Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA – a Bayesian approach

<p>Abstract</p> <p>Background</p> <p>Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge.</p> <p>Results</p> <p>A computing tool (ArrayLeaRNA) has been developed for gene expression analysis. It implements a Bayesian approach which is based on the Gumbel distribution and uses printed genomic DNA control features for normalization and for estimation of the parameters of the Bayesian model and prior knowledge from predicted operon structure. The method is compared with two other approaches: the classical LOWESS normalization followed by a two fold cut-off criterion and the OpWise method (Price, et al. 2006. BMC Bioinformatics. 7, 19), a published Bayesian approach also using predicted operon structure. The three methods were compared on experimental datasets with prior knowledge of gene expression. With ArrayLeaRNA, data normalization is carried out according to the genomic features which reflect the results of equally transcribed genes; also the statistical significance of the difference in expression is based on the variability of the equally transcribed genes. The operon information helps the classification of genes with low confidence measurements.</p> <p>ArrayLeaRNA is implemented in Visual Basic and freely available as an Excel add-in at <url>http://www.ifr.ac.uk/safety/ArrayLeaRNA/</url></p> <p>Conclusion</p> <p>We have introduced a novel Bayesian model and demonstrated that it is a robust method for analysing microarray expression profiles. ArrayLeaRNA showed a considerable improvement in data normalization, in the estimation of the experimental variability intrinsic to each hybridization and in the establishment of a clear boundary between non-changing and differentially expressed genes. The method is applicable to data derived from hybridizations of labelled cDNA samples as well as from hybridizations of labelled cDNA with genomic DNA and can be used for the analysis of datasets where differentially regulated genes predominate.</p

Hierarchically organized Li-Al-LDH nano-flakes: a low-temperature approach to seal porous anodic oxide on aluminum alloys

This work suggests a low-temperature sealing approach for tartaric–sulfuric acid (TSA) anodized AA2024 based on hierarchically organized Li–Al-layered double hydroxide (LDH) structures. The new proposed sealing is expected to be directly competitive to the standard hot water sealing (HWS) approaches because of its reduced treatment temperature and high protection efficiency. A hierarchical organization of in situ formed LDH nano-flakes across the depth length of the TSA pores, from the macrodown to the nano-size range, was observed with transmission electron microscopy (TEM). Electrochemical impedance spectroscopy (EIS) studies showed that the densely packed LDH arrangement at the porous oxide layer is directly related to the drastically improved barrier properties of TSA. Moreover, LDH flakelike structures worked as “smart” reservoirs for corrosion inhibiting vanadium species (VOx) that are released on demand upon the onset of corrosion. This was confirmed using a scanning vibrating electrode technique (SVET), giving relevant insights into the time-resolved release activity of VOx and the formation of the passivation layer on cathodic intermetallics, corroborated with EDX and analytical Raman spectroscopy. Passive and active corrosion protection was imparted to the anodic layer via new Li–Al-LDH structures with long-term protection exceeding that of standard HWS procedures.This work has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement no. 645676 project MULTISURF. Dr M. Mohedano is grateful to MICINN (Spain) for nancial support via Proyecto Retos Jovenes Investigadores MAT2015-73355-JIN. Dr S. V. Lamaka acknowledges the nancial support of Alexander von Humboldt Foundation via Experienced Researcher Grant. Dr J. Tedim thanks FCT for the researcher grant IF/00347/2013. This work was developed in the scope of the project CICECO – Aveiro Institute of Materials, POCI-01-0145-FEDER-007679 (Ref. FCT UID/CTM/50011/2013), nanced by national funds through the FCT/MEC and when applicable co-nanced by FEDER under the PT2020 Partnership Agreement. Dr D. Mata would like to thank Dr Nico Scharnagl for the Raman scientic discussions. Authors acknowledge Mr Maksim Starykevich for carrying out the GDOES analyses

Natural Organic Matter Removal by Heterogeneous Catalytic Wet Peroxide Oxidation (CWPO)

NOM usually reaches drinking water supply sources through metabolic reactions and soil leaching. It has been, in general, considered that NOM is still one of the most problematic contaminants present in this kind of influents. Therefore, in the present chapter, most relevant technologies used for removal of NOM and its constituents from water have been examined, emphasizing in the past few years. An overview of the recent research studies dealing the NOM removal by catalytic wet peroxide oxidation and other closely related heterogeneous Fenton-like AOPs is presented. As revealed from recent literature reports, heterogeneous Fenton processes including CWPO are still emerging, promising catalytic technologies for NOM removal from water. A wide variety of catalytic solids reported within the past few years has been examined focusing on their potential in the NOM removal from water. Main findings offered by several types of catalysts like zeolites, Fe-functionalized activated carbons, carbon nanotubes, but mainly pillared and other clay minerals have been critically discussed emphasizing on the NOM removal by CWPO