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

A hepatitis A epidemic occurred among men who have sex with men (MSM) in Japan in 2017–2018. In this study, we employ a parsimonious mathematical model to epidemiologically investigate the dynamics of infection, aiming to evaluate the effectiveness of campaign-based interventions among MSM to raise awareness of the situation. A mathematical model describing a mixture of human-to-human transmission

Sexually transmitted infections (STIs) have remained a worldwide public health threat. It is difficult to control the spread of STIs, not only because of heterogeneous sexual transmission between men and women but also because of the complicated effects of sexual transmission among men who have sex with men (MSM) and mother-to-child transmission. Many studies point to the existence of a ‘bisexual bridge’

Travelers play a role in triggering epidemics of imported dengue fever because they can carry the virus to other countries during the incubation period. If a traveler carrying dengue virus visits open green space and is bitten by mosquitoes, a local outbreak can ensue. In the present study, we aimed to understand the movement patterns of international travelers in Tokyo using mobile phone data, with

This study aimed to jointly model HIV disease progression patterns based on viral load (VL) among adult ART patients adjusting for the time-varying “incremental transients states” variable, and the CD4 cell counts orthogonal variable in a single 5-stage time-homogenous multistate Markov model. We further jointly mapped the relative risks of HIV disease progression outcomes (detectable VL (VL ≥ 50copies/uL)

Nondepolarizing neuromuscular blocking drugs (NDNBs) are clinically used to produce muscle relaxation during general anesthesia. To better understand clinical properties of NDNBs, comparative in vitro pharmacologic studies have been performed. In these studies, a receptor binding model, which relies on the assumption that the inhibition, i.e., the effect of an NDNB, is proportional to the receptor

At the moment we have more than 177 million cases and 3.8 million deaths (as of June 2021) around the world and vaccination represents the only hope to control the pandemic. Imperfections in planning vaccine acquisition and difficulties in implementing distribution among the population, however, have hampered the control of the virus so far. We propose a new mathematical model to estimate the impact

In Japan, a part of confirmed patients’ samples have been screened for the variant of concern (VOC), including the variant alpha with N501Y mutation. The present study aimed to estimate the actual number of cases with variant alpha and reconstruct the epidemiological dynamics. The number of cases with variant alpha out of all PCR confirmed cases was estimated, employing a hypergeometric distribution

Individuals with asymptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can propagate the virus unknowingly and thus have been a focus of public health attentions since the early stages of the pandemic. Understanding viral transmissibility among asymptomatic individuals is critical for successful control of coronavirus disease 2019 (COVID-19). The present study aimed to

Cancer is one of the leading death causes globally with about 8.2 million deaths per year and an increase in numbers in recent years. About 90% of cancer deaths do not occur due to primary tumors but due to metastases, of which most are not clinically identifiable because of their relatively small size at primary diagnosis and limited technical possibilities. However, therapeutic decisions are formed

The COVID-19 pandemic poses a serious threat to global health, and pathogenic mutations are a major challenge to disease control. We developed a statistical framework to explore the association between molecular-level mutation activity of SARS-CoV-2 and population-level disease transmissibility of COVID-19. We estimated the instantaneous transmissibility of COVID-19 by using the time-varying reproduction

An amendment to this paper has been published and can be accessed via the original article.

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

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

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. The main purpose of the present study is to investigate

An amendment to this paper has been published and can be accessed via the original article.

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

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

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

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. 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

To employ the benchmark dose (BMD) method in toxicological risk assessment, it is critical to understand how the BMD lower bound for reference dose calculation is selected following statistical fitting procedures of multiple mathematical models. The purpose of this study was to compare the performances of various combinations of model exclusion and selection criteria for quantal response data. Simulation-based

Currently, due to the huge progress in the field of information technologies and computer equipment, it is important to use modern approaches of artificial intelligence in order to process extensive chemical information at creating new drugs with desired properties. The interdisciplinary of research creates additional difficulties in creating new drugs. Currently, there are no universal algorithms

Seasonal influenza poses a significant public health and economic burden, associated with the outcome of infection and resulting complications. The true burden of the disease is difficult to capture due to the wide range of presentation, from asymptomatic cases to non-respiratory complications such as cardiovascular events, and its seasonal variability. An understanding of the magnitude of the true

HIV infected patients may experience many intermediate events including between-event transition throughout their follow up. Through modelling these transitions, we can gain a deeper understanding of HIV disease process and progression and of factors that influence the disease process and progression pathway. In this work, we present transition-specific parametric multi-state models to describe HIV

On December 31, 2019, the World Health Organization was alerted to the occurrence of cases of pneumonia in Wuhan, Hubei Province, China, that were caused by an unknown virus, which was later identified as a coronavirus and named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to estimate the reproductive number of SARS-CoV-2 in the Hubei Province and evaluate the risk of

Genes, proteins, or cells influence each other and consequently create patterns, which can be increasingly better observed by experimental biology and medicine. Thereby, descriptive methods of statistics and bioinformatics sharpen and structure our perception. However, additionally considering the interconnectivity between biological elements promises a deeper and more coherent understanding of melanoma

BACKGROUND This paper intends to check whether and how a hypothetical dengue vaccine could contribute to issue of evolution of bacteria resistance against antibiotics by reducing the number of patients that would inappropriately being treated with antibiotics. METHODS We use a new mathematical model that combines, in a novel way, two previously published papers, one on the evolution of resistance against

BACKGROUND Tuberculosis (TB) is one of the most important health topics in the world. Directly observed treatment and short course chemotherapy (DOTS) strategy combines medicine care and modern health system firmly, and it has been carried out by World Health Organization (WHO) since 1997. In the struggle with TB, China has promoted the process of controlling the disease actively, and the full coverage

BACKGROUND Alzheimer's disease (AD) is a degenerative brain disease. A novel agent-based modelling framework was developed in NetLogo 3D to provide fundamental insights into the potential mechanisms by which a microbe (eg. Chlamydia pneumoniae) may play a role in late-onset AD. The objective of our initial model is to simulate one possible spatial and temporal pathway of bacterial propagation via the

BACKGROUND CpGs, the major methylation sites in vertebrate genomes, exhibit a high mutation rate from the methylated form of CpG to TpG/CpA and, therefore, influence the evolution of genome composition. However, the quantitative effects of CpG to TpG/CpA mutations on the evolution of genome composition in terms of the dinucleotide frequencies/proportions remain poorly understood. RESULTS Based on the

BACKGROUND Aging is a fundamental biological process, where key bio-markers interact with each other and synergistically regulate the aging process. Thus aging dysfunction will induce many disorders. Finding aging markers and re-constructing networks based on multi-omics data (i.e. methylation, transcriptional and so on) are informative to study the aging process. However, optimizing the model to predict

BACKGROUND Autophagy is an evolutionarily conserved intracellular process that is used for delivering proteins and organelles to the lysosome for degradation. For decades, autophagy has been speculated to regulate amyloid-β peptide (Aβ) accumulation, which is involved in Alzheimer's disease (AD); however, specific autophagic effects on the Aβ kinetics only have begun to be explored. RESULTS We develop

Estimating HIV incidence is crucial for monitoring the epidemiology of this infection, planning screening and intervention campaigns, and evaluating the effectiveness of control measures. However, owing to the long and variable period from HIV infection to the development of AIDS and the introduction of highly active antiretroviral therapy, accurate incidence estimation remains a major challenge. Numerous

Variations of gene expression levels play an important role in tumors. There are numerous methods to identify differentially expressed genes in high-throughput sequencing. Several algorithms endeavor to identify distinctive genetic patterns susceptable to particular diseases. Although these processes have been proved successful, the probability that the number of non-differentially expressed genes

Background Glucose tolerance testing is a tool used to estimate glucose effectiveness and insulin sensitivity in diabetic patients. The importance of such tests has prompted the development and utilisation of mathematical models that describe glucose kinetics as a function of insulin activity. The hormone glucagon, also plays a fundamental role in systemic plasma glucose regulation and is secreted

BACKGROUND Gravity, especially hypergravity, can affect the morphology of membranes, and further influence most biological processes. Since vesicle structures are relatively simple, the vesicle can be treated as a vital model to study the mechanical properties of membranes in most cases. Basic research on membrane tension has become a vital research topic in cellular biomechanics. METHODS In this study

BACKGROUND Associations between disease characteristics and payer-relevant outcomes can be difficult to establish for rare and progressive chronic diseases with sparse available data. We developed an exploratory bridging model to predict premature mortality from disease characteristics, and using inclusion body myositis (IBM) as a representative case study. METHODS Candidate variables that may be potentially

BACKGROUND Autophagy and apoptosis are two important physiological processes that determine cell survival or death in response to different stress signals. The regulatory mechanisms of these two processes share B-cell lymphoma-2 family proteins and AMBRA1, which are present in both the endoplasmic reticulum and mitochondria. B-cell lymphoma-2 family proteins sense different stresses and interact with

BACKGROUND Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are two coronaviruses with demonstrated potential to generate significant nosocomial outbreaks. In particular, MERS continues to pose a significant threat in the Middle East since 2012. Currently, no licensed vaccine or drug treatment is available to treat patients infected with either coronavirus. However

BACKGROUND Existed mathematical models of individual adaptation are mostly reductionist by nature. Researchers usually a priori consider the subject adapted basing only on the fact of continued or prolonged influence of the harmful factor. This paper describes a method that allows assessing the physiological adaptedness to experimental challenges on the basis of holistic approach and quantitative criteria

BACKGROUND Photothermal therapy is a local treatment method for cancer and the heat energy generated from it could destroy the tumor cells. This study is aimed to investigate the temperature distribution in tumor tissue and surrounding health tissue of tumor bearing mice applying mathematical simulation model. Tumor bearing mice treated by laser combined with or without indocyanine green. Monte Carlo

BACKGROUND The transbilayer sterol distribution between both plasma membrane (PM) leaflets has long been debated. Recent studies in mammalian cells and in yeast show that the majority of sterol resides in the inner PM leaflet. Since sterol flip-flop in model membranes is rapid and energy-independent, a mechanistic understanding for net enrichment of sterol in one leaflet is lacking. Import of ergosterol

BACKGROUND After proteolysis, the majority of released amino acids from dietary protein are transported to the liver for gluconeogenesis or to peripheral tissues where they are used for protein synthesis and eventually catabolized, producing ammonia as a byproduct. High ammonia levels in the brain are a major contributor to the decreased neural function that occurs in several pathological conditions

BACKGROUND The mathematical design of optimal therapies to fight cancer is an important research field in today's Biomathematics and Biomedicine given its relevance to formulate patient-specific treatments. Until now, however, cancer optimal therapies have considered that malignancy exclusively depends on the drug concentration and the number of cancer cells, ignoring that the faster the cancer grows

BACKGROUND There is an increasing need for complex computational models to perform in silico experiments as an adjunct to in vitro and in vivo experiments in immunology. We introduce Microscopic Stochastic Immune System Simulator (MiStImm), an agent-based simulation tool, that is designed to study the self-nonself discrimination of the adaptive immune system. MiStImm can simulate some components of

BACKGROUND The increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory

After publication of the original article.

BACKGROUND Social contact surveys can greatly help in quantifying the heterogeneous patterns of infectious disease transmission. The present study aimed to conduct a contact survey in Japan, offering estimates of contact by age and location and validating a social contact matrix using a seroepidemiological dataset of influenza. METHODS An internet-based questionnaire survey was conducted, covering

BACKGROUND Mathematical models of diseases may provide a unified approach for establishing effective treatment strategies based on fundamental pathophysiology. However, models that are useful for clinical practice must overcome the massive complexity of human physiology and the diversity of patients' environmental conditions. With the aim of modeling a complex disease, we choose sepsis, which is highly

BACKGROUND The application of effective vaccines against pig cysticercosis and mass chemotherapy against pig cysticercosis and human taeniasis have shown the feasibility of interrupting the parasite's life cycle in endemic areas. METHODS A mathematical model that divides the population into susceptible, infected, and vaccinated individuals is formulated. The model is based upon the life cycle of the

BACKGROUND Clinical studies have shown that all-trans retinoic acid (RA), which is often used in treatment of cancer patients, improves hemostatic parameters and bleeding complications such as disseminated intravascular coagulation (DIC). However, the mechanisms underlying this improvement have yet to be elucidated. In vitro studies have reported that RA upregulates thrombomodulin (TM) expression on

BACKGROUND Clostridium difficile (C. difficile) infection is an important cause of healthcare-associated diarrhea. Several factors such as admission of colonized patients, levels of serum antibodies in patients, and control strategies may involve in determining the prevalence and the persistence of C. difficile in a hospital unit. METHODS We develop mathematical models based on deterministic and stochastic

BACKGROUND Mathematical modeling is now frequently used in outbreak investigations to understand underlying mechanisms of infectious disease dynamics, assess patterns in epidemiological data, and forecast the trajectory of epidemics. However, the successful application of mathematical models to guide public health interventions lies in the ability to reliably estimate model parameters and their corresponding

BACKGROUND The Smad7 protein is negative regulator of the TGF-β signaling pathway, which is upregulated in patients with breast cancer. miRNAs regulate proteins expressions by arresting or degrading the mRNAs. The purpose of this work is to identify a miRNAs profile that regulates the expression of the mRNA coding for Smad7 in breast cancer using the data from patients with breast cancer obtained from

BACKGROUND Personalized medicine for patients receiving radiation therapy remains an elusive goal due, in part, to the limits in our understanding of the underlying mechanisms governing tumor response to radiation. The purpose of this study was to develop a kinetic model, in the context of locally advanced lung cancer, connecting cancer cell subpopulations with tumor volumes measured during the course

BACKGROUND Mathematical modeling has achieved a broad interest in the field of biology. These models represent the associations among the metabolism of the biological phenomenon with some mathematical equations such that the observed time course profile of the biological data fits the model. However, the estimation of the unknown parameters of the model is a challenging task. Many algorithms have been

BACKGROUND Japan has a rapidly decreasing population, with ultra-low fertility and extremely fast aging. The rapid dynamics constitute a warning that change in the industrial structure may be unable to meet the changing pace of age-dependent demand. METHODS The present study estimated the supply-demand imbalance by industrial sector, and we investigated the effectiveness of possible countermeasures

BACKGROUND Many biological soft tissues are hydrated porous hyperelastic materials, which consist of a complex solid skeleton with fine voids and fluid filling these voids. Mechanical interactions between the solid and the fluid in hydrated porous tissues have been analyzed by finite element methods (FEMs) in which the mixture theory was introduced in various ways. Although most of the tissues are

BACKGROUND In the classical pathway of retinoic acid (RA) mediated gene transcription, RA binds to a nuclear hormone receptor dimer composed of retinoic acid receptor (RAR) and retinoid X receptor (RXR), to induce the expression of its downstream target genes. In addition to nuclear receptors, there are other intracellular RA binding proteins such as cellular retinoic acid binding proteins (CRABP1

BACKGROUND Embryo transfer (ET) is a key step of assisted reproductive procedures, where the transferred medium containing the embryos is injected into the uterine cavity through a transcervical catheter and blended with intrauterine fluid in the uterine cavity. This procedure determines the delivery sites of embryos in the uterine cavity and has crucial impact on the implantation. Due to practical