Theoretical Biology and Medical Modelling最新文献

{"title":"Correction to: Statistical field theory of the transmission of nerve impulses.","authors":"Gianluigi Zangari Del Balzo","doi":"10.1186/s12976-021-00141-2","DOIUrl":"https://doi.org/10.1186/s12976-021-00141-2","url":null,"abstract":"","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-021-00141-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25441067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A mathematical model of circadian rhythms and dopamine.","authors":"Ruby Kim,&nbsp;Michael C Reed","doi":"10.1186/s12976-021-00139-w","DOIUrl":"https://doi.org/10.1186/s12976-021-00139-w","url":null,"abstract":"<p><strong>Background: </strong>The superchiasmatic nucleus (SCN) serves as the primary circadian (24hr) clock in mammals and is known to control important physiological functions such as the sleep-wake cycle, hormonal rhythms, and neurotransmitter regulation. Experimental results suggest that some of these functions reciprocally influence circadian rhythms, creating a highly complex network. Among the clock's downstream products, orphan nuclear receptors REV-ERB and ROR are particularly interesting because they coordinately modulate the core clock circuitry. Recent experimental evidence shows that REV-ERB and ROR are not only crucial for lipid metabolism but are also involved in dopamine (DA) synthesis and degradation, which could have meaningful clinical implications for conditions such as Parkinson's disease and mood disorders.</p><p><strong>Methods: </strong>We create a mathematical model consisting of differential equations that express how the circadian variables are influenced by light, how REV-ERB and ROR feedback to the clock, and how REV-ERB, ROR, and BMAL1-CLOCK affect the dopaminergic system. The structure of the model is based on the findings of experimentalists.</p><p><strong>Results: </strong>We compare our model predictions to experimental data on clock components in different light-dark conditions and in the presence of genetic perturbations. Our model results are consistent with experimental results on REV-ERB and ROR and allow us to predict the circadian variations in tyrosine hydroxylase and monoamine oxidase seen in experiments. By connecting our model to an extant model of dopamine synthesis, release, and reuptake, we are able to predict circadian oscillations in extracellular DA and homovanillic acid that correspond well with experimental observations.</p><p><strong>Conclusions: </strong>The predictions of the mathematical model are consistent with a wide variety of experimental observations. Our calculations show that the mechanisms proposed by experimentalists by which REV-ERB, ROR, and BMAL1-CLOCK influence the DA system are sufficient to explain the circadian oscillations observed in dopaminergic variables. Our mathematical model can be used for further investigations of the effects of the mammalian circadian clock on the dopaminergic system. The model can also be used to predict how perturbations in the circadian clock disrupt the dopaminergic system and could potentially be used to find drug targets that ameliorate these disruptions.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-021-00139-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25381643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstructing the household transmission of influenza in the suburbs of Tokyo based on clinical cases.","authors":"Masaya M Saito,&nbsp;Nobuo Hirotsu,&nbsp;Hiroka Hamada,&nbsp;Mio Takei,&nbsp;Keisuke Honda,&nbsp;Takamichi Baba,&nbsp;Takahiro Hasegawa,&nbsp;Yoshitake Kitanishi","doi":"10.1186/s12976-021-00138-x","DOIUrl":"https://doi.org/10.1186/s12976-021-00138-x","url":null,"abstract":"<p><strong>Background: </strong>Influenza is a public health issue that needs to be addressed strategically. The assessment of detailed infectious profiles is an important part of this effort. Household transmission data play a key role in estimating such profiles. We used diagnostic and questionnaire-based data on influenza patients at a Japanese clinic to estimate the detailed infectious period (as well as incubation period, symptomatic and infectious periods, and extended infectious period after recovery) and the secondary attack ratio (SAR) of influenza for households of various sizes based on a modified Cauchemez-type model.</p><p><strong>Results: </strong>The data were from enrolled patients with confirmed influenza who were treated at the Hirotsu Clinic (Kawasaki, Japan) with a neuraminidase inhibitor (NAI) during six northern hemisphere influenza seasons between 2010 and 2016. A total of 2342 outpatients, representing 1807 households, were included. For influenza type A, the average incubation period was 1.43 days (95% probability interval, 0.03-5.32 days). The estimated average symptomatic and infective period was 1.76 days (0.33-4.62 days); the extended infective period after recovery was 0.25 days. The estimated SAR rose from 20 to 32% as household size increased from 3 to 5. For influenza type B, the average incubation period, average symptomatic and infective period, and extended infective period were estimated as 1.66 days (0.21-4.61), 2.62 days (0.54-5.75) and 1.00 days, respectively. The SAR increased from 12 to 21% as household size increased from 3 to 5.</p><p><strong>Conclusion: </strong>All estimated periods of influenza type B were longer than the corresponding periods for type A. However, the SAR for type B was less than that for type A. These results may reflect Japanese demographics and treatment policy. Understanding the infectious profiles of influenza is necessary for assessing public health measures.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25357136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Numerical modeling in arterial hemodynamics incorporating fluid-structure interaction and microcirculation.","authors":"Fan He,&nbsp;Lu Hua,&nbsp;Tingting Guo","doi":"10.1186/s12976-021-00136-z","DOIUrl":"https://doi.org/10.1186/s12976-021-00136-z","url":null,"abstract":"<p><strong>Background: </strong>The effects of arterial wall compliance on blood flow have been revealed using fluid-structure interaction in last decades. However, microcirculation is not considered in previous researches. In fact, microcirculation plays a key role in regulating blood flow. Therefore, it is very necessary to involve microcirculation in arterial hemodynamics.</p><p><strong>Objective: </strong>The main purpose of the present study is to investigate how wall compliance affects the flow characteristics and to establish the comparisons of these flow variables with rigid wall when microcirculation is considered.</p><p><strong>Methods: </strong>We present numerical modeling in arterial hemodynamics incorporating fluid-structure interaction and microcirculation. A novel outlet boundary condition is employed to prescribe microcirculation in an idealised model.</p><p><strong>Results: </strong>The novel finding in this work is that wall compliance under the consideration of microcirculation leads to the increase of wall shear stress in contrast to rigid wall, contrary to the traditional result that wall compliance makes wall shear stress decrease when a constant or time dependent pressure is specified at an outlet.</p><p><strong>Conclusions: </strong>This work provides the valuable study of hemodynamics under physiological and realistic boundary conditions and proves that wall compliance may have a positive impact on wall shear stress based on this model. This methodology in this paper could be used in real model simulations.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-021-00136-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38837096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Required concentration index quantifies effective drug combinations against hepatitis C virus infection.","authors":"Yusuke Kakizoe,&nbsp;Yoshiki Koizumi,&nbsp;Yukino Ikoma,&nbsp;Hirofumi Ohashi,&nbsp;Takaji Wakita,&nbsp;Shingo Iwami,&nbsp;Koichi Watashi","doi":"10.1186/s12976-021-00137-y","DOIUrl":"https://doi.org/10.1186/s12976-021-00137-y","url":null,"abstract":"","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-021-00137-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38841107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Required concentration index quantifies effective drug combinations against hepatitis C virus infection.","authors":"Yusuke Kakizoe,&nbsp;Yoshiki Koizumi,&nbsp;Yukino Ikoma,&nbsp;Hirofumi Ohashi,&nbsp;Takaji Wakita,&nbsp;Shingo Iwami,&nbsp;Koichi Watashi","doi":"10.1186/s12976-020-00135-6","DOIUrl":"https://doi.org/10.1186/s12976-020-00135-6","url":null,"abstract":"<p><p>Successful clinical drug development requires rational design of combination treatments based on preclinical data. Anti-hepatitis C virus (HCV) drugs exhibit significant diversity in antiviral effect. Dose-response assessments can be used to determine parameters profiling the diverse antiviral effect during combination treatment. In the current study, a combined experimental and mathematical approaches were used to compare and score different combinations of anti-HCV treatments. A \"required concentration index\" was generated and used to rank the antiviral profile of possible double- and triple-drug combinations against HCV genotype 1b and 2a. Rankings varied based on target HCV genotype. Interestingly, multidrug (double and triple) treatment not only augmented antiviral activity, but also reduced genotype-specific efficacy, suggesting another advantage of multidrug treatment. The current study provides a quantitative method for profiling drug combinations against viral genotypes, to better inform clinical drug development.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-020-00135-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38801543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis and forecast of dengue incidence in urban Colombo, Sri Lanka.","authors":"Kkwh Erandi,&nbsp;Ssn Perera,&nbsp;A C Mahasinghe","doi":"10.1186/s12976-020-00134-7","DOIUrl":"https://doi.org/10.1186/s12976-020-00134-7","url":null,"abstract":"<p><strong>Background: </strong>Understanding the dynamical behavior of dengue transmission is essential in designing control strategies. Mathematical models have become an important tool in describing the dynamics of a vector borne disease. Classical compartmental models are well-known method used to identify the dynamical behavior of spread of a vector borne disease. Due to use of fixed model parameters, the results of classical compartmental models do not match realistic nature. The aim of this study is to introduce time in varying model parameters, modify the classical compartmental model by improving its predictability power.</p><p><strong>Results: </strong>In this study, per-capita vector density has been chosen as the time in varying model parameter. The dengue incidences, rainfall and temperature data in urban Colombo are analyzed using Fourier mathematical analysis tool. Further, periodic pattern of the reported dengue incidences and meteorological data and correlation of dengue incidences with meteorological data are identified to determine climate data-driven per-capita vector density parameter function. By considering that the vector dynamics occurs in faster time scale compares to host dynamics, a two dimensional data-driven compartmental model is derived with aid of classical compartmental models. Moreover, a function for per-capita vector density is introduced to capture the seasonal pattern of the disease according to the effect of climate factors in urban Colombo.</p><p><strong>Conclusions: </strong>The two dimensional data-driven compartmental model can be used to predict weekly dengue incidences upto 4 weeks. Accuracy of the model is evaluated using relative error function and the model can be used to predict more than 75% accurate data.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-020-00134-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38794709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A numerical simulation of air flow in the human respiratory system for various environmental conditions.","authors":"Alibek Issakhov,&nbsp;Yeldos Zhandaulet,&nbsp;Aizhan Abylkassymova,&nbsp;Assylbek Issakhov","doi":"10.1186/s12976-020-00133-8","DOIUrl":"https://doi.org/10.1186/s12976-020-00133-8","url":null,"abstract":"<p><p>The functions of the nasal cavity are very important for maintaining the internal environment of the lungs since the inner walls of the nasal cavity control the temperature and saturation of the inhaled air with water vapor until the nasopharynx is reached. In this paper, three-dimensional computational studies of airflow transport in the models of the nasal cavity were carried out for the usual inspiratory velocity in various environmental conditions. Three-dimensional numerical results are compared with experimental data and calculations of other authors. Numerical results show that during normal breathing, the human nose copes with heat and relative moisture metabolism in order to balance the intra-alveolar conditions. It is also shown in this paper that a normal nose can maintain balance even in extreme conditions, for example, in cold and hot weather. The nasal cavity accelerates heat transfer by narrowing the air passages and swirls from the nasal concha walls of the inner cavity.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-020-00133-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38788183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Statistical field theory of the transmission of nerve impulses.","authors":"Gianluigi Zangari Del Balzo","doi":"10.1186/s12976-020-00132-9","DOIUrl":"https://doi.org/10.1186/s12976-020-00132-9","url":null,"abstract":"<p><strong>Background: </strong>Stochastic processes leading voltage-gated ion channel dynamics on the nerve cell membrane are a sufficient condition to describe membrane conductance through statistical mechanics of disordered and complex systems.</p><p><strong>Results: </strong>Voltage-gated ion channels in the nerve cell membrane are described by the Ising model. Stochastic circuit elements called \"Ising Neural Machines\" are introduced. Action potentials are described as quasi-particles of a statistical field theory for the Ising system.</p><p><strong>Conclusions: </strong>The particle description of action potentials is a new point of view and a powerful tool to describe the generation and propagation of nerve impulses, especially when classical electrophysiological models break down. The particle description of action potentials allows us to develop a new generation of devices to study neurodegenerative and demyelinating diseases as Multiple Sclerosis and Alzheimer's disease, even integrated by connectomes. It is also suitable for the study of complex networks, quantum computing, artificial intelligence, machine and deep learning, cryptography, ultra-fast lines for entanglement experiments and many other applications of medical, physical and engineering interest.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-020-00132-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38788924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of natural disasters on the spread of COVID-19: a geospatial, agent-based epidemiology model","authors":"M. V. W. de Vries, L. Rambabu","doi":"10.1101/2020.09.12.20193433","DOIUrl":"https://doi.org/10.1101/2020.09.12.20193433","url":null,"abstract":"Natural disasters and infectious diseases result in widespread disruption to human health and livelihood. At the scale of a global pandemic, the co-occurrence of natural disasters is inevitable. However, the impact of natural disasters on the spread of COVID-19 has not been extensively evaluated through epidemiological modelling. We create an agent-based epidemiology model based on COVID-19 clinical, epidemiological, and geographic data. We first model 35 scenarios with varying natural disaster timing and duration for a COVID-19 outbreak in a theoretical region. We then evaluate the potential effect of an eruption of Vesuvius volcano on the spread of COVID-19 in Campania, Italy. In a majority of cases, the occurrence of a natural disaster increases the number of disease related fatalities. For a natural disaster fifty days after infection onset, the median increase in fatalities is 2, 59, and 180% for a 2, 14, and 31-day long natural disaster respectively, when compared to the no natural disaster scenario. For the Campania case, the median increase in fatalities is 1.1 and 2.4 additional fatalities per 100,000 for eruptions on day 1 and 100 respectively, and 60.0 additional fatalities per 100,000 for an eruption close to the peak in infections (day 50). Our results show that the occurrence of a natural disaster in most cases leads to an increase in infection related fatalities, with wide variance in possible outcomes depending on the timing of the natural disaster relative to the peak in infections and the duration of the natural disaster.","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44225059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}