Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism

Background Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distributions. Even though existing methods use transcript abundances as a proxy for enzyme activity, each method uses a different hypothesis and assumptions. Most methods implicitly assume a proportionality between transcript levels and flux through the corresponding function, although these proportionality constant(s) are often not explicitly mentioned nor discussed in any of the published methods. E-Flux is one such method and, in this algorithm, flux bounds are related to expression data, so that reactions associated with highly expressed genes are allowed to carry higher flux values. Results Here, we extended E-Flux and systematically evaluated the impact of an assumed proportionality constant on model predictions. We used data from published experiments with Escherichia coli and Saccharomyces cerevisiae and we compared the predictions of the algorithm to measured extracellular and intracellular fluxes. Conclusion We showed that detailed modelling using a proportionality constant can greatly impact the outcome of the analysis. This increases accuracy and allows for extraction of better physiological information.

Simplified Relation Model of Soil Saturation Permeability Coefficient and Air-Entry Value and Its Application

Based on the Tao and Kong (TK) model and the fractal model of the soil–water characteristic curve, a simplified model of the relationship between the saturated permeability coefficient and the air-entry value is established in this study: ks = k0ψa−2. It is shown that the saturated permeability coefficient of soil is determined by its maximum pore size. In order to facilitate the mutual prediction of saturation permeability coefficient and air-entry value, based on the data of five types of soil in the UNSODA database, the comprehensive proportionality constant k0 of the five types of soil were obtained: sand k0 = 0.03051; clay k0 = 0.001878; loam k0 = 0.001426; sandy loam k0 = 0.009301; and silty clay loam k0 = 0.0007055. Based on the obtained comprehensive proportionality constant k0 and the relationship model between saturated permeability coefficient and air intake value, the air-entry value of five kinds of soils in the existing literature and the SoilVision database were calculated. Comparing the calculated air-entry value with the measured one, the results showed that the model simplifies the traditional air-entry value prediction method to some extent and can effectively predict the air-entry value of different types of soil. On the whole, the model better predicts the air-entry value for sandy, clay, and silty clay loam than loam and sandy loam.

Flow of a Fluid with Pressure-Dependent Viscosity through Variable Permeability Porous Layer

In this work, we consider flow of a fluid with pressure-dependent viscosity down an inclined porous plane with variable permeability that is incorporated in the pressure-dependent drag coefficient. We provide a solution to a recently developed flow model, and study the effects of flow and domain parameters (viscosity control parameter, permeability proportionality constant, and angle of inclination) on the flow characteristics. Suitability of a variable permeability model that considers permeability proportional to the flow velocity is investigated. Results show that large values of the permeability proportionality constant have little or no effects on flow characteristics.

Mathematical Model for Describing Corn Grain Dehydration Kinetics after a Nixtamalization Process

In this research, the mathematical model associated with the hydrothermal dehydration process of Nixtamalized Corn Grains (NCG) with different Steeping Time (ST) values, allows the fitting of experimental data with initial moisture M0 and the equilibrium moisture ME as a function of Isothermal Dehydration Time (IDT). The moisture percentage for any time t and dehydration rate (isolines M(t) and isolines vI respectively) of the NCG is shown by means of matrix graphics as a simultaneous function of IDT and ST. The relationship between initial dehydration rate v0 and initial moisture M0 establishes as a function of ST. Also, the mathematical model associated with the solution of the second Fick’s law allows calculating the diffusivity rate vk (H2O molecules out of NCG) and verify that the rate of change in moisture and the dynamical proportionality constant k has a non-linear dependence on the IDT and that k is directly proportional to Deff. The k values strongly relate to ST and the calcium ions percentage into NCG according to solubility lime values into cooking water (or nejayote) as a function of decreasing temperature when ST increases.

PreDarwinian evolution, prebiotic change: a principle of least selection

Evolution prior to its Darwinian era was an age of variation. Events allowed by starting materials, chemistry and physics were realized, directed by intrinsic probabilities. In this landscape, a principle of least selection defines the most probable evolutionary path. For selection from a population where x varies, the rate of x evolution dx/dt = αΔμ. μ is the population mean of the selected property x, [alpha] a proportionality constant. Explicit equations for selected change Δμ are presented. Simple results exist for frequent cases; for example, selection for x ≥ a threshold. Maximizing Δμ minimizes need for selection. Least selections for x demand maximal selection dependence on x, maximal x standard deviation σ, and maximal lower x threshold (consistent with the need for a survivor). Least selection is free of the cost of natural selection, thus can support rapid advance. Least selection also unites previous seemingly independent optima. As examples, evolution via ′starting bloc selection [prime] and ′chance utility′ (where selection spans a minimal change) and ′near-ideal reactions′ (where variable reactant supplies create easy reactions) occur via transitory paths of least selection. ′Bayesian convergence′ is guaranteed by least selection′s extremum (which sharply defines evolution′s path). [prime]Distribution fitness′ (where specific outcomes are selected among multiple concurrent variations) is least selection of rare functional minorities. Inheritance of encoded chemical capabilities first evolves because templating and catalysis are close, potentially joined in a single molecular complex. Least selection defines directions, biostructures define destinations in likely pathways of preDarwinian evolution.

ESTIMATION OF INTERIOR TEMPERATURE OF AN ELECTRIC OVEN

This paper is aimed at estimating interior temperature of an electric oven with respect to the jacket temperature. A discrete dynamic model of first order difference equation is described for the system. Kalman filtering technique is applied to the discrete dynamic model for estimation of the interior temperature. A computer program is written to simulate the system. It was observed that the estimates of the interior temperatures are directly proportional to estimates of the Jacket temperatures with proportionality constant of 0.0009. With this method it is therefore possible to obtain the interior temperature of the electric oven at any given time.

NEW RENEWABLE SOURCE: REST ENERGY OF THE ELECTRON SPIN

The intrinsic properties of electrons are fundamental for the progress of science. The relationship between electron mass and its electric charge and spin is poorly explored. Thus, through the Relativistic Quantum Theory, we have investigated the equivalence between mc² and qc², where m and q are, respectively, the mass and the electric charge of the electron. We demonstrated that ∆E = mc² ≡ Aqc², where A (A = 5.68562964 × 10−12KgC−1) is the proportionality constant obtained through the ratio of the spin g-factor and the gyromagnetic ratio for a free electron. The alignment of the spin magnetic dipole moment with the magnetic field ceases the electron precession movement. Therefore, the kinetic energy, associated with the precession, is dissipated with an intensity equal to mc². This result is promising for the production of clean and sustainable energy, besides new technological applications.

PROSPECTIVE PRIMARY SCHOOL TEACHERS’ ACTIVITIES WHEN DEALING WITH MATHEMATICS MODELLING TASKS

The current teaching of mathematics is guided by recommendations that suggest the implementation of various activities in order to raise the understanding of mathematical knowledge. This diversity is related to the characteristics of the tasks proposed in the learning contexts. Among all tasks, the modelling ones call for the application of activities through different representations. So, it is important that teacher training courses promote experiences involving prospective teachers with this type of task. Based on this assumption, we intend to identify the activities that prospective primary school teachers perform in solving modelling tasks, the difficulties experienced in these tasks and the value of the models they determine. From the analysis of the resolutions of two tasks, we find that the prospective teachers translate the information of the data available in tables through graphs and analytical expressions. Some discuss models that determine which best fits the data. In the activities carried out, difficulties arise in determining the proportionality constant that best translates the problem situation, discussing the reasonableness of the values generated by the model, and sketching the graph of the model that best fits the experimental data. As for the usefulness of the model they determine, few prospective teachers are predicting outcomes.

A calibration method for monitoring bedload transport rate using Japanese pipe-type hydrophone considering installation condition and aging

<p>Observation of bedload is quite important for understanding temporal and spatial variation of sediment transport in mountainous regions. In government-owned mountain watersheds in Japan, Japanese pipe-type hydrophones (Hydrotech Co., Ltd.) have been installed as a surrogate monitoring tool since about 2009 and continuous observations have been conducted. According to positive correlation between sound pressure and bedload transport rate, observed sound pressure is used to be integrated with respect to time and its value is converted into bedload transport rate using proportionality constant. However, it remains challenging to obtain precise bedload transport rate with high accuracy, because we should consider the difference of the way to fix the hydrophone on river bed among installed sites, deformation of steel pipe due to collision of sediment particles, and the difference of initial performance and aging of microphone. Hence, we have to calibrate frequently the proportionality constant. In this study, we investigate a calibration method which is easily conducted by engineers. Because it takes time and effort to obtain time integral of sound pressure, we try to calibrate the proportionality constant with the maximum sound pressure, which can be obtained easily.</p>