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Journals Theoretical Biology & Medical ...

Theoretical Biology & Medical Modelling

https://read.qxmd.com/read/32669115/ontological-model-of-multi-agent-smart-system-for-predicting-drug-properties-based-on-modified-algorithms-of-artificial-immune-systems
#21
JOURNAL ARTICLE
Galina Samigulina, Zarina Samigulina
BACKGROUND: 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 and software for predicting the "structure-property" dependence of drug compounds that can take into account the needs of specialists in this field...
July 20, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32646444/quantifying-the-annual-incidence-and-underestimation-of-seasonal-influenza-a-modelling-approach
#22
JOURNAL ARTICLE
Zachary McCarthy, Safia Athar, Mahnaz Alavinejad, Christopher Chow, Iain Moyles, Kyeongah Nah, Jude D Kong, Nishant Agrawal, Ahmed Jaber, Laura Keane, Sam Liu, Myles Nahirniak, Danielle St Jean, Razvan Romanescu, Jessica Stockdale, Bruce T Seet, Laurent Coudeville, Edward Thommes, Anne-Frieda Taurel, Jason Lee, Thomas Shin, Julien Arino, Jane Heffernan, Ayman Chit, Jianhong Wu
BACKGROUND: 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 annual incidence of influenza is important to support prevention and control policy development and to evaluate the impact of preventative measures such as vaccination...
July 10, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32571361/modelling-hiv-disease-process-and-progression-in-seroconversion-among-south-africa-women-using-transition-specific-parametric-multi-state-model
#23
JOURNAL ARTICLE
Zelalem G Dessie, Temesgen Zewotir, Henry Mwambi, Delia North
BACKGROUND: 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 disease process and progression. METHODS: The data is from an ongoing prospective cohort study conducted amongst adult women who were HIV-infected in KwaZulu-Natal, South Africa...
June 23, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32498721/risk-estimation-of-the-sars-cov-2-acute-respiratory-disease-outbreak-outside-china
#24
JOURNAL ARTICLE
Soyoung Kim, Sunhwa Choi, Youngsuk Ko, Moran Ki, Eunok Jung
BACKGROUND: 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 an acute respiratory coronavirus disease (COVID-19) outbreak outside China by using a mathematical model and stochastic simulations...
June 5, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32410672/computational-models-of-melanoma
#25
REVIEW
Marco Albrecht, Philippe Lucarelli, Dagmar Kulms, Thomas Sauter
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. For instance, integrative network-based tools and well-grounded inductive in silico research reveal disease mechanisms, stratify patients, and support treatment individualization...
May 14, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32404100/modelling-the-effect-of-a-dengue-vaccine-on-reducing-the-evolution-of-resistance-against-antibiotic-due-to-misuse-in-dengue-cases
#26
JOURNAL ARTICLE
Ana Kurauchi, Claudio Jose Struchiner, Annelies Wilder-Smith, Eduardo Massad
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 antibiotics and one classical Ross-Macdonald model for dengue transmission...
May 13, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32362279/modeling-and-dynamic-analysis-of-tuberculosis-in-mainland-china-from-1998-to-2017-the-effect-of-dots-strategy-and-further-control
#27
JOURNAL ARTICLE
Siyu Liu, Yingjie Bi, Yawen Liu
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 of DOTS strategy has been reached around 2004. Mathematical modeling is a very useful tool to study the transmission of diseases...
May 4, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32290858/an-agent-based-model-to-investigate-microbial-initiation-of-alzheimer-s-via-the-olfactory-system
#28
JOURNAL ARTICLE
Shalini Sundar, Carly Battistoni, Ryan McNulty, Fernando Morales, Jonathan Gorky, Henry Foley, Prasad Dhurjati
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 olfactory system, which may then lead to AD symptoms. The model maps the bacteria infecting cells from the nasal cavity and the olfactory epithelium, through the olfactory bulb and into the olfactory cortex and hippocampus regions of the brain...
April 15, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32264909/methylation-driven-model-for-analysis-of-dinucleotide-evolution-in-genomes
#29
JOURNAL ARTICLE
Jian-Hong Sun, Shi-Meng Ai, Shu-Qun Liu
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 neutral theory of molecular evolution, we propose a methylation-driven model (MDM) that allows predicting the changes in frequencies/proportions of the 16 dinucleotides and in the GC content of a genome given the known number of CpG to TpG/CpA mutations...
April 8, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32197622/the-self-organization-model-reveals-systematic-characteristics-of-aging
#30
JOURNAL ARTICLE
Yin Wang, Tao Huang, Yixue Li, Xianzheng Sha
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 aging have not been performed systemically, although it is critical to identify potential molecular mechanism of aging related diseases...
March 20, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/32102666/computational-modeling-of-the-effects-of-autophagy-on-amyloid-%C3%AE-peptide-levels
#31
JOURNAL ARTICLE
Kyungreem Han, Soon Ho Kim, MooYoung Choi
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 a mathematical model for autophagy with respect to Aβ kinetics and perform simulations to understand the quantitative relationship between Aβ levels and autophagy activity...
February 26, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31964392/modeling-methods-for-estimating-hiv-incidence-a-mathematical-review
#32
REVIEW
Xiaodan Sun, Hiroshi Nishiura, Yanni Xiao
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 estimation methods have been proposed in epidemiological modeling studies, and here we review commonly-used methods for estimation of HIV incidence...
January 22, 2020: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31865918/ugm-a-more-stable-procedure-for-large-scale-multiple-testing-problems-new-solutions-to-identify-oncogene
#33
REVIEW
Chengyou Liu, Leilei Zhou, Yuhe Wang, Shuchang Tian, Junlin Zhu, Hang Qin, Yong Ding, Hongbing Jiang
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 measured by false discovery rate (FDR) has a large standard deviation, and the misidentification rate (type I error) grows rapidly when the number of genes to be detected become larger...
December 23, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31829209/modelling-the-effects-of-glucagon-during-glucose-tolerance-testing
#34
JOURNAL ARTICLE
Ross A Kelly, Molly J Fitches, Steven D Webb, S R Pop, Stewart J Chidlow
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 reciprocally to insulin, stimulating catabolic glucose utilisation. However, regulation of glucagon secretion by α-cells is impaired in type-1 and type-2 diabetes through pancreatic islet dysfunction...
December 12, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31801614/response-of-membrane-tension-to-gravity-in-an-approximate-cell-model
#35
JOURNAL ARTICLE
Lili Wang, Weiyi Chen, Hongmei Guo, Airong Qian
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, a new vesicle model is proposed to quantitatively investigate the response of membrane tension to gravity...
December 5, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31694651/development-and-validation-of-a-bayesian-survival-model-for-inclusion-body-myositis
#36
JOURNAL ARTICLE
Gorana Capkun, Jens Schmidt, Shubhro Ghosh, Harsh Sharma, Thomas Obadia, Ana de Vera, Valery Risson, Billy Amzal
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 associated with premature mortality were identified by disease experts and from the IBM literature...
November 7, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31665034/autophagy-and-apoptosis-are-regulated-by-stress-on-bcl2-by-ambra1-in-the-endoplasmic-reticulum-and-mitochondria
#37
JOURNAL ARTICLE
Bojie Yang, Quansheng Liu, Yuanhong Bi
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 AMBRA1 to regulate autophagy and apoptosis, which are respectively mediated by Beclin1 and Caspases...
October 29, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31587665/evaluating-the-potential-impact-of-targeted-vaccination-strategies-against-severe-acute-respiratory-syndrome-coronavirus-sars-cov-and-middle-east-respiratory-syndrome-coronavirus-mers-cov-outbreaks-in-the-healthcare-setting
#38
JOURNAL ARTICLE
Fatima Abdirizak, Rayleen Lewis, Gerardo Chowell
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, there are some MERS vaccines in the preclinical stage of development. We sought to evaluate the potential impact of targeted vaccination strategies for mitigating SARS and MERS outbreaks in healthcare settings using simple mathematical models and detailed historic transmission trees describing the progression of past nosocomial outbreaks of SARS and MERS...
October 7, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31500635/the-effect-of-group-a-streptococcal-carrier-on-the-epidemic-model-of-acute-rheumatic-fever
#39
JOURNAL ARTICLE
Natsuda Yokchoo, Nichaphat Patanarapeelert, Klot Patanarapeelert
BACKGROUND: Group A streptococcus (GAS) is the most frequent cause of bacterial pharyngitis in school-aged children. The postinfection sequel as acute rheumatic fever (ARF) and rheumatic heart disease that cause morbidity and mortality among young people is public health concerns in several developing countries. Asymptomatic carriage state of GAS is not fully understood in terms of host and bacterial factors. Although the ability of transmitting GAS of the asymptomatic carriers is relatively low, they may present the reservoir of the epidemic...
September 10, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/31477131/a-quantitative-method-for-estimating-the-adaptedness-in-a-physiological-study
#40
JOURNAL ARTICLE
Vladimir N Melnikov
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. METHODS: The suggested method comprises simple equations and incorporates into the model an indicator that differentiates functions in regard to their significance for determining physiological adaptedness considered as an outcome of the adaptive process...
September 3, 2019: Theoretical Biology & Medical Modelling
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