Quantitative proteome analysis in cardiovascular physiology and pathology. I. Data processing

Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. It has been found that the silver-stained readout offers a convenient approach for quantitation if a linear range for gel loading is defined. In addition, a broad range of a 10-fold input (loading 20-200 microg per gel) fulfills the linearity criteria, although at the lowest input (20 microg) a portion of protein species will remain undetected. The method is reliable and reproducible within a range of 65-200 microg input. The normalization procedure using the sum of all spot intensities from a silver-stained 2D pattern has been shown to be less reliable than other approaches, namely, normalization through median or through involvement of interquartile range. A special refinement of the normalization through virtual segmentation of pattern, and calculation of normalization factor for each stratum provides highly satisfactory results. The presented results not only provide evidence for the usefulness of silver-stained gels for quantitative evaluation, but they are directly applicable to the research endeavor of monitoring alterations in cardiovascular pathophysiology.

The applicability of non-local LCI data for LCA

This study evaluated how applicable European Life Cycle Inventory (LCI) data are to assessing the environmental impacts of the life cycle of Brazilian triple superphosphate (TSP). The LCI data used for the comparison were local Brazilian LCI data, European LCI data in its original version from the ecoinvent database and a modified version of the European LCI data, which had been adapted to better account for the Brazilian situation. We compared the three established datasets at the level of the inventory as well as for their environmental impacts, i.e. at the level of Life Cycle Environmental Assessment (LCIA). The analysis showed that the European LCIs (both the original and the modified ones) considered a broader spectrum of background processes and environmental flows (inputs and outputs). Nevertheless, TSP production had in all three cases similar values for the consumption of the main raw materials. The LCIA results obtained for the datasets showed important differences as well. Therefore we concluded that the European data in general lead to much higher environmental impacts than the Brazilian data. The differences between the LCIA results obtained with the Brazilian and the European data can be basically explained by the methodological differences underlying the data. The small differences at the LCI level for selected inputs and outputs between the Brazilian and the European LCIs from ecoinvent indicate that the latter can be regarded as applicable for characterizing the Brazilian TSP.

Decision-usefulness of ideal cost- and ideal value accounting for valuation and stewardship

This paper contrasts the decision-usefulness of prototype accounting regimes based on perfect accounting for value, i.e. ideal value accounting (IVA), and perfect matching of cost, i.e. ideal cost accounting (ICA). The regimes are analyzed in the context of a firm with overlapping capacity investments where projects earn excess returns and residual income is utilized as performance indicator. Provided that IVA and ICA systematically differ based on the criterion of unconditional conservatism, we assess their respective decision-usefulness for different valuation- and stewardship-scenarios. Assuming that addressees solely observe current accounting data of the firm, ICA provides information which is useful for valuation and stewardship without reservation whereas IVA entails problems under specific assumptions.

Population structure, inbreeding and local adaptation within an endangered riverine specialist: the nase (Chondrostoma nasus)

Chondrostoma nasus is a cyprinid fish with highly specialized, ecologically and geographically distinct, ontogenetic trophic niches. Nase population numbers across their Swiss range have shown massive declines and many localized extinctions. Here we integrate data from different genetic markers with phenotypic and demographic data to survey patterns of neutral and adaptive genetic diversity in all extant (and one extinct) Swiss nase populations, with the aim to delineate intraspecific conservation units (CUs) and to inform future population management strategies. We discovered two major genetically and geographically distinct population groupings. The first population grouping comprises nase inhabiting rivers flowing into Lake Constance; the second comprises nase populations from Rhine drainages below Lake Constance. Within these clusters there is generally limited genetic differentiation among populations. Genomic outlier scans based on 256–377 polymorphic AFLP loci revealed little evidence of local adaptation both within and among population clusters, with the exception of one candidate locus identified in scans involving the inbred Schanzengraben population. However, significant phenotypic differentiation in body shape between certain populations suggests a need for more intensive future studies of local adaptation. Our data strongly suggests that the two major population groups should be treated as distinct CUs, with any supplemental stocking and reintroductions sourced only from within the range of the CU concerned.

A global radiosonde and tracked balloon archive on 16 pressure levels (GRASP) back to 1905 – Part 1: Merging and interpolation to 00:00 and 12:00 GMT

Many observed time series of the global radiosonde or PILOT networks exist as fragments distributed over different archives. Identifying and merging these fragments can enhance their value for studies on the three-dimensional spatial structure of climate change. The Comprehensive Historical Upper-Air Network (CHUAN version 1.7), which was substantially extended in 2013, and the Integrated Global Radiosonde Archive (IGRA) are the most important collections of upper-air measurements taken before 1958. CHUAN (tracked) balloon data start in 1900, with higher numbers from the late 1920s onward, whereas IGRA data start in 1937. However, a substantial fraction of those measurements have not been taken at synoptic times (preferably 00:00 or 12:00 GMT) and on altitude levels instead of standard pressure levels. To make them comparable with more recent data, the records have been brought to synoptic times and standard pressure levels using state-of-the-art interpolation techniques, employing geopotential information from the National Oceanic and Atmospheric Administration (NOAA) 20th Century Reanalysis (NOAA 20CR). From 1958 onward the European Re-Analysis archives (ERA-40 and ERA-Interim) available at the European Centre for Medium-Range Weather Forecasts (ECMWF) are the main data sources. These are easier to use, but pilot data still have to be interpolated to standard pressure levels. Fractions of the same records distributed over different archives have been merged, if necessary, taking care that the data remain traceable back to their original sources. If possible, station IDs assigned by the World Meteorological Organization (WMO) have been allocated to the station records. For some records which have never been identified by a WMO ID, a local ID above 100 000 has been assigned. The merged data set contains 37 wind records longer than 70 years and 139 temperature records longer than 60 years. It can be seen as a useful basis for further data processing steps, most notably homogenization and gridding, after which it should be a valuable resource for climatological studies. Homogeneity adjustments for wind using the NOAA-20CR as a reference are described in Ramella Pralungo and Haimberger (2014). Reliable homogeneity adjustments for temperature beyond 1958 using a surface-data-only reanalysis such as NOAA-20CR as a reference have yet to be created. All the archives and metadata files are available in ASCII and netCDF format in the PANGAEA archive

Granular computing as a tool of human data interaction - a cognitive cities use case

The article proposes granular computing as a theoretical, formal and methodological basis for the newly emerging research field of human–data interaction (HDI). We argue that the ability to represent and reason with information granules is a prerequisite for data legibility. As such, it allows for extending the research agenda of HDI to encompass the topic of collective intelligence amplification, which is seen as an opportunity of today’s increasingly pervasive computing environments. As an example of collective intelligence amplification in HDI, we introduce a collaborative urban planning use case in a cognitive city environment and show how an iterative process of user input and human-oriented automated data processing can support collective decision making. As a basis for automated human-oriented data processing, we use the spatial granular calculus of granular geometry.

Doppler Orbit Determination of Deep Space Probes by the Bernese GNSS Software: First Results of the Combined Orbit Determination from DSN and Inter-Satellite Ka-Band Data from the Grail Mission

Navigation of deep space probes is most commonly operated using the spacecraft Doppler tracking technique. Orbital parameters are determined from a series of repeated measurements of the frequency shift of a microwave carrier over a given integration time. Currently, both ESA and NASA operate antennas at several sites around the world to ensure the tracking of deep space probes. Just a small number of software packages are nowadays used to process Doppler observations. The Astronomical Institute of the University of Bern (AIUB) has recently started the development of Doppler data processing capabilities within the Bernese GNSS Software. This software has been extensively used for Precise Orbit Determination of Earth orbiting satellites using GPS data collected by on-board receivers and for subsequent determination of the Earth gravity field. In this paper, we present the currently achieved status of the Doppler data modeling and orbit determination capabilities in the Bernese GNSS Software using GRAIL data. In particular we will focus on the implemented orbit determination procedure used for the combined analysis of Doppler and intersatellite Ka-band data. We show that even at this earlier stage of the development we can achieve an accuracy of few mHz on two-way S-band Doppler observation and of 2 µm/s on KBRR data from the GRAIL primary mission phase.