Scenario dependence of linear site-effect factors for short-period response spectral ordinates

Ground‐motion models for response spectral ordinates commonly partition site‐response effects into linear and nonlinear components. The nonlinear components depend upon the earthquake scenario being considered implicitly through the use of the expected level of excitation at some reference horizon. The linear components are always assumed to be independent of the earthquake scenario. This article presents empirical and numerical evidence as well as a theoretical explanation for why the linear component of site response depends upon the magnitude and distance of the earthquake scenario. Although the impact is most pronounced for small‐magnitude scenarios, the finding has significant implications for a number of applications of more general interest including the development of site‐response terms within ground‐motion models, the estimation of ground‐motion variability components ϕS2SϕS2S and ϕSSϕSS , the construction of partially nonergodic models for site‐specific hazard assessments, and the validity of the convolution approach for computing surface hazard curves from those at a reference horizon, among others. All of these implications are discussed in the present article

Development of pGEMINI, a Plant Gateway Destination Vector Allowing the Simultaneous Integration of Two cDNA via a Single LR-Clonase Reaction

Gateway technology has been used to facilitate the generation of a large number of constructs for the modification of plants for research purposes. However, many of the currently available vectors only allow the integration of a single cDNA of interest into an expression clone. The ability to over-express multiple genes in combination is essential for the study of plant development where several transcripts have a role to play in one or more metabolic processes. The tools to carry out such studies are limited, and in many cases rely on the incorporation of cDNA into expression systems via conventional cloning, which can be both time consuming and laborious. To our knowledge, this study reports on the first development of a vector allowing the simultaneous integration of two independent cDNAs via a single LR-clonase reaction. This vector “pGEMINI” represents a powerful molecular tool offering the ability to study the role of multi-cDNA constructs on plant development, and opens up the process of gene stacking and the study of gene combinations through transient or stable transformation procedures

Developing a model for the prediction of ground motions due to earthquakes in the Groningen gas field

Major efforts are being undertaken to quantify seismic hazard and risk due to production-induced earthquakes in the Groningen gas field as the basis for rational decision-making about mitigation measures. An essential element is a model to estimate surface ground motions expected at any location for each earthquake originating within the gas reservoir. Taking advantage of the excellent geological and geophysical characterisation of the field and a growing database of ground-motion recordings, models have been developed for predicting response spectral accelerations, peak ground velocity and ground-motion durations for a wide range of magnitudes. The models reflect the unique source and travel path characteristics of the Groningen earthquakes, and account for the inevitable uncertainty in extrapolating from the small observed magnitudes to potential larger events. The predictions of ground-motion amplitudes include the effects of nonlinear site response of the relatively soft near-surface deposits throughou t the field

Genome sequence of foot-and-mouth disease virus serotype O lineage ind-2001d collected in vietnam in 2015

© 2017 Arzt et al. In 2015, foot-and-mouth disease (FMD) virus lineage Ind-2001 was detected for the first time in Southeast Asia. This report contains the first nearcomplete genome sequence of a viral isolate from this lineage collected from an outbreak in Vietnam. This novel incursion has substantial implications for regional FMD control measures

Derivation of a near-surface damping model for the Groningen gas field

Seismic damping of near-surface deposits is an important input to site-response analysis for seismic hazard assessment. In Groningen, the Netherlands, gas production from a reservoir at 3 km depth causes seismicity. Above the gas field, an 800 m thick layer of unconsolidated sediments exist, which consists of a mixture of sand, gravel, clay and peat strata. Shear waves induced at 3 km depth experience most of their anelastic attenuation in these loose sediments. A good estimate of damping is therefore crucial for modeling realistic ground-motion levels. In Groningen, we take advantage of a large network of 200 m deep vertical arrays to estimate damping from recordings of the induced events. As a first step, we apply seismic interferometry by deconvolution to estimate local transfer functions over these vertical arrays. Subsequently, two different methods are employed. The first is the ’up-going’ method, where the amplitude decay of the retrieved up-going wave is used. The second is the ’up-down’ method, where the amplitude difference between retrieved up- and down-going waves is utilized. For the up-going method, the amplitude of the up-going direct wave is affected by both elastic and anelastic effects. In order to estimate the anelastic attenuation it is necessary to remove the elastic amplification first. Despite the fact that elastic compensation could be determined quite accurately, non-physical damping values were estimated for a number of boreholes. Likely, the underlying cause was small differences in effective response functions of geophones at different depths. It was found that the up-down method is more robust. With this method, elastic propagation corrections are not needed. In addition, small differences in in situ geophone response are irrelevant because the up- and down-going waves retrieved at the same geophone, are used. For the 1D case we showed that for estimating the local transfer function, the complex reverberations need to be included in the interferometric process. Only when this is done, the transfer function does not contain elastic transmission loss and Q estimation can be made without knowing the soil profile in detail. Uncertainty in the estimated damping was found from the signal-to-noise ratio of the estimated transfer function. The Q profiles estimated with the up-down method were used to derive a damping model for the top 200 m of the entire Groningen field. A scaling relation was derived by comparing estimated Q profiles with low-strain damping profiles that were constructed using published models for low-strain damping linked to soil properties. This scaling relation, together with the soil-properties based damping model, allowed up-scaling of the model to each grid-cell in the Groningen field. For depths below 200 m, damping was derived from the attenuation of the microseism over Groningen. The mean damping model, over a frequency band between 2 and 20 Hz, was estimated to be 2.0% (0-50 m depth), 1.3% (50-100 m), 0.66% (100-150 m), 0.57% (150-200 m) and 0.5% (200-580 m)

Liquefaction hazard of the Groningen region of the Netherlands due to induced seismicity

The operator of the Groningen gas field is leading an effort to quantify the seismic hazard and riskof the region due to induced earthquakes, includingoverseeing one of the most comprehensive liquefaction hazard studies performedgloballyto date. Due tothe unique characteristics of the seismic hazard and the geologic deposits in Groningen, efforts first focused on developing relationships for a Groningen-specific liquefaction triggering model. The liquefaction hazard was then assessedusing a Monte Carlo method, wherein a range of credibleevent scenarios were considered in computingliquefaction damage-potentialhazard curves. Thiseffort entailed the use of a regional stochastic seismic source model,ground motion prediction equation,site response model,and geologic model that were developed as part of the broader regional seismic hazardassessment.“No-to-Minor Surficial Liquefaction Manifestations”arepredicted for mostsites across the study areafor a 75-year return period. The only sites where “Moderate Surficial Liquefaction Manifestations” are predicted are in the town of Zandeweer, with only some of the sites in the townbeing predicted to experience this severityof liquefactionfor thisreturn period

Using molecular data for epidemiological inference: assessing the prevalence of Trypanosoma brucei rhodesiense in Tsetse in Serengeti, Tanzania

Background: Measuring the prevalence of transmissible Trypanosoma brucei rhodesiense in tsetse populations is essential for understanding transmission dynamics, assessing human disease risk and monitoring spatio-temporal trends and the impact of control interventions. Although an important epidemiological variable, identifying flies which carry transmissible infections is difficult, with challenges including low prevalence, presence of other trypanosome species in the same fly, and concurrent detection of immature non-transmissible infections. Diagnostic tests to measure the prevalence of T. b. rhodesiense in tsetse are applied and interpreted inconsistently, and discrepancies between studies suggest this value is not consistently estimated even to within an order of magnitude. Methodology/Principal Findings: Three approaches were used to estimate the prevalence of transmissible Trypanosoma brucei s.l. and T. b. rhodesiense in Glossina swynnertoni and G. pallidipes in Serengeti National Park, Tanzania: (i) dissection/microscopy; (ii) PCR on infected tsetse midguts; and (iii) inference from a mathematical model. Using dissection/microscopy the prevalence of transmissible T. brucei s.l. was 0% (95% CI 0–0.085) for G. swynnertoni and 0% (0–0.18) G. pallidipes; using PCR the prevalence of transmissible T. b. rhodesiense was 0.010% (0–0.054) and 0.0089% (0–0.059) respectively, and by model inference 0.0064% and 0.00085% respectively. Conclusions/Significance: The zero prevalence result by dissection/microscopy (likely really greater than zero given the results of other approaches) is not unusual by this technique, often ascribed to poor sensitivity. The application of additional techniques confirmed the very low prevalence of T. brucei suggesting the zero prevalence result was attributable to insufficient sample size (despite examination of 6000 tsetse). Given the prohibitively high sample sizes required to obtain meaningful results by dissection/microscopy, PCR-based approaches offer the current best option for assessing trypanosome prevalence in tsetse but inconsistencies in relating PCR results to transmissibility highlight the need for a consensus approach to generate meaningful and comparable data

Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

Background Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far not been performed. Results Using a combination of long- and short-read sequencing, we establish that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit. DNA methylation dynamics at these haplotypes are dichotomous and life-stage specific: at one haplotype, the DNA methylation state is sensitive to the in utero environment, but refractory to post-weaning influences, whereas other haplotypes entropically gain DNA methylation during aging only. On the other hand, individual rDNA units in human show limited evidence of genetic haplotypes, and hence little discernible correlation between genetic and epigenetic states. However, in both species, adjacent units show similar epigenetic profiles, and the overall epigenetic state at rDNA is strongly positively correlated with the total rDNA copy number. Analysis of different mouse inbred strains reveals that in some strains, such as 129S1/SvImJ, the rDNA copy number is only approximately 150 copies per diploid genome and DNA methylation levels are < 5%. Conclusions Our work demonstrates that rDNA-associated genetic variation has a considerable influence on rDNA epigenetic state and consequently rRNA expression outcomes. In the future, it will be important to consider the impact of inter-individual rDNA (epi)genetic variation on mammalian phenotypes and diseases