Whole Genome Sequencing was performed on the proband (me!) and three healthy family members: one paternal uncle and two maternal aunts. First-degree relatives were not available. Paired-FASTQ files were inputted to a GATK pipeline, according to GATK best practices workflows (R). After the generation of unmapped BAM from paired-FASTQ, a BAM file was obtained for each participant. The four GRCh38 BAM files were then submitted to joint variant calling along with other 50 genomes from the 1000 Genomes Project, used to maximize the signal/noise ratio. These analyses were all performed on the NHGRI AnVIL platform that offers virtual machines with optimized GATK configuration.
The resulting gVCF was submitted to Seqr for family filtering. Family filtering based on a dominant pattern of inheritance was performed with a threshold of zero for both QUAL and allele balance (quality filtering is performed in a following step). The result was downloaded and submitted to a custom R script (reported at the end of this page). The script filters out variants harbored by genes with a probability of being dominant below 0.5 (DOMINO score); it also eliminates calls with QUAL below 30. It then collects the remaining calls in a VCF file for submission to CADD GRCh38 v1.7 (R). The file containing the scores is then inputted again to the script that adds them to the Seqr output. Filtering is then performed as follows: the script retains only calls with CADD≥22.8, Eigen≥0, PolyPhen≥0.45, and SIFT≤0.05. Filtering is performed only when scores are available: so, for instance, a call with no available scores is kept.
Table. Results of Seqr permissive De Novo Dominant search on WGS, after filtering performed by my R script (see below). In the WES column: NA indicates that the variant is not present in the VCF file of WES, which can be due either to the fact that the position was not genotyped or to the fact that it was found homozygous for the reference allele; Y indicates that the position is present in WES with the same genotype. Same for 23&ME.
This pipeline selects four variants (see table). Two of them are present in a whole-exome performed on the proband, too. The other two are not present on WES and since only the VCF file is available for WES, we cannot say if they are absent because they were not genotyped or because the proband is homozygous for the reference allele. I then used reactome.org to select for each gene the pathway where its protein is involved in the higher number of reactions. Only CIC was not included in any pathway by Reactome, but it has been recently reported the involvement of CIC in folate transport into the brain and a few rare mutations in this gene have been proposed as causative for cerebral folate deficiency (R). None of the variants of the table has been associated with known diseases. The mitochondrial chromosome was analyzed by a custom R script, as detailed elsewhere (R), and nothing relevant was found. I’m currently performing further studies on these results and I am analyzing the structural variants of the proband.
# file name: Seqr_Dominant
#
# Rome 09th December 2023
#
#-------------------------------------------------------------------------------
# This script filters the results of Seqr's De Novo/Dominant Restrictive search
#-------------------------------------------------------------------------------
#
#-------------------------------------------------------------------------------
# Thresholds
#-------------------------------------------------------------------------------
#
co_CADD<-22.8 # a CADD phred score below co_CADD is considered tolerated
co_Eigen<-0 # a Eigen score below co_EIGEN is considered tolerated
co_PolyPhen<-0.45 # a PolyPhen score below co_PolyPhen is considered tolerated
co_SIFT<-0.05 # a SIFT score ABOVE co_SIFT is considered tolerated
#
PAD<-0.5 # Cut-off for probability of being Autosomal Disease (PAD)
#
co_Qual<-30 # threshold for quality score
#
#-------------------------------------------------------------------------------
# This function adds the probability of being a dominant gene
#-------------------------------------------------------------------------------
#
DOMINO<-function(variants) {
#
# Read the genes with their relative Domino probabilities
#
genes<-read.csv(file="C:/Users/macpa/OneDrive/Appunti/Genetics/Domino/DOMINO_GENEID_feb_2019.txt",sep="\t")
colnames(genes)<-c("SYMBOL","gene","Domino")
#
# For each variant assign the DOMINO score of its gene (if any)
#
string<-"SYMBOL"
if (substr(variants$gene[1],1,4)=="ENSG") string<-"gene"
variants<-merge(variants,genes,by=string,all.x=T)
}
#
#-------------------------------------------------------------------------------
# This function generates a VCF file for CADD submission
#-------------------------------------------------------------------------------
#
VCF<-function(variants) {
#
variants<-variants[,2:5]
variants$id<-rep(".",length(variants[,1]))
temporary<-c("chrom","pos","id","ref","alt")
variants<-variants[,temporary]
write.table(variants,file="DeNovoDominant_permissive.vcf",quote=F,
row.names=F,col.names=F,sep="\t")
}
#
#-------------------------------------------------------------------------------
# Read the seqr file and assign the domino probability
#-------------------------------------------------------------------------------
#
seqr_dom<-read.csv(file="DeNovoDominant_permissive.tsv", sep="\t", header = TRUE)
#
seqr_dom<-DOMINO(seqr_dom)
#
#-------------------------------------------------------------------------------
# Remove variants based on their Domino probability and quality
#-------------------------------------------------------------------------------
#
seqr_dom<-subset.data.frame(seqr_dom, Domino>=PAD | is.na(Domino)==T )
#
seqr_dom<-subset.data.frame(seqr_dom, gq_1>=co_Qual)
#
#-------------------------------------------------------------------------------
# Write file for CADD submission
#-------------------------------------------------------------------------------
#
VCF(seqr_dom)
#
#-------------------------------------------------------------------------------
# Read file after CADD submission
#-------------------------------------------------------------------------------
#
f.name<-gzfile("DeNovoDominant_permissive_CADD.tsv.gz")
CADDed<-read.csv(file=f.name,sep="\t",skip=1,comment.char=" ")
colnames(CADDed)<-c("chrom","pos","ref","alt","rawscore","cadd")
#
#-------------------------------------------------------------------------------
# Add cadd score
#-------------------------------------------------------------------------------
#
seqr_dom<-merge(seqr_dom,CADDed,by=c("chrom","pos","ref","alt"),all.x=T)
#
#-------------------------------------------------------------------------------
# Remove variants based on their in silico scores
#-------------------------------------------------------------------------------
#
seqr_dom<-subset.data.frame(seqr_dom, cadd.y>=co_CADD | is.na(cadd.y)==T )
seqr_dom<-subset.data.frame(seqr_dom, eigen>=co_Eigen | is.na(eigen)==T )
seqr_dom<-subset.data.frame(seqr_dom, polyphen>=co_PolyPhen | is.na(polyphen)==T )
seqr_dom<-subset.data.frame(seqr_dom, sift<=co_SIFT | is.na(sift)==T )
#
#-------------------------------------------------------------------------------
# Write output
#-------------------------------------------------------------------------------
#
write.table(seqr_dom,file="DeNovoDominant_permissive_filt.tsv",quote=F,row.names=F,col.names=T,sep="\t")
si chiama progressione aritmetica quando, comunque si scelga 
, si ha:
assume il nome di ragione aritmetica. Altresì, una successione si dice geometrica quando 
di ragione geometrica. E dunque la menzionata successione di esborsi con cui tassare gli autori molesti è una progressione geometrica, non aritmetica. 
. Therefore, we conclude that the volume of the four-dimensional hypersphere that includes the Universe, according to Dante Alighieri, is 
, which is about 
. It is not clear what the meaning of this analysis might be, if any: Dante did not know geometry with more than three dimensions, to my knowledge. But one implication is that a three-dimensional being can not move from one sky of the Ptolemaic system to the other (because they are in different three-dimensional spaces) unless he finds a way to move along the fourth dimension. I think that this would resonate with Dante’s mind and that this would agree with what he had envisioned: he can accomplish his ascent to God only because of external intervention and help from Beatrice. 
where Y is my status (the higher the value, the less the symptoms), t is air temperature (°C) and T is absolute air temperature (K). This regression model approximates the flux of thermic energy between my body and the environment, when indoors, but with two different signs for the coefficients of t and of 
. I have used then the best regression model to predict the score over the year in several cities. These predictions can be used to find the optimal spot to live in, as a function of the month of the year. 
. In another study, I simulated summerish conditions in a room for five months, during cold months, by means of a heat pump, an infrared lamp, an air moisturizer, and mylar panels (
. RM = Rome; AR = Arona, Tenerife, Spain; RO = Rosario, Argentina; BA = Buenos Aires, Argentina; AS = Asunción, Paraguay; CO = Corrientes, Argentina; SM = Santa Maria, Cape Verde. 
, and model 
. These three models have a physical meaning; namely, they express the flux of thermic energy between my body and the environment. The human body must balance the energy exchanged with the environment to maintain thermic homeostasis. The power P exchanged with the environment can be written as 
where 
is the power absorbed from the Sun, and the other addend is the radiant power exchanged with the environment, whit 
a constant that expresses radiant and geometrical properties of both my body and of the environment. While 
is radiant power in the form of short wave radiation (wavelength below 3 
), the other addend represents radiant power exchanged by bodies at low temperatures with a wavelength above 3 
? One first approximation might be the absolute temperature of the air, because in warm months, with the windows open, the objects surrounding us tend to acquire a superficial temperature similar to that of the air. To show that point, I analyzed the power emitted by the soil in Rome, during the year 2020, and the temperature of the air (data from ARPALAZIO). If we indicate J the daily mean power emitted per surface unit by the soil in the hemispace, the Stefan-Boltzmann law states that
is the Stefan-Boltzmann constant, and 
is the absolute temperature of the soil. If the assertion that the temperature of the soil is about the same as the temperature of the air was correct, the regression for the following linear model should have a very low p value of the F test:
. For further details on these calculations, see (
è la velocità angolare (vedi 
e la si prolunga in modo che sia tangente in ogni suo punto al valore del campo delle velocità in quello stesso punto, si ottiene una elica, comunque si scelga P (Figura 1). L’elica cioè descrive proprio la matrice matematica del moto dei corpi nello spazio, oltre ad essere, come visto, una costante nelle forme naturali, microscopiche, nanoscopiche, e macroscopiche. E sebbene queste nozioni di cinematica siano posteriori ai Philosophiae Naturalis Principia Mathematica (1687), gli artisti hanno sempre usato l’elica esattamente per suggerire una idea di moto, senza contare il fatto che l’elica sembra anche inscrivere in sé ulteriori connotazioni emotive e significati. L’elica, che non ha piani di simmetria (sebbene abbia punti di simmetria), è stata usata per animare le forme simmetrche, a un certo punto della storia dell’arte, essendo la simmetria forse il criterio di bellezza originario, quello a cui allude il poeta-pittore William Blake: “What immortal hand or eye could frame thy fearful simmetry?” (
è il versore relativo al campo vettoriale in Eq. 1. Il codice funziona qualunque sia il campo vettoriale inserito nella funzione interna allo script (vectorial_field). Ho scritto questo codice nel 2021, come dimostrazione del metodo di ricostruzione delle fibre di materia bianca nella risonanza magnetica cerebrale con trattografia (
. While the absence of correlation can be used to rule out causation, the presence of correlation does not mean automatically causation. Moreover, since air density and dry air density are strongly inversely correlated with air temperature, the correlations with air density might be driven by the correlation with air temperature (and vice-versa). In order to further investigate the nature of these correlations, I planned a second study, this time performed inside a chamber where I could manipulate the temperature of the air, the content of water in the air, and the amount of infrared radiation I was hit by. I called this chamber “Summer Simulator” because I used several devices to obtain, during the months from December to May, the conditions that we usually have in Rome during summer. I lived inside the simulator while I collected a functionality score, three times per day, and while I measured (every 10 minutes) the temperature of the air, relative humidity, and atmospheric pressure. The data for the months from January to April were used to study how my symptoms correlated with the environmental parameters I could directly measure and those that I could mathematically derive.
. The temperature was controlled by a heat pump (Electrolux EXP26U558HW) that collects air from inside the room, divides it into two fluxes, transfers heat from one to the other (by cycles of compression-evaporation of refrigerant R290), and releases the warmer flux inside and the other one outside the window. The humidity was controlled by two/three ultrasonic mist humidifiers that release mist which is then turned into vapor in a fraction that depends on the temperature of the air (Figure 2). 
). 
is given by
![I_\xi\,=\,\frac{e\Pi(1-4b^2)\sqrt{1-4c^2}}{8\pi hLbc[F(\arctan\sqrt{\frac{1-4c^2}{4c^2}},\sqrt{\frac{1-4b^2}{1-4c^2}})-E(\arctan\sqrt{\frac{1-4c^2}{4c^2}},\sqrt{\frac{1-4b^2}{1-4c^2}})]}](https://s0.wp.com/latex.php?latex=I_%5Cxi%5C%2C%3D%5C%2C%5Cfrac%7Be%5CPi%281-4b%5E2%29%5Csqrt%7B1-4c%5E2%7D%7D%7B8%5Cpi+hLbc%5BF%28%5Carctan%5Csqrt%7B%5Cfrac%7B1-4c%5E2%7D%7B4c%5E2%7D%7D%2C%5Csqrt%7B%5Cfrac%7B1-4b%5E2%7D%7B1-4c%5E2%7D%7D%29-E%28%5Carctan%5Csqrt%7B%5Cfrac%7B1-4c%5E2%7D%7B4c%5E2%7D%7D%2C%5Csqrt%7B%5Cfrac%7B1-4b%5E2%7D%7B1-4c%5E2%7D%7D%29%5D%7D&bg=ffffff&fg=000000&s=0&c=20201002)
is the power absorbed by the device (about 800 W, according to the measurements performed by a power meter) and where F and E are the elliptic functions of the first and second kind, respectively (
which is reached for b = 0.49, c = 0.36 (assuming c < b < 0.5).
from O, is reported in figure 6, where it can be seen that the maximum of 
is reached for 
and its value is about 376 
. 
, for 
is the molecular weight of water, 
is the molecular weight of dry air, 
is the constant of gasses, and where we express temperature in °C and pressure in hPa. These formulae are taken from chapter 4 of the Guide to Instruments and Methods of Observation by the World Meteorological Organization (
; see figure 7. 
on the vertical plane by the left side of my bed, according to a mathematical model of the lamp (figure 6). This radiation was then partially reflected by the surfaces covered in mylar of my infrared chamber, so that it hit my body from other directions too, even though I have not built a model for the whole infrared chamber, yet.
, my infrared heater emits in the range 
. So, my artificial source of radiation does not simulate the radiation from the Earth, if we consider the wavelength (while it does from the point of view of the total power, as we will see in a following study, already concluded). But it could be considered that the radiation from the lamp did end up hitting the walls of my room, which in turn released their thermic energy as long wave infrared radiation. It is conceivable then that both in the Summer Simulator and in real summer, my improvements might be driven by far infrared radiation. Another possibility is that the improvement was due to the infrared radiation emitted by my body (long wave infrared radiation) and reflected back to me by the mylar coating of the infrared chamber. 
paolo maccallini 