Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation

BACKGROUND: Publicly accessible EST libraries contain valuable information that can be utilized for studies of tissue-specific gene expression and processing of individual genes. This information is, however, confounded by multiple systematic effects arising from the procedures used to generate these libraries. RESULTS: We used alignment of ESTs against a reference set of transcripts to estimate the size distributions of the cDNA inserts and sampled mRNA transcripts in individual EST libraries and show how these measurements can be used to inform quantitative comparisons of libraries. While significant attention has been paid to the effects of normalization and substraction, we also find significant biases in transcript sampling introduced by the combined procedures of reverse transcription and selection of cDNA clones for sequencing. Using examples drawn from studies of mRNA 3'-processing (cleavage and polyadenylation), we demonstrate effects of the transcript sampling bias, and provide a method for identifying libraries that can be safely compared without bias. All data sets, supplemental data, and software are available at our supplemental web site [1]. CONCLUSION: The biases we characterize in the transcript sampling of EST libraries represent a significant and heretofore under-appreciated source of false positive candidates for tissue-, cell type-, or developmental stage-specific activity or processing of genes. Uncorrected, quantitative comparison of dissimilar EST libraries will likely result in the identification of statistically significant, but biologically meaningless changes

Study of the Far Wake of a Large Ship

A large dataset of high-resolution photographic images of far wakes of a volunteer observing ship (Royal Caribbean’s Explorer of the Seas) has been acquired under various meteorological conditions and ship operation modes. This work presents the description of instrumentation, methodology, and the results of the experiment. Environmental and ship operation factors that affect appearance and geometric properties of ship wakes in photographic and satellite-based radar images have been analyzed. The photo imagery reveals an asymmetry of the wake depending on wind direction relative to the ship course. In addition, a good agreement between the averaged shape of the wakes measured from the photographic images and a few available satellite-based radar images of the wake of the same ship has been found

Performance Evaluation of Vision-Based Algorithms for MAVs

An important focus of current research in the field of Micro Aerial Vehicles (MAVs) is to increase the safety of their operation in general unstructured environments. Especially indoors, where GPS cannot be used for localization, reliable algorithms for localization and mapping of the environment are necessary in order to keep an MAV airborne safely. In this paper, we compare vision-based real-time capable methods for localization and mapping and point out their strengths and weaknesses. Additionally, we describe algorithms for state estimation, control and navigation, which use the localization and mapping results of our vision-based algorithms as input.Comment: Presented at OAGM Workshop, 2015 (arXiv:1505.01065

Validation and assimilation of Seasat altimeter wave heights using the WAM wave model

The mutual consistency of the Seasat global data sets of scatterometer winds and altimeter wave heights is investigated for the complete Seasat period using the third-generation wave model WAM. The wave model was driven by surface (1000 hPa) wind and surface stress fields constructed by the Goddard Laboratory for Atmospheres (GLA) by assimilation of the scatterometer winds in an atmospheric model. For the 10-day period September 7?17 the intercomparison was extended to two further scatterometer wind fields: a 1000-hPa assimilated wind field from the European Centre for Medium-Range Weather Forecasts and a subjectively analyzed 19.5-m-height surface wind field from the Jet Propulsion Laboratory. On the global average, the modeled and observed wave heights agree reasonably well. Regional differences, however, can be large and sometimes exceed 40%. The errors are attributed mainly to deficiencies in the forcing wind fields. Low wind speeds are found to be overestimated and high wind speeds underestimated by the Seasat scatterometer algorithm. The friction velocities of the GLA model are found to be significantly underestimated in the high-wind belt of the southern hemisphere. The analysis demonstrates the diagnostic advantages of applying a wave model for the quality assessment of satellite wind and wave data. A preliminary wave data assimilation scheme is presented in which the wave field is updated without changing the forcing wind field. A considerable improvement of the computed wave field is achieved, particularly in regions in which the wave energy is dominated by swell. However, a more general assimilation scheme including modifications of the wind field is needed to upgrade wind sea forecasts

A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif

BACKGROUND: The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to identify and extract large sets of putative 3'-processing sites for mRNA from ten metazoan species, including Homo sapiens, Canis familiaris, Rattus norvegicus, Mus musculus, Gallus gallus, Danio rerio, Takifugu rubripes, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans. In order to further delineate the details of the mRNA-protein interaction, we obtained and multiply aligned CstF-64 protein sequences from the same species. RESULTS: We characterized the sequence content and specific positioning of putative DSEs across the range of organisms studied. Our analysis characterized the downstream element (DSE) as two distinct parts – a proximal UG-rich element and a distal U-rich element. We find that while the U-rich element is largely conserved in all of the organisms studied, the UG-rich element is not. Multiple alignment of the CstF-64 RNA recognition motif revealed that, while it is highly conserved throughout metazoans, we can identify amino acid changes that correlate with observed variation in the sequence content and positioning of the DSEs. CONCLUSION: Our analysis confirms the early reports of separate U- and UG-rich DSEs. The correlated variations in protein sequence and mRNA binding sequences provide novel insights into the interactions between the precursor mRNA and the 3'-processing machinery

Reactive Crystallization Kinetics of K2SO4 from Picromerite-Based MgSO4 and KCl

In this work, the kinetic parameters, the degrees of initial supersaturation (S0) and the profiles of supersaturation (S) were determined for the reactive crystallization of K2SO4 from picromerite (K2SO4.MgSO4.6H2O) and KCl. Different reaction temperatures between 5 and 45 °C were considered, and several process analytical techniques were applied. Along with the solution temperature, the crystal chord length distribution (CLD) was continuously followed by an FBRM probe, images of nucleation and growth events as well as the crystal morphology were captured, and the absorbance of the solution was measured via ATR-FTIR spectroscopy. In addition, the ion concentrations were analyzed. It was found that S0 is inversely proportional to the reactive crystallization temperature in the K+, Mg2+/Cl−, SO42−//H2O system at 25 °C, where S0 promotes nucleation and crystal growth of K2SO4 leading to a bimodal CLD. The CLD was converted to square-weighted chord lengths for each S0 to determine the secondary nucleation rate (B), crystal growth rate (G), and suspension density (MT). By correlation, from primary nucleation rate (Bb) and G with S0, the empirical parameters b = 3.61 and g = 4.61 were obtained as the order of primary nucleation and growth, respectively. B versus G and MT were correlated to the reaction temperature providing the rate constants of B and respective activation energy, E = 69.83 kJ∙mol−1. Finally, a general Equation was derived that describes B with parameters KR = 13,810.8, i = 0.75 and j = 0.71. The K2SO4 crystals produced were of high purity, containing maximal 0.51 wt% Mg impurity, and were received with ~73% yield at 5 °C

Synthesis and spectral studies of 5-[3-(1,2,4-triazolyl-azo]-2,4-dihydroxybenzaldehyde(TA)and its Schiff bases with 1,3-diaminopropane(TAAP)and 1,6-diaminohexane(TAAH).Their analytical application for spectrophotometric microdetermination of cobalt(II).

Cataloged from PDF version of article.The new azo compound 5-[3-(1,2,4-triazolyl-azo]-2,4-dihydroxy-benzaldehyde (TA) and its Schiff bases with 1,3-diaminopropane (TAAP) and 1,6-diaminohexane (TAAH) have been synthesized. The bands of diagnostic importance in the IR and the main signals in 1 H NMR spectra are assigned. The electronic absorption spectra in pure organic solvents of different polarity and in buffer solutions of varying pH are investigated. The quantitative description of the solvent effect on the electronic absorption spectra is studied and their acid ionization constants are determined. Also, a new simple and sensitive method for the spectrophotometric microdetermination of Co(II) using these compounds (TA, TAAP and TAAH) as new chromogenic reagents is established. The developed method is successfully used for the determination of trace amounts of cobalt in authentic samples and calculation of the distribution ratio of cobalt adsorbed on bentonite and kaolinite clay minerals. 2004 Elsevier Ltd. All rights reserved

Are patient-centered care values as reflected in teaching scenarios really being taught when implemented by teaching faculty? A discourse analysis on an Indonesian medical school's curriculum

<p>Abstract</p> <p>Background</p> <p>According to The Indonesian Medical Council, 2006, Indonesian competence-based medical curriculum should be oriented towards family medicine. We aimed to find out if the educational goal of patient-centered care within family medicine (comprehensive care and continuous care) were adequately transferred from the expected curriculum to implemented curriculum and teaching process.</p> <p>Methods</p> <p>Discourse analysis was done by 3 general practitioners of scenarios and learning objectives of an Indonesian undergraduate medical curriculum. The coders categorized those sentences into two groups: met or unmet the educational goal of patient-centered care.</p> <p>Results</p> <p>Text analysis showed gaps in patient-centered care training between the scenarios and the learning objectives which were developed by both curriculum committee and the block planning groups and the way in which the material was taught. Most sentences in the scenarios were more relevant to patient-centered care while most sentences in the learning objectives were more inclined towards disease-perspectives.</p> <p>Conclusions</p> <p>There is currently a discrepancy between expected patient-centered care values in the scenario and instructional materials that are being used.</p

Staphylococcus aureus und seine Genotypen als Mastitiserreger der Milchkuh – eine Übersicht

INTRODUCTION In the last decade the knowledge on Staphylococcus aureus as the etiologic agent of chronic mastitis in dairy cattle has increased. Molecular biology and increasingly whole genome sequencing provide an advanced technology far beyond the classical, phenotypic bacteriology. Staphylococcus aureus has different characteristics, thus clinical and epidemiological properties are massively dependent on the genotypes. In Switzerland, Staphylococcus aureus genotype B (GTB) is a common genotype that causes infectious mastitis. Often, half and more cows of the herd are infected. Conversely, genotype C (GTC) and some of the other Staphylococcus aureus genotypes are classified less problematic because they affect individual cows and only one mammary gland quarter. Since Staphylococcus aureus GTB causes herd problems, the associated costs are high in the dairy industry. This applies in particular in the alpine region, because GTB-positive and -negative cows are not separated during milking and the infectious pathogen can spread rapidly. The pathogen is transferred by contaminated milking liners. Staphylococcus aureus GTB is highly associated with the mammary gland. In contrast, the skin and the udder are identified as the reservoir for Staphylococcus aureus GTC and the other genotypes. Staphylococcus aureus GTC is a classic infectious pathogen in wounds and occasionally in mammary glands.Im letzten Jahrzehnt konnte viel neues Wissen zu Sta-phylococcus aureus als Mastitiserreger der Milchkuh erar-beitet werden. Dies hat vor allem damit zu tun, dass mit der Molekularbiologie und zunehmend auch mit der Vollgenomsequenzierung und der Bioinformatik völlig neue Analyseverfahren zur Verfügung stehen, die weit über diejenigen der klassischen, phänotypischen Bakte-riologie hinausgehen. Staphylococcus aureus ist nicht mehr ein Bakterium mit den immer gleichen Eigen-schaften, vielmehr hängen die klinischen und epidemio-logischen Eigenschaften massiv von den Genotypen von Staphylococcus aureus ab. In der Schweiz ist Staphylococcus aureus Genotyp B (GTB) der einzige Genotyp, der bei der Kuh ansteckende Mastitiden verursacht. Dabei sind oft die Hälfte und mehr Kühe eines Betriebes infiziert. Dagegen verursachen Genotyp C (GTC) und alle an-dern Genotypen in der Schweiz ausschliesslich Einzelviertelerkrankungen bei einzelnen Kühen. Da Staphylococcus aureus GTB Herdenprobleme verursacht, sind die damit verbundenen Kosten in der Milchwirt-schaft hoch. Dies trifft vor allem auf diejenigen Regio-nen der Schweiz zu, wo die Kühe gealpt werden, denn die Alpung selbst stellt das grösste Infektionsrisiko dar: hier kann sich der sehr ansteckende Erreger rasch aus-breiten, weil die GTB-positiven und -negativen Kühe beim Melken durchmischt werden. Dabei wird der Er-reger dann durch die kontaminierten Zitzengummis auf andere Kühe übertragen. Staphylococcus aureus GTB ist hochgradig euterassoziert. GTC und die übrigen Geno-typen dagegen kolonisieren hauptsächlich die Haut und verursachen gelegentlich auch Mastitiden. Daneben ist Staphylococcus aureus GTC ein klassischer Wunderreger

Competitive Sorption of Inorganics impurities from Aqueous Solutions onto Boric Acid: Implications on its Crystal Growth

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