Papers by Jacques Demongeot
HAL (Le Centre pour la Communication Scientifique Directe), 2007
Following the Hodge decomposition of regular vector fields we can decompose the second member of ... more Following the Hodge decomposition of regular vector fields we can decompose the second member of any Liénard system into 2 (non unique) polynomials, first corresponding to potential and second to Hamiltonian dynamics. This polynomial Hodge decomposition is called potential-Hamiltonian, denoted PH-decomposition, and we give it for any polynomial differential system of dimension 2. We will give in a further Note an algorithm expliciting the PH-decomposition in the neighborhood of particular orbits like a limit-cycle for Liénard systems, the method being applicable for any polynomial differential system of dimension 2. Un système de Liénard est un système différentiel du second ordre, défini sur ℜ 2 , du type : dx /dt = y , dy/dt = -g(x)+yf (x) où g et f sont des polynômes. Un tel système est susceptible dêtre décomposé, de manière non unique, en 2 parties polynomiales, l'une potentielle et l'autre hamiltonienne, c'est-à-dire qu'il existe deux polynômes P et H, définis sur ℜ 2 à valeurs dans ℜ , vérifiant dx /dt = -∂P/∂x + ∂H/∂y , dy/dt = -∂P/∂y -∂H/∂x. On montre, en utilisant la décomposition de Hodge des champs de vecteurs réguliers, que le second membre d'un tel système est décomposable en 2 polynômes, l'un correspondant à une dynamique de gradient et l'autre à une dynamique hamiltonienne. Cette décomposition de Hodge polynomiale est appelée potentielle-hamiltonienne, notée PH-décomposition, et nous en donnons la formule pour tout système différentiel polynomial du plan. Nous donnerons, dans une Note ultérieure, un algorithme permettant d'obtenir une formule explicite de la PH-décomposition au voisinage d'orbites particulières, telles qu'un cycle limite dans le cas des systèmes de Liénard, la méthode étant applicable à tout système différentiel polynomial du plan. Les systèmes de Liénard sont des Equations Différentielles Ordinaires de Dimension 2 (2D-EDO) du type : dx/dt = y, dy/dt = -g(x) + yf (x), où f et g sont des polynômes. Le système de van der Pol (cf. Figure ) en est un bon exemple [2-4], utilisé pour modéliser de nombreux systèmes biologiques régulés, dont le système cardiaque. Les polynômes g et f d'un système de van der Pol
International Journal of Molecular Sciences
The development of phylogenetic trees based on RNA or DNA sequences generally requires a precise ... more The 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. In this article, we propose revisiting a classic phylogeny of archaea from only the information on the succession of nucleotides of their entire genome. For this purpose, we use a new tool, the unsupervised classifier Maxwell, whose principle lies in the Burrows–Wheeler compression transform, and we show its efficiency in clustering whole archaeal genomes.
Diseases
Objective: The objective of this article is to develop a robust method for forecasting the transi... more Objective: 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. Results: This score is applied to the retro-prediction of endemic/epidemic transitions of COVID-19 outbreak in seven various countries for which the first PCA component has a good predicting power. Conclusion: This research offers a valuable tool for early epidemic detection, aiding in effective public health responses.
Pathogens
The formulation of mathematical models using differential equations has become crucial in predict... more The 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. A reaction–diffusion system is a mathematical model that describes the evolution of a phenomenon subjected to two processes: a reaction process, in which different substances are transformed, and a diffusion process, which causes their distribution in space. This article provides a mathematical study of the Susceptible, Exposed, Infected, Recovered, and Vaccinated population model of the COVID-19 pandemic using the bias of reaction–diffusion equations. Both local and global asymptotic stability conditions ...
International Journal of Molecular Sciences
It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-str... more It 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. To maximize the potential explanatory value of this hypothesis, we speculate boldly about the origins of several of the fundamental characteristics and briefly describe the main methods or treatments applied. The principal prediction of the paper is that the highly constrained, conformational changes will occur preferentially in dsDNA, dsRNA and hybrid RNA-DNA circlets that are below a critical size (e.g., 306 bp) and that these will favor the polymerization of precursors into RNA and DNA. We conclude that the Circlet hypothesis and the Ring World therefore have the attraction of offering the same solution t...
The statistical analysis found that the mortality rate of COVID-19 infection experienced a signif... more The statistical analysis found that the mortality rate of COVID-19 infection experienced a significant decline in the early stage of the epidemic. We suspect that the sharp deterioration of virus toxicity is related to point mutation and the deletion of the untranslated region of the virus genome. Through sequence analysis of mega-genome data, we found that the genome length of COVID-19 was deleted, which mainly occurred in the untranslated regions at both ends. Sequence similarity analysis further indicated that short UTR length strain emerged by deleting strain with long sequence length. This process is irreversible; the genome with a short sequence length could not restore to the long sequence length. By studying the relationship between genome length and mortality, we found a good correlation between them statistically, which demonstrated that the deletion of the untranslated region of the virus significantly affected the toxicity of the virus. We extracted the viral genome leng...
We extend the classical approach in supervised classification based on the local likelihood estim... more We extend the classical approach in supervised classification based on the local likelihood estimation to the functional covariates case. The estimation procedure of the functional parameter (slope parameter) in the linear model when the covariate is of functional kind is investigated. We show, on simulated as well on real data, that classification error rates estimated using test samples, and the estimation procedure by local likelihood seem to lead to better estimators than the classical kernel estimation. In addition, this approach is no longer assuming that the linear predictors have a specific parametric form. However, this approach also has two drawbacks. Indeed, it was more expensive and slower than the kernel regression. Thus, as mentioned earlier, kernels other than the Gaussian kernel can lead to a divergence of the Newton-Raphson algorithm. In contrast, using a Gaussian kernel, 4 to 6 iterations are then sufficient to achieve convergence.
Psychology, 2021
ment of individuals' psyches, creating a group entity having its own identity. In the slow-open g... more ment of individuals' psyches, creating a group entity having its own identity. In the slow-open groups, the participants are mainly subject to clan loyalties.
Psychology, 2021
will give here only a short reminder. The study's objective is to explore the existence and the e... more will give here only a short reminder. The study's objective is to explore the existence and the evolution of common behavior of the participants to four slow open groups taking part in a Dialectical Behavior Therapy (DBT) skills training. Two groups were composed of adolescents and two of their respective parents. We analyzed their evolution via the answers to the "absurd" questionnaire.
Aide informatisée aux soins, surveillance et éducation thérapeutique à domicile
Technologies biomédicales, 2016
L'aide a domicile en SESPAO (Surveillance, Education et Soins Personnalises Assistes par Ordi... more L'aide a domicile en SESPAO (Surveillance, Education et Soins Personnalises Assistes par Ordinateur) propose de nombreuses applications utiles pour le suivi des personnages âgees a domicile. Cette technologie permet entre autres la detection d'une chute, d'un malaise ou d'un episode pouvant necessiter une intervention, la surveillance d'un etat stabilise ou encore l'entree progressive dans une pathologie a l'aide de l'observation d'un certain nombres de symptomes. Apres un etat des lieux des differents capteurs existants en SESPAO et de leurs environnements virtuels, cet article interroge sur la portee ethique de ces technologies et offre une piste de reflexion sur les avancees futures.
SummaryBackgroundThe COVID-19 epidemic, which started in late December 2019 and rapidly spread th... more SummaryBackgroundThe COVID-19 epidemic, which started in late December 2019 and rapidly spread throughout the world, was accompanied by an unprecedented release of reported case data. Our objective is to propose a fresh look at this data by coupling a phenomenological description to the epidemiological dynamics.MethodsWe use a phenomenological model to describe and regularize the data. This model can be matched by a single mathematical model reproducing the epidemiological dynamics with a time-dependent transmission rate. We provide a method to compute this transmission rate and reconstruct the changes in the social interactions between people as well as changes in host-pathogen interactions. This method is applied to the cumulative case data of 8 different geographic areas.FindingsWe reconstruct the transmission rate from the data, therefore we are in position to understand the contribution of the dynamical effects of social interactions (contacts between individuals) and the contr...
The Lancet Public Health, 2021
Background The objective of this study was to better understand the factors associated with the h... more Background The objective of this study was to better understand the factors associated with the heterogeneity of in-hospital COVID-19 morbidity and mortality across France, one of the countries most affected by COVID-19 in the early months of the pandemic. Methods This geo-epidemiological analysis was based on data publicly available on government and administration websites for the 96 administrative departments of metropolitan France between March 19 and May 11, 2020, including Public Health France, the Regional Health Agencies, the French national statistics institute, and the Ministry of Health. Using hierarchical ascendant classification on principal component analysis of multidimensional variables, and multivariate analyses with generalised additive models, we assessed the associations between several factors (spatiotemporal spread of the epidemic between Feb 7 and March 17, 2020, the national lockdown, demographic population structure, baseline intensive care capacities, baseline population health and health-care services, new chloroquine and hydroxychloroquine dispensations, economic indicators, degree of urbanisation, and climate profile) and in-hospital COVID-19 incidence, mortality, and case fatality rates. Incidence rate was defined as the cumulative number of in-hospital COVID-19 cases per 100 000 inhabitants, mortality rate as the cumulative number of in-hospital COVID-19 deaths per 100 000, and case fatality rate as the cumulative number of in-hospital COVID-19 deaths per cumulative number of in-hospital COVID-19 cases. Findings From March 19 to May 11, 2020, hospitals in metropolitan France notified a total of 100 988 COVID-19 cases, including 16 597 people who were admitted to intensive care and 17 062 deaths. There was an overall cumulative in-hospital incidence rate of 155•6 cases per 100 000 inhabitants (range 19•4-489•5), in-hospital mortality rate of 26•3 deaths per 100 000 (1•1-119•2), and in-hospital case fatality rate of 16•9% (4•8-26•2). We found clear spatial heterogeneity of in-hospital COVID-19 incidence and mortality rates, following the spread of the epidemic. After multivariate adjustment, the delay between the first COVID-19-associated death and the onset of the national lockdown was positively associated with in-hospital incidence (adjusted standardised incidence ratio 1•02, 95% CI 1•01-1•04), mortality (adjusted standardised mortality ratio 1•04, 1•02-1•06), and case fatality rates (adjusted standardised fatality ratio 1•01, 1•01-1•02). Mortality and case fatality rates were higher in departments with older populations (adjusted standardised ratio for populations with a high proportion older than aged >85 years 2•17 [95% CI 1•20-3•90] for mortality and 1•43 [1•08-1•88] for case fatality rate). Mortality rate was also associated with incidence rate (1•0004, 1•0002-1•001), but mortality and case fatality rates did not appear to be associated with baseline intensive care capacities. We found no association between climate and in-hospital COVID-19 incidence, or between economic indicators and in-hospital COVID-19 incidence or mortality rates. Interpretation This ecological study highlights the impact of the epidemic spread, national lockdown, and reactive adaptation of intensive care capacities on the spatial distribution of COVID-19 morbidity and mortality. It provides information for future geo-epidemiological analyses and has implications for preparedness and response policies to current and future epidemic waves in France and elsewhere.
Like in many countries and regions, spread of the COVID-19 pandemic has exhibited important spati... more Like in many countries and regions, spread of the COVID-19 pandemic has exhibited important spatial heterogeneity across France, one of the most affected countries so far.To better understand factors associated with incidence, mortality and lethality heterogeneity across the 96 administrative departments of metropolitan France, we thus conducted a geo-epidemiological analysis based on publicly available data, using hierarchical ascendant classification (HAC) on principal component analysis (PCA) of multidimensional variables, and multivariate analyses with generalized additive models (GAM).Our results confirm a marked spatial heterogeneity of in-hospital COVID-19 incidence and mortality, following the North East – South West diffusion of the epidemic. The delay elapsed between the first COVID-19 associated death and the onset of the national lockdown on March 17th, 2020, appeared positively associated with in-hospital incidence, mortality and lethality. Mortality was also strongly a...
The article is devoted to the parameters identification in the SI model. We consider several meth... more The article is devoted to the parameters identification in the SI model. We consider several methods, starting with an exponential fit of the early cumulative data of Sars-CoV2 in mainland China. The present methodology provides a way to compute the parameters at the early stage of the epidemic. Next, we establish an identifiability result. Then we use the Bernoulli-Verhulst model as a phenomenological model to fit the data and derive some results on the parameters identification. The last part of the paper is devoted to some numerical algorithms to fit a daily piecewise constant rate of transmission.
Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies, 2019
This paper proposes a non-invasive, acoustic-based method to i) automatically detect sounds throu... more This paper proposes a non-invasive, acoustic-based method to i) automatically detect sounds through a neckworn microphone providing a stream of acoustic input comprising of a) swallowing-related, b) speech and c) other ambient sounds (noise); ii) classify and detect swallowing-related sounds, speech or ambient noise within the acoustic stream. The above three types of acoustic signals were recorded from subjects, without any clinical symptoms of dysphagia, with a microphone attached to the neck at a pre-studied position midway between the Laryngeal Prominence and the Jugular Notch. Frequency-based analysis detection algorithms were developed to distinguish the above three types of acoustic signals with an accuracy of 86.09%. Integrated automatic detection algorithms with classification based on Gaussian Mixture Model (GMM) using the Expectation Maximisation algorithm (EM), achieved an overall validated recognition rate of 87.60% which increased to 88.87 recognition accuracy if the validated false alarm classifications were also to be included. The proposed approach thus enables the recovery from ambient signals, detection and time-stamping of the acoustic footprints of the swallowing process chain and thus further analytics to characterise the swallowing process in terms of consistency, normality and possibly risk-assessing and localising the level of any swallowing abnormality i.e. the dysphagia. As such this helps reduce the need for invasive techniques for the examination and evaluation of patient's swallowing process and enables diagnostic clinical evaluation based only on acoustic data analytics and non-invasive clinical observations.
Journal of Medical Systems, 2020
The world population ageing is on the rise, which has led to an increase in the demand for medica... more The world population ageing is on the rise, which has led to an increase in the demand for medical care due to diseases and symptoms prevalent in health centers. One of the most prevalent symptoms prevalent in older adults is falls, which affect one-third of patients each year and often result in serious injuries that can lead to death. This paper describes the design of a fall detection system for elderly households living alone using very low resolution thermal sensor arrays. The algorithms implemented were LSTM, GRU, and Bi-LSTM; the last one mentioned being that which obtained the best results at 93% in accuracy. The results obtained aim to be a valuable tool for accident prevention for those patients that use it and for clinicians who manage the data.
IEEE Journal of Translational Engineering in Health and Medicine, 2018
Pressure ulcers (PU) are known to be a high-cost disease with a risk of severe morbidity. This pa... more Pressure ulcers (PU) are known to be a high-cost disease with a risk of severe morbidity. This paper evaluates a new clinical strategy based on an innovative medical device [Tongue Display Unit (TDU)] that implements perceptive supplementation in order to reduce prolonged excessive pressure, recognized as one of the main causes of PU. A randomized, controlled, and parallel-group trial was carried out with 12 subjects with spinal cord injuries (SCI). Subjects were assigned to the control (without TDU, n = 6) or intervention (with TDU, n = 5) group. Each subject took part in two sessions, during which the subject, seated on a pressure map sensor, watched a movie for one hour. The TDU was activated during the second session of the intervention group. Intention-to-treat analysis showed that the improvement in adequate weight shifting between the two sessions was higher in the intervention group (0.84 [0.24; 0.89]) than in the control group (0.01 [−0.01; 0.09]; p = 0.004) and that the ratio of prolonged excessive pressure between the two sessions was lower in the intervention group (0.74 [0.37; 1.92]) than in the control group (1.72 [1.32; 2.56]; p = 0.06). The pressure map sensor was evaluated as being convenient for use in daily life; however, this was not the case for the TDU. This paper shows that persons with SCI could benefit from a system based on perceptive supplementation that alerts and guides the user on how to adapt their posture in order to reduce prolonged excessive pressure, one of the main causes of PU.
The Science of Nature, 2019
Deaminations (A->G, C->T) increase with DNA singlestrandedness during replication, presumably cre... more Deaminations (A->G, C->T) increase with DNA singlestrandedness during replication, presumably creating spontaneous genomic mutational and nucleotide frequency gradients. Alternatively, genes are positioned to avoid deaminations. Deamination gradients affect directly mitogene third codon positions; conserved vertebrate mitochondrial tRNA and protein coding gene arrangements minimize deaminations in anticodons, and first and second codon positions in mitogenes. Here we describe deamination gradients across theoretical minimal RNA rings, 22 nucleotide-long RNAs designed to simulate prebiotic RNAs. These RNA rings code for a start/stop codon and a single codon for each amino acid, and form stem-loop hairpins slowing degradation. They resemble consensus tRNAs, defining potential anticodons and cognate amino acids. Theoretical minimal RNA rings are not designed to include deamination gradients, yet deamination gradients occur in RNA rings. tRNA homology produces stronger evidence for deamination gradients than RNA ring homology defined by coding properties. Deamination gradients start at predicted RNA ring anticodons, corresponding to known homologies between mitochondrial tRNAs and replication origins, and between bacterial tRNA synthetases and mitochondrial DNA polymerase gamma. Deamination gradients are strongest for RNA rings with predicted anticodons matching cognate amino acids that integrated early the genetic code. Presumably protections against deaminations evolved while amino acids integrated the genetic code. Results confirm tRNA-RNA ring homologies. Coding constraints defining RNA rings presumably produce deamination gradients starting at predicted anticodons. Hence, the universal genetic code determines nucleotide deamination gradients in theoretical minimal RNA rings, suggesting adaptation to prevent consequences of deamination mutations. Results also indicate that the genetic code's structure determined evolution of tRNAs, their cognates, tRNA synthetases, and polymerases.
Advances in Applied Mathematics, 2018
This paper addresses the question of the impact of the boundary on the dynamical behaviour of fin... more This paper addresses the question of the impact of the boundary on the dynamical behaviour of finite Boolean automata networks on Z 2. The evolution over discrete time of such networks is governed by a specific stochastic threshold non-linear transition rule derived from the classical rule of formal neural networks. More precisely, the networks considered in this paper are finite but the study is done for arbitrarily large sizes. Moreover, the boundary impact is viewed as a classical definition of a phase transition in probability theory, characterising in our context the fact that a network admits distinct asymptotic behaviours when different boundary instances are assumed. The main contribution of this paper is the highlight of a formula for a necessary condition for boundary sensitivity, whose sufficiency and necessity are entirely proven with natural constraints on interaction potentials.
IRBM, 2018
Aiming for autonomous living for the people after a stroke is the challenge these days especially... more Aiming for autonomous living for the people after a stroke is the challenge these days especially for swallowing disorders or dysphagia. It is in this context that the e-swallhome project proposes to develop tools, from hospital care until the patient returns home, which are able to monitor in real time the process of swallowing. This paper proposes a non-invasive acoustic based method to differentiate between swallowing sounds and other sounds in normal ambient environment during food intake. Gaussian Mixture Models (GMM) adapted through the Expectation Maximization (EM) algorithm was employed for classification and test combination using the leave-one-out approach according to the small amount of data in our database. Results provide a good recognition rate of 100 %.
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Papers by Jacques Demongeot