From 77f52a80877bdcb389329b47794ddc9643744afb Mon Sep 17 00:00:00 2001 From: Gabriella Azzopardi Date: Tue, 11 May 2021 10:20:47 +0000 Subject: [PATCH] Introduce About page --- cara/apps/calculator/__init__.py | 13 ++++ cara/apps/templates/about.html.j2 | 55 +++++++++++++++++ cara/apps/templates/common_text.md.j2 | 72 +++++++++++++++++++++++ cara/apps/templates/index.html.j2 | 2 +- cara/apps/templates/layout.html.j2 | 6 +- cara/tests/apps/calculator/test_webapp.py | 1 - 6 files changed, 146 insertions(+), 3 deletions(-) create mode 100644 cara/apps/templates/about.html.j2 diff --git a/cara/apps/calculator/__init__.py b/cara/apps/calculator/__init__.py index 37c2e48c..57376206 100644 --- a/cara/apps/calculator/__init__.py +++ b/cara/apps/calculator/__init__.py @@ -127,6 +127,18 @@ class LandingPage(BaseRequestHandler): self.finish(report) +class AboutPage(BaseRequestHandler): + def get(self): + template_environment = self.settings["template_environment"] + template = template_environment.get_template("about.html.j2") + report = template.render( + user=self.current_user, + active_page="about", + text_blocks=template_environment.globals['common_text'] + ) + self.finish(report) + + class CalculatorForm(BaseRequestHandler): def get(self): template = self.settings["template_environment"].get_template( @@ -171,6 +183,7 @@ def make_app( urls: typing.Any = [ (r'/?', LandingPage), (r'/_c/(.*)', CompressedCalculatorFormInputs), + (r'/about', AboutPage), (r'/static/(.*)', StaticFileHandler, {'path': static_dir}), (prefix + r'/?', CalculatorForm), (prefix + r'/report', ConcentrationModel), diff --git a/cara/apps/templates/about.html.j2 b/cara/apps/templates/about.html.j2 new file mode 100644 index 00000000..3ff6222d --- /dev/null +++ b/cara/apps/templates/about.html.j2 @@ -0,0 +1,55 @@ +{% extends "page.html.j2" %} + +{% block contents %} + +

Airborne Transmission of SARS-CoV-2


+Currently, the existing public health measures point to the importance of proper building and environmental engineering control measures, such as proper Indoor Air Quality (IAQ). +This pandemic clearly raised increased awareness on airborne transmission of respiratory viruses in indoor settings. +Out of the main modes of viral transmission, the airborne route of SARS-CoV-2 seems to have a significant importance to the spread of COVID-19 infections world-wide, hence proper guidance to building engineers or facility managers, on how to prevent on-site transmission, is essential.
+For information on the Airborne Transmission of SARS-CoV-2, feel free to check out the HSE Seminar: https://cds.cern.ch/record/2743403.
+Slides available in https://indico.cern.ch/event/968258/. + +

What is CARA?


+CARA stands for COVID Airborne Risk Assessment and was developed in the spring of 2020 to better understand and quantify the risk of long-range airborne spread of SARS-CoV-2 virus in workplaces. CARA comes with different applications that allow more or less flexibility in the input parameters: + + +The mathematical and physical model simulate the long-range airborne spread of SARS-CoV-2 virus in a finite volume, assuming a homogenous mixture, and estimates the risk of COVID-19 infection therein. The results DO NOT include short-range airborne exposure (where the physical distance plays a factor) nor the other known modes of SARS-CoV-2 transmission. Hence, the output from this model is only valid when the other recommended public health & safety instructions are observed, such as adequate physical distancing, good hand hygiene and other barrier measures.
+

The methodology, mathematical equations and parameters of the model are described here: https://edms.cern.ch/ui/file/2566402/1/CARA_Deterministic_parameters_2020.pdf.

+ +The model used is based on scientific publications relating to airborne transmission of infectious diseases, virology, epidemiology and aerosol science. It can be used to compare the effectiveness of different airborne-related risk mitigation measures. + +The tool helps assess the potential dose of infectious airborne viruses in indoor gatherings, with people seated, standing, moving around, while breathing, speaking or shouting/singing. The model is based on the Wells-Riley model of aerosol disease transmission, which assumes a fixed value for the average infectious dose. The dose-response models for respiratory diseases is more accurate, although since this parameter for SARS-CoV-2 is not known so far, the Wells-Riley method is recommended in the health science community (see References). +The methodology of the model is divided into three parts: +
    +
  1. Estimating the emission rate of infectious viruses.
    2. +
  2. Modeling the concentration evolution of viruses within a given volume and consequent inhalation dose during the exposure time.
    3. +
  3. Estimating the probability of a COVID-19 infection, the expected number of new cases arising from the transmission event and the basic reproduction rate (R0).
    4. +
+Parts #1 and #3 are mainly based on methods published in scientific papers (see References), and cover the medical aspects, which is not the core competencies of the authors. The ‘heart and soul’ of CARA lies within the Part #2 and the concentration modelling, which is based on a mass-balance differential equation solved for a constant emission rate and time-dependent exchange rate (e.g. natural ventilation flow rate). Other aspects, e.g., the biological decay of the virus in the air, gravitational settlement of the aerosols, mechanical supply of fresh air, effect of HEPA filtration, among others, are also included.
+ +

What is the aim of CARA?


+Although the user is able to calculate the infection probability of a stand-alone event with a pre-defined set of protection measures, the main utility of CARA is to compare the relative impact of different measures and/or combination of measure. For example: + + +

Authors:


+{{ text_blocks['Authors'] }} + +

Acknowledgements:


+{{ text_blocks['Acknowledgements'] }} + +

References:


+{{ text_blocks['References'] }} + +
+
+ +{% endblock contents %} diff --git a/cara/apps/templates/common_text.md.j2 b/cara/apps/templates/common_text.md.j2 index e69de29b..3bffc818 100644 --- a/cara/apps/templates/common_text.md.j2 +++ b/cara/apps/templates/common_text.md.j2 @@ -0,0 +1,72 @@ +## Authors + +

Andre Henriques1, Marco Andreini1, Gabriella Azzopardi2, James Devine3, Philip Elson4, Nicolas Mounet2, Markus Kongstein Rognlien2, Nicola Tarocco5


+ +1HSE Unit, Occupational Health & Safety Group, CERN
+2Beams Department, Accelerators and Beam Physics Group, CERN
+3Experimental Physics Department, Safety Office, CERN
+4Beams Department, Controls Group, CERN
+5Information Technology Department, Collaboration, Devices & Applications Group, CERN
+ +## Acknowledgements + +We wish to thank CERN’s HSE Unit, Beams Department, Experimental Physics Department, Information Technology Department, Industry, Procurement and Knowledge Transfer Department and International Relations Sector for their support to the study. Thanks to Doris Forkel-Wirth, Benoit Delille, Walid Fadel, Olga Beltramello, Letizia Di Giulio, Evelyne Dho, Wayne Salter, Benoit Salvant and colleagues from the COVID working group for providing expert advice and extensively testing the model. Finally, we wish to thank Fabienne Landua and the design service for preparing the illustrations and Alessandro Raimondo, Ana Padua and Manuela Cirilli from the Knowledge Transfer Group for their continuous support. Our compliments towards the work and research performed by world leading scientists in this domain: Prof. Manuel Gameiro, Prof. Shelly Miller, Prof. Linsey Marr, Prof. Jose Jimenez, Dr. Lidia Morawska, Prof Yuguo Li et al. – their scientific contribution was indispensable for this project. + +## References + +[1] Jimenez, J. (2020), COVID-19 Data Dives: Why Arguments Against SARS-CoV-2 Aerosol Transmission Don't Hold Water https://www.medscape.com/viewarticle/934837?src=uc_mscpedt&faf=1.
+[2] Jimenez, J. (2020), Summary of the Evidence For and Against the Routes of Transmission of SARS-CoV-2. https://tinyurl.com/aerosol-pros-cons.
+[3] Miller SL, Nazaroff WW, Jimenez JL, et al. Transmission of SARS-CoV-2 by inhalation of respiratory aerosol in the Skagit Valley Chorale superspreading event. Indoor Air. 2020;00:1–10. https://doi.org/10.1111/ina.12751.
+[4] Gameiro da Silva, Manuel. (2020). An analysis of the transmission modes of COVID-19 in light of the concepts of Indoor Air Quality. 10.13140/RG.2.2.28663.78240.
+[5] Stephanie Taylor, (2019). Optimize Occupant Health, Building Energy Performance and Your Revenue Through Indoor-Air Hydration.
+[6] REHVA COVID-19 guidance document, April 3, 2020.
+[7] Morawska, L, Milton, D. It Is Time to Address Airborne Transmission of Coronavirus Disease 2019 (COVID-19), Clinical Infectious Diseases, , ciaa939, https://doi.org/10.1093/cid/ciaa939.
+[8] Wei, Jianjian & Li, Yuguo. (2015). Enhanced spread of expiratory droplets by turbulence in a cough jet. Building and Environment. 93. 10.1016/j.buildenv.2015.06.018.
+[9] Doremalen N et al. (2020). Aerosol and surface stability of HCoV-19 (SARS-CoV-6 2) compared to SARS-CoV-1. doi:10.1101/2020.03.09.20033217.
+[10] Bourouiba L., Turbulent Gas Clouds and Respiratory Pathogen Emissions: Potential Implications for Reducing Transmission of COVID-19. JAMA. Published online March 26, 2020. doi:10.1001/jama.2020.4756.
+[11] Fauci A. 2020. Transmission of SARS-CoV-2, Citizen by CNN.
+[12] Chen W. 9, Zhang N., et al. (2020) Short-range airborne route dominates exposure of respiratory infection during close contact. Building and Environment, Volume 176, 10.1016/j.buildenv.2020.10685.
+[13] Office of the Prime Minister and the Ministry of Health, Labor and Welfare of Japan, 2020.
+[14] World Health Organization holds news conference on coronavirus outbreak – 2/11/2020, min 41:40 - https://youtu.be/edvsh6x_f4Q.
+[15] WHO (2020). Transmission of SARS-CoV-2: implications for infection prevention precautions. WHO/2019-nCoV/Sci_Brief/Transmission_modes/2020.3.
+[16] Chapin, C. (1912). The sources and modes of infection. The Library of Congress urn:oclc:record:1085180298.
+[17] CERN Instruction on COVID-19 Health and Safety Measures, EDMS N. 2370903.
+[18] CERN instructions on COVID-19 related health and safety measures – Appendix A on HVAC, EDMS N. 2389839.
+[19] CDC, Scientific Brief: SARS-CoV-2 and Potential Airborne Transmission. https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-brief-sars-cov-2.html.
+[20] Li, Yuguo et al. (2020). Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant. 10.1101/2020.04.16.20067728.
+[21] Lu J, Gu J, Li K, et al. COVID-19 outbreak associated with air conditioning in restaurant, Guangzhou, China, 2020. Emerg Infect Dis. CDC - Volume 26, Number 7, 10.3201/eid2607.200764.
+[22] Shen Y, Li C, Dong H, et al. Community Outbreak Investigation of SARS-CoV-2 Transmission Among Bus Riders in Eastern China. JAMA Intern Med. Published online September 01, 2020. doi:10.1001/jamainternmed.2020.5225.
+[23] Park S, Kim Y, Yi S, et al. Coronavirus Disease Outbreak in Call Center, South Korea. Emerging Infectious Diseases. 2020;26(8):1666-1670. doi:10.3201/eid2608.201274.
+[24] Liu, Y., Ning, Z., Chen, Y. et al. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals. Nature (2020). 10.1038/s41586-020-2271-3.
+25] Twitter @EmmanuelMacron https://twitter.com/EmmanuelMacron/status/1316485827715829762?s=20.
+[26] Gao, X., Li, Y. and Leung, G.M., 2009. Ventilation control of indoor transmission of airborne diseases in an urban community. Indoor and Built Environment , 18(3), pp.205 -218.
+[27] Zhu S, Jenkins S, Addo K, et al. Ventilation and laboratory confirmed acute respiratory infection (ARI) rates in college residence halls in College Park, Maryland. Environment International. 2020;137:105537. doi:10.1016/j.envint.2020.105537.
+[28] Perry J.L., et al. Submicron and Nanoparticulate Matter Removal by HEPA-Rated Media Filters and Packed Beds of Granular Materials. NASA/TM—2016–218224.
+[29] Julian W. Tang, et al. (2009) A schlieren optical study of the human cough with and without wearing masks for aerosol infection control J . R. Soc. Interface.6S727–S736. 10.1098/rsif.2009.0295.focus.
+[30] Buonanno, G., et al. (2020) “Estimation of airborne viral emission: Quanta emission rate of SARS-CoV-2 for infetion risk assessment”, https://doi.org/10.1016/j.envint.2020.105794.
+[31] Buonanno, G., et al. (2020) “Quantitative assessment of the risk of airborne transmission of SARS-CoV-2 infection: Prospective and retrospective applications ”, https://doi.org/10.1016/j.envint.2020.106112.
+[32] Gammaitoni, L. et al. (1997) “Using a mathematical model to evaluate the efficacy of TB control measures.”, Emerg. Infect. Dis. (1997), pp. 335-342, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2627642.
+[33] Huang, J.T., et al. (2007) “Evaluation of the Efficiency of Medical Masks and the Creation of New Medical Masks.”, J. Int. Medical Research, 35: 213 – 223, https://doi.org/10.1177/147323000703500205.
+[34] Morawska, L. et al. (2009), “Size distribution and sites of origin of droplets expelled from the human respiratory tract during expiratory activities”, J. Aerosol Science, 256-269, https://doi.org/10.1016/j.jaerosci.2008.11.002.
+[35] Riley, E.C., et al. (1978), “Airborne spread of measles in a suburban elementary school.”, Am. J. Epidemiol. 107, 421–432, https://doi.org/10.1093/oxfordjournals.aje.a112560.
+[36] Sze To, G.N., Chao, C.Y.H. (2010). “Review and comparison between the Wells-Riley and dose-response approaches to risk assessment of infectious respiratory diseases.” Indoor Air 20, 2–16. https://doi.org/10.1111/j.1600-0668.2009.00621.x.
+[37] Wells, W.F., (1934). “On airborne infection: study II. Droplets and Droplet nuclei.” Am. J. Epidemiol. 20, 611–618. https://doi.org/10.1093/oxfordjournals.aje.a118097.
+[38] Wells, W.F. (1955). “Airborne contagion and air hygiene. Cambridge, MA: Harvard University Press”, https://doi.org/10.1111/j.1746-1561.1955.tb08015.x.
+[39] EL PAIS, An analysis of three Covid-19 outbreaks: how they happened and how they can be avoided. https://english.elpais.com/spanish_news/2020-06-17/an-analysis-of-three-covid-19-outbreaks-how-they-happened-and-how-they-can-be-avoided.html?ssm=TW_CC.
+[40] WHO. Avoid the three C’s – Be aware of different levels of risk in different settings. https://www.who.int/images/default-source/wpro/countries/malaysia/infographics/three-3cs/final-avoid-the-3-cs-poster.tmb-1920v.jpg?sfvrsn=638335c1_1.
+[41] Miller, S. Germicidal Ultraviolet Light (Radiation) for Reducing Disease Transmission. https://shellym80304.files.wordpress.com/2020/05/isiaq-guv-2-compiled.pdf +[42] CDC. How COVID-19 Spreads. https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/how-covid-spreads.html.
+[43] Thomas, Y. et al. (2014). Survival of influenza virus on human fingers. Clin Microbiol Infect ;20: O58–O64 10.1111/1469-0691.12312.
+[44] Tang, J. (2020). The Guardian, Understanding 'aerosol transmission' could be key to controlling coronavirus. https://www.theguardian.com/commentisfree/2020/oct/28/understanding-aerosol-transmission-key-controlling-coronavirus-wash-hands.
+[45] Johnson, G.R. et al. Modality of human expired aerosol size distributions. Journal of Aerosol Science 42 (2011) 839–851840, doi:10.1016/j.jaerosci.2011.07.009.
+[46] Li, Yuguo (2020). SARS-CoV-2 airborne transmission is opportunistic and ventilation works. University of Hong Kong. COVID-19 zoom conference. https://www.hku.hk/f/upload/21292/HKU%20Covid-19%20Zoom%20conference.pdf.
+[47] Marr, L. (2020). Aerosol and Transmission of Respiratory Viruses 101, Airborne Transmission of SARS-CoV-2: A Virtual Workshop. https://www.nationalacademies.org/event/08-26-2020/airborne-transmission-of-sars-cov-2-a-virtual-workshop?s=09 .
+[48] Morawska, L. (2006). Droplet fate in indoor environments, or can we prevent the spread of infection?. Indoor Air, Volume: 16, Issue: 5, Pages: 335-347, doi:10.1111/j.1600-0668.2006.00432.x.
+[49] Marr, L.C., Tang, J.W., Van Mullekom, J., et al., 2019, Mechanistic insights into the effect of humidity on airborne influenza virus survival, transmission and incidence, J Roy Soc Interface. https://doi.org/10.1098/rsif.2018.0298.
+[50] Roy C, Milton D, Airborne Transmission of Communicable Infection — The Elusive Pathway, N Engl J Med 2004; 350:1710-1712, doi: 10.1056/NEJMp04805.
+[51] Hui, K. P. Y. et al. (2020), Tropism, replication competence, and innate immune responses of the coronavirus SARS-CoV-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures, Lancet Respir Med, Volume 8, Issue 7, Pages 687-695, doi:10.1016/S2213-2600(20)30193-4.
+[52] Morawska, Lidia & Cao, Junji. (2020). Airborne transmission of SARS-CoV-2: The world should face the reality. Environment International. 139. 105730. 10.1016/j.envint.2020.105730.
+[53] Milton D.,, A Rosetta Stone for Understanding Infectious Drops and Aerosols, Journal of the Pediatric Infectious Diseases Society, Volume 9, Issue 4, 1 September 2020, Pages 413–415, https://doi.org/10.1093/jpids/piaa079.
+[54] Leung, N.H.L et al. Respiratory virus shedding in exhaled breath and efficacy of face masks. Nat Med (2020). 10.1038/s41591-020-0843-2.
+[55] Asadi, S., Cappa, C.D., Barreda, S. et al. Efficacy of masks and face coverings in controlling outward aerosol particle emission from expiratory activities. Sci Rep 10, 15665 (2020). https://doi.org/10.1038/s41598-020-72798-7.
+[56] Endo A, Abbott S et al. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China [version 3; peer review: 2 approved]. Wellcome Open Res 2020, 5:67. doi:10.12688/wellcomeopenres.15842.3.
diff --git a/cara/apps/templates/index.html.j2 b/cara/apps/templates/index.html.j2 index 2e814fd1..b75b529d 100644 --- a/cara/apps/templates/index.html.j2 +++ b/cara/apps/templates/index.html.j2 @@ -22,7 +22,7 @@

CARA is a risk assessment tool developed to model the concentration of viruses in enclosed spaces, in order to inform space-management decisions. It does this by simulating the long-range airborne spread SARS-CoV-2 virus in a finite volume, assuming homogenous mixing, and it estimates the risk of COVID-19 infection therein. - Please see the about page for more details on the methodology, assumptions and limitations of CARA. + Please see the About page for more details on the methodology, assumptions and limitations of CARA.

The full CARA source code can be accessed freely under an Apache 2.0 open source license from our code repository. diff --git a/cara/apps/templates/layout.html.j2 b/cara/apps/templates/layout.html.j2 index be46f836..a5fe95ea 100644 --- a/cara/apps/templates/layout.html.j2 +++ b/cara/apps/templates/layout.html.j2 @@ -155,7 +155,11 @@ - +

  • + + About + +
    • diff --git a/cara/tests/apps/calculator/test_webapp.py b/cara/tests/apps/calculator/test_webapp.py index ca7a893a..d8a8d6d7 100644 --- a/cara/tests/apps/calculator/test_webapp.py +++ b/cara/tests/apps/calculator/test_webapp.py @@ -31,7 +31,6 @@ async def test_user_guide(http_server_client): assert resp.code == 200 -@pytest.mark.xfail(reason="about page not yet implemented") async def test_about(http_server_client): resp = await http_server_client.fetch('/about') assert resp.code == 200