:name">&nbsp;
Development of Automated Patch Clamp Technique to Investigate CFTR Chloride
Channel Function
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Frontiers in Pharmacology</i>
<b property="issueNumber" typeof="PublicationIssue"> 8</b>
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2017">2017</time>).
<a className="doi" href="https://doi.org/10.3389/fphar.2017.00195"> doi: 10.3389/fphar.2017.00195</a>
</li>
{/*<!-- Citation num 5--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-5">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> DuBridge, R. B.</span>
<span property="schema:Name"> Tang, P.</span>
<span property="schema:Name"> Hsia, H. C.</span>
<span property="schema:Name"> Leong, P. M.</span>
<span property="schema:Name"> Miller, J. H.</span>
<span property="schema:Name"> Calos, M. P.</span>
</span>
<span property="schema:name">&nbsp;
Analysis of mutation in human cells by using an Epstein-Barr virus shuttle
system.
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Molecular and Cellular Biology</i>
<b property="issueNumber" typeof="PublicationIssue"> 7</b>
,&nbsp;<span property="schema:pageBegin"> 379</span>-<span property="schema:pageEnd">387</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 1987">1987</time>).
</li>
{/*<!-- Citation num 6--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-6">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Qin, J. Y.</span>
<span property="schema:Name"> Zhang, L.</span>
<span property="schema:Name"> Clift, K. L.</span>
<span property="schema:Name"> Hulur, I.</span>
<span property="schema:Name"> Xiang, A. P.</span>
<span property="schema:Name"> Ren, B.</span>
<span property="schema:Name"> Lahn, B. T.</span>
</span>
<span property="schema:name">&nbsp;
Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible
Promoter
</span>.
<i property="schema:publisher" typeof="schema:Organization"> PLOS ONE</i>
<b property="issueNumber" typeof="PublicationIssue"> 5</b>
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2010">2010</time>).
<a className="doi" href="https://doi.org/10.1371/journal.pone.0010611"> doi: 10.1371/journal.pone.0010611</a>
</li>
{/*<!-- Citation num 7--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-7">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Bulcaen, M.</span>
<span property="schema:Name"> Kortleven, P.</span>
<span property="schema:Name"> Liu, R. B.</span>
<span property="schema:Name"> Maule, G.</span>
<span property="schema:Name"> Dreano, E.</span>
<span property="schema:Name"> Kelly, M.</span>
<span property="schema:Name"> Ensinck, M. M.</span>
<span property="schema:Name"> et al.</span>
</span>
<span property="schema:name">&nbsp;Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells</span>.
<i property="schema:publisher" typeof="schema:Organization"> Cell Reports Medicine</i>
<b property="issueNumber" typeof="PublicationIssue"> 5</b>
<span property="schema:pageBegin">101544</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2024">2024</time>).
<a className="doi" href="https://doi.org/https://doi.org/10.1016/j.xcrm.2024.101544"> doi: https://doi.org/10.1016/j.xcrm.2024.101544</a>
</li>
{/*<!-- Citation num 8--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-8">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Ensinck, M.</span>
<span property="schema:Name"> De Keersmaecker, L.</span>
<span property="schema:Name"> Heylen, L.</span>
<span property="schema:Name"> Ramalho, A. S.</span>
<span property="schema:Name"> Gijsbers, R.</span>
<span property="schema:Name"> Farré, R.</span>
<span property="schema:Name"> De Boeck, K.</span>
<span property="schema:Name"> et al.</span>
</span>
<span property="schema:name">&nbsp;
Phenotyping of Rare CFTR Mutations Reveals Distinct Trafficking and
Functional Defects
</span>.
<i property="schema:publisher" typeof="schema:Organization"> Cells</i>
<b property="issueNumber" typeof="PublicationIssue"> 9</b>
<span property="schema:pageBegin">754</span>&nbsp;
(<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2020">2020</time>).
<a className="doi" href="https://doi.org/10.3390/cells9030754"> doi: 10.3390/cells9030754</a>
</li>
{/*<!-- Citation num 9--> */}
<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-9">
<span property="schema:author" typeof="schema:Organisation">
<span property="schema:Name"> Zoya Ignatova</span>.
</span>
<span property="schema:name">Research Group Ignatova at the Institute of Biochemistry and Molecular Biology.</span>
<i property="schema:publisher" typeof="schema:Organization">Hamburg University</i>
&nbsp;(<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2023">2023</time>).
</li>
{/*<!-- Citation num 10--> */}
<li typeof="schema:Book" role="doc-biblioentry" property="schema:citation" id="desc-10">
<span property="schema:author" typeof="schema:Person">
<span property="schema:Name"> Mennella, V.</span>
</span>
<span property="schema:name">&nbsp;Cilia: methods and protocols.</span>
<i property="schema:publisher" typeof="schema:Organization">&nbsp;Humana Press</i>
&nbsp;(<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2024">2024</time>).
</li>
</ol>
</Section>
......
......@@ -5,6 +5,7 @@
"lib": ["ES2020", "DOM", "DOM.Iterable"],
"module": "ESNext",
"skipLibCheck": true,
"noImplicitAny": false,
/* Bundler mode */
"moduleResolution": "bundler",
......
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