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Mathematical modelling

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https://www.readbyqxmd.com/read/28340243/finite-time-parametric-identification-for-the-model-representing-the-metabolic-and-genetic-regulatory-effects-of-sequential-aerobic-respiration-and-anaerobic-fermentation-processes-in-escherichia-coli
#1
Alfonso Sepúlveda-Gálvez, Jesús Agustín Badillo-Corona, Isaac Chairez
Mathematical modelling applied to biological systems allows for the inferring of changes in the dynamic behaviour of organisms associated with variations in the environment. Models based on ordinary differential equations are most commonly used because of their ability to describe the mechanisms of biological systems such as transcription. The disadvantage of using this approach is that there is a large number of parameters involved and that it is difficult to obtain them experimentally. This study presents an algorithm to obtain a finite-time parameter characterization of the model used to describe changes in the metabolic behaviour of Escherichia coli associated with environmental changes...
March 17, 2017: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/28339789/early-treatment-gains-for-antibiotic-administration-and-within-human-host-time-series-data
#2
Todd R Young, Erik M Boczko
As technological improvements continue to infiltrate and impact medical practice, it has become possible to non-invasively collect dense physiological time series data from individual patients in real time. These advances continue to improve physicians' ability to detect and to treat infections early. One important benefit of early detection and treatment of nascent infections is that it leads to earlier resolution. In response to current and anticipated advances in data capture, we introduce the Early Treatment Gain (ETG) as a measure to quantify this benefit...
February 18, 2017: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/28339681/on-tear-film-breakup-tbu-dynamics-and-imaging
#3
Richard J Braun, Tobin A Driscoll, Carolyn G Begley, P Ewen King-Smith, Javed I Siddique
We report the results of some recent experiments to visualize tear film dynamics. We then study a mathematical model for tear film thinning and tear film breakup (TBU), a term from the ocular surface literature. The thinning is driven by an imposed tear film thinning rate which is input from in vivo measurements. Solutes representing osmolarity and fluorescein are included in the model. Osmolarity causes osmosis from the model ocular surface, and the fluorescein is used to compute the intensity corresponding closely to in vivo observations...
February 20, 2017: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/28335425/linear-mathematical-model-for-seam-tracking-with-an-arc-sensor-in-p-gmaw-processes
#4
Wenji Liu, Liangyu Li, Ying Hong, Jianfeng Yue
Arc sensors have been used in seam tracking and widely studied since the 80s and commercial arc sensing products for T and V shaped grooves have been developed. However, it is difficult to use these arc sensors in narrow gap welding because the arc stability and sensing accuracy are not satisfactory. Pulse gas melting arc welding (P-GMAW) has been successfully applied in narrow gap welding and all position welding processes, so it is worthwhile to research P-GMAW arc sensing technology. In this paper, we derived a linear mathematical P-GMAW model for arc sensing, and the assumptions for the model are verified through experiments and finite element methods...
March 14, 2017: Sensors
https://www.readbyqxmd.com/read/28335399/an-eddy-current-testing-platform-system-for-pipe-defect-inspection-based-on-an-optimized-eddy-current-technique-probe-design
#5
Damhuji Rifai, Ahmed N Abdalla, Ramdan Razali, Kharudin Ali, Moneer A Faraj
The use of the eddy current technique (ECT) for the non-destructive testing of conducting materials has become increasingly important in the past few years. The use of the non-destructive ECT plays a key role in the ensuring the safety and integrity of the large industrial structures such as oil and gas pipelines. This paper introduce a novel ECT probe design integrated with the distributed ECT inspection system (DSECT) use for crack inspection on inner ferromagnetic pipes. The system consists of an array of giant magneto-resistive (GMR) sensors, a pneumatic system, a rotating magnetic field excitation source and a host PC acting as the data analysis center...
March 13, 2017: Sensors
https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#6
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334538/modelling-studies-of-inhomogeneity-effects-during-laser-flash-photolysis-experiments-a-reaction-diffusion-approach
#7
Eva Doka, Gabor Lente
This works present a rigorous mathematical study of the effect of unavoidable inhomogeneities in laser flash photolysis experiments. There are two different kinds of inhomegenities: the first arises from diffusion, whereas the second one has geometric origins (the shapes of the excitation and detection light beams). Both of these are taken into account in our reported model, which gives rise to a set of reaction-diffusion type partial differential equations. These equations are solved by a specially developed finite volume method...
March 23, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28334424/frequency-and-function-in-the-basal-ganglia-the-origins-of-beta-and-gamma-band-activity
#8
Alexander Blenkinsop, Sean Anderson, Kevin Gurney
Neural oscillations in the basal ganglia are well studied yet remain poorly understood. Behavioural correlates of spectral activity are well described, yet a quantitative hypothesis linking time domain dynamics and spectral properties to basal ganglia function has been lacking. We show, for the first time, that a unified description is possible by interpreting previously ignored structure in data describing GPi responses to cortical stimulation. These data were used to expose a pair of distinctive neuronal responses to the stimulation...
March 23, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28334268/an-algorithmic-perspective-of-de-novo-cis-regulatory-motif-finding-based-on-chip-seq-data
#9
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
Transcription factors are proteins that bind to specific DNA sequences and play important roles in controlling the expression levels of their target genes. Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. Chromatin immunoprecipitation sequencing (ChIP-seq) technology can generate large-scale experimental data for such protein-DNA interactions, providing an unprecedented opportunity to identify TFBSs (a...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334223/is-bamm-flawed-theoretical-and-practical-concerns-in-the-analysis-of-multi-rate-diversification-models
#10
Daniel L Rabosky, Jonathan S Mitchell, Jonathan Chang
BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a statistical framework that uses reversible jump MCMC to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore and coauthors (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (1) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (2) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (3) diversification rate estimates from BAMM are unreliable...
February 21, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334014/the-quaternary-lidocaine-derivative-qx-314-in-combination-with-bupivacaine-for-long-lasting-nerve-block-efficacy-toxicity-and-the-optimal-formulation-in-rats
#11
Qinqin Yin, Jun Li, Qingshan Zheng, Xiaolin Yang, Rong Lv, Longxiang Ma, Jin Liu, Tao Zhu, Wensheng Zhang
OBJECTIVE: The quaternary lidocaine derivative (QX-314) in combination with bupivacaine can produce long-lasting nerve blocks in vivo, indicating potential clinical application. The aim of the study was to investigate the efficacy, safety, and the optimal formulation of this combination. METHODS: QX-314 and bupivacaine at different concentration ratios were injected in the vicinity of the sciatic nerve in rats; bupivacaine and saline served as controls (n = 6~10)...
2017: PloS One
https://www.readbyqxmd.com/read/28334005/multi-scale-model-of-drug-induced-adaptive-resistance-of-gram-negative-bacteria-to-polymyxin-b
#12
Wojciech Krzyzanski, Gauri G Rao
The purpose of this report is to apply multi-scale modeling using the theory of physiologically structured populations (PSP) to develop a mathematical model for antimicrobial resistance based on a heterogeneous distribution of receptors and affinities among bacterial cells. The theory has been tested on data obtained from an in vitro static time-kill infection model analyzing the pharmacodynamics of polymyxin B against Gram-negative bacteria. The drug binding parameter KD (dissociation equilibrium constant) is assumed to vary between the bacterial cells...
2017: PloS One
https://www.readbyqxmd.com/read/28333588/multiassociative-memory-recurrent-synapses-increase-storage-capacity
#13
Marcelo Matheus Gauy, Florian Meier, Angelika Steger
The connection density of nearby neurons in the cortex has been observed to be around 0.1, whereas the longer-range connections are present with much sparser density (Kalisman, Silberberg, & Markram, 2005). We propose a memory association model that qualitatively explains these empirical observations. The model we consider is a multiassociative, sparse, Willshaw-like model consisting of binary threshold neurons and binary synapses. It uses recurrent synapses for iterative retrieval of stored memories. We quantify the usefulness of recurrent synapses by simulating the model for small network sizes and by doing a precise mathematical analysis for large network sizes...
March 23, 2017: Neural Computation
https://www.readbyqxmd.com/read/28333370/influence-of-nickel-titanium-rotary-systems-with-varying-tapers-on-the-biomechanical-behaviour-of-maxillary-first-premolars-under-occlusal-forces-a-finite-element-analysis-study
#14
S Askerbeyli Ors, A Serper
AIM: To evaluate the effect of three nickel-titanium (Ni-Ti) rotary systems with varying tapers on stress distribution and to analyse potential fracture patterns as well as the volume of fracture-susceptible regions in two-rooted maxillary premolars. METHODOLOGY: The root canals of three single-rooted premolars were prepared with either HeroShaper (Micro-Mega, Besançon, France) to (size 30, .04 taper), Revo-S (Micro-Mega) to AS30 (size 30, .06 taper) or ProTaper Universal (Dentsply Maillefer, Ballaigeus, Switzerland) to F3 (size 30, ...
March 23, 2017: International Endodontic Journal
https://www.readbyqxmd.com/read/28332207/the-eyes-and-vision-of-butterflies
#15
Kentaro Arikawa
Butterflies use colour vision when searching for flowers. Unlike the trichromatic retinas of humans (blue, green, and red cones; plus rods) and honeybees (ultraviolet, blue, and green photoreceptors), butterfly retinas typically have six or more photoreceptor classes with distinct spectral sensitivities. The eyes of the Japanese yellow swallowtail (Papilio xuthus) contain ultraviolet, violet, blue, green, red and broad-band receptors, with each ommatidium housing nine photoreceptor cells in one of three fixed combinations...
March 22, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28332104/exhaustive-mathematical-analysis-of-simple-clinical-measurements-for-childhood-pneumonia-diagnosis
#16
Keegan Kosasih, Udantha Abeyratne
BACKGROUND: Pneumonia is the leading cause of mortality for children below 5 years of age. The majority of these occur in poor countries with limited access to diagnosis. The World Health Organization (WHO) criterion for pneumonia is the de facto method for diagnosis. It is designed targeting a high sensitivity and uses easy to measure parameters. The WHO criterion has poor specificity. METHODS: We propose a method using common measurements (including the WHO parameters) to diagnose pneumonia at high sensitivity and specificity...
March 22, 2017: World Journal of Pediatrics: WJP
https://www.readbyqxmd.com/read/28330985/a-mechanically-coupled-reaction-diffusion-model-that-incorporates-intra-tumoural-heterogeneity-to-predict-in-vivo-glioma-growth
#17
David A Hormuth, Jared A Weis, Stephanie L Barnes, Michael I Miga, Erin C Rericha, Vito Quaranta, Thomas E Yankeelov
While gliomas have been extensively modelled with a reaction-diffusion (RD) type equation it is most likely an oversimplification. In this study, three mathematical models of glioma growth are developed and systematically investigated to establish a framework for accurate prediction of changes in tumour volume as well as intra-tumoural heterogeneity. Tumour cell movement was described by coupling movement to tissue stress, leading to a mechanically coupled (MC) RD model. Intra-tumour heterogeneity was described by including a voxel-specific carrying capacity (CC) to the RD model...
March 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28330920/immanent-conditions-determine-imminent-collapses-nutrient-regimes-define-the-resilience-of-macroalgal-communities
#18
Jordi Boada, Rohan Arthur, David Alonso, Jordi F Pagès, Albert Pessarrodona, Silvia Oliva, Giulia Ceccherelli, Luigi Piazzi, Javier Romero, Teresa Alcoverro
Predicting where state-changing thresholds lie can be inherently complex in ecosystems characterized by nonlinear dynamics. Unpacking the mechanisms underlying these transitions can help considerably reduce this unpredictability. We used empirical observations, field and laboratory experiments, and mathematical models to examine how differences in nutrient regimes mediate the capacity of macrophyte communities to sustain sea urchin grazing. In relatively nutrient-rich conditions, macrophyte systems were more resilient to grazing, shifting to barrens beyond 1 800 g m(-2) (urchin biomass), more than twice the threshold of nutrient-poor conditions...
March 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28330886/preclinical-diagnosis-predicting-its-ability-to-improve-control-of-farm-to-farm-foot-and-mouth-disease-transmission-in-cattle
#19
Noel Nelson, David J Paton, Simon Gubbins, Claire Colenutt, Emma Brown, Sophia Hodgson, Jose L Gonzales
Foot-and-mouth disease (FMD) can cause large disruptive epidemics in livestock. Current eradication measures rely on the rapid clinical detection and removal of infected herds. Here, we have evaluated the potential for preclinical diagnosis during reactive surveillance to reduce the risk of between farm transmission. We used data from transmission experiments in cattle where both individual animal samples, such as blood, probang, saliva or nasal swabs, and herd level samples, such as air samples, were taken daily during the course of infection...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330291/optimization-of-culture-conditions-by-response-surface-methodology-and-unstructured-kinetic-modeling-for-bioactive-metabolite-production-by-nocardiopsis-litoralis-vsm-8
#20
Ushakiranmayi Managamuri, Muvva Vijayalakshmi, Sudhakar Poda, V S Rama Krishna Ganduri, R Satish Babu
Response surface methodology-based central composite design on five variables incubation time, pH, temperature, sucrose concentration, and soya peptone concentration was employed for optimization of the production of bioactive compounds by Nocardiopsis litoralis strain VSM 8. The main quadratic effects and interactions of the five variables on the production of bioactive metabolites were investigated. A second-order polynomial model produced a satisfied fit for experimental data with regard to the production of the bioactive metabolites...
December 2016: 3 Biotech
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