Mathematical Linear Programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer.

Genes are transcribed into various RNA molecules, and a portion of them called messenger RNA (mRNA) is then translated into proteins in the process known as gene expression. Gene expression is a high-energy demanding process, and aberrant expression changes often manifest into pathophysiology. Therefore, gene expression is tightly regulated by several factors at different levels. MicroRNAs (miRNAs) are one of the powerful post-transcriptional regulators involved in key biological processes and diseases. They inhibit the translation of their mRNA targets or degrade them in a sequence-specific manner, and hence control the rate of protein synthesis. In recent years, in response to experimental limitations, several computational methods have been proposed to predict miRNA target genes based on sequence complementarity and structural features. However, these predictions yield a large number of false positives. Integration of gene and miRNA expression data drastically alleviates this problem. Here, I describe a mathematical linear modeling approach to identify miRNA targets at the genome scale using gene and miRNA expression data. Mathematical modeling is faster and more scalable to genome-level compared to conventional statistical modeling approaches.

Optimum contribution for mate selection in Santa Inês sheep

The objective of this research was to simulate the genetic gains expected comparing random mating strategies and mate selection by optimum contribution with different penalty levels in the inbreeding rate of Santa Inês sheep. The optimum contribution theory was thus applied to optimize genetic gain in the long term in twelve selection groups by selectively mating 500 females with the respective males, increasingly penalizing the increase in inbreeding in the objective function. Genetic algorithms were used to find the optimum contribution. Optimization was achieved via EVA software. Selection candidates had their contribution defined into four treatments, using different values to weigh the genetic merit and penalize increases in inbreeding. This made it possible to measure the degree of control over those parameters that can be obtained with this methodology. This selection offers different levels of genetic gain, which are achievable from restrictions on the coancestry. The number of males selected and their distribution into selection groups varied according to the penalty attributed to inbreeding in the objective function. Mate selection using optimum contribution should be adopted when aiming to limit the increase in inbreeding. Increasing the exchange of genetic material between groups is recommended to elevate genetic gain and maintain control over inbreeding.

A comparative energy and exergy optimization of a supercritical-CO2 Brayton cycle and Organic Rankine Cycle combined system using swarm intelligence algorithms.

This article presents a multivariable optimization of the energy and exergetic performance of a power generation system, which is integrated by a supercritical Brayton Cycle using carbon dioxide, and a Simple Organic Rankine Cycle (SORC) using toluene, with reheater ( S - C O 2 R H - S O R C ), and without reheater ( S - C O 2 N R H - S O R C ) using the PSO algorithm. A thermodynamic model of the integrated system was developed from the application of mass, energy and exergy balances to each component, which allowed the calculation of the exergy destroyed a fraction of each equipment, the power generated, the thermal and exergetic efficiency of the system. In addition, through a sensitivity analysis, the effect of the main operational and design variables on thermal efficiency and total exergy destroyed was studied, which were the objective functions selected in the proposed optimization. The results show that the greatest exergy destruction occurs at the thermal source, with a value of 97 kW for the system without Reheater (NRH), but this is reduced by 92.28% for the system with Reheater (RH). In addition, by optimizing the integrated cycle for a particle number of 25, the maximum thermal efficiency of 55.53% (NRH) was achieved, and 56.95% in the RH system. Likewise, for a particle number of 15 and 20 in the PSO algorithm, exergy destruction was minimized to 60.72 kW (NRH) and 112.06 kW (RH), respectively. Comparative analyses of some swarm intelligence optimization algorithms were conducted for the integrated S-CO2-SORC system, evaluating performance indicators, where the PSO optimization algorithm was favorable in the analyses, guaranteeing that it is the ideal algorithm to solve this case study.