jekyll-theme-ici3d 0.1.0

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data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2023 International Clinics on Infectious Disease Dynamics and Data (ICI3D)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# jekyll-theme-ici3d
+
+This theme captures the cross-workshop templates, styles, and data for the Internation Clinics on Infectious Disease Dynamics and Data, [ICI3D](https://www.ici3d.org)
+
+Welcome to your new Jekyll theme! In this directory, you'll find the files you need to be able to package up your theme into a gem. Put your layouts in `_layouts`, your includes in `_includes`, your sass files in `_sass` and any other assets in `assets`.
+
+## Installation
+
+To use this theme in an ICI3D site:
+
+ 1. Add this line to workshop site `Gemfile`:
+
+```ruby
+gem "jekyll-theme-ici3d"
+```
+
+ 2. Add this line to the site `_config.yml`:
+
+```yaml
+theme: jekyll-theme-ici3d
+```
+
+ 3. Execute:
+
+```bash
+$ bundle # to have bundler install it for you OR
+$ gem install jekyll-theme-ici3d # use this to install yourself
+```
+
+## Usage
+
+TODO: Write usage instructions here. Describe your available layouts, includes, sass and/or assets.
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/jekyll-theme-ici3d. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](https://www.contributor-covenant.org/) code of conduct.
+
+## Development
+
+To set up your environment to develop this theme, run `bundle install`.
+
+Your theme is setup just like a normal Jekyll site! To test your theme, run `bundle exec jekyll serve` and open your browser at `http://localhost:4000`. This starts a Jekyll server using your theme. Add pages, documents, data, etc. like normal to test your theme's contents. As you make modifications to your theme and to your content, your site will regenerate and you should see the changes in the browser after a refresh, just like normal.
+
+When your theme is released, only the files in `_layouts`, `_includes`, `_sass` and `assets` tracked with Git will be bundled.
+
+To add a custom directory to your theme-gem, please edit the regexp in `jekyll-theme-ici3d.gemspec` accordingly.
+
+## License
+
+The theme is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/_data/publications/pulliam2012.yml

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+---
+title: Agricultural intensification, priming for persistence, and the emergence of Nipah virus, a lethal bat-borne zoonosis
+authors: <b>Pulliam</b>, Epstein, <b>Dushoff</b>, Rahman, Bunning, Jamaluddin, Hyatt, Field, Dobson, Daszak, and the Henipavirus Ecology Research Group
+link: http://dx.doi.org/10.1098/rsif.2011.0223
+doi: 10.1098/rsif.2011.0223
+journal: Journal of the Royal Society Interface
+year: 2012
+---
+
+<script type="text/javascript" src="https://d1bxh8uas1mnw7.cloudfront.net/assets/embed.js"></script>
+
+<div data-badge-popover="right" data-badge-type="donut" data-doi="{{ page.doi }}" data-hide-no-mentions="true" data-hide-less-than="3" class="altmetric-embed"></div>

data/_data/team/ackley.yml

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+---
+name: Sarah Ackley
+type: i3d_toAfrica
+role: I3D Research Exchange Scholar
+home: USA
+former: PhD student in Epidemiology, UCSF
+position: PhD student in Epidemiology
+affiliation: University of California – San Francisco (UCSF)
+img: scholars/ackley.jpg
+year: 2014
+host: South African Centre for Epidemiological Modelling and Analysis
+mentor: Prof. John Hargrove
+project: estimating tsetse fly mortality from entomological surveillance data
+outputs:
+  - title: A dynamic model for estimating adult female mortality from ovarian dissection data for the tsetse fly <em>Glossina pallidipes</em> Austen sampled in Zimbabwe
+    authors: <em>Ackley, SF</em> and <b>JW Hargrove</b>
+    link: https://doi.org/10.1371/journal.pntd.0005813
+    journal: PLoS Neglected Tropical Diseases
+    year: 2017
+  - title: Mortality estimates from ovarian age distributions of the tsetse fly <em>Glossina pallidipes</em> Austen sampled in Zimbabwe suggest the need for new analytical approaches
+    authors: <b>Hargrove, JW</b> and <em>SF Ackley</em>
+    link: http://journals.cambridge.org/abstract_S0007485315000073
+    journal: Bulletin of Entomological Research
+    year: 2015
+---

data/_data/team/are.yml

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+---
+name: Elisha Are, MSc
+type: mentor
+role: Mentor
+img: mentors/are.jpg
+position: Postdoctoral Fellow & Term Lecturer
+affiliation: Mathematics Department, Simon Fraser University, Canada
+degrees:
+  - degree: PhD
+    discipline: Mathematical Biology
+    institution: Stellenbosch University
+    year: 2015
+  - degree: MSc
+    discipline: Mathematics
+    institution: University of Ilorin
+    year: 2015
+  - degree: BSc
+    discipline: Mathematics
+    institution: University of Ilorin
+    year: 2013
+bio: Elisha B. Are is an infectious disease modeller, currently working as a postdoctoral research fellow in the Department of Mathematics, Simon Fraser University, British Columbia. He also holds a research associate position with the South African Centre for Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University.  Before taking up his current position at SFU, he completed his PhD in Mathematical biology at Stellenbosch University, South Africa. His PhD thesis focused on using mathematical models to quantify and predict the impact of climate change on tsetse and trypanosomiasis in Africa. He has six years of experience as a faculty member in the Mathematics Department, at Federal University Oye-Ekiti, Nigeria. He is currently interested in  understanding the role of several evolutionary, epidemiological and behavioral factors in shaping the transition of the COVID-19 pandemic to endemicity.
+---

data/_data/team/beauclair.yml

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+---
+name: Roxanne Beauclair
+type: i3d_toNA
+role: I3D Research Exchange Scholar
+home: South Africa
+former: PhD student, University of Ghent and SACEMA
+position: PhD student
+affiliation: University of Ghent and SACEMA
+img: scholars/beauclair.png
+year: 2016
+host: McMaster University
+mentor: Prof. Jonathan Dushoff
+project: evaluating the effect of age-mixing patterns on HIV transmission in Malawi
+---

data/_data/team/bekele.yml

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+---
+name: Bewketu Bekele
+type: i3d_toNA
+role: I3D Research Exchange Scholar
+home: Ethiopia
+former: Lecturer, Debre Markos University in Ethiopia
+position: Lecturer
+affiliation: Debre Markos University in Ethiopia
+img: scholars/bekele.jpg
+year: 2016
+host: McMaster University
+mentor: Prof. Jonathan Dushoff
+project: epidemic dynamics of HIV with treatment dropout
+---

data/_data/team/bellan.yml

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+---
+name: Steve Bellan, MPH, PhD
+type: founding
+role: Faculty Member, MMED and DAIDD clinics
+involvement: Faculty Member, MMED and DAIDD clinics
+position: Assistant Professor of Epidemiology and Biostatistics
+affiliation: University of Georgia, Athens, GA, USA
+img: team/bellan.jpg
+summary: Steve was a founding member of the ICI3D Core Faculty and served as Program Director from 2016-2018.
+icons: yes
+github: sbellan61
+orcid: 0000-0002-4110-272X
+linkedin: steven-bellan-36536229
+gscholar: LVbjeXEAAAAJ
+twitter: lechaquel
+website: http://bellanlab.uga.edu
+degrees:
+  - degree: PhD
+    discipline: Environmental Science, Policy, and Management
+    institution: UC Berkeley
+    year: 2012
+  - degree: MPH
+    discipline: Epidemiology
+    institution: UC Berkeley
+    year: 2008
+  - degree: AB
+    discipline: Ecology and Evolutionary Biology
+    institution: Princeton University
+    year: 2006
+papers:
+  - title: The statistical power and validity of Ebola vaccine trials in Sierra Leone - A simulation study of trial design and analysis
+    authors: <b>Bellan</b>, <b>Pulliam</b>, <b>Pearson</b>, Champredon, Fox, Skrip, Galvani, Gambhir, Lopman, <b>Porco</b>, Meyers, <b>Dushoff</b>
+    link: http://bellanlab.publichealth.uga.edu/wp-content/uploads/2016/09/BellanEtAl-SLEbola-LancetID-2015.pdf
+    journal: Lancet Infectious Diseases
+    year: 2015
+  - title: Re-assessment of HIV-1 acute phase infectivity - adjusting for biases with simulated cohorts
+    authors: <b>Bellan</b>, <b>Dushoff</b>, Galvani, Meyers
+    link: http://bellanlab.publichealth.uga.edu/wp-content/uploads/2016/09/Bellan-et-al-HIV-Acute-Infectivity-2015.pdf
+    journal: PLOS Medicine
+    year: 2015
+  - title: Extra-couple HIV transmission in sub-Saharan Africa - a mathematical modelling study of survey data
+    authors: <b>Bellan</b>, Fiorella, Melesse, Getz, <b>Williams</b>, <b>Dushoff</b>
+    journal: The Lancet
+    year: 2013
+bio: Steve served as the ICI3D Program Director from 2016-2018. He was involved as an organizer and instructor of the MMED and DAIDD clinics from 2009, after attending precursor workshops in 2007-2008 as a student. Steve’s background includes logistically challenging field work studying anthrax and rabies outbreaks in Namibian wildlife, as well as experience with a variety of mathematical, statistical and computational methods. His research projects span numerous pathogens and are united under the overarching theme of using mechanistic modeling and high performance computing to plan and interpret empirical studies. One of Steve’s projects centered on understanding heterogeneity in HIV transmissibility across individuals, explaining the dramatic variation in HIV epidemic severity across Africa. A second project aimed to optimally navigate the scientific and ethical tradeoffs involved in vaccine efficacy trials during emerging epidemics of pathogens such as the Ebola and Zika viruses. Steve was formerly an Assistant Professor of Epidemiology and Biostatistics at the University of Georgia.
+---

data/_data/team/bolton.yml

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+---
+name: Larisse Bolton, PhD
+type: workshop
+role: Faculty Member, DAIDD 2021
+involvement: Faculty Member, DAIDD clinic
+position: Researcher
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, South Africa
+img: mentors/bolton.jpg
+degrees:
+  - degree: PhD
+    discipline: Applied Mathematics
+    institution: University of the Free State
+    year: 2017
+  - degree: MSc
+    discipline: Mathematics and Applied Mathematics
+    institution: University of the Free State
+    year: 2009
+  - degree: BSc (Hons)
+    discipline: Mathematics and Applied Mathematics
+    institution: University of the Free State
+    year: 2008
+  - degree: BSc
+    discipline: Chemistry
+    institution: University of the Free State
+    year: 2007
+papers:
+  - title: Mind the gap - Patterns of red blood cell product usage in South Africa, 2014 - 2019
+    authors: <b>Bolton</b>, van den Berg, Swanevelder, <b>Pulliam</b>
+    link: http://dx.doi.org/10.7196%2FSAMJ.2021.v111i10.15658
+    journal: South African Medical Journal
+    year: 2021
+bio: Larisse Bolton holds a BSc in Chemistry and a PhD in Applied Mathematics from the University of the Free State in Bloemfontein, South Africa.  Her postgraduate research focused on the application of mathematical modelling in oncology using different approaches – model adaptation and model construction.  She was a postdoctoral research fellow at the DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA) in Stellenbosch from 2018-2021 and now holds the position of Researcher at SACEMA. Her current research focuses on blood systems analysis. She has been assessing blood product usage and demand in South Africa and is developing a predictive model for red blood cell product usage. The model will be used to investigate various scenarios of health system structuring.
+---

data/_data/team/borchering.yml

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+---
+name: Rebecca Borchering, PhD
+type: director
+role: ICI3D Co-Director
+role.old: Faculty Member, MMED and DAIDD clinics
+role.older: Faculty Member, DAIDD 2015-2019, MMED 2016-2019, 2021
+involvement: Faculty Member, MMED and DAIDD clinics
+position: Postdoctoral researcher, the Huck Institutes of the Life Sciences
+affiliation: The Pennsylvania State University, State College, PA, USA
+img: team/borchering.jpg
+summary: Rebecca received her PhD in Mathematics from the University of Florida (UF) in 2017 and is now a postdoctoral researcher in the in the Huck Institutes of the Life Sciences at the Pennsylvania State University. She completed a postdoc in the UF Department of Biology in 2017-2019 and a postdoc in the University of Georgia Odum School of ecology in 2019-2020. She was an MMED participant in 2014, served as the ICI3D Program Assistant for the 2015-2016 academic year, and joined the Workshop Faculty in 2015.
+icons: yes
+github: rborchering
+gscholar: JvBiQQYAAAAJ
+website: https://rebeccaborchering.com
+degrees:
+  - degree: PhD
+    discipline: Mathematics
+    institution: University of Florida
+    year: 2017
+  - degree: MS
+    discipline: Mathematics
+    institution: University of Florida
+    year: 2014
+  - degree: BS
+    discipline: Mathematics
+    institution: Arizona State University
+    year: 2011
+  - degree: BA
+    discipline: Philosophy
+    institution: Arizona State University
+    year: 2011
+bio: Rebecca is a postdoctoral researcher in the Huck Institutes of the Life Sciences at the Pennsylvania State University. She earned a PhD in Mathematics from the University of Florida in May 2017, focusing on stochastic processes of invasion and extinction, with particular applications for seasonal rabies virus dynamics. She previously held postdoctoral positions at the Emerging Pathogens Institute and Department of Biology at the University of Florida and at the Odum School of Ecology at the University of Georgia. Her research interests center around infectious disease modeling and public health applications. She is interested in the dynamics of co-circulating pathogens and her previous work includes investigating the effects of the 2015/2016 Zika epidemic in Latin America on endemic dengue dynamics and the emergence of novel influenza B viruses in the United States. Currently, she helps lead multi-model efforts to inform decision support in the face of uncertainty during the COVID-19 pandemic. She works on both the Multiple Models for Outbreak Decision Support (<a href = "https://midasnetwork.us/mmods/">MMODS</a>) and the <a href = "https://covid19scenariomodelinghub.org/">COVID-19 Scenario Modeling Hub</a> projects.
+papers:
+  - title: Resource-driven encounters and the induction of disease among consumers
+    authors: <b>Borchering</b>, <b>Bellan</b>, Flynn, <b>Pulliam</b>, McKinley
+    link: http://rsif.royalsocietypublishing.org/content/14/135/20170555
+    journal: Journal of the Royal Society Interface
+    year: 2017
+  - title: Continuum Approximation of Invasion Probabilities
+    authors: <b>Borchering</b>, McKinley
+    link: https://epubs.siam.org/doi/abs/10.1137/17M1155259
+    journal: Multiscale Modeling & Simulation
+    year: 2018
+  - title: Impacts of Zika emergence in Latin America on endemic dengue transmission
+    authors: <b>Borchering</b>, Huang, Mier-y-Teran-Romero, Rojas, Rodriguez-Barraquer, Katzelnick, Martinez, King, Cinkovich, Lessler, Cummings
+    link: https://doi.org/10.1038/s41467-019-13628-x
+    journal: Nature Communications
+    year: 2019
+  - title:  COVID-19 reopening strategies at the county level in the face of uncertainty - multiple models for outbreak decision support
+    authors: Shea, <b>Borchering</b>, Probert, Howerton, Bogich, Li, van Panhuis <em>et al</em>
+    link: https://doi.org/10.1101/2020.11.03.20225409
+    journal: medRxiv
+    year: 2020
+  - title:   Anomalous influenza seasonality in the United States and the emergence of novel influenza B/Victoria viruses
+    authors: <b>Borchering</b>, Gunning, Gokhale, Weedop, Saidpour, Brett, Rohani
+    link: https://doi.org/10.1073/pnas.2012327118
+    journal: Proceedings of the National Academy of Sciences
+    year: 2021
+  - title:  Modeling of future COVID-19 cases, hospitalizations, and deaths, by vaccination rates and nonpharmaceutical intervention scenarios — United States, April–September 2021
+    authors: <b>Borchering</b>, Viboud, Howerton, Smith, Truelove, Reich <em>et al</em>
+    link: https://www.cdc.gov/mmwr/volumes/70/wr/mm7019e3.htm
+    journal: MMWR
+    year: 2021
+---

data/_data/team/brook.yml

@@ -0,0 +1,15 @@
+---
+name: Cara Brook
+type: inactive
+role: Faculty Member, DAIDD 2015, MMED 2016
+involvement: Faculty Member, MMED and DAIDD clinics
+position: Miller Postdoctoral Fellow, Department of Integrative Biology
+affiliation: Univeristy of California - Berkeley, CA, USA
+position.old: PhD candidate, Department of Ecology and Evolutionary Biology
+affiliation.old: Princeton University, Princeton, NJ, USA
+img: team/brook.jpg
+summary: Cara is a Postdoctoral Fellow in the Department of Integrative Biology at Univeristy of California - Berkeley. She was an MMED participant in June 2015 and joined the Workshop Faculty in December 2015.
+icons: no
+github: carabrook
+website: http://www.princeton.edu/eeb/people/display_person.xml?netid=caraeb&display=Graduate
+---

data/_data/team/brown.yml

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+---
+name: Lauren Brown, BSc (Hons)
+type: mentor
+role: Mentor
+img: mentors/brown.jpg
+position: MSc candidate in Applied Mathematics<br>South African Centre for Epidemiological Modelling and Analysis
+affiliation: Stellenbosch University, Stellenbosch, South Africa
+degrees:
+  - degree: BSc Honours
+    discipline: Biomathematics
+    institution: Stellenbosch University
+    year: 2020
+  - degree: BSc
+    discipline: Mathematics
+    institution: Stellenbosch University
+    year: 2019
+bio: Lauren Brown is an MSc candidate at SACEMA. She recently submitted her thesis to Stellenbosch University, titled "Mathematical modelling of tuberculosis in South Africa - investigating the impact of interventions on population-level incidence and mortality." Her thesis was co-supervised by Dr Cari van Schalkwyk and Dr Florian Marx. She holds a BSc degree in Biomathematics, majoring in Biochemistry and Applied Mathematics, and a BSc Honours degree in the same. She will join SACEMA as a Junior Researcher in January 2023.
+---

data/_data/team/bruce.yml

@@ -0,0 +1,26 @@
+---
+name: Faikah Bruce, MSc
+type: evaluator
+role: ICI3D Program Evaluator
+position: Training Coordinator
+involvement: Faculty Member, MMED clinic
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, South Africa
+img: team/bruce.jpg
+summary: Faikah is a PhD candidate in the Department of Mathematics at Stellenbosch University and SACEMA's Training Coordinator. She was an MMED participant in 2011, served as an MMED mentor in 2012-2014, and joined the Workshop Faculty in 2015. She now serves as the ICI3D Program Evaluator.
+degrees:
+  - degree: MSc
+    discipline: Mathematical Sciences
+    institution: Stellenbosch University
+    year: 2013
+  - degree: Postgraduate Diploma
+    discipline: Mathematical Sciences
+    institution: African Institute for Mathematical Sciences – South Africa
+    year: 2010
+  - degree: BSc (Hons)
+    discipline: Applied Mathematics
+    institution: Nelson Mandela University
+    year: 2007
+icons: no
+github: faikah
+bio: Faikah obtained her BSc and BSc Hon in Applied Mathematics at Nelson Mandela University, Port Elizabeth, South Africa in 2008. She continued her studies to obtain a postgraduate diploma in Mathematical Sciences from the African Institute for Mathematical Sciences – South Africa in 2010, then proceeded to join the South African Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA) to obtain a Master of Science in Mathematical Sciences from Stellenbosch University in 2013. She is currently serves as SACEMA's Training Coordinator and, in this role, as the ICI3D Program Evaluator. She is also a PhD student at Stellenbosch University. She was an MMED participant in 2011, served as an MMED mentor in 2012-2014, and joined the Workshop Faculty in 2015. Her research so far has focused on the development and use of mathematical models to characterize, understand, and eventually to manage the epidemic of HIV and other sexually transmitted infections in South Africa. She is currently developing a stochastic, individual-based model to simulate the impact of various HIV prevention methods on the incidence of HIV and HSV-2, and their interaction, among adolescents. She has developed a risk scoring algorithm that aims to help individuals better understand their risk of acquiring HIV and how they could decrease this risk by adopting various HIV mitigation strategies. This application has been used in a project (part of the CHAMPS project) that assessed the acceptability of HIV pre-exposure prophylaxis among adolescents in Masiphumelele, South Africa. The application was developed as part of her PhD.
+---

data/_data/team/brucePA.yml

@@ -0,0 +1,9 @@
+---
+name: Faikah Bruce, MSc
+type: admin
+role: ICI3D Program Assistant (Africa)
+position: PhD candidate
+affiliation: South African Centre for Epidemiological Modelling and Analysis
+img: team/bruce.jpg
+summary: Faikah is a PhD candidate in the Department of Mathematics at Stellenbosch University. She was an MMED participant in 2011, served as an MMED mentor in 2012-2014, and joined the Workshop Faculty in 2015. Since January 2018, she also serves as the ICI3D Program Assistant for Africa, coordinating logistical aspects of the program for African participants and overseeing local logistics for the MMED clinic.
+---

data/_data/team/deleo.yml

@@ -0,0 +1,49 @@
+---
+name: Giulio De Leo, PhD
+type: workshop
+role: Faculty Member, DAIDD 2022
+involvement: Faculty Member, DAIDD clinic
+position: Professor
+affiliation: Department of Earth System Science and Department of Oceans<br>Stanford Doerr School of Sustainability<br>Stanford University
+img: team/deleo.jpg
+summary: Giulio De Leo is a disease ecologist interested in investigating factors and processes driving the dynamics of coupled natural and human systems and using this knowledge to identify levers for health and conservation, i.e., ecological interventions that can improve human wellbeing and the health of the environment that underpins it.  In the last ten years, he has been particularly interested in investigating how the development of water management infrastructures to support agricultural expansion and intensification may increase the risk of transmission of schistosomiasis, one of the most important of the so called Neglected Tropical Diseases.  He co-founded "The Upstream Alliance - partners in schistosomiasis reduction" and the [Stanford Program for Disease Ecology](https://ecohealthsolutions.stanford.edu/), Health and the Environment, with the goal of developing ecological solutions to control infectious diseases with an important environmental component in their transmission cycle.
+gscholar: lmmq0XsAAAAJ
+twitter:
+cv:
+degrees:
+  - degree: PhD
+    discipline: Ecology
+    institution: University of Parma, Italy
+    year: 1993
+  - degree: MS and BS
+    discipline: Environmental Engineering
+    institution: Politecnico di Milano, Italy
+    year: 1989
+papers:
+  - title: Filamentous bacteriophages and the competitive interaction between <em>Pseudomonas aeruginosa</em> strains under antibiotic treatment - a modeling study
+    authors: Pourtois, Kratochvil, Chen, Haddock, Burgener, <b>De Leo</b>, Bollyky
+    link: https://journals.asm.org/doi/10.1128/mSystems.00193-21
+    journal: mSystems
+    year: 2021
+  - title: Cost-effectiveness of combining drug and environmental treatments for environmentally transmitted diseases
+    authors: Francois, Sokolow, <b>De Leo</b>, Sanchirco
+    link: https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0966
+    journal: Proceedings of the Royal Society B
+    year: 2020
+  - title: Concomitant Immunity and worm senescence may drive schistosomiasis epidemiological patterns - an eco-evolutionary perspective
+    authors: Buck, <b>De Leo</b>, Sokolow
+    link: https://doi.org/10.3389/fimmu.2020.00160
+    journal: Frontiers in Microbiology
+    year: 2020
+  - title: Modelled effects of prawn aquaculture on poverty alleviation and schistosomiasis control
+    authors: Hoover, Sokolow , Kemp, Sanchirico, Lund, Jones, Higginson, Riveau, Savaya, Coyle, Wood, Micheli, Casagrandi, Mari, Gatto, Rinaldo, Perez-Saez, Rohr, Sagi, Remais, <b>De Leo</b>
+    link: https://www.nature.com/articles/s41893-019-0301-7
+    journal: Nature Sustainability
+    year: 2019
+  - title: Disease ecology, health and the environment - a framework to account for ecological and socio-economic drivers in the control of neglected tropical diseases
+    authors: Garchitorena, Sokolow, Roche, Ngonghala, Jocque, Lund, Barry, Mordecai, Daily, Jones, Andrews, Bendavid, Luby, LaBeaud, Seetah, Guégan,  Bonds, <b>De Leo</b>
+    link: http://dx.doi.org/10.1098/rstb.2016.0128
+    journal: Philosophical Transactions of the Royal Society B
+    year: 2017
+bio: Giulio De Leo is a disease ecologist interested in investigating factors and processes driving the dynamics of coupled natural and human systems and using this knowledge to identify levers for health and conservation, i.e., ecological interventions that can improve human wellbeing and the health of the environment that underpins it.  In the last ten years, he has been particularly interested in investigating how the development of water management infrastructures to support agricultural expansion and intensification may increase the risk of transmission of schistosomiasis, one of the most important of the so called Neglected Tropical Diseases.  He co-founded "The Upstream Alliance - partners in schistosomiasis reduction" and the [Stanford Program for Disease Ecology](https://ecohealthsolutions.stanford.edu/), Health and the Environment, with the goal of developing ecological solutions to control infectious diseases with an important environmental component in their transmission cycle.
+---

data/_data/team/delva.yml

@@ -0,0 +1,15 @@
+---
+name: Wim Delva, MD, PhD
+type: inactive
+role: Faculty Member, MMED 2010-2012, 2016
+involvement: Faculty Member, MMED clinic
+position: Deputy Director for Research
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, South Africa
+img: team/delva.jpg
+summary: Wim is the Deputy Director for Research at SACEMA and a Senior Lecturer of Mathematics at Stellenbosch University. He was on the faculty of the inaugural MMED clinic in 2010 and has been on the Workshop Faculty since the ICI3D Program started in 2012.
+icons: no
+github: wdelva
+orcid:
+linkedin: wimdelva
+gscholar: 7tUIcCIAAAAJ
+---

data/_data/team/dushoff.yml

@@ -0,0 +1,52 @@
+---
+name: Jonathan Dushoff, PhD
+type: director
+role: Clinic Director for DAIDD 2022
+role.old: ICI3D Co-Director<br>Program Director for North America
+involvement: Faculty Member, MMED and DAIDD clinics
+position: Professor of Biology
+affiliation: Department of Biology <br>Department of Mathematics and Statistics <br>McMaster University, Hamilton, ON, Canada
+img: team/dushoff.jpg
+summary: Jonathan is a Professor of Biology in the Department of Biology and Department of Mathematics and Statistics at McMaster University. He has been on the ICI3D Core Faculty since the program started in 2012. He became Program Director for North America in 2018 and is currently Co-Director of the ICI3D Program.
+icons: yes
+github: dushoff
+gscholar: yVwAcxMAAAAJ
+twitter: jd_mathbio
+website: http://www.biology.mcmaster.ca/dushoff/
+degrees:
+  - degree: PhD
+    discipline: Ecology and Evolutionary Biology
+    institution: Princeton University
+    year: 1997
+  - degree: BA
+    discipline: Mathematics and Environmental Studies
+    institution: University of Pennsylvania
+    year: 1986
+papers:
+  - title: Ebola control - effect of asymptomatic infection and acquired immunity
+    authors: <b>Bellan</b>, <b>Pulliam</b>, <b>Dushoff</b>, Meyers
+    link: https://www.ncbi.nlm.nih.gov/pubmed/25390569
+    journal: The Lancet
+    year: 2014
+  - title: Reevaluating cumulative HIV-1 viral load as a prognostic predictor - predicting opportunistic infection incidence and mortality in a Ugandan cohort
+    authors: Sempa, <b>Dushoff</b>, Daniels, Castelnuovo, Kiragga, Nieuwoudt, <b>Bellan</b>
+    link: https://www.ncbi.nlm.nih.gov/pubmed/27188943
+    journal: American Journal of Epidemiology
+    year: 2016
+  - title: Two approaches to forecast Ebola synthetic epidemics
+    authors: Champredon, Li, Bolker, <b>Dushoff</b>
+    link: https://www.ncbi.nlm.nih.gov/pubmed/28325495
+    journal: Epidemics
+    year: 2017
+  - title: Two approaches to forecast Ebola synthetic epidemics
+    authors: Champredon, Li, Bolker, <b>Dushoff</b>
+    link: https://www.ncbi.nlm.nih.gov/pubmed/28325495
+    journal: Epidemics
+    year: 2017
+  - title: Do pubmed search
+    authors: All Pubmed indexed papers
+    link: https://pubmed.ncbi.nlm.nih.gov/?term=dushoff+J*%5BAuthor%5D
+    journal: Various journals and co-authors
+    year: 1995–
+bio: Jonathan is a Professor of Biology at McMaster University in Hamilton, Canada, with cross appointments in the Department of Mathematics and Statistics, and the Institute for Infectious Disease Research. He has taught short courses annually in South Africa since 2007, starting with predecessors of the MMED clinic, and has been involved from the beginning in building and maintaining the ICI3D program. Jonathan has a broad interest in understanding the dynamics of infectious diseases by combining theoretical, statistical and computational approaches. Current interests include HIV control and the HIV treatment cascade; control of canine rabies; disease forecasting; and understanding the role of transmission intervals in disease dynamics.
+---

data/_data/team/ervin.yml

@@ -0,0 +1,10 @@
+---
+name: Sara Ervin, MA
+type: inactiveadmin
+role: ICI3D Program Assistant (North America)
+position: Administrative Associate
+affiliation: Department of Epidemiology and Biostatistics<br>University of Georgia
+img: team/ervin.jpg
+summary: Sara is an administrative assistant in the Department of Epidemiology and Biostatistics at the University of Georgia in Athens, GA, USA. She also serves as the ICI3D Program Assistant for North America, coordinating logistical aspects of the program for North American participants and overseeing local logistics for the DAIDD clinic.
+website: https://www.publichealth.uga.edu/epibio/about/directory/staff/sara_ervin
+---

data/_data/team/faikah.yml

@@ -0,0 +1,26 @@
+---
+name: Faikah Bruce, MSc
+type: inactive
+role: Faculty Member, MMED 2015-2016, MMED 2018
+involvement: Faculty Member, MMED clinic
+position: PhD candidate, South African Centre for Epidemiological Modelling and Analysis
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, South Africa
+img: team/bruce.jpg
+summary: Faikah is a PhD candidate in the Department of Mathematics at Stellenbosch University. She was an MMED participant in 2011, served as an MMED mentor in 2012-2014, and joined the Workshop Faculty in 2015.
+degrees:
+  - degree: MSc
+    discipline: Mathematical Sciences
+    institution: Stellenbosch University
+    year: 2013
+  - degree: Postgraduate Diploma
+    discipline: Mathematical Sciences
+    institution: African Institute for Mathematical Sciences – South Africa
+    year: 2010
+  - degree: BSc (Hons)
+    discipline: Applied Mathematics
+    institution: Nelson Mandela University
+    year: 2007
+icons: no
+github: faikah
+bio: Faikah obtained her BSc and BSc Hon in Applied Mathematics at Nelson Mandela University, Port Elizabeth, South Africa in 2008. She continued her studies to obtain a postgraduate diploma in Mathematical Sciences from the African Institute for Mathematical Sciences – South Africa in 2010, then proceeded to join the South African Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA) to obtain a Master of Science in Mathematical Sciences from Stellenbosch University in 2013. Still with SACEMA, she is currently a PhD student at Stellenbosch University. She was an MMED participant in 2011, served as an MMED mentor in 2012-2014, and joined the Workshop Faculty in 2015. She is currently serving as the ICI3D Program Assistant. Her research so far has focused on the development and use of mathematical models to characterize, understand, and eventually to manage the epidemic of HIV and other sexually transmitted infections in South Africa. She is currently developing a stochastic, individual-based model to simulate the impact of various HIV prevention methods on the incidence of HIV and HSV-2, and their interaction, among adolescents. She has developed a risk scoring algorithm that aims to help individuals better understand their risk of acquiring HIV and how they could decrease this risk by adopting various HIV mitigation strategies. This application has been used in a project (part of the CHAMPS project) that assessed the acceptability of HIV pre-exposure prophylaxis among adolescents in Masiphumelele, South Africa. The application was developed as part of her PhD.
+---

data/_data/team/grebe.yml

@@ -0,0 +1,36 @@
+---
+name: Eduard Grebe, PhD
+type: inactive
+role: Faculty Member, MMED 2018
+involvement: Faculty Member, MMED clinic
+position: Research Associate
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, South Africa
+img: team/grebe.jpg
+summary: Eduard is a Staff Scientist at Vitalant Research Institute and Research Associate at SACEMA. He was an MMED participant in 2016 and joined the Workshop Faculty in 2018.
+github: eduardgrebe
+orcid:
+linkedin:
+gscholar:
+twitter:
+impactstory:
+website:
+cv:
+degrees:
+  - degree: PhD
+    discipline: Economics
+    institution: University of Cape Town
+    year: 2012
+  - degree: MA
+    discipline: Philosophy
+    institution: Stellenbosch University
+    year: 2012
+  - degree: BA Hons
+    discipline: Philosophy
+    institution: Stellenbosch University
+    year: 2004
+  - degree: BA
+    discipline: Value and Policy Studies
+    institution: Stellenbosch University
+    year: 2002
+bio: Eduard is a Researcher at SACEMA who works primarily on HIV incidence estimation. He was the principal analyst for the CEPHIA collaboration, an international consortium established to independently evaluate HIV incidence assays (i.e. laboratory tests for ‘recent’ HIV infection, used in cross-sectional incidence estimation) and serves on the World Health Organisation’s technical working group on HIV incidence assays. He is also the maintainer of the open source inctools package for the R statistical programming language, which provides implementations of standard methods for cross- sectional incidence estimation and for ‘calibrating’ tests for recent infection. He has a background in social science, having obtained his PhD in economics from the University of Cape Town for work on HIV/AIDS policy and civil society health activism in Sub-Saharan Africa.
+---

data/_data/team/hargrove.yml

@@ -0,0 +1,36 @@
+---
+name: John Hargrove, PhD
+type: founding
+position: Senior Research Fellow
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, South Africa
+img: team/hargrove.jpg
+role: Faculty Member, MMED and DAIDD clinics
+summary: John is a Senior Research Fellow at the South African Centre for Epidemiological Modelling and Analysis (SACEMA) and Professor Emeritus of Mathematics at Stellenbosch University. He served as the Director of SACEMA from 2006-2010 and has been on the ICI3D Core Faculty since the program started in 2012.
+github: jhargrove
+gscholar: JhzWOuMAAAAJ
+degrees:
+  - degree: PhD
+    discipline: Insect Physiology
+    institution: University of London
+    year: 1973
+  - degree: MS
+    discipline: Biomathematics
+    institution: UC Los Angeles
+    year: 1981
+  - degree: BA (Honours)
+    discipline: Zoology
+    institution: University of Oxford
+    year: 1968
+papers:
+  - title: Heightened HIV antibody responses in postpartum women as exemplified by recent infection assays - implications for incidence estimates
+    authors: <b>Hargrove JW</b>, <b>van Schalkwyk C</b>, Humphrey JH, Mutasa K, Ntozini R, Owen SM, Masciotra S, Parekh BS, Duong YT, Dobbs T, Kilmarx PH, Gonese E
+    link: http://online.liebertpub.com/doi/abs/10.1089/AID.2016.0319
+    journal: AIDS Research and Human Retroviruses
+    year: in press
+  - title: Mortality estimates from ovarian age distributions of the tsetse fly <em>Glossina pallidipes</em> Austen sampled in Zimbabwe suggest the need for new analytical approaches
+    authors: <b>Hargrove JW</b>, Ackley SF
+    link: http://bellanlab.publichealth.uga.edu/wp-content/uploads/2016/09/Bellan-et-al-HIV-Acute-Infectivity-2015.pdf
+    journal: Bulletin of Entomological Research
+    year: 2015
+bio: John is a Professor Emeritus of Mathematical Sciences at Stellenbosch University and was the inaugural director of the South African Centre for Epidemiological Modelling and Analysis (SACEMA). The precursors for MMED and DAIDD were launched in 2006 at the beginning of his directorship and he has been involved continuously as an instructor in the programme since then. Over the past nearly 50 years John has combined fieldwork and mathematical epidemiology to understand the population dynamics and control of tsetse flies, the vectors of Human African Trypanosomiasis. His current interests are in the modelling population dynamics, with a particular focus on how increasing temperatures in Africa will affect tsetse distribution. This work involves improving estimation of mortality in adult and immature stages of the fly. Since 1999 he has also focused on the analysis and modelling of data in the world of HIV. Current interest are in improving the use of biomarkers for the accurate estimation of HIV incidence.
+---