ALBERT

Description: Well-developed karst aquifers consist of highly conductive conduits and a relatively low permeability fractured and/or porous rock matrix and therefore behave as a dual-hydraulic system. Groundwater flow within highly permeable strata is rapid and transient and depends on local flow conditions, i.e., pressurized or nonpressurized flow. The characterization of karst aquifers is a necessary and challenging task because information about hydraulic and spatial conduit properties is poorly defined or unknown. To investigate karst aquifers, hydraulic stresses such as large recharge events can be simulated with hybrid (coupled discrete continuum) models. Since existing hybrid models are simplifications of the system dynamics, a new karst model (ModBraC) is presented that accounts for unsteady and nonuniform discrete flow in variably saturated conduits employing the Saint-Venant equations. Model performance tests indicate that ModBraC is able to simulate (1) unsteady and nonuniform flow in variably filled conduits, (2) draining and refilling of conduits with stable transition between free-surface and pressurized flow and correct storage representation, (3) water exchange between matrix and variably filled conduits, and (4) discharge routing through branched and intermeshed conduit networks. Subsequently, ModBraC is applied to an idealized catchment to investigate the significance of free-surface flow representation. A parameter study is conducted with two different initial conditions: (1) pressurized flow and (2) free-surface flow. If free-surface flow prevails, the systems is characterized by (1) a time lag for signal transmission, (2) a typical spring discharge pattern representing the transition from pressurized to free-surface flow, and (3) a reduced conduit-matrix interaction during free-surface flow.

Description: In this study the potential of an inversion approach based on hydraulic travel time and hydraulic attenuation tomography was assessed. Both hydraulic travel time and hydraulic attenuation tomography are based on the transformation of the transient groundwater flow equation into the eikonal equation using an asymptotic approach. The eikonal equation allows the calculation of pressure propagation and attenuation along trajectories, which is computationally efficient. The attenuation and travel time-based inversion approaches are naturally complementary: hydraulic travel times are determined by the hydraulic diffusivity, a combination of hydraulic conductivity and specific storage, whereas the attenuation is determined solely by specific storage. The potential of our hydraulic tomographical approach was investigated at a well-characterized sand and gravel aquifer located in the Leine River valley near Göttingen, Germany. The database for the hydraulic inversion consists of 392 cross-well slug interference tests performed between five wells, in which the positions of the sources (injection ports) and the receivers (observation ports), isolated with double packer systems, were varied between tests. The results have shown that the combination of hydraulic travel time and hydraulic attenuation tomography allows the reconstruction of the diffusivity and storage distribution in two and three dimensions with a resolution and accuracy superior to that possible with type curve analysis.

Description: Background: New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis. Results: We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository. Conclusions: The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the "house keeping" abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse, complementary techniques are combined and correlated.

Description: In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the Simultaneous Iterative Reconstruction Technique algorithm, using a ray tracing technique with curved trajectories. The experimental set up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. The experiments were performed at a well-characterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.

Description: The morphology of the flanks of the Southwest Indian Ridge holds a record of seafloor formation and abyssal hill generation at an ultraslow spreading rate. Statistical analysis of compiled bathymetry and gravity data from the flanks of the Southwest Indian Ridge from 54°E to 67°E provides estimates of abyssal hill morphologic character and inferred crustal thickness. The extent of the compiled data encompasses a spreading rate change from slow to ultraslow at ∼24 Ma, a significant inferred variation in sub-axis mantle temperature, and a patchwork of volcanic and non-volcanic seafloor, making the Southwest Indian Ridge an ideal and unique location to characterize abyssal hills generated by ultraslow spreading and to examine the effect of dramatic spreading rate change on seafloor morphology. Root mean square abyssal hill height in ultraslow spreading seafloor ranges from ∼280 m to ∼320 m and is on average ∼80 m greater than found for slow-spreading seafloor. Ultraslow spreading abyssal hill width ranges from ∼4 km to ∼12 km, averaging ∼8 km. Abyssal hill height and width increases west-to-east in both slow and ultraslow spreading seafloor, corresponding to decreasing inferred mantle temperature. Abyssal hills persist in non-volcanic seafloor and extend continuously from volcanic to non-volcanic terrains. We attribute the increase of abyssal hill height and width to strengthening of the mantle portion of the lithosphere as the result of cooler sub-axial mantle temperature and conclude that abyssal hill height is primarily controlled by the strength of the mantle component of the lithosphere rather than spreading rate.

Description: Probabilistic Boolean network (PBN) modelling is a semi-quantitative approach widely used for thestudy of the topology and dynamic aspects of biological systems. The combined use of rule-basedrepresentation and probability makes PBN appealing for large-scale modelling of biological networkswhere degrees of uncertainty need to be considered.A considerable expansion of our knowledge in the field of theoretical research on PBN can be observedover the past few years, with a focus on network inference, network intervention and control. Withrespect to areas of applications, PBN is mainly used for the study of gene regulatory networks thoughwith an increasing emergence in signal transduction, metabolic, and also physiological networks. Atthe same time, a number of computational tools, facilitating the modelling and analysis of PBNs, arecontinuously developed.A concise yet comprehensive review of the state-of-the-art on PBN modelling is offered in this ar-ticle, including a comparative discussion on PBN versus similar models with respect to conceptsand biomedical applications. Due to their many advantages, we consider PBN to stand as a suitablemodelling framework for the description and analysis of complex biological systems, ranging frommolecular to physiological levels.

Description: Several factors influence land availability for the growth of short rotation coppices (SRC) with fast-growing tree species, including the nationwide availability of agricultural land, economic efficiency, ecological impacts, political boundaries and environmental protection regulations. In this study, we analysed the growing potential of poplar and willow SRC for bioenergy purposes in Germany without negative ecological impacts or land use conflicts. The potential biomass production using SRC on agricultural land in Germany was assessed taking into account ecological, ethical, political and technical restrictions. Using a geographic information system (GIS), digital site maps, climate data and a digital terrain model, the SRC biomass production potential on cropland and grassland was estimated using water supply and mean temperature during the growing season as parameters. From this analysis, a yield model for SRC was developed based on the analysed growth data and site information of 62 short rotation plantations in Germany and France. To assess the technical, ethical and ecological potential of SRC, restrictions in protected areas, technical constraints and competition with food and feed production were investigated. Our results revealed that approximately 18% (2.12 Mio. ha) of cropland and 54% (2.5 Mio. ha) of grassland in Germany were highly suitable for SRC plantations, providing favourable water supplies and mean temperatures during the growing season. These identified sites produced an average yield of more than 14 tons of dry matter per hectare per year. Due to local climate and soil conditions, the federal states in northern and eastern Germany had the highest theoretical SRC potential for agricultural land. After considering all ecological, ethical, political and technical restrictions, as well as future climate predictions, 5.7% (680 000 ha) of cropland and 33% (1.5 Mio. ha) of grassland in Germany were classified as suitable for biomass production with fast-growing tree species in SRC.

Description: The Southwest Indian Ridge (SWIR) is an ultraslow spreading end-member of mid-ocean ridge system. We use airgun shooting data recorded by ocean bottom seismometers (OBS) and multi-beam bathymetry to obtain a detailed three-dimensional (3D) P -wave tomographic model centered at 49°39′E near the active hydrothermal “Dragon Flag” vent. Results are presented in the form of a 3D seismic traveltime inversion over the center and both ends of a ridge segment. We show that the crustal thickness, defined as the depth to the 7-km/s-isovelocity contour, decreases systematically from the center (~7.0–8.0 km) toward the segment ends (~3.0–4.0 km). This variation is dominantly controlled by thickness changes in the lower crustal layer. We interpret this variation as due to focusing of the magmatic activity at the segment center. The across-axis velocity model documents a strong asymmetrical structure involving oceanic detachment faulting. A locally corrugated oceanic core complex (Dragon Flag OCC) on the southern ridge flank is characterized by high shallow crustal velocities and a strong vertical velocity gradient. We infer that this OCC may be predominantly made of gabbros. We suggest that detachment faulting is a prominent process of slow-spreading oceanic crust accretion even in magmatically robust ridge sections. Hydrothermal activity at the Dragon Flag vents is located next to the detachment fault termination. We infer that the detachment fault system provides a pathway for hydrothermal convection.

Description: Background: A close match of the HLA alleles between donor and recipient is an important prerequisite for successful unrelated hematopoietic stem cell transplantation. To increase the chances of finding an unrelated donor, registries recruit many hundred thousands of volunteers each year. Many registries with limited resources have had to find a trade-off between cost and resolution and extent of typing for newly recruited donors in the past. Therefore, we have taken advantage of recent improvements in NGS to develop a workflow for low-cost, high-resolution HLA typing. Results: We have established a straightforward three-step workflow for high-throughput HLA typing: Exons 2 and 3 of HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 are amplified by PCR on Fluidigm Access Array microfluidic chips. Illumina sequencing adapters and sample specific tags are directly incorporated during PCR. Upon pooling and cleanup, 384 samples are sequenced in a single Illumina MiSeq run. We developed "neXtype" for streamlined data analysis and HLA allele assignment. The workflow was validated with 1140 samples typed at 6 loci. All neXtype results were concordant with the Sanger sequences, demonstrating error-free typing of more than 6000 HLA loci. Current capacity in routine operation is 12,000 samples per week. Conclusions: The workflow presented proved to be a cost-efficient alternative to Sanger sequencing for high-throughput HLA typing. Despite the focus on cost efficiency, resolution exceeds the current standards of Sanger typing for donor registration.