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<div style="font-family: Calibri, sans-serif; font-size: 14px; "><br>
Hi,</div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; ">Actually,  <span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; "><span style="line-height: 1.1em; background-color: rgb(249, 249, 249); ">"/gate/output/analysis/recordSeptalPenetration"
 and "</span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; "><span style="line-height: 1.1em; background-color: rgb(249, 249, 249); ">/gate/output/analysis/setSeptalVolumeName" </span><span class="Apple-style-span" style="font-size: 14px; font-family: Calibri, sans-serif; "> are
 commands that are not intended to work with "parallelebeam" command. </span></span>Those 2 previous commands work with the "old classical" geometry. Moreover, I think that parallelbeam collimator is modelling a leaf collimator (not cast one that is to say
 that septal thichness is double in y direction that "oblique" direction ).</div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; ">In order to record septal photons, you need to set to true "<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; "><span style="line-height: 1.1em; background-color: rgb(249, 249, 249); ">recordSeptalPenetration"
 flag and to explicitely name the volume you want to track the septal informations (usually the collimator but it may not). Additionnaly, you have to set output as ROOT file.</span></span></div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; "><span style="line-height: 1.1em; background-color: rgb(249, 249, 249); "> </span></span></div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; ">All the best.</div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; ">Ludovic</div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; "><span class="Apple-style-span" style="font-size: 14px; font-family: Calibri, sans-serif; "><br>
</span></span></div>
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<span style="font-weight:bold">De : </span>Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca">carluri@phas.ubc.ca</a>><br>
<span style="font-weight:bold">Date : </span>Wed, 13 Mar 2013 14:35:37 -0700<br>
<span style="font-weight:bold">À : </span>Jonathan Moody <<a href="mailto:jbm139@gmail.com">jbm139@gmail.com</a>><br>
<span style="font-weight:bold">Cc : </span>"<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>
<span style="font-weight:bold">Objet : </span>Re: [Gate-users] Parallel Hole Collimator<br>
</div>
<div><br>
</div>
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<div dir="ltr">I wasn't setting up a root file as an output...Thanks for letting me know now I guess that solves everything.
<div><br>
</div>
<div style="">Carlos</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Mar 13, 2013 at 1:54 PM, Jonathan Moody <span dir="ltr">
<<a href="mailto:jbm139@gmail.com" target="_blank">jbm139@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Carlos,<br>
<br>
From the Gate source code it looks like setting "recordSeptalPenetration" to true should create new branches called "septalNb" in the Hit and Singles tree of the output root file.  It does not look like this septal data is available with any other type of output. 
 You don't see the "septalNb" branches in the root file?<br>
--<br>
Jon
<div>
<div class="h5"><br>
<br>
<br>
On 3/13/2013 1:39 PM, Carlos Uribe wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Jon,
<div><br>
</div>
<div>Yes the collimator is attached to the phantomSD.  </div>
<div><br>
</div>
<div>When I run my code with the </div>
<div><br>
</div>
<div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/recordSeptalPenetration true</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/setSeptalVolumeName collimator</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:14.296875px">I don't get errors or anything like that...the code works fine.  I just don't get any output related to septal penetration information.</span></div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Mar 13, 2013 at 7:44 AM, Jon Moody <span dir="ltr">
<<a href="mailto:jbmoody@umich.edu" target="_blank">jbmoody@umich.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>I have not used this feature.  When you said you tried it and it didn't work what happened?<br>
Was the collimator attached to the phantomSD by the command<br>
<br>
/gate/collimator/attachPhantomSD<br>
<br>
--<br>
Jon
<div>
<div><br>
<br>
On 3/12/2013 5:52 PM, Carlos Uribe wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Thanks for the reply Jonathan..
<div><br>
</div>
<div>
<div style="font-family:arial,sans-serif;font-size:13px">Do you know then how can I use </div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/recordSeptalPenetration true</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/setSeptalVolumeName collimator</span></div>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">with this way of specifying the collimator?</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div style="font-family:arial,sans-serif;font-size:13px"><span style="line-height:1.1em;background-color:rgb(249,249,249)">Carlos</span></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Mar 12, 2013 at 11:18 AM, Jonathan Moody <span dir="ltr">
<<a href="mailto:jbm139@gmail.com" target="_blank">jbm139@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Carlos,<br>
<br>
I think "parallelbeam" collimator construction has not been working right since Gate v.5.0.0, so the other option is to use cubicArray and linear repeaters as Giuseppe mentioned.  In this case, the septal thickness is defined implicitly in the two repeatVectors. 
 For hexagonal shaped holes the second and third components of the cubicArray repeatVector are:<br>
<br>
Ry = hole_diameter + septal_thickness<br>
Rz = Ry * sqrt(3)<br>
<br>
where hole_diameter is defined across the flat sides.  The corresponding two components of the linear repeatVector are:<br>
<br>
Ly = Ry / 2 <br>
Lz = Rz / 2 <br>
<br>
(the x-components of both repeatVectors are 0).  Then the cubicArray repeatNumberY/Z determine the number of holes in each direction divided by 2.<br>
--<br>
Jon
<div>
<div><br>
<br>
<br>
On 3/12/2013 1:16 PM, Carlos Uribe wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Hi Giuseppe,
<div><br>
</div>
<div>Thanks for your reply...I tried it but it still doesn't solve the problem.</div>
<div><br>
</div>
<div>I know that I can use your specified macro to create a collimator step by step.  However, I do want to use the option given in the guide using the </div>
<div><br>
</div>
<div>/gate/SPECThead/daughters/insert parallelbeam<br>
</div>
<div><br>
</div>
<div>This has a parameter that specifies the septal thickness</div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/colli/geometry/setSeptalThickness 0.2 cm </span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">I guess I will be able to track the septal penetration using</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/recordSeptalPenetration true</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)">/gate/output/analysis/setSeptalVolumeName collimator</span></div>
<div><span style="line-height:1.1em;background-color:rgb(249,249,249)"><br>
</span></div>
<div><font color="#000000"><span style="line-height:14.296875px">I've tried this using the macro that you suggested and it doesn't work.  I assume that you need to set the septal thickness shown in the guide's example.  If there's another way that someone knows
 to make it work please let me know.</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px"><br>
</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px">Thanks,</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px"><br>
</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px">Carlos</span></font></div>
<div><font color="#000000"><span style="line-height:14.296875px"><br>
</span></font></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Mar 12, 2013 at 5:26 AM, Giuseppe Magro <span dir="ltr">
<<a href="mailto:beppe.magro@gmail.com" target="_blank">beppe.magro@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div><br>
</div>
/gate/colli/setMaterial Lead<br>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">(instead of setMaterialName)</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Example (shielding as mother volume):</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
<div class="gmail_extra">#=====================================</div>
<div class="gmail_extra">#    Collimator</div>
<div class="gmail_extra">#=====================================</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/shielding/daughters/name collimator</div>
<div class="gmail_extra">/gate/shielding/daughters/insert box</div>
<div class="gmail_extra">/gate/collimator/geometry/setXLength 3. cm</div>
<div class="gmail_extra">/gate/collimator/geometry/setYLength 19. cm</div>
<div class="gmail_extra">/gate/collimator/geometry/setZLength 28. cm</div>
<div class="gmail_extra">/gate/collimator/placement/setTranslation  -2. 0. 0. cm</div>
<div class="gmail_extra">/gate/collimator/setMaterial Lead</div>
<div class="gmail_extra">/gate/collimator/vis/setColor red</div>
<div class="gmail_extra">/gate/collimator/vis/forceWireframe</div>
<div class="gmail_extra">/gate/collimator/describe</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/collimator/daughters/name hole</div>
<div class="gmail_extra">/gate/collimator/daughters/insert hexagone</div>
<div class="gmail_extra">/gate/hole/geometry/setHeight 3. cm</div>
<div class="gmail_extra">/gate/hole/geometry/setRadius .15 cm</div>
<div class="gmail_extra">/gate/hole/placement/setRotationAxis 0 1 0</div>
<div class="gmail_extra">/gate/hole/placement/setRotationAngle 90 deg</div>
<div class="gmail_extra">/gate/hole/placement/setTranslation 0. -0.25 -0.25 cm #</div>
<div class="gmail_extra">/gate/hole/setMaterial Air</div>
<div class="gmail_extra">/gate/hole/describe</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/hole/repeaters/insert cubicArray</div>
<div class="gmail_extra">/gate/hole/cubicArray/setRepeatNumberX 1</div>
<div class="gmail_extra">/gate/hole/cubicArray/setRepeatNumberY 18 #9</div>
<div class="gmail_extra">/gate/hole/cubicArray/setRepeatNumberZ 27 #9</div>
<div class="gmail_extra">/gate/hole/cubicArray/setRepeatVector 0. 1. 1. cm</div>
<div class="gmail_extra">/gate/hole/cubicArray/autoCenter true #false </div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">/gate/hole/repeaters/insert linear</div>
<div class="gmail_extra">/gate/hole/linear/setRepeatNumber 2</div>
<div class="gmail_extra">/gate/hole/linear/setRepeatVector 0. 0.5 0.5 cm</div>
<div class="gmail_extra">/gate/hole/linear/autoCenter false </div>
<div><br>
</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Giuseppe M.</div>
<div>PhD Student - CNAO <br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 12 March 2013 12:00, <span dir="ltr"><<a href="mailto:gate-users-request@lists.opengatecollaboration.org" target="_blank">gate-users-request@lists.opengatecollaboration.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
   1. Parallel hole Collimator (Carlos Uribe)<br>
   2. Re: ASCII output (Carlos Uribe)<br>
   3. Re: Process for Photon Evaporation (Hermann Fuchs)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 11 Mar 2013 11:31:41 -0700<br>
From: Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca" target="_blank">carluri@phas.ubc.ca</a>><br>
To: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
        <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: [Gate-users] Parallel hole Collimator<br>
Message-ID:<br>
        <CAPJy_1TcFTKwiEpu_Zicc=+<a href="mailto:UKYN3hfHMjvhumfzWL6AxyZ%2B1Sg@mail.gmail.com" target="_blank">UKYN3hfHMjvhumfzWL6AxyZ+1Sg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello everyone,<br>
<br>
I'm following the user's guide<br>
<a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Defining_a_system" target="_blank">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Defining_a_system</a><br>
trying to model a parallel hole collimator.<br>
<br>
The guide shows the following example:<br>
<br>
/gate/SPECThead/daughters/name colli<br>
<br>
#specify that the parallel beam collimator setup must be used<br>
/gate/SPECThead/daughters/insert parallelbeam<br>
<br>
#set the collimator material<br>
/gate/colli/setMaterialName Lead<br>
<br>
#set the collimator dimensions<br>
/gate/colli/geometry/setDimensionX 70 cm<br>
/gate/colli/geometry/setDimensionY 80 cm<br>
<br>
#set the thickness of the collimator<br>
/gate/colli/geometry/setHeight 3 cm<br>
<br>
#specify the hole radius<br>
/gate/colli/geometry/setInnerRadius 0.5 cm<br>
<br>
#set the septal thickness to the required distance between the holes<br>
/gate/colli/geometry/setSeptalThickness 0.2 cm<br>
/gate/colli/placement/alignToX<br>
/gate/colli/placement/setRotationAxis 0 0 1<br>
/gate/colli/placement/setRotationAngle -90 deg<br>
<br>
<br>
I'm getting a problem as follows:<br>
<br>
/opt/simulation/gate_v6.2/source/geometry/src/GateVVolume.cc (l.179): The<br>
material of the volume side hole 1 is not defined.<br>
<br>
Anyone knows how to fix this?<br>
<br>
Thanks,<br>
<br>
--<br>
Carlos F Uribe<br>
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Message: 2<br>
Date: Mon, 11 Mar 2013 12:40:11 -0700<br>
From: Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca" target="_blank">carluri@phas.ubc.ca</a>><br>
To: samira nezhad <<a href="mailto:sn90113@gmail.com" target="_blank">sn90113@gmail.com</a>><br>
Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
        <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: Re: [Gate-users] ASCII output<br>
Message-ID:<br>
        <CAPJy_1QZT9uYF1VmobA3Mk2xMfS_2MRTmQfv41x=<a href="mailto:2nVvdJ2ssg@mail.gmail.com" target="_blank">2nVvdJ2ssg@mail.gmail.com</a>><br>
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<br>
I had the same problem and here is how I fixed it<br>
<br>
In the <a href="http://GateConfiguration.h.in" target="_blank">GateConfiguration.h.in</a> <<a href="http://gateconfiguration.h.in/" target="_blank">http://gateconfiguration.h.in/</a>> file found<br>
within the home folder of Gate, change this line:<br>
<br>
<br>
#cmakedefine GATE_USE_FILE        @GATE_USE_FILE@<br>
<br>
<br>
to this:<br>
<br>
#cmakedefine GATE_ANALYSIS_USE_FILE        @GATE_ANALYSIS_USE_FILE@<br>
<br>
<br>
Recompile Gate and it should now work!<br>
<br>
Cheers,<br>
<br>
Carlos<br>
<br>
<br>
On Sun, Mar 10, 2013 at 3:10 AM, samira nezhad <<a href="mailto:sn90113@gmail.com" target="_blank">sn90113@gmail.com</a>> wrote:<br>
<br>
> Dear all,<br>
><br>
> I need to ASCII output but by gate6.2 i couldn't get it .<br>
> when use this command<br>
>  /gate/output/ascii/enable<br>
><br>
> It gives this error message:<br>
><br>
> COMMAND NOT FOUND<br>
><br>
> I appreciate if you guide me, thanks in advance<br>
><br>
> Best regards,<br>
><br>
><br>
><br>
> _______________________________________________<br>
> Gate-users mailing list<br>
> <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
><br>
> --<br>
> Carlos F Uribe<br>
><br>
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Message: 3<br>
Date: Tue, 12 Mar 2013 10:11:10 +0100<br>
From: Hermann Fuchs <<a href="mailto:hermann.fuchs@meduniwien.ac.at" target="_blank">hermann.fuchs@meduniwien.ac.at</a>><br>
To: Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca" target="_blank">carluri@phas.ubc.ca</a>><br>
Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
        <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: Re: [Gate-users] Process for Photon Evaporation<br>
Message-ID:<br>
        <<a href="mailto:1363079470.5371.3.camel@strahlen41.strahlen.meduniwien.ac.at" target="_blank">1363079470.5371.3.camel@strahlen41.strahlen.meduniwien.ac.at</a>><br>
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<br>
That is an interesting question.<br>
<br>
Could you keep me informed on your findings?<br>
If it isn't already in Gate it should be easy to add.<br>
Just contact me and I can help you with this or implement it for you.<br>
<br>
Best reards,<br>
Hermann<br>
<br>
On Fri, 2013-03-08 at 12:22 -0800, Carlos Uribe wrote:<br>
> Hello everybody,<br>
><br>
><br>
><br>
> Can anyone please tell me which process to add to my Physics list in<br>
> order to see the de-exitation of the metastable daughter?<br>
><br>
><br>
> The parent follows a beta-minus decay which works great except I don't<br>
> see the gammas generated by the metastable daughter.<br>
><br>
><br>
> I am using<br>
> /gate/physics/addProcess RadioactiveDecay<br>
><br>
><br>
> but apparently, Geant4 handles the meta-stable states through the<br>
> existing photo-evaporation code;<br>
><br>
><br>
><br>
> How do I set the photon evaporation process?<br>
><br>
><br>
> Thanks in advance,<br>
> --<br>
><br>
><br>
> Carlos F Uribe<br>
><br>
> _______________________________________________<br>
> Gate-users mailing list<br>
> <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
<br>
<br>
--<br>
-------------<br>
DI Hermann Fuchs<br>
Christian Doppler Laboratory for Medical Radiation Research for Radiation Oncology<br>
Department of Radiation Oncology<br>
Medical University Vienna<br>
W?hringer G?rtel 18-20<br>
A-1090 Wien<br>
<br>
Tel.  <a href="tel:%2B%2043%20%2F%201%20%2F%2040%20400%207271" value="+431404007271" target="_blank">+ 43 / 1 / 40 400 7271</a><br>
Mail. <a href="mailto:hermann.fuchs@meduniwien.ac.at" target="_blank">hermann.fuchs@meduniwien.ac.at</a><br>
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End of Gate-users Digest, Vol 82, Issue 20<br>
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-- <br>
Carlos F Uribe </a></blockquote>
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-- <br>
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-- <br>
Carlos F Uribe </div>
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