Modernizing Legacy Physics Applications for Reuse in Web and SOA

This paper concerns the application of recent information technologies for creating a software system for numerical simulations in the domain of plasma physics and in particular metal vapor lasers. The presented work is connected with performing modernization of legacy physics software for reuse on the web and inside a Service-Oriented Architecture environment. Applied and described is the creation of Java front-ends of legacy C++ and FORTRAN codes. Then the transformation of some of the scientific components into web services, as well as the creation of a web interface to the legacy application, is presented. The use of the BPEL language for managing scientific workflows is also considered.

Global compilation of benthic data sets I

Approaches to quantify the organic carbon accumulation on a global scale generally do not consider the small-scale variability of sedimentary and oceanographic boundary conditions along continental margins. In this study, we present a new approach to regionalize the total organic carbon (TOC) content in surface sediments (<5 cm sediment depth). It is based on a compilation of more than 5500 single measurements from various sources. Global TOC distribution was determined by the application of a combined qualitative and quantitative-geostatistical method. Overall, 33 benthic TOC-based provinces were defined and used to process the global distribution pattern of the TOC content in surface sediments in a 1°x1° grid resolution. Regional dependencies of data points within each single province are expressed by modeled semi-variograms. Measured and estimated TOC values show good correlation, emphasizing the reasonable applicability of the method. The accumulation of organic carbon in marine surface sediments is a key parameter in the control of mineralization processes and the material exchange between the sediment and the ocean water. Our approach will help to improve global budgets of nutrient and carbon cycles.

Database of the GLAMAP project

A uniform chronology for foraminifera-based sea surface temperature records has been established in more than 120 sediment cores obtained from the equatorial and eastern Atlantic up to the Arctic Ocean. The chronostratigraphy of the last 30,000 years is mainly based on published d18O records and 14C ages from accelerator mass spectrometry, converted into calendar-year ages. The high-precision age control provides the database necessary for the uniform reconstruction of the climate interval of the Last Glacial Maximum within the GLAMAP-2000 project.

Glacial North Atlantic: Sea surface conditions reconstructed by GLAMAP 2000

The response of the tropical ocean to global climate change and the extent of sea ice in the glacial nordic seas belong to the great controversies in paleoclimatology. Our new reconstruction of peak glacial sea surface temperatures (SSTs) in the Atlantic is based on census counts of planktic foraminifera, using the Maximum Similarity Technique Version 28 (SIMMAX-28) modern analog technique with 947 modern analog samples and 119 well-dated sediment cores. Our study compares two slightly different scenarios of the Last Glacial Maximum (LGM), the Environmental Processes of the Ice Age: Land, Oceans, Glaciers (EPILOG), and Glacial Atlantic Ocean Mapping (GLAMAP 2000) time slices. The comparison shows that the maximum LGM cooling in the Southern Hemisphere slightly preceeded that in the north. In both time slices sea ice was restricted to the north western margin of the nordic seas during glacial northern summer, while the central and eastern parts were ice-free. During northern glacial winter, sea ice advanced to the south of Iceland and Faeroe. In the central northern North Atlantic an anticyclonic gyre formed between 45° and 60°N, with a cool water mass centered west of Ireland, where glacial cooling reached a maximum of >12°C. In the subtropical ocean gyres the new reconstruction supports the glacial-to-interglacial stability of SST as shown by CLIMAP Project Members (CLIMAP) [1981]. The zonal belt of minimum SST seasonality between 2° and 6°N suggests that the LGM caloric equator occupied the same latitude as today. In contrast to the CLIMAP reconstruction, the glacial cooling of the tropical east Atlantic upwelling belt reached up to 6°-8°C during Northern Hemisphere summer. Differences between these SIMMAX-based and published U37[k]- and Mg/Ca-based equatorial SST records are ascribed to strong SST seasonalities and SST signals that were produced by different planktic species groups during different seasons.

Global data compilation of benthic data sets II

In this study we present a global distribution pattern and budget of the minimum flux of particulate organic carbon to the sea floor (J POC alpha). The estimations are based on regionally specific correlations between the diffusive oxygen flux across the sediment-water interface, the total organic carbon content in surface sediments, and the oxygen concentration in bottom waters. For this, we modified the principal equation of Cai and Reimers [1995] as a basic monod reaction rate, applied within 11 regions where in situ measurements of diffusive oxygen uptake exist. By application of the resulting transfer functions to other regions with similar sedimentary conditions and areal interpolation, we calculated a minimum global budget of particulate organic carbon that actually reaches the sea floor of ~0.5 GtC yr**-1 (>1000 m water depth (wd)), whereas approximately 0.002-0.12 GtC yr**-1 is buried in the sediments (0.01-0.4% of surface primary production). Despite the fact that our global budget is in good agreement with previous studies, we found conspicuous differences among the distribution patterns of primary production, calculations based on particle trap collections of the POC flux, and J POC alpha of this study. These deviations, especially located at the southeastern and southwestern Atlantic Ocean, the Greenland and Norwegian Sea and the entire equatorial Pacific Ocean, strongly indicate a considerable influence of lateral particle transport on the vertical link between surface waters and underlying sediments. This observation is supported by sediment trap data. Furthermore, local differences in the availability and quality of the organic matter as well as different transport mechanisms through the water column are discussed.

Prevalence and control of Clostridium difficile in patients with cystic fibrosis

The aim of this thesis was to investigate the high prevalence of Clostridium difficile in patients with cystic fibrosis (CF), and to control its dissemination. To determine the carriage rate of C. difficile in CF patients, 60 patients were tested for C. difficile and its toxin. In total, 50% of patients were found to be asymptomatic carriers of C. difficile despite toxin being detected in 31.66% of patients. Ribotyping of the C. difficile isolates revealed 16 distinct ribotypes, including the hyper virulent RT078. All isolates were sensitive to both Vancomycin and Metronidazole. The effect of CF and its treatment on the gut microbiota of CF patients was assessed by 16s sequencing of the gut microbiota of 68 CF patients. When compared to a healthy control group, CF patient gut microbiota was found to be less diverse and had an increased Firmicutes to Bacteriodetes ratio. Interestingly, CF patients who were carriers of C. difficile had a less diverse gut microbiota than C. difficile negative CF patients. Multilocus sequence typing was found to be comparable to PCR-ribotyping for typing C. difficile isolates from high risk patient groups. The sequence type ST 26 is potentially associated with CF patients as all seven isolates were found in this group and this sequence type has been previously reported in CF patients in a geographically distinct study. The bacteriophage ФCD6356 was assessed as a targeted antimicrobial against C. difficile in an ex-vivo model of the human distal colon. Despite reducing viable C. difficile by 1.75 logs over 24 hours, this bacteriophage was not suitable due to its lysogenic nature. Following treatment, all surviving C. difficile were immune to reinfection due to prophage integration. However, the ФCD6356 encoded endolysin was capable of reducing viable C. difficile by 2.9 over 2 hours in vitro after being cloned and expressed in Escherichia coli.

Geochemical analysis of surface sediments from the ocean floor and from sea ice in the northern Atlantic and Arctic Oceans

Barium in marine terrigenous surface sediments of the European Nordic Seas is analysed to evaluate its potential as palaeoproductivity proxy. Biogenic Ba is calculated from Ba and Al data using a conventional approach. For the determination of appropriate detrital Ba/Al ratios a compilation of Ba and Al analyses in rocks and soils of the catchments surrounding the Nordic Seas is presented. The resulting average detrital Ba/Al ratio of 0.0070 is similar to global crustal average values. In the southern Nordic Seas the high input of basaltic material with a low Ba/Al ratio is evident from high values of magnetic susceptibility and low Al/Ti ratios. Most of the Ba in the marine surface sediments is of terrigenous and not of biogenic origin. Variability in the lithogenic composition has been considered by the application of regionally varying Ba/Al ratios. The biogenic Ba values are comparable with those observed in the central Arctic Ocean, they are lower than in other oceanic regions. Biogenic Ba values are correlated with other productivity proxies and with oceanographic data for a validation of the applicability in paleoceanography. In the Iceland Sea and partly in the marginal sea-ice zone of the Greenland Sea elevated values of biogenic Ba indicate seasonal phytoplankton blooms. In both areas paleoproductivities may be reconstructed based on Ba and Al data of sediment cores.

Magnetic susceptibility and ice-rafted debris in surface sediments of the Nordic Sea

Magnetic susceptibility and ice-rafted debris of surface sediments in the Nordic Seas were investigated to reconstruct source areas and recent transport pathways of magnetic minerals. From the distribution of magnetic susceptibility and ice-rafted debris and published data on petrographic tracers for iceberg drift, we reconstructed a counter-clockwise iceberg drift pattern during cooler phases in the Holocene, which is similar to conceptual and numerical models for Weichselian iceberg drift. The release of basaltic debris at Scoresby Sund played a significant role for the magnetic signature of stadial/interstadial events during isotope stage 3 recorded in sediment cores of the Nordic Seas.