From 4353c84120cc1857ff630fd9b3ff796deab62f9c Mon Sep 17 00:00:00 2001
From: Liliana Sanfilippo <liliana.sanfilippo@uni-bielefeld.de>
Date: Sun, 29 Sep 2024 11:42:11 +0200
Subject: [PATCH] authors = dictio['editor']
---
code/cit.py | 5 +-
code/methods.bib | 270 +++++++++++++++++++++++++++++++++++++++++++++++
code/output.txt | 14 +++
3 files changed, 288 insertions(+), 1 deletion(-)
create mode 100644 code/methods.bib
diff --git a/code/cit.py b/code/cit.py
index d6a3ceab..f37d1bd9 100644
--- a/code/cit.py
+++ b/code/cit.py
@@ -215,7 +215,10 @@ 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...")
- authors = dictio['author']
+ if 'authors' in dictio:
+ authors = dictio['author']
+ elif 'editor' in dictio:
+ authors = dictio['editor']
makeauthors(authors, out)
# out.write("\t" + "\t" +"<span property=\"schema:Name\"> " + aut + "</span>."+ "\n")
# out.write("\t" +"</span>"+ "\n")
diff --git a/code/methods.bib b/code/methods.bib
new file mode 100644
index 00000000..e4e19fdb
--- /dev/null
+++ b/code/methods.bib
@@ -0,0 +1,270 @@
+[1]
+@article{article,
+ title = {Die Entwicklung der Patch-Clamp-Technik},
+ author = {Roth, F. C., Numberger, M., and Draguhn, A.},
+ year = 2023,
+ month = {{}},
+ journal = {Springer eBooks},
+ volume = {{}},
+ pages = {1--14},
+ doi = {10.1007/978-3-662-66053-9}
+}
+[2]
+@book{dallas_patch_2021,
+ title = {Patch clamp electrophysiology: methods and protocols},
+ shorttitle = {Patch clamp electrophysiology},
+ year = 2021,
+ publisher = {Humana Press},
+ address = {New York},
+ series = {Methods in molecular biology},
+ number = 2188,
+ isbn = {978-1-07-160818-0 978-1-07-160820-3},
+ language = {en},
+ editor = {Dallas, Mark and Bell, Damian}
+}
+[3]
+@article{PRIEL20073893,
+ title = {
+ Ionic Requirements for Membrane-Glass Adhesion and Giga Seal Formation in
+ Patch-Clamp Recording
+ },
+ author = {
+ Avi Priel and Ziv Gil and Vincent T. Moy and Karl L. Magleby and Shai D.
+ Silberberg
+ },
+ year = 2007,
+ journal = {Biophysical Journal},
+ volume = 92,
+ number = 11,
+ pages = {3893--3900},
+ doi = {10.1529/biophysj.106.099119},
+ issn = {0006-3495},
+ url = {https://www.sciencedirect.com/science/article/pii/S000634950771189X},
+ abstract = {
+ Patch-clamp recording has revolutionized the study of ion channels,
+ transporters, and the electrical activity of small cells. Vital to this
+ method is formation of a tight seal between glass recording pipette and cell
+ membrane. To better understand seal formation and improve practical
+ application of this technique, we examine the effects of divalent ions,
+ protons, ionic strength, and membrane proteins on adhesion of membrane to
+ glass and on seal resistance using both patch-clamp recording and atomic
+ force microscopy. We find that H+, Ca2+, and Mg2+ increase adhesion force
+ between glass and membrane (lipid and cellular), decrease the time required
+ to form a tight seal, and increase seal resistance. In the absence of H+
+ (10−10M) and divalent cations (<10−8M), adhesion forces are greatly reduced
+ and tight seals are not formed. H+ (10−7M) promotes seal formation in the
+ absence of divalent cations. A positive correlation between adhesion force
+ and seal formation indicates that high resistance seals are associated with
+ increased adhesion between membrane and glass. A similar ionic dependence of
+ the adhesion of lipid membranes and cell membranes to glass indicates that
+ lipid membranes without proteins are sufficient for the action of ions on
+ adhesion.
+ }
+}
+[4]
+@article{10.3389/fphar.2017.00195,
+ title = {
+ Development of Automated Patch Clamp Technique to Investigate CFTR Chloride
+ Channel Function
+ },
+ author = {
+ Billet, Arnaud and Froux, Lionel and Hanrahan, John W. and Becq, Frederic
+ },
+ year = 2017,
+ journal = {Frontiers in Pharmacology},
+ volume = 8,
+ doi = {10.3389/fphar.2017.00195},
+ issn = {1663-9812},
+ url = {
+ https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2017.00195
+ }
+}
+New5.
+@article{DuBridge_Tang_Hsia_Leong_Miller_Calos_1987,
+ title = {
+ Analysis of mutation in human cells by using an Epstein-Barr virus shuttle
+ system.
+ },
+ author = {
+ DuBridge, R B and Tang, P and Hsia, H C and Leong, P M and Miller, J H and
+ Calos, M P
+ },
+ year = 1987,
+ month = jan,
+ journal = {Molecular and Cellular Biology},
+ volume = 7,
+ number = 1,
+ pages = {379–387},
+ issn = {0270-7306},
+ abstractnote = {
+ We developed highly sensitive shuttle vector systems for detection of
+ mutations formed in human cells using autonomously replicating derivatives of
+ Epstein-Barr virus (EBV). EBV vectors carrying the bacterial lacI gene as the
+ target for mutation were established in human cells and later returned to
+ Escherichia coli for rapid detection and analysis of lacI mutations. The
+ majority of the clonal cell lines created by establishment of the lacI-EBV
+ vector show spontaneous LacI- frequencies of less than 10(-5) and are
+ suitable for studies of induced mutation. The ability to isolate clonal lines
+ represents a major advantage of the EBV vectors over transiently replicating
+ shuttle vectors (such as those derived from simian virus 40) for the study of
+ mutation. The DNA sequence changes were determined for 61 lacI mutations
+ induced by exposure of one of the cell lines to N-nitroso-N-methylurea. A
+ total of 33 of 34 lacI nonsense mutations and 26 of 27 missense mutations
+ involve G X C to A X T transitions. These data provide support for the
+ mutational theory of cancer.
+ }
+}
+[New6].
+@article{Qin_Zhang_Clift_Hulur_Xiang_Ren_Lahn_2010,
+ title = {
+ Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible
+ Promoter
+ },
+ author = {
+ Qin, Jane Yuxia and Zhang, Li and Clift, Kayla L. and Hulur, Imge and Xiang,
+ Andy Peng and Ren, Bing-Zhong and Lahn, Bruce T.
+ },
+ year = 2010,
+ month = may,
+ journal = {PLOS ONE},
+ publisher = {Public Library of Science},
+ volume = 5,
+ number = 5,
+ pages = {e10611},
+ doi = {10.1371/journal.pone.0010611},
+ issn = {1932-6203},
+ abstractnote = {
+ Constitutive promoters are used routinely to drive ectopic gene expression.
+ Here, we carried out a systematic comparison of eight commonly used
+ constitutive promoters (SV40, CMV, UBC, EF1A, PGK and CAGG for mammalian
+ systems, and COPIA and ACT5C for Drosophila systems). We also included in the
+ comparison the TRE promoter, which can be activated by the rtTA
+ transcriptional activator in a doxycycline-inducible manner. To make our
+ findings representative, we conducted the comparison in a variety of cell
+ types derived from several species. We found that these promoters vary
+ considerably from one another in their strength. Most promoters have fairly
+ consistent strengths across different cell types, but the CMV promoter can
+ vary considerably from cell type to cell type. At maximal induction, the TRE
+ promoter is comparable to a strong constitutive promoter. These results
+ should facilitate more rational choices of promoters in ectopic gene
+ expression studies.
+ },
+ 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
+ organoidsâ€).
+ }
+}
+new8.
+@article{Ensinck_Deeersmaecker_Heylen_Ramalho_Gijsbers_Far,
+ title = {
+ Phenotyping of Rare CFTR Mutations Reveals Distinct Trafficking and
+ Functional Defects
+ },
+ author = {
+ Ensinck, Marjolein and De Keersmaecker, Liesbeth and Heylen, Lise and
+ Ramalho, Anabela S. and Gijsbers, Rik and Farré, Ricard and De Boeck, Kris
+ and Christ, Frauke and Debyser, Zeger and Carlon, Marianne S.
+ },
+ year = 2020,
+ month = mar,
+ journal = {Cells},
+ volume = 9,
+ number = 3,
+ pages = 754,
+ doi = {10.3390/cells9030754},
+ issn = {2073-4409},
+ abstractnote = {
+ Background. The most common CFTR mutation, F508del, presents with multiple
+ cellular defects. However, the possible multiple defects caused by many rarer
+ CFTR mutations are not well studied. We investigated four rare CFTR mutations
+ E60K, G85E, E92K and A455E against well-characterized mutations, F508del and
+ G551D, and their responses to corrector VX-809 and/or potentiator VX-770.
+ Methods. Using complementary assays in HEK293T stable cell lines, we
+ determined maturation by Western blotting, trafficking by flow cytometry
+ using extracellular 3HA-tagged CFTR, and function by halide-sensitive YFP
+ quenching. In the forskolin-induced swelling assay in intestinal organoids,
+ we validated the effect of tagged versus endogenous CFTR. Results. Treatment
+ with VX-809 significantly restored maturation, PM localization and function
+ of both E60K and E92K. Mechanistically, VX-809 not only raised the total
+ amount of CFTR, but significantly increased the traffic efficiency, which was
+ not the case for A455E. G85E was refractory to VX-809 and VX-770 treatment.
+ Conclusions. Since no single model or assay allows deciphering all defects at
+ once, we propose a combination of phenotypic assays to collect rapid and
+ early insights into the multiple defects of CFTR variants.
+ },
+ language = {eng}
+}
+[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}
+}
+new10.
+@book{Mennella_2024,
+ title = {Cilia: methods and protocols},
+ year = 2024,
+ publisher = {Humana Press},
+ address = {New York, NY},
+ isbn = {978-1-07-163507-0},
+ abstractnote = {
+ This volume covers the latest advancements in the study of ciliary
+ complexity. Protocols cover genomic, proteomic, imaging, and functional
+ analysis of different ciliated tissues and their wide applicability in cilia
+ biology. Chapters in this book primarily focus on methods to study
+ multiciliated cells, and discuss topics such as SARS-CoV-2 infections of
+ human primary nasal multiciliated epithelial cells; expansion microscopy of
+ ciliary proteins; live-imaging centriole amplification in mouse brain
+ multiciliated cells; biophysical properties of cilia motility; and
+ mucociliary transport device construction. Written in the highly successful
+ Methods in Molecular Biology series format, chapters include introductions to
+ their respective topics, lists of the necessary materials and reagents,
+ step-by-step, readily reproducible laboratory protocols, and tips on
+ troubleshooting and avoiding known pitfalls. Cutting-edge and thorough,
+ Cilia: Methods and Protocols is a valuable resource for researchers who are
+ interested in learning more about this developing field.
+ },
+ language = {eng}
+}
diff --git a/code/output.txt b/code/output.txt
index 49f41668..64bcf0f7 100644
--- a/code/output.txt
+++ b/code/output.txt
@@ -1,2 +1,16 @@
{/*<!-- 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"> Die Entwicklung der Patch-Clamp-Technik</span>.
+ <i property="schema:publisher" typeof="schema:Organization"> Springer eBooks</i>
+ <b property="issueNumber" typeof="PublicationIssue"> </b>
+ , <span property="schema:pageBegin"> 1</span>-<span property="schema:pageEnd">14</span>
+ (<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">
--
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