Why I study my own disease

Why I study my own disease

A lot of patients have asked me why I use my little energies to study my disease, instead of just waiting for science to conquer it.

There are many reasons, the first one being that I am desperate because of the cognitive disability that is worse than death. I am not concerned about the physical limitations, at all, even though I have been mostly housebound for the last 20 years. Another reason is that I like computational biology, and I started studying engineering before getting sick with the idea of switching to bioengineering after graduating. So, this is my job.

The other point is that even though I fit the criteria for ME/CFS, I have a rare disease, granted that ME/CFS is not a rare disease: it has a prevalence of 0.4% according to some studies, so it is relatively common. Then why am I a rare patient? Let’s do some calculations: since the median age at onset is 36.6 years with a standard deviation of 12.3 years, the proportion of males is 19% and the proportion of those who are housebound for most of their disease is 25% (R), the probability for a ME/CFS patient of having my same characteristics is (assuming that these are all independent random variables) given by p=0.0075. So, less than 1 out of 100 ME/CFS patients has my type of illness. If we consider also that pain or aching in muscles is present in 59% of patients and it is mostly absent in my case, the above-mentioned probability is even lower: p=0.0031. Which means that only 3 ME/CFS patients out of 1’000 have my illness.

Taken all these data together, the prevalence of my disease in the general population becomes 1/100’000, which means that I have a rare disease, according to the European definition (where a disease is defined rare if it has a prevalence ≤1/2’000) [R]. In the US a disease is defined rare only if it has a prevalence ≤1/200’000, though [R].

And besides that, it is pretty obvious that I am a unique case. I have never found a patient like me, so far. It can also be noted that in Italy, given a population of 60 million inhabitants, those who have my condition are only 600. This might be the reason why I haven’t met them, yet.

This means that I am probably the only one who is studying my disease, on the planet! This is why I’m doing what I’m doing.

91569815_10220268929849855_9111778109215997952_o

Above, my personal book of immunology, built page by page, paper by paper. I have three other books about this discipline. One of them was a gift from a neurologist that perhaps thought that gift was the only thing she could do to save me. Another one is a very sophisticated text on cutting edge immunology. But this one is the best one because I have selected and read each one of its pages. It is by no means a complete book, it is mainly focused on B cells and B cell autoimmunity, but it has been very useful.

I have built several other books like this, on computational methods in immunology, on metabolism, on neurosciences, on microbiology, and on some diseases: Lyme, ME/CFS, mast cell activation, POTS…

I have learned a great deal, even though outside academia. But I had no choice, I have been too sick and too slow to study at university: I had only a few weeks in which I could study, and then months or years in which I had to wait. This has been my routine. Moreover, given the lack of energy and time, I had to study only what was truly important for my health. Because my goal was to cure myself and save me from a lifetime of cognitive disability.

Testing hypotheses

Testing hypotheses

Introduction

My ME/CFS improves during summer, in the period of the year that goes from May/June to the end of September. I don’t know why. I have several hypotheses. One possible reason for the improvement in summer is an interaction between the light from the Sun and some parts of my physiology, the immune system for instance. We know that ME/CFS tends to have an oscillating course in most of the patients (Chu L. et al. 2019), but the presence of a seasonal pattern in this patient population has not been investigated so far, to my knowledge. And yet, if you ask directly to patients, many of them say that they feel better in summer. Unfortunately, we don’t have scientific data on that, this is an area worth investigating with some carefully done survey.

Seasonal variation of the immune system

The immune system has a high degree of variation for several reasons (Brodin P et Davis MM 2017). In particular, there are studies about the seasonal fluctuations in the expression of some crucial genes of the immune response (Dopico XC et al. 2014).

How does this regulation happen? Different mechanisms are possible, some of them might be related to changes in the light we receive from the Sun as the Earth rotates around it. We know that the length of the day has an effect on innate immunity: the more the hours of light, the lower the power of the innate immune system (Pierre K. et al. 2016). We also know that ultraviolet radiation, particularly UVB, is an agonist for the aryl hydrocarbon receptor (AhR) (Navid F. et al. 2013). This receptor seems to reduce the expression of the major histocompatibility complex II (MHC II) in dendritic cells (DCs), thus reducing their antigen-presenting activity (Rothhammer V. et Quintana F.J. 2019). UVB might be able to reach dendritic cells when they are circulating near the skin, during summer, thus inhibiting their antigen-presenting activity. Infrared radiation, on the other hand, seems to have an effect on energy metabolism: in Fall we lose a significant amount of infrared radiation in a wavelength range (0.7-1.0 nm) that is known to have an effect on mitochondrial activity (Nguyen L.M. et al. 2013) and it might perhaps have an indirect effect on immunity too.

As further proof of seasonal fluctuation in immunity, some immunological diseases have this kind of seasonality: Rheumatoid arthritis (Nagamine R. et al. 2014) and Rheumatic fever (Coelho Mota C.C. et al. 2010) are two examples. Moreover, the prevalence of Multiple Sclerosis is directly proportional to the latitude (Simpson S. et al. 2011). We also know that there is seasonal fluctuation in serum autoantibodies (Luong T.H. et al. 2001).

Of course, sunlight might be just one of the variables into play. The other aspect I am considering is the seasonal distribution of some common pathogens. Streptococcus, Enteroviruses and Fungi of the genus Penicillium are known to have a seasonal distribution with a peak in Fall and/or Winter (Ana S.G. et al. 2006), (Salort-Pons M et al. 2018), (Coelho Mota C.C. et al. 2010). Common influenza has this pattern too. Rheumatic fever, a disease due to an abnormal immune response to Streptococcus, has its flares in Fall because Streptococcus is more common in that period of the year (Coelho Mota C.C. et al. 2010). I am currently investigating my immunosignature, measured with an array of 150.000 random peptides, to see if I can find some relevant pathogen in my case. You can find this study here.

An experiment

I moved from Rome (Italy) to Rosario (Argentina) at the beginning of January. I was very sick and I steadily improved after about 40 days. I became a less severe ME/CFS patients and I could work several hours a day and care for myself, granted that I did not exceed with aerobic exercise. At the end of March, I started deteriorating as it usually happens at the end of September, when I am in Rome. In order to study this phenomenon, I have built a complete model of solar radiation at sea level, which considers the inclination of sunrays in function of the latitude and of the day of the year. It takes into account the effect of the atmosphere (both diffusion and absorption) and the eccentricity of the orbit (Maccallini P. 2019). If you look at the figure below (a byproduct of my mathematical model) you can see that when I started deteriorating in Rosario, the power of sunrays at noon in that city was still as high as it is in Rome during the summer solstice (this is due to the fact that the Earth is closer to the Sun in this period and to the fact that Rosario is closer to the Equator than Rome is).

Rome_vs_Rosario

So I have to discard the original idea that the power within the infrared range, or the ultraviolet radiation, or the visible one is responsible for my improvement in summer. If I still have to consider that sunlight has something to do with my improvement, I must conclude that it is the length of the day the relevant parameter: I may need more than 12 hours of light to feel better. Why? Because the longer the day, the lower the strength of the innate immunity. This is now my working hypothesis and I will start from the following mathematical model to pursue this research: (Pierre K. et al. 2016).

I will also use full-spectrum lamps early in the morning and in the evening to reproduce a 15 hours day, so to dampen down my innate immune system in a safe, drug-free way. I have to reproduce a day of 15 hours and see what happens. In the figure below the hours of the day at dawn and at dusk and the length of the day for Rome, for each day of the year (this is also a plot from my model).

ore di luce

What follows is the script I have coded in order to plot the first figure of this post. More details on this model of solar radiation are here: (Maccallini P. 2019). As a further note, I would like to acknowledge that I started pursuing this avenue in the summer of 2009: I was building the mathematical model of solar radiation (see figure below, made in 2009) but as the summer finished, I turned into a statue and I had to stop working on it. When I improved, about a year later I started working on the systematic analysis of the mechanical equilibrium of planar structures (it is a chapter of this book). I am proud of that analysis, but it has not been very useful for my health…

trigonometria sferica 2

% file name = sun emissive power sea level Rosario vs Roma
% date of creation = 07/11/2019
% sun emissive power per unit area, per unit wavelength at sea level
clear all
% three parameters of the orbit
A = 6.69*( 10^(-9) ); % 1/km
B = 1.12*( 10^(-10) ); % 1/km
delta = pi*313/730;
% the two parameters of Plunk's law
C_1 = 3.7415*( 10^(-16) ); % W*m^2
C_2 = 1.4388*( 10^(-2) ); % mK
% Stefan-Boltzmann parameter ( W/( (m^2)*(K^4) ) )
SB = 5.670*( 10^(-8) );
% radius of the photosphere (m)
R_S = 696*(10^6); % m
% temperature of the photosphere (K)
T_S = 5875;
% conversion of units of measurments
N = 20; % dots for the equator
R = 3.8; % radius of the orbit
ro_E = 1.3; % radius of the earth
lambda_Rosario = -32*pi/180; % latitude of Rosario (radiants)
lambda_Roma = 41*pi/180; % latitude of Rome (radiants)
delta = 23.45*pi/180; % tilt angle
% the array of theta
theta(1) = 0; % winter solstice (21/22 December)
i_ws = 1;
day = 2*pi/365;
days = [1:1:366];
for i = 2:366
theta(i) = theta(i-1) + day;
if ( abs( theta(i) - (pi/2) ) <= day )
i_se = i; % spring equinox (20 March)
endif
if ( abs( theta(i) - pi ) <= day )
i_ss = i; % summer solstice (20/21 June)
endif
if ( abs( theta(i) - (3*pi/2) ) <= day )
i_ae = i; % autumn equinox (22/23 September)
endif
endfor
% the array of the radius (m)
for i=1:1:366
o_omega (i) = (10^3)/[ A + ( B*sin(theta(i) + delta ) ) ]; % m
endfor
% the array of the wavelength in micron
N = 471;
L(1) = 0.3;
L(N) = 5.0;
delta_L = ( L(N) - L(1) )/(N-1);
for j = 2:N-1
L (j) = L(j-1) + delta_L;
endfor
% the array of beta*L
load beta_int.mat S
% the array of L in metres
L_m = L*( 10^(-6) );
% angle psi
psi(1) = 0;
minute = pi/(12*60);
for i = 2:(24*60)+1
psi(i) = psi(i-1) + minute;
endfor
% -----------------------------------------------------------------------------
% Rosario
lambda = lambda_Rosario
% angle between n and r at noon in Rosario
for i= [i_ws, i_ae, i_ss, i_se]
for j=1:(24*60) + 1
% scalar product between n and r
scalar_p(j) = [cos(lambda)*sin(psi(j))*cos(delta) + sin(lambda)*sin(delta)]*( -cos(theta(i)) )+ [(-1)*cos(lambda)*cos(psi(j))]*( -sin(theta(i)) );
endfor
% value of psi at noon
for j=1:(24*60) + 1
if ( ( scalar_p(j) ) == ( max( scalar_p ) ) )
j_noon = j;
psi_noon (i) = psi(j);
endif
endfor
% angle between n and r at noon
cos_gamma (i) = scalar_p(j_noon);
endfor
% the array of the emissive power (W/(m^2)*micron) in Rosario
for i = i_se:i_se
for j=1:N
num = C_1*( (R_S)^2 );
den = ( (L_m(j)^5)*( (e^(C_2/( L_m(j)*T_S ))) - 1)*( (o_omega(i))^2 ) )*10^6;
power(j,i) = ( num/den )*( e^(-S(j)/cos_gamma (i)) );
endfor
% plotting
plot (L (1:N), power(1:N,i), '-r', "linewidth", 2)
xlabel('wavelenght ({\mu})');
ylabel('W/m^{2}{\mu}');
axis ([0.3,5,0,1500])
grid on
endfor
hold on
% -----------------------------------------------------------------------------
% Rome
lambda = lambda_Roma
% angle between n and r at noon in Rosario
for i= [i_ws, i_ae, i_ss, i_se]
for j=1:(24*60) + 1
% scalar product between n and r
scalar_p(j) = [cos(lambda)*sin(psi(j))*cos(delta) + sin(lambda)*sin(delta)]*( -cos(theta(i)) )+ [(-1)*cos(lambda)*cos(psi(j))]*( -sin(theta(i)) );
endfor
% value of psi at noon
for j=1:(24*60) + 1
if ( ( scalar_p(j) ) == ( max( scalar_p ) ) )
j_noon = j;
psi_noon (i) = psi(j);
endif
endfor
% angle between n and r at noon
cos_gamma (i) = scalar_p(j_noon);
endfor
% the array of the emissive power (W/(m^2)*micron) in Rosario
for i = [i_ae, i_ss]
for j=1:N
num = C_1*( (R_S)^2 );
den = ( (L_m(j)^5)*( (e^(C_2/( L_m(j)*T_S ))) - 1)*( (o_omega(i))^2 ) )*10^6;
power(j,i) = ( num/den )*( e^(-S(j)/cos_gamma (i)) );
endfor
endfor
hold on
plot (L (1:N), power(1:N,i_ae), '-k', "linewidth", 2)
plot (L (1:N), power(1:N,i_ss), '--k', "linewidth", 2)
legend ('spring equinox in Rosario', 'autumn equinox in Rome', 'summer solstice in Rome', "location",'NORTHEAST')
hold on
plot ([0.4,0.4], [0,1500], '--k', "linewidth", 1)
plot ([0.7,0.7], [0,1500], '--k', "linewidth", 1)

Back home

Back home

Continuation of this post.

Forty-four hours of travelling, in total, from Rosario to Rome, by pullman, by plane, and by train. With 40 kilos of books and papers.

I had a flight for Rome that was programmed to take off from Ezeiza, the International airport of Buenos Aires, on April 13th, but I decided to take the one organized by the Italian government for March 23th, a special flight set up to bring back home Italian citizens abroad, before a complete shut down of international flights from Argentina to our country. There were no flights from Rosario, my city, to Buenos Aires, though, but I managed to find a company that organizes transportations by pullman from one city to the other, in Argentina: Tienda Leon.

So, on March 22nd, I moved to Ezeiza where I waited several hours before sitting on my chair, on a brand new Boeing 787 bearing the colours of the Italian company Neos.

While at the airport, I met most of the Italians that were going to get the same flight, all wearing their masks. Some of them with some very fancy models, that made them look like a Star Wars character. I was there, well aware that I was going far beyond the limit set by my disease. I had to lay down continuously and I could see how frail I was in comparison with the other passengers waiting for the flight. No one knew how sick I was, I told nobody. No one knew that I have been living in my bedroom for most of the last 20 years. And that this was the very first long travel abroad for me.

I have just received the notification that my flight for April 13th has been cancelled, so my choice to come back as soon as possible has been a wise one. I took that decision also because of the advice from the diplomatic offices of the Italian Consulate in Rosario.

A friend has crafted the picture above, not knowing how much Indiana Jones has meant for me when I was a teenager. But, even though an appealing adventure, the tragedy behind it is real, it is not a movie. Once in Milan, I could start seeing the effects of the pandemic in the eyes of the staff of the airport of Malpensa: the fear and the concern. Then I moved from Milan to Fiumicino, where I found a train for Rome, my city. A city that I left two and a half months ago full of life and noise, now empty as in a dream.

 

From Argentina to Italy, during a pandemic

From Argentina to Italy, during a pandemic

It has been a great ride, my almost-three-month period here in Rosario, next to the huge slowly flowing river of Paranà. This is a city full of life, embraced by the warmest summer I have ever seen. Populated by wonderful citizens.

WhatsApp Image 2020-03-09 at 09.37.08

I have been living in an apartment where the sun awakes me very early in the morning, through a wide window next to my bed. I could see the roofs of the centre of the city as I opened my eyes, including the top of the Monumento National a la Bandera, a gigantic building that celebrates this great nation. For the second half of the day, I had the light from the opposite window and I could follow its changes, while I was working, as the hours passed by; I saw every day the same magic ritual: as the photons from our star went through thicker layers of the atmosphere, they changed their frequency, turning redder and redder, culminating in a warm explosion, just before the night.

And in the meanwhile, news from Italy was scarier and scarier and the hypothesis that the new coronavirus could reach this continent was more obvious as the weeks passed by. Now we have the virus here, and president Alberto Fernandez has declared the state of quarantine from March 20th.

At that point, the connection between Argentina and other countries (including Italy) has become uncertain; my flight planned for March 28th has been cancelled and I have decided to get one of the special flights organized by the Italian government to bring back its citizens from Argentina, before a complete shut down of international travels. So I had about 48 hours to find a means of transport from Rosario to the airport in Buenos Aires, where the flight will take off tomorrow, at 1:00 AM.

But there was no way I could find a flight from Rosario to Buenos Aires in such a short time, also because of the shut down of Argentina, and no trains were available. Fortunately enough I have found a Pullman, and I am going to leave this apartment in a few hours.

My come back to Italy is becoming more and more adventurous also because I will land in Milan, one of the places most hit by the infection in the whole planet. There I have to reach Rome. I have been able to find a plane from Milan to Rome, so it will be possible to be at home on the evening of March 23rd. I have to avoid to get the virus though, during this travel. I will be exposed to it for sure, so I am taking any possible measure to ensure my safeness.

This travel to Argentina has been a success. My health has improved, even though now I am deteriorating again, as was expected, as the light of the summer of the southern hemisphere becomes weaker. But I have been able to use my new energies to write and submit a paper on the cingulate cortex in ME/CFS, I have gone further with my studies on the analysis of the immunosignature (measured using random peptides) in my own serum (R), I have started the study of a mathematical model for the diffusion of Coronavirus 19 among the Italian population (R). I have learnt a great deal about computational neuroanatomy (R) and neurosciences in general. I have finished a complete model for solar radiation at sea level (R) and I might have found one of the environmental parameters that determine my improvement during summer. And yes, I have also been able to draw a portrait.

WhatsApp Image 2020-03-18 at 10.07.35

The adventure in the realm of science and art has been great, now I have to live the adventure of coming back home going through a world that is facing one of the greatest health challenges of the last century.

 

A Mathematical model for the diffusion of Coronavirus 19 among the Italian population

A Mathematical model for the diffusion of Coronavirus 19 among the Italian population

Abstract

In this document, I propose a distribution for the number of infected subjects in Italy during the outbreak of Coronavirus 19. To do that I find a logistic curve for the number of deaths due to this virus, in Italy. I also use a density of probability for the fatality rate and one for the number of days from infection to death. These functions have been built using recently published statistical data on the Chinese outbreak.   

Download the paper (pdf)