Submission of content to a digital object repository using a configurable workflow system

The prototype of a workflow system for the submission of content to a digital object repository is here presented. It is based entirely on open-source standard components and features a service-oriented architecture. The front-end consists of Java Business Process Management (jBPM), Java Server Faces (JSF), and Java Server Pages (JSP). A Fedora Repository and a mySQL data base management system serve as a back-end. The communication between front-end and back-end uses a SOAP minimal binding stub. We describe the design principles and the construction of the prototype and discuss the possibilities and limitations of work ow creation by administrators. The code of the prototype is open-source and can be retrieved in the project escipub at http://sourceforge.ne

Record occurrence and record values in daily and monthly temperatures

We analyze the occurrence and the values of record-breaking temperatures in daily and monthly temperature observations. Our aim is to better understand and quantify the statistics of temperature records in the context of global warming. Similar to earlier work we employ a simple mathematical model of independent and identically distributed random variables with a linearly growing expectation value. This model proved to be useful in predicting the increase (decrease) in upper (lower) temperature records in a warming climate. Using both station and re-analysis data from Europe and the United States we further investigate the statistics of temperature records and the validity of this model. The most important new contribution in this article is an analysis of the statistics of record values for our simple model and European reanalysis data. We estimate how much the mean values and the distributions of record temperatures are affected by the large scale warming trend. In this context we consider both the values of records that occur at a certain time and the values of records that have a certain record number in the series of record events. We compare the observational data both to simple analytical computations and numerical simulations. We find that it is more difficult to describe the values of record breaking temperatures within the framework of our linear drift model. Observations from the summer months fit well into the model with Gaussian random variables under the observed linear warming, in the sense that record breaking temperatures are more extreme in the summer. In winter however a significant asymmetry of the daily temperature distribution hides the effect of the slow warming trends. Therefore very extreme cold records are still possible in winter. This effect is even more pronounced if one considers only data from subpolar regions.Comment: 16 pages, 20 figures, revised version, published in Climate Dynamic

Initialization and Ensemble Generation for Decadal Climate Predictions: A Comparison of Different Methods

Five initialization and ensemble generation methods are investigated with respect to their impact on the prediction skill of the German decadal prediction system “Mittelfristige Klimaprognose” (MiKlip). Among the tested methods, three tackle aspects of model‐consistent initialization using the ensemble Kalman filter, the filtered anomaly initialization, and the initialization method by partially coupled spin‐up (MODINI). The remaining two methods alter the ensemble generation: the ensemble dispersion filter corrects each ensemble member with the ensemble mean during model integration. And the bred vectors perturb the climate state using the fastest growing modes. The new methods are compared against the latest MiKlip system in the low‐resolution configuration (Preop‐LR), which uses lagging the climate state by a few days for ensemble generation and nudging toward ocean and atmosphere reanalyses for initialization. Results show that the tested methods provide an added value for the prediction skill as compared to Preop‐LR in that they improve prediction skill over the eastern and central Pacific and different regions in the North Atlantic Ocean. In this respect, the ensemble Kalman filter and filtered anomaly initialization show the most distinct improvements over Preop‐LR for surface temperatures and upper ocean heat content, followed by the bred vectors, the ensemble dispersion filter, and MODINI. However, no single method exists that is superior to the others with respect to all metrics considered. In particular, all methods affect the Atlantic Meridional Overturning Circulation in different ways, both with respect to the basin‐wide long‐term mean and variability and with respect to the temporal evolution at the 26° N latitude

Sleep duration and its role in the aetiology of cardio-metabolic health outcomes

An adequate amount of sleep is believed to be important for optimal health and functioning throughout life and changes in sleep duration were found to be associated with several especially cardio-metabolic - health outcomes in adults as well as in children. The factors that influence sleep duration are multi-factorial and the interplay between sleep duration and other factors in the aetiology of cardio-metabolic outcomes is complex and not fully understood yet. Internationally comparable data from children aged 2 to 9 years participating in the IDEFICS study has been analysed to investigate on differences in and determinants of sleep duration as well as on the association between sleep duration and overweight in children. Systematic reviews give an insight in the literature on the longitudinal relationship between sleep duration and weight status in children and adults on the one hand, and on the epidemiological evidence regarding sleep duration and cardiovascular mortality on the other hand. A meta-analysis has been conducted to quantify the dose dependency of the association between sleep duration and cardiovascular mortality. Nocturnal sleep duration differed significantly (P < 0.001) by up to 1.7 hours between countries in univariate as well as in multivariate analysis. Disparities between Northern, Southern and Eastern Europe were striking, with children from Northern countries sleeping the longest. The factor that was found to mainly affect children s sleep duration was country affiliation. Age also had a significant effect in all models, but accounted for less change in sleep duration than country. No association was found with behavioral aspects or environmental factors, such as season or daylight. A negative association of sleep duration with a higher probability of being overweight was revealed. This relationship was attenuated by an adjustment for geographic region, whereas no effect modification by region was found. Generally the association appeared to be much stronger in school children than in preschool children. The relationship between sleep duration and weight status can not only be seen in children but also in adults even if the results are less consistent with increasing age. The meta-analysis showed a clear dose-effect relationship of sleep duration on cardiovascular mortality. For stroke and cardiovascular diseases in general (CVD) the association could mainly be seen with sleep durations of more than 7.5 hours and the direction of the relationship seemed to be similar in men and in women. For coronary heart disease (CHD)the effects of sleep duration were generally stronger, but differed between sexes, with short sleep duration being associated with CHD to a higher extent in men than in women. In contrast, long sleep duration seemed to increase the risk in women, while no significant effect was seen in men. In conclusion we suggested a twofold effect of sleep duration on cardiovascular outcomes: directly and indirectly via the effect of overweight. Furthermore, investigation on sleep duration as a tracking risk factor for cardio-metabolic outcomes as well as internationally comparable studies to give insight in regional aspects of sleep duration was proposed. Such research might create the basis for specific and appropriate public health actions with regard to sleep induced cardio-metabolic conditions

Stream fish populations in a watershed scale context for fish community dynamics in central Appalachian watersheds

In this study we first conducted a three pass removal study to estimate electrofishing capture probabilities for species and size classes of fish common in the Cheat River and Tygart River watersheds of West Virginia. We then calculated models of capture probabilities for 12 species that were divided into two size classes based on site-specific physico-chemical variables. We took these capture probability models and applied them to a watershed scale study in the Cheat River and Tygart Valley River watersheds of West Virginia. We sampled across the two watersheds with the objective of quantifying and relating juvenile and adult distributions within species along a stream size continuum. The 14 species that were included in the study we found to be mostly non-uniformly distributed across the watershed. We used general stream size to categorize where the concentrations of each species and size class were, in relation to the watershed and each other. Our analyses determined among species variations in the degree of overlap of juvenile and adult distributions within species. We generally related watershed population and community level organization to the within species juvenile and adult distributions

Evolutionary and functional analysis of gene expression regulation in Drosophila melanogaster

Die in dieser Dissertation präsentierten Ergebnisse tragen aus dem Blickwinkel der Evolutionsbiologie zu unserem Verständnis der Regulation von Genexpression bei. Ich verwende einen bestens bekannten Modellorganismus, die Fruchtfliege Drosophila melanogaster, nicht nur als Objekt der Beobachtung, sondern auch als ein genetisches Manipulationswerkzeug, und untersuche drei verschiedene Aspekte des Prozesses, durch den die in der DNA gespeicherte Information förmlich „entfesselt“ oder umgesetzt wird zu biologischem Sinn, letztlich also zu Form und Funktion. In Kapitel 1 zeige ich zunächst, dass eine Inaktivierung des X-Chromosomes (und somit Genregulation auf chromosomaler Ebene) in der männlichen Keimbahn von D. melanogaster stattfindet. Im Gegensatz zur X-Inaktivierung in weiblichen Säugetieren, wo dies in den somatischen Zellen als Mechanismus zur Dosiskompensation auftritt, ist diese Art der Inaktivierung auf die Spermatogenese beschränkt und wurde wahrscheinlich während der Genomevolution als eine Möglichkeit etabliert, schädliche Auswirkungen in Zusammenhang mit Sexualantagonismus zu umgehen. Durch P-Element-vermittelte Keimbahntransformation erhielt ich fast 50 unabhängige Insertionen eines testisspezifischen Reportergenkonstrukts und untersuchte die dazugehörigen Reportergenaktivitäten durch Messung der Enzymaktivität und durch quantitative RT-PCR. Autosomale Insertionen dieses Konstrukts zeigten das erwartete Muster hoher männchen- und testisspezifischer Expression. Insertionen auf dem X-Chromosom zeigten dagegen wenig bzw. gar keine Expression des Transgens. Da die X-chromosomalen Insertionen die euchromatischen Abschnitte des Chromosoms abdeckten (bestimmt durch inverse PCR), konnte eine systematische Bevorzugung bestimmter Regionen bei Insertionen, die ein Fehlen von Expression auf dem X-Chromosom hätte erklären können, ausgeschlossen werden. Der Effekt scheint eine globale Eigenschaft des X-Chromosomes zu sein. Lediglich die Testisspezifität des transgenen Konstrukts ist für das Erscheinen des Effekts erforderlich, was somit eine Selektionshypothese für die X-Inaktivierung erhärtet sowie einige Beobachtungen erklären könnte, die im Zusammenhang mit der Verteilung von im Männchen und Testis exprimierten Genen im Drosophila-Genom gemacht wurden. In Kapitel 2 untersuche ich dann mutmaßliche cis-regulatorische Sequenzen und ihr Vermögen, allelspezifische Genexpression zu steuern. Nachdem Microarray-Studien umfangreiche Variabilität im Primärmerkmal Genexpression in unterschiedlichsten Taxa aufgedeckt haben, ist eine naheliegende Frage, mit der sich Evolutionsbiologen konfrontiert sehen, die nach der dieser Variabilität zugrunde liegenden genetischen Quelle. Neben epigenetischen Mechanismen gibt es einen Disput darüber, ob regulatorische Sequenzen nahe des exprimierten Gens (cis-Faktoren) und anderswo im Genom kodierte Faktoren (trans-Faktoren) einen qualitativ und quantitativ unterschiedlichen Beitrag zur Variabilität der Genexpression liefern. Hierzu wählte ich ein Gen von D. melanogaster, das nachweislich konsistente Expressionsunterschiede zwischen afrikanischen und nicht-afrikanischen („kosmopolitischen“) Stämmen zeigt, und klonierte die entsprechenden stromaufwärts flankierend gelegenen Teile jeweils in ein bakterielles Reportergenkonstrukt, um – nach erfolgreicher Integration ins Fruchtfliegengenom – direkt die von ihnen gesteuerte Auswirkung auf die Genexpression zu vergleichen. Der beobachtete Effekt war klein, jedoch signifikant, und zeigte sich nur in transgenen Fliegen, die ein X-Chromosom des afrikanischen Ausgangsstammes besaßen. Dies legt den Schluss nahe, dass zusätzlich zu den cis-regulatorischen Faktoren auch noch trans-Faktoren (vor allem auf dem X-Chromosom) zu dem zwischen den Stämmen beobachteten Expressionsunterschied beitragen. Letztendlich untersuche ich in Kapitel 3 das Phänomen des Codon bias durch seinen Zusammenhang mit Genexpression. Aufgrund der Redundanz des genetischen Codes werden viele der proteinogenen Aminosäuren durch mehr als ein Codon kodiert. Dies ermöglicht es, synonyme Codons in einer kodierenden Gensequenz auszutauschen, ohne dabei die Aminosäurensequenz des kodierten Polypeptids zu verändern. Ob dies Konsequenzen für die produzierte Proteinmenge hat (Translationseffizienz) ist Gegenstand dieses Kapitels. Ich verglich dabei die von zwei Allelen des Gens Alkoholdehydogenase (Adh) (von D. melanogaster) vermittelte Enzymaktivität direkt miteinander, welche sich in sieben Leucin-Codons unterschieden. Es ergab sich nahezu kein Unterschied in der ADH-Enzymaktivität, obwohl eines der Allele aus gänzlich optimalen Leucin-Codons bestand und das andere sieben suboptimale Leucin-Codons enthielt. Da Letzteres die Wildtypform von Adh war, legen die Ergebnisse den Schluss nahe, dass das Adh-Gen in seiner Leucin-Codonzusammensetzung (und vielleicht auch in seiner Codonzusammensetzung allgemein) bereits ausreichend optimiert ist. Weitere Versuche, die Zahl der optimalen Leucin-Codons zu erhöhen, können sogar einen Negativeffekt hinsichtlich der Enzymproduktion haben; dies möglicherweise aufgrund einer Sättigung des tRNA-Pools und/oder der Konsequenzen veränderter mRNA-Sekundärstrukturen