Characterization and simulation of cDNA microarray spots using a novel mathematical model

<p>Abstract</p> <p>Background</p> <p>The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been suggested to increase the accuracy of microarray gene expression data, it is necessary to obtain reliable microarray images by improving wet-lab experiments. As the first step of a cDNA microarray experiment, spotting cDNA probes is critical to determining the quality of spot images.</p> <p>Results</p> <p>We developed a governing equation of cDNA deposition during evaporation of a drop in the microarray spotting process. The governing equation included four parameters: the surface site density on the support, the extrapolated equilibrium constant for the binding of cDNA molecules with surface sites on glass slides, the macromolecular interaction factor, and the volume constant of a drop of cDNA solution. We simulated cDNA deposition from the single model equation by varying the value of the parameters. The morphology of the resulting cDNA deposit can be classified into three types: a doughnut shape, a peak shape, and a volcano shape. The spot morphology can be changed into a flat shape by varying the experimental conditions while considering the parameters of the governing equation of cDNA deposition. The four parameters were estimated by fitting the governing equation to the real microarray images. With the results of the simulation and the parameter estimation, the phenomenon of the formation of cDNA deposits in each type was investigated.</p> <p>Conclusion</p> <p>This study explains how various spot shapes can exist and suggests which parameters are to be adjusted for obtaining a good spot. This system is able to explore the cDNA microarray spotting process in a predictable, manageable and descriptive manner. We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays.</p

Consequences of H-dimerization on the photophysics and photochemistry of oxacarbocyanines

The photophysical/photochemical behaviour of the monomers and the H dimers of four oxacarbocyanines (dyes D-G in the scheme) was investigated in water. In contrast with the usually observed effect of H dimerization, the dimers of dyes D-G were found to fluoresce with efficiencies comparable to or larger than those of the corresponding monomers. Analysis of the decay paths of the lowest excited singlet state showed, however, that dimerization causes a decrease of the radiative rate constants and an enhancement of intersystem crossing to the triplet manifold, as expected from application of exciton theory to a model H dimer. Twisting about one of the polymethine bonds contributes to the decay from the spectroscopic minimum of monomers, though yielding a rather small amount of a distorted cis isomer. The process is inhibited in dimers, likely due to a pronounced increase of activation energy connected with a loss of van der Waals attractive energy at the twisted geometry

The Eucalyptus Firewood: Understanding Consumers' Behaviour and Motivations

Italy is one of the world’s major importers of firewood, despite the large amount of Italian eucalyptus plantations that could satisfy part of the country’s internal demand. The demand is critical for farmers to understand developing market dynamics and people’s willingness to buy a product is related to several parameters, including different supply methods. This study aimed to analyse the willingness to consume domestic eucalyptus firewood, and the related motivations of consumers considering the preferred supply method. Data was collected through a web‐survey and analysed applying a multilevel regression. In general, the sample showed that attention is paid to both the type of wood and its origin, and that there is a preference for loose firewood as a supply method. Our findings suggest that factors such as age, experience, and familiarity with a product, the supply method, attitude towards novelty, provenience, and energetic density of firewood have an important role in shaping individual inclination towards consuming domestic eucalyptus firewood. This implies that the owners of eucalyptus plantations should target mostly young and detail‐oriented consumers, and should also try to clearly give information regarding the origin of the product and its technical characteristics

An Italian Explorative Study of Willingness to Pay for a New Functional Pasta Featuring Opuntia ficus indica

Opuntia ficus indica is a source of vitamins and minerals, and recently, it has been used as ingredient to make a new functional pasta. Italy produces the highest amount of pasta in the world and it is also the second-highest producer of opuntia globally. This study sought to identify the consumer willingness to pay for pasta featuring Opuntia ficus indica and to understand what factors influence their choice. This study is the first in food research to analyze consumers’ willingness to pay for a new functional pasta featuring Opuntia ficus indica. Data were collected by using a web-based survey; the sample was composed of 342 consumers and an ordered logistic regression model was applied. The findings showed that the educational and higher income levels of respondents play important roles in the willingness to pay for functional pasta. Moreover, the healthy and nutritional features of functional pasta together with the respondents’ willingness to eat it, their curiosity towards this new food and their need to get more information about functional pasta should improve consumers’ willingness to pay for it. The findings should be useful for firms to draw marketing strategies considering the positive consumers’ attitude toward the use of Opuntia ficus indica in pasta production

Italian Consumer Preferences for Eucalyptus Honey: An Exploratory Study

The growing concern for environmental issues has underlined the need to promote sustain able consumption and production. Taking into consideration the three pillars of sustainability, honey should be seen as an important food from a sustainability perspective. Among honey varieties, the eucalyptus one is becoming increasingly popular with people for its aroma and the plant’s therapeutic properties. However, the beekeeping sector in Italy does not yet have sufficient knowledge and understanding of consumer needs with a view to increasing earnings. This paper aimed to analyze the drivers that make people pick eucalyptus honey and tries to investigate which extrinsic and intrinsic quality attributes affect consumer behavior. Data came from an online survey of 403 Italian honey consumers. An ordered Probit model was applied. The results show that consumers consider the taste, viscosity, therapeutic properties, brand reputation, variety, geographical indication, Italian origin, and organic certification of honey as the most important factors that drive the consump tion of eucalyptus honey. The findings of the study should help the beekeepers and provide them with the right tools of communication, such as quality or sustainability labeling, thereby increasing their competitiveness

Solvent dependent iodide oxidation in metal-halide perovskite precursor solutions

Solar cell absorbing layers made of metal-halide perovskites (MHPs) are usually deposited from solution phase precursors, which is one of the reasons why these materials received huge research attention in the last few years. A detailed knowledge of the solution chemistry is critical to understand the formation of MHP thin films and thus to control their optoelectronic properties and the reproducibility issues that usually affect their synthesis. In this regard, the concentration of triiodide, I-3(-), is one factor known to have an influence on regulating important aspects such as the particle size in the solution and the defect concentration in the film. In this study, we highlight an underestimated source of I-3(-), namely the iodide salt solutions ubiquitously employed in MHP synthetic routes, which not only lead to the formation of I-3(-) but also detracts available I- for the MHP synthesis, thus establishing under-stoichiometric conditions. Particularly, we show how the oxidation of I- to I-3(-) changes in time with both the iodide salt counter-cation (K+, CH3NH3+) and the used solvent, meaning that variable quantities of I-3(-) are found depending on the synthesis conditions, with enhanced oxidation found in the gamma-butyrolactone (GBL) solvent. Though these differences are generally small, we shed light on a hidden and ever-present reaction which is likely to be related to the overall processing quality of MHP thin films