From 74e55ab3f2639a2e5522d559f2c770b06c38e470 Mon Sep 17 00:00:00 2001
From: Liliana Sanfilippo <liliana.sanfilippo@uni-bielefeld.de>
Date: Thu, 26 Sep 2024 10:03:53 +0200
Subject: [PATCH] cit
---
code/cit.py | 49 ++--
code/output.txt | 436 +++++++++++++++++++++++++++-
code/safety-bibtex.bib | 645 +++++++++++++++++++++++++++++++++++++++++
3 files changed, 1108 insertions(+), 22 deletions(-)
create mode 100644 code/safety-bibtex.bib
diff --git a/code/cit.py b/code/cit.py
index 301908a7..900293a0 100644
--- a/code/cit.py
+++ b/code/cit.py
@@ -64,27 +64,29 @@ def main():
en_x = library.entries[x]
print("Filling dictionary for entry "+ str(startnum+count) + "")
- # Direkt auf die Einträge zugreifen, da es sich um ein Dictionary handelt
+
for key, value in en_x.items():
key_low = key.lower()
dictio[key_low] = value
- # Überprüfung auf den Typ des Eintrags über 'ENTRYTYPE'
+ print("Checking Entry type of "+ str(startnum+count) + "")
if en_x['ENTRYTYPE'] == "article":
articleHTML(dictio, (startnum+count), out)
elif en_x['ENTRYTYPE'] == "misc":
miscHTML(dictio, (startnum+count), out)
elif en_x['ENTRYTYPE'] == "book":
bookHTML(dictio, (startnum+count), out)
+ elif en_x['ENTRYTYPE'] == "inbook":
+ bookHTML(dictio, (startnum+count), out)
count += 1;
except Exception as e:
- print(f"An unexpected error occurred: {e}")
+ print(f"An unexpected error occurred: {e} in line 83")
except Exception as e:
- print(f"An unexpected error occurred: {e}")
+ print(f"An unexpected error occurred: {e} in line 85")
except FileNotFoundError:
- print(f"Error: The file '{args.input}' was not found.")
+ print(f"Error: The file '{args.input}' was not found. line 87")
if len(problemlist)>0:
print("- - - - - - - - - - - - - - - - - ")
print("REMAINING ERRORS:")
@@ -103,22 +105,26 @@ def articleHTML(dictio, x, out):
out.write("<li typeof=\"schema:ScolarlyArticle\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x) + "\">"+ "\n")
out.write("\t" + "<span property=\"schema:author\" typeof=\"schema:Person\">"+ "\n")
- print("Just a sec, seperating authors...")
+ print("Just a sec, separating authors...")
authors = dictio['author']
authors = authors.replace(" and ", "|")
liste = authors.split("|")
for a in liste:
try:
- #print("processing " + a)
first = None
last = None
name = None
if ',' in a:
s = a.split(", ")
- first = s[1]
- first_sh = first[0]
- last = s[0]
- name = last + ", " + first_sh + "."
+ if len(s) > 1:
+ first = s[1]
+ first_sh = first[0]
+ last = s[0]
+ name = last + ", " + first_sh + "."
+ else:
+ # Falls es nur einen Nachnamen gibt
+ last = s[0]
+ name = last + ", "
else:
s = a.split()
if len(s) == 2:
@@ -130,17 +136,17 @@ def articleHTML(dictio, x, out):
leng = len(s)
last = s[leng-1]
first = ''
- for n in s:
- if n != s[-1]:
- first = first + n[0] + '.'
- name = last + ", " + first
+ for n in s[:-1]: # Alle bis auf den letzten Namen
+ first += n[0] + '.'
+ name = last + ", " + first
if a == liste[-1]:
- out.write("\t" + "\t" +"<span property=\"schema:Name\"> " +name + "</span>"+ "\n")
+ out.write("\t" + "\t" + "<span property=\"schema:Name\"> " + name + "</span>" + "\n")
else:
- out.write("\t" +"\t" +"<span property=\"schema:Name\"> " +name + "</span>;"+ "\n")
+ out.write("\t" + "\t" + "<span property=\"schema:Name\"> " + name + "</span>;" + "\n")
except Exception as e:
print(f"An unexpected error occurred: {e} see " + a)
+
out.write("\t" +"</span>"+ "\n")
out.write("\t" + "<span property=\"schema:name\"> "+dictio['title']+ ". </span>"+ "\n")
out.write("\t" +"<i property=\"schema:publisher\" typeof=\"schema:Organization\"> "+ dictio['journal'] +"</i>"+ "\n")
@@ -210,7 +216,14 @@ def bookHTML(dictio, x, out):
aut = dictio['author']
out.write("\t" + "\t" +"<span property=\"schema:Name\"> " + aut + "</span>."+ "\n")
out.write("\t" +"</span>"+ "\n")
- out.write("\t" + "<span property=\"schema:name\"> "+dictio['title']+ ".</span>"+ "\n")
+ if 'title' in dictio:
+ out.write("\t" + "<span property=\"schema:name\"> "+dictio['title']+ ".</span>"+ "\n")
+ elif 'booktitle' in dictio:
+ out.write("\t" + "<span property=\"schema:name\"> "+dictio['booktitle']+ ".</span>"+ "\n")
+ else:
+ print(f"No title or booktitle found for entry {x}")
+ problemlist.append(f"Check for missing title or booktitle at entry {x}")
+
out.write("\t" +"<i property=\"schema:publisher\" typeof=\"schema:Organization\"> "+ dictio['publisher'] +"</i>"+ "\n")
year = dictio['year']
out.write("\t" + " (<time property=\"schema:datePublished\" datatype=\"xsd:gYear\" dateTime=\"" + year + "\">"+year+"</time>)."+ "\n")
diff --git a/code/output.txt b/code/output.txt
index c7503f22..e515e341 100644
--- a/code/output.txt
+++ b/code/output.txt
@@ -1,15 +1,20 @@
{/*<!-- 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"> Cloarec-Ung, F.</span>;
+ <span property="schema:Name">
+Cloarec-Ung, F.</span>;
<span property="schema:Name"> Beaulieu, J.</span>;
<span property="schema:Name"> Suthananthan, A.</span>;
- <span property="schema:Name"> Lehnertz, B.</span>;
<span property="schema:Name"> Sauvageau, G.</span>;
<span property="schema:Name"> Sheppard, H.</span>;
- <span property="schema:Name"> Knapp, D.</span>
+ <span property="schema:Name"> Knapp,
+David J. H. F.
+, </span>
</span>
- <span property="schema:name"> Near-perfect precise on-target editing of human hematopoietic stem and progenitor cells. </span>
+ <span property="schema:name">
+Near-perfect precise on-target editing of human hematopoietic stem and
+progenitor cells
+. </span>
<i property="schema:publisher" typeof="schema:Organization"> eLife</i>
<b property="issueNumber" typeof="PublicationIssue"> 12</b>,
<span property="schema:pageBegin">RP91288</span>
@@ -20,3 +25,426 @@
{/*<!-- Citation num 2--> */}
<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-2">
<span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name">
+Nelson, J.</span>;
+ <span property="schema:Name"> Randolph, P.</span>;
+ <span property="schema:Name"> Shen, S.</span>;
+ <span property="schema:Name"> Everette,
+Kelcee A., </span>;
+ <span property="schema:Name"> Chen, P.</span>;
+ <span property="schema:Name"> Anzalone, A.</span>;
+ <span property="schema:Name"> An, M.</span>;
+ <span property="schema:Name"> Chen, J.</span>;
+ <span property="schema:Name"> Hsu, A.</span>;
+ <span property="schema:Name"> Liu, D.</span>
+ </span>
+ <span property="schema:name"> Engineered pegRNAs improve prime editing efficiency. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Nature Biotechnology</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 40</b>,
+ <span property="schema:pageBegin">402–410</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2022">2022</time>).
+ <a className="doi" href="https://doi.org/10.1038/s41587-021-01039-7"> doi: 10.1038/s41587-021-01039-7</a>
+</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">
+Doench, J.</span>;
+ <span property="schema:Name"> Fusi, N.</span>;
+ <span property="schema:Name"> Sullender, M.</span>;
+ <span property="schema:Name"> Hegde, M.</span>;
+ <span property="schema:Name"> Donovan, K.</span>;
+ <span property="schema:Name"> Smith, I.</span>;
+ <span property="schema:Name"> Tothova,
+Zuzana, </span>;
+ <span property="schema:Name"> Wilen, C.</span>;
+ <span property="schema:Name"> Orchard, R.</span>;
+ <span property="schema:Name"> Virgin, H.</span>;
+ <span property="schema:Name"> Root, D.</span>
+ </span>
+ <span property="schema:name">
+Optimized sgRNA design to maximize activity and minimize off-target effects
+of CRISPR-Cas9
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Nature Biotechnology</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 34</b>,
+ <span property="schema:pageBegin">184–191</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2016">2016</time>).
+ <a className="doi" href="https://doi.org/10.1038/nbt.3437"> doi: 10.1038/nbt.3437</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">
+White, N.</span>;
+ <span property="schema:Name"> Sadeeshkumar, H.</span>;
+ <span property="schema:Name"> Sun, A.</span>;
+ <span property="schema:Name"> Sudarsan, N.</span>
+ </span>
+ <span property="schema:name">
+Na+ riboswitches regulate genes for diverse physiological processes in
+bacteria
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Nature Chemical Biology</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 18</b>,
+ <span property="schema:pageBegin">878–885</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2022">2022</time>).
+ <a className="doi" href="https://doi.org/10.1038/s41589-022-01086-4"> doi: 10.1038/s41589-022-01086-4</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"> Iwawaki, T.</span>;
+ <span property="schema:Name"> Akai, R.</span>
+ </span>
+ <span property="schema:name">
+Analysis of the XBP1 splicing mechanism using endoplasmic reticulum
+stress-indicators
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Biochemical and Biophysical Research Communications</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 350</b>,
+ <span property="schema:pageBegin">709–715</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2006">2006</time>).
+ <a className="doi" href="https://doi.org/10.1016/j.bbrc.2006.09.100"> doi: 10.1016/j.bbrc.2006.09.100</a>
+</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">
+Zhang, Y.</span>;
+ <span property="schema:Name"> Lin, S.</span>;
+ <span property="schema:Name"> Yao, J.</span>;
+ <span property="schema:Name"> Cai, W.</span>;
+ <span property="schema:Name"> Chen, H.</span>;
+ <span property="schema:Name"> Wang, Z.</span>;
+ <span property="schema:Name"> Song, W.</span>
+ </span>
+ <span property="schema:name">
+XBP1 splicing contributes to endoplasmic reticulum stress-induced human islet
+amyloid polypeptide up-regulation
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Genes & Diseases</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 11</b>,
+ <span property="schema:pageBegin">101148</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2023">2023</time>).
+ <a className="doi" href="https://doi.org/10.1016/j.gendis.2023.101148"> doi: 10.1016/j.gendis.2023.101148</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">
+Wei, T.</span>;
+ <span property="schema:Name"> Sun, Y.</span>;
+ <span property="schema:Name"> Cheng, Q.</span>;
+ <span property="schema:Name"> Chatterjee, S.</span>;
+ <span property="schema:Name"> Traylor,
+Zachary, </span>;
+ <span property="schema:Name"> Johnson, L.</span>;
+ <span property="schema:Name"> Coquelin, M.</span>;
+ <span property="schema:Name"> Wang, J.</span>;
+ <span property="schema:Name"> Lian, X.</span>;
+ <span property="schema:Name"> Wang, X.</span>;
+ <span property="schema:Name"> Xiao, Y.</span>;
+ <span property="schema:Name"> Hodges,
+Craig A., </span>;
+ <span property="schema:Name"> Siegwart, D.</span>
+ </span>
+ <span property="schema:name">
+Lung {SORT} {LNPs} enable precise homology-directed repair mediated
+{CRISPR}/{Cas} genome correction in cystic fibrosis models
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Nature Communications</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 14</b>,
+ <span property="schema:pageBegin">7322</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2023">2023</time>).
+ <a className="doi" href="https://doi.org/10.1038/s41467-023-42948-2"> doi: 10.1038/s41467-023-42948-2</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"> Ibrahim, M.</span>;
+ <span property="schema:Name"> Ramadan, E.</span>;
+ <span property="schema:Name"> Elsadek, N.E.</span>;
+ <span property="schema:Name"> Shimizu, S.E.E.a.T.</span>;
+ <span property="schema:Name"> Ando, H.</span>;
+ <span property="schema:Name"> Ishima, Y.</span>;
+ <span property="schema:Name"> Elgarhy, O.H.</span>;
+ <span property="schema:Name"> Sarhan, H.A.</span>;
+ <span property="schema:Name"> Hussein, A.K.</span>;
+ <span property="schema:Name"> Ishida, T.</span>
+ </span>
+ <span property="schema:name">
+Polyethylene glycol (PEG): The nature, immunogenicity, and role in the
+hypersensitivity of PEGylated products
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Journal of Controlled Release</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 351</b>,
+ <span property="schema:pageBegin"> 215</span>-<span property="schema:pageEnd">230</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2022">2022</time>).
+ <a className="doi" href="https://doi.org/https://doi.org/10.1016/j.jconrel.2022.09.031"> doi: https://doi.org/10.1016/j.jconrel.2022.09.031</a>
+</li>
+
+{/*<!-- Citation num 9--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-9">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name">
+Jiang, A.</span>;
+ <span property="schema:Name"> Witten, J.</span>;
+ <span property="schema:Name"> Raji, I.</span>;
+ <span property="schema:Name"> Eweje, F.</span>;
+ <span property="schema:Name"> Meng, S.</span>;
+ <span property="schema:Name"> Oladimeji, F.</span>;
+ <span property="schema:Name"> Hu, Y.</span>;
+ <span property="schema:Name"> Langer, R.</span>;
+ <span property="schema:Name"> Anderson, D.</span>
+ </span>
+ <span property="schema:name">
+Combinatorial development of nebulized {mRNA} delivery formulations for the
+lungs
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Nature Nanotechnology</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 19</b>,
+ <span property="schema:pageBegin"> 364</span>-<span property="schema:pageEnd">375</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2024">2024</time>).
+ <a className="doi" href="https://doi.org/10.1038/s41565-023-01548-3"> doi: 10.1038/s41565-023-01548-3</a>
+</li>
+
+{/*<!-- Citation num 10--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-10">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name">
+Vilà -González, M.</span>;
+ <span property="schema:Name"> Pinte, L.</span>;
+ <span property="schema:Name"> Fradique, R.</span>;
+ <span property="schema:Name"> Causa,
+Erika, </span>;
+ <span property="schema:Name"> Kool, H.</span>;
+ <span property="schema:Name"> Rodrat, M.</span>;
+ <span property="schema:Name"> Morell, C.</span>;
+ <span property="schema:Name"> Porter, L.</span>;
+ <span property="schema:Name"> Guo, W.</span>;
+ <span property="schema:Name"> Maeshima, R.</span>;
+ <span property="schema:Name"> McCaughan, F.</span>;
+ <span property="schema:Name"> Granata, A.</span>;
+ <span property="schema:Name"> Sheppard,
+David N., </span>;
+ <span property="schema:Name"> Floto, R.</span>;
+ <span property="schema:Name"> Rawlins, E.</span>;
+ <span property="schema:Name"> Cicuta, P.</span>
+ </span>
+ <span property="schema:name">
+In vitro platform to model the function of ionocytes in the human airway
+epithelium
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Respiratory Research</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 25</b>,
+ <span property="schema:pageBegin">180</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2024">2024</time>).
+ <a className="doi" href="https://doi.org/10.1186/s12931-024-02800-7"> doi: 10.1186/s12931-024-02800-7</a>
+</li>
+
+{/*<!-- Citation num 11--> */}
+<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-11">
+ <span property="schema:author" typeof="schema:Organisation">
+ <span property="schema:Name"> Paris, Katherine</span>.
+ </span>
+ <span property="schema:name"> Genome Editing and Biological Weapons: Assessing the Risk of Misuse.</span>
+ <i property="schema:publisher" typeof="schema:Organization"> Springer Nature Switzerland AG</i>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2023">2023</time>).
+</li>
+
+{/*<!-- Citation num 12--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-12">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name"> Wickiser, J.</span>
+ </span>
+ <span property="schema:name">
+The democratization of biology: how CRISPR and synthetic biology usher in new
+biosecurity threats
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Defense Horizons</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 85</b>,
+ <span property="schema:pageBegin"> 1</span>-<span property="schema:pageEnd">16</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2020">2020</time>).
+</li>
+
+{/*<!-- Citation num 13--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-13">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name"> Cohen, J.</span>;
+ <span property="schema:Name"> Desai, T.</span>
+ </span>
+ <span property="schema:name">
+Security implications of CRISPR-enabled genome editing: New weapons of mass
+disruption?
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Journal of Bioethical Inquiry</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 16</b>,
+ <span property="schema:pageBegin"> 219</span>-<span property="schema:pageEnd">228</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2019">2019</time>).
+ <a className="doi" href="https://doi.org/10.1007/s11673-019-09914-5"> doi: 10.1007/s11673-019-09914-5</a>
+</li>
+
+{/*<!-- Citation num 14--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-14">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name"> Doudna, J.</span>;
+ <span property="schema:Name"> Charpentier, E.</span>
+ </span>
+ <span property="schema:name">
+The rise of synthetic biology: New biosecurity risks and regulatory
+challenges
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Nature Reviews Genetics</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 21</b>,
+ <span property="schema:pageBegin"> 144</span>-<span property="schema:pageEnd">156</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2020">2020</time>).
+ <a className="doi" href="https://doi.org/10.1038/s41576-019-0182-7"> doi: 10.1038/s41576-019-0182-7</a>
+</li>
+
+{/*<!-- Citation num 15--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-15">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name"> Shwartz, M.</span>;
+ <span property="schema:Name"> Conklin, B.</span>
+ </span>
+ <span property="schema:name">
+Public perception of CRISPR and genome editing: Misconceptions and media
+portrayal
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Journal of Science Communication</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 18</b>,
+ <span property="schema:pageBegin">A02</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2019">2019</time>).
+ <a className="doi" href="https://doi.org/10.22323/2.18040202"> doi: 10.22323/2.18040202</a>
+</li>
+
+{/*<!-- Citation num 16--> */}
+<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-16">
+ <span property="schema:author" typeof="schema:Organisation">
+ <span property="schema:Name"> Chadwick, Ruth F.</span>.
+ </span>
+ <span property="schema:name"> Encyclopedia of applied ethics.</span>
+ <i property="schema:publisher" typeof="schema:Organization"> Academic Press</i>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2012">2012</time>).
+</li>
+
+{/*<!-- Citation num 17--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-17">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name"> Rubeis, G.</span>;
+ <span property="schema:Name"> Steger, F.</span>
+ </span>
+ <span property="schema:name"> Risks and benefits of human germline genome editing: An ethical analysis. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Asian Bioethics Review</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 10</b>,
+ <span property="schema:pageBegin">133–141</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2018">2018</time>).
+ <a className="doi" href="https://doi.org/10.1007/s41649-018-0056-x"> doi: 10.1007/s41649-018-0056-x</a>
+</li>
+
+{/*<!-- Citation num 18--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-18">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name"> Ansah, E.</span>
+ </span>
+ <span property="schema:name">
+Ethical Challenges and Controversies in the Practice and Advancement of Gene
+Therapy
+. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Advances in Cell and Gene Therapy</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 2022</b>,
+ <span property="schema:pageBegin">1–5</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2022">2022</time>).
+ <a className="doi" href="https://doi.org/10.1155/2022/1015996"> doi: 10.1155/2022/1015996</a>
+</li>
+
+{/*<!-- Citation num 19--> */}
+<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-19">
+ <span property="schema:author" typeof="schema:Organisation">
+ <span property="schema:Name"> Pugh, Jonathan</span>.
+ </span>
+ <span property="schema:name"> Autonomy, Rationality, and Contemporary Bioethics.</span>
+ <i property="schema:publisher" typeof="schema:Organization"> Oxford University PressOxford</i>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2020">2020</time>).
+</li>
+
+{/*<!-- Citation num 20--> */}
+<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-20">
+ <span property="schema:author" typeof="schema:Organisation">
+ <span property="schema:Name"> Gstraunthaler, Gerhard and Lindl, Toni</span>.
+ </span>
+ <span property="schema:name"> Allgemeine Aspekte der Primärkultur.</span>
+ <i property="schema:publisher" typeof="schema:Organization"> Springer</i>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2013">2013</time>).
+</li>
+
+{/*<!-- Citation num 21--> */}
+<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-21">
+ <span property="schema:author" typeof="schema:Organisation">
+ <span property="schema:Name"> Thiele, F.</span>.
+ </span>
+ <span property="schema:name"> International Encyclopedia of the Social & Behavioral Sciences.</span>
+ <i property="schema:publisher" typeof="schema:Organization"> Elsevier</i>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2001">2001</time>).
+</li>
+
+{/*<!-- Citation num 22--> */}
+<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-22">
+ <span property="schema:author" typeof="schema:Organisation">
+ <span property="schema:Name"> Gethmann, C.F.</span>.
+ </span>
+ <span property="schema:name"> Research: Ethical Aspects of Long-term Responsibilities.</span>
+ <i property="schema:publisher" typeof="schema:Organization"> Elsevier</i>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2001">2001</time>).
+</li>
+
+{/*<!-- Citation num 23--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-23">
+ <span property="schema:author" typeof="schema:Person">
+ <span property="schema:Name">
+Kiani, A.</span>;
+ <span property="schema:Name"> Pheby, D.</span>;
+ <span property="schema:Name"> Henehan, G.</span>;
+ <span property="schema:Name"> Brown, R.</span>;
+ <span property="schema:Name"> Sykora, P.</span>;
+ <span property="schema:Name"> Marks, R.</span>;
+ <span property="schema:Name"> Falsini, B.</span>;
+ <span property="schema:Name"> Miertus, S.</span>;
+ <span property="schema:Name"> Lorusso, L.</span>;
+ <span property="schema:Name"> Tartaglia, G.</span>;
+ <span property="schema:Name"> Ergoren, M.</span>;
+ <span property="schema:Name"> Dundar, M.</span>;
+ <span property="schema:Name"> Michelini, S.</span>;
+ <span property="schema:Name"> Malacarne, D.</span>;
+ <span property="schema:Name"> Dautaj, A.</span>;
+ <span property="schema:Name"> Donato, K.</span>;
+ <span property="schema:Name"> Medori, M.</span>;
+ <span property="schema:Name"> Beccari, T.</span>;
+ <span property="schema:Name"> Samaja, M.</span>;
+ <span property="schema:Name"> Connelly, S.</span>;
+ <span property="schema:Name"> Martin, D.</span>;
+ <span property="schema:Name"> Morresi, A.</span>;
+ <span property="schema:Name"> Bacu, A.</span>;
+ <span property="schema:Name"> Herbst,
+Karen L., </span>;
+ <span property="schema:Name"> Kapustin, M.</span>;
+ <span property="schema:Name"> Stuppia, L.</span>;
+ <span property="schema:Name"> Lumer, L.</span>;
+ <span property="schema:Name"> Bertelli, M.</span>;
+ <span property="schema:Name"> GROUP, I.B.S.</span>
+ </span>
+ <span property="schema:name"> Ethical considerations regarding animal experimentation. </span>
+ <i property="schema:publisher" typeof="schema:Organization"> Journal of Preventive Medicine and Hygiene</i>
+ <b property="issueNumber" typeof="PublicationIssue"> 63</b>,
+ <span property="schema:pageBegin">E255–E266</span>
+ (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2022">2022</time>).
+ <a className="doi" href="https://doi.org/10.15167/2421-4248/jpmh2022.63.2S3.2768"> doi: 10.15167/2421-4248/jpmh2022.63.2S3.2768</a>
+</li>
+
diff --git a/code/safety-bibtex.bib b/code/safety-bibtex.bib
new file mode 100644
index 00000000..b5a4e9c5
--- /dev/null
+++ b/code/safety-bibtex.bib
@@ -0,0 +1,645 @@
+@article{Cloarec-Ung_Beaulieu_Suthananthan_Lehnertz_Sauvageau_Sheppard_Knapp_2024,
+ title = {
+ Near-perfect precise on-target editing of human hematopoietic stem and
+ progenitor cells
+ },
+ author = {
+ Cloarec-Ung, Fanny-Mei and Beaulieu, Jamie and Suthananthan, Arunan and
+ Lehnertz, Bernhard and Sauvageau, Guy and Sheppard, Hilary M. and Knapp,
+ David J. H. F.
+ },
+ year = 2024,
+ month = jun,
+ journal = {eLife},
+ volume = 12,
+ pages = {RP91288},
+ doi = {10.7554/eLife.91288},
+ issn = {2050-084X},
+ abstractnote = {
+ Precision gene editing in primary hematopoietic stem and progenitor cells
+ (HSPCs) would facilitate both curative treatments for monogenic disorders as
+ well as disease modelling. Precise efficiencies even with the CRISPR/Cas
+ system, however, remain limited. Through an optimization of guide RNA
+ delivery, donor design, and additives, we have now obtained mean precise
+ editing efficiencies >90% on primary cord blood HSCPs with minimal toxicity
+ and without observed off-target editing. The main protocol modifications
+ needed to achieve such high efficiencies were the addition of the DNA-PK
+ inhibitor AZD7648, and the inclusion of spacer-breaking silent mutations in
+ the donor in addition to mutations disrupting the PAM sequence. Critically,
+ editing was even across the progenitor hierarchy, did not substantially
+ distort the hierarchy or affect lineage outputs in colony-forming cell assays
+ or the frequency of high self-renewal potential long-term culture initiating
+ cells. As modelling of many diseases requires heterozygosity, we also
+ demonstrated that the overall editing and zygosity can be tuned by adding in
+ defined mixtures of mutant and wild-type donors. With these optimizations,
+ editing at near-perfect efficiency can now be accomplished directly in human
+ HSPCs. This will open new avenues in both therapeutic strategies and disease
+ modelling.
+ },
+ language = {eng}
+}
+@article{Nelson_Randolph_Shen_Everette_Chen_Anzalone_An_Newby_Chen_Hsu_et,
+ title = {Engineered pegRNAs improve prime editing efficiency},
+ author = {
+ Nelson, James W. and Randolph, Peyton B. and Shen, Simon P. and Everette,
+ Kelcee A. and Chen, Peter J. and Anzalone, Andrew V. and An, Meirui and
+ Newby, Gregory A. and Chen, Jonathan C. and Hsu, Alvin and Liu, David R.
+ },
+ year = 2022,
+ month = mar,
+ journal = {Nature Biotechnology},
+ publisher = {Nature Publishing Group},
+ volume = 40,
+ number = 3,
+ pages = {402–410},
+ doi = {10.1038/s41587-021-01039-7},
+ issn = {1546-1696},
+ rights = {
+ 2021 The Author(s), under exclusive licence to Springer Nature America, Inc.
+ },
+ abstractnote = {
+ Prime editing enables the installation of virtually any combination of point
+ mutations, small insertions or small deletions in the DNA of living cells. A
+ prime editing guide RNA (pegRNA) directs the prime editor protein to the
+ targeted locus and also encodes the desired edit. Here we show that
+ degradation of the 3′ region of the pegRNA that contains the reverse
+ transcriptase template and the primer binding site can poison the activity of
+ prime editing systems, impeding editing efficiency. We incorporated
+ structured RNA motifs to the 3′ terminus of pegRNAs that enhance their
+ stability and prevent degradation of the 3′ extension. The resulting
+ engineered pegRNAs (epegRNAs) improve prime editing efficiency 3–4-fold in
+ HeLa, U2OS and K562 cells and in primary human fibroblasts without increasing
+ off-target editing activity. We optimized the choice of 3′ structural motif
+ and developed pegLIT, a computational tool to identify non-interfering
+ nucleotide linkers between pegRNAs and 3′ motifs. Finally, we showed that
+ epegRNAs enhance the efficiency of the installation or correction of
+ disease-relevant mutations.
+ },
+ language = {en}
+}
+@article{Doench_Fusi_Sullender_Hegde_Vaimberg_Donovan_Smith_Tothova_Wilen_Orchard_et,
+ title = {
+ Optimized sgRNA design to maximize activity and minimize off-target effects
+ of CRISPR-Cas9
+ },
+ author = {
+ Doench, John G. and Fusi, Nicolo and Sullender, Meagan and Hegde, Mudra and
+ Vaimberg, Emma W. and Donovan, Katherine F. and Smith, Ian and Tothova,
+ Zuzana and Wilen, Craig and Orchard, Robert and Virgin, Herbert W. and
+ Listgarten, Jennifer and Root, David E.
+ },
+ year = 2016,
+ month = feb,
+ journal = {Nature Biotechnology},
+ publisher = {Nature Publishing Group},
+ volume = 34,
+ number = 2,
+ pages = {184–191},
+ doi = {10.1038/nbt.3437},
+ issn = {1546-1696},
+ rights = {2015 Springer Nature America, Inc.},
+ abstractnote = {
+ Genome-wide sgRNA libraries based on rules for on-target activity improve
+ results of Cas9-based screens and facilitate a further refinement of on- and
+ off-target prediction algorithms.
+ },
+ language = {en}
+}
+@article{White_Sadeeshkumar_Sun_Sudarsan_Breaker_2022,
+ title = {
+ Na+ riboswitches regulate genes for diverse physiological processes in
+ bacteria
+ },
+ author = {
+ White, Neil and Sadeeshkumar, Harini and Sun, Anna and Sudarsan, Narasimhan
+ and Breaker, Ronald R.
+ },
+ year = 2022,
+ month = aug,
+ journal = {Nature Chemical Biology},
+ publisher = {Nature Publishing Group},
+ volume = 18,
+ number = 88,
+ pages = {878–885},
+ doi = {10.1038/s41589-022-01086-4},
+ issn = {1552-4469},
+ rights = {2022 The Author(s)},
+ abstractnote = {
+ Only one protein factor is known that senses Na+ and controls gene
+ expression. The Breaker Laboratory describes a bacterial riboswitch class
+ selective for Na+ that regulates genes important for Na+ homeostasis, pH
+ maintenance, osmotic stress response and ATP synthesis.
+ },
+ language = {en}
+}
+@article{Iwawaki_Akai_2006,
+ title = {
+ Analysis of the XBP1 splicing mechanism using endoplasmic reticulum
+ stress-indicators
+ },
+ author = {Iwawaki, Takao and Akai, Ryoko},
+ year = 2006,
+ month = nov,
+ journal = {Biochemical and Biophysical Research Communications},
+ volume = 350,
+ number = 3,
+ pages = {709–715},
+ doi = {10.1016/j.bbrc.2006.09.100},
+ issn = {0006-291X},
+ abstractnote = {
+ Under endoplasmic reticulum (ER) stress conditions, XBP1 mRNA is processed by
+ unconventional splicing and translated into a functional transcription
+ factor. ER stress-specific XBP1 splicing is also known to be activated by
+ IRE1. However, many aspects of the molecular mechanism of XBP1 splicing
+ remain to be elucidated. We previously developed an indicator system that
+ enabled detection of XBP1 splicing using fluorescent proteins as the reporter
+ signals. Here, we use a modification of this method that employs modified ER
+ stress-indicators and mutant IRE1 in vivo and in vitro to analyze XBP1
+ splicing mechanisms. Our analyses suggest that the 506–579nt region of the
+ XBP1 mRNA is necessary and sufficient for XBP1 splicing, that XBP1 splicing
+ can occur in the cytoplasm, and that cleavage and ligation of XBP1 mRNA
+ during splicing may occur as a coupled reaction.
+ }
+}
+@article{Zhang_Lin_Yao_Cai_Chen_Aierken_Wang_Song_2023,
+ title = {
+ XBP1 splicing contributes to endoplasmic reticulum stress-induced human islet
+ amyloid polypeptide up-regulation
+ },
+ author = {
+ Zhang, Yun and Lin, Susan and Yao, Jing and Cai, Wantong and Chen, Huaqiu and
+ Aierken, Ailikemu and Wang, Zhe and Song, Weihong
+ },
+ year = 2023,
+ month = oct,
+ journal = {Genes & Diseases},
+ volume = 11,
+ number = 5,
+ pages = 101148,
+ doi = {10.1016/j.gendis.2023.101148},
+ issn = {2352-4820},
+ abstractnote = {
+ As a pathological hallmark of type 2 diabetes mellitus (T2DM), islet amyloid
+ is formed by the aggregation of islet amyloid polypeptide (IAPP). Endoplasmic
+ reticulum (ER) stress interacts with IAPP aggregates and has been implicated
+ in the pathogenesis of T2DM. To examine the role of ER stress in T2DM, we
+ cloned the hIAPP promoter and analyzed its promoter activity in human
+ β-cells. We found that ER stress significantly enhanced hIAPP promoter
+ activity and expression in human β-cells via triggering X-box binding protein
+ 1 (XBP1) splicing. We identified a binding site of XBP1 in the hIAPP
+ promoter. Disruption of this binding site by substitution or deletion
+ mutagenesis significantly diminished the effects of ER stress on hIAPP
+ promoter activity. Blockade of XBP splicing by MKC3946 treatment inhibited ER
+ stress-induced hIAPP up-regulation and improved human β-cell survival and
+ function. Our study uncovers a link between ER stress and IAPP at the
+ transcriptional level and may provide novel insights into the role of ER
+ stress in IAPP cytotoxicity and the pathogenesis of T2DM.
+ }
+}
+@article{wei_lung_2023,
+ title = {
+ Lung {SORT} {LNPs} enable precise homology-directed repair mediated
+ {CRISPR}/{Cas} genome correction in cystic fibrosis models
+ },
+ author = {
+ Wei, Tuo and Sun, Yehui and Cheng, Qiang and Chatterjee, Sumanta and Traylor,
+ Zachary and Johnson, Lindsay T. and Coquelin, Melissa L. and Wang, Jialu and
+ Torres, Michael J. and Lian, Xizhen and Wang, Xu and Xiao, Yufen and Hodges,
+ Craig A. and Siegwart, Daniel J.
+ },
+ year = 2023,
+ month = nov,
+ journal = {Nature Communications},
+ volume = 14,
+ number = 1,
+ pages = 7322,
+ doi = {10.1038/s41467-023-42948-2},
+ issn = {2041-1723},
+ url = {https://www.nature.com/articles/s41467-023-42948-2},
+ urldate = {2024-04-16},
+ copyright = {2023 The Author(s)},
+ note = {Publisher: Nature Publishing Group},
+ abstract = {
+ Approximately 10\% of Cystic Fibrosis (CF) patients, particularly those with
+ CF transmembrane conductance regulator (CFTR) gene nonsense mutations, lack
+ effective treatments. The potential of gene correction therapy through
+ delivery of the CRISPR/Cas system to CF-relevant organs/cells is hindered by
+ the lack of efficient genome editor delivery carriers. Herein, we report
+ improved Lung Selective Organ Targeting Lipid Nanoparticles (SORT LNPs) for
+ efficient delivery of Cas9 mRNA, sgRNA, and donor ssDNA templates, enabling
+ precise homology-directed repair-mediated gene correction in CF models.
+ Optimized Lung SORT LNPs deliver mRNA to lung basal cells in Ai9 reporter
+ mice. SORT LNP treatment successfully corrected the CFTR mutations in
+ homozygous G542X mice and in patient-derived human bronchial epithelial cells
+ with homozygous F508del mutations, leading to the restoration of CFTR protein
+ expression and chloride transport function. This proof-of-concept study will
+ contribute to accelerating the clinical development of mRNA LNPs for CF
+ treatment through CRISPR/Cas gene correction.
+ },
+ language = {en},
+ keywords = {Biomedical engineering, CRISPR-Cas9 genome editing, Gene delivery}
+}
+8:
+@article{IBRAHIM2022215,
+ title = {
+ Polyethylene glycol (PEG): The nature, immunogenicity, and role in the
+ hypersensitivity of PEGylated products
+ },
+ author = {
+ Mohamed Ibrahim and Eslam Ramadan and Nehal E. Elsadek and Sherif E. Emam and
+ Taro Shimizu and Hidenori Ando and Yu Ishima and Omar Helmy Elgarhy and Hatem
+ A. Sarhan and Amal K. Hussein and Tatsuhiro Ishida
+ },
+ year = 2022,
+ journal = {Journal of Controlled Release},
+ volume = 351,
+ pages = {215--230},
+ doi = {https://doi.org/10.1016/j.jconrel.2022.09.031},
+ issn = {0168-3659},
+ url = {https://www.sciencedirect.com/science/article/pii/S0168365922006265},
+ keywords = {
+ Polyethylene glycol (PEG), anti-PEG antibodies, Hypersensitivity, COVID-19
+ mRNA vaccines, complement activation-related pseudoallergy (CARPA)
+ },
+ abstract = {
+ Polyethylene glycol (PEG) is a versatile polymer that is widely used as an
+ additive in foods and cosmetics, and as a carrier in PEGylated therapeutics.
+ Even though PEG is thought to be less immunogenic, or perhaps even
+ non-immunogenic, with a variety of physicochemical properties, there is
+ mounting evidence that PEG causes immunogenic responses when conjugated with
+ other materials such as proteins and nanocarriers. Under these conditions,
+ PEG with other materials can result in the production of anti-PEG antibodies
+ after administration. The antibodies that are induced seem to have a
+ deleterious impact on the therapeutic efficacy of subsequently administered
+ PEGylated formulations. In addition, hypersensitivity to PEGylated
+ formulations could be a significant barrier to the utility of PEGylated
+ products. Several reports have linked the presence of anti-PEG antibodies to
+ incidences of complement activation-related pseudoallergy (CARPA) following
+ the administration of PEGylated formulations. The use of COVID-19 mRNA
+ vaccines, which are composed mainly of PEGylated lipid nanoparticles (LNPs),
+ has recently gained wide acceptance, although many cases of post-vaccination
+ hypersensitivity have been documented. Therefore, our review focuses not only
+ on the importance of PEGs and its great role in improving the therapeutic
+ efficacy of various medications, but also on the hypersensitivity reactions
+ attributed to the use of PEGylated products that include PEG-based mRNA
+ COVID-19 vaccines.
+ }
+}
+9:
+@article{jiang_combinatorial_2024,
+ title = {
+ Combinatorial development of nebulized {mRNA} delivery formulations for the
+ lungs
+ },
+ author = {
+ Jiang, Allen Y. and Witten, Jacob and Raji, Idris O. and Eweje, Feyisayo and
+ MacIsaac, Corina and Meng, Sabrina and Oladimeji, Favour A. and Hu, Yizong
+ and Manan, Rajith S. and Langer, Robert and Anderson, Daniel G.
+ },
+ year = 2024,
+ month = mar,
+ journal = {Nature Nanotechnology},
+ volume = 19,
+ number = 3,
+ pages = {364--375},
+ doi = {10.1038/s41565-023-01548-3},
+ issn = {1748-3387, 1748-3395},
+ url = {https://www.nature.com/articles/s41565-023-01548-3},
+ urldate = {2024-09-10},
+ language = {en}
+}
+10:
+@article{vila-gonzalez_vitro_2024,
+ title = {
+ In vitro platform to model the function of ionocytes in the human airway
+ epithelium
+ },
+ author = {
+ Vilà -González, Marta and Pinte, Laetitia and Fradique, Ricardo and Causa,
+ Erika and Kool, Heleen and Rodrat, Mayuree and Morell, Carola Maria and
+ Al-Thani, Maha and Porter, Linsey and Guo, Wenrui and Maeshima, Ruhina and
+ Hart, Stephen L. and McCaughan, Frank and Granata, Alessandra and Sheppard,
+ David N. and Floto, R. Andres and Rawlins, Emma L. and Cicuta, Pietro and
+ Vallier, Ludovic
+ },
+ year = 2024,
+ month = apr,
+ journal = {Respiratory Research},
+ volume = 25,
+ number = 1,
+ pages = 180,
+ doi = {10.1186/s12931-024-02800-7},
+ issn = {1465-993X},
+ url = {
+ https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-024-02800-7
+ },
+ urldate = {2024-09-10},
+ abstract = {
+ Background  Pulmonary ionocytes have been identified in the airway epithelium
+ as a small population of ion transporting cells expressing high levels of
+ CFTR (cystic fibrosis transmembrane conductance regulator), the gene mutated
+ in cystic fibrosis. By providing an infinite source of airway epithelial
+ cells (AECs), the use of human induced pluripotent stem cells (hiPSCs) could
+ overcome some challenges of studying ionocytes. However, the production of
+ AEC epithelia containing ionocytes from hiPSCs has proven difficult. Here, we
+ present a platform to produce hiPSCderived AECs (hiPSC-AECs) including
+ ionocytes and investigate their role in the airway epithelium.
+
+ Methods  hiPSCs were differentiated into lung progenitors, which were
+ expanded as 3D organoids and matured by air-liquid interface culture as
+ polarised hiPSC-AEC epithelia. Using CRISPR/Cas9 technology, we generated a
+ hiPSCs knockout (KO) for FOXI1, a transcription factor that is essential for
+ ionocyte specification. Differences between FOXI1 KO hiPSC-AECs and their
+ wild-type (WT) isogenic controls were investigated by assessing gene and
+ protein expression, epithelial composition, cilia coverage and motility, pH
+ and transepithelial barrier properties.
+
+ Results  Mature hiPSC-AEC epithelia contained basal cells, secretory cells,
+ ciliated cells with motile cilia, pulmonary neuroendocrine cells (PNECs) and
+ ionocytes. There was no difference between FOXI1 WT and KO hiPSCs in terms of
+ their capacity to differentiate into airway progenitors. However, FOXI1 KO
+ led to mature hiPSC-AEC epithelia without ionocytes with reduced capacity to
+ produce ciliated cells.
+
+ Conclusion  Our results suggest that ionocytes could have role beyond
+ transepithelial ion transport by regulating epithelial properties and
+ homeostasis in the airway epithelium.
+ },
+ language = {en}
+}
+11:
+
+@book{book,
+ title = {Genome Editing and Biological Weapons: Assessing the Risk of Misuse},
+ author = {Paris, Katherine},
+ year = 2023,
+ month = {01},
+ publisher = {Springer Nature Switzerland AG},
+ pages = {},
+ doi = {10.1007/978-3-031-21820-0},
+ isbn = {978-3-031-21819-4}
+}
+12:
+@article{wickiser2020biosecurity,
+ title = {
+ The democratization of biology: how CRISPR and synthetic biology usher in new
+ biosecurity threats
+ },
+ author = {Wickiser, Jason K., et al.},
+ year = 2020,
+ journal = {Defense Horizons},
+ volume = 85,
+ pages = {1--16},
+ url = {
+ https://ndupress.ndu.edu/Media/News/News-Article-View/Article/2386026/democratization-of-biology-crispr-synthetic-biology-new-biosecurity-threats/
+ }
+}
+13:
+@article{cohen2019security,
+ title = {
+ Security implications of CRISPR-enabled genome editing: New weapons of mass
+ disruption?
+ },
+ author = {Cohen, Jon and Desai, Tej},
+ year = 2019,
+ journal = {Journal of Bioethical Inquiry},
+ publisher = {Springer},
+ volume = 16,
+ number = 2,
+ pages = {219--228},
+ doi = {10.1007/s11673-019-09914-5},
+ url = {https://doi.org/10.1007/s11673-019-09914-5}
+}
+14:
+@article{doudna2020synthetic,
+ title = {
+ The rise of synthetic biology: New biosecurity risks and regulatory
+ challenges
+ },
+ author = {Doudna, Jennifer A. and Charpentier, Emmanuelle},
+ year = 2020,
+ journal = {Nature Reviews Genetics},
+ publisher = {Nature},
+ volume = 21,
+ number = 3,
+ pages = {144--156},
+ doi = {10.1038/s41576-019-0182-7},
+ url = {https://www.nature.com/articles/s41576-019-0182-7}
+}
+15:
+@article{shwartz2019public,
+ title = {
+ Public perception of CRISPR and genome editing: Misconceptions and media
+ portrayal
+ },
+ author = {Shwartz, Mark and Conklin, Brian},
+ year = 2019,
+ journal = {Journal of Science Communication},
+ volume = 18,
+ number = 4,
+ pages = {A02},
+ doi = {10.22323/2.18040202},
+ url = {https://jcom.sissa.it/archive/18/04/JCOM_1804_2019_A02}
+}
+16:
+@book{Chadwick_2012,
+ title = {Encyclopedia of applied ethics},
+ author = {Chadwick, Ruth F.},
+ year = 2012,
+ publisher = {Academic Press},
+ address = {London},
+ isbn = {978-0-12-373932-2},
+ edition = {2nd ed},
+ language = {eng}
+}
+17:
+@article{Rubeis_Steger_2018,
+ title = {Risks and benefits of human germline genome editing: An ethical analysis},
+ author = {Rubeis, Giovanni and Steger, Florian},
+ year = 2018,
+ month = jul,
+ journal = {Asian Bioethics Review},
+ volume = 10,
+ number = 2,
+ pages = {133–141},
+ doi = {10.1007/s41649-018-0056-x},
+ issn = {1793-8759, 1793-9453},
+ language = {en}
+}
+18:
+@article{Ansah_2022,
+ title = {
+ Ethical Challenges and Controversies in the Practice and Advancement of Gene
+ Therapy
+ },
+ author = {Ansah, Emmanuel Owusu},
+ year = 2022,
+ month = aug,
+ journal = {Advances in Cell and Gene Therapy},
+ volume = 2022,
+ pages = {1–5},
+ doi = {10.1155/2022/1015996},
+ issn = {2573-8461},
+ rights = {https://creativecommons.org/licenses/by/4.0/},
+ abstractnote = {
+ One of the most important technologies in modern medicine is gene therapy,
+ which allows therapeutic genes to be introduced into cells of the body. The
+ approach involves genetics and recombinant DNA techniques that allow
+ manipulating vectors for delivery of exogenous material to target cells. The
+ efficacy and safety of the delivery system are a key step towards the success
+ of gene therapy. Somatic cell gene therapy is the easiest in terms of
+ technology and the least problematic in terms of ethics. Although genetic
+ manipulation of germline cells at the gene level has the potential to
+ permanently eradicate certain hereditary disorders, major ethical issues such
+ as eugenics, enhancement, mosaicism, and the transmission of undesirable
+ traits or side effects to patients’ descendants currently stymie its
+ development, leaving only somatic gene therapy in the works. However, moral,
+ social, and ethical arguments do not imply that germline gene therapy should
+ be banned forever. This review discusses in detail the current challenges
+ surrounding the practice of gene therapy, focusing on the moral arguments and
+ scientific claims that affect the advancement of the technology. The review
+ also suggests precautionary principles as a means to navigate ethical
+ uncertainties.
+ },
+ editor = {Miao, Carol H.},
+ language = {en}
+}
+19:
+@book{Pugh_2020,
+ title = {Autonomy, Rationality, and Contemporary Bioethics},
+ author = {Pugh, Jonathan},
+ year = 2020,
+ month = apr,
+ publisher = {Oxford University PressOxford},
+ doi = {10.1093/oso/9780198858584.001.0001},
+ isbn = {978-0-19-885858-4},
+ url = {https://academic.oup.com/book/33778},
+ edition = 1,
+ rights = {https://creativecommons.org/licenses/by-nc-nd/4.0/},
+ abstractnote = {
+ Abstract Personal autonomy is often lauded as a key value in
+ contemporary Western bioethics, and the claim that there is an important
+ relationship between autonomy and rationality is often treated as an
+ uncontroversial claim in this sphere. Yet, there is also considerable
+ disagreement about how we should cash out the relationship between
+ rationality and autonomy. In particular, it is unclear whether a rationalist
+ view of autonomy can be compatible with legal judgments that enshrine a
+ patient’s right to refuse medical treatment, regardless of whether ‘… the
+ reasons for making the choice are rational, irrational, unknown or even
+ non-existent’. This book brings recent philosophical work on the nature of
+ rationality to bear on the question of how we should understand autonomy in
+ contemporary bioethics. In doing so, the author develops a new framework for
+ thinking about the concept, one that is grounded in an understanding of the
+ different roles that rational beliefs and rational desires have to play in
+ personal autonomy. Furthermore, the account outlined here allows for a deeper
+ understanding of different forms of controlling influence, and the
+ relationship between our freedom to act, and our capacity to decide
+ autonomously. The author contrasts his rationalist account with other
+ prominent accounts of autonomy in bioethics, and outlines the revisionary
+ implications it has for various practical questions in bioethics in which
+ autonomy is a salient concern, including questions about the nature of
+ informed consent and decision-making capacity.
+ },
+ language = {en}
+}
+20:
+@inbook{Gstraunthaler_Lindl_2013,
+ title = {Allgemeine Aspekte der Primärkultur},
+ author = {Gstraunthaler, Gerhard and Lindl, Toni},
+ year = 2013,
+ booktitle = {Zell- und Gewebekultur: Allgemeine Grundlagen und spezielle Anwendungen},
+ publisher = {Springer},
+ address = {Berlin, Heidelberg},
+ pages = {151–162},
+ doi = {10.1007/978-3-642-35997-2_16},
+ isbn = {978-3-642-35997-2},
+ url = {https://doi.org/10.1007/978-3-642-35997-2_16},
+ abstractnote = {
+ Definitionsgemäß versteht man unter Primärkultur alle In-vitro-Züchtungen von
+ Zellen, Geweben und Organen, die direkt aus dem Organismus entnommen wurden.
+ Wird diese Erstkultur weiter subkultiviert, spricht man von einer
+ Sekundärkultur und in weiterer Folge bereits von einer Zelllinie (Schaeffer,
+ 1990) (Abb. 16-1). In den meisten Fällen kann eine Primärkultur nicht mehr
+ weitergezüchtet werden (Abschn. 16.2). Während eine Organkultur nicht in
+ ihrer Struktur- und Organisationseinheit zerstört werden soll (Kap. 23), ist
+ die Gewebekultur von einer mehr oder minder starken Desintegration aus einem
+ Organismus abhängig. Für die Gewinnung einer Zellkultur ist eine vollständige
+ Dissoziation des Gewebes bzw. des Organs in Einzelzellen notwendig.
+ },
+ editor = {Gstraunthaler, Gerhard and Lindl, Toni},
+ language = {de}
+}
+21:
+@book{book1,
+ author = {Thiele, F.},
+ year = 2001,
+ booktitle = {International Encyclopedia of the Social & Behavioral Sciences},
+ publisher = {Elsevier},
+ pages = {13224–13227},
+ doi = {10.1016/B0-08-043076-7/00191-1},
+ isbn = {978-0-08-043076-8},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B0080430767001911},
+ rights = {https://www.elsevier.com/tdm/userlicense/1.0/},
+ language = {en}
+}
+22:
+@inbook{Gethmann_2001,
+ title = {Research: Ethical Aspects of Long-term Responsibilities},
+ author = {Gethmann, C.F.},
+ year = 2001,
+ booktitle = {International Encyclopedia of the Social & Behavioral Sciences},
+ publisher = {Elsevier},
+ pages = {13227–13231},
+ doi = {10.1016/B0-08-043076-7/00159-5},
+ isbn = {978-0-08-043076-8},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B0080430767001595},
+ rights = {https://www.elsevier.com/tdm/userlicense/1.0/},
+ language = {en}
+}
+23:
+@article{Kiani_Pheby_Henehan_Brown_Sieving_Sykora_Marks_Falsini_Capodicasa_Miertus_et,
+ title = {Ethical considerations regarding animal experimentation},
+ author = {
+ Kiani, Aysha Karim and Pheby, Derek and Henehan, Gary and Brown, Richard and
+ Sieving, Paul and Sykora, Peter and Marks, Robert and Falsini, Benedetto and
+ Capodicasa, Natale and Miertus, Stanislav and Lorusso, Lorenzo and
+ Dondossola, Daniele and Tartaglia, Gianluca Martino and Ergoren, Mahmut
+ Cerkez and Dundar, Munis and Michelini, Sandro and Malacarne, Daniele and
+ Bonetti, Gabriele and Dautaj, Astrit and Donato, Kevin and Medori, Maria
+ Chiara and Beccari, Tommaso and Samaja, Michele and Connelly, Stephen
+ Thaddeus and Martin, Donald and Morresi, Assunta and Bacu, Ariola and Herbst,
+ Karen L. and Kapustin, Mykhaylo and Stuppia, Liborio and Lumer, Ludovica and
+ Farronato, Giampietro and Bertelli, Matteo and INTERNATIONAL BIOETHICS STUDY
+ GROUP
+ },
+ year = 2022,
+ month = jun,
+ journal = {Journal of Preventive Medicine and Hygiene},
+ volume = 63,
+ number = {2 Suppl 3},
+ pages = {E255–E266},
+ doi = {10.15167/2421-4248/jpmh2022.63.2S3.2768},
+ issn = {2421-4248},
+ abstractnote = {
+ Animal experimentation is widely used around the world for the identification
+ of the root causes of various diseases in humans and animals and for
+ exploring treatment options. Among the several animal species, rats, mice and
+ purpose-bred birds comprise almost 90% of the animals that are used for
+ research purpose. However, growing awareness of the sentience of animals and
+ their experience of pain and suffering has led to strong opposition to animal
+ research among many scientists and the general public. In addition, the
+ usefulness of extrapolating animal data to humans has been questioned. This
+ has led to Ethical Committees’ adoption of the “four Rs†principles
+ (Reduction, Refinement, Replacement and Responsibility) as a guide when
+ making decisions regarding animal experimentation. Some of the essential
+ considerations for humane animal experimentation are presented in this review
+ along with the requirement for investigator training. Due to the ethical
+ issues surrounding the use of animals in experimentation, their use is
+ declining in those research areas where alternative in vitro or in silico
+ methods are available. However, so far it has not been possible to dispense
+ with experimental animals completely and further research is needed to
+ provide a road map to robust alternatives before their use can be fully
+ discontinued.
+ },
+ language = {eng}
+}
--
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