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https://www.readbyqxmd.com/read/28822135/kinetic-modeling-of-photorespiration
#1
Honglong Zhao, Yi Xiao, Xin-Guang Zhu
Dynamic systems modeling is a method to study systematic properties of a complex system. The basic principles, procedures, and tools available to develop a dynamic systems model of complex metabolic processes are detailed. Here, a photosynthetic carbon metabolism model, which includes the Calvin Benson cycle, photorespiration, and starch and sucrose synthesis pathways, is used as an example to illustrate the whole process of model development.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28822069/characterization-of-ofloxacin-interaction-with-mutated-a91v-quinolone-resistance-determining-region-of-dna-gyrase-in-mycobacterium-leprae-through-computational-simulation
#2
J Nisha, V Shanthi
Mycobacterium leprae, the causal agent of leprosy is non-cultivable in vitro. Thus, the assessment of antibiotic activity against Mycobacterium leprae depends primarily upon the time-consuming mouse footpad system. The GyrA protein of Mycobacterium leprae is the target of the antimycobacterial drug, Ofloxacin. In recent times, the GyrA mutation (A91V) has been found to be resistant to Ofloxacin. This phenomenon has necessitated the development of new, long-acting antimycobacterial compounds. The underlying mechanism of drug resistance is not completely known...
August 18, 2017: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28822005/a-supply-model-for-nurse-workforce-projection-in-malaysia
#3
Zuraida Abal Abas, Mohamad Raziff Ramli, Mohamad Ishak Desa, Nordin Saleh, Ainul Nadziha Hanafiah, Nuraini Aziz, Zaheera Zainal Abidin, Abdul Samad Shibghatullah, Ahmad Fadzli Nizam Abdul Rahman, Haslinda Musa
The paper aims to provide an insight into the significance of having a simulation model to forecast the supply of registered nurses for health workforce planning policy using System Dynamics. A model is highly in demand to predict the workforce demand for nurses in the future, which it supports for complete development of a needs-based nurse workforce projection using Malaysia as a case study. The supply model consists of three sub-models to forecast the number of registered nurses for the next 15 years: training model, population model and Full Time Equivalent (FTE) model...
August 18, 2017: Health Care Management Science
https://www.readbyqxmd.com/read/28821842/direct-learning-hidden-excited-state-interaction-patterns-from-ab-initio-dynamics-and-its-implication-as-alternative-molecular-mechanism-models
#4
Fang Liu, Likai Du, Dongju Zhang, Jun Gao
The excited states of polyatomic systems are rather complex, and often exhibit meta-stable dynamical behaviors. Static analysis of reaction pathway often fails to sufficiently characterize excited state motions due to their highly non-equilibrium nature. Here, we proposed a time series guided clustering algorithm to generate most relevant meta-stable patterns directly from ab initio dynamic trajectories. Based on the knowledge of these meta-stable patterns, we suggested an interpolation scheme with only a concrete and finite set of known patterns to accurately predict the ground and excited state properties of the entire dynamics trajectories, namely, the prediction with ensemble models (PEM)...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821802/dispersive-regimes-of-the-dicke-model
#5
Diego Barberena, Lucas Lamata, Enrique Solano
We study two dispersive regimes of the Dicke model in the dynamics of N two-level atoms interacting with a bosonic mode for long interaction times. Firstly, we analyze the model for the regime in which the qubit frequencies are equal and smaller than the mode frequency, and for values of the coupling strength similar or larger than the mode frequency, namely, the deep strong coupling regime. Secondly, we address an interaction that is dependent on the photon number, where the coupling strength is comparable to the geometric mean of the qubit and mode frequencies...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821762/multi-tissue-interactions-in-an-integrated-three-tissue-organ-on-a-chip-platform
#6
Aleksander Skardal, Sean V Murphy, Mahesh Devarasetty, Ivy Mead, Hyun-Wook Kang, Young-Joon Seol, Yu Shrike Zhang, Su-Ryon Shin, Liang Zhao, Julio Aleman, Adam R Hall, Thomas D Shupe, Andre Kleensang, Mehmet R Dokmeci, Sang Jin Lee, John D Jackson, James J Yoo, Thomas Hartung, Ali Khademhosseini, Shay Soker, Colin E Bishop, Anthony Atala
Many drugs have progressed through preclinical and clinical trials and have been available - for years in some cases - before being recalled by the FDA for unanticipated toxicity in humans. One reason for such poor translation from drug candidate to successful use is a lack of model systems that accurately recapitulate normal tissue function of human organs and their response to drug compounds. Moreover, tissues in the body do not exist in isolation, but reside in a highly integrated and dynamically interactive environment, in which actions in one tissue can affect other downstream tissues...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821647/plasticity-beyond-v1-reinforcement-of-motion-perception-upon-binocular-central-retinal-lesions-in-adulthood
#7
Kalina Burnat, Tjing-Tjing Hu, Małgorzata Kossut, Ulf T Eysel, Lutgarde Arckens
Induction of a central retinal lesion in both eyes of adult mammals is a model for macular degeneration and leads to retinotopic map reorganization in the primary visual cortex (V1). Here we characterized the spatio-temporal dynamics of molecular activity levels in the central and peripheral representation of five higher order visual areas, V2/18, V3/19, V4/21a,V5/PMLS, area 7, and V1/17, in adult cats with central 10° retinal lesions (both sexes), by means of real-time PCR for the neuronal activity reporter gene zif268...
August 16, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28820904/parametric-studies-of-metabolic-cooperativity-in-escherichia-coli-colonies-strain-and-geometric-confinement-effects
#8
Joseph R Peterson, John A Cole, Zaida Luthey-Schulten
Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise due to the subtle interplay between microenvironmental conditions and the cells' regulatory machinery, often involving cascades of intra- and extracellular signalling molecules. In the simplest of cases, as demonstrated in a recent study of the model organism Escherichia coli, metabolic cross-feeding can arise in monoclonal colonies of bacteria driven merely by spatial heterogeneity in the availability of growth substrates; namely, acetate, glucose and oxygen...
2017: PloS One
https://www.readbyqxmd.com/read/28820467/aquaporin-4-functionality-and-virchow-robin-space-water-dynamics-physiological-model-for-neurovascular-coupling-and-glymphatic-flow
#9
REVIEW
Tsutomu Nakada, Ingrid L Kwee, Hironaka Igarashi, Yuji Suzuki
The unique properties of brain capillary endothelium, critical in maintaining the blood-brain barrier (BBB) and restricting water permeability across the BBB, have important consequences on fluid hydrodynamics inside the BBB hereto inadequately recognized. Recent studies indicate that the mechanisms underlying brain water dynamics are distinct from systemic tissue water dynamics. Hydrostatic pressure created by the systolic force of the heart, essential for interstitial circulation and lymphatic flow in systemic circulation, is effectively impeded from propagating into the interstitial fluid inside the BBB by the tightly sealed endothelium of brain capillaries...
August 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28820263/hydrodynamic-steering-in-protein-association-revisited-surprisingly-minuscule-effects-of-considerable-torques
#10
Jan Marek Antosiewicz, Kamil Kamiński, Maciej Dlugosz
We investigate the previously postulated hydrodynamic steering phenomenon, resulting from complication of molecular shapes, its magnitude and possible relevance for protein-ligand and protein-protein diffusional encounters, and the kinetics of diffusion-controlled association. We consider effects of hydrodynamic interactions in a prototypical model system consisting of a cleft enzyme and an elongated substrate, and real protein-protein complexes, that of barnase and barstar, and human growth hormone and its binding protein...
August 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28820195/photoelectron-spectroscopy-of-isolated-luciferin-and-infraluciferin-anions-in-vacuo-competing-photodetachment-photofragmentation-and-internal-conversion
#11
Joanne L Woodhouse, Mariana Assmann, Michael A Parkes, Helen Grounds, Steven J Pacman, James C Anderson, Graham A Worth, Helen H Fielding
The electronic structure and excited-state dynamics of the ubiquitous bioluminescent probe luciferin and its furthest red-shifted analogue infraluciferin have been investigated using photoelectron spectroscopy and quantum chemistry calculations. In our electrospray ionization source, the deprotonated anions are formed predominantly in their phenolate forms and are directly relevant to studies of luciferin and infraluciferin as models for their unstable oxyluciferin and oxyinfraluciferin emitters. Following photoexcitation in the range 357-230 nm, we find that internal conversion from high-lying excited states to the S1(1ππ*) state competes efficiently with electron detachment...
August 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28819462/virtual-factory-framework-for-supporting-production-planning-and-control
#12
Deogratias Kibira, Guodong Shao
Developing optimal production plans for smart manufacturing systems is challenging because shop floor events change dynamically. A virtual factory incorporating engineering tools, simulation, and optimization generates and communicates performance data to guide wise decision making for different control levels. This paper describes such a platform specifically for production planning. We also discuss verification and validation of the constituent models. A case study of a machine shop is used to demonstrate data generation for production planning in a virtual factory...
2017: IFIP Advances in Information and Communication Technology
https://www.readbyqxmd.com/read/28818644/radioecological-assessment-and-radiometric-dating-of-sediment-cores-from-dynamic-sedimentary-systems-of-pra-and-volta-estuaries-ghana-along-the-equatorial-atlantic
#13
E Klubi, J M Abril, E Nyarko, A Laissaoui, M Benmansour
The Volta and Pra estuaries (Ghana, West Africa) are dynamical sedimentary systems whose natural equilibrium is being affected by anthropogenic activities. This paper reports depth-distributions of (210)Pb, (226)Ra, (234)Th, (40)K, (228)Ra and (137)Cs for two sediment cores from these estuaries. Bulk densities were not steady-state and well correlated with (40)K (p < 0.00005). Unsupported (210)Pb profiles were incomplete, non-monotonic and showed large fluctuations. The assumptions involved in the common (210)Pb-based dating models were not meet in these dynamical scenarios, and the use of (137)Cs as a time-marker is difficult in Equatorial and South-Hemisphere countries due to its low fallout rates...
August 14, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28818613/network-analysis-a-new-way-of-understanding-psychopathology
#14
Eduardo Fonseca-Pedrero
Current taxonomic systems are based on a descriptive and categorical approach where psychopathological symptoms and signs are caused by a hypothetical underlying mental disorder. In order to circumvent the limitations of classification systems, it is necessary to incorporate new conceptual and psychometric models that allow to understand, analyze and intervene in psychopathological phenomena from another perspective. The main goal was to present a new approach called network analysis for its application in the field of psychopathology...
August 14, 2017: Revista de Psiquiatrí́a y Salud Mental
https://www.readbyqxmd.com/read/28818602/operational-modelling-of-bigeye-tuna-thunnus-obesus-spatial-dynamics-in-the-indonesian-region
#15
P Lehodey, I Senina, T A Wibawa, O Titaud, B Calmettes, A Conchon, B Tranchant, P Gaspar
With INDESO, Indonesia has implemented a system for the monitoring and management of its tuna resources. Despite increasing catch, very few is known about the dynamics and real abundance of tuna species in the Indonesian waters and adjacent oceanic regions. The SEAPODYM model was implemented in an operational chain of production for the Indonesian region to simulate tuna spatial dynamics in realtime. This challenging objective imposed developing a global scale model at coarse resolution to provide initial and boundaries conditions of the regional model...
August 14, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28818579/developing-integrated-pbpk-pd-coupled-mechanistic-pathway-model-mirna-bdnf-an-approach-towards-system-toxicology
#16
Raju Prasad Sharma, Marta Schuhmacher, Vikas Kumar
Integration of a dynamic signal transduction pathway into the tissue dosimetry model is a major advancement in the area of computational toxicology. This paper illustrates the ways to incorporate the use of existing system biological model in the field of toxicology via its coupling to the Physiological based Pharmacokinetics and Pharmacodynamics (PBPK/PD) model.This expansion framework of integrated PBPK/PD coupled mechanistic system pathway model can be called as system toxicology that describes the kinetics of both -the chemicals and -biomolecules, help us to understand the dynamic and steady-state behaviors of molecular pathways under perturbed condition...
August 14, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28818496/nonlinear-dynamical-systems-comment-on-modeling-human-behavior-in-economics-and-social-science-by-marina-dolfin-leone-leonida-and-nisrine-outada
#17
Nicola Bellomo, Ahmed Elaiw
No abstract text is available yet for this article.
August 3, 2017: Physics of Life Reviews
https://www.readbyqxmd.com/read/28818467/mathematical-modelling-and-analysis-of-the-brassinosteroid-and-gibberellin-signalling-pathways-and-their-interactions
#18
Henry R Allen, Mariya Ptashnyk
The plant hormones brassinosteroid (BR) and gibberellin (GA) have important roles in a wide range of processes involved in plant growth and development. In this paper we derive and analyse new mathematical models for the BR signalling pathway and for the crosstalk between the BR and GA signalling pathways. To analyse the effects of spatial heterogeneity of the signalling processes, along with spatially-homogeneous ODE models we derive coupled PDE-ODE systems modelling the temporal and spatial dynamics of molecules involved in the signalling pathways...
August 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28817705/cell-surface-dynamics-and-cellular-distribution-of-endogenous-fcrn
#19
Lena D'Hooghe, Andrew D Chalmers, Sam Heywood, Paul Whitley
A major role for FcRn is the salvage of pinocytosed IgG and albumin from a degradative fate in lysosomes. FcRn achieves this by binding IgG in a pH-dependent manner in acidic endosomes and recycling it to the plasma membrane to be released at neutral pH. This is important in maintaining high serum IgG and albumin levels and has the potential to be exploited to modulate the pharmacokinetics of antibody-based therapeutics. Although FcRn is responsible for the recycling of IgG, the dynamic behaviour of endogenous FcRn is not well understood...
2017: PloS One
https://www.readbyqxmd.com/read/28817666/assessing-the-sustainable-development-and-intensification-potential-of-beef-cattle-production-in-sumbawa-indonesia-using-a-system-dynamics-approach
#20
Dahlanuddin, Benjamin Henderson, Kanar Dizyee, Hermansyah, Andrew Ash
The intensification of beef cattle production in dryland areas of East Indonesia has the potential to substantially raise the incomes of smallholder farmers that dominate the sector. In this study we assess the potential for intensifying beef production on Sumbawa Island, by introducing a household feedlot production system (2-20 animals) based on the Leucaena leucocephala (leucanea) tree legume as an improved source of feed. We used a system dynamics approach to model the entire value chain, accounting for herd dynamics, demand dynamics and seasonality...
2017: PloS One
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