An epidemic calculator for COVID infections

To a non-expert as most of us comprehending the numbers, the forecasts and the epidemiological parameters presented in the literature may be quite a challenge. I found online a very interesting calculator for COVID that addresses this gap in our understanding.

Figure 1. A calculator to be used to measure one’s risk of exposure to the disease for any given day of the epidemic

The variables for transmission dynamics that can be modified are:

• population inputs: size of population, number of initial infections
• basic reproduction number (measure of contagiousness) : the number of secondary infections each infected individual produces
• transmission times: length of incubation period, duration patient is infectious

The variables for clinical dynamics that can be modified are:

• mortality statistics: fatality rate, time from end of incubation to death
• recovery times : length of hospital stay, recovery time for mild cases
• case statistics: hospitalization rate, time to hospitalization

One may drag horizontally the line for the day of intervention in order to decrease the transmission and then the parameters for susceptible cases, exposed cases, infectious cases, population no longer infectious, fully recovered cases, number of active hospitalizations and fatality rate values will change accordingly.

The infectious disease is mathematically modelled using a compartmental model. The population is assigned to one of the four compartments: susceptible (S), exposed(E), infectious (I) and recovered(R). A mathematical set of equations is used to model the progress of people from one compartment to another. The model runs either on a set of ordinary differential equations (deterministic) or using a stochastic framework (more close to reality).

I attended many online meetings about various models for the clinical data available for COVID cases and I found this model as quite suitable. This epidemiologic calculator uses the SEIR model which assumes that S+E+I+R=N where N is constant as it is assumed that the birth and death rates are equal. I hope this calculator may be of assistance in better administrating the situation with this pandemic.

Happy Easter everyone!

The situation for COVID-19 cases in countries in Europe - 7 April 2020

COVID-19 affects everyone’s life and routine. The meetings started to become virtual meetings. The streets are empty, the offices are empty but the virtual world is very busy. I didn’t see an open communication with the public about the real situation in any of the countries that I have an eye on, The Netherlands where I live, UK and most importantly Romania, my home country.

Yesterday, randomly, I had a virtual meeting with the data science team from a company in Rotterdam that promotes a visualisation tool that can provide predictive insights to the government of any country. The tool can estimate the effects of non pharmaceutical interventions based on the understanding of the outbreak hotspots all over the world.

This is how I had a closer look at the resources that people have as reliable source of information on the number of confirmed cases and deaths in each country. This main source of reliable information represents the list of situation reports provided by the World Health Organisation. Yesterday, April 7, another situation report was released.

The number of confirmed cases and the number of deaths reported for each country are sureal. This is how I started to look at the data in Excel. I had problems to understand how much is too much, how can I interpret these values. One would not find as fair to say that the same value for confirmed cases for a small country has the same weight as for a country with a larger population. This is why I added another column, that of confirmed population for that country in 2020.

Maybe not all have time to do this research and this is the reason why I decided to share with you my Excel sheet with the raw data in the link above. I personally wanted to see which is the percentage of the population for each European country that represents the confirmed cases. I was surprised to see, in figure 1, that in fact we discuss here about less than 1% of the population for that country.

Figure 1. The total number of confirmed cases until April 7 versus the total population of the reported country

Later on I had a look at the total number of deaths until April 7 versus the total population of the reported country. Figure 2 presents the situation for these cases. The greatest value, with a small anomaly in San Marino at 0.1%, represents 0.03% of the total population for that country.

Figure 2. The total number of deaths until April 7 versus the total population of the reported country

Last but not least, one can have the “barometer” of the immune system per country, which is the percentage from the total number of confirmed cases until April 7 that represents the total number of deaths. Figure 3 shows that a maximum of 13% of the confirmed cases actually end up with the death of the patient.

Figure 3. The total number of deaths from the total number of confirmed cases until April 7

I know that people are not statistics but the fear that is in the air nowadays is a little bit pushed too far. People start to need a psychologist in order to handle the current lifestyle in isolation in the privacy of your own home. This doesn’t mean that we should not be cautious as before with the hygiene but I think that we also deserve to enjoy ourselves a little bit more now that Easter is coming.

Merry Christmas everyone!

STRP – The Conference for The Curious

The man and the machine are more and more connected though new apps and new devices. The behaviour and the way of thinking of a biological system needs to be translated in lines of code so that the quality of life of people is further increased. More and more biological data needs to be collected, processed, analysed and interpreted. This provides ample reason for STRP to focus on Senses & Sensors in the Biennial of 2017, where both scientists and local people are invited to indulge in their own sense of curiosity.

Video 1. Conference for The Curious – the presentation video created by OddOne for STRP and distributed on Vimeo

During the STRP Conference for The Curious : Senses & Sensors on 28 March 2017, high profile international speakers explored this theme from different perspectives. Artists and designers, writers and scientists, and nonetheless coders are gathered to show a glimpse on how are interpreted the complex processes through which the world around us is perceived both by human and machine. Together they outlined the contours of new developments in today’s sensory systems, and shared their thoughts on how this could influence us. The talk for each presenter was recorded and posted online through YouTube and it is accessible through the link attached to their individual name.

The moderator of the first part of the day is Isolde Hallensleben (NL), who is a main contributor to the development of the TU/e Innovation Space, a place for challenged-based, interdisciplinary and hands-on education.

Photo 1. Conference for The Curious – curiosity

The first presenter, Claire L. Evans (US), a musician and a writer, brings us to our attention that in science fiction music is shown as the universal language of communication, and it is a way to quantify and transmit the emotional and cultural impact of life.

Photo 2. Conference for The Curious – the presentations

The second presenter, Tobias Revell (UK) is an internationally-exhibited artist, designer and programme director for Graphic Design Communication at London College of Communication. He focuses on the interplay between mythology and contemporary technology.

Photo 3. Conference for The Curious – the human and the cup of tea

The third presenter, Tom Pursey (UK) is the co-founder and creative director of Flying Object, a London-based creative agency that developed the prize winning exhibition Tate Sensorium in 2015.

Photo 4. Conference for the Curious – let’s make sense of the future now

To Sissel Tolaas (NO), the fourth presenter, the nose knows a lot more than most of us know. After studying and working at the universities in Oslo, Warsaw, Moscow, Saint Petersburg, Oxford and Princeton, Sissel works actively and focuses on the topic of smell, smell and language communication since 1990, within different sciences, fields of art and other disciplines. Sissel believes that smell is a crucial component to define, understand and move within a specific environment and now creates in the lab “the alphabet for the nose”.

Photo 5. Conference for The Curious – the workshops

The moderator for the second part of the day is Koert van Mensvoort, an artist and philosopher best known for his work on the philosophical concept of Next Nature. He introduces and moderates the highlight of the Conference for the Curious - the keynote by Kevin Kelly (US), the founding executive editor of Wired magazine, and the author of bestsellers such as What Technology Wants (2010) and The Inevitable(2016).

Video 2. Conference for The Curious – the program

The Conference for The Curious was the meeting place for 2 days with in-depth talks and interviews for creators and thinkers, do-ers and experts, who are shifting every day the borders of current knowledge within their field of expertise through novel techniques and devices.

STRP - Musical communication and cognitive behaviour

The ubiquity of music in everyday life, and the corresponding diversification of musical behaviour are the reasons why there it is an increased interest in studying the music psychology in the last 20 years. [Hargreaves, 2002]. The meaningful information that is shared through any form of communication may also be shared in a form of organised sounds that represents the music [Thaut, M, 2008]. I find it fascinating what a big influence music has in my everyday life. There are various philosophical questions regarding music. Does music represent humanity? How can music express emotions? How is music perceived emotionally by the listener?

Claire L. Evans, a musician and a writer, brings us to our attention, at the STRP festival, that in science fiction music is shown as the universal language of communication, and it is a way to quantify and transmit the emotional and cultural impact of life. Can music be produced in a way that does not represent a human culture? What musical segment can one send in space to represent the various cultural backgrounds present on Earth? Does music influence the emotional side of non-human, even animals? Which instruments should be used to create abstract music?

Video set. Conference for the curious - Claire L. Evans - The sound of post-human music

When we listen to music various parts of our brain are triggered. The auditory cortex perceives and analyses the sounds in the first stages of listening to sounds. The motor cortex and the cerebellum are working to create the movement in dancing, for foot tapping, and playing an instrument. The sensory cortex provides tactile feedback from playing an instrument and dancing. The visual cortex is triggered for reading the musical notes, for looking at a performer's movements in dancing. The hippocampus is responsible for the memory for music, for the musical experiences and for the context in which music is provided. The prefrontal cortex processes expectations for the musical play. The nucleus accumbens and the amygdala create the emotional reaction to the music. The corpus callosum connects the left and the right hemispheres of the brain.

Various studies showed interesting facts about the effect that music has on us. An individual, after listening to a piece of music charged with either positive or negative emotions, perceives a neutral face as either happy, after a positive piece of music, or sad, after a negative piece. A moderate intensity level for the ambient music may improve creativity. Our music choices may predict parts of our personality, like extraversion, self esteem, hard-working, the emotional stability. Music is a significant distraction while in traffic. Cyclists who listen to music require 7% less oxygen than the people who cycle in silence for the same route. Classical music may improve visual attention.

Music can stimulate complex processes in the brain and the progress achieved with the patient may be then transferred to non-musical methods for therapy. Rhythmic activities that involve the movement of the body proved to facilitate the early recovery for patients suffering from with stroke, for patients with the Parkinson's disease, cerebral palsy and with traumatic brain injury. The recovery of speech functions is also done quicker through music. Music may help rebuild the damaged brain pathways or even build new ones to restore the normal functionality of the human body.

References:

Thaut M. (2008) “Rhythm, Music, and the Brain: Scientific Foundations and Clinical Applications”

Hargreaves D.J., MacDonald R., and Miell D.E. (2005) “Musical communication”

STRP - the eye and optical instruments

We use the accessory visual structures every day, but not many think of studying the structure in fine detail. The eyes capture a lot of information, part of it is stored in the conscious part of our brain, and part remains in the subconscious. People study this part of the human anatomy and sensors are developed based on the findings provided by the research.

Figure 1 . The human iris, front view. Copyright (2008) Gray's Anatomy

When a collimated beam of light or laser passes through one or several apertures, or if it encounters an obstacle, it spreads out and, due to diffraction, various resulting patterns are captured on a circular canvas.

Figure 2 . The optical patterns on the semi-circular canvas

The polygonal mesh is the core tool to analyse both solid surfaces and for simulation of internal body parts.

Figure 3 . The polygonal mesh

The equivalent electrical circuit of the entire human body may be developed by putting together the equivalent electrical circuits of each of the body parts.Each part has different values for the resistance, capacitance and inductance. The physiology engine may be tested by switching on and off electrical circuits for various parts of the body.

Figure 4 . The equivalent electrical circuit for the entire human body

People, from young to old, have the opportunity to touch and experience the effects of the basic elements for high level research. I find it fascinating that people, in a nice sunny afternoon, can take their family out at this event and play with tools designed in a child-friendly manner, and probably without a full understanding of the science in the background, have access to knowledge that people in other countries, like me, only dream to see.

References :

Gray's Anatomy: The Anatomical Basis of Clinical Practice ( 2008 ), 40th edition, Churchill-Livingstone, Elsevier.