ALBERT

Description: Quasistatic deformation experiments in the laboratory are key to determining the poroelastic moduli of rocks. For microinhomogeneous porous rocks, it is a challenge to determine a complete set of poroelastic parameters. This is because an additional parameter is required that quantifies the effect of microinhomogeneities because then the unjacketed bulk and pore moduli are no longer the same as the bulk modulus of the solid phase. We found that measurements for the drained and unjacketed bulk moduli together with Skempton’s pore-pressure build-up coefficient were sufficient to determine the solid-phase bulk modulus and the microinhomogeneity parameter. The latter served as a direct measure for the deviation from Biot-Gassmann prediction for the undrained bulk modulus. We applied the results to a set of measured poroelastic moduli in which microinhomogeneities have been made responsible for a non-Gassmann rock behavior. Accordingly, our estimate for the microinhomogeneity parameter quantified the deviation from the Biot-Gassmann prediction.

Description: Author(s): J. D. Rameau, J. Smedley, E. M. Muller, T. E. Kidd, and P. D. Johnson Electron emission from the negative electron affinity (NEA) surface of hydrogen terminated, boron doped diamond in the [100] orientation is investigated using angle resolved photoemission spectroscopy (ARPES). ARPES measurements using 16 eV synchrotron and 6 eV laser light are compared and found t... [Phys. Rev. Lett. 106, 137602] Published Wed Mar 30, 2011

Description: The Biot-Gassmann (BG) poroelasticity theory is based on the assumption of a microhomogeneous solid frame. This means that it considers the solid frame to be homogeneous at the pore-scale level. If the solid frame is built out of two or more solid constituents at the pore-scale level, then the porous rock can be considered microinhomogeneous. Although in a macroscopic sense, it still is homogeneous. Porosity changes during deformation of microinhomogeneous rocks lead to poroelastic compressibilities that are not compatible with the BG theory. The key to modeling the compressive response of microinhomogeneous rocks is the porosity perturbation equation known from the volume-averaging-based poroelasticity framework. This porosity perturbation equation entails an effective stress coefficient that can be different from unity. Only if this porosity effective stress coefficient equals unity can the porosity perturbation equation implicit to Biot’s theory be recovered. The porosity perturbation equation was reconciled with the poroelastic compressibility definitions suitable for pressure-cell experiments. These compressibilities were parameterized in terms of the porosity effective stress coefficient. The results provide a means to consistently interpret pressure-cell experiments on Berea sandstone samples in which a difference between the unjacketed bulk and pore compressibilities has been found.

Description: Motivation: High-throughput molecular data provide a wealth of information that can be integrated into network analysis. Several approaches exist that identify functional modules in the context of integrated biological networks. The objective of this study is 2-fold: first, to assess the accuracy and variability of identified modules and second, to develop an algorithm for deriving highly robust and accurate solutions. Results: In a comparative simulation study accuracy and robustness of the proposed and established methodologies are validated, considering various sources of variation in the data. To assess this variation, we propose a jackknife resampling procedure resulting in an ensemble of optimal modules. A consensus approach summarizes the ensemble into one final module containing maximally robust nodes and edges. The resulting consensus module identifies and visualizes robust and variable regions by assigning support values to nodes and edges. Finally, the proposed approach is exemplified on two large gene expression studies: diffuse large B-cell lymphoma and acute lymphoblastic leukemia. Contact: marcus.dittrich@biozentrum.uni-wuerzburg.de or tobias.mueller@biozentrum.uni-wuerzburg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Seismic attenuation and dispersion in layered sedimentary structures are often interpreted in terms of the classical White model for wave-induced pressure diffusion across the layers. However, this interlayer flow is severely dependent on the properties of the interface separating two layers. This interface behaviour can be described by a pressure jump boundary condition involving a non-vanishing interfacial impedance. In this paper, we incorporate the interfacial impedance into the White model by solving a boundary value problem in the framework of quasi-static poroelasticity. We show that the White model predictions for attenuation and dispersion substantially change. These changes can be attributed to petrophysically plausible scenarios such as imperfect hydraulic contacts or the presence of capillarity.

Description: Seismic waves propagating in porous rocks saturated with two immiscible fluids can be strongly attenuated. Predicting saturation effects on seismic responses requires a sound understanding of attenuation and velocity dependencies on the fluid distribution. Decoding these effects involves interpreting laboratory experiments, analyzing well-log data, and performing numerical simulations. Despite striking differences among scales, flow regimes, and frequency bands, some aspects of wave attenuation can be explained with a single mechanism — wave-induced pressure diffusion. Different facets of wave-induced pressure diffusion can be revealed across scales.

Description: The WHO has recently classified Neisseria gonorrhoeae as a super-bacterium due to the rapid spread of antibiotic resistant derivatives and an overall dramatic increase in infection incidences. Genome sequencing has identified potential genes, however, little is known about the transcriptional organization and the presence of non-coding RNAs in gonococci. We performed RNA sequencing to define the transcriptome and the transcriptional start sites of all gonococcal genes and operons. Numerous new transcripts including 253 potentially non-coding RNAs transcribed from intergenic regions or antisense to coding genes were identified. Strikingly, strong antisense transcription was detected for the phase-variable opa genes coding for a family of adhesins and invasins in pathogenic Neisseria , that may have regulatory functions. Based on the defined transcriptional start sites, promoter motifs were identified. We further generated and sequenced a high density Tn5 transposon library to predict a core of 827 gonococcal essential genes, 133 of which have no known function. Our combined RNA-Seq and Tn-Seq approach establishes a detailed map of gonococcal genes and defines the first core set of essential gonococcal genes.

Description: Motivation: With 〉8 million new cases in 2010, particularly documented in developing countries, tuberculosis (TB) is still a highly present pandemic and often terminal. This is also due to the emergence of antibiotic-resistant strains (MDR-TB and XDR-TB) of the primary causative TB agent Mycobacterium tuberculosis (MTB). Efforts to develop new effective drugs against MTB are restrained by the unique and largely impermeable composition of the mycobacterial cell wall. Results: Based on a database of antimycobacterial substances (CDD TB), 3815 compounds were classified as active and thus permeable. A data mining approach was conducted to gather the physico-chemical similarities of these substances and delimit them from a generic dataset of drug-like molecules. On the basis of the differences in these datasets, a regression model was generated and implemented into the online tool MycPermCheck to predict the permeability probability of small organic compounds. Discussion: Given the current lack of precise molecular criteria determining mycobacterial permeability, MycPermCheck represents an unprecedented prediction tool intended to support antimycobacterial drug discovery. It follows a novel knowledge-driven approach to estimate the permeability probability of small organic compounds. As such, MycPermCheck can be used intuitively as an additional selection criterion for potential new inhibitors against MTB. Based on the validation results, its performance is expected to be of high practical value for virtual screening purposes. Availability : The online tool is freely accessible under the URL http://www.mycpermcheck.aksotriffer.pharmazie.uni-wuerzburg.de Contact : sotriffer@uni-wuerzburg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The sulfated polysaccharide dermatan sulfate (DS) forms proteoglycans with a number of distinct core proteins. Iduronic acid-containing domains in DS have a key role in mediating the functions of DS proteoglycans. Two tissue-specific DS epimerases, encoded by DSE and DSEL , and a GalNAc-4- O -sulfotransferase encoded by CHST14 are necessary for the formation of these domains. CHST14 mutations were previously identified for patients with the musculocontractural type of Ehlers–Danlos syndrome (MCEDS). We now identified a homozygous DSE missense mutation (c.803C〉T, p.S268L) by the positional candidate approach in a male child with MCEDS, who was born to consanguineous parents. Heterologous expression of mutant full-length and soluble recombinant DSE proteins showed a loss of activity towards partially desulfated DS. Patient-derived fibroblasts also showed a significant reduction in epimerase activity. The amount of DS disaccharides was markedly decreased in the conditioned medium and the cell fraction from cultured fibroblasts of the patient when compared with a healthy control subject, whereas no apparent difference was observed in the chondroitin sulfate (CS) chains from the conditioned media. However, the total amount of CS disaccharides in the cell fraction from the patient was increased ~1.5-fold, indicating an increased synthesis or a reduced conversion of CS chains in the cell fraction. Stable transfection of patient fibroblasts with a DSE expression vector increased the amount of secreted DS disaccharides. DSE deficiency represents a specific defect of DS biosynthesis. We demonstrate locus heterogeneity in MCEDS and provide evidence for the importance of DS in human development and extracellular matrix maintenance.

Description: When a porous medium is permeated by open fractures, wave-induced flow between pores and fractures can cause significant attenuation and dispersion. Most studies of this phenomenon assume that pores and fractures are saturated with the same fluid. In some situations, particularly when a fluid such as water or carbon dioxide is injected into a tight hydrocarbon reservoir, fractures may be filled with a different fluid (with capillary forces preventing fluid mixing). Here we develop a model for wave propagation in a porous medium with aligned fractures where pores and fractures are filled with different fluids. The fractured medium is modelled as a periodic system of alternating layers of two types: thick porous layers representing the background, and very thin and highly compliant porous layers representing fractures. A dispersion equation for the P -wave propagating through a layered porous medium is derived using Biot's theory of wave propagation in periodically stratified poroelastic media. By taking the limit of zero thickness and zero normal stiffness of the thin layers, we obtain expressions for dispersion and attenuation of the P waves. The results show that in the low-frequency limit the elastic properties of such a medium can be described by Gassmann's equation with a composite fluid, whose bulk modulus is a harmonic (Wood) average of the moduli of the two fluids. The dispersion is relatively large when the fluid in both pores and fractures is liquid, and also when the pores are filled with a liquid but fractures are filled with a highly compressible gas. An intermediate case exists where the fluid in the pores is liquid while the fluid in the fractures has a bulk modulus between those of liquid and gas. In this intermediate case no dispersion is observed. This can be explained by observing that for uniform saturation, wave-induced compression causes flow from fractures into pores due to the high compliance of the fractures. Conversely, when pores are filled with a liquid but fractures are filled with gas, the fluid will flow from pores into fractures due to the high compressibility of gas. Thus, there exists an intermediate fracture fluid compressibility such that no flow can be induced and hence no dispersion or attenuation is observed.