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  • 1
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    Hot Embossed Microtopographic Gradients Reveal Morphological Cues That Guide the Settlement of Zoospores (2013)
    American Chemical Society (ACS)
    In: Langmuir
    Details
    Publication Date: 2013-01-16
    Description: Langmuir DOI: 10.1021/la303832u
    Print ISSN: 0743-7463
    Electronic ISSN: 1520-5827
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 2
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    Path Durations for Use in the Stochastic-Method Simulation of Ground Motions (2014)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2014-10-04
    Description: The stochastic method of ground-motion simulation assumes that the energy in a target spectrum is spread over a duration D T . D T is generally decomposed into the duration due to source effects ( D S ) and to path effects ( D P ). For the most commonly used source, seismological theory directly relates D S to the source corner frequency, accounting for the magnitude scaling of D T . In contrast, D P is related to propagation effects that are more difficult to represent by analytic equations based on the physics of the process. We are primarily motivated to revisit D T because the function currently employed by many implementations of the stochastic method for active tectonic regions underpredicts observed durations, leading to an overprediction of ground motions for a given target spectrum. Further, there is some inconsistency in the literature regarding which empirical duration corresponds to D T . Thus, we begin by clarifying the relationship between empirical durations and D T as used in the first author’s implementation of the stochastic method, and then we develop a new D P relationship. The new D P function gives significantly longer durations than in the previous D P function, but the relative contribution of D P to D T still diminishes with increasing magnitude. Thus, this correction is more important for small events or subfaults of larger events modeled with the stochastic finite-fault method.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 3
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    Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-26
    Description: Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" 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/PMC3760481/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Henriet, Simon -- Mungpakdee, Sutada -- Aury, Jean-Marc -- Da Silva, Corinne -- Brinkmann, Henner -- Mikhaleva, Jana -- Olsen, Lisbeth Charlotte -- Jubin, Claire -- Canestro, Cristian -- Bouquet, Jean-Marie -- Danks, Gemma -- Poulain, Julie -- Campsteijn, Coen -- Adamski, Marcin -- Cross, Ismael -- Yadetie, Fekadu -- Muffato, Matthieu -- Louis, Alexandra -- Butcher, Stephen -- Tsagkogeorga, Georgia -- Konrad, Anke -- Singh, Sarabdeep -- Jensen, Marit Flo -- Huynh Cong, Evelyne -- Eikeseth-Otteraa, Helen -- Noel, Benjamin -- Anthouard, Veronique -- Porcel, Betina M -- Kachouri-Lafond, Rym -- Nishino, Atsuo -- Ugolini, Matteo -- Chourrout, Pascal -- Nishida, Hiroki -- Aasland, Rein -- Huzurbazar, Snehalata -- Westhof, Eric -- Delsuc, Frederic -- Lehrach, Hans -- Reinhardt, Richard -- Weissenbach, Jean -- Roy, Scott W -- Artiguenave, Francois -- Postlethwait, John H -- Manak, J Robert -- Thompson, Eric M -- Jaillon, Olivier -- Du Pasquier, Louis -- Boudinot, Pierre -- Liberles, David A -- Volff, Jean-Nicolas -- Philippe, Herve -- Lenhard, Boris -- Roest Crollius, Hugues -- Wincker, Patrick -- Chourrout, Daniel -- Z01 LM000073-12/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Institut de Genomique, Genoscope, Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097902" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA Transposable Elements ; DNA, Intergenic ; Exons ; Gene Order ; Genes, Duplicate ; Genes, Homeobox ; *Genome ; Introns ; Invertebrates/classification/genetics ; Molecular Sequence Data ; Recombination, Genetic ; Spliceosomes/metabolism ; Synteny ; Urochordata/anatomy & histology/classification/*genetics/immunology ; Vertebrates/classification/genetics
    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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  • 4
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    Critical Parameters Affecting Bias and Variability in Site-Response Analyses Using KiK-net Downhole Array Data (2013)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2013-06-08
    Description: Because of the limited number of strong-motion records that have measured ground response at large strains, any statistical analyses of seismic site-response models subject to strong ground motions are severely limited by a small number of observations. Recent earthquakes in Japan, including the M w  9.0 Tohoku earthquake of March 2011, have substantially increased the observations of strong-motion records that can be used to compare alternative site-response models at large strains and can subsequently provide insight into the accuracy and precision of site-response models. Using the Kiban-Kyoshin network (KiK-net) downhole array data in Japan, we analyze the accuracy (bias) and variability (precision) resulting from common site-response modeling assumptions, and we identify critical parameters that significantly contribute to the uncertainty in site-response analyses. We perform linear and equivalent-linear site-response analyses at 100 KiK-net sites using 3720 ground motions ranging in amplitude from weak to strong; 204 of these records have peak ground accelerations greater than at the ground surface. We find that the maximum shear strain in the soil profile, the observed peak ground acceleration at the ground surface, and the predominant spectral period of the surface ground motion are the best predictors of where the evaluated models become inaccurate and/or imprecise. The peak shear strains beyond which linear analyses become inaccurate in predicting surface pseudospectral accelerations (PSA; presumably as a result of nonlinear soil behavior) are a function of vibration period and are between 0.01% and 0.1% for periods 〈0.5 s. Equivalent-linear analyses become inaccurate at peak strains of ~0.4% over this range of periods. We find that, for the sites and ground motions considered, site-response residuals at spectral periods 〉0.5 s do not display noticeable effects of nonlinear soil behavior. Online Material: Site-specific information and model residuals at 100 KiK-net stations.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 5
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    A VS30 Map for California with Geologic and Topographic Constraints (2014)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2014-10-04
    Description: For many earthquake engineering applications, site response is estimated through empirical correlations with the time-averaged shear-wave velocity to 30 m depth ( V S 30 ). These applications therefore depend on the availability of either site-specific V S 30 measurements or V S 30 maps at local, regional, and global scales. Because V S 30 measurements are sparse, a proxy frequently is needed to estimate V S 30 at unsampled locations. We present a new V S 30 map for California, which accounts for observational constraints from multiple sources and spatial scales, such as geology, topography, and site-specific V S 30 measurements. We apply the geostatistical approach of regression kriging (RK) to combine these constraints for predicting V S 30 . For the V S 30 trend, we start with geology-based V S 30 values and identify two distinct trends between topographic gradient and the residuals from the geology V S 30 model. One trend applies to deep and fine Quaternary alluvium, whereas the second trend is slightly stronger and applies to Pleistocene sedimentary units. The RK framework ensures that the resulting map of California is locally refined to reflect the rapidly expanding database of V S 30 measurements throughout California. We compare the accuracy of the new mapping method to a previously developed map of V S 30 for California. We also illustrate the sensitivity of ground motions to the new V S 30 map by comparing real and scenario ShakeMaps with V S 30 values from our new map to those for existing V S 30 maps. Online Material: California statewide V S 30 and ShakeMaps for Loma Prieta.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 6
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    OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: We report the development of OikoBase ( http://oikoarrays.biology.uiowa.edu/Oiko/ ), a tiling array-based genome browser resource for Oikopleura dioica , a metazoan belonging to the urochordates, the closest extant group to vertebrates. OikoBase facilitates retrieval and mining of a variety of useful genomics information. First, it includes a genome browser which interrogates 1260 genomic sequence scaffolds and features gene, transcript and CDS annotation tracks. Second, we annotated gene models with gene ontology (GO) terms and InterPro domains which are directly accessible in the browser with links to their entries in the GO ( http://www.geneontology.org/ ) and InterPro ( http://www.ebi.ac.uk/interpro/ ) databases, and we provide transcript and peptide links for sequence downloads. Third, we introduce the transcriptomics of a comprehensive set of developmental stages of O. dioica at high resolution and provide downloadable gene expression data for all developmental stages. Fourth, we incorporate a BLAST tool to identify homologs of genes and proteins. Finally, we include a tutorial that describes how to use OikoBase as well as a link to detailed methods, explaining the data generation and analysis pipeline. OikoBase will provide a valuable resource for research in chordate development, genome evolution and plasticity and the molecular ecology of this important marine planktonic organism.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Expansion of Cyclin D and CDK1 Paralogs in Oikopleura dioica, a Chordate Employing Diverse Cell Cycle Variants (2011)
    Oxford University Press
    Details
    Publication Date: 2011-07-06
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    The Gumbel hypothesis test for left censored observations using regional earthquake records as an example (2011)
    Copernicus
    Details
    Publication Date: 2011-01-11
    Description: Annual maximum (AM) time series are incomplete (i.e., censored) when no events are included above the assumed censoring threshold (i.e., magnitude of completeness). We introduce a distrtibutional hypothesis test for left-censored Gumbel observations based on the probability plot correlation coefficient (PPCC). Critical values of the PPCC hypothesis test statistic are computed from Monte-Carlo simulations and are a function of sample size, censoring level, and significance level. When applied to a global catalog of earthquake observations, the left-censored Gumbel PPCC tests are unable to reject the Gumbel hypothesis for 45 of 46 seismic regions. We apply four different field significance tests for combining individual tests into a collective hypothesis test. None of the field significance tests are able to reject the global hypothesis that AM earthquake magnitudes arise from a Gumbel distribution. Because the field significance levels are not conclusive, we also compute the likelihood that these field significance tests are unable to reject the Gumbel model when the samples arise from a more complex distributional alternative. A power study documents that the censored Gumbel PPCC test is unable to reject some important and viable Generalized Extreme Value (GEV) alternatives. Thus, we cannot rule out the possibility that the global AM earthquake time series could arise from a GEV distribution with a finite upper bound, also known as a reverse Weibull distribution. Our power study also indicates that the binomial and uniform field significance tests are substantially more powerful than the more commonly used Bonferonni and false discovery rate multiple comparison procedures.
    Print ISSN: 1561-8633
    Electronic ISSN: 1684-9981
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 9
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    Multiscale Site-Response Mapping: A Case Study of Parkfield, California (2011)
    Seismological Society of America
    Details
    Publication Date: 2011-05-29
    Description: The scale of previously proposed methods for mapping site-response ranges from global coverage down to individual urban regions. Typically, spatial coverage and accuracy are inversely related. We use the densely spaced strong-motion stations in Parkfield, California, to estimate the accuracy of different site-response mapping methods and demonstrate a method for integrating multiple site-response estimates from the site to the global scale. This method is simply a weighted mean of a suite of different estimates, where the weights are the inverse of the variance of the individual estimates. Thus, the dominant site-response model varies in space as a function of the accuracy of the different models. For mapping applications, site-response models should be judged in terms of both spatial coverage and the degree of correlation with observed amplifications. Performance varies with period, but in general the Parkfield data show that: (1) where a velocity profile is available, the square-root-of-impedance (SRI) method outperforms the measured V (sub S30) (30 m divided by the S-wave travel time to 30 m depth) and (2) where velocity profiles are unavailable, the topographic slope method outperforms surficial geology for short periods, but geology outperforms slope at longer periods. We develop new equations to estimate site response from topographic slope, derived from the Next Generation Attenuation (NGA) database.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America
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  • 10
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    Regional Correlations of VS30 and Velocities Averaged Over Depths Less Than and Greater Than 30 Meters (2011)
    Seismological Society of America
    Details
    Publication Date: 2011-12-01
    Description: Using velocity profiles from sites in Japan, California, Turkey, and Europe, we find that the time-averaged shear-wave velocity to 30 m (V (sub S30) ), used as a proxy for site amplification in recent ground-motion prediction equations (GMPEs) and building codes, is strongly correlated with average velocities to depths less than 30 m (V (sub Sz) , with z being the averaging depth). The correlations for sites in Japan (corresponding to the KiK-net network) show that V (sub S30) is systematically larger for a given V (sub Sz) than for profiles from the other regions. The difference largely results from the placement of the KiK-net station locations on rock and rocklike sites, whereas stations in the other regions are generally placed in urban areas underlain by sediments. Using the KiK-net velocity profiles, we provide equations relating V (sub S30) to V (sub Sz) for z ranging from 5 to 29 m in 1-m increments. These equations (and those for California velocity profiles given in Boore, 2004b) can be used to estimate V (sub S30) from V (sub Sz) for sites in which velocity profiles do not extend to 30 m. The scatter of the residuals decreases with depth, but, even for an averaging depth of 5 m, a variation in logV (sub S30) of + or -1 standard deviation maps into less than a 20% uncertainty in ground motions given by recent GMPEs at short periods. The sensitivity of the ground motions to V (sub S30) uncertainty is considerably larger at long periods (but is less than a factor of 1.2 for averaging depths greater than about 20 m). We also find that V (sub S30) is correlated with V (sub Sz) for z as great as 400 m for sites of the KiK-net network, providing some justification for using V (sub S30) as a site-response variable for predicting ground motions at periods for which the wavelengths far exceed 30 m.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America
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