jekyll-theme-ici3d 0.1.0

data/_includes/partners.html

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+<!-- OUR PARTNERS -->
+<section class="clients" id="partners">
+  <div class="heading-center">
+    <h2 class="section-heading">PARTNERS</h2>
+    <p class="lead">Consortium institutions and institutional partners</p>
+    <hr>
+  </div>
+  <div class="container">
+    <ul class="list-inline list-client-logo" >
+      <li>
+       </li>
+      <li>
+        <a href="http://www.sacema.org/"><img src="{{site.url}}/assets/img/partners/SACEMA_228.png" title="SACEMA (Consortium Institution)" style="width:480px" /></a>
+      </li>
+      <li>
+        <a href="http://www.midas.us/"><img src="{{site.url}}/assets/img/partners/MIDAS.png" title="MIDAS Coordinating Center (Consortium Institution)" style="height:100px"/></a>
+      </li>
+      <li>
+      </li>
+      {% if false %}
+      <li>
+        <a href="http://www.uga.edu/"><img src="{{site.url}}/assets/img/partners/UGA_228.png" title="University of Georgia (Consortium Institution)" style="width:480px"/></a>
+      </li>
+      {%endif%}
+      <li>
+       </li>
+    </ul>
+    <hr>
+  </div>
+  <div class="container">
+    <ul class="list-inline list-client-logo" >
+      <li>
+        <a href="http://www.aims.ac.za/"><img src="{{site.url}}/assets/img/partners/AIMS-SA.jpg" title="AIMS-South Africa (Institutional Partner)" style="height:114px; width:567px"/></a>
+      </li>
+      <li>
+        <a href="https://cema.africa/"><img src="{{site.url}}/assets/img/partners/CEMA_UN.png" title="CEMA (Institutional Partner)" style="height:114px; width:385px;" /></a>
+      </li>
+      <li>
+       </li>
+      {% if false %}
+      <li>
+        <a href="http://www.cidid.org/"><img src="{{site.url}}/assets/img/partners/CIDID_long.png" title="CIDID (Institutional Partner)" style="height:114px; width:385px;" /></a>
+      </li>
+      {%endif%}
+    </ul>
+    <hr>
+  </div>
+  <div class="container">
+    <ul class="list-inline list-client-logo">
+      {% if false %}
+      <li>
+        <a href="http://proctor.ucsf.edu/"><img src="{{site.url}}/assets/img/partners/Proctor.png" title="The Francis I. Proctor Foundation for Research in Ophthalmology (Institutional Partner)"/></a>
+      </li>
+      <li>
+        <a href="http://www.ucsf.edu/"><img src="{{site.url}}/assets/img/partners/UCSF.png" title="University of California - San Francisco (Institutional Partner)" style="height:114px; width:175px"/></a>
+      </li>
+      {%endif%}
+      <li>
+        <a href="http://www.colby.edu/"><img src="{{site.url}}/assets/img/partners/Colby.png" title="Colby College (Institutional Partner)" /></a>
+      </li>
+      <li>
+        <a href="http://www.mcmaster.ca/"><img src="{{site.url}}/assets/img/partners/McMaster.jpg" title="McMaster Univeristy (Institutional Partner)" style="height:114px; width:206px"/></a>
+      </li>
+      <li>
+        <a href="http://www.psu.edu/"><img src="{{site.url}}/assets/img/partners/PSU.png" title="Pennsylvania State Univeristy (Institutional Partner)" style="height:114px"/></a>
+      </li>
+      {% if false %}
+      <li>
+        <a href="http://www.ufl.edu/"><img src="{{site.url}}/assets/img/partners/UF.png" title="University of Florida (Institutional Partner)" /></a>
+      </li>
+      {%endif%}
+    </ul>
+  </div>
+</section>
+<!-- END OUR PARTNERS -->

data/_includes/profile.html

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+{% assign key = page.relative_path | split: '/' | last | split: '.' | first %}
+{% assign person = site.data.team[key] %}
+
+<div class="col-md-10 col-md-offset-1">
+  <div class="team-member media" style="font-size:18px">
+    <img src="{{site.url}}{{site.path}}/assets/img/{{person.img}}" class="media-object img-circle pull-left" alt="{{ person.name }}" height="140" />
+    <div class="media-body">
+      <h3 class="media-heading team-name">{{ person.name }}</h3>
+      <strong>{{ person.role }}</strong>
+      <hr class="pull-left">
+      <div class="clearfix"></div>
+      {% if person.type contains "i3d"%}
+      <p style="font-size:14px"><b>Project:</b> {{person.project}}
+      <br><b>Host:</b> {{person.mentor}}, {{person.host}}
+      <br><b>Current position:</b> {{person.position}}, {{person.affiliation}}</p>
+      {% else %}
+      <p style="font-size:14px"> <b>{{ person.position }}<br>{{ person.affiliation }}</b></p>
+      <p style="font-size:14px">
+      {% for dd in person.degrees %}
+        <em>{{ dd.degree }} in {{ dd.discipline }}, {{ dd.institution }} ({{ dd.year }})</em><br>
+      {% endfor %}
+      </p>
+      <p style="font-size:14px"><b>About:</b> {% if person.bio contains "" %}{{ person.bio }}{% else %}{{ person.summary }}{% endif %}</p>
+      {% endif %}
+      {% if person.outputs.size > 0 %}
+      <h4> Output{% if person.outputs.size > 1 %}s{% endif %}:</h4>
+      {% for pp in person.outputs %}
+      <p style="font-size:14px">{{ pp.authors }}. ({{ pp.year }}) <a href="{{ pp.link }}">{{ pp.title }}</a>. <em>{{ pp.journal }}</em></p>
+      {% endfor %}
+      {% endif %}
+      {% if person.papers.size > 0 %}
+      <h4> Selected publication{% if person.papers.size > 1 %}s{% endif %}:</h4>
+      {% for pp in person.papers %}
+      <p style="font-size:14px">{{ pp.authors }}. ({{ pp.year }}) <a href="{{ pp.link }}">{{ pp.title }}</a>. <em>{{ pp.journal }}</em></p>
+      {% endfor %}
+      {% endif %}
+      {% if person.icons == "yes" %}
+      <ul class="list-inline social-icon">
+        {%if person.gscholar contains ""%}
+        <li><a href="https://scholar.google.com/citations?user={{ person.gscholar }}"><i class="ai ai-google-scholar" style="font-size:28px"></i></a></li>
+        {%endif%}
+        {%if person.twitter contains ""%}
+        <li><a href="https://twitter.com/{{ person.twitter }}"><i class="fa fa-twitter" style="font-size:30px"></i></a></li>
+        {%endif%}
+        {%if person.linkedin contains ""%}
+        <li><a href="https://za.linkedin.com/in/{{ person.linkedin }}"><i class="fa fa-linkedin" style="font-size:30px"></i></a></li>
+        {%endif%}
+        {%if person.orcid contains ""%}
+        <li><a href="http://orcid.org/{{ person.orcid }}"><i class="ai ai-orcid" style="font-size:30px"></i></a></li>
+        {%endif%}
+        {%if person.impactstory contains ""%}
+        <li><a href="https://impactstory.org/u/{{ person.impactstory }}"><i class="ai ai-impactstory" style="font-size:30px"></i></a></li>
+        {%endif%}
+        {%if person.github contains ""%}
+        <li><a href="https://github.com/{{ person.github }}"><i class="fa fa-github" style="font-size:30px"></i></a></li>
+        {%endif%}
+        {%if person.website contains ""%}
+        <li><a href="{{ person.website }}"><i class="fa fa-globe" style="font-size:30px"></i></a></li>
+        {%endif%}
+        {%if person.cv contains ""%}
+        <li><a href="{{ person.cv }}"><i class="fa fa-file" style="font-size:26px"></i></a></li>
+        {%endif%}
+      </ul>
+      {% endif %}
+  </div><!-- media-body -->
+</div><!-- team-member media -->
+</div><!-- col-md-5 col-md-offset-2 -->

data/_includes/publications/faculty.md

@@ -0,0 +1,13 @@
+<div markdown='1'>
+
+**Pulliam, JRC**, **SE Bellan** [p], M Gambhir, LA Meyers, and **J Dushoff**. (2015) [Evaluating Ebola vaccine trials: insights from simulation](http://www.sciencedirect.com/science/article/pii/S1473309915003035). _**The Lancet Infectious Diseases**_ 15(10): 1134. doi:10.1016/S1473-3099(15)00303-5
+
+**Bellan, SE** [p], **JRC Pulliam**, CAB Pearson [p], D Champredon [g], SJ Fox [g], L Skrip [p], AP Galvani, M Gambhir, BA Lopman, **TC Porco**, LA Meyers, and **J Dushoff**. (2015) [Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis](http://dx.doi.org/10.1016/S1473-3099%2815%2970139-8). _**The Lancet Infectious Diseases**_ 15(6): 703-710. doi: 10.1016/S1473-3099(15)70139-8.
+
+**Bellan, SE** [p], **J Dushoff**, AP Galvani, LA Meyers. (2015) [Reassessment of HIV-1 acute phase infectivity: accounting for heterogeneity and study design with simulated cohorts](http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001801). _**PLoS Medicine**_ 12(3): e1001801. doi: 10.1371/journal.pmed.1001801
+
+**Bellan, SE** [p], **JRC Pulliam**, **J Dushoff**, and LA Meyers. (2014) [Ebola control: effect of asymptomatic infection and acquired immunity](http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2814%2961839-0/fulltext). _**The Lancet**_ 384(9953): 1499-1500. doi: 10.1016/S0140-6736(14)61839-0
+
+**Bellan, SE** [p], **JRC Pulliam**, **J Dushoff**, and LA Meyers. (2014) [Ebola vaccine trials: the ethical mandate for a therapeutic safety net](http://bmj.com/cgi/content/full/bmj.g7518?ijkey=qHj1rqPkFuwxnAk&keytype=ref). _**The British Medical Journal**_ 349: g7518. doi: http://dx.doi.org/10.1136/bmj.g7518
+
+</div>

data/_includes/publications/instructional.md

@@ -0,0 +1,5 @@
+<div markdown='1'>
+
+**Bellan, SE** [g], **JRC Pulliam**, **JC Scott**, **J Dushoff**, and the MMED Organizing Committee. (2012) [How to make epidemiological training infectious](http://10.1371/journal.pbio.1001295). _**PLoS Biology**_ 10(4): e1001295. doi:10.1371/journal.pbio.1001295.
+
+</div>

data/_includes/publications/participant.md

@@ -0,0 +1,33 @@
+<div markdown='1'>
+
+_Marx, F_ [p], T Cohen, NA Menzies, JA Salomon, G Theron, and R Yaesoubi. (2020) [Cost-effectiveness of post-treatment follow-up examinations and secondary prevention of tuberculosis in a high-incidence setting – a model-based analysis](https://doi.org/10.1016/S2214-109X(20)30227-8). _**The Lancet Global Health**_ 8: e1223-33. doi: 10.1016/S2214-109X(20)30227-8
+
+Black, A, F Sitas, _T Chibrawara_ [g], _Z Gill_ [g], _M Kubjane_ [g], and **BG Williams**. (2019) [HIV-attributable causes of death in the medical ward at the Chris Hani Baragwanath Hospital, South Africa](https://doi.org/10.1371/journal.pone.0215591). _**PLOS ONE**_ 14(5): e0215591. doi: 10.1371/journal.pone.0215591
+
+_Beauclair, R_ [g], **J Dushoff**, and **W Delva**. (2018) [Partner age differences and associated sexual risk behaviours among adolescent girls and young women in a cash transfer programme for schooling in Malawi](https://doi.org/10.1186/s12889-018-5327-7). _**BMC Public Health**_ 18: 403. doi: 10.1186/s12889-018-5327-7
+
+_Grantz, KH_, _W Chabaari_ [g], _RK Samuel_ [g], _B Gershom_ [g], L Blum, L Worden, SK Ackley, F Liu, TM Lietman, AP Galvani, L Prajna, and **TC Porco**. (2018) [Spatial distribution of leprosy in India: an ecological study](https://doi.org/10.1186/s40249-018-0402-y). _**Infectious Diseases of Poverty**_ 7: 20. doi: 10.1186/s40249-018-0402-y
+
+_Fox, SJ_ [g], JC Miller, and LA Meyers. (2017) [Seasonality in risk of pandemic influenza emergence](https://doi.org/10.1371/journal.pcbi.1005749). _**PLoS Computational Biology**_ 13(10): e1005749. doi: 10.1371/journal.pcbi.1005749
+
+_Borchering, RK_ [g], **SE Bellan**, JM Flynn [g], **JRC Pulliam**, and SA McKinley. (2017) [Resource-driven encounters among consumers and implications for the spread of infectious disease](http://rsif.royalsocietypublishing.org/content/14/135/20170555). _**Journal of the Royal Society Interface**_ 14(135). doi: 10.1098/rsif.2017.0555
+
+_Ackley, SF_ [g] and **JW Hargrove**. (2017) [A dynamic model for estimating adult female mortality from ovarian dissection data for the tsetse fly _Glossina pallidipes_ Austen sampled in Zimbabwe](https://doi.org/10.1371/journal.pntd.0005813). _**PLoS Neglected Tropical Diseases**_ 11(8): e0005813. doi: 10.1371/journal.pntd.0005813
+
+_Lord, JS_ [p], _Z Mthombothi_ [g], _VK Lagat_ [g], _F Atuhaire_ [g], and **JW Hargrove**. (2017) [Host-seeking efficiency can explain population dynamics of the tsetse fly _Glossina morsitans morsitans_ in response to host density decline](https://doi.org/10.1371/journal.pntd.0005730). _**PLoS Neglected Tropical Diseases**_ 11(7): e0005730. doi: 10.1371/journal.pntd.0005730
+
+_Means, A_ [g], _K Risher_ [g], _E Ujeneza_ [g], _I Maposa_, _J Nondi_, and **SE Bellan** [p]. (2016) [Impact of age and sex on CD4+ cell count trajectories following treatment initiation: an analysis of the Tanzanian HIV treatment database](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0164148). _**PLoS ONE**_ 11(10): e0164148. doi: 10.1371/journal.pone.0164148
+
+_Sempa, JB_ [g], **J Dushoff**, MJ Daniels, M Nieuwoudt, and **SE Bellan** [p]. (2016) [Reevaluating cumulative HIV-1 viral load as a prognostic predictor: predicting opportunistic infection incidence and mortality in a Ugandan cohort](http://aje.oxfordjournals.org/cgi/reprint/kwv303?ijkey=KxcBzzl10c7eRVS&keytype=ref). _**American Journal of Epidemiology**_ 184(1): 67-77. doi: 10.1093/aje/kwv303
+
+_Ying, R_ [g], RM Granich, S Gupta, and **BG Williams**. (2016) [CD4 cell count: Declining value for antiretroviral therapy eligibility](http://cid.oxfordjournals.org/content/early/2016/01/28/cid.civ1224.full). _**Clinical Infectious Diseases**_. Published online ahead of print: January 29, 2016. doi: 10.1093/cid/civ1224
+
+_Brook, CE_ [g], _R Beauclair_ [g], _O Ngwenya_, L Worden, M Ndeffo-Mbah, TM Lietman, SK Satpathy, AP Galvani, and **TC Porco**. (2015) [Spatial heterogeneity in projected leprosy trends in India](http://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-015-1124-7). _**Parasites and Vectors**_ 8:542-552. doi:10.1186/s13071-015-1124-7
+
+Enanoria WTA, L Worden, F Liu [p], D Gao [p], _S Ackley_ [g], **JC Scott**, M Deiner, _E Mwebaze_ [p], W Ip, TM Lietman, and **TC Porco**. (2015) [Evaluating subcriticality during the Ebola epidemic in West Africa](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140651). _**PLoS ONE**_ 10(10): e0140651. doi:10.1371/journal.pone.0140651
+
+**Hargrove, JW** and _SF Ackley_ [g]. (2015) [Mortality estimates from ovarian age distributions of the tsetse fly _Glossina pallidipes_ Austen sampled in Zimbabwe suggest the need for new analytical approaches](http://journals.cambridge.org/abstract_S0007485315000073). _**Bulletin of Entomological Research**_ 105(3): 294-304.
+
+**Bellan, SE** [g], _K Fiorella_ [g], _D Melesse_ [g], W Getz, **BG Williams**, and **J Dushoff**. (2012) [Extra-couple HIV transmission in sub-Saharan Africa: a mathematical modelling study of survey data](http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2812%2961960-6/fulltext). _**The Lancet**_ 381(9877): 1561-1569. doi:10.1016/S0140-6736(12)61960-6.
+
+</div>

data/_includes/talk.html

@@ -0,0 +1,12 @@
+<div class="team-member media" style="font-size:18px">
+  <img src="{{site.url}}{{site.path}}/assets/img/{{page.img}}" class="media-object img-circle pull-left" alt="{{ page.name }}" height="115" />
+  <div class="media-body">
+    <h3 class="media-heading team-name">{{ page.name }}</h3>
+    <strong>{{ page.topic }}</strong>
+    <hr class="pull-left">
+    <div class="clearfix"></div>
+    <p style="font-size:14px"> {{ page.session }}</p>
+    <p style="font-size:14px"><b>Abstract:</b> {{ page.abstract }}</p>
+    <p style="font-size:14px"><b>About:</b> {{ page.bio }}</p><br>
+</div><!-- media-body -->
+</div><!-- team-member media -->

data/_includes/topTable.html

@@ -0,0 +1,6 @@
+
+<div class="container-fluid"  align="left">
+      <!-- Three columns of text below the carousel -->
+      <div class="row">
+        <div class="col-lg-6">
+          <div markdown="1">

data/_includes/upcoming.html

@@ -0,0 +1,43 @@
+<!-- BOXED CONTENT -->
+<section>
+  <div class="heading-center" id="upcoming">
+    <h2 class="section-heading">UPCOMING EVENTS</h2>
+    <p class="lead">Application required</p>
+    <hr>
+  </div>
+  <div class="container">
+    <div class="row">
+      <!---div class="col-md-6">
+        <div class="boxed-content">
+          <h4 id="mmed">Clinic on Software Engineering for the Applied Mathematical Sciences</h4>
+          <img class="img-circle" src="{{ site.absoluteurl }}{{ site.baseurl }}/images/protea.jpg" alt="Western Cape" style="width: 180px; height: 180px;">
+          <br><br>
+          <p>Annually in South Africa, Kenya, or Rwanda</p>
+          <h2><a href="{{ site.absoluteurl }}{{ site.baseurl }}/seams/" title="SEAMS">SEAMS</a></h2>
+          <a href="{{ site.absoluteurl }}{{ site.baseurl }}/seams/" class="btn btn-primary btn-outline btn-rounded-2x">View details &raquo;</a>
+        </div>
+      </div--->
+      <div class="col-md-6">
+        <div class="boxed-content">
+          <h4 id="mmed">Clinic on the Meaningful Modeling of Epidemiological Data</h4>
+          <img class="img-circle" src="{{ site.absoluteurl }}{{ site.baseurl }}/images/cape.jpg" alt="Western Cape" style="width: 180px; height: 180px;">
+          <br><br>
+          <p>Annually in Cape Town, South Africa<br>Upcoming clinic: 26 June - 8 July, 2023</p>
+          <h2><a href="{{ site.absoluteurl }}{{ site.baseurl }}/mmed/" title="MMED">MMED</a></h2>
+          <a href="{{ site.absoluteurl }}{{ site.baseurl }}/mmed/" class="btn btn-primary btn-outline btn-rounded-2x">View details &raquo;</a>
+        </div>
+      </div>
+      <div class="col-md-6">
+        <div class="boxed-content">
+          <h4 id="daidd">Clinic on Dynamical Approaches to Infectious Disease Data</h4>
+          <img class="img-circle" src="{{ site.absoluteurl }}{{ site.baseurl }}/images/protea.jpg" alt="DAIDD" style="width: 180px; height: 180px;">
+          <br><br>
+          <p>Annually in December, Virtual on Microsoft Teams<br>Upcoming clinic: Dates TBA</p>
+          <h2><a href="{{ site.absoluteurl }}{{ site.baseurl }}/daidd/" title="DAIDD">DAIDD</a></h2>
+          <a href="{{ site.absoluteurl }}{{ site.baseurl }}/daidd/" class="btn btn-primary btn-outline btn-rounded-2x">View details &raquo;</a>
+        </div>
+      </div>
+    </div>
+  </div>
+</section>
+<!-- END BOXED CONTENT -->

data/_layouts/clinic.liquid

@@ -0,0 +1,43 @@
+<!DOCTYPE html>
+<html lang="en" class="fullscreen">
+{%include head.html%}
+  <body>
+	<!-- WRAPPER -->
+	 <div class="wrapper">
+     {%include navbar.html%}
+     {%include clinicNavbar.html%}
+     {%include header.html%}
+     {% if page.alertmsg contains "" %}
+        <div class="alert alert-{{page.alerttype}} alert-dismissible" role="alert">
+          							<button type="button" class="close" data-dismiss="alert"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
+          <div class="container padding-left=0px padding-right=0px">
+          <p style="font-size:16px; margin:0px">
+            {{ page.alertmsg }}
+          </p>
+        </div>
+      </div>
+     {%endif%}
+     <!-- PAGE CONTENT -->
+ 		<div class="page-content">
+ 			<div class="container">
+        <h1><span style="color: #15378a">{{page.subtitle}}</span></h1>
+
+         {{ content }}
+       </div>
+     </div>
+     <!-- END PAGE CONTENT -->
+         {% include footer.html %}
+    </div>
+    <!-- END WRAPPER -->
+    <!-- JAVASCRIPTS -->
+    <script src="{{ site.url }}/assets/js/jquery-2.1.1.min.js"></script>
+    <script src="{{ site.url }}/assets/js/bootstrap.min.js"></script>
+    <script src="{{ site.url }}/assets/js/plugins/slick/slick.min.js"></script>
+    <script src="{{ site.url }}/assets/js/plugins/easing/jquery.easing.min.js"></script>
+    <script src="{{ site.url }}/assets/js/plugins/scrollto/jquery.localscroll-1.2.7-min.js"></script>
+    <script src="{{ site.url }}/assets/js/plugins/scrollto/jquery.scrollTo-1.4.3.1-min.js"></script>
+    <script src="{{ site.url }}/assets/js/plugins/autohidingnavbar/jquery.bootstrap-autohidingnavbar.min.js"></script>
+    <script src="{{ site.url }}/assets/js/repute-scripts.js"></script>
+
+  </body>
+</html>