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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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    Revisions to Some Parameters Used in Stochastic-Method Simulations of Ground Motion (2015)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2015-04-01
    Description: The stochastic method of ground-motion simulation specifies the amplitude spectrum as a function of magnitude ( M ) and distance ( R ). The manner in which the amplitude spectrum varies with M and R depends on physical-based parameters that are often constrained by recorded motions for a particular region (e.g., stress parameter, geometrical spreading, quality factor, and crustal amplifications), which we refer to as the seismological model. The remaining ingredient for the stochastic method is the ground-motion duration. Although the duration obviously affects the character of the ground motion in the time domain, it also significantly affects the response of a single-degree-of-freedom oscillator. Recently published updates to the stochastic method include a new generalized double-corner-frequency source model, a new finite-fault correction, a new parameterization of duration, and a new duration model for active crustal regions. In this article, we augment these updates with a new crustal amplification model and a new duration model for stable continental regions. Random-vibration theory (RVT) provides a computationally efficient method to compute the peak oscillator response directly from the ground-motion amplitude spectrum and duration. Because the correction factor used to account for the nonstationarity of the ground motion depends on the ground-motion amplitude spectrum and duration, we also present new RVT correction factors for both active and stable regions. Online Material: Files of coefficients for evaluating distance ( D rms ), time-domain–to–random-vibration ratios, and SMSIM parameter files.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 4
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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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  • 5
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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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  • 6
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    Uncertainty in VS30-Based Site Response (2016)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2016-04-07
    Description: Methods that account for site response range in complexity from simple linear categorical adjustment factors to sophisticated nonlinear constitutive models. Seismic-hazard analysis usually relies on ground-motion prediction equations (GMPEs); within this framework site response is modeled statistically with simplified site parameters that include the time-averaged shear-wave velocity to 30 m ( V S 30 ) and basin depth parameters. Because V S 30 is not known in most locations, it must be interpolated or inferred through secondary information such as geology or topography. In this article, we analyze a subset of stations for which V S 30 has been measured to address effects of V S 30 proxies on the uncertainty in the ground motions as modeled by GMPEs. The stations we analyze also include multiple recordings, which allow us to compute the repeatable site effects (or empirical amplification factors [EAFs]) from the ground motions. Although all methods exhibit similar bias, the proxy methods only reduce the ground-motion standard deviations at long periods when compared to GMPEs without a site term, whereas measured V S 30 values reduce the standard deviations at all periods. The standard deviation of the ground motions are much lower when the EAFs are used, indicating that future refinements of the site term in GMPEs have the potential to substantially reduce the overall uncertainty in the prediction of ground motions by GMPEs.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 7
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    Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-14
    Description: Polycistronic mRNAs transcribed from operons are resolved via the trans -splicing of a spliced-leader (SL) RNA. Trans -splicing also occurs at monocistronic transcripts. The phlyogenetically sporadic appearance of trans -splicing and operons has made the driving force(s) for their evolution in metazoans unclear. Previous work has proposed that germline expression drives operon organization in Caenorhabditis elegans , and a recent hypothesis proposes that operons provide an evolutionary advantage via the conservation of transcriptional machinery during recovery from growth arrested states. Using a modified cap analysis of gene expression protocol we mapped sites of SL trans -splicing genome-wide in the marine chordate Oikopleura dioica . Tiled microarrays revealed the expression dynamics of trans -spliced genes across development and during recovery from growth arrest. Operons did not facilitate recovery from growth arrest in O. dioica . Instead, we found that trans -spliced transcripts were predominantly maternal. We then analyzed data from C. elegans and Ciona intestinalis and found that an enrichment of trans -splicing and operon gene expression in maternal mRNA is shared between all three species, suggesting that this may be a driving force for operon evolution in metazoans. Furthermore, we found that the majority of known terminal oligopyrimidine (TOP) mRNAs are trans -spliced in O. dioica and that the SL contains a TOP-like motif. This suggests that the SL in O. dioica confers nutrient-dependent translational control to trans -spliced mRNAs via the TOR-signaling pathway. We hypothesize that SL- trans -splicing provides an evolutionary advantage in species that depend on translational control for regulating early embryogenesis, growth and oocyte production in response to nutrient levels.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Geotechnical Effects of the 2015 Magnitude 7.8 Gorkha, Nepal, Earthquake and Aftershocks (2015)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2015-10-29
    Description: This article summarizes the geotechnical effects of the 25 April 2015 M  7.8 Gorkha, Nepal, earthquake and aftershocks, as documented by a reconnaissance team that undertook a broad engineering and scientific assessment of the damage and collected perishable data for future analysis. Brief descriptions are provided of ground shaking, surface fault rupture, landsliding, soil failure, and infrastructure performance. The goal of this reconnaissance effort, led by Geotechnical Extreme Events Reconnaissance, is to learn from earthquakes and mitigate hazards in future earthquakes.
    Print ISSN: 0895-0695
    Electronic ISSN: 1938-2057
    Topics: Geosciences
    Published by Seismological Society of America (SSA)
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  • 9
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    Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioral problems (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-01
    Description: Next generation genomic technologies have made a significant contribution to the understanding of the genetic architecture of human neurodevelopmental disorders. Copy number variants (CNVs) play an important role in the genetics of intellectual disability (ID). For many CNVs, and copy number gains in particular, the responsible dosage-sensitive gene(s) have been hard to identify. We have collected 18 different interstitial microduplications and 1 microtriplication of Xq25. There were 15 affected individuals from 6 different families and 13 singleton cases, 28 affected males in total. The critical overlapping region involved the STAG2 gene, which codes for a subunit of the cohesin complex that regulates cohesion of sister chromatids and gene transcription. We demonstrate that STAG2 is the dosage-sensitive gene within these CNVs, as gains of STAG2 mRNA and protein dysregulate disease-relevant neuronal gene networks in cells derived from affected individuals. We also show that STAG2 gains result in increased expression of OPHN1 , a known X-chromosome ID gene. Overall, we define a novel cohesinopathy due to copy number gain of Xq25 and STAG2 in particular.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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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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