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<p>Since John is taking the lead on the new version, my suggestion
is to let him do it the way that will be most efficient for him. I
think everyone, including John, have noted your concerns.<br>
</p>
<div class="moz-signature">
<div style="line-height:16px; margin:6px 0; padding:8px 8px 8px
8px; border-top:1px #aeb1a6 dotted; border-bottom:1px #aeb1a6
dotted; font-face: Calibri, Verdana; font-size:11px;
color:grey;">
<font ;="" font-style="bold" size="2.5px;" color="#0049FF">Tomas
Helikar, Ph.D.</font> <br>
Susan J. Rosowski Associate Professor <br>
Department of Biochemistry | University of Nebraska-Lincoln <br>
m: <a href="callto:402-547-8904" style="color:rgb(0, 136, 204)
!important;">402-547-8904</a> | o: <a href="callto:402-472-3530" style="color:rgb(0, 136, 204)
!important;">402-472-3530</a><br>
<a href="http://www.postbox-inc.com" style="color:rgb(0, 136,
204) !important; text-decoration:none !important;
border-bottom:1px dotted #AAA;">www.helikarlab.org</a> | <a href="http://helikarlab.org" style="color:rgb(0, 136, 204)
!important; text-decoration:none !important; border-bottom:1px
dotted #AAA;">cellcollective.org</a><br>
twitter: <a href="http://twitter.com/helikarlab" style="color:rgb(0, 136, 204) !important; text-decoration:none
!important; border-bottom:1px dotted #AAA;">@helikarlab</a>, <a href="http://twitter.com/biocollective" style="color:rgb(0,
136, 204) !important; text-decoration:none !important;
border-bottom:1px dotted #AAA;">@biocollective</a>
</div>
</div>
<div class="moz-cite-prefix">On 5/18/21 9:27 AM, Jacob Barhak wrote:<br>
</div>
<blockquote type="cite" cite="mid:CAM_y+3Tysce7W_zKOFb__KeKT2tBb38U5a2irJEMRjRB_+BF3g@mail.gmail.com">
<div>
<font face="sans-serif" color="#FF6347">Non-NU Email</font>
<hr>
</div>
<div dir="ltr">So Tomas,
<div><br>
</div>
<div>Before starting editing, to save time it is important that
we establish what is going to be edited - I voiced my concern
over the large deletions in Johns version more than once -
there is a real problem there - many authors may be completely
eliminated in the name of style - I don't like it - so John
has to decide how he spends his time - first just define what
sections you want to contribute in - this will help John
comprehend the magnitude of the task - he promised editorial
services for two weeks - so before we start wasting time with
edits, lets see the entire picture. </div>
<div><br>
</div>
<div>Tomas, what you like may be something I dislike or
something I do not care about, and eventually we all have to
agree - and there are about 20 of us - this is a legal
requirement for copyright transfer. The task here is time
consuming and I do not envy John and it is important we all
help him realize the task before he spends time on it.</div>
<div><br>
</div>
<div>And please reply to all - there are some contributors that
are listed in only one list and some that may not have signed
up - they all need to be aware of what we are doing. </div>
<div><br>
</div>
<div>Hopefully you identified the sections you want to
contribute to - please state those to move this forward
quicker.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, May 18, 2021 at 9:08
AM Tomas Helikar <<a href="mailto:thelikar2@unl.edu" moz-do-not-send="true">thelikar2@unl.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>I suggest we use John's version - the flow has begun to
improve there and he'll be bringing the content over from
the submitted version.</p>
<p>At the top of each of the other version, there should be
big red "DO NOT EDIT THIS VERSION" and a link to John's
version that will be the running draft where our efforts
should focus.</p>
<p>Best,<br>
</p>
<div>
<div style="line-height:16px;margin:6px
0px;padding:8px;border-top:1px dotted
rgb(174,177,166);border-bottom:1px dotted
rgb(174,177,166);font-size:11px;color:grey"> <font size="2.5px;" color="#0049FF">Tomas Helikar, Ph.D.</font>
<br>
Susan J. Rosowski Associate Professor <br>
Department of Biochemistry | University of
Nebraska-Lincoln <br>
m: <a href="callto:402-547-8904" style="color:rgb(0,136,204)" target="_blank" moz-do-not-send="true">402-547-8904</a> | o: <a href="callto:402-472-3530" style="color:rgb(0,136,204)" target="_blank" moz-do-not-send="true">402-472-3530</a><br>
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</div>
</div>
<div>On 5/18/21 9:05 AM, Jacob Barhak wrote:<br>
</div>
<blockquote type="cite">
<div> <font face="sans-serif" color="#FF6347">Non-NU
Email</font>
<hr> </div>
<div dir="ltr">Yes Sheriff,
<div><br>
</div>
<div>You have a good point. Here are the versions of
the paper that I recall.
<div><br>
</div>
<div>1. The version we all approved - I suggest we use
this: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1IMEgmdNkx-2DEsnOjGuegpenSIMmKIkK00Lc8Gred3QxM_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=FanQUPp95Lqx2G9Ojb6SLVQzkZS6mrqBIt_W-zgW8_Q&e=" target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a></div>
<div>2. John Gennari version: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=" target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2</a></div>
<div>3. Rahuman Sheriff version: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh_edit&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=yaBZO6lyEXDKmMXfrDPDqy10sDgl0FQgkFFMO3_iShg&e=" target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit</a></div>
<div>4. Alexander Kulesza version <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1U-5FlTHrV6STXWNT3GiCepvsLk1WdYgzN5_view&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=6gQoAQCH7F2WOy92A0xjfWmCMUjW7onPku8BYcIsY9Y&e=" target="_blank" moz-do-not-send="true">https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view</a></div>
<div>5. Original Model Reproducibility, Credibility,
Standardization subgroup version <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq-5FW0py7t4PNVLo_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=QH6Rgy4why7ib2YGE2T5AA61L68xDE1K-ySoCdKV9ew&e=" target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing</a></div>
<div>6. Original Integration subgroup version: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1voUSrSpv3AZlC1T-2DBLa3W4wzHQ5vEdJCVrBbwMUTDiQ_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=WPFW1D-ECFULPKl8uijQsNA58J5V7TNynIc9OeqCiBE&e=" target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing</a></div>
<div><br>
</div>
<div>The last two versions hold the original
discussions before the merge to the version on top.
The history of those contain most contributions -
however it will take hours to figure out where each
text portion is located in the new version. Yet the
new version also includes many modifications. And I
believe Hana has another version of proofs that were
never made public - we did this revision and proof
process before, yet I think she sent me her version
privately. I may be mistaken - it was a long time
ago. </div>
<div><br>
</div>
<div>Hopefully this list will help understand the
undertaking and save time.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, May 18, 2021
at 8:34 AM Rahuman Sheriff <<a href="mailto:sheriff@ebi.ac.uk" target="_blank" moz-do-not-send="true">sheriff@ebi.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>Dear John G,
<div>Many thanks for the update.</div>
<div>I like the new ordering :)</div>
<div><br>
</div>
<div>@Jacob, as you mentioned you have 6 versions,
could you please add the link to those versions in
John G document, so they are all inked.</div>
<div>I give consent to to rephrase my contribution
or even remove part or all of my contribution to
the white paper and present the ideas in other
sections if required to make the paper coherent
and flow well.</div>
<div><br>
</div>
<div>The white paper has a great collections of
ideas, I hope we can get it into a good shape
soon for submission and benefit the scientific
community.</div>
<div><br>
</div>
<div>Best regards</div>
<div>Sheriff</div>
<div><br>
</div>
<div><br>
<blockquote type="cite">
<div>On 18 May 2021, at 13:28, James Osborne
<<a href="mailto:jmosborne@unimelb.edu.au" target="_blank" moz-do-not-send="true">jmosborne@unimelb.edu.au</a>>
wrote:</div>
<br>
<div>
<div dir="ltr">Sorry I wasn't on the call
Yesterday (it was 1 am for me so not really
achievable). Looking at the emails looks
like it was useful.
<div><br>
</div>
<div>Happy to help how I can, in terms of
areas as someone on the multicellular side
of life i'm probably most use on 3 but
happy to support others.</div>
<div><br>
</div>
<div>James </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue,
May 18, 2021 at 3:12 PM John Gennari <<a href="mailto:gennari@uw.edu" target="_blank" moz-do-not-send="true">gennari@uw.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>
<div>
<div style="font-size:12px;text-align:left;font-family:Helvetica,Arial,sans-serif"><strong>
<table style="width:100%;float:left" cellspacing="0" cellpadding="0" border="0">
<tbody>
<tr>
<td style="color:red"><b>External
email: </b>Please
exercise caution</td>
</tr>
</tbody>
</table>
</strong><br>
</div>
<hr> </div>
<p><br>
</p>
<p>All: About 9 of us had a lively Zoom
meeting today to chat about the
manuscript. By the end, it was a
productive meeting, and I'm hoping
that this email will capture some key
outputs from the meeting. I apologize
if I said some things that were a bit
"inflammatory". Obviously 2 years
would be much too long to get this
paper out-the door. <br>
</p>
<p>I saw two outcomes. First, we had
some nice ideas and discussion about
re-ordering (initiated by Tomas
Helikar). In the below, I'm going to
propose one possible ordering, but
this is certainly a work-in-progress.
The reason that I think ordering is
important is that it will give us a
much better ability to write a strong
concluding section, where we talk
about themes and the larger arc of our
ideas. <br>
</p>
<p>Second, we agreed that we should
nominate "point persons" who would be
in charge of at least the initial cut
of each of the subsections. As Jacob
pointed out, this information should
be easy to get from older email and
history of the development of the
paper. During the zoom meeting, we
associated some co-authors with some
sections, but our coverage wasn't
perfect (see challenge #12). Hopefully
people will "stand up" and admit that
some section of text is theirs. <br>
</p>
<p>So in the below, I include the
original title of the section, a few
words about the content of that
section, and then a name (or several
names) of co-authors who will be the
"point person" to make sure that the
appropriate content is included.
Obviously, all co-authors can and
should chime in on any part of the
text, but the point person should make
sure that the key ideas are included.
<br>
</p>
<p>The basic ordering idea for the dozen
challenges was to follow the
life-cycle of model development,
execution, sharing and integration,
and eventually implementation. So... <br>
</p>
<p>*********************************************<br>
</p>
<p><b>(1) "</b><b>Data</b><b> and
measurement definitions</b>". Before
you can build a model, you must have
data. So data availability and
measurement standards is the place to
start. <br>
</p>
<p><b>People: </b>Hana D, Jacob B<br>
</p>
<p><b>(2) "</b><b>The variety of
modeling languages</b>" This is
about the choice of modeling
languages, such as using SBML, CellML,
or Matlab. As I said on the phone
call, this is sort of about
"syntax"--how do you write down your
model? <br>
</p>
<p><b>People:</b> John G, Jon K, Rahuman
S.</p>
<p><b>(3) "</b><b>The variety of
modeling paradigms and scales"</b><b>
</b>Separately from modeling syntax,
we must acknowledge modeling paradigms
with very different semantics. Some
clear examples are PDEs versus ODEs
versus rule-based systems (and
obviously one can combine these).
Certainly semantics might impact
syntax (the prior challenge), in that
certain modeling language might be
appropriate only for some paradigms.</p>
<p>People: James G, Eric F (?) <br>
</p>
<p><b>(4) "</b><b>Units standardization</b>"
A common reason that models are not
reproducible are errors in units, or
misunderstanding about units, or
simply a lack of information about
units. <br>
</p>
<p>People: Jacob B, Hana D</p>
<p><b>(5) "</b><b>A lack of annotations
in models</b>". Once researchers
publish models, they must annotate the
model so that others can understand
it. Quality annotation is essential
for both search and reproducibility. <br>
</p>
<p>People: John G.</p>
<p><b>(6) "</b><b>Models are hard to
locate"</b> If your goal is to
reproduce, understand and possibly
reuse or integrate some other model,
one must first find that model. This
requires annotation (prior section)
and repositories (Physiome Model
Repository, BioModels) and search
platforms (ModeleXchange). <br>
</p>
<p>People: Jon K, John G.</p>
<p><b>(7) "</b><b>Common platforms to
execute models" </b>A model is
pretty worthless as a static object.
For folk to understand and reproduce
models they must be executable. Alas,
there is no single or consistent way
of executing a model -- and of course,
this interacts direction with section
#2 and #3, above: Execution platforms
are usually only for one modeling
paradigm, and often for one modeling
language. The BioSimulators work goes
here.</p>
<p>People: Jon K. <br>
</p>
<p><b>(8) "</b><b>Credibility </b><b>and
validity of models</b>" Once a model
is published, how do folk know it is
right? Model validation is a big topic
and challenge. Credibility follows (in
part) from validation, but also
requires transparency and
reproducibility, etc. <br>
</p>
<p>People: John Rice, Jon K, Jacob B</p>
<p><b>(9) "</b><b>Environments to adapt
and integrate models</b>" As I see
it, one of the end-targets for this
manuscript is to better enable model
integration, to build better models.
There are many challenges with the
task of integrating two (or more)
models. (One that has recently been
discussed is that even if model A and
model B are valid and correct, there
is no guarantee that the combined
model A+B is correct. I liked what
William Waites and Katherine Morse
posted on this subject.) This section
is where SBML-comp and SemGen
environments can be mentioned.</p>
<p>People: John G.</p>
<p>(<b>10) "Challenges for stochastic
models" </b>Special challenges
specific to stochaistic modeling. An
obvious point to mention is
repeatability -- stochastic models
don't necessarily give the same
results with the same inputs. <br>
</p>
<p>People: James G., Eric F<br>
</p>
<p><b>(11) "Licensing barriers" </b>Issues
around "open source" and CC0
licensing. <br>
</p>
<p>People: Jacob B<br>
</p>
<p><b>(12) "Barriers to model
implementations and applications"</b>
(I might suggest this be re-phrased
for better clarity). What this section
should discuss are challenges is
getting a community to actually use
models for "real-world" applications
or decision making. This is more of a
cultural/societal challenge, and thus
seems like a nice big-picture way to
end. <br>
</p>
<p><b>People: ?? </b>I don't have any
names here...<br>
</p>
<p>*********************************************</p>
<p>We didn't really talk much about it
in the Zoom meeting, but there have
been ideas tossed around about a
"baker's dozen", i.e., adding a 13th
challenge. We could also potentially
merge some of the above. <br>
</p>
<p class="MsoNormal">The "point persons"
listed above is obviously a subset of
co-authors. That's fine and
appropriate. Just for transparency, I
follow what I think is pretty standard
policy for authorship issues, and
nicely summarized by the<span style="font-family:Helvetica,sans-serif">
International Committee of Medical
Journal Editors (ICMJE); see 2019
updated document at </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.icmje.org_icmje-2Drecommendations.pdf&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=l29d3A9PItAUv4N0WkCuREqes9tSKSW7sk5GDEo6VBA&e=" target="_blank" moz-do-not-send="true">http://www.icmje.org/icmje-recommendations.pdf</a>
(Or see, below my signature, a summary
of the key points of this document). <br>
</p>
<p class="MsoNormal">Finally, I've made
the document editable by all at <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=" target="_blank" moz-do-not-send="true">
https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2</a>
<br>
<span style="font-family:Helvetica,sans-serif"></span></p>
<div><br>
</div>
<p>-John G.<br>
==========================================================================<br>
Associate Professor & Graduate
Program Director <a href="mailto:gennari@uw.edu" target="_blank" moz-do-not-send="true">
<gennari@uw.edu></a><br>
Dep't of Biomedical Informatics
and
telephone:206-616-6641<br>
Medical Education, box
358047 <br>
University of Washington<br>
Seattle, WA 98109-4714 <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__faculty.washington.edu_gennari_&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h8T10a2oOTChEmXp5dGxDnAIghmjMroKsXSfcbIH9Y&e=" target="_blank" moz-do-not-send="true">
http://faculty.washington.edu/gennari/</a><br>
==========================================================================<br>
<br>
</p>
<div><br>
</div>
<p class="MsoNormal" style="margin-left:0.25in"><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">The
ICMJE recommends that authorship be
based on the following 4 criteria: </span></p>
<p style="margin-left:0.75in"> <span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>1.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Substantial
contributions to the conception or
design of the work; or the
acquisition, analysis, or
interpretation of data for the work;
AND</span></p>
<p style="margin-left:0.75in"> <span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>2.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Drafting
the work or revising it critically
for important intellectual content;
AND </span></p>
<p style="margin-left:0.75in"> <span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>3.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Final
approval of the version to be
published; AND </span></p>
<p style="margin-left:0.75in"> <span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>4.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Agreement
to be accountable for all aspects of
the work in ensuring that questions
related to the accuracy or integrity
of any part of the work are
appropriately investigated and
resolved.</span></p>
<p style="margin-left:0.75in"> <span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><br>
</span></p>
<div><br>
</div>
<p><br>
</p>
</div>
</blockquote>
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<pre>_______________________________________________
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