Merge branch 'master' into survey-table

.gitignore

@@ -7,6 +7,7 @@ _site/
 .sass-cache/
 .jekyll-cache/
 .jekyll-metadata
+vendor/
 
 ### Python ###
 # Byte-compiled / optimized / DLL files

Gemfile.lock

@@ -197,14 +197,14 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
-    mini_portile2 (2.5.0)
+    mini_portile2 (2.5.1)
     minima (2.5.1)
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
     minitest (5.14.1)
     multipart-post (2.1.1)
-    nokogiri (1.11.1)
+    nokogiri (1.11.5)
       mini_portile2 (~> 2.5.0)
       racc (~> 1.4)
     octokit (4.18.0)

_data/navigation.yml

@@ -18,6 +18,8 @@
     link: /members/
   - name: Join
     link: /join/
+- name: Publications
+  link: /publications/
 - name: Contact
   link: "#contact"
 

_data/pubs.yml

@@ -0,0 +1,27 @@
+- title: "More Than Smell—COVID-19 Is Associated With Severe Impairment of Smell, Taste, and Chemesthesis"
+  abstract: "Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19–79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change ±100) revealed a mean reduction of smell (−79.7 ± 28.7, mean ± standard deviation), taste (−69.0 ± 32.6), and chemesthetic (−37.3 ± 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis. The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms."
+  link: https://doi.org/10.1093/chemse/bjaa041
+  materials: https://osf.io/a3vkw/
+  journal: Chemical Senses
+  yearPublished: 2020
+  imageloc: /assets/img/pub/2020-parma.png
+  webID: 101
+
+- title: "Recent Smell Loss Is the Best Predictor of COVID-19 Among Individuals With Recent Respiratory Symptoms"
+  abstract: "In a preregistered, cross-sectional study, we investigated whether olfactory loss is a reliable predictor of COVID-19 using a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0–100 visual analog scales (VAS) for participants reporting a positive (C19+; n = 4148) or negative (C19−; n = 546) COVID-19 laboratory test outcome. Logistic regression models identified univariate and multivariate predictors of COVID-19 status and post-COVID-19 olfactory recovery. Both C19+ and C19− groups exhibited smell loss, but it was significantly larger in C19+ participants (mean ± SD, C19+: −82.5 ± 27.2 points; C19−: −59.8 ± 37.7). Smell loss during illness was the best predictor of COVID-19 in both univariate and multivariate models (ROC AUC = 0.72). Additional variables provide negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms (e.g., fever). Olfactory recovery within 40 days of respiratory symptom onset was reported for ~50% of participants and was best predicted by time since respiratory symptom onset. We find that quantified smell loss is the best predictor of COVID-19 amongst those with symptoms of respiratory illness. To aid clinicians and contact tracers in identifying individuals with a high likelihood of having COVID-19, we propose a novel 0–10 scale to screen for recent olfactory loss, the ODoR-19. We find that numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4 < OR < 10). Once independently validated, this tool could be deployed when viral lab tests are impractical or unavailable."
+  link: https://doi.org/10.1093/chemse/bjaa081
+  materials: https://github.com/GCCR/gccr002
+  journal: Chemical Senses
+  yearPublished: 2020
+  imageloc: /assets/img/pub/2020-Gerkin.png
+  webID: 102
+
+- title: "Smell and taste changes are early indicators of the COVID-19 pandemic and political decision effectiveness"
+  abstract: "In response to the COVID-19 pandemic, many governments have taken drastic measures to avoid an overflow of intensive care units. Accurate metrics of disease spread are critical for the reopening strategies. Here, we show that self-reports of smell/taste changes are more closely associated with hospital overload and are earlier markers of the spread of infection of SARS-CoV-2 than current governmental indicators. We also report a decrease in self-reports of new onset smell/taste changes as early as 5 days after lockdown enforcement. Cross-country comparisons demonstrate that countries that adopted the most stringent lockdown measures had faster declines in new reports of smell/taste changes following lockdown than a country that adopted less stringent lockdown measures. We propose that an increase in the incidence of sudden smell and taste change in the general population may be used as an indicator of COVID-19 spread in the population."
+  link: https://doi.org/10.1038/s41467-020-18963-y
+  materials: https://osf.io/gew7p/
+  journal: Nature Communications
+  yearPublished: 2020
+  imageloc: /assets/img/pub/2020-Pierron.png
+  webID: 103
+

_sass/main.scss

@@ -4,11 +4,28 @@
 .partners-logo {
   max-width: 180px;
 }
+
 .big-line-breaks br {
   display: block;
   margin-top: 15px;
   content: " ";
 }
+
+.publication-img {
+  max-width: 180px;
+  border: 2px solid #555;
+  box-shadow: 5px 10px 18px grey;
+  margin-top: 30px;
+  margin-bottom: 30px;
+  margin-right: 30px;
+  margin-left: 30px;
+  float: left;
+
+  @media(min-width:992px) {
+    float: none;
+    }
+}
+
 // literature page
 .color-covid19 {background-color: #f78686;}
 .color-viral {background-color: #ffd175;}
@@ -17,10 +34,12 @@
 .color-genes {background-color: #75a3ff;}
 .color-smell {background-color: #79db86;}
 .color-taste {background-color: #a8916c;}
+
 // survey table
 .survey-table {margin: 0 auto;}
 .survey-table td {padding: 5px 20px;}
 @media (max-width: 768px) {
   .survey-table td {padding: 5px;}
 }
 .survey-table img {width: 64px;}
+

_scripts/requirements.txt

@@ -28,7 +28,7 @@ openpyxl==3.0.5
 packaging==20.4
 pandas==1.1.2
 pathlib==1.0.1
-Pillow==8.1.1
+Pillow==8.2.0
 pyparsing==2.4.7
 pyproj==2.6.1.post1
 python-dateutil==2.8.1
@@ -60,5 +60,5 @@ protobuf==3.13.0
 pyasn1==0.4.8
 pyasn1-modules==0.2.8
 requests-oauthlib==1.3.0
-rsa==4.6
+rsa==4.7
 uritemplate==3.0.1

_surveys/fr.md

@@ -1,6 +1,6 @@
 ---
 title: Français
-description: Participez à l'étude du GCCR !
+description: Participez aux études du GCCR !
 lang: fr_FR   # https://www.unicode.org/cldr/charts/latest/supplemental/language_territory_information.html
 language: French
 hello: Bonjour !
@@ -10,6 +10,19 @@ contact: Pour plus d'informations à propos de cette étude, merci de contacter
 leader_email: [email protected]
 survey_url: https://psusensory.compusensecloud.com/edu/login.aspx?t=be8c9203-1e43-4933-aad2-bf6b9ffe159e
 short_url: https://bit.ly/3a1A7b0
+selfcheck_url: http://riech-check.de/
+take_selfcheck: Faire l'auto-évaluation
+share_selfcheck: Partager l'auto-évaluation
+selfcheck_response: Compte tenu de votre réponse, vous êtes invité à
+selfcheck_choices: [
+    "Je souffre actuellement d'une maladie respiratoire (COVID-19, grippe, rhume)",
+    "J'ai souffert, au cours des deux dernières semaines, d'une maladie respiratoire (COVID-19, grippe, rhume)",
+    "J'ai souffert d'une maladie respiratoire (COVID-19, grippe, rhume), il y a de cela plus de 2 semaines",
+    "J'ai été malade et maintenant je veux surveiller mon odorat et mon sens du goût",
+    "Je veux surveiller mon odorat et mon sens du goût"
+]
+contact_selfcheck: Pour plus d'informations sur notre test d'évaluation des odeurs et des saveurs, veuillez contacter Kathrin Ohla
+email_selfcheck: [email protected]
 ---
 Le GCCR est un groupement de 600 scientifiques, cliniciens et personnes physiques ou morales couvrant plus de 50 pays. Il a été créé pour répondre à la pandémie de COVID19. 
 

index.html

@@ -108,6 +108,7 @@ <h2 class="section-heading text-uppercase">Mission</h2>
 
 
 <!-- Partners -->
+<!--
 <section class="py-5">
   <div class="container">
     <div class="col-md-3 col-sm-3">
@@ -123,3 +124,4 @@ <h2 class="section-heading text-uppercase">Mission</h2>
     </div>
   </div>
 </section>
+-->

publications.html

@@ -0,0 +1,66 @@
+---
+title: Publications
+description: GCCR Publications 
+sitemap:
+  priority: 0.8
+---
+<!-- Created by KWC on 210606 -->
+<!-- Data derived from the pubs.yml file -->
+
+<!-- Publications -->
+<section class="page-section" id="intro">
+    <div class="container">
+
+        <div class="col-lg-12 col-md-12 col-sm-12 text-left">
+          <h2 class="section-heading text-uppercase text-center">GCCR Publications</h2>
+
+            {% for pubitem in site.data.pubs %}
+            <div class="container">
+                <div class="row">
+<!--                <div class="col-lg-12 col-md-12 col-sm-12"> -->
+                <!-- Paper icon (css in main.scss) -->
+
+                <div class="col-lg-4 col-md-5 col-sm-12"> 
+                    <a href="{{ pubitem.link }}" target="_blank">
+                    <img class="img-fluid publication-img" src="{{ pubitem.imageloc }}" alt="{{ pubitem.title }}">
+                    </a>
+                </div>
+                <!-- Paper Data -->
+                <div class="col-lg-8 col-md-7 col-sm-12"> 
+                    <nav>
+                      <div class="nav nav-tabs" id="nav-tab" role="tablist">
+                        <a class="nav-link active" id="nav-home-tab{{ pubitem.webID }}" data-toggle="tab" href="#nav-home{{ pubitem.webID }}" role="tab" aria-controls="nav-home{{ pubitem.webID }}" aria-selected="true">Info</a>
+                        <a class="nav-link" id="nav-profile-tab{{ pubitem.webID }}" data-toggle="tab" href="#nav-profile{{ pubitem.webID }}" role="tab" aria-controls="nav-profile{{ pubitem.webID }}" aria-selected="false">Abstract</a>
+                        <a class="nav-link" id="nav-contact-tab{{ pubitem.webID }}" data-toggle="tab" href="#nav-contact{{ pubitem.webID }}" role="tab" aria-controls="nav-contact{{ pubitem.webID }}" aria-selected="false">Resources</a>
+                      </div>
+                    </nav>
+                    <div class="tab-content" id="nav-tabContent">
+                      <div class="tab-pane fade show active" id="nav-home{{ pubitem.webID }}" role="tabpanel" aria-labelledby="nav-home-tab{{ pubitem.webID }}">
+                          <br>
+                          <p><b> {{ pubitem.title }}</b></p>
+                          <p><i>{{ pubitem.yearPublished }} {{ pubitem.journal }}</i></p>
+                          <p> <a href="{{ pubitem.link}}" target="_blank"> Paper link </a>
+                      </div>
+                      <div class="tab-pane fade" id="nav-profile{{ pubitem.webID }}" role="tabpanel" aria-labelledby="nav-profile-tab{{ pubitem.webID }}">
+                      <p> {{ pubitem.abstract }} </p>  
+
+                      </div>
+                      <div class="tab-pane fade" id="nav-contact{{ pubitem.webID }}" role="tabpanel" aria-labelledby="nav-contact-tab{{ pubitem.webID }}">
+                      <br>
+                      <p> Data and code avaliable <a href="{{ pubitem.materials }}" target="_blank">here</a>
+                      </div>
+                    </div>
+
+<!--                </div>-->
+                </div>
+
+            </div>
+            <br>
+            </div>
+            {% endfor %}
+
+
+      </div>
+  </div>
+</section>
+<!--<script src="/assets/js/literature.js"></script>-->