Application of a correlation correction factor in a microarray cross-platform reproducibility study

Background Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations. Results In this paper, three technical replicate microarrays were hybridized to each of three platforms. The three platforms were then analyzed to assess both intra- and cross-platform reproducibility. We present various methods for examining intra-platform reproducibility. We also examine cross-platform reproducibility using Pearson\u27s correlation. Additionally, we previously developed a correction factor for Pearson\u27s correlation which is applicable when X and Y are measured with error. Herein we demonstrate that correcting for measurement error by estimating the disattenuated correlation substantially improves cross-platform correlations. Conclusion When estimating cross-platform correlation, it is essential to thoroughly evaluate intra-platform reproducibility as a first step. In addition, since measurement error is present in microarray gene expression data, methods to correct for attenuation are useful in decreasing the bias in cross-platform correlation estimates

Synthesis, structure, and opto-electronic properties of organic-based nanoscale heterojunctions

Enormous research effort has been put into optimizing organic-based opto-electronic systems for efficient generation of free charge carriers. This optimization is mainly due to typically high dissociation energy (0.1-1 eV) and short diffusion length (10 nm) of excitons in organic materials. Inherently, interplay of microscopic structural, chemical, and opto-electronic properties plays crucial role. We show that employing and combining advanced scanning probe techniques can provide us significant insight into the correlation of these properties. By adjusting parameters of contact- and tapping-mode atomic force microscopy (AFM), we perform morphologic and mechanical characterizations (nanoshaving) of organic layers, measure their electrical conductivity by current-sensing AFM, and deduce work functions and surface photovoltage (SPV) effects by Kelvin force microscopy using high spatial resolution. These data are further correlated with local material composition detected using micro-Raman spectroscopy and with other electronic transport data. We demonstrate benefits of this multi-dimensional characterizations on (i) bulk heterojunction of fully organic composite films, indicating differences in blend quality and component segregation leading to local shunts of photovoltaic cell, and (ii) thin-film heterojunction of polypyrrole (PPy) electropolymerized on hydrogen-terminated diamond, indicating covalent bonding and transfer of charge carriers from PPy to diamond

Cellobiose Dehydrogenase Aryl Diazonium Modified Single Walled Carbon Nanotubes: Enhanced Direct Electron Transfer through a Positively Charged Surface

One of the challenges in the field of biosensors and biofuel cells is to establish a highly efficient electron transfer rate between the active site of redox enzymes and electrodes to fully access the catalytic potential of the biocatalyst and achieve high current densities. We report on very efficient direct electron transfer (DET) between cellobiose dehydrogenase (CDH) from Phanerochaete sordida (PsCDH) and surface modified single walled carbon nanotubes (SWCNT). Sonicated SWCNTs were adsorbed on the top of glassy carbon electrodes and modified with aryl diazonium salts generated in situ from p-aminobenzoic acid and p-phenylenediamine, thus featuring at acidic pH (3.5 and 4.5) negative or positive surface charges. After adsorption of PsCDH, both electrode types showed excellent long-term stability and very efficient DET. The modified electrode presenting p-aminophenyl groups produced a DET current density of 500,mu A cm(-2) at 200 mV vs normal hydrogen reference electrode (NHE) in a 5 mM lactose solution buffered at pH 3.5. This is the highest reported DET value so far using a CDH modified electrode and comes close to electrodes using mediated electron transfer. Moreover, the onset of the electrocatalytic current for lactose oxidation started at 70 mV vs NHE, a potential which is 50 mV lower compared to when unmodified SWCNTs were used. This effect potentially reduces the interference by oxidizable matrix components in biosensors and increases the open circuit potential in biofuel cells. The stability of the electrode was greatly increased compared with unmodified but cross-linked SWCNTs electrodes and lost only 15% of the initial current after 50 h of constant potential scanning

Transdisciplinary sustainability: the Council for Frontiers of Knowledge

This paper introduces the work and diversity of the Council for Frontiers of Knowledge (CFK). In a series of vignettes relating to the intellectual interests of some of the leading academics working with the CFK, both the mission and the trans- disciplinary oversight of the agency are explored

Electrospinning and stabilization of fully hydrolyzed poly(vinyl alcohol) fibers

Fully (99+ %) hydrolyzed poly(vinyl alcohol) (PVA) was electrospun from water using Triton X-100 surfactant to lower the surface tension. The diameter of the electrospun PVA fibers ranged from 100 to 700 nm. Treatment of the PVA fiber mats with methanol for 8 h stabilized the fibers against disintegration in contact with water. In addition, the mats showed increased mechanical strength due to increased crystallinity following post-spinning treatment with methanol. We suggest that methanol treatment serves to increase the degree of crystallinity, and hence the number of physical cross-links in the electrospun PVA fibers. This may occur by removal of residual water within the fibers by the alcohol, allowing PVA - water hydrogen bonding to be replaced by intermolecular polymer hydrogen bonding resulting in additional crystallization. Potential applications of electrospun PVA include filters, precursors to graphitic fibers, and biomedical materials

Application of a correlation correction factor in a microarray cross-platform reproducibility study-5

<p><b>Copyright information:</b></p><p>Taken from "Application of a correlation correction factor in a microarray cross-platform reproducibility study"</p><p>http://www.biomedcentral.com/1471-2105/8/447</p><p>BMC Bioinformatics 2007;8():447-447.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2211756.</p><p></p>on among the three platforms

Application of a correlation correction factor in a microarray cross-platform reproducibility study-3

<p><b>Copyright information:</b></p><p>Taken from "Application of a correlation correction factor in a microarray cross-platform reproducibility study"</p><p>http://www.biomedcentral.com/1471-2105/8/447</p><p>BMC Bioinformatics 2007;8():447-447.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2211756.</p><p></p> to the 1,288 genes in common among the three platforms

Application of a correlation correction factor in a microarray cross-platform reproducibility study-0

<p><b>Copyright information:</b></p><p>Taken from "Application of a correlation correction factor in a microarray cross-platform reproducibility study"</p><p>http://www.biomedcentral.com/1471-2105/8/447</p><p>BMC Bioinformatics 2007;8():447-447.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2211756.</p><p></p> to the 1,288 genes in common among the three platforms

Application of a correlation correction factor in a microarray cross-platform reproducibility study-1

<p><b>Copyright information:</b></p><p>Taken from "Application of a correlation correction factor in a microarray cross-platform reproducibility study"</p><p>http://www.biomedcentral.com/1471-2105/8/447</p><p>BMC Bioinformatics 2007;8():447-447.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2211756.</p><p></p>n among the three platforms