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https://www.readbyqxmd.com/read/29164873/plasma-protein-turnover-rates-in-rats-using-stable-isotope-labeling-global-proteomics-and-activity-based-protein-profiling
#1
Jordan Ned Smith, Kimberly J Tyrrell, Joshua R Hansen, Dennis George Thomas, Taylor A Murphree, Anil K Shukla, Teresa Luders, James M Madden, YunYing Li, Aaron T Wright, Paul D Piehowski
Protein turnover is important for general health on cellular and organism scales providing a strategy to replace old, damaged, or dysfunctional proteins. Protein turnover also informs of biomarker kinetics, as a better understanding of synthesis and degradation of proteins increases the clinical utility of biomarkers. Here, turnover rates of plasma proteins in rats were measured in vivo using a pulse-chase stable isotope labeling experiment. During the pulse, rats (n=5) were fed 13C6-labeled lysine ("heavy") feed for 23 days to label proteins...
November 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29163325/an-illustration-of-the-exploratory-structural-equation-modeling-esem-framework-on-the-passion-scale
#2
István Tóth-Király, Beáta Bõthe, Adrien Rigó, Gábor Orosz
While exploratory factor analysis (EFA) provides a more realistic presentation of the data with the allowance of item cross-loadings, confirmatory factor analysis (CFA) includes many methodological advances that the former does not. To create a synergy of the two, exploratory structural equation modeling (ESEM) was proposed as an alternative solution, incorporating the advantages of EFA and CFA. The present investigation is thus an illustrative demonstration of the applicability and flexibility of ESEM. To achieve this goal, we compared CFA and ESEM models, then thoroughly tested measurement invariance and differential item functioning through multiple-indicators-multiple-causes (MIMIC) models on the Passion Scale, the only measure of the Dualistic Model of Passion (DMP) which differentiates between harmonious and obsessive forms of passion...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/29162003/feedforward-approximations-to-dynamic-recurrent-network-architectures
#3
Dylan R Muir
Recurrent neural network architectures can have useful computational properties, with complex temporal dynamics and input-sensitive attractor states. However, evaluation of recurrent dynamic architectures requires solving systems of differential equations, and the number of evaluations required to determine their response to a given input can vary with the input or can be indeterminate altogether in the case of oscillations or instability. In feedforward networks, by contrast, only a single pass through the network is needed to determine the response to a given input...
November 21, 2017: Neural Computation
https://www.readbyqxmd.com/read/29161870/modeling-transcriptional-co-regulation-of-mammalian-circadian-clock
#4
Yanqin Wang, Xin Ni, Jie Yan, Ling Yang
The circadian clock is a self-sustaining oscillator that has a period of about 24 hours at the molecular level. The oscillator is a transcription-translation feedback loop system composed of several genes. In this paper, a scalar nonlinear differential equation with two delays, modeling the transcriptional co-regulation in mammalian circadian clock, is proposed and analyzed. Sufficient conditions are established for the asymptotic stability of the unique nontrivial positive equilibrium point of the model by studying an exponential polynomial characteristic equation with delay-dependent coefficients...
October 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161866/a-mathematical-model-of-stem-cell-regeneration-with-epigenetic-state-transitions
#5
Qiaojun Situ, Jinzhi Lei
In this paper, we study a mathematical model of stem cell regeneration with epigenetic state transitions. In the model, the heterogeneity of stem cells is considered through the epigenetic state of each cell, and each epigenetic state defines a subpopulation of stem cells. The dynamics of the subpopulations are modeled by a set of ordinary differential equations in which epigenetic state transition in cell division is given by the transition probability. We present analysis for the existence and linear stability of the equilibrium state...
October 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161859/theoretical-investigation-on-models-of-circadian-rhythms-based-on-dimerization-and-proteolysis-of-per-and-tim
#6
Jifa Jiang, Qiang Liu, Lei Niu
Circadian rhythms of physiology and behavior are widespread\break mechanisms in many organisms. The internal biological rhythms are driven by molecular clocks, which oscillate with a period nearly but not exactly 24 hours. Many classic models of circadian rhythms are based on a time-delayed negative feedback, suggested by the protein products inhibiting transcription of their own genes. In 1999, based on stabilization of PER upon dimerization, Tyson et al. [J. J. Tyson, C. I. Hong, C. D. Thron, B. Novak, Biophys...
October 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161855/global-dynamics-of-a-vector-host-epidemic-model-with-age-of-infection
#7
Yan-Xia Dang, Zhi-Peng Qiu, Xue-Zhi Li, Maia Martcheva
In this paper, a partial differential equation (PDE) model is proposed to explore the transmission dynamics of vector-borne diseases. The model includes both incubation age of the exposed hosts and infection age of the infectious hosts which describe incubation-age dependent removal rates in the latent period and the variable infectiousness in the infectious period, respectively. The reproductive number R0 is derived. By using the method of Lyapunov function, the global dynamics of the PDE model is further established, and the results show that the basic reproduction number R0 determines the transmission dynamics of vector-borne diseases: the disease-free equilibrium is globally asymptotically stable if R0 ≤ 1, and the endemic equilibrium is globally asymptotically stable if R0 > 1...
October 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161847/formulation-of-the-protein-synthesis-rate-with-sequence-information
#8
Wenjun Xia, Jinzhi Lei
Translation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here, we investigate the kinetics of translation at the molecular level by a stochastic simulation model. The model explicitly includes RNA sequences, ribosome dynamics, the tRNA pool and biochemical reactions involved in the translation elongation. The results show that the translation efficiency is mainly limited by the available ribosome number, translation initiation and the translation elongation time...
April 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161841/effect-of-rotational-grazing-on-plant-and-animal-production
#9
Mayee Chen, Junping Shi
It is a common understanding that rotational cattle grazing provides better yields than continuous grazing, but a quantitative analysis is lacking in agricultural literature. In rotational grazing, cattle periodically move among paddocks in contrast to continuous grazing, in which the cattle graze on a single plot for the entire grazing season. We construct a differential equation model of vegetation grazing on a fixed area to show that production yields and stockpiled forage are greater for rotational grazing than continuous grazing...
April 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161839/the-potential-impact-of-a-prophylactic-vaccine-for-ebola-in-sierra-leone
#10
Erin N Bodine, Connor Cook, Mikayla Shorten
The 2014 outbreak of Ebola virus disease (EVD) in West Africa was multinational and of an unprecedented scale primarily affecting the countries of Guinea, Liberia, and Sierra Leone. One of the qualities that makes EVD of high public concern is its potential for extremely high mortality rates (up to 90%). A prophylactic vaccine for ebolavirus (rVSV-ZEBOV) has been developed, and clinical trials show near-perfect efficacy. We have developed an ordinary differential equations model that simulates an EVD epidemic and takes into account (1) transmission through contact with infectious EVD individuals and deceased EVD bodies, (2) the heterogeneity of the risk of becoming infected with EVD, and (3) the increased survival rate of infected EVD patients due to greater access to trained healthcare providers...
April 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161833/prediction-of-influenza-peaks-in-russian-cities-comparing-the-accuracy-of-two-seir-models
#11
Vasiliy N Leonenko, Sergey V Ivanov
This paper is dedicated to the application of two types of SEIR models to the influenza outbreak peak prediction in Russian cities. The first one is a continuous SEIR model described by a system of ordinary differential equations. The second one is a discrete model formulated as a set of difference equations, which was used in the Baroyan-Rvachev modeling framework for the influenza outbreak prediction in the Soviet Union. The outbreak peak day and height predictions were performed by calibrating both models to varied-size samples of long-term data on ARI incidence in Moscow, Saint Petersburg, and Novosibirsk...
February 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161828/numerical-solution-of-a-spatio-temporal-gender-structured-model-for-hantavirus-infection-in-rodents
#12
Raimund Bürger, Gerardo Chowell, Elvis Gavilán, Pep Mulet, Luis M Villada
In this article we describe the transmission dynamics of hantavirus in rodents using a spatio-temporal susceptible-exposed-infective-recovered (SEIR) compartmental model that distinguishes between male and female subpopulations [L.J.S. Allen, R.K. McCormack and C.B. Jonsson, Bull. Math. Biol. 68 (2006), 511--524]. Both subpopulations are assumed to differ in their movement with respect to local variations in the densities of their own and the opposite gender group. Three alternative models for the movement of the male individuals are examined...
February 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161303/nonlinear-dynamics-of-early-atherosclerotic-plaque-formation-may-determine-the-efficacy-of-high-density-lipoproteins-hdl-in-plaque-regression
#13
Alexander D Chalmers, Christina A Bursill, Mary R Myerscough
We use a computational model to explore the effect of foam cell accumulation on plaque regression following an increase in high density lipoprotein (HDL) influx into the plaque. Atherosclerotic plaque formation is the outcome of cellular and cytokine responses to low density lipoproteins (LDL) that penetrate the artery wall following an injury to the endothelium and become modified. We modelled the cells and cytokines that are most important in plaque formation using partial differential equations. The model includes monocytes and macrophages, foam cells, macrophage chemoattractants, endothelium-stimulating cytokines, modified low density lipoproteins (mod LDL) and HDL...
2017: PloS One
https://www.readbyqxmd.com/read/29159321/lie-group-analysis-of-magnetohydrodynamic-tangent-hyperbolic-fluid-flow-towards-a-stretching-sheet-with-slip-conditions
#14
Zakir Ullah, Gul Zaman
In this paper, we studied MHD two dimensional flow of an incompressible tangent hyperbolic fluid flow and heat transfer towards a stretching sheet with velocity and thermal slip. Lie group analysis is used to develop new similarity transformation, using these similarity transformation the governing nonlinear partial differential equation are reduced into a system of coupled nonlinear ordinary differential equation. The obtained system is solved numerically by applying shooting method. Effects of pertinent parameters on the velocity and temperature profiles, skin friction, local Nusselt number are graphically presented and discussed...
November 2017: Heliyon
https://www.readbyqxmd.com/read/29158608/a-fully-coupled-space-time-multiscale-modeling-framework-for-predicting-tumor-growth
#15
Mohammad Mamunur Rahman, Yusheng Feng, Thomas E Yankeelov, J Tinsley Oden
Most biological systems encountered in living organisms involve highly complex heterogeneous multi-component structures that exhibit different physical, chemical, and biological behavior at different spatial and temporal scales. The development of predictive mathematical and computational models of multiscale events in such systems is a major challenge in contemporary computational biomechanics, particularly the development of models of growing tumors in humans. The aim of this study is to develop a general framework for tumor growth prediction by considering major biological events at tissue, cellular, and subcellular scales...
June 15, 2017: Computer Methods in Applied Mechanics and Engineering
https://www.readbyqxmd.com/read/29158597/a-new-paradigm-in-modelling-the-evolution-of-a-stand-via-the-distribution-of-tree-sizes
#16
Petras Rupšys, Edmundas Petrauskas
Our study focusses on investigating a modern modelling paradigm, a bivariate stochastic process, that allows us to link individual tree variables with growth and yield stand attributes. In this paper, our aim is to introduce the mathematics of mixed effect parameters in a bivariate stochastic differential equation and to describe how such a model can be used to aid our understanding of the bivariate height and diameter distribution in a stand using a large dataset provided by the Lithuanian National Forest Inventory (LNFI)...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29157162/discrete-stochastic-analogs-of-erlang-epidemic-models
#17
Wayne M Getz, Eric R Dougherty
Erlang differential equation models of epidemic processes provide more realistic disease-class transition dynamics from susceptible (S) to exposed (E) to infectious (I) and removed (R) categories than the ubiquitous SEIR model. The latter is itself is at one end of the spectrum of Erlang SE[Formula: see text]I[Formula: see text]R models with [Formula: see text] concatenated E compartments and [Formula: see text] concatenated I compartments. Discrete-time models, however, are computationally much simpler to simulate and fit to epidemic outbreak data than continuous-time differential equations, and are also much more readily extended to include demographic and other types of stochasticity...
December 2018: Journal of Biological Dynamics
https://www.readbyqxmd.com/read/29156121/the-toxmatrix-chemo-genomic-profiling-identifies-interactions-that-reveal-mechanisms-of-toxicity
#18
Zhi-Bin Tong, Ruili Huang, Yuhong Wang, Carleen Klumpp-Thomas, John Braisted, Zina Itkin, Paul Shinn, Menghang Xia, Anton Simeonov, David Gerhold
A chemical genomics 'Toxmatrix' method was developed to elucidate mechanisms of cytotoxicity using neuronal models. Quantitative high-throughput screening (qHTS) was applied to systematically screen each toxicant against a panel of 70 modulators, drugs or chemicals that act on a known target, to identify interactions that either protect or sensitize cells to each toxicant. Thirty-two toxicants were tested at 10 concentrations for cytotoxicity to SH-SY5Y human neuroblastoma cells, with results fitted to the Hill equation to determine an IC50 for each toxicant...
November 20, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/29155837/reduced-order-modeling-and-analysis-of-the-human-complement-system
#19
Adithya Sagar, Wei Dai, Mason Minot, Rachel LeCover, Jeffrey D Varner
Complement is an important pathway in innate immunity, inflammation, and many disease processes. However, despite its importance, there are few validated mathematical models of complement activation. In this study, we developed an ensemble of experimentally validated reduced order complement models. We combined ordinary differential equations with logical rules to produce a compact yet predictive model of complement activation. The model, which described the lectin and alternative pathways, was an order of magnitude smaller than comparable models in the literature...
2017: PloS One
https://www.readbyqxmd.com/read/29155822/heavy-atom-effect-on-optically-excited-triplet-state-kinetics
#20
Christian Hintze, Tobias O Morgen, Malte Drescher
In several fields of research, like e.g. photosensitization, photovoltaics, organic electroluminescent devices, dynamic nuclear polarization, or pulsed dipolar electron paramagnetic resonance spectroscopy, triplet state kinetics play an important role. It is therefore desirable to tailor the kinetics of photoexcited triplet states, e.g. by exploiting the intramolecular heavy-atom effect, and to determine the respective kinetic parameters. In this work, we set out to systematically investigate the photoexcited triplet state kinetics of a series of haloanthracenes by time-resolved electron paramagnetic resonance spectroscopy in combination with synchronized laser excitation...
2017: PloS One
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