XML-Verarbeitung auf Grafikkarten

Die Extensible Markup Language (XML) ist ein weit verbreitetes, strukturiertes Format zur Datenspeicherung und zum Datenaustausch. Die Komplexität und die Menge der zu verarbeitenden XML-Daten hat in den vergangenen Jahren erheblich zugenommen, und sowohl in der Wissenschaft wie auch in der Wirtschaft wird an Verfahren zur schnellen Verarbeitung von XML gearbeitet. In einigen Arbeiten werden auch Verfahren zur parallelen Verarbeitung von XML mittels üblicher Mehrkern-CPUs entwickelt. Seit einigen Jahren gewinnt die parallele Verarbeitung allgemeiner Probleme mittels Grafikprozessoren (GPUs) an Bedeutung. GPUs ähneln in ihrer Architektur und Arbeitsweise dem bekannten Single Instruction Multiple Data-Prinzip. Daher sind GPUs besonders gut geeignet für die Verarbeitung massiv-datenparalleler Probleme wie etwa der Matrixmultiplikation oder der Bildverarbeitung. XML-Dokumente bzw. XML-Datenmodelle haben eine baumartige Struktur und folglich basieren viele der Verfahren zur Verarbeitung von XML auf dieser Baumstruktur. Solche Strukturen und Verfahren können jedoch wegen der Architektur von GPUs nicht trivial von CPUs auf GPUs übertragen werden, selbst wenn es sich um Verfahren zur parallelen Verarbeitung mittels Mehrkern-CPUs handelt. Daher existieren bisher kaum Arbeiten, die die parallele Verarbeitung von XML mittels GPUs untersuchen. In der vorliegenden Arbeit wird anhand einer konkreten XML-Anwendung, der Transformation von XML-Dokumenten mit XSLT, untersucht, inwieweit die Verarbeitung von XML an die massiv-parallele Architektur von GPUs angepasst werden kann. Dazu wird zunächst ein Konzept zur XSLT-Verarbeitung durch GPUs entworfen und danach werden die vier wichtigsten in diesem Konzept eingesetzten neuen Verfahren vorgestellt: ein schnelles Sortierverfahren für GPUs, ein Verfahren um GPUs als asynchrone Koprozessoren für die CPU einsetzen zu können, ein Verfahren um XPath-Ausdrücke parallel auszuwerten und schließlich ein Verfahren zur XSLT-Verarbeitung mittels GPUs. In umfangreichen Tests wird gezeigt, dass mit den hier dargelegten Verfahren die Nutzung von GPUs für die XPath- und XSLT-Verarbeitung in vielen Fällen zu einer Leistungssteigerung gegenüber der Verarbeitung durch Mehrkern-CPUs führt. Es ist demnach möglich, GPUs auch zur Verarbeitung von XML gewinnbringend einzusetzen

Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean

Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1–C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods

Demographic, clinical and antibody characteristics of patients with digital ulcers in systemic sclerosis: data from the DUO Registry

OBJECTIVES: The Digital Ulcers Outcome (DUO) Registry was designed to describe the clinical and antibody characteristics, disease course and outcomes of patients with digital ulcers associated with systemic sclerosis (SSc). METHODS: The DUO Registry is a European, prospective, multicentre, observational, registry of SSc patients with ongoing digital ulcer disease, irrespective of treatment regimen. Data collected included demographics, SSc duration, SSc subset, internal organ manifestations, autoantibodies, previous and ongoing interventions and complications related to digital ulcers. RESULTS: Up to 19 November 2010 a total of 2439 patients had enrolled into the registry. Most were classified as either limited cutaneous SSc (lcSSc; 52.2%) or diffuse cutaneous SSc (dcSSc; 36.9%). Digital ulcers developed earlier in patients with dcSSc compared with lcSSc. Almost all patients (95.7%) tested positive for antinuclear antibodies, 45.2% for anti-scleroderma-70 and 43.6% for anticentromere antibodies (ACA). The first digital ulcer in the anti-scleroderma-70-positive patient cohort occurred approximately 5 years earlier than the ACA-positive patient group. CONCLUSIONS: This study provides data from a large cohort of SSc patients with a history of digital ulcers. The early occurrence and high frequency of digital ulcer complications are especially seen in patients with dcSSc and/or anti-scleroderma-70 antibodies

Food utilisation and digestive ability of aquatic and semi-terrestrial crayfishes, Cherax destructor and Engaeus sericatus (Astacidae, Parastacidae)

Both Engaeus sericatus and Cherax destructor are omnivorous crayfishes consuming a variety of food items. Materials identified in the faeces of both E. sericatus and C. destructor consisted of mainly plant material with minor amounts of arthropod animals, algae and fungi. The morphology of the gastric mill of C. destructor suggests that it is mainly involved in crushing of food material while the gastric mill of E. sericatus appears to be better suited to cutting of food material. Given this, the gastric mill of E. sericatus may be better able to cut the cellulose and hemicellulose fibres associated with fibrous plant material. In contrast, the gastric mill of C. destructor appears to be more efficient in grinding soft materials such as animal protein and algae. Both species accumulated high amounts of lipids in their midgut glands (about 60% of the dry mass) which were dominated by triacylglycerols (81&ndash;82% of total lipids). The dominating fatty acids were 16:0, 16:1(n-7), 18:1(n-9), 18:2(n-6), and 18:3(n-3). The two latter fatty acids can only be synthesised by plants, and are thus indicative of the consumption of terrestrial plants by the crayfishes. The similarity analysis of the fatty acid patterns showed three distinct clusters of plants and each of the crayfish species. The complement of digestive enzymes, proteinases, total cellulase, endo-&beta;-1,4-glucanase, &beta;-glucosidase, laminarinase and xylanase within midgut gland suggests that both C. destructor and E. sericatus are capable of hydrolysing a variety of substrates associated with an omnivorous diet. Higher activities of total cellulase, endo-&beta;-1,4-glucanase and &beta;-glucosidase indicate that E. sericatus is better able to hydrolyse cellulose within plant material than C. destructor. In contrast to E. sericatus, higher total protease and N-acetyl-&beta;-d-glucosaminidase activity in the midgut gland of C. destructor suggests that this species is better able to digest animal materials in the form of arthropods. Differences in total cellulase and gastric mill morphology suggest that E. sericatus is more efficient at digesting plant material than C. destructor. However, the contents of faecal pellets and the fatty acid compositions seem to indicate that both species opportunistically feed on the most abundant and easily accessible food items.<br /

Schlussbericht des Forschungsprojekts 'Studium neben dem Beruf'

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