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AgRad50.lyx
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AgRad50.lyx
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#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 544
\begin_document
\begin_header
\save_transient_properties true
\origin unavailable
\textclass classicthesis
\begin_preamble
\usepackage{pdfpages}
\usepackage{currfile-abspath}
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\use_default_options true
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\end_header
\begin_body
\begin_layout Chapter
Zn(II) to Ag(I) swap in Rad50 zinc hook domain leads to highly stable interprote
in complex disruption through the formation of Ag
\begin_inset script subscript
\begin_layout Plain Layout
x
\end_layout
\end_inset
(Cys)
\begin_inset script subscript
\begin_layout Plain Layout
y
\end_layout
\end_inset
cores
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
chaptermark{
\backslash
protect
\backslash
parbox{0.9
\backslash
linewidth}{Zn(II) to Ag(I) swap in Rad50 zinc hook domain leads to highly
stable interprotein complex disruption through the formation of Ag
\backslash
textsubscript{x}(Cys)
\backslash
textsubscript{y} cores}}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset CommandInset label
LatexCommand label
name "chap:AgRad50"
\end_inset
\end_layout
\begin_layout Standard
\shape smallcaps
Olga Kerber
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
*
\end_layout
\end_inset
, Józef Ba Tran
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
*
\end_layout
\end_inset
, Alicja Misiaszek
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
*
\end_layout
\end_inset
, Aleksandra Cho
\shape default
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
-
\end_layout
\end_inset
\shape smallcaps
rą
\shape default
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status open
\begin_layout Plain Layout
\backslash
-
\end_layout
\end_inset
\shape smallcaps
żew
\shape default
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status open
\begin_layout Plain Layout
\backslash
-
\end_layout
\end_inset
\shape smallcaps
ska
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
*
\end_layout
\end_inset
, Wojciech Bal
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
†
\end_layout
\end_inset
and Artur Krężel
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
*
\end_layout
\end_inset
\shape default
\begin_inset Newline newline
\end_inset
\begin_inset Flex CT - Spaced Low Small Caps
status open
\begin_layout Plain Layout
\shape smallcaps
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
*
\end_layout
\end_inset
\shape default
Department of Chemical Biology, Faculty of Biotechnology, University of
Wrocław, F.
Joliot-Curie 14a, 50-383 Wrocław, Poland
\end_layout
\end_inset
\begin_inset Newline newline
\end_inset
\begin_inset Flex CT - Spaced Low Small Caps
status open
\begin_layout Plain Layout
\shape smallcaps
\begin_inset script superscript
\begin_layout Plain Layout
\shape smallcaps
*
\end_layout
\end_inset
\shape default
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskieg
o 5a, 02-106 Warsaw, Poland
\end_layout
\end_inset
\begin_inset Newline newline
\end_inset
\shape italic
Inorganic Chemistry
\shape default
\size small
\size default
2023 62, 4076–4087
\begin_inset VSpace medskip
\end_inset
\end_layout
\begin_layout Section
Brief history and bibliometric data
\end_layout
\begin_layout Standard
Bringing this article to publication was, of the other articles I co-authored,
the hardest.
Initially, we wanted to publish the article in
\emph on
Chemical Communications
\emph default
, as a continuation of the project devoted to the investigation of the role
of Ag(I) on the intraprotein zinc-binding sites, where previously an article
about the formation of
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
ce{Ag_nS_n}
\end_layout
\end_inset
clusters in
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{zf}
\end_layout
\end_inset
was described.
Finally, after several iterations involving the exchange of criticism from
reviewers, the manuscript, and responses to the reviewers' objections,
the article was published in
\emph on
Inorganic Chemistry
\emph default
(
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{if}
\end_layout
\end_inset
of 5.436, March 6, 2023).
\begin_inset Newline newline
\end_inset
I have mixed feelings as I think about the publication of this article.
My reservations about the peer-review process became even stronger after
this article.
In the 21st century, with the ability to exchange information cheaply,
and expressly, and where the cost of publishing information online is very
low, the peer-review process as a rule should be completely transparent.
In addition, the rule should be the possibility to criticize an article
\emph on
after
\emph default
it has been published, without having to write another article in which,
one refers to the criticized publication.
The publication process for this article was quite tedious due to the incompete
nce of one of the reviewers—the prolonged review did not bring anything
new, did not improve our article, but only increased the time in review.
Also, this article, is the last article included in this thesis and I am
very pleased to have collaborated on it with my lab-mates, whom I saw every
day (provided there were no pandemic restrictions).
This successful cooperation between us was one of the reasons why the time
spent on experiments, data processing, and writing the manuscript, was
far less than the time this article spent in review.
\begin_inset Newline newline
\end_inset
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
begin{pycode}[sessionA]
\end_layout
\begin_layout Plain Layout
from scholarly import scholarly
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
num2words = {1: 'once',
\end_layout
\begin_layout Plain Layout
2: 'two',
\end_layout
\begin_layout Plain Layout
3: 'three',
\end_layout
\begin_layout Plain Layout
4: 'four',
\end_layout
\begin_layout Plain Layout
5: 'five',
\end_layout
\begin_layout Plain Layout
6: 'six',
\end_layout
\begin_layout Plain Layout
7: 'seven',
\end_layout
\begin_layout Plain Layout
8: 'eight',
\end_layout
\begin_layout Plain Layout
9: 'nine',
\end_layout
\begin_layout Plain Layout
10: 'ten',
\end_layout
\begin_layout Plain Layout
11: 'eleven',
\end_layout
\begin_layout Plain Layout
12: 'twelve',
\end_layout
\begin_layout Plain Layout
13: 'thirteen',
\end_layout
\begin_layout Plain Layout
14: 'fourteen',
\end_layout
\begin_layout Plain Layout
15: 'fifteen',
\end_layout
\begin_layout Plain Layout
16: 'sixteen',
\end_layout
\begin_layout Plain Layout
17: 'seventeen',
\end_layout
\begin_layout Plain Layout
18: 'eighteen',
\end_layout
\begin_layout Plain Layout
19: 'nineteen',
\end_layout
\begin_layout Plain Layout
20: 'twenty',
\end_layout
\begin_layout Plain Layout
30: 'thirty',
\end_layout
\begin_layout Plain Layout
40: 'forty',
\end_layout
\begin_layout Plain Layout
50: 'fifty',
\end_layout
\begin_layout Plain Layout
60: 'sixty',
\end_layout
\begin_layout Plain Layout
70: 'seventy',
\end_layout
\begin_layout Plain Layout
80: 'eighty',
\end_layout
\begin_layout Plain Layout
90: 'ninety',
\end_layout
\begin_layout Plain Layout
0: 'zero'}
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
def n2w(n):
\end_layout
\begin_layout Plain Layout
try:
\end_layout
\begin_layout Plain Layout
return (num2words[n])
\end_layout
\begin_layout Plain Layout
except KeyError:
\end_layout
\begin_layout Plain Layout
try:
\end_layout
\begin_layout Plain Layout
return ((num2words[n-n % 10]) + ' ' + (num2words[n % 10].lower()))
\end_layout
\begin_layout Plain Layout
except KeyError:
\end_layout
\begin_layout Plain Layout
return ('Number out of range')
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
search_query = scholarly.search_single_pub(
\end_layout
\begin_layout Plain Layout
'Zn(II) to Ag(I) Swap in Rad50 Zinc Hook Domain Leads to Interprotein
Complex Disruption through the Formation of Highly Stable Agx(Cys)y Cores')
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
num_citations = search_query['num_citations']
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
if num_citations <= 10:
\end_layout
\begin_layout Plain Layout
if num_citations == 0:
\end_layout
\begin_layout Plain Layout
print("As the article was published recently, it is not surprising
that it is not yet cited (as of
\backslash
\backslash
today).")
\end_layout
\begin_layout Plain Layout
elif num_citations == 1:
\end_layout
\begin_layout Plain Layout
print(f'The article was published recently, however, it was already
cited {n2w(num_citations)} (as of
\backslash
\backslash
today).')
\end_layout
\begin_layout Plain Layout
else:
\end_layout
\begin_layout Plain Layout
print(f'The article was published recently, however, it was already
cited {n2w(num_citations)} times (as of
\backslash
\backslash
today).')
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
else:
\end_layout
\begin_layout Plain Layout
print(f'The article was warmly recieved in the scientific community
and was cited by {num_citations} other articles so far (as of
\backslash
\backslash
today).')
\end_layout
\begin_layout Plain Layout
\backslash
end{pycode}
\end_layout
\begin_layout Plain Layout
\end_layout
\end_inset
\begin_inset Foot
status open
\begin_layout Plain Layout
\begin_inset Flex URL
status open
\begin_layout Plain Layout
https://scholar.google.com/
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Section
Summary
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
ExplSyntaxOn
\end_layout
\begin_layout Plain Layout
% call python script, here I assume the binary name is python3
\end_layout
\begin_layout Plain Layout
\backslash
sys_shell_now:x {cd~
\backslash
thesispath~
\backslash
string&
\backslash
string&~conda~activate~thesis~
\backslash
string&
\backslash
string&~ python~Scripts
\backslash
string
\backslash
Ag_vs_Hg_popularity
\backslash
string.py}
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
\backslash
ExplSyntaxOff
\end_layout
\end_inset
\end_layout
\begin_layout Standard
The medical use of silver, both as an Ag(0) and as compounds of Ag(I) is
known for millennia, the ancient Persians, Phoenicians, Greeks, Romans,
and others were recorded to utilize various forms of silver to preserve
both food and water, the custom practiced through World War II.
The first preserved records of the medical use of silver come from ancient
Macedonians, who attempted to treat infections with silver plates.
Hippocrates, the Father of Medicine, was supposed to use silver preparations
to treat ulcers and promote wound healing.
Before the introduction of antibiotics, silver, and various silver compounds
were the most available antimicrobial agents.
\begin_inset CommandInset citation
LatexCommand citep
key "AlexanderWesley2009"
literal "true"
\end_inset
The toxicity of silver is low compared to most of the other heavy metals,
which allows the use of silver in various utility goods, e.
g.
jewelry, silverware, or as a food additive.
However, it has been shown that high doses of silver given parenterally,
can cause convulsions or even death.
\begin_inset CommandInset citation
LatexCommand citep
key "AlexanderWesley2009"
literal "true"
\end_inset
Though the silver toxicity is low, the organisms usually lack the mechanisms
for silver detoxification, and in the case of the human body, when silver
is delivered (e.g., injection, ingestion, or applied topically) silver is
accumulated irreversibly.
The condition caused by sustained silver exposure (and light
\begin_inset Foot
status open
\begin_layout Plain Layout
Like in a photography sunlight causes the decomposition of colorless silver
compounds to Ag(0) or silver sulfides.
\end_layout
\end_inset
) is called argyria.
By 1939
\begin_inset CommandInset citation
LatexCommand citeauthor
key "Hill1939"
literal "true"
\end_inset
have identified 357 cases of recorded argyria, all of the recorded cases,
except for the irreversible bluish skin tone, had a benign course of the
disease.
\begin_inset CommandInset citation
LatexCommand citep
key "Hill1939"
literal "true"
\end_inset
Despite low toxicity, the number of publications dedicated to silver toxicity
by the year increases (
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:ag_hg_count"
plural "false"
caps "false"
noprefix "false"
\end_inset
), possibly the reason for this is the use of silver in everyday articles
(e.g., use of silver in deodorants, sportswear, anti-smoking pills), of which
a lot of these items utilize
\begin_inset ERT
status open
\begin_layout Plain Layout
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glspl{agnp}
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\end_inset
.
\end_layout
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\begin_inset Float figure
wide false
sideways false
status open
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\begin_inset Graphics
filename gfx/ag_hg_count.png
lyxscale 40
width 100line%
\end_inset
\begin_inset Caption Standard
\begin_layout Plain Layout
\begin_inset CommandInset label
LatexCommand label
name "fig:ag_hg_count"
\end_inset
Number of publications devoted to silver or mercury toxicity aggregated
in PubMed (accessed
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
today
\end_layout
\end_inset
)
\begin_inset CommandInset citation
LatexCommand citep
key "Sayers2022"
literal "true"
\end_inset
, blue and orange lines respectively.
Note that since 2013 (marked as a dashed line) more publications are devoted
to the toxicity of silver than mercury.
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
The oligodynamic effect, which is the property of some metals to have a
biocidal effect, in the case of silver is mainly caused by the bioactive
species – Ag(I).
The antimicrobial properties of
\begin_inset ERT