Vaccination has been widely recognized as an effective measure for preventing infectious diseases. To facilitate quantitative research into the activation of adaptive immune responses in the human body by vaccines, it is important to develop an appropriate mathematical model, which can provide valuable guidance for vaccine development. In this study, we constructed a novel mathematical model to simulate the dynamics of antibody levels following vaccination, based on principles from immunology.
View Article and Find Full Text PDFBackground: Predicting the endemic/epidemic transition during the temporal evolution of a contagious disease.
Methods: Indicators for detecting the transition endemic/epidemic, with four scalars to be compared, are calculated from the daily reported news cases: coefficient of variation, skewness, kurtosis, and entropy. The indicators selected are related to the shape of the empirical distribution of the new cases observed over 14 days.
In this review, we successively present the methods for phenomenological modeling of the evolution of reported and unreported cases of COVID-19, both in the exponential phase of growth and then in a complete epidemic wave. After the case of an isolated wave, we present the modeling of several successive waves separated by endemic stationary periods. Then, we treat the case of multi-compartmental models without or with age structure.
View Article and Find Full Text PDFWe hypothesize that the first ancestral "protocell" molecular structures, i.e., the first RNAs and peptides that gradually transformed into real cells once the Earth had cooled sufficiently for organic molecules to appear, have left traces in the RNAs and the genes in present cells.
View Article and Find Full Text PDFThis study introduces a specialized Automatic Speech Recognition (ASR) system, leveraging the Whisper Large-v2 model, specifically adapted for radiological applications in the French language. The methodology focused on adapting the model to accurately transcribe medical terminology and diverse accents within the French language context, achieving a notable Word Error Rate (WER) of 17.121%.
View Article and Find Full Text PDFBackground: Hereditary angioedema (HAE) is a potentially life-threatening disorder characterized by recurrent episodes of subcutaneous or submucosal swelling. HAE with normal C1 inhibitor (HAE-nC1-INH) is an underdiagnosed condition. Although the association with genetic variants has been identified for some families, the genetic causes in many patients with HAE-nC1-INH remain unknown.
View Article and Find Full Text PDFInfectious diseases, such as Dengue fever, pose a significant public health threat. Developing a reliable mathematical model plays a crucial role in quantitatively elucidating the kinetic characteristics of antibody-virus interactions. By integrating previous models and incorporating the antibody dynamic theory, we have constructed a novel and robust model that can accurately simulate the dynamics of antibodies and viruses based on a comprehensive understanding of immunology principles.
View Article and Find Full Text PDFDVGs (Defective Viral Genomes) are prevalent in RNA virus infections. In this investigation, we conducted an analysis of high-throughput sequencing data and observed widespread presence of DVGs in SARS-CoV-2. Comparative analysis between SARS-CoV-2 and diverse DNA viruses revealed heightened susceptibility to damage and increased sequencing sample heterogeneity within the SARS-CoV-2 genome.
View Article and Find Full Text PDFBackground: The current ribosome has evolved from the primitive stages of life on Earth. Its function is to build proteins and on the basis of this role, we are looking for a universal common ancestor to the ribosome which could: i) present optimal combinatorial properties, and ii) have left vestiges in the current molecules composing the ribosome (rRNA or r-proteins) or helping in its construction and functioning.
Methods: Genomic public databases are used for finding the nucleotide sequences of rRNAs and mRNA of r-proteins and statistical calculations are performed on the occurrence in these genes of some pentamers belonging to the RNA proposed as optimal ribosome ancestor.
The chronological age used in demography describes the linear evolution of the life of a living being. The chronological age cannot give precise information about the exact developmental stage or aging processes an organism has reached. On the contrary, the biological age (or epigenetic age) represents the true evolution of the tissues and organs of the living being.
View Article and Find Full Text PDFThe development of phylogenetic trees based on RNA or DNA sequences generally requires a precise and limited choice of important RNAs, e.g., messenger RNAs of essential proteins or ribosomal RNAs (like 16S), but rarely complete genomes, making it possible to explain evolution and speciation.
View Article and Find Full Text PDFObjective: The objective of this article is to develop a robust method for forecasting the transition from endemic to epidemic phases in contagious diseases using COVID-19 as a case study.
Methods: Seven indicators are proposed for detecting the endemic/epidemic transition: variation coefficient, entropy, dominant/subdominant spectral ratio, skewness, kurtosis, dispersion index and normality index. Then, principal component analysis (PCA) offers a score built from the seven proposed indicators as the first PCA component, and its forecasting performance is estimated from its ability to predict the entrance in the epidemic exponential growth phase.
We have employed mathematical modeling techniques to construct a comprehensive framework for elucidating the intricate response mechanisms of the immune system, facilitating a deeper understanding of B-cell clonal deletion and somatic hypermutation. Our improved model introduces innovative mechanisms that shed light on positive and negative selection processes during T-cell and B-cell development. Notably, clonal deletion is attributed to the attenuated immune stimulation exerted by self-antigens with high binding affinities, rendering them less effective in eliciting subsequent B-cell maturation and differentiation.
View Article and Find Full Text PDFInfectious diseases such as SARS-CoV-2 pose a considerable threat to public health. Constructing a reliable mathematical model helps us quantitatively explain the kinetic characteristics of antibody-virus interactions. A novel and robust model is developed to integrate antibody dynamics with virus dynamics based on a comprehensive understanding of immunology principles.
View Article and Find Full Text PDFThere are several theories on the origin of life, which differ by choosing the preponderant factor of emergence: main function (autocatalysis versus replication), initial location (black smokers versus ponds) or first molecule (RNA versus DNA). Among the two last ones, the first assumes that an RNA world involving a collaboration of small RNAs with amino-acids pre-existed and the second that DNA-enzyme-lipid complexes existed first. The debate between these classic theories is not closed and the arguments for one or the other of these theories have recently fueled a debate in which the two have a high degree of likelihood.
View Article and Find Full Text PDFVaccines (Basel)
December 2022
Background: The adventure of the mRNA vaccine began thirty years ago in the context of influenza. This consisted in encapsulating the mRNA coding for a viral protein in a lipid particle. We show how the mRNA encoding S protein has been modified for that purpose in the context of the anti-SARS-CoV-2 vaccination.
View Article and Find Full Text PDFThe formulation of mathematical models using differential equations has become crucial in predicting the evolution of viral diseases in a population in order to take preventive and curative measures. In December 2019, a novel variety of Coronavirus (SARS-CoV-2) was identified in Wuhan, Hubei Province, China, which causes a severe and potentially fatal respiratory syndrome. Since then, it has been declared a pandemic by the World Health Organization and has spread around the globe.
View Article and Find Full Text PDFSARS-CoV-2 has caused tremendous deaths globally. It is of great value to predict the evolutionary direction of SARS-CoV-2. In this paper, we proposed a novel mathematical model that could predict the evolutionary trend of SARS-CoV-2.
View Article and Find Full Text PDFBiology (Basel)
December 2022
Background: The age of infection plays an important role in assessing an individual's daily level of contagiousness, quantified by the daily reproduction number. Then, we derive an autoregressive moving average model from a daily discrete-time epidemic model based on a difference equation involving the age of infection. Novelty: The article's main idea is to use a part of the spectrum associated with this difference equation to describe the data and the model.
View Article and Find Full Text PDFIt is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that small, double-stranded, polynucleotide circlets have special catalytic properties. We then use this proposal as the basis for a 'view from here' that we term the Circlet hypothesis as part of a broader Ring World.
View Article and Find Full Text PDFtRNAs presumably accreted into modern ribosomal RNAs. Previous analyses showed similar secondary structures for ancient rRNA subelements and theoretical minimal RNA rings, candidate tRNA ancestors rationally designed from tRNA-unrelated principles. Here, analyses test which tRNA secondary structure subelements resemble ancient/recent rRNA subelements.
View Article and Find Full Text PDFIt was noticed that the mortality rate of SARS-CoV-2 infection experienced a significant declination in the early stage of the epidemic. We suspect that the sharp deterioration of virus toxicity is related to the deletion of the untranslated region (UTR) of the virus genome. It was found that the genome length of SARS-CoV-2 engaged a significant truncation due to UTR deletion after a mega-sequence analysis.
View Article and Find Full Text PDFThe end of the acute phase of the COVID-19 pandemic is near in some countries as declared by World Health Organization (WHO) in January 2022 based on some studies in Europe and South Africa despite unequal distribution of vaccines to combat the disease spread globally. The heterogeneity in individual age and the reaction to biological and environmental changes that has been observed in COVID-19 dynamics in terms of different reaction to vaccination by age group, severity of infection per age group, hospitalization and Intensive Care Unit (ICU) records show different patterns, and hence, it is important to improve mathematical models for COVID-19 pandemic prediction to account for different proportions of ages in the population, which is a major factor in epidemic history. We aim in this paper to estimate, using the Usher model, the lifespan loss due to viral infection and ageing which could result in pathological events such as infectious diseases.
View Article and Find Full Text PDFIn this article we study the efficacy of vaccination in epidemiological reconstructions of COVID-19 epidemics from reported cases data. Given an epidemiological model, we developed in previous studies a method that allowed the computation of an instantaneous transmission rate that produced an exact fit of reported cases data of the COVID-19 outbreak. In this article, we improve the method by incorporating vaccination data.
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