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Mathematical modelling

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https://www.readbyqxmd.com/read/28723080/an-orthogonal-multi-input-integration-system-to-control-gene-expression-in-escherichia-coli
#1
Fabio Annunziata, Antoni Matyjaszkiewicz, Gianfranco Fiore, Claire Grierson, Lucia Marucci, Mario di Bernardo, Nigel Savery
In many biotechnological applications, it is useful for gene expression to be regulated by multiple signals, as this allows the programming of complex behaviour. Here we implement, in Escherichia coli, a system that compares the concentration of two signal molecules, and tunes GFP expression proportionally to their relative abundance. The computation is performed via molecular titration between an orthogonal σ factor and its cognate anti-σ factor. We use mathematical modelling and experiments to show that the computation system is predictable and able to adapt GFP expression dynamically to a wide range of combinations of the two signals, and our model qualitatively captures most of these behaviours...
July 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28722824/local-equilibrium-and-retardation-revisited
#2
Scott K Hansen, Velimir V Vesselinov
In modeling solute transport with mobile-immobile mass transfer (MIMT), it is common to use an advection-dispersion equation (ADE) with a retardation factor, or retarded ADE. This is commonly referred to as making the local equilibrium assumption (LEA). Assuming local equilibrium, Eulerian textbook treatments derive the retarded ADE, ostensibly exactly. However, other authors have presented rigorous mathematical derivations of the dispersive effect of MIMT, applicable even in the case of arbitrarily fast mass transfer...
July 19, 2017: Ground Water
https://www.readbyqxmd.com/read/28722541/nox-emission-calculations-for-bulk-carriers-by-using-engine-power-probabilities-as-weighting-factors
#3
Chih-Wen Cheng, Jian Hua, Daw-Shang Hwang
An important marine pollution issue identified by the International Maritime Organization is NOx emissions; however, the stipulated method for determining the NOx certification value does not reflect the actual high emission factors of slow-speed two-stroke diesel engines over long-term slow steaming. In this study, an accurate method is presented for calculating the NOx emission factors and total amount of NOx emissions by using the actual power probabilities of the diesel engines in four types of bulk carriers...
July 19, 2017: Journal of the Air & Waste Management Association
https://www.readbyqxmd.com/read/28721941/blood-glucose-concentration-control-for-type-1-diabetic-patients-a-non-linear-suboptimal-approach
#4
Yazdan Batmani
In this study, a closed-loop treatment strategy is proposed for the control of blood glucose levels in type 1 diabetic patients. Toward this end, a non-linear technique for designing suboptimal tracking controllers, called the state-dependent Riccati equation tracker, is used based on a mathematical model of the glucose-insulin regulatory system. Since two state variables of the utilised model are not available to the controller, a non-linear filter is also designed to estimate these variables using the measured blood glucose concentration...
August 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28721940/isolation-characterisation-and-enzymatic-activity-of-streptomyces-sp-and-its-ph-control-during-fermentation-process
#5
Balraj Baskaran, Arulmozhi Muthukumarasamy
Streptomyces sp. with grey white mycelium was isolated from Kodiyakkarai marine segment of east coastal of India. The isolate produced spiny spores and did not produce any diffusible pigments. Various biochemical tests were carried out to confirm the isolate classification. The amylolytic enzyme activity was estimated using the isolated strain which was confirmed by golden yellowish zone formation after using the Gram's iodine stain. The amount of amylase produced by the isolate was 6.15 U/ml. Higher living cells always produce better enzymes, so that the process parameters especially pH was maintained in fermentation chamber for higher growth and also for large-scale growth...
August 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28721471/evaluations-of-interventions-using-mathematical-models-with-exponential-and-non-exponential-distributions-for-disease-stages-the-case-of-ebola
#6
Xiaojing Wang, Yangyang Shi, Zhilan Feng, Jingan Cui
Many mathematical models for the disease transmission dynamics of Ebola have been developed and studied, particularly during and after the 2014 outbreak in West Africa. Most of these models are systems of ordinary differential equations (ODEs). One of the common assumptions made in these ODE models is that the duration of disease stages, such as latent and infectious periods, follows an exponential distribution. Gamma distributions have also been used in some of these models. It has been demonstrated that, when the models are used to evaluate disease control strategies such as quarantine or isolation, the models with exponential and Gamma distribution assumptions may generate contradictory results (Feng et al...
July 18, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28721470/an-alternative-to-moment-closure
#7
Ingemar Nåsell
Moment closure methods are widely used to analyze mathematical models. They are specifically geared toward derivation of approximations of moments of stochastic models, and of similar quantities in other models. The methods possess several weaknesses: Conditions for validity of the approximations are not known, magnitudes of approximation errors are not easily evaluated, spurious solutions can be generated that require large efforts to eliminate, and expressions for the approximations are in many cases too complex to be useful...
July 18, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28721129/anti-m%C3%A3-llerian-hormone-amh-as-a-good-predictor-of-time-of-menopause
#8
REVIEW
Aleksandra Kruszyńska, Jadwiga Słowińska-Srzednicka
Anti-Müllerian hormone (AMH) in women is secreted by granulosa cells in late preantral and small antral follicles. AMH seems to be a very stable marker having some advantages over other biochemical and biophysical markers and is very useful in the assessment of ovarian reserve. AMH measurement may be used in cases of premature ovarian failure, including iatrogenic, due to treatment for cancer, hypogonadotropic hypogonadism, and lastly, in polycystic ovary syndrome (PCOS). It is also a very specific marker of ovarian tumors - folliculomas...
June 2017: Przeglad Menopauzalny, Menopause Review
https://www.readbyqxmd.com/read/28720897/a-predictive-mathematical-modeling-approach-for-the-study-of-doxorubicin-treatment-in-triple-negative-breast-cancer
#9
Matthew T McKenna, Jared A Weis, Stephanie L Barnes, Darren R Tyson, Michael I Miga, Vito Quaranta, Thomas E Yankeelov
Doxorubicin forms the basis of chemotherapy regimens for several malignancies, including triple negative breast cancer (TNBC). Here, we present a coupled experimental/modeling approach to establish an in vitro pharmacokinetic/pharmacodynamic model to describe how the concentration and duration of doxorubicin therapy shape subsequent cell population dynamics. This work features a series of longitudinal fluorescence microscopy experiments that characterize (1) doxorubicin uptake dynamics in a panel of TNBC cell lines, and (2) cell population response to doxorubicin over 30 days...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720696/persistent-organic-pollutants-impair-insulin-secretory-function-of-pancreatic-beta-cells-human-and-in-vitro-evidence
#10
Yu-Mi Lee, Chae-Myeong Ha, Se-A Kim, Themis Thoudam, Young-Ran Yoon, Dae-Jung Kim, Hyeon-Chang Kim, Hyo-Bang Moon, Sungmi Park, In-Kyu Lee, Duk-Hee Lee
Persistent organic pollutants (POPs), especially organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs), have emerged as a new risk factor of type 2 diabetes (T2D). We evaluated whether chronic exposure to low-dose POPs affects insulin secretory function of beta-cells in humans and in vitro cells. Serum concentrations of OCPs and PCBs were measured in 200 nondiabetic adults. Mathematical-model-based insulin secretion indices were estimated using a 2-hour 7-sample oral glucose tolerance test. Insulin secretion by INS1E beta-cells was measured after 48-hour treatment with 3 OCPs or a PCB mixture...
July 18, 2017: Diabetes
https://www.readbyqxmd.com/read/28720536/a-diffusing-wave-spectroscopy-study-of-pharmaceutical-emulsions-for-physical-stability-assessment
#11
Andreas Niederquell, Alexandra H E Machado, Martin Kuentz
Emulsions are broadly used in pharmaceutics either as intermediate products or as final dosage forms. Such disperse systems are only kinetically stabilized and therefore early detection of physical instability is highly desirable. This work employed diffusing wave spectroscopy (DWS) to study a series of model emulsions that were categorized, based on their composition, as either "simple" or "complex". DWS data were compared with results of droplet size imaging, apparent viscosity obtained by microfluidics, and near-infrared (NIR) analytical centrifugation...
July 15, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28720456/mechanistic-mathematical-models-an-underused-platform-for-hpv-research
#12
REVIEW
Marc D Ryser, Patti E Gravitt, Evan R Myers
Health economic modeling has become an invaluable methodology for the design and evaluation of clinical and public health interventions against the human papillomavirus (HPV) and associated diseases. At the same time, relatively little attention has been paid to a different yet complementary class of models, namely that of mechanistic mathematical models. The primary focus of mechanistic mathematical models is to better understand the intricate biologic mechanisms and dynamics of disease. Inspired by a long and successful history of mechanistic modeling in other biomedical fields, we highlight several areas of HPV research where mechanistic models have the potential to advance the field...
June 2017: Papillomavirus Research
https://www.readbyqxmd.com/read/28720023/early-motor-development-and-cognitive-abilities-among-mexican-preschoolers
#13
Erika Osorio-Valencia, Luisa Torres-Sánchez, Lizbeth López-Carrillo, Stephen J Rothenberg, Lourdes Schnaas
Psychomotricity plays a very important role in children's development, especially for learning involving reading-writing and mathematical calculations. Evaluate motor development in children 3 years old and its relationship with their cognitive abilities at the age of 5 years. Based on a cohort study, we analyzed the information about motor performance evaluated at 3 years old by Peabody Motor Scale and cognitive abilities at 5 years old. The association was estimated using linear regression models adjusted by mother's intelligence quotient, sex, Bayley mental development index at 18 months, and quality of the environment at home (HOME scale)...
July 18, 2017: Child Neuropsychology: a Journal on Normal and Abnormal Development in Childhood and Adolescence
https://www.readbyqxmd.com/read/28719607/stress-induced-mutagenesis-stress-diversity-facilitates-the-persistence-of-mutator-genes
#14
Marta Lukačišinová, Sebastian Novak, Tiago Paixão
Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28718662/prediction-of-porosity-of-food-materials-during-drying-current-challenges-and-future-directions
#15
Mohammad U H Joardder, C Kumar, M A Karim
Pore formation in food samples is a common physical phenomenon observed during dehydration processes. The pore evolution during drying significantly affects the physical properties and quality of dried foods. Therefore, it should be taken into consideration when predicting transport processes in the drying sample. Characteristics of pore formation depend on the drying process parameters, product properties and processing time. Understanding the physics of pore formation and evolution during drying will assist in accurately predicting the drying kinetics and quality of food materials...
July 18, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28717995/ovomucin-nanoparticles-promising-carriers-for-mucosal-delivery-of-drugs-and-bioactive-compounds
#16
Ali Akbari, Jianping Wu
Ovomucin, with a similar structure to mucin and gelation ability at room temperature, is a potential mucosal carrier. To evaluate this potential, the mucoadhesive property of ovomucin was studied by the tensile strength and rheology methods, and compared with three known mucoadhesive polymers, chitosan, polyacrylic acid (PAA), and alginate. Ovomucin particles were basically spherical in shape with an average size of ~572, 235 and 54 nm prepared at pH 5, 6.5, and 9, respectively. The absolute value of the zeta potential increased from ~ -51 mV at pH 5 to ~ -59 and -91 mV at pH 6...
July 17, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28717163/titin-mediated-thick-filament-activation-through-a-mechanosensing-mechanism-introduces-sarcomere-length-dependencies-in-mathematical-models-of-rat-trabecula-and-whole-ventricle
#17
Lorenzo Marcucci, Takumi Washio, Toshio Yanagida
Recent experimental evidence in skeletal muscle demonstrated the existence of a thick-filament mechanosensing mechanism, acting as a second regulatory system for muscle contraction, in addition to calcium-mediated thin filament regulation. These two systems cooperate to generate force, but the extent to which their interaction is relevant in physiologically contracting muscle was not yet assessed experimentally. Therefore, we included both regulatory mechanisms in a mathematical model of rat trabecula and whole ventricle...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717156/patterned-arrangements-of-olfactory-receptor-gene-expression-in-zebrafish-are-established-by-radial-movement-of-specified-olfactory-sensory-neurons
#18
Xalid Bayramli, Yiğit Kocagöz, Uğurcan Sakizli, Stefan H Fuss
Spatial restriction of olfactory receptor (OR) gene expression in peripheral sense organs is a common phenomenon across species, suggesting that zonal OR expression somehow contributes to olfactory function. In zebrafish OR expression patterns reminiscent of zones occur as concentric domains with preferred diameters for different ORs. However, the function and the developmental origin of the pattern are unknown. Here we investigate olfactory sensory neuron (OSN) neurogenesis in the adult zebrafish olfactory epithelium (OE) to understand how the zonally organized OR pattern is established and maintained during the lifetime of the animal...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717042/modeling-the-kinetics-of-the-permeation-of-antibacterial-agents-into-growing-bacteria-and-its-interplay-with-efflux
#19
Wright W Nichols
A mathematical model of the passive permeation of a novel solute into bacteria is developed that explicitly accounts for intracellular dilution through growth. A bacterial cell envelope permeability coefficient of >10(-8) cm(2)s(-1) approx., is predicted to ensure passive permeation into rapidly replicating bacterial cells. The relative importance of the permeability coefficients of the cytoplasmic and outer membranes of Gram-negative bacteria in determining the overall envelope permeability coefficient is analyzed quantitatively...
July 17, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28716945/evaluating-optimal-therapy-robustness-by-virtual-expansion-of-a-sample-population-with-a-case-study-in-cancer-immunotherapy
#20
Syndi Barish, Michael F Ochs, Eduardo D Sontag, Jana L Gevertz
Cancer is a highly heterogeneous disease, exhibiting spatial and temporal variations that pose challenges for designing robust therapies. Here, we propose the VEPART (Virtual Expansion of Populations for Analyzing Robustness of Therapies) technique as a platform that integrates experimental data, mathematical modeling, and statistical analyses for identifying robust optimal treatment protocols. VEPART begins with time course experimental data for a sample population, and a mathematical model fit to aggregate data from that sample population...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
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