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  • 1
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    Stochastic regridding of geological models for flow simulation (2016)
    Canadian Society of Petroleum Geologists (CSPG)
    Details
    Publication Date: 2016-03-29
    Description: Regridding geological models to a higher resolution for flow simulation is an important problem in geostatistical modeling. For practical reasons, over a large area, models can only be built at a relatively coarse resolution. Subsequently, the resolution of specified regions of interest must be increased before upscaling for flow modeling. The construction of a high-resolution model of the entire reservoir at the beginning of the evaluation may be impractical because of computational and time constraints. It is standard practice to implement nearest neighbor interpolation to increase the resolution of models. Although it is a simple practical solution, nearest neighbor interpolation introduces spatial continuity artifacts that are often unrealistic. This paper proposes an automatic stochastic regridding approach based on simulation. The simulation is conditioned to the initial coarse resolution model/realization. The process includes the extraction of specified regions of interest, definition of corresponding local variography, and implementation of Sequential Gaussian Simulation (SGS) and/or Sequential Indicator Simulation (SIS) to characterize continuous and categorical variables, respectively. In each specified region, the local variography can be defined by either implementing automatic fitting algorithms or assigning the global variography initially used to build the coarse resolution model. The regridding process is automated. The advantage of this approach over the conventional nearest neighbor interpolation is in the improvement in the realistic spatial variability features of small scale geologic heterogeneity. The benefits of obtaining a proper regridded model are discussed in a case study of a fluvial reservoir in the McMurray formation. One of the main reasons for generating high resolution models is in the appropriate characterization of small scale impermeable geobodies such as remnant shales. The coarse resolution models are not able to properly characterize the small scale geologic features of the shales; more amount of information is required to characterize smaller scale features. The metric of performance considered is the effective vertical permeability. The automated stochastic regridding workflow described in this paper is available on a Fortran platform with additional scripting which will be distributed upon request. Note that the terms "regridding" and "stochastic regridding" are used interchangeably and both refer to the proposed workflow of modeling at higher resolution.
    Print ISSN: 0007-4802
    Electronic ISSN: 0007-4802
    Topics: Geosciences
    Published by Canadian Society of Petroleum Geologists (CSPG)
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  • 2
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    Digestive Organ in the Female Reproductive Tract Borrows Genes from Multiple Organ Systems to Adopt Critical Functions (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-30
    Description: Persistent adaptive challenges are often met with the evolution of novel physiological traits. Although there are specific examples of single genes providing new physiological functions, studies on the origin of complex organ functions are lacking. One such derived set of complex functions is found in the Lepidopteran bursa copulatrix, an organ within the female reproductive tract that digests nutrients from the male ejaculate or spermatophore. Here, we characterized bursa physiology and the evolutionary mechanisms by which it was equipped with digestive and absorptive functionality. By studying the transcriptome of the bursa and eight other tissues, we revealed a suite of highly expressed and secreted gene products providing the bursa with a combination of stomach-like traits for mechanical and enzymatic digestion of the male spermatophore. By subsequently placing these bursa genes in an evolutionary framework, we found that the vast majority of their novel digestive functions were co-opted by borrowing genes that continue to be expressed in nonreproductive tissues. However, a number of bursa-specific genes have also arisen, some of which represent unique gene families restricted to Lepidoptera and may provide novel bursa-specific functions. This pattern of promiscuous gene borrowing and relatively infrequent evolution of tissue-specific duplicates stands in contrast to studies of the evolution of novelty via single gene co-option. Our results suggest that the evolution of complex organ-level phenotypes may often be enabled (and subsequently constrained) by changes in tissue specificity that allow expression of existing genes in novel contexts, such as reproduction. The extent to which the selective pressures encountered in these novel roles require resolution via duplication and sub/neofunctionalization is likely to be determined by the need for specialized reproductive functionality. Thus, complex physiological phenotypes such as that found in the bursa offer important opportunities for understanding the relative role of pleiotropy and specialization in adaptive evolution.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Short-Term Plant Community Responses to Warming and Defoliation in a Northern Temperate Grassland (2012)
    International Scholarly Research Network (ISRN)
    Details
    Publication Date: 2012-06-21
    Description: Little is known about the short-term impacts of warming on native plant community dynamics in the northern Canadian prairies. This study examined the immediate effects of elevated temperature and defoliation on plant community diversity, composition, and biomass within a native rough fescue (Festuca hallii (Vasey) Piper) grassland over two growing seasons. We used open-top chambers to simulate climate change and defoliated vegetation in midsummer of the first year to simulate biomass loss associated with periodic ungulate grazing. Warming marginally increased plant species diversity and changed community composition shortly after treatment, but effects were not apparent the second year, and there were no apparent impacts on plant biomass. Nonetheless, warming may have impacted community diversity indirectly through reduced soil moisture content, a pattern that persisted into the second year. Overall, this northern temperate grassland demonstrated limited community-level changes to warming even in the presence of defoliation.
    Print ISSN: 2090-4614
    Electronic ISSN: 2090-4622
    Topics: Biology
    Published by International Scholarly Research Network (ISRN)
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  • 4
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    Common regulatory variation impacts gene expression in a cell type-dependent manner (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-01
    Description: Studies correlating genetic variation to gene expression facilitate the interpretation of common human phenotypes and disease. As functional variants may be operating in a tissue-dependent manner, we performed gene expression profiling and association with genetic variants (single-nucleotide polymorphisms) on three cell types of 75 individuals. We detected cell type-specific genetic effects, with 69 to 80% of regulatory variants operating in a cell type-specific manner, and identified multiple expressive quantitative trait loci (eQTLs) per gene, unique or shared among cell types and positively correlated with the number of transcripts per gene. Cell type-specific eQTLs were found at larger distances from genes and at lower effect size, similar to known enhancers. These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867218/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867218/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dimas, Antigone S -- Deutsch, Samuel -- Stranger, Barbara E -- Montgomery, Stephen B -- Borel, Christelle -- Attar-Cohen, Homa -- Ingle, Catherine -- Beazley, Claude -- Gutierrez Arcelus, Maria -- Sekowska, Magdalena -- Gagnebin, Marilyne -- Nisbett, James -- Deloukas, Panos -- Dermitzakis, Emmanouil T -- Antonarakis, Stylianos E -- 077011/Wellcome Trust/United Kingdom -- 077046/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Sep 4;325(5945):1246-50. doi: 10.1126/science.1174148. Epub 2009 Jul 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19644074" target="_blank"〉PubMed〈/a〉
    Keywords: Allelic Imbalance ; B-Lymphocytes ; Cell Line ; Enhancer Elements, Genetic ; Fibroblasts ; Gene Expression Profiling ; *Gene Expression Regulation ; Gene Frequency ; Genotype ; Humans ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; RNA, Messenger/genetics/metabolism ; *Regulatory Elements, Transcriptional ; Statistics, Nonparametric ; T-Lymphocytes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    A measure of facies mixing in data upscaling to account for information loss in the estimation of petrophysical variables (2016)
    Geological Society of London
    Details
    Publication Date: 2016-05-14
    Description: Blocking facies information to a constant length prior to three-dimensional (3D) modelling is necessary with current 3D geostatistical modelling techniques. The high-resolution information from core and well logging must be upscaled to unify the scale to a target scale considered in building the 3D numerical models. A downside is the inevitable loss of information when the majority facies is assigned to each upscaled interval. The loss of such information could become problematic when dealing with small shale barriers in the middle of the reservoir or at the boundary of the facies transitions. This paper addresses the information loss by retaining as much information as possible in the upscaling process and proposes a metric to account for small-scale information that is mixed during the process: such a metric is referred to as facies mixing measure (FMM). Retaining more information in the upscaling process and utilizing that information to better model petrophysical properties is an important contribution. FMM is calculated during the upscaling step and is treated as a secondary property during petrophysical property modelling. Cross-validation with two different datasets demonstrates improvements in porosity estimation.
    Print ISSN: 1354-0793
    Topics: Chemistry and Pharmacology , Geosciences
    Published by Geological Society of London
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  • 6
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    Domains of genome-wide gene expression dysregulation in Down's syndrome (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-04-18
    Description: Trisomy 21 is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in trisomy 21, and to eliminate the noise of genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for trisomy 21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either upregulated or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins' fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of Down's syndrome and normal littermate mouse fibroblasts also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall position of LADs was not altered in trisomic cells; however, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results indicate that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome, and that GEDDs may therefore contribute to some trisomy 21 phenotypes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Letourneau, Audrey -- Santoni, Federico A -- Bonilla, Ximena -- Sailani, M Reza -- Gonzalez, David -- Kind, Jop -- Chevalier, Claire -- Thurman, Robert -- Sandstrom, Richard S -- Hibaoui, Youssef -- Garieri, Marco -- Popadin, Konstantin -- Falconnet, Emilie -- Gagnebin, Maryline -- Gehrig, Corinne -- Vannier, Anne -- Guipponi, Michel -- Farinelli, Laurent -- Robyr, Daniel -- Migliavacca, Eugenia -- Borel, Christelle -- Deutsch, Samuel -- Feki, Anis -- Stamatoyannopoulos, John A -- Herault, Yann -- van Steensel, Bas -- Guigo, Roderic -- Antonarakis, Stylianos E -- U54HG007010/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Apr 17;508(7496):345-50. doi: 10.1038/nature13200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Genetic Medicine and Development, University of Geneva Medical School, University Hospitals of Geneva, 1211 Geneva, Switzerland [2]. ; Department of Genetic Medicine and Development, University of Geneva Medical School, University Hospitals of Geneva, 1211 Geneva, Switzerland. ; Center for Genomic Regulation, University Pompeu Fabra, 08003 Barcelona, Spain. ; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands. ; AneuPath 21, Institut de Genetique Biologie Moleculaire et Cellulaire, Translational medicine and Neuroscience program, IGBMC, ICS, PHENOMIN, CNRS, INSERM, Universite de Strasbourg, UMR7104, UMR964, 1 rue Laurent Fries, 67404 Illkirch, France. ; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. ; Stem Cell Research Laboratory, Department of Obstetrics and Gynecology, Geneva University Hospitals, 1211 Geneva, Switzerland. ; FASTERIS SA, 1228 Plan-les-Ouates, Switzerland. ; 1] Department of Genetic Medicine and Development, University of Geneva Medical School, University Hospitals of Geneva, 1211 Geneva, Switzerland [2] Swiss Institute of Bioinfomatics, 1211 Geneva, Switzerland. ; DOE Joint Genome Institute, Walnut Creek, California 94598, USA. ; 1] Department of Genetic Medicine and Development, University of Geneva Medical School, University Hospitals of Geneva, 1211 Geneva, Switzerland [2] iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24740065" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Chromatin/chemistry/metabolism ; Chromosomes, Human, Pair 21/genetics ; Chromosomes, Mammalian/genetics ; DNA Replication Timing ; Down Syndrome/*genetics/pathology ; Female ; Fetus/cytology ; Fibroblasts ; Gene Expression Regulation/*genetics ; Genome/*genetics ; Histones/chemistry/metabolism ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Lysine/metabolism ; Male ; Methylation ; Mice ; Transcriptome/*genetics ; Twins, Monozygotic/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Letourneau, Audrey -- Santoni, Federico A -- Bonilla, Ximena -- Sailani, M Reza -- Gonzalez, David -- Kind, Jop -- Chevalier, Claire -- Thurman, Robert -- Sandstrom, Richard S -- Hibaoui, Youssef -- Garieri, Marco -- Popadin, Konstantin -- Falconnet, Emilie -- Gagnebin, Maryline -- Gehrig, Corinne -- Vannier, Anne -- Guipponi, Michel -- Farinelli, Laurent -- Robyr, Daniel -- Migliavacca, Eugenia -- Borel, Christelle -- Deutsch, Samuel -- Feki, Anis -- Stamatoyannopoulos, John A -- Herault, Yann -- van Steensel, Bas -- Guigo, Roderic -- Antonarakis, Stylianos E -- England -- Nature. 2016 Mar 17;531(7594):400. doi: 10.1038/nature16135. Epub 2015 Dec 2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26633627" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Short-Term Plant Community Responses to Warming and Defoliation in a Northern Temperate Grassland (2012)
    International Scholarly Research Network (ISRN)
    Details
    Publication Date: 2012-08-16
    Description: Little is known about the short-term impacts of warming on native plant community dynamics in the northern Canadian prairies. This study examined the immediate effects of elevated temperature and defoliation on plant community diversity, composition, and biomass within a native rough fescue (Festuca hallii (Vasey) Piper) grassland over two growing seasons. We used open-top chambers to simulate climate change and defoliated vegetation in midsummer of the first year to simulate biomass loss associated with periodic ungulate grazing. Warming marginally increased plant species diversity and changed community composition shortly after treatment, but effects were not apparent the second year, and there were no apparent impacts on plant biomass. Nonetheless, warming may have impacted community diversity indirectly through reduced soil moisture content, a pattern that persisted into the second year. Overall, this northern temperate grassland demonstrated limited community-level changes to warming even in the presence of defoliation.
    Print ISSN: 2090-4614
    Electronic ISSN: 2090-4622
    Topics: Biology
    Published by International Scholarly Research Network (ISRN)
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  • 9
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    Short-Term Plant Community Responses to Warming and Defoliation in a Northern Temperate Grassland (2012)
    International Scholarly Research Network (ISRN)
    Details
    Publication Date: 2012-10-17
    Description: Little is known about the short-term impacts of warming on native plant community dynamics in the northern Canadian prairies. This study examined the immediate effects of elevated temperature and defoliation on plant community diversity, composition, and biomass within a native rough fescue (Festuca hallii (Vasey) Piper) grassland over two growing seasons. We used open-top chambers to simulate climate change and defoliated vegetation in midsummer of the first year to simulate biomass loss associated with periodic ungulate grazing. Warming marginally increased plant species diversity and changed community composition shortly after treatment, but effects were not apparent the second year, and there were no apparent impacts on plant biomass. Nonetheless, warming may have impacted community diversity indirectly through reduced soil moisture content, a pattern that persisted into the second year. Overall, this northern temperate grassland demonstrated limited community-level changes to warming even in the presence of defoliation.
    Print ISSN: 2090-4614
    Electronic ISSN: 2090-4622
    Topics: Biology
    Published by International Scholarly Research Network (ISRN)
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  • 10
    Electronic Resource
    Electronic Resource
    Osmium subcarbonyls on .gamma.-alumina: characterization of the metal-support bonding by infrared, nuclear magnetic resonance, and x-ray absorption spectroscopies (1993)
    s.l. : American Chemical Society
    Langmuir 9 (1993), S. 1284-1289 
    Details
    ISSN: 1520-5827
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/la00029a022
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    Paper (German National Licenses)
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