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  • Artikel  (23)
  • Wiley  (15)
  • Oxford University Press  (8)
  • American Chemical Society (ACS)
  • Nature Publishing Group (NPG)
  • 2010-2014  (14)
  • 2000-2004  (7)
  • 1990-1994  (2)
  • Architektur, Bauingenieurwesen, Vermessung  (12)
  • Informatik  (8)
  • Wissenschaftskunde und Wissenschaftsorganisation, Hochschul- und Universitätswesen, Museumswissenschaft  (3)
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  • Artikel  (23)
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  • 1
    Publikationsdatum: 2014-11-05
    Beschreibung: ABSTRACT A primary concern for geologic carbon storage is the potential for leakage of stored carbon dioxide (CO 2 ) into the shallow subsurface where it could degrade the quality of groundwater and surface water. In order to predict and mitigate the potentially negative impacts of CO 2 leakage, it is important to understand the physical processes that CO 2 will undergo as it moves through naturally heterogeneous porous media formations. Previous studies have shown that heterogeneity can enhance the evolution of gas phase CO 2 in some cases, but the conditions under which this occurs have not yet been quantitatively defined, nor tested through laboratory experiments. This study quantitatively investigates the effects of geologic heterogeneity on the process of gas phase CO 2 evolution in shallow aquifers through an extensive set of experiments conducted in a column that was packed with layers of various test sands. Soil moisture sensors were utilized to observe the formation of gas phase near the porous media interfaces. Results indicate that the conditions under which heterogeneity controls gas phase evolution can be successfully predicted through analysis of simple parameters, including the dissolved CO 2 concentration in the flowing water, the distance between the heterogeneity and the leakage location, and some fundamental properties of the porous media. Results also show that interfaces where a less permeable material overlies a more permeable material affect gas phase evolution more significantly than interfaces with the opposite layering.
    Print ISSN: 0043-1397
    Digitale ISSN: 1944-7973
    Thema: Architektur, Bauingenieurwesen, Vermessung , Geographie
    Publiziert von Wiley im Namen von American Geophysical Union (AGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2011-06-19
    Beschreibung: We present a predictive, multiscale modeling framework for chemotaxis in porous media. This model results from volume averaging the governing equations for bacterial transport at the microscale and is expressed in terms of effective medium coefficients that are predicted from the solution of the associated closure problems. As a result, the averaged chemotactic velocity is an explicit function of the attractant concentration field and diffusivity, rather than an empirical effective chemotactic sensitivity coefficient. The model was validated by comparing the transverse bacterial concentration profiles with experimental measurements for Escherichia coli HCB1 in a T-sensor. The averaged chemotactic velocity predicted by the model was found to be within the range of values reported in the literature. Reasonable agreement (approximately 10% mean absolute error) between theory and experiments was found for several flow rates. In order to assess the potential for decreasing the computational demands of the model, the macroscale domain was divided into subdomains for the coupling of bacterial transport to that of the attractant. Sensitivity analysis was performed regarding the number of subdomains chosen, and the results indicate that bacterial transport (as measured by concentration profiles) was not highly affected by this choice. Overall, these results suggest that the predictive, multiscale modeling framework is reliable for modeling chemotaxis in porous media when chemotactic transport is significant compared to convective transport.
    Print ISSN: 0043-1397
    Digitale ISSN: 1944-7973
    Thema: Architektur, Bauingenieurwesen, Vermessung , Geographie
    Publiziert von Wiley im Namen von American Geophysical Union (AGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2013-02-13
    Beschreibung: Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms. Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis. Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html . Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2012-08-29
    Beschreibung: Improvements in our ability to model runoff from glaciers remain an important scientific goal. This paper describes a new temperature-radiation-index glacier melt model specifically enhanced for use in High-Arctic environments, utilising high temporal and spatial resolution datasets while retaining relatively modest data requirements. The model employs several physically constrained parameters and was tuned using a lidar-derived surface elevation model of Midtre Lovénbreen, meteorological data from sites spanning ~70% of the glacier's area-altitude distribution, and periodic ablation surveys during the 2005 melt season. The model explained 80% of the variance in observed ablation across the glacier, an improvement of ~40% on a simplified energy balance model (EBM), yet equivalent to the performance of a full EBM employed at the same location. Model performance was assessed further by comparing potential and measured runoff from the catchment, and through application to an earlier (2004) melt season. The additive model form and consideration of a priori parameters for the Arctic locality were shown to be beneficial, with a planimetry correction eliminating systematic errors in potential runoff. Further parameterisations defining modelled incident radiation failed to yield significant improvements to model output. Our results suggest that such enhanced melt models may perform well for singular melt seasons, yet are highly sensitive to the choice of lapse rates and their transferability to different locations and seasons may be limited. While modelling ablation requires detailed consideration of the transition between snow- and ice-melt, our study suggests that description of the ratio between radiative and turbulent heat fluxes may provide a useful step towards dynamic parameterisation of melt factors in temperature-index models. Copyright © 2012 John Wiley & Sons, Ltd.
    Print ISSN: 0885-6087
    Digitale ISSN: 1099-1085
    Thema: Architektur, Bauingenieurwesen, Vermessung , Geographie
    Publiziert von Wiley
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2013-07-17
    Beschreibung: Background: Homology-based taxonomic assignment is impeded by differences between the unassigned read and reference database, forcing a rank-specific classification to the closest (and possibly incorrect) reference lineage. This assignment may be correct only to a general rank (e.g. order) and incorrect below that rank (e.g. family and genus). Algorithms like LCA avoid this by varying the predicted taxonomic rank based on matches to a set of taxonomic references. LCA and related approaches can be conservative, especially if best matches are taxonomically widespread because of events such as lateral gene transfer (LGT). Results: Our extension to LCA called SPANNER (similarity profile annotater) uses the set of best homology matches (the LCA Profile) for a given sequence and compares this profile with a set of profiles inferred from taxonomic reference organisms. SPANNER provides an assignment that is less sensitive to LGT and other confounding phenomena. In a series of trials on real and artificial datasets, SPANNER outperformed LCA-style algorithms in terms of taxonomic precision and outperformed best BLAST at certain levels of taxonomic novelty in the dataset. We identify examples where LCA made an overly conservative prediction, but SPANNER produced a more precise and correct prediction. Conclusions: By using profiles of homology matches to represent patterns of genomic similarity that arise because of vertical and lateral inheritance, SPANNER offers an effective compromise between taxonomic assignment based on best BLAST scores, and the conservative approach of LCA and similar approaches. Availability: C++ source code and binaries are freely available at http://kiwi.cs.dal.ca/Software/SPANNER . Contact: beiko@cs.dal.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2013-06-03
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2003-04-01
    Print ISSN: 0302-3427
    Digitale ISSN: 1471-5430
    Thema: Wissenschaftskunde und Wissenschaftsorganisation, Hochschul- und Universitätswesen, Museumswissenschaft
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 1993-10-01
    Print ISSN: 0302-3427
    Digitale ISSN: 1471-5430
    Thema: Wissenschaftskunde und Wissenschaftsorganisation, Hochschul- und Universitätswesen, Museumswissenschaft
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2002-06-01
    Print ISSN: 0302-3427
    Digitale ISSN: 1471-5430
    Thema: Wissenschaftskunde und Wissenschaftsorganisation, Hochschul- und Universitätswesen, Museumswissenschaft
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2014-10-29
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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