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Theoretical Biology & Medical Modelling

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https://read.qxmd.com/read/30764845/analysis-of-the-role-of-thrombomodulin-in-all-trans-retinoic-acid-treatment-of-coagulation-disorders-in-cancer-patients
#1
Hamed Ghaffari, Jeffrey D Varner, Linda R Petzold
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 the endothelial cell surface. The objective of this study was to investigate how and to what extent the TM concentration changes after RA treatment in cancer patients, and how this variation influences the blood coagulation cascade...
February 14, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30704484/modeling-clostridium-difficile-in-a-hospital-setting-control-and-admissions-of-colonized-and-symptomatic-patients
#2
Farida Chamchod, Prasit Palittapongarnpim
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 frameworks to investigate the effects of control strategies for colonized and symptomatic patients and admissions of colonized and symptomatic patients on the prevalence and the persistence of C...
January 31, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30642334/assessing-parameter-identifiability-in-compartmental-dynamic-models-using-a-computational-approach-application-to-infectious-disease-transmission-models
#3
Kimberlyn Roosa, Gerardo Chowell
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 uncertainty. Here, we present and illustrate a simple computational method for assessing parameter identifiability in compartmental epidemic models...
January 14, 2019: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30594253/model-based-on-ga-and-dnn-for-prediction-of-mrna-smad7-expression-regulated-by-mirnas-in-breast-cancer
#4
Edgar Manzanarez-Ozuna, Dora-Luz Flores, Everardo Gutiérrez-López, David Cervantes, Patricia Juárez
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 the Cancer Genome Atlas Project. METHODS: We develop an automatic search method based on genetic algorithms to find a predictive model based on deep neural networks (DNN) which fit the set of biological data and apply the Olden algorithm to identify the relative importance of each miRNAs...
December 29, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30587218/kinetic-modeling-of-tumor-regression-incorporating-the-concept-of-cancer-stem-like-cells-for-patients-with-locally-advanced-lung-cancer
#5
Hualiang Zhong, Stephen Brown, Suneetha Devpura, X Allen Li, Indrin J Chetty
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 of radiation treatment for understanding treatment outcome for individual patients...
December 27, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30348205/finite-element-analysis-of-biological-soft-tissue-surrounded-by-a-deformable-membrane-that-controls-transmembrane-flow
#6
Satoko Hirabayashi, Masami Iwamoto
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 surrounded by deformable membranes that control transmembrane flows, the boundaries of the tissues have been treated as rigid and/or freely permeable in these studies...
December 10, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30373604/novel-neural-network-application-for-bacterial-colony-classification
#7
Lei Huang, Tong Wu
BACKGROUND: Bacterial colony morphology is the first step of classifying the bacterial species before sending them to subsequent identification process with devices, such as VITEK 2 automated system and mass spectrometry microbial identification system. It is essential as a pre-screening process because it can greatly reduce the scope of possible bacterial species and will make the subsequent identification more specific and increase work efficiency in clinical bacteriology. But this work needs adequate clinical laboratory expertise of bacterial colony morphology, which is especially difficult for beginners to handle properly...
December 2, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30449280/mathematical-model-of-the-life-cycle-of-taenia-cysticercosis-transmission-dynamics-and-chemotherapy-part-1
#8
Marco V José, Juan R Bobadilla, Norma Y Sánchez-Torres, Juan Pedro Laclette
BACKGROUND: Taenia solium is the aetiological agent of human taeniasis, pig cysticercosis and human neurocysticercosis, which are serious public health problems, especially in developing countries. METHODS: A mathematical model of the transmission dynamics of taeniasis-cysticercosis is formulated. The model consists of a coupled system of differential equations, which are density-dependent equations for describing the flow of the parasite through the life cycle...
November 19, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30392468/a-modified-particle-swarm-optimization-algorithm-for-parameter-estimation-of-a-biological-system
#9
Raziyeh Mosayebi, Fariba Bahrami
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 developed for parameter estimation, but none of them is entirely capable of finding the best solution...
November 5, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30382893/demographic-supply-demand-imbalance-in-industrial-structure-in-the-super-aged-nation-japan
#10
Naoki Kishida, Hiroshi Nishiura
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. To quantify the demographic burden of different industry experts, we employed the dependency ratio to calculate the supply and demand of each industrial sector and occupation...
November 1, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30322383/identification-of-influential-proteins-in-the-classical-retinoic-acid-signaling-pathway
#11
Hamed Ghaffari, Linda R Petzold
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 and CRABP2) and cytochrome P450 (CYP) enzymes, whose contributions to the RA signaling pathway have not been fully understood...
October 16, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30290814/numerical-simulation-of-embryo-transfer-how-the-viscosity-of-transferred-medium-affects-the-transport-of-embryos
#12
Dali Ding, Weiping Shi, Yang Shi
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 restrictions and ethical issues, it is often difficult to perform an in vivo study in humans to examine factors that affect the motions and delivery of embryos during ET...
October 5, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30269687/osmotic-and-diffusive-flows-in-single-file-pores-new-approach-to-modeling-pore-occupancy-states
#13
Gordon Kepner
BACKGROUND: The relation between osmotic permeability, Pf , diffusion permeability, Pd , and the number of water molecules, Np , in the single-file membrane pore remains an open question. Theoretical analyses, empirical studies on aquaporins and nanotubes, and molecular dynamics simulations have yet to provide a consensus view. RESULTS: This paper presents a new combinatorial analysis of the different pore states formed from water molecules and the presence of a vacancy that differs from the several previous combinatorial approaches to analyzing pore states...
October 1, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30196793/modern-and-traditional-approaches-combined-into-an-effective-gray-box-mathematical-model-of-full-blood-acid-base
#14
Filip Ježek, Jiří Kofránek
BACKGROUND: The acidity of human body fluids, expressed by the pH, is physiologically regulated in a narrow range, which is required for the proper function of cellular metabolism. Acid-base disorders are common especially in intensive care, and the acid-base status is one of the vital clinical signs for the patient management. Because acid-base balance is connected to many bodily processes and regulations, complex mathematical models are needed to get insight into the mixed disorders and to act accordingly...
September 10, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30173664/a-conceptual-model-for-optimizing-vaccine-coverage-to-reduce-vector-borne-infections-in-the-presence-of-antibody-dependent-enhancement
#15
Biao Tang, Xi Huo, Yanni Xiao, Shigui Ruan, Jianhong Wu
BACKGROUND: Many vector-borne diseases co-circulate, as the viruses from the same family are also transmitted by the same vector species. For example, Zika and dengue viruses belong to the same Flavivirus family and are primarily transmitted by a common mosquito species Aedes aegypti. Zika outbreaks have also commonly occurred in dengue-endemic areas, and co-circulation and co-infection of both viruses have been reported. As recent immunological cross-reactivity studies have confirmed that convalescent plasma following dengue infection can enhance Zika infection, and as global efforts of developing dengue and Zika vaccines are intensified, it is important to examine whether and how vaccination against one disease in a large population may affect infection dynamics of another disease due to antibody-dependent enhancement...
September 3, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30122157/application-of-bayesian-evidence-synthesis-to-modelling-the-effect-of-ketogenic-therapy-on-survival-of-high-grade-glioma-patients
#16
Rainer J Klement, Prasanta S Bandyopadhyay, Colin E Champ, Harald Walach
BACKGROUND: Ketogenic therapy in the form of ketogenic diets or calorie restriction has been proposed as a metabolic treatment of high grade glioma (HGG) brain tumors based on mechanistic reasoning obtained mainly from animal experiments. Given the paucity of clinical studies of this relatively new approach, our goal is to extrapolate evidence from the greater number of animal studies and synthesize it with the available human data in order to estimate the expected effects of ketogenic therapy on survival in HGG patients...
August 20, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30064447/a-mathematical-model-for-zika-virus-transmission-dynamics-with-a-time-dependent-mosquito-biting-rate
#17
Parinya Suparit, Anuwat Wiratsudakul, Charin Modchang
BACKGROUND: Mathematical modeling has become a tool used to address many emerging diseases. One of the most basic and popular modeling frameworks is the compartmental model. Unfortunately, most of the available compartmental models developed for Zika virus (ZIKV) transmission were designed to describe and reconstruct only past, short-time ZIKV outbreaks in which the effects of seasonal change to entomological parameters can be ignored. To make an accurate long-term prediction of ZIKV transmission, the inclusion of seasonal effects into an epidemic model is unavoidable...
August 1, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/30008270/determinants-of-viral-load-rebound-on-hiv-aids-patients-receiving-antiretroviral-therapy-results-from-south-africa
#18
Claris Shoko, Delson Chikobvu
BACKGROUND: Antiretroviral therapy (ART) has become the standard of care for patients with HIV infection in South Africa and has led to the reduction in AIDS related morbidity and mortality. In developing countries, the nucleosides reverse transcriptase inhibitors (NRTIs) class are widely used because of their low production costs. However patients treated with NRTIs develop varying degree of toxicity after long-term therapy. For this study patients are administered with a triple therapy of two NRTIs and one non-nucleoside reverse transcriptase inhibitor (NNRTI)...
July 16, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/29961429/modeling-the-elevated-risk-of-yellow-fever-among-travelers-visiting-brazil-2018
#19
Yohei Sakamoto, Takayuki Yamaguchi, Nao Yamamoto, Hiroshi Nishiura
BACKGROUND: Unlike the epidemic of yellow fever from 2016 to 17 in Brazil mostly restricted to the States of Minas Gerais and Espirito Santo, the epidemic from 2017 to 18 mainly involved São Paulo and Rio de Janeiro and resulted in multiple international disseminations. To understand mechanisms behind this observation, the present study analyzed the distribution of imported cases from Brazil, 2018. METHODS: A statistical model was employed to capture the risk of importing yellow fever by returning international travelers from Brazil...
July 2, 2018: Theoretical Biology & Medical Modelling
https://read.qxmd.com/read/29925399/a-model-of-hematopoietic-bone-marrow-apoptosis-during-growth-factor-deprivation-in-combination-with-a-cytokine
#20
Christina L Mouser, Eliana S Antoniou, Evros K Vassiliou
BACKGROUND: The process by which blood cells are formed is referred to as hematopoiesis. This process involves a complex sequence of phases that blood cells must complete. During hematopoiesis, a small fraction of cells undergo cell death. Causes of cell death are dependent upon various factors; one such factor being growth factor deprivation. METHODS: In this paper, a mathematical model of hematopoiesis during growth factor deprivation is presented. The model consists of a set of three coupled differential delay equations...
June 21, 2018: Theoretical Biology & Medical Modelling
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