An experimental evaluation of a loop versus a reference design for two-channel microarrays

Motivation: Despite theoretical arguments that socalled "loop designs" of two-channel DNA microarray experiments are more efficient, biologists keep on using "reference designs". We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicor). In each case, both a loop and a reference design were performed using the same RNA preparations with the aim to study their relative efficiency. Results: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example by taking log-ratios or including spot-effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice

In-water lidar simulations: the ALADIN ADM-Aeolus backscattered signal at 355 nm

The Lidar Ocean Color (LiOC) Monte Carlo code has been developed to simulate the in-water propagation of the lidar beam emitted by the ALADIN ADM-Aeolus instrument in the ultraviolet (UV) spectral region (∼ 355 nm). To this end, LiOC accounts for reflection/transmission processes at the sea surface, absorption and multiple scattering in the water volume, and reflection from the sea bottom. The water volume components included in the model are pure seawater, Chlorophyll-a concentration (Chl-a), Colored Dissolved Organic Matter (CDOM), and/or a generic absorbing species. By considering the transmission/reception measurement geometry of ALADIN ADM-Aeolus, the study documents the variability of the normalized backscattered signal in different bio-optical conditions. The potential for data product retrieval based on information at 355 nm is considered by developing a demonstrative lookup table to estimate the absorption budget exceeding that explained by Chl-a. Results acknowledge the interest of space programs in exploiting UV bands for ocean color remote sensing, as, for instance, addressed by the PACE mission of NASA

Validation of standard and alternative satellite ocean-color chlorophyll products off Western Iberia

Chlorophyll a concentration (Chl) product validation off theWestern Iberian coast is here undertaken by directly comparing remote sensing data with in situ surface reference values. Both standard and recently developed alternative algorithms are considered for match-up data analysis. The investigated standard products are those produced by the MERIS (algal 1 and algal 2) and MODIS (OC3M) algorithms. The alternative data products include those generatedwithin the CoastColour Project and Ocean Color Climate Change Initiative (OC-CCI) funded by ESA, as well as a neural net model trained with field measurements collected in the Atlantic off Portugal (MLPATLP). Statistical analyses showed that satellite Chl estimates tend to be larger than in situ reference values. The study also revealed that a non-uniform Chl distribution in the water column can be a concurring factor to the documented overestimation tendency when considering larger optical depth match-up stations. Among standard remote sensing products, MODIS OC3M and MERIS algal 2 yield the best agreement with in situ data. The performance of MLPATLP highlights the capability of regional solutions to further improve Chl retrieval by accounting for environmental specificities. Results also demonstrate the relevance of oceanographic regions such as the Nazaré area to evaluate how complex hydrodynamic conditions can influence the quality of Chl products.This studywas performed in the framework of HabSpot FCT Project, PTDC/MAR/100348/2008 and European Space Agency projects DUE CoastColour (ESRIN/AO/1-6141/09/l-EC) and Climate Change Iniciative — Ocean Color (AO-1/6207/09/I-LG). The work has been also partially supported by the European Space Agency within the framework of the MERIS Validation Activities under contract n. 12595/09/I-OL, and sampling activities benefited from European projects HERMES (GOCE-CT-2005-511234) and Hermione (EC contract 226354) support. We would like to thank NASA OBPG for the MODIS data and ESA Project AOPT-2423 for providing MERIS full resolution images. Ana C. Brito was funded by a Portuguese Post-doc grant from FCT (BPD/63017/2009) and by the Investigador FCT Program (IF/00331/2013). Davide D'Alimonte was funded by Investigador FCT Program (IF/00541/2013).info:eu-repo/semantics/publishedVersio

Exploring the potential of Aeolus lidar mission for ocean color applications

The Atmospheric Laser Doppler Instrument (ALADIN) onboard the Aeolus wind mission was the first High Spectral Resolution Lidar operating in the Ultra Violet (UV) region deployed in space. This study explores and documents the feasibility of deriving ocean optical properties using data from ALADIN. A three steps (i.e. data screening, analytical estimation of the total in-water signal contribution, Look Up Table-based estimation of the in-water attenuation) retrieval algorithm was developped combining data analysis and signal simulations from a radiative transfer model. The algorithm has been implemented using the signal acquired by the Mie channel, and tested for 1-year of Aeolus observations. This approach allowed estimating the first Aeolus derived Ocean Color (OC) products in terms of the total in-water signal contribution and the in-water attenuation term in a spectral region (355 nm) not covered, during Aeolous lifetime, by operational OC products. The validation process involved comparing these products with both Biogeochemical-Argo (BGC-Argo) field measurements and satellite OC dataset distributed by ESA Ocean Color Climate Change Initiative across a set of 7 selected oceanic regions representing diverse open-ocean scenarios. These validation exercises attested the general accordance between OC reference measurements and the proposed Aeolus OC parameters. Thus, this study was able to provide statistical evidence of the sensitivity of the retrieved Aeolus in-water lidar attenuation term to the CDOM variability on a temporal/seasonal and spatial/regional basis. A preliminary estimation of the uncertainty associated to the retrieved quality controlled Klid, was performed assuming the radiometric noise as unique source of uncertainty. As a result, a median/average value of absolute relative percent difference of about 50/80% was obtained. Limits of the developed technique, possible improvements, potential adaptation to planned/future space lidar missions are discussed

Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue

<p>Abstract</p> <p>Background</p> <p>Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial for revealing interesting gene expression patterns and functional relationships of coexpressed genes. Such screening helps to gain deeper insights into regulatory behavior and cellular responses, as will be discussed for expression data of developing barley endosperm tissue. For that purpose, high-throughput multidimensional scaling (HiT-MDS), a recent method for similarity-preserving data embedding, is substantially refined and used for (a) assessing the quality and reliability of centroid gene expression patterns, and for (b) derivation of functional relationships of coexpressed genes of endosperm tissue during barley grain development (0–26 days after flowering).</p> <p>Results</p> <p>Temporal expression profiles of 4824 genes at 14 time points are faithfully embedded into two-dimensional displays. Thereby, similar shapes of coexpressed genes get closely grouped by a correlation-based similarity measure. As a main result, by using power transformation of correlation terms, a characteristic cloud of points with bipolar sandglass shape is obtained that is inherently connected to expression patterns of pre-storage, intermediate and storage phase of endosperm development.</p> <p>Conclusion</p> <p>The new HiT-MDS-2 method helps to create global views of expression patterns and to validate centroids obtained from clustering programs. Furthermore, functional gene annotation for developing endosperm barley tissue is successfully mapped to the visualization, making easy localization of major centroids of enriched functional categories possible.</p

Comparing and Contrasting the Uses of Two Graphical Tools for Displaying Patterns of Multi-Party Competition

The article aims at comparing two tools for displaying, in graphical form, information about vote outcomes in multiparty elections at the constituency level. One was proposed by Nagayama and introduced to the English-speaking world by Reed, who applied this method to Japanese and Italian election data. Reed labels the method Nagayama diagrams. Recently, Taagepera has shown how the domain of potential uses of Nagayama diagrams can be expanded significantly. A second graphical device has been used by a number of authors for various types of election analyses, but is not that well known in the comparative parties literature. This method, which uses barycentric coordinates (i.e. triangular) rather than the more familiar rectangular coordinates, has gone under a variety of names (e.g. trilinear plot, toroidal diagram and simplex representation): In this work both methods tare used to visually present election data (by constituency) for the Italian national elections of 1994, 1996 and 2001. It is shown how different types of information may be readily gleaned from the two types of graph, and, perhaps most importantly, the paper illustrates how it I spossible to improve the ready intuitive interpretability of each type of graph by specifying boundary constraints to define particular regions of the graph \u2013 a technique called \u2018segmentation\u2019

Comparing and contrasting the uses of two graphical tools for displaying patterns of multiparty competition: Nagayama diagrams and simplex representations

4sìWe compare two tools for displaying, in graphical form, information about vote outcomes in multiparty elections at the constituency level. One was recently proposed by Nagayama and introduced to the English-speaking world by Reed, who applied this method to Japanese and Italian election data. Reed labels the method Nagayama diagrams. Recently, Taagepera has shown how the domain of potential uses of Nagayama diagrams can be expanded significantly. A second graphical device has been used by a number of authors for various types of election analyses, but is not that well known in the comparative parties literature. This method, which uses barycentric coordinates (i.e. triangular) rather than the more familiar rectangular coordinates, has gone under a variety of names (e.g. trilinear plot, toroidal diagram and simplex representation), but we have chosen to use the last of these labels. We make use of both methods to visually present election data (by constituency) for the Italian national elections of 1994, 1996 and 2001. We show how different types of information may be readily gleaned from the two types of graph, and, perhaps most importantly, illustrate how we may improve the ready intuitive interpretability of each type of graph by specifying boundary constraints to define particular regions of the graph - a technique we call 'segmentation'.reservedmixedB. GROFMAN;A. CHIARAMONTE;R. D'ALIMONTE;S. FELDB., Grofman; A., Chiaramonte; D'Alimonte, Roberto; S., Fel