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Faire une suggestion Affiner la recherche Interroger des sources externesAt the crossroads of epidemiology and biology: bridging the gap between SARS-CoV-2 viral strain properties and epidemic wave characteristics / Florian Poydenot
Titre : At the crossroads of epidemiology and biology: bridging the gap between SARS-CoV-2 viral strain properties and epidemic wave characteristics Type de document : texte imprimé Auteurs : Florian Poydenot, Auteur ; Alice Lebreton, Auteur ; Jacques Haiech, Auteur ; Bruno Andreotti, Auteur Editeur : arXiv Année de publication : 2021 Note générale : 26 pages, 5 figures; Langues : Anglais (eng) Catégories : 570 Biologie générale, sciences de la vie Tags : 'Populations and Evolution (q-bio.PE) Biological Physics (physics.bio-ph) (q-bio.PE) (physics.bio-ph) COVID19 SARS-CoV-2 epidemiology PFU GU viral load' Index. décimale : 570 Résumé : The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish relationships between epidemiological data and the characteristics of the virus strain responsible for the epidemic wave concerned. We have carried out this study on the Wuhan, Alpha, Delta and Omicron strains allowing us to illustrate the evolution of the relationships we have highlighted according to these different viral strains. We addressed the following questions: 1) How can the mean infectious dose (one quantum, by definition in epidemiology) be measured and expressed as an amount of viral RNA molecules (in genome units, GU) or as a number of replicative viral particles (in plaque-forming units, PFU)? 2) How many infectious quanta are exhaled by an infected person per unit of time? 3) How many infectious quanta are exhaled, on average, integrated over the whole contagious period? 4) How do these quantities relate to the epidemic reproduction rate R as measured in epidemiology, and to the viral load, as measured by molecular biological methods? 5) How has the infectious dose evolved with the different strains of SARS-CoV-2? We make use of state-of-the-art modelling, reviewed and explained in the appendix of the article (Supplemental Information, SI), to answer these questions using data from the literature in both epidemiology and virology. We have considered the modification of these relationships according to the vaccination status of the population. We hope that this work will allow a better integration of data from different fields (virology, epidemiology, and immunology) to anticipate the evolution of the epidemic in the case of COVID-19, but also in respiratory pathologies transmissible in an airborne manner. En ligne : https://arxiv.org/abs/2301.12975 Format de la ressource électronique : At the crossroads of epidemiology and biology: bridging the gap between SARS-CoV-2 viral strain properties and epidemic wave characteristics [texte imprimé] / Florian Poydenot, Auteur ; Alice Lebreton, Auteur ; Jacques Haiech, Auteur ; Bruno Andreotti, Auteur . - arXiv, 2021.
26 pages, 5 figures;
Langues : Anglais (eng)
Catégories : 570 Biologie générale, sciences de la vie Tags : 'Populations and Evolution (q-bio.PE) Biological Physics (physics.bio-ph) (q-bio.PE) (physics.bio-ph) COVID19 SARS-CoV-2 epidemiology PFU GU viral load' Index. décimale : 570 Résumé : The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish relationships between epidemiological data and the characteristics of the virus strain responsible for the epidemic wave concerned. We have carried out this study on the Wuhan, Alpha, Delta and Omicron strains allowing us to illustrate the evolution of the relationships we have highlighted according to these different viral strains. We addressed the following questions: 1) How can the mean infectious dose (one quantum, by definition in epidemiology) be measured and expressed as an amount of viral RNA molecules (in genome units, GU) or as a number of replicative viral particles (in plaque-forming units, PFU)? 2) How many infectious quanta are exhaled by an infected person per unit of time? 3) How many infectious quanta are exhaled, on average, integrated over the whole contagious period? 4) How do these quantities relate to the epidemic reproduction rate R as measured in epidemiology, and to the viral load, as measured by molecular biological methods? 5) How has the infectious dose evolved with the different strains of SARS-CoV-2? We make use of state-of-the-art modelling, reviewed and explained in the appendix of the article (Supplemental Information, SI), to answer these questions using data from the literature in both epidemiology and virology. We have considered the modification of these relationships according to the vaccination status of the population. We hope that this work will allow a better integration of data from different fields (virology, epidemiology, and immunology) to anticipate the evolution of the epidemic in the case of COVID-19, but also in respiratory pathologies transmissible in an airborne manner. En ligne : https://arxiv.org/abs/2301.12975 Format de la ressource électronique : Exemplaires (5)
Code-barres Cote Support Localisation Section Disponibilité 5 570 POY Cartes et plans Biblio Libre Albums Enfants Exclu du prêt 6 570 POY Cartes et plans Biblio Libre Albums Enfants Exclu du prêt 7 570 POY Cartes et plans Biblio Libre Albums Enfants Exclu du prêt 8 570 POY Cartes et plans Biblio Libre Albums Enfants Exclu du prêt 10 570 POY Cartes et plans Biblio Libre Albums Enfants Exclu du prêt
Titre : Device for measuring the plant physiology and electrophysiology Type de document : document électronique Auteurs : Serge Kernbach, Auteur Editeur : arXiv Langues : Anglais (eng) Catégories : 575 Anatomie et physiologie végétales Tags : 'measuring physiological electrophysiological plants physiologie spectroscopy plantes bio-physiological'. Index. décimale : 575 Résumé : This paper briefly describes the device - the phytosensor - for measuring physiological and electrophysiological parameters of plants. This system is developed as a bio-physiological sensor in precise agriculture, as a tool in plant research and environmental biology, and for plant enthusiasts in smart home or entertainment applications. The phytosentor measures main physiological parameters such as the leaf transpiration rate, sap flow, tissue conductivity and frequency response, biopotentials (action potentials and variation potentials), and can conduct electrochemical impedance spectroscopy with organic tissues. Soil moisture and temperature, air quality (CO2, NO2, O3 and other sensors on I2C bus), and general environmental parameters (light, temperature, humidity, air pressure, electromagnetic and magnetic fields) are also recorded in real time. In addition to phytosensing, the device can also perform phytoactuation, i.e. execute electrical or light stimulation of plants, control irrigation and lighting modes, conduct fully autonomous experiments with complex feedback-based and adaptive scenarios in robotic or biohybrid systems. This article represents the revised and extended version of original paper and includes some descriptions and images from the FloraRobotica and BioHybrids projects. En ligne : https://arxiv.org/abs/2206.10459 Format de la ressource électronique : Device for measuring the plant physiology and electrophysiology [document électronique] / Serge Kernbach, Auteur . - arXiv, [s.d.].
Langues : Anglais (eng)
Catégories : 575 Anatomie et physiologie végétales Tags : 'measuring physiological electrophysiological plants physiologie spectroscopy plantes bio-physiological'. Index. décimale : 575 Résumé : This paper briefly describes the device - the phytosensor - for measuring physiological and electrophysiological parameters of plants. This system is developed as a bio-physiological sensor in precise agriculture, as a tool in plant research and environmental biology, and for plant enthusiasts in smart home or entertainment applications. The phytosentor measures main physiological parameters such as the leaf transpiration rate, sap flow, tissue conductivity and frequency response, biopotentials (action potentials and variation potentials), and can conduct electrochemical impedance spectroscopy with organic tissues. Soil moisture and temperature, air quality (CO2, NO2, O3 and other sensors on I2C bus), and general environmental parameters (light, temperature, humidity, air pressure, electromagnetic and magnetic fields) are also recorded in real time. In addition to phytosensing, the device can also perform phytoactuation, i.e. execute electrical or light stimulation of plants, control irrigation and lighting modes, conduct fully autonomous experiments with complex feedback-based and adaptive scenarios in robotic or biohybrid systems. This article represents the revised and extended version of original paper and includes some descriptions and images from the FloraRobotica and BioHybrids projects. En ligne : https://arxiv.org/abs/2206.10459 Format de la ressource électronique : Genetic Composition of Supercritical Branching Populations under Power Law Mutation Rates / Vianney Brouard
Titre : Genetic Composition of Supercritical Branching Populations under Power Law Mutation Rates Type de document : document électronique Auteurs : Vianney Brouard, Auteur Editeur : arXiv Année de publication : 2023 Langues : Anglais (eng) Catégories : 576 Évolution, génétique:576.01 Philosophie et théorie de la génétique et de l'évolution Tags : 'cancer evolution multitype branching processes finite graph , long time behavior power law mutation rates population genetics génétique Évolution Populations and Evolution (q-bio.PE)'. Résumé : We aim at understanding the evolution of the genetic composition of cancer cell populations. To this aim, we consider a branching individual based model representing a cell population where cells divide, die and mutate along the edges of a finite directed graph (V,E). The process starts with only one cell of trait 0. Following typical parameter values in cancer cell populations we study the model under large population and power law mutation rates limit, in the sense that the mutation probabilities are parameterized by negative powers of n and the typical sizes of the population of our interest are positive powers of n. Under non-increasing growth rate condition (namely the growth rate of any sub-population is smaller than the growth rate of trait 0), we describe the time evolution of the first-order asymptotics of the size of each sub-population on the log(n) time scale, as well as in the random time scale at which the initial population, resp. the total population, reaches the size nt. In particular, such results allow to characterize whose mutational paths along the edges of the graph are actually contributing to the size order of the sub-populations. Without any condition on the growth rate, we describe the time evolution of the orders of magnitude of each sub-population. Adapting techniques from Durrett and Mayberry 2011, we show that these converges to positive deterministic non-decreasing piecewise linear continuous functions, whose slopes are given by an algorithm. En ligne : https://arxiv.org/abs/2309.12055 Format de la ressource électronique : Genetic Composition of Supercritical Branching Populations under Power Law Mutation Rates [document électronique] / Vianney Brouard, Auteur . - arXiv, 2023.
Langues : Anglais (eng)
Catégories : 576 Évolution, génétique:576.01 Philosophie et théorie de la génétique et de l'évolution Tags : 'cancer evolution multitype branching processes finite graph , long time behavior power law mutation rates population genetics génétique Évolution Populations and Evolution (q-bio.PE)'. Résumé : We aim at understanding the evolution of the genetic composition of cancer cell populations. To this aim, we consider a branching individual based model representing a cell population where cells divide, die and mutate along the edges of a finite directed graph (V,E). The process starts with only one cell of trait 0. Following typical parameter values in cancer cell populations we study the model under large population and power law mutation rates limit, in the sense that the mutation probabilities are parameterized by negative powers of n and the typical sizes of the population of our interest are positive powers of n. Under non-increasing growth rate condition (namely the growth rate of any sub-population is smaller than the growth rate of trait 0), we describe the time evolution of the first-order asymptotics of the size of each sub-population on the log(n) time scale, as well as in the random time scale at which the initial population, resp. the total population, reaches the size nt. In particular, such results allow to characterize whose mutational paths along the edges of the graph are actually contributing to the size order of the sub-populations. Without any condition on the growth rate, we describe the time evolution of the orders of magnitude of each sub-population. Adapting techniques from Durrett and Mayberry 2011, we show that these converges to positive deterministic non-decreasing piecewise linear continuous functions, whose slopes are given by an algorithm. En ligne : https://arxiv.org/abs/2309.12055 Format de la ressource électronique :
Titre : Holocrine Secretion and Kino Flow in Angiosperms: Their Role and Physiological Advantages in Plant Defence Mechanisms Type de document : document électronique Auteurs : Paulo Cabrita, Auteur Editeur : arXiv Année de publication : 2020 Note générale : 69 pages, 7 figures, 2 Tables Langues : Anglais (eng) Catégories : 575 Anatomie et physiologie végétales :575.2 Transformations génétiques des plantes Tags : 'cambium gum, kino veins unsteady Stokes equation laminar flow physiologie '. Index. décimale : 575 Résumé : Kino is a plant exudate, rich in polyphenols, produced by several angiosperms in reaction to injury of the cambium. It flows out of kino veins, which compose an anatomically distinct continuous system of tangentially anastomosing canals produced by the cambium upon damage, encircling plant stems and branches. Kino is loaded into the vein lumen by autolysis of a cambiform epithelium lined by suberized cells that separate kino veins from the surrounding axial parenchyma. A model describing kino flow is presented to investigate how vein distribution and structure, as well as the loading, solidification, and viscosity of kino affect flow. Considering vein anatomy, viscosity, and a time-dependent loading of kino, the unsteady Stokes equation was applied. Qualitatively, kino flow is similar to resin flow observed on conifers. There is an increase in flow towards the vein open end, with both pressure and flow depending on the vein dimensions, properties, and loading of kino. However, kino veins present a much smaller specific resistance to flow compared to resin ducts. Also, unlike resin loading in conifers, the loading of kino is not pressure-driven. The pressure and pressure gradient required to drive an equally fast flow are smaller than what is observed on the resin ducts of conifers. These results agree with previous observations on some angiosperms and suggest that flow within internal secretory systems derived from autolysing epithelia may have lower metabolic energy costs; thus presenting physiological advantages and possibly constituting an evolutionary step of angiosperms in using internal secretory systems in plant defence mechanisms compared to resin flow in conifers. Understanding of how these physiological and morphological parameters affect kino flow might be useful for selecting species and developing more sustainable and economically viable methods of tapping gum and gum resin in angiosperms. En ligne : https://arxiv.org/abs/1902.09308 Format de la ressource électronique : Holocrine Secretion and Kino Flow in Angiosperms: Their Role and Physiological Advantages in Plant Defence Mechanisms [document électronique] / Paulo Cabrita, Auteur . - arXiv, 2020.
69 pages, 7 figures, 2 Tables
Langues : Anglais (eng)
Catégories : 575 Anatomie et physiologie végétales :575.2 Transformations génétiques des plantes Tags : 'cambium gum, kino veins unsteady Stokes equation laminar flow physiologie '. Index. décimale : 575 Résumé : Kino is a plant exudate, rich in polyphenols, produced by several angiosperms in reaction to injury of the cambium. It flows out of kino veins, which compose an anatomically distinct continuous system of tangentially anastomosing canals produced by the cambium upon damage, encircling plant stems and branches. Kino is loaded into the vein lumen by autolysis of a cambiform epithelium lined by suberized cells that separate kino veins from the surrounding axial parenchyma. A model describing kino flow is presented to investigate how vein distribution and structure, as well as the loading, solidification, and viscosity of kino affect flow. Considering vein anatomy, viscosity, and a time-dependent loading of kino, the unsteady Stokes equation was applied. Qualitatively, kino flow is similar to resin flow observed on conifers. There is an increase in flow towards the vein open end, with both pressure and flow depending on the vein dimensions, properties, and loading of kino. However, kino veins present a much smaller specific resistance to flow compared to resin ducts. Also, unlike resin loading in conifers, the loading of kino is not pressure-driven. The pressure and pressure gradient required to drive an equally fast flow are smaller than what is observed on the resin ducts of conifers. These results agree with previous observations on some angiosperms and suggest that flow within internal secretory systems derived from autolysing epithelia may have lower metabolic energy costs; thus presenting physiological advantages and possibly constituting an evolutionary step of angiosperms in using internal secretory systems in plant defence mechanisms compared to resin flow in conifers. Understanding of how these physiological and morphological parameters affect kino flow might be useful for selecting species and developing more sustainable and economically viable methods of tapping gum and gum resin in angiosperms. En ligne : https://arxiv.org/abs/1902.09308 Format de la ressource électronique :
Titre : In silico prediction of protein flexibility with local structure approach Type de document : document électronique Auteurs : Tarun Narwani, Auteur ; Catherine Etchebest, Auteur ; Pierrick Craveur, Auteur Editeur : Elsevier Autre Editeur : arXiv Importance : Volume 165, Pages 150-155 Format : Langues : Anglais (eng) Catégories : 572 Biochimie Tags : 'Amino acid Structural alphabet Long structural prototypes Protein folds Disorder Bioinformatics Structural bioinformatics Software Support vector machines Evolutionary information Protein data bank Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM)' Index. décimale : 572 Résumé : Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility and predicts them as rigid or flexible.PredyFlexy stands differently from other approaches as it relies on the definition of protein flexibility (i) not only taken from crystallographic data, but also (ii) from Root Mean Square Fluctuation (RMSFs) observed in Molecular Dynamics simulations. It also uses a specific representation of protein structures, named Long Structural Prototypes (LSPs). From Position-Specific Scoring Matrix, the 120 LSPs are predicted with a good accuracy and directly used to predict (i) the protein flexibility in three categories (flexible, intermediate and rigid), (ii) the normalized B-factors, (iii) the normalized RMSFs, and (iv) a confidence index. Prediction accuracy among these three classes is equivalent to the best two class prediction methods, while the normalized B-factors and normalized RMSFs have a good correlation with experimental and in silico values. Thus, PredyFlexy is a unique approach, which is of major utility for the scientific community. It support parallelization features and can be run on a local cluster using multiple cores.The entire project is available under an open-source license at this http URL. En ligne : https://arxiv.org/abs/1908.05120 Format de la ressource électronique : In silico prediction of protein flexibility with local structure approach [document électronique] / Tarun Narwani, Auteur ; Catherine Etchebest, Auteur ; Pierrick Craveur, Auteur . - Elsevier : arXiv, [s.d.] . - Volume 165, Pages 150-155 ; PDF.
Langues : Anglais (eng)
Catégories : 572 Biochimie Tags : 'Amino acid Structural alphabet Long structural prototypes Protein folds Disorder Bioinformatics Structural bioinformatics Software Support vector machines Evolutionary information Protein data bank Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM)' Index. décimale : 572 Résumé : Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility and predicts them as rigid or flexible.PredyFlexy stands differently from other approaches as it relies on the definition of protein flexibility (i) not only taken from crystallographic data, but also (ii) from Root Mean Square Fluctuation (RMSFs) observed in Molecular Dynamics simulations. It also uses a specific representation of protein structures, named Long Structural Prototypes (LSPs). From Position-Specific Scoring Matrix, the 120 LSPs are predicted with a good accuracy and directly used to predict (i) the protein flexibility in three categories (flexible, intermediate and rigid), (ii) the normalized B-factors, (iii) the normalized RMSFs, and (iv) a confidence index. Prediction accuracy among these three classes is equivalent to the best two class prediction methods, while the normalized B-factors and normalized RMSFs have a good correlation with experimental and in silico values. Thus, PredyFlexy is a unique approach, which is of major utility for the scientific community. It support parallelization features and can be run on a local cluster using multiple cores.The entire project is available under an open-source license at this http URL. En ligne : https://arxiv.org/abs/1908.05120 Format de la ressource électronique :
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