Innovative GenExpA software for selecting suitable reference genes for reliable normalization of gene expression in melanoma

The algorithms commonly used to select the best stable reference gene in RT-qPCR data analysis have their limitations. We showed that simple selection of the reference gene or pair of genes with the lowest stability value from the pool of potential reference genes—a commonly used approach—is not sufficient to accurately and reliably normalize the target gene transcript and can lead to biologically incorrect conclusions. For reliable assessment of changes in a target gene expression level, we propose our innovative GenExpA software, which works in a manner independent of the experimental model and the normalizer used. GenExpA software selects the best reference by combining the NormFinder algorithm with progressive removal of the least stable gene from the candidate genes in a given experimental model and in the set of daughter models assigned to it. The reliability of references is validated based on the consistency of the statistical analyses of normalized target gene expression levels through all models, described by the coherence score (CS). The use of the CS value imparts a new quality to qPCR analysis because it clarifies how low the stability value of reference must be in order for biologically correct conclusions to be drawn. We tested our method on qPCR data for the B4GALT genes family in melanoma, which is characterized by a high mutation rate, and in melanocytes. GenExpA is available at https://github.com/DorotaHojaLukowicz/GenExpA or https://www.sciencemarket.pl/baza-programow-open-source#oferty

Investigation of the processes accompanying ionbeam lithography of self-assembled organic monolayer

Litografia jonowa jest techniką stosowaną do wytwarzania nanostruktur, w której wykorzystuje się zogniskowaną wiązkę jonów do przeniesienia wzoru na modyfikowany materiał. W niniejszej pracy zastosowano modelowanie komputerowe metodą dynamiki molekularnej do symulacji procesów zachodzących podczas uderzenia pocisku w powierzchnię materiału. Porównano efektywność rozpylania wiązką klastrową (C60) oraz atomową (Bi) dla układów Au(111) i BP3/Au(111). Badania miały na celu odpowiedzenie na pytanie, która wiązka posiada lepsze własności pod kątem zastosowania w litografii jonowej. Na podstawie przeprowadzonych symulacji stwierdzono, że wiązka klastrowa posiada lepsze własności.Ion-beam Lithography is a technique applied to create nanostructures, which uses a focused ion beam to transfer the pattern to the material that is being modified. Molecular dynamics computer simulations have been used to model processes occurring during collisions of a keV projectile with the surface of the material. The effectiveness of sputtering induced by cluster (C60) and atomic (Bi) projectiles of Au (111) and BP3/Au (111) systems has been probed. The main goal of this study was to answer the question which beam is more appropriate for application in the ion-beam lithography. Based on the simulations it has been found that a beam composed from cluster projectiles has better properties

The research on the influence of modulus of elasticity and surface morphology on angular distributions of sputtered atoms from chosen metals in ion gas cluster litography

W niniejszej pracy zastosowano modelowanie komputerowe metodą dynamiki molekularnej do symulacji procesów zachodzących podczas uderzenia gazowego pocisku klastrowego w powierzchnię wybranych metali. Przeprowadzone badania miały na celu odpowiedzenie na pytanie dlaczego rozkłady kątowe molibdenu różnią się od wyników dla innych metali. Na podstawie przeprowadzonych symulacji stwierdzono, że decydujący wpływ ma morfologia powierzchni.Molecular dynamics computer simulations have been used to model processes occurring during collisions of a ion gas cluster with the surface of selected metals. The aim this study is to explain why angular distributions of atoms sputtered from molibdenium differ from results for other metals. Conducted computer simulations have shown that surface morphology is a determining factor

A Review on Optimization of Active Power Filter Placement and Sizing Methods

Distortions of current and voltage waveforms from a sinusoidal shape are, not only a source of technical problems, but also have serious economic effects. Their occurrence is related to the common use of loads with nonlinear current-voltage characteristics. These are both high-power loads (most often power electronic switching devices supplying high-power drives), but also widely used low-power loads (power supplies, chargers, energy-saving light sources). The best way to eliminate these distortions is to use active power filters. The cost of these devices is relatively high. Therefore, scientists all over the world are conducting research aimed at developing techniques for the proper placement of these devices, in order to minimize their investment costs. The best solution to this problem is to use optimization techniques. This paper compares the methods and criteria used by the authors of publications dealing with this topic. The summary also indicates a possible direction for further work

A Review on Optimization of Active Power Filter Placement and Sizing Methods

Distortions of current and voltage waveforms from a sinusoidal shape are, not only a source of technical problems, but also have serious economic effects. Their occurrence is related to the common use of loads with nonlinear current-voltage characteristics. These are both high-power loads (most often power electronic switching devices supplying high-power drives), but also widely used low-power loads (power supplies, chargers, energy-saving light sources). The best way to eliminate these distortions is to use active power filters. The cost of these devices is relatively high. Therefore, scientists all over the world are conducting research aimed at developing techniques for the proper placement of these devices, in order to minimize their investment costs. The best solution to this problem is to use optimization techniques. This paper compares the methods and criteria used by the authors of publications dealing with this topic. The summary also indicates a possible direction for further work