Site response and attenuation in the Puget Lowland, Washington State

USGS Publications Warehouse

Pratt, T.L.; Brocher, T.M.

2006-01-01

Simple spectral ratio (SSR) and horizontal-to-vertical (HN) site-response estimates at 47 sites in the Puget Lowland of Washington State document significant attenuation of 1.5- to 20-Hz shear waves within sedimentary basins there. Amplitudes of the horizontal components of shear-wave arrivals from three local earthquakes were used to compute SSRs with respect to the average of two bedrock sites and H/V spectral ratios with respect to the vertical component of the shear-wave arrivals at each site. SSR site-response curves at thick basin sites show peak amplifications of 2 to 6 at frequencies of 3 to 6 Hz, and decreasing spectra amplification with increasing frequency above 6 Hz. SSRs at nonbasin sites show a variety of shapes and larger resonance peaks. We attribute the spectral decay at frequencies above the amplification peak at basin sites to attenuation within the basin strata. Computing the frequency-independent, depth-dependent attenuation factor (Qs,int) from the SSR spectral decay between 2 and 20 Hz gives values of 5 to 40 for shallow sedimentary deposits and about 250 for the deepest sedimentary strata (7 km depth). H/V site responses show less spectral decay than the SSR responses but contain many of the same resonance peaks. We hypothesize that the H/V method yields a flatter response across the frequency spectrum than SSRs because the H/V reference signal (vertical component of the shear-wave arrivals) has undergone a degree of attenuation similar to the horizontal component recordings. Correcting the SSR site responses for attenuation within the basins by removing the spectral decay improves agreement between SSR and H/V estimates.

Examination of the site amplification factor of OBS and their application to magnitude estimation and ground-motion prediction for EEW

NASA Astrophysics Data System (ADS)

Hayashimoto, N.; Hoshiba, M.

2013-12-01

1. Introduction Ocean bottom seismograph (OBS) is useful for making Earthquake Early Warning (EEW) earlier. However, careful handling of these data is required because the installation environment of OBSs may be different from that of land stations. Site amplification factor is an important factor to estimate the magnitudes, and to predict ground motions (e.g. seismic intensity) in EEW. In this presentation, we discuss the site amplification factor of OBS in the Tonankai area of Japan from these two points of view. 2. Examination of magnitude correction of OBS In the EEW of JMA, the magnitude is estimated from the maximum amplitude of the displacement in real time. To provide the fast magnitude estimation, the magnitude-estimation algorithm switches from the P to S formula (Meew(P) to Meew(S)) depending on the expected S-phase arrival (Kamigaichi,2004). To estimate the magnitude correction for OBS, we determine Meew(P) and Meew(S) at OBSs and compare them with JMA magnitude (Mjma). We find Meew(S) at OBS is generally larger than Mjma by approximately 0.6. The slight differences of spatial distribution of Meew(S) amplification are also found among other OBSs. From the numerical simulations, Nakamura et al. (MGR,submitted) pointed out that the oceanic layer and the low-velocity sediment layers causes the large amplifications in low frequency range (0.1-0.2Hz) at OBSs. We conclude that the site effect of OBS characterized by such a low velocity sediment layers causes those amplification of Magnitude. 3. The frequency-dependent site factor of OBS estimated from Fourier spectrum ratio and their application for prediction of seismic intensity of land station We compare Fourier spectra of S-wave portion on OBSs with those on adjacent land stations. Station pair whose distance is smaller than 50 km is analyzed, and we obtain that spectral ratio of land station (MIEH05 of the KiK-net/NIED) to OBS (KMA01 of the DONET/JAMSTEC) is 5-20 for frequencies 10-20Hz for both horizontal and vertical components, whereas it is approximately 0.2 at less than 2Hz for the horizontal component, which corresponds to the relative site amplification factors in the frequency domain. In addition, we compare the accuracies of expected seismic intensity of land stations using the average of seismic intensity difference with those using the spectral ratio as the empirical amplification factor. In an example of station pair mentioned above, the RMS of the difference between measured and predicted seismic intensity is improved by about 38% by using a spectral ratio as the amplification factor. These results indicate that the frequency-dependent site factor is crucial factor to predict seismic intensity from OBS data, and also show that OBS can be used as front stations in the method for prediction of ground motion based on the real-time monitoring (Hoshiba, 2013). Acknowledgement: Waveform data were obtained from the JMA network, DONET of the JAMSTEC, K-net and KiK-net of the NIED.

Peak ground motion predictions with empirical site factors using Taiwan Strong Motion Network recordings

NASA Astrophysics Data System (ADS)

Chung, Jen-Kuang

2013-09-01

A stochastic method called the random vibration theory (Boore, 1983) has been used to estimate the peak ground motions caused by shallow moderate-to-large earthquakes in the Taiwan area. Adopting Brune's ω-square source spectrum, attenuation models for PGA and PGV were derived from path-dependent parameters which were empirically modeled from about one thousand accelerograms recorded at reference sites mostly located in a mountain area and which have been recognized as rock sites without soil amplification. Consequently, the predicted horizontal peak ground motions at the reference sites, are generally comparable to these observed. A total number of 11,915 accelerograms recorded from 735 free-field stations of the Taiwan Strong Motion Network (TSMN) were used to estimate the site factors by taking the motions from the predictive models as references. Results from soil sites reveal site amplification factors of approximately 2.0 ~ 3.5 for PGA and about 1.3 ~ 2.6 for PGV. Finally, as a result of amplitude corrections with those empirical site factors, about 75% of analyzed earthquakes are well constrained in ground motion predictions, having average misfits ranging from 0.30 to 0.50. In addition, two simple indices, R 0.57 and R 0.38, are proposed in this study to evaluate the validity of intensity map prediction for public information reports. The average percentages of qualified stations for peak acceleration residuals less than R 0.57 and R 0.38 can reach 75% and 54%, respectively, for most earthquakes. Such a performance would be good enough to produce a faithful intensity map for a moderate scenario event in the Taiwan region.

Nonlinear and linear site response and basin effects in Seattle for the M 6.8 Nisqually, Washington, earthquake

USGS Publications Warehouse

Frankel, A.D.; Carver, D.L.; Williams, R.A.

2002-01-01

We used recordings of the M 6.8 Nisqually earthquake and its ML 3.4 aftershock to study site response and basin effects for 35 locations in Seattle, Washington. We determined site amplification from Fourier spectral ratios of the recorded horizontal ground motions, referenced to a soft-rock site. Soft-soil sites (generally National Earthquake Hazard Reduction Program [NEHRP] class E) on artificial fill and young alluvium have the largest 1-Hz amplifications (factors of 3-7) for both the mainshock and aftershock. These amplifications are correlated with areas of higher damage from the mainshock to major buildings and liquefaction. There are several indications of nonlinear response at the soft-soil sites for the mainshock ground motions, despite relatively modest peak accelerations in the S waves of 15%-22%g. First, the mainshock spectral ratios do not show amplification at 2-8 Hz as do the aftershock spectral ratios. Spectral peaks at frequencies below 2 Hz generally occur at lower frequencies for the mainshock spectral ratios than for the aftershock ratios. At one soft-soil site, there is a clear shift of the resonant frequency to a lower frequency for the mainshock compared with the aftershock. The frequency of this resonance increases in the coda of the mainshock record, indicating that the site response during the weaker motions of the coda is more linear than that of the initial S wave. Three of the soft-soil sites display cusped, one-sided mainshock accelerograms after the S wave. These soft-soil sites also show amplification at 10-20 Hz in the S wave, relative to the rock site, that is not observed for the aftershock. The cusped waveforms and 10-20-Hz amplification are symptomatic of nonlinear response at the soft-soil sites. These sites had nearby liquefaction. The largest amplifications for 0.5 Hz occur at soft-soil sites on the southern portion of the Seattle Basin. Stiff-soil sites (NEHRP classes D and C) on Pleistocene-age glacial deposits display similar spectral amplification for the mainshock and aftershock, indicating approximately linear response. The stiff-soil sites generally have moderate amplification (factors of 1.1-2.4) at 0.5 and 1 Hz. Amplifications at 1 and 5 Hz for all sites generally increase with decreasing shear-wave velocity measured in the top 30 m (Vs 30). However, larger amplifications at 0.5 and 1 Hz for sites with similar Vs 30 values are observed for sites in the Seattle Basin, illustrating the amplification from the deeper (>30 m) sediments and the contribution from basin surface waves. Record sections for the mainshock and aftershock show that basin surface waves produce the peak velocities for many of the sites in the Seattle Basin and often dominate the amplitude at 1 Hz and lower frequencies.

Site Amplification Characteristics of the Several Seismic Stations at Jeju Island, in Korea, using S-wave Energy, Background Noise, and Coda waves from the East Japan earthquake (Mar. 11th, 2011) Series.

NASA Astrophysics Data System (ADS)

Seong-hwa, Y.; Wee, S.; Kim, J.

2016-12-01

Observed ground motions are composed of 3 main factors such as seismic source, seismic wave attenuation and site amplification. Among them, site amplification is also important factor and should be considered to estimate soil-structure dynamic interaction with more reliability. Though various estimation methods are suggested, this study used the method by Castro et. al.(1997) for estimating site amplification. This method has been extended to background noise, coda waves and S waves recently for estimating site amplification. This study applied the Castro et. al.(1997)'s method to 3 different seismic waves, that is, S-wave Energy, Background Noise, and Coda waves. This study analysed much more than about 200 ground motions (acceleration type) from the East Japan earthquake (March 11th, 2011) Series of seismic stations at Jeju Island (JJU, SGP, HALB, SSP and GOS; Fig. 1), in Korea. The results showed that most of the seismic stations gave similar results among three types of seismic energies. Each station showed its own characteristics of site amplification property in low, high and specific resonance frequency ranges. Comparison of this study to other studies can give us much information about dynamic amplification of domestic sites characteristics and site classification.

Models and methods to characterize site amplification from a pair of records

USGS Publications Warehouse

Safak, E.

1997-01-01

The paper presents a tutorial review of the models and methods that are used to characterize site amplification from the pairs of rock- and soil-site records, and introduces some new techniques with better theoretical foundations. The models and methods discussed include spectral and cross-spectral ratios, spectral ratios for downhole records, response spectral ratios, constant amplification factors, parametric models, physical models, and time-varying filters. An extensive analytical and numerical error analysis of spectral and cross-spectral ratios shows that probabilistically cross-spectral ratios give more reliable estimates of site amplification. Spectral ratios should not be used to determine site amplification from downhole-surface recording pairs because of the feedback in the downhole sensor. Response spectral ratios are appropriate for low frequencies, but overestimate the amplification at high frequencies. The best method to be used depends on how much precision is required in the estimates.

Shear Wave Velocity and Site Amplification Factors for 25 Strong-Motion Instrument Stations Affected by the M5.8 Mineral, Virginia, Earthquake of August 23, 2011

USGS Publications Warehouse

Kayen, Robert E.; Carkin, Brad A.; Corbett, Skye C.; Zangwill, Aliza; Estevez, Ivan; Lai, Lena

2015-01-01

Vertical one-dimensional shear wave velocity (Vs) profiles are presented for 25 strong-motion instrument sites along the Mid-Atlantic eastern seaboard, Piedmont region, and Appalachian region, which surround the epicenter of the M5.8 Mineral, Virginia, Earthquake of August 23, 2011. Testing was performed at sites in Pennsylvania, Maryland, West Virginia, Virginia, the District of Columbia, North Carolina, and Tennessee. The purpose of the study is to determine the detailed site velocity profile, the average velocity in the upper 30 meters of the profile (VS,30), the average velocity for the entire profile (VS,Z), and the National Earthquake Hazards Reduction Program (NEHRP) site classification. The Vs profiles are estimated using a non-invasive continuous-sine-wave method for gathering the dispersion characteristics of surface waves. A large trailer-mounted active source was used to shake the ground during the testing and produce the surface waves. Shear wave velocity profiles were inverted from the averaged dispersion curves using three independent methods for comparison, and the root-mean square combined coefficient of variation (COV) of the dispersion and inversion calculations are estimated for each site.

Empirical evidence for acceleration-dependent amplification factors

USGS Publications Warehouse

Borcherdt, R.D.

2002-01-01

Site-specific amplification factors, Fa and Fv, used in current U.S. building codes decrease with increasing base acceleration level as implied by the Loma Prieta earthquake at 0.1g and extrapolated using numerical models and laboratory results. The Northridge earthquake recordings of 17 January 1994 and subsequent geotechnical data permit empirical estimates of amplification at base acceleration levels up to 0.5g. Distance measures and normalization procedures used to infer amplification ratios from soil-rock pairs in predetermined azimuth-distance bins significantly influence the dependence of amplification estimates on base acceleration. Factors inferred using a hypocentral distance norm do not show a statistically significant dependence on base acceleration. Factors inferred using norms implied by the attenuation functions of Abrahamson and Silva show a statistically significant decrease with increasing base acceleration. The decrease is statistically more significant for stiff clay and sandy soil (site class D) sites than for stiffer sites underlain by gravely soils and soft rock (site class C). The decrease in amplification with increasing base acceleration is more pronounced for the short-period amplification factor, Fa, than for the midperiod factor, Fv.

Combined estimation of kappa and shear-wave velocity profile of the Japanese rock reference

NASA Astrophysics Data System (ADS)

Poggi, Valerio; Edwards, Benjamin; Fäh, Donat

2013-04-01

The definition of a common soil or rock reference is a key issue in probabilistic seismic hazard analysis (PSHA), microzonation studies, local site-response analysis and, more generally, when predicted or observed ground motion is compared for sites of different characteristics. A scaling procedure, which accounts for a common reference, is then necessary to avoid bias induced by the differences in the local geology. Nowadays methods requiring the definition of a reference condition generally prescribe the characteristic of a rock reference, calibrated using indirect estimation methods based on geology or on surface proxies. In most cases, a unique average shear-wave velocity value is prescribed (e.g. Vs30 = 800m/s as for class A of the EUROCODE8). Some attempts at defining the whole shape of a reference rock velocity profile have been described, often without a clear physical justification of how such a selection was performed. Moreover, in spite of its relevance in affecting the high-frequency part of the spectrum, the definition of the associated reference attenuation is in most cases missing or, when present, still remains quite uncertain. In this study we propose an approach that is based on the comparison between empirical anelastic amplification functions from spectral modeling of earthquakes and average S-wave velocities computed using the quarter-wavelength approach. The method is an extension of the approach originally proposed by Poggi et al. (2011) for Switzerland, and is here applied to Japan. For the analysis we make use of a selection of 36 stiff-soil and rock sites from the Japanese KiK-net network, for which a measured velocity profile is available. With respect to the previous study, however, we now analyze separately the elastic and anelastic contributions of the estimated empirical amplification. In a first step - which is consistent with the original work - only the elastic part of the amplification spectrum is considered. This procedure allows the retrieval of the shape of the velocity profile that is characterized by no relative amplification within the network. Subsequently, the contribution of intrinsic attenuation is analyzed, disaggregated from the anelastic function by using the frequency independent (and site-dependent) attenuation operator kappa (κ). By comparing the dependency of κ with the quarter-wavelength velocity at selected sites, a frequency-dependent predictive equation is established to model the attenuation characteristics of an arbitrary rock or stiff-soil velocity model, such as the reference model obtained in the first step. The result of this application can be used to model the site-dependent attenuation for any rock and stiff-soil site for which an estimation of the velocity profile or its corresponding quarter-wavelength velocity representation is available. As an additional output of the present study, we also propose a simplified method to estimate kappa from the average velocity estimates over the first 30m (Vs30). We provide an example of such predictions for a range of Vs30 velocities up to 2000m/s.

Observation of aftershocks of the 2003 Tokachi-Oki earthquake for estimation of local site effects

NASA Astrophysics Data System (ADS)

Yamanaka, Hiroaki; Motoki, Kentaro; Etoh, Kiminobu; Murayama, Masanari; Komaba, Nobuhiko

2004-03-01

Observation of aftershocks of the 2003 Tokachi-Oki earthquake was conducted in the southern part of the Tokachi basin in Hokkaido, Japan for estimation of local site effects. We installed accelerographs at 12 sites in Chokubetsu, Toyokoro, and Taiki areas, where large strong motion records were obtained during the main shock at stations of the K-NET and KiK-net. The stations of the aftershock observation are situated with different geological conditions and some of the sites were installed on Pleistocene layers as reference sites. The site amplifications are investigated using spectral ratio of S-waves from the aftershocks. The S-wave amplification factor is dominant at a period of about 1 second at the site near the KiK-net site in Toyokoro. This amplification fits well with calculated 1D amplification of S-wave in alluvial layers with a thickness of 50 meters. In addition to the site effects, we detected nonlinear amplification of the soft soils only during the main shock. The site effects at the strong motion site of the K-NET at Chokubetsu have a dominate peak at a period of 0.4 seconds. This amplification is due to soft soils having a thickness of about 13 meters. Contrary to the results at the two areas, site effects are not significantly different at the stations in the Taiki area, because of similarity on surface geological conditions.

New methods to characterize site amplification

USGS Publications Warehouse

Safak, Erdal

1993-01-01

Methods alternative to spectral ratios are introduced to characterize site amplification. The methods are developed by using a range of models, from the simple constant amplification model to the time-varying filter model. Examples are given for each model by using a pair of rock- and soil-site recordings from the Loma Prieta earthquake.

VS30, site amplifications and some comparisons: The Adapazari (Turkey) case

NASA Astrophysics Data System (ADS)

Ozcep, Tazegul; Ozcep, Ferhat; Ozel, Oguz

The aim of this study was to investigate the role of VS30 in site amplifications in the Adapazari region, Turkey. To fulfil this aim, amplifications from VS30 measurements were compared with earthquake data for different soil types in the seismic design codes. The Adapazari area was selected as the study area, and shear-wave velocity distribution was obtained by the multichannel analysis of surface waves (MASWs) method at 100 sites for the top 50 m of soil. Aftershock data following the Mw 7.4 Izmit earthquake of 17 August 1999 gave magnitudes between 4.0 and 5.6 at six stations installed in and around the Adapazari Basin, at Babalı, Şeker, Genç, Hastane, Toyota and Imar. This data was used to estimate site amplifications by the reference-station method. In addition, the fundamental periods of the station sites were estimated by the single station method. Site classifications based on VS30 in the seismic design codes were compared with the fundamental periods and amplification values. It was found that site amplifications (from earthquake data) and relevant spectra (from VS30) are not in good agreement for soils in Adapazari (Turkey).

Describing Site Amplification for Surface Waves in Realistic Basins

NASA Astrophysics Data System (ADS)

Bowden, D. C.; Tsai, V. C.

2017-12-01

Standard characterizations of site-specific site response assume a vertically-incident shear wave; given a 1D velocity profile, amplification and resonances can be calculated based on conservation of energy. A similar approach can be applied to surface waves, resulting in an estimate of amplification relative to a hard rock site that is different in terms of both amount of amplification and frequency. This prediction of surface-wave site amplification has been well validated through simple simulations, and in this presentation we explore the extent to which a 1D profile can explain observed amplifications in more realistic scenarios. Comparisons of various simple 2D and 3D simulations, for example, allow us to explore the effect of different basin shapes and the relative importance of effects such as focusing, conversion of wave-types and lateral surface wave resonances. Additionally, the 1D estimates for vertically-incident shear waves and for surface waves are compared to spectral ratios of historic events in deep sedimentary basins to demonstrate the appropriateness of the two different predictions. This difference in amplification responses between the wave types implies that a single measurement of site response, whether analytically calculated from 1D models or empirically observed, is insufficient for regions where surface waves play a strong role.

Seismic site-response characterization of high-velocity sites using advanced geophysical techniques: application to the NAGRA-Net

NASA Astrophysics Data System (ADS)

Poggi, V.; Burjanek, J.; Michel, C.; Fäh, D.

2017-08-01

The Swiss Seismological Service (SED) has recently finalised the installation of ten new seismological broadband stations in northern Switzerland. The project was led in cooperation with the National Cooperative for the Disposal of Radioactive Waste (Nagra) and Swissnuclear to monitor micro seismicity at potential locations of nuclear-waste repositories. To further improve the quality and usability of the seismic recordings, an extensive characterization of the sites surrounding the installation area was performed following a standardised investigation protocol. State-of-the-art geophysical techniques have been used, including advanced active and passive seismic methods. The results of all analyses converged to the definition of a set of best-representative 1-D velocity profiles for each site, which are the input for the computation of engineering soil proxies (traveltime averaged velocity and quarter-wavelength parameters) and numerical amplification models. Computed site response is then validated through comparison with empirical site amplification, which is currently available for any station connected to the Swiss seismic networks. With the goal of a high-sensitivity network, most of the NAGRA stations have been installed on stiff-soil sites of rather high seismic velocity. Seismic characterization of such sites has always been considered challenging, due to lack of relevant velocity contrast and the large wavelengths required to investigate the frequency range of engineering interest. We describe how ambient vibration techniques can successfully be applied in these particular conditions, providing practical recommendations for best practice in seismic site characterization of high-velocity sites.

Empirical Site Amplification Factors Incorporating Soil Nonlinearity in Taiwan

NASA Astrophysics Data System (ADS)

Kuo, C. H.; Chung, C. H.; Che-Min, L.; Huang, J. Y.; Wen, K. L.

2017-12-01

Characteristics of site amplifications caused by both crustal and subduction earthquakes are important in Taiwan. For example, seismic waves were amplified and led to significant building damages in the Taipei Basin by the 1986 Hualien offshore (subduction interface) and the 1999 Chi-Chi earthquakes (crustal), for which the epicentral distances were about 100 km. To understand local site amplifications in Taiwan, empirical site amplification factors for horizontal ground motions are studied using recently constructed strong motion and site databases for the free-field TSMIP stations in Taiwan. Records of large magnitude earthquakes of ML larger than six from 1994 to 2014 were selected for this study. Site amplification factors at site conditions with Vs30 of 120 m/s to 1500 m/s and base accelerations up to 0.7g were inferred from intensity ratios of station pairs within specific distances. The reference site condition is assumed as Vs30 of 760 m/s (B/C boundary). Preliminary results indicate: 1. Soil nonlinearity is more obviously at short periods (PGA, Sa0.3) than long periods (PGV, Sa1.0). 2. Soil nonlinearity is significant for stations belong to site classes of B, C, D, and E in Taiwan. 3. Effect of station-pair distance is seen at short periods (PGA and Sa0.3). 4. No significant different is found in site amplifications of crustal and subduction earthquakes. The result could be a reference for the Fa and Fv in Taiwan's building code.

Estimation of empirical site amplification factors in Taiwan

NASA Astrophysics Data System (ADS)

Chung, Chi-Hsuan; Wen, Kuo-Liang; Kuo, Chun-Hsiang

2017-04-01

Lots of infrastructures are under construction in metropolises in Taiwan in recent years and thus leads to increasement of population density and urbanization in those area. Taiwan island is located in plate boundaries in which the high seismicity is caused by active tectonic plates. The Chi-Chi earthquake (Mw 7.6) in 1999 caused a fatality of more than 2000, and the Meinong earthquake (Mw 6.5) in 2016 caused a fatality of 117 in Tainan city as well as damages on hundreds of buildings. The cases imply seismic vulnerability of urban area. During the improvements for seismic hazard analysis and seismic design, consideration of seismic site amplifications in different site conditions is one of important issues. This study used selected and processed strong motion records observed by the TSMIP network. The site conditions considered as Vs30 used in this study were investigated at most stations (Kuo et al. 2012; Kuo et al. 2016). Since strong motion records and site conditions are both available, we are able to use the data to analyze site amplifications of seismic waves at different periods. The result may be a reference for future modification of seismic design codes to decrease potential seismic hazards and losses. We adopted the strong motion and site database of the SSHAC (Senior Seismic Hazard Analysis Committee) Level 3 project in Taiwan. The selected significant crustal and subduction events of magnitude larger than six for analysis. The amplification factors of PGA, PGV, PGD, and spectra acceleration at 0.3, 1.0, and 3.0 seconds were evaluated using the processed strong motions. According to the recommendation of SSHAC Level 3 project, the site condition of Vs30 = 760 m/s is considered as the reference rock site in this study. The stations with Vs30 between 600 m/s and 900 m/s and used as the reference rock sites in reality. For each event, we find a reference rock site and other site within a certain distance (region dependent) to calculate site amplifications of ground motions. Relationships of site amplification factors and Vs30 are therefore derived for strong motions by regression analysis. Soil nonlinearity (decrease of amplifications) has to be considered at soft soil sites during a strong shaking. We also discuss amplification factors in terms of different intensities if data is available.

Site characterization and site response in Port-au-Prince, Haiti

USGS Publications Warehouse

Hough, Susan E.; Yong, Alan K.; Altidor, Jean Robert; Anglade, Dieuseul; Given, Douglas D.; Mildor, Saint-Louis

2011-01-01

Waveform analysis of aftershocks of the Mw7.0 Haiti earthquake of 12 January 2010 reveals amplification of ground motions at sites within the Cul de Sac valley in which Port-au-Prince is situated. Relative to ground motions recorded at a hard-rock reference site, peak acceleration values are amplified by a factor of approximately 1.8 at sites on low-lying Mio-Pliocene deposits in central Port-au-Prince and by a factor of approximately 2.5–3 on a steep foothill ridge in the southern Port-au-Prince metropolitan region. The observed amplitude, predominant periods, variability, and polarization of amplification are consistent with predicted topographic amplification by a steep, narrow ridge. A swath of unusually high damage in this region corresponds with the extent of the ridge where high weak-motion amplifications are observed. We use ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) imagery to map local geomorphology, including characterization of both near-surface and of small-scale topographic structures that correspond to zones of inferred amplification.

Characterization of 13 microsatellite loci for the deep-sea coral, Lophelia pertusa (Linnaeus 1758), from the western North Atlantic Ocean and Gulf of Mexico

USGS Publications Warehouse

Morrison, C.L.; Eackles, M.S.; Johnson, Robin L.; King, T.L.

2008-01-01

A suite of 13 polymorphic tri- and tetranucleotide microsatellite loci were isolated from the ahermatypic deep-sea coral, Lophelia pertusa. Among 51 individuals collected from three disjunct oceanic regions, allelic diversity ranged from six to 38 alleles and averaged 9.1 alleles per locus. Observed heterozygosity ranged from 9.1 to 96.8% and averaged 62.3% in the Gulf of Mexico population. For some loci, amplification success varied among collections, suggesting regional variation in priming site sequences. Four loci showed departures from Hardy–Weinberg equilibrium in certain collections which may reflect nonrandom mating.

Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

PubMed

Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

2018-02-06

A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

Ground Motions Simulations and Site Effects in the Quito Basin (Ecuador)

NASA Astrophysics Data System (ADS)

Courboulex, F.; Castro-Cruz, D.; Laurendeau, A.; Bonilla, L. F.; Bertrand, E.; Mercerat, D.; Alvarado, A. P.

2017-12-01

The city of Quito (3M inhabitants), capital of Ecuador has been damaged several times in the past by large earthquakes. It is built on the hanging-wall of an active reverse fault, constituting a piggy-back basin. The deep structure of this basin and its seismic response remains badly known. We first use the recordings of 170 events on 18 accelerometers from the Quito permanent network and perform spectral ratio analysis. We find that the southern part of Quito shows strong site amplification at low frequency ( 0.35 Hz). Yet, high frequency ( 5 Hz) amplifications also exist, but exhibit a complex spatial variability. We then propose a new calibrated method based on empirical Green's functions (EGF) to simulate the ground motions due to a future earthquake in Quito. The idea is to use the results of a global database of source time functions (i.e., the SCARDEC database, Vallée and Douet, 2016; Courboulex et al., 2016) to define the average values and the variability of the stress-drop ratio parameter, which strongly affects the resulting simulations. We test the method on a Mw 7.8 event, similar in location and focal mechanism to the Pedernales earthquake that occurred on April 16th 2016 on the subduction zone. For this aim, we use the recordings of 6 aftershocks of magnitude 5.6 to 6.2 as EGF's. The predicted Fourier spectra, peak values and response spectra we obtain are in good agreement with real data from the 2016 event recorded on the Quito network. With the constraints we impose on stress-drop ratios, we expect that the simulated ground motions be representative of the variability of other Pedernales-type events that could occur in the future. Our results also well reproduce the low frequency site effects amplification in the south of the basin. This amplification could be particularly dangerous in the case of a mega subduction earthquake, like the one that struck Ecuador in 1906.

The effect of classroom amplification on the signal-to-noise ratio in classrooms while class is in session.

PubMed

Larsen, Jeffery B; Blair, James C

2008-10-01

The purpose of this study was to measure the signal-to-noise ratios in classrooms while class was in session and students were interacting with the teacher and each other. Measurements of noise and reverberation were collected for 5 different classrooms in 3 different schools while class was in session. Activities taking place during the measurements were recorded to compare with sound level measures. The use of infrared classroom amplification was compared with no amplification. The results revealed that when classroom amplification was used, students heard the teacher's voice at a level that was an average of 13 dB above the noise floor as compared to an average of +2 dB above the noise floor without amplification.

Low-velocity zone and topography as a source of site amplification effect on Tarzana hill, California

USGS Publications Warehouse

Graizer, V.

2009-01-01

Tarzana station is located in the foothills of the Santa Monica Mountains in California near the crest of a low (<20 m) natural hill with gentle slopes. The hill is about 500 m in length by 130 m in width and is formed of extremely weathered shale at the surface to fresh at depth. Average S-wave is about 250 m/s in the top 17-18 m, and S- and P-wave velocities significantly increase below this depth. According to the NEHRP classification based on VS30???300 m/s it is a site class D. Strong-motion instrumentation at Tarzana consisted of an accelerograph at the top of the hill, a downhole instrument at 60 m depth, and an accelerograph at the base of the hill. More than 20 earthquakes were recorded by at least three instruments at Tarzana from 1998 till 2003. Comparisons of recordings and Fourier spectra indicate strong directional resonance in a direction perpendicular to the strike of the hill. The dominant peaks in ground motion amplification on the top of the hill relative to the base are at frequencies ???3.6 and 8-9 Hz for the horizontal components. Our hypothesis is that the hill acts like a wave trap. This results in an amplification at predominant frequencies f=V/4 h (h is layer's thickness) at f???3.6 Hz for S-waves (using average VS17=246 m/s and h=17 m) and f???7.9 Hz for P-waves (using average VP17=535 m/s and h=17 m). As was shown by Bouchon and Barker [Seismic response of a hill: the example of Tarzana, California. Bull Seism Soc Am 1996;86(1A):66-72], topography of this hill amplifies and polarizes ground motion in the frequency range of 3-5 Hz. Hill acts as a magnifying polarizing glass: It polarizes ground motion in the direction perpendicular to the strike of the hill and also amplifies ground motions that had been also amplified by a low-velocity layer.

Comparisons of Low-Strain Amplification at Soft-Sediment, Hard-Rock, Topographic, and Fault-Zone Sites in the Hayward Fault Zone, California

NASA Astrophysics Data System (ADS)

Catchings, R.; Strayer, L. M.; Goldman, M.

2014-12-01

We used a temporary network of approximately 600 seismographs to record a seismic source generated by the collapse of a 13-story building near the active trace of the Hayward Fault. These data allow us to evaluate variations in ground shaking across a series of 30 2-km-long radial arrays centered on the seismic source. Individual seismographs were spaced at 200-m intervals, forming a series of 360°concentric arrays around the seismic source. The data show variations in amplification caused by (1) soft sediments within the East Bay alluvial plain (EBAP), (2) hard rocks within the East Bay hills (EBH), (3) low-velocity rocks within the Hayward Fault zone (HFZ), and (4) topography. Given that ground shaking varies strongly with distance from the source, the concentric arrays allowed us to measure variations in ground shaking as a function of azimuth at fixed distances from the source. On individual linear profiles within the concentric arrays, we observed decreases in peak ground velocity (PGV) across the HFZ and other faults within the EBH. However, for a given distance from the source, we observe four to five fold amplification from the EBAP sites compared to most sites in the EBH. Topographic and fault-zone amplification effects within the EBH, however, are greater than the EBAP sediment amplification. Thus, for future earthquakes, shaking at many sites within the EBH may be significantly stronger than many sites within the EBAP. These observations suggest amplification can be expected in unconsolidated sediments, but topographic and fault-zone amplification can be larger. This confirms the importance of site effects for hazard mitigation and in interpreting MMI for future and historical earthquakes.

Regional correlations of VS30 averaged over depths less than and greater than 30 meters

USGS Publications Warehouse

Boore, David M.; Thompson, Eric M.; Cadet, Héloïse

2011-01-01

Using velocity profiles from sites in Japan, California, Turkey, and Europe, we find that the time-averaged shear-wave velocity to 30 m (VS30), 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 (VSz, with z being the averaging depth). The correlations for sites in Japan (corresponding to the KiK-net network) show that VSz is systematically larger for a given VSz 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 VS30 to VSz 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 VS30 from VSz 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 logVS30 of ±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 VS30 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 VS30 is correlated with VSz for z as great as 400 m for sites of the KiK-net network, providing some justification for using VS30 as a site-response variable for predicting ground motions at periods for which the wavelengths far exceed 30 m.

Optimization of strand displacement amplification-sensitized G-quadruplex DNAzyme-based sensing system and its application in activity detection of uracil-DNA glycosylase.

PubMed

Du, Yi-Chen; Jiang, Hong-Xin; Huo, Yan-Fang; Han, Gui-Mei; Kong, De-Ming

2016-03-15

As an isothermal nucleic acid amplification technique, strand displacement amplification (SDA) reaction has been introduced in G-quadruplex DNAzyme-based sensing system to improve the sensing performance. To further provide useful information for the design of SDA-amplified G-quadruplex DNAzyme-based sensors, the effects of nicking site number in SDA template DNA were investigated. With the increase of the nicking site number from 1 to 2, enrichment of G-quadruplex DNAzyme by SDA is changed from a linear amplification to an exponential amplification, thus greatly increasing the amplification efficiency and subsequently improving the sensing performance of corresponding sensing system. The nicking site number cannot be further increased because more nicking sites might result in high background signals. However, we demonstrated that G-quadruplex DNAzyme enrichment efficiency could be further improved by introducing a cross-triggered SDA strategy, in which two templates each has two nicking sites are used. To validate the proposed cross-triggered SDA strategy, we used it to develop a sensing platform for the detection of uracil-DNA glycosylase (UDG) activity. The sensor enables sensitive detection of UDG activity in the range of 1 × 10(-4)-1 U/mL with a detection limit of 1 × 10(-4)U/mL. Copyright © 2015 Elsevier B.V. All rights reserved.

J-SHIS - an integrated system for knowing seismic hazard information in Japan

NASA Astrophysics Data System (ADS)

Azuma, H.; Fujiwara, H.; Kawai, S.; Hao, K. X.; Morikawa, N.

2015-12-01

An integrated system of Japan seismic hazard information station (J-SHIS) was established in 2005 for issuing and exchanging information of the National Seismic Hazard Maps for Japan that are based on seismic hazard assessment (SHA). A simplified app, also named J-SHIS, for smartphones is popularly used in Japan based on the integrated system of http://www.j-shis.bosai.go.jp/map/?lang=en. "Smartphone tells hazard" is realized on a cellphone, a tablet and/or a PC. At a given spot, the comprehensive information of SHA map can be easily obtained as below: 1) A SHA probability at given intensity (JMA=5-, 5+, 6-, 6+) within 30 years. 2) A site amplification factor varies within 0.5 ~ 3.0 and expectation is 1 based on surface geology map information. 3) A depth of seismic basement down to ~3,000m based on deeper borehole and geological structure. 4) Scenario earthquake maps: By choosing an active fault, one got the average case for different parameters of the modeling. Then choose a case, you got the shaking map of intensity with color scale. "Seismic Hazard Karte tells more hazard" is another app based on website of http://www.j-shis.bosai.go.jp/labs/karte/. (1) For every mesh of 250m x 250m, professional service SHA information is provided over national-world. (2) With five ranks for eight items, comprehensive SHA information could be delivered. (3) Site amplification factor with an average index is given. (4) Deeper geologic structure modeling is provided with borehole profiling. (5) A SHA probability is assessed within 30 and/or 50 years for the given site. (6) Seismic Hazard curves are given for earthquake sources from inland active fault, subduction zone, undetermined and their summarization. (7) The JMA seismic intensities are assessed in long-term averaged periods of 500-years to ~100,000 years. The app of J-SHIS can be downloaded freely from http://www.j-shis.bosai.go.jp/app-jshis.

Variability of site response in Seattle, Washington

USGS Publications Warehouse

Hartzell, S.; Carver, D.; Cranswick, E.; Frankel, A.

2000-01-01

Ground motion from local earthquakes and the SHIPS (Seismic Hazards Investigation in Puget Sound) experiment is used to estimate site amplification factors in Seattle. Earthquake and SHIPS records are analyzed by two methods: (1) spectral ratios relative to a nearby site on Tertiary sandstone, and (2) a source/site spectral inversion technique. Our results show site amplifications between 3 and 4 below 5 Hz for West Seattle relative to Tertiary rock. These values are approximately 30% lower than amplification in the Duwamish Valley on artificial fill, but significantly higher than the calculated range of 2 to 2.5 below 5 Hz for the till-covered hills east of downtown Seattle. Although spectral amplitudes are only 30% higher in the Duwamish Valley compared to West Seattle, the duration of long-period ground motion is significantly greater on the artificial fill sites. Using a three-dimensional displacement response spectrum measure that includes the effects of ground-motion duration, values in the Duwamish Valley are 2 to 3 times greater than West Seattle. These calculations and estimates of site response as a function of receiver azimuth point out the importance of trapped surface-wave energy within the shallow, low-velocity, sedimentary layers of the Duwamish Valley. One-dimensional velocity models yield spectral amplification factors close to the observations for till sites east of downtown Seattle and the Duwamish Valley, but underpredict amplifications by a factor of 2 in West Seattle. A two-dimensional finite-difference model does equally well for the till sites and the Duwamish Valley and also yields duration estimates consistent with the observations for the Duwamish Valley. The two-dimensional model, however, still underpredicts amplification in West Seattle by up to a factor of 2. This discrepancy is attributed to 3D effects, including basin-edge-induced surface waves and basin-geometry-focusing effects, caused by the proximity of the Seattle thrust fault and the sediment-filled Seattle basin.

Terrain Classification of Aster gDEM for Seismic Microzonation of Port-Au Haiti, Using - and - Based Analytic Methods

NASA Astrophysics Data System (ADS)

Yong, A.; Hough, S. E.; Cox, B. R.; Rathje, E. M.; Bachhuber, J.; Hulslander, D.; Christiansen, L.; Abrams, M.

2010-12-01

The aftermath of the M7.0 Haiti earthquake of 12 January 2010 witnessed an impressive scientific response from the international community. In addition to conventional post-earthquake investigations, there was also an unprecedented reliance on remote-sensing technologies for scientific investigation and damage assessment. These technologies include sensors from both aerial and space-borne observational platforms. As part of the Haiti earthquake response and recovery effort, we develop a seismic zonation map of Port-au-Prince based on high-resolution satellite imagery as well as data from traditional seismographic monitoring stations and geotechnical site characterizations. Our imagery consists of a global digital elevation model (gDEM) of Hispaniola derived from data recorded by NASA-JPL's Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) instrument onboard the multi-platform satellite Terra. To develop our model we also consider recorded waveforms from portable seismographic stations (Hough et al., in review) and 36 geotechnical shear-wave velocity surveys (Cox et al., in review). Following a similar approach developed by Yong et al. (2008; Bull. Seism Soc. Am.), we use both pixel- and object- based imaging analytic methods to systematically identify and extract local terrain features that are expected to amplify seismic ground motion. Using histogram-stretching techniques applied to the rDEM values, followed by multi-resolution, segmentations of the imagery into terrain types, we systematically classify the terrains of Hispaniola. By associating available Vs30 (average shear-wave velocity in the upper 30 meter depth) calculated from the MASW (Multi-channel Analysis of Surface Wave) survey method, we develop a first-order site characterization map. Our results indicate that the terrain-based Vs30 estimates are significantly associated with amplitudes recorded at station sites. We also find that the damage distribution inferred from UNOSAT (UNITAR Operational Satellite Applications Program) data matches our estimates. However, the strongest amplifications are observed at two stations on a foothill ridge, where Vs30 values indicate that amplification should be relatively lower. Hough et al. (2010, this session) conclude that the observations can be explained by topographic amplification along a steep, narrow ridge. On the basis of these preliminary results, we conclude that the terrain-based framework, which characterizes topographic amplification as well as sediment-induced amplification, is needed to develop a microzonation map for Port-au-Prince.

Linear and exponential TAIL-PCR: a method for efficient and quick amplification of flanking sequences adjacent to Tn5 transposon insertion sites.

PubMed

Jia, Xianbo; Lin, Xinjian; Chen, Jichen

2017-11-02

Current genome walking methods are very time consuming, and many produce non-specific amplification products. To amplify the flanking sequences that are adjacent to Tn5 transposon insertion sites in Serratia marcescens FZSF02, we developed a genome walking method based on TAIL-PCR. This PCR method added a 20-cycle linear amplification step before the exponential amplification step to increase the concentration of the target sequences. Products of the linear amplification and the exponential amplification were diluted 100-fold to decrease the concentration of the templates that cause non-specific amplification. Fast DNA polymerase with a high extension speed was used in this method, and an amplification program was used to rapidly amplify long specific sequences. With this linear and exponential TAIL-PCR (LETAIL-PCR), we successfully obtained products larger than 2 kb from Tn5 transposon insertion mutant strains within 3 h. This method can be widely used in genome walking studies to amplify unknown sequences that are adjacent to known sequences.

Anomalous amplification of a homodyne signal via almost-balanced weak values.

PubMed

Liu, Wei-Tao; Martínez-Rincón, Julián; Viza, Gerardo I; Howell, John C

2017-03-01

We propose precision measurements of ultra-small angular velocities of a mirror within a modified Sagnac interferometer, where the counter-propagating beams are spatially separated, using the recently proposed technique of almost-balanced weak values amplification (ABWV) [Phys. Rev. Lett.116, 100803 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.100803]. The separation between the two beams provides additional amplification with respect to using collinear beams in a Sagnac interferometer. Within the same setup, the weak-value amplification technique is also performed for comparison. Much higher amplification factors can be obtained using the almost-balanced weak values technique, with the best one achieved in our experiments being as high as 1.2×10⁷. In addition, the amplification factor monotonically increases with decreasing of the post-selection phase for the ABWV case in our experiments, which is not the case for weak-value amplification (WVA) at small post-selection phases. Both techniques consist of measuring the angular velocity. The sensitivity of the ABWV technique is ∼38  nrad/s per averaged pulse for a repetition rate of 1 Hz and ∼33  nrad/s per averaged pulse for the WVA technique.

Site Amplification in the Central U.S.: Towards and understanding of factors influencing the site effect

NASA Astrophysics Data System (ADS)

Yassminh, R.; Sandvol, E. A.

2017-12-01

We have mapped site amplification using a Reverse Two Station (RTS) approach across much of the Central United States. We have found several unexpected results including a lack of amplification in Paleozoic basins such as the Illinois and Michigan basins. In general, we found that the amplification of high frequency regional waves is related to the topography. We also suggest that the HVSR spectra are primarily a function of the shallow velocity structure. The Central United States Seismic Observatory (CUSSO) is a vertical seismic array located adjacent to the central segment of the NMSZ. CUSSO data gives us the opportunity to understand the amplification of the ground motion at different depths within the uppermost crust. Simulating ground motions throughout the CUSSO borehole and examining the factors affecting the ground amplification, such as the velocity and thicknesses of the model layers and the source sizes, is an effective way to understand the role different factors playing in modifying the ground motion for both the local and regional seismic phases. We have used the spectral-element method (SEMs) with a 1D crustal velocity structure derived from logging data taken from CUSSO borehole. This model is comprised of near surface sediment layers and a Paleozoic basement. Utilizing the software package SPECFEM2D with virtual seismometers located on the surface and in the bottom of the different sediment layers, we have computed the true synthetic site amplification for frequencies between 0.01-3 Hz. For the local model, we have tested the sensitivity of the ground motion amplification to the source magnitude. For frequencies>0.6, the ground motions have been amplified with decreasing the magnitudes while for HZ<0.6 the the horizontal amplification increases with increasing the magnitudes. The effect of the velocity of the upper 30m was tested and the result shows that decreasing the Vs30m resulted in amplifying of the ground motion and decreasing of the resonant frequency. The velocity of the lower part of the sediment basin modifies the ground motion amplification and the result shows that increasing the velocity resulted in shifting the horizontal amplification peak frequency toward a lower frequency and increasing the amplification for frequencies >2Hz.

Quantifying the uncertainty in site amplification modeling and its effects on site-specific seismic-hazard estimation in the upper Mississippi embayment and adjacent areas

USGS Publications Warehouse

Cramer, C.H.

2006-01-01

The Mississippi embayment, located in the central United States, and its thick deposits of sediments (over 1 km in places) have a large effect on earthquake ground motions. Several previous studies have addressed how these thick sediments might modify probabilistic seismic-hazard maps. The high seismic hazard associated with the New Madrid seismic zone makes it particularly important to quantify the uncertainty in modeling site amplification to better represent earthquake hazard in seismic-hazard maps. The methodology of the Memphis urban seismic-hazard-mapping project (Cramer et al., 2004) is combined with the reference profile approach of Toro and Silva (2001) to better estimate seismic hazard in the Mississippi embayment. Improvements over previous approaches include using the 2002 national seismic-hazard model, fully probabilistic hazard calculations, calibration of site amplification with improved nonlinear soil-response estimates, and estimates of uncertainty. Comparisons are made with the results of several previous studies, and estimates of uncertainty inherent in site-amplification modeling for the upper Mississippi embayment are developed. I present new seismic-hazard maps for the upper Mississippi embayment with the effects of site geology incorporating these uncertainties.

Elastic-wave propagation and site amplification in the Salt Lake Valley, Utah, from simulated normal faulting earthquakes

USGS Publications Warehouse

Benz, H.M.; Smith, R.B.

1988-01-01

The two-dimensional seismic response of the Salt Lake valley to near- and far-field earthquakes has been investigated from simulations of vertically incident plane waves and from normal-faulting earthquakes generated on the basin-bounding Wasatch fault. The plane-wave simulations were compared with observed site amplifications in the Salt Lake valley, based on seismic recordings from nuclear explosions in southern Nevada, that show 10 times greater amplification with the basin than measured values on hard-rock sites. Synthetic seismograms suggest that in the frequency band 0.3 to 1.5 Hz at least one-half the site amplitication can be attributed to the impedance contrast between the basin sediments and higher velocity basement rocks. -from Authors

New Downhole Strong-Motion Data Recorded at Tarzana Array

NASA Astrophysics Data System (ADS)

Graizer, V.; Shakal, A.; Haddadi, H.

2001-12-01

Significantly amplified ground accelerations at the Tarzana station were recorded during many, but not all, earthquakes (e.g., Shakal et al., 1988). Peak horizontal ground acceleration at the Tarzana station during the M7.1 Hector Mine earthquake was almost twice as large as the accelerations recorded at nearby stations. After the Northridge earthquake the California Strong Motion Instrumentation Program (CSMIP) significantly increased instrumentation at Tarzana to study the unusual site amplification effect. Current instrumentation at Tarzana consists of an accelerograph at the top of Tarzana hill (Tarzana - Cedar Hill B), a downhole instrument at 60 m depth, and an accelerograph at the foot of the hill (Tarzana - Clubhouse), 180 m from the Cedar Hill B station. The original station, Tarzana - Cedar Hill Nursery A, was lost in 1999 due to construction. Thirteen events, including the Hector Mine earthquake, were simultaneously recorded by these instruments at Tarzana. The downhole instrument (A) was used as a reference site to compare the amplification effects at the top of Tarzana hill (B) and at the foot of the hill (C). Spectral amplification from the bottom of the hole to the top of the hill (B/A) and to the foot of the hill (C/A) is similar along the component parallel to the strike of Tarzana hill. But B/A is almost double C/A along the component transverse to the strike of the hill in period range from 0.04 to 0.8 sec (1.2 to 25 Hz). Comparison of the response spectra demonstrates clear directional site response resonance (perpendicular to the strike of the hill) at Tarzana. In contrast to accelerations recorded during the Mw 7.1 Hector Mine earthquake (high frequency part of seismic signal), displacements (relatively low frequency part of seismic signal) demonstrate almost no site amplification from the bottom of the hole to the surface (B/A) at periods greater than 1.5 sec, in either direction. Ground displacements at other CSMIP downhole arrays which recorded the Hector Mine earthquake also demonstrate almost no near-surface site amplification at long periods. Comparison of empirical and theoretical site amplification effects at Tarzana was performed using SHAKE91 modeling motion separately in the longitudinal and transverse directions. The source of the site amplification that produces large motions at Tarzana is still under investigation. The topography, shear-wave velocity profile and three-dimensional structure of the site apparently all contribute to the higher amplification of ground motion at the Tarzana site. The studies of Tarzana were co-funded by CSMIP and by the National Science Foundation (NSF) through the Resolution of Site Response Issues from the Northridge Earthquake Project (ROSRINE).

Amplification of seismic waves by the Seattle basin, Washington State

USGS Publications Warehouse

Pratt, T.L.; Brocher, T.M.; Weaver, C.S.; Creager, K.C.; Snelson, C.M.; Crosson, R.S.; Miller, K.C.; Trehu, A.M.

2003-01-01

Recordings of the 1999 Mw 7.6 Chi-Chi (Taiwan) earthquake, two local earthquakes, and five blasts show seismic-wave amplification over a large sedimentary basin in the U.S. Pacific Northwest. For weak ground motions from the Chi-Chi earthquake, the Seattle basin amplified 0.2- to 0.8-Hz waves by factors of 8 to 16 relative to bedrock sites west of the basin. The amplification and peak frequency change during the Chi-Chi coda: the initial S-wave arrivals (0-30 sec) had maximum amplifications of 12 at 0.5-0.8 Hz, whereas later arrivals (35-65 sec) reached amplifications of 16 at 0.3-0.5 Hz. Analysis of local events in the 1.0- to 10.0-Hz frequency range show fourfold amplifications for 1.0-Hz weak ground motion over the Seattle basin. Amplifications decrease as frequencies increase above 1.0 Hz, with frequencies above 7 Hz showing lower amplitudes over the basin than at bedrock sites. Modeling shows that resonance in low-impedance deposits forming the upper 550 m of the basin beneath our profile could cause most of the observed amplification, and the larger amplification at later arrival times suggests surface waves also play a substantial role. These results emphasize the importance of shallow deposits in determining ground motions over large basins.

Regional correlations of V s30 and velocities averaged over depths less than and greater than 30 meters

USGS Publications Warehouse

Boore, D.M.; Thompson, E.M.; Cadet, H.

2011-01-01

Using velocity profiles from sites in Japan, California, Turkey, and Europe, we find that the time-averaged shear-wave velocity to 30 m (V 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 Sz, with z being the averaging depth). The correlations for sites in Japan (corresponding to the KiK-net network) show that V S30 is systematically larger for a given V 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 S30 to V 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 S30 from V 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 log V S30 of 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 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 S30 is correlated with V Sz for z as great as 400 m for sites of the KiK-net network, providing some justification for using V S30 as a site-response variable for predicting ground motions at periods for which the wavelengths far exceed 30 m.

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

PubMed

Waszak, Sebastian M; Kilpinen, Helena; Gschwind, Andreas R; Orioli, Andrea; Raghav, Sunil K; Witwicki, Robert M; Migliavacca, Eugenia; Yurovsky, Alisa; Lappalainen, Tuuli; Hernandez, Nouria; Reymond, Alexandre; Dermitzakis, Emmanouil T; Deplancke, Bart

2014-01-15

High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. The R package abs filter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter

Prognostic relevance of Fédération Nationale des Centres de Lutte Contre le Cancer grade and MDM2 amplification levels in dedifferentiated liposarcoma: a study of 50 cases.

PubMed

Jour, George; Gullet, Ashley; Liu, Mingdong; Hoch, Benjamin L

2015-01-01

Dedifferentiated liposarcoma represents a form of liposarcoma composed of a non-lipogenic sarcoma associated with well-differentiated liposarcoma. The prognostic significance of histological grading of the dedifferentiated component remains to be elucidated due to vague grading criteria employed in previous studies. Molecular markers of tumor behavior, including amplification levels of murine double minute-2 (MDM2) and cyclin-dependent kinase-4 (CDK4) genes, have been explored in a limited number of cases. Here we investigate whether 'Fédération Nationale des Centres de Lutte Contre le Cancer' (FNCLCC) grade and MDM2 gene amplification levels have prognostic value in dedifferentiated liposarcoma in terms of local recurrence and disease-specific survival. Fifty cases were retrieved, reviewed and FNCLCC grade was scored for the dedifferentiated component. Testing for MDM2 gene amplification was performed by fluorescence in situ hybridization. Amplification was categorized as high level (≥20 copies) and as low level (<20 copies). Follow-up data was obtained through chart review. Log-rank test and Cox proportional hazard models were used to determine the effect of grade and level of MDM2 amplification on outcomes. Our series includes 50 patients (male n=28, female n=22) with an average age of 63 years (range, 28-88) and a median follow-up of 28 months (range, 2-120). Tumors were graded as grade 1 (6%), grade 2 (58%), and grade 3 (36%). When adjusted for age, sex, site, tumor size, and margin status, grade 3 patients had a higher recurrence rate than grades 1 and 2 (HR=2.07, 95% CI: 1.24, 7.62; P=0.015). Patients with high-level MDM2 amplification had higher recurrence rate on univariate analysis (P=0.028), but not on multivariate analysis (HR=1.69, 95% CI: 0.73, 3.94; P=0.221). FNCLCC grade 3 dedifferentiation confers a worse prognosis in dedifferentiated liposarcoma in terms of local recurrence. MDM2 amplification level remains a useful diagnostic tool in dedifferentiated liposarcoma, but has no prognostic value in terms of local recurrence.

Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

ERIC Educational Resources Information Center

Esernio-Jenssen, Debra; Barnes, Marilyn

2011-01-01

The American Academy of Pediatrics recommends that site-specific cultures be obtained, when indicated, for sexually victimized children. Nucleic acid amplification testing is a highly sensitive and specific methodology for identifying sexually transmitted infections. Nucleic acid amplification tests are also less invasive than culture, and this…

Site effects in Port-au-Prince (Haiti) from the analysis of spectral ratio and numerical simulations.

USGS Publications Warehouse

St. Fleur, Sadrac; Bertrand, Etienne; Courboulex, Francoise; Mercier de Lépinay, Bernard; Deschamps, Anne; Hough, Susan E.; Cultrera, Giovanna; Boisson, Dominique; Prepetit, Claude

2016-01-01

To provide better insight into seismic ground motion in the Port‐au‐Prince metropolitan area, we investigate site effects at 12 seismological stations by analyzing 78 earthquakes with magnitude smaller than 5 that occurred between 2010 and 2013. Horizontal‐to‐vertical spectral ratio on earthquake recordings and a standard spectral ratio were applied to the seismic data. We also propose a simplified lithostratigraphic map and use available geotechnical and geophysical data to construct representative soil columns in the vicinity of each station that allow us to compute numerical transfer functions using 1D simulations. At most of the studied sites, spectral ratios are characterized by weak‐motion amplification at frequencies above 5 Hz, in good agreement with the numerical transfer functions. A mismatch between the observed amplifications and simulated response at lower frequencies shows that the considered soil columns could be missing a deeper velocity contrast. Furthermore, strong amplification between 2 and 10 Hz linked to local topographic features is found at one station located in the south of the city, and substantial amplification below 5 Hz is detected near the coastline, which we attribute to deep and soft sediments as well as the presence of surface waves. We conclude that for most investigated sites in Port‐au‐Prince, seismic amplifications due to site effects are highly variable but seem not to be important at high frequencies. At some specific locations, however, they could strongly enhance the low‐frequency content of the seismic ground shaking. Although our analysis does not consider nonlinear effects, we thus conclude that, apart from sites close to the coast, sediment‐induced amplification probably had only a minor impact on the level of strong ground motion, and was not the main reason for the high level of damage in Port‐au‐Prince.

Seismic risk assessment of architectural heritages in Gyeongju considering local site effects

NASA Astrophysics Data System (ADS)

Park, H.-J.; Kim, D.-S.; Kim, D.-M.

2013-02-01

A seismic risk assessment is conducted for cultural heritage sites in Gyeongju, the capital of Korea's ancient Silla Kingdom. Gyeongju, home to UNESCO World Heritage sites, contains remarkable artifacts of Korean Buddhist art. An extensive geotechnical survey including a series of in situ tests is presented, providing pertinent soil profiles for site response analyses on thirty cultural heritage sites. After the shear wave velocity profiles and dynamic material properties were obtained, site response analyses were carried out at each historical site and the amplification characteristics, site period, and response spectrum of the site were determined for the earthquake levels of 2400 yr and 1000 yr return periods based on the Korean seismic hazard map. Response spectrum and corresponding site coefficients obtained from site response analyses considering geologic conditions differ significantly from the current Korean seismic code. This study confirms the importance of site-specific ground response analyses considering local geological conditions. Results are given in the form of the spatial distribution of bedrock depth, site period, and site amplification coefficients, which are particularly valuable in the context of a seismic vulnerability study. This study presents the potential amplification of hazard maps and provides primary data on the seismic risk assessment of each cultural heritage.

Divided-pulse nonlinear amplification and simultaneous compression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hao, Qiang; Zhang, Qingshan; Sun, Tingting

2015-03-09

We report on a fiber laser system delivering 122 fs pulse duration and 600 mW average power at 1560 nm by the interplay between divided pulse amplification and nonlinear pulse compression. A small-core double-clad erbium-doped fiber with anomalous dispersion carries out the pulse amplification and simultaneously compresses the laser pulses such that a separate compressor is no longer necessary. A numeric simulation reveals the existence of an optimum fiber length for producing transform-limited pulses. Furthermore, frequency doubling to 780 nm with 240 mW average power and 98 fs pulse duration is achieved by using a periodically poled lithium niobate crystal at roommore » temperature.« less

Exponential isothermal amplification of nucleic acids and amplified assays for proteins, cells, and enzyme activities.

PubMed

Reid, Michael S; Le, X Chris; Zhang, Hongquan

2018-04-27

Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in-situ assay applications. These amplification techniques eliminate the need for temperature cycling required for polymerase chain reaction (PCR) while achieving comparable amplification yield. We highlight here recent advances in exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. We discuss design strategies, enzyme reactions, detection techniques, and key features. Incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from non-specific template interactions, must be addressed to further improve isothermal and exponential amplification techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

3D Ground-Motion Simulations for Magnitude 9 Earthquakes on the Cascadia Megathrust: Sedimentary Basin Amplification, Rupture Directivity, and Ground-Motion Variability

NASA Astrophysics Data System (ADS)

Frankel, A. D.; Wirth, E. A.; Marafi, N.; Vidale, J. E.; Stephenson, W. J.

2017-12-01

We have produced broadband (0-10 Hz) synthetic seismograms for Mw 9 earthquakes on the Cascadia subduction zone by combining synthetics from 3D finite-difference simulations at low frequencies (≤ 1 Hz) and stochastic synthetics at high frequencies (≥ 1 Hz). These synthetic ground motions are being used to evaluate building response, liquefaction, and landslides, as part of the M9 Project of the University of Washington, in collaboration with the U.S. Geological Survey. The kinematic rupture model is composed of high stress drop sub-events with Mw 8, similar to those observed in the Mw 9.0 Tohoku, Japan and Mw 8.8 Maule, Chile earthquakes, superimposed on large background slip with lower slip velocities. The 3D velocity model is based on active and passive-source seismic tomography studies, seismic refraction and reflection surveys, and geologic constraints. The Seattle basin portion of the model has been validated by simulating ground motions from local earthquakes. We have completed 50 3D simulations of Mw 9 earthquakes using a variety of hypocenters, slip distributions, sub-event locations, down-dip limits of rupture, and other parameters. For sites not in deep sedimentary basins, the response spectra of the synthetics for 0.1-6.0 s are similar, on average, to the values from the BC Hydro ground motion prediction equations (GMPE). For periods of 7-10 s, the synthetic response spectra exceed these GMPE, partially due to the shallow dip of the plate interface. We find large amplification factors of 2-5 for response spectra at periods of 1-10 s for locations in the Seattle and Tacoma basins, relative to sites outside the basins. This amplification depends on the direction of incoming waves and rupture directivity. The basin amplification is caused by surface waves generated at basin edges from incoming S-waves, as well as amplification and focusing of S-waves and surface waves by the 3D basin structure. The inter-event standard deviation of response spectral amplitudes from the synthetics is larger for sites nearer the coast, because of their higher sensitivity to the sub-event locations and rupture directivity. The total standard deviations of spectral accelerations from 30 simulations for periods greater than 2 s are similar to those determined in the BC Hydro GMPE from strong-motion recordings in subduction zones.

A study of possible ground-motion amplification at the Coyote Lake Dam, California

USGS Publications Warehouse

Boore, D.M.; Graizer, V.M.; Tinsley, J.C.; Shakal, A.F.

2004-01-01

The abutment site at the Coyote Lake Dam recorded an unusually large peak acceleration of 1.29g during the 1984 Morgan Hill earthquake. Following this earthquake another strong-motion station was installed about 700 m downstream from the abutment station. We study all events (seven) recorded on these stations, using ratios of peak accelerations, spectral ratios, and particle motion polarization (using holograms) to investigate the relative ground motion at the two sites. We find that in all but one case the motion at the abutment site is larger than the downstream site over a broad frequency band. The polarizations are similar for the two sites for a given event, but can vary from one event to another. This suggests that the dam itself is not strongly influencing the records. Although we can be sure that the relative motion is usually larger at the abutment site, we cannot conclude that there is anomalous site amplification at the abutment site. The downstream site could have lower-than-usual near-surface amplifications. On the other hand, the geology near the abutment site is extremely complex and includes fault slivers, with rapid lateral changes in materials and presumably seismic velocities. For this reason alone, the abutment site should not be considered a normal free-field site.

Search for methylation-sensitive amplification polymorphisms in mutant figs.

PubMed

Rodrigues, M G F; Martins, A B G; Bertoni, B W; Figueira, A; Giuliatti, S

2013-07-08

Fig (Ficus carica) breeding programs that use conventional approaches to develop new cultivars are rare, owing to limited genetic variability and the difficulty in obtaining plants via gamete fusion. Cytosine methylation in plants leads to gene repression, thereby affecting transcription without changing the DNA sequence. Previous studies using random amplification of polymorphic DNA and amplified fragment length polymorphism markers revealed no polymorphisms among select fig mutants that originated from gamma-irradiated buds. Therefore, we conducted methylation-sensitive amplified polymorphism analysis to verify the existence of variability due to epigenetic DNA methylation among these mutant selections compared to the main cultivar 'Roxo-de-Valinhos'. Samples of genomic DNA were double-digested with either HpaII (methylation sensitive) or MspI (methylation insensitive) and with EcoRI. Fourteen primer combinations were tested, and on an average, non-methylated CCGG, symmetrically methylated CmCGG, and hemimethylated hmCCGG sites accounted for 87.9, 10.1, and 2.0%, respectively. MSAP analysis was effective in detecting differentially methylated sites in the genomic DNA of fig mutants, and methylation may be responsible for the phenotypic variation between treatments. Further analyses such as polymorphic DNA sequencing are necessary to validate these differences, standardize the regions of methylation, and analyze reads using bioinformatic tools.

Neo-Deterministic Seismic Hazard Assessment at Watts Bar Nuclear Power Plant Site, Tennessee, USA

NASA Astrophysics Data System (ADS)

Brandmayr, E.; Cameron, C.; Vaccari, F.; Fasan, M.; Romanelli, F.; Magrin, A.; Vlahovic, G.

2017-12-01

Watts Bar Nuclear Power Plant (WBNPP) is located within the Eastern Tennessee Seismic Zone (ETSZ), the second most naturally active seismic zone in the US east of the Rocky Mountains. The largest instrumental earthquakes in the ETSZ are M 4.6, although paleoseismic evidence supports events of M≥6.5. Events are mainly strike-slip and occur on steeply dipping planes at an average depth of 13 km. In this work, we apply the neo-deterministic seismic hazard assessment to estimate the potential seismic input at the plant site, which has been recently targeted by the Nuclear Regulatory Commission for a seismic hazard reevaluation. First, we perform a parametric test on some seismic source characteristics (i.e. distance, depth, strike, dip and rake) using a one-dimensional regional bedrock model to define the most conservative scenario earthquakes. Then, for the selected scenario earthquakes, the estimate of the ground motion input at WBNPP is refined using a two-dimensional local structural model (based on the plant's operator documentation) with topography, thus looking for site amplification and different possible rupture processes at the source. WBNNP features a safe shutdown earthquake (SSE) design with PGA of 0.18 g and maximum spectral amplification (SA, 5% damped) of 0.46 g (at periods between 0.15 and 0.5 s). Our results suggest that, although for most of the considered scenarios the PGA is relatively low, SSE values can be reached and exceeded in the case of the most conservative scenario earthquakes.

Amplification of earthquake ground motions in Washington, DC, and implications for hazard assessments in central and eastern North America

USGS Publications Warehouse

Pratt, Thomas L.; Horton, J. Wright; Munoz, Jessica; Hough, Susan E.; Chapman, Martin C.; Olgun, C. Guney

2017-01-01

The extent of damage in Washington, DC, from the 2011 Mw 5.8 Mineral, VA, earthquake was surprising for an epicenter 130 km away; U.S. Geological Survey “Did-You-Feel-It” reports suggest that Atlantic Coastal Plain and other unconsolidated sediments amplified ground motions in the city. We measure this amplification relative to bedrock sites using earthquake signals recorded on a temporary seismometer array. The spectral ratios show strong amplification in the 0.7 to 4 Hz frequency range for sites on sediments. This range overlaps with resonant frequencies of buildings in the city as inferred from their heights, suggesting amplification at frequencies to which many buildings are vulnerable to damage. Our results emphasize that local amplification can raise moderate ground motions to damaging levels in stable continental regions, where low attenuation extends shaking levels over wide areas and unconsolidated deposits on crystalline metamorphic or igneous bedrock can result in strong contrasts in near-surface material properties.

Microtremor exploration for shallow S-wave velocity structure in Bandung Basin, Indonesia

NASA Astrophysics Data System (ADS)

Pramatadie, Andi Muhamad; Yamanaka, Hiroaki; Chimoto, Kosuke; Afnimar Collaboration; Koketsu, Kazuki; Sakaue, Minoru; Miyake, Hiroe; Sengara, I. Wayan; Sadisun, Imam A.

2017-05-01

We have conducted a microtremor survey for shallow S-wave velocity profiles to be used for seismic hazard evaluation in the Bandung Basin, Indonesia. In the survey, two arrays were deployed temporarily at each of 29 sites, by installing seven vertical sensors in triangular configurations with side lengths from 1 to 16 m. Records of vertical microtremors from each array were used to estimate Rayleigh wave phase velocity spectra using the spatial autocorrelation method, as well as the horizontal-to-vertical spectral ratio obtained at the centre of the arrays. Phase velocities at sites on the basin margin exhibit higher values than those obtained in the central part of the basin, in a frequency range of 7 to 30 Hz. The phase velocity data were used to deduce S-wave velocity profiles of shallow soil using a hybrid heuristic inversion method. We validated our inversion models by comparing observed horizontal-to-vertical spectral ratios with ellipticities of the fundamental mode of Rayleigh waves, calculated for the inversion models. The S-wave velocity profiles in the area can be characterised by two soft layers over a firm engineering basement that has an S-wave velocity of 500 m/s. The S-wave velocities of the two layers are 120 and 280 m/s on average. The distribution of the averaged S-wave velocity in the top 30 m clearly indicates low values in the eastern central part and high values in the edge of the basin. The amplification is large in the areas with low velocity layers. In addition, we have proposed an empirical relation between the amplification factor and the topographical slope in the area.

Calibration of Subsurface Amplification Factors Using Surface/Borehole Strong-motion Records from the KiK-net

NASA Astrophysics Data System (ADS)

Hayashida, T.; Tajima, F.

2007-12-01

The Real-time Earthquake Information System (REIS, Horiuchi et al., 2005) detects earthquakes and determines event parameters using the Hi-net (High-sensitivity seismograph network Japan) data in Japan. The system also predicts the arrival time and seismic intensity at a given site before ground motions arrive. Here, the seismic intensity is estimated based on the intensity magnitude which is derived from data of the Hi-net. As the Hi-net stations are located in the boreholes, intensity estimation on the ground surface is evaluated using a constant for subsurface amplification. But the estimated intensities based on the conventionally used amplification constants are not always in agreement with those observed at specific sites on the ground surface. The KiK-net (KIBAN Kyoshin network Japan) consists of strong motion instruments. Each station has two sets of accelerometers, one set is installed on the ground surface and the other one is co-located with a Hi-net station in the borehole. We use data recorded at the KiK-net stations to calibrate subsurface site amplification factors between the borehole and the ground surface. We selected data recorded for over 200 events during the period of 1997 to 2006 in Hiroshima prefecture and calculated the ratios of peak velocity amplitudes on the ground surface ( Asurf) to those in the borehole ( Abor). The subsurface amplification varies from station to station showing dependency on the propagation distance as well as on the incident direction of seismic waves. Results suggest that the site amplification factors shall be described as a function of distance and incident direction, and are not constants. Thus, we derived empirical amplification formulas between Asurf and the peak velocity amplitudes on the engineering bedrock ( Abed) as a function of distance in place of the conventionally used amplification constants. Here, the engineering bedrock is defined as the depth where the S- wave velocity is 600 m/s. The estimated intensities show substantial improvement in the accuracy at most stations as compared with those calculated using conventional constants. When the amplification dependence on the incident direction was accounted for, the estimated intensities somewhat improved. This calibration will help an earthquake early warning system such as REIS provide more accurate intensity estimates.

Systematic Site Characterization at Seismic Stations combined with Empirical Spectral Modeling: critical data for local hazard analysis

NASA Astrophysics Data System (ADS)

Michel, Clotaire; Hobiger, Manuel; Edwards, Benjamin; Poggi, Valerio; Burjanek, Jan; Cauzzi, Carlo; Kästli, Philipp; Fäh, Donat

2016-04-01

The Swiss Seismological Service operates one of the densest national seismic networks in the world, still rapidly expanding (see http://www.seismo.ethz.ch/monitor/index_EN). Since 2009, every newly instrumented site is characterized following an established procedure to derive realistic 1D VS velocity profiles. In addition, empirical Fourier spectral modeling is performed on the whole network for each recorded event with sufficient signal-to-noise ratio. Besides the source characteristics of the earthquakes, statistical real time analyses of the residuals of the spectral modeling provide a seamlessly updated amplification function w.r. to Swiss rock conditions at every station. Our site characterization procedure is mainly based on the analysis of surface waves from passive experiments and includes cross-checks of the derived amplification functions with those obtained through spectral modeling. The systematic use of three component surface-wave analysis, allowing the derivation of both Rayleigh and Love waves dispersion curves, also contributes to the improved quality of the retrieved profiles. The results of site characterisation activities at recently installed strong-motion stations depict the large variety of possible effects of surface geology on ground motion in the Alpine context. Such effects range from de-amplification at hard-rock sites to amplification up to a factor of 15 in lacustrine sediments with respect to the Swiss reference rock velocity model. The derived velocity profiles are shown to reproduce observed amplification functions from empirical spectral modeling. Although many sites are found to exhibit 1D behavior, our procedure allows the detection and qualification of 2D and 3D effects. All data collected during the site characterization procedures in the last 20 years are gathered in a database, implementing a data model proposed for community use at the European scale through NERA and EPOS (www.epos-eu.org). A web stationbook derived from it can be accessed through the interface www.stations.seismo.ethz.ch.

Interfacial polymerization for colorimetric labeling of protein expression in cells.

PubMed

Lilly, Jacob L; Sheldon, Phillip R; Hoversten, Liv J; Romero, Gabriela; Balasubramaniam, Vivek; Berron, Brad J

2014-01-01

Determining the location of rare proteins in cells typically requires the use of on-sample amplification. Antibody based recognition and enzymatic amplification is used to produce large amounts of visible label at the site of protein expression, but these techniques suffer from the presence of nonspecific reactivity in the biological sample and from poor spatial control over the label. Polymerization based amplification is a recently developed alternative means of creating an on-sample amplification for fluorescence applications, while not suffering from endogenous labels or loss of signal localization. This manuscript builds upon polymerization based amplification by developing a stable, archivable, and colorimetric mode of amplification termed Polymer Dye Labeling. The basic concept involves an interfacial polymer grown at the site of protein expression and subsequent staining of this polymer with an appropriate dye. The dyes Evans Blue and eosin were initially investigated for colorimetric response in a microarray setting, where both specifically stained polymer films on glass. The process was translated to the staining of protein expression in human dermal fibroblast cells, and Polymer Dye Labeling was specific to regions consistent with desired protein expression. The labeling is stable for over 200 days in ambient conditions and is also compatible with modern mounting medium.

The thermal history of human fossils and the likelihood of successful DNA amplification.

PubMed

Smith, Colin I; Chamberlain, Andrew T; Riley, Michael S; Stringer, Chris; Collins, Matthew J

2003-09-01

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.

REVIEW ARTICLE: A comparison of site response techniques using earthquake data and ambient seismic noise analysis in the large urban areas of Santiago de Chile

NASA Astrophysics Data System (ADS)

Pilz, Marco; Parolai, Stefano; Leyton, Felipe; Campos, Jaime; Zschau, Jochen

2009-08-01

Situated in an active tectonic region, Santiago de Chile, the country's capital with more than six million inhabitants, faces tremendous earthquake risk. Macroseismic data for the 1985 Valparaiso event show large variations in the distribution of damage to buildings within short distances, indicating strong effects of local sediments on ground motion. Therefore, a temporary seismic network was installed in the urban area for recording earthquake activity and a study was carried out aiming to estimate site amplification derived from horizontal-to-vertical (H/V) spectral ratios from earthquake data (EHV) and ambient noise (NHV), as well as using the standard spectral ratio (SSR) technique with a nearby reference station located on igneous rock. The results lead to the following conclusions: (1) The analysis of earthquake data shows significant dependence on the local geological structure with respect to amplitude and duration. (2) An amplification of ground motion at frequencies higher than the fundamental one can be found. This amplification would not be found when looking at NHV ratios alone. (3) The analysis of NHV spectral ratios shows that they can only provide a lower bound in amplitude for site amplification. (4) P-wave site responses always show lower amplitudes than those derived by S waves, and sometimes even fail to provide some frequencies of amplification. (5) No variability in terms of time and amplitude is observed in the analysis of the H/V ratio of noise. (6) Due to the geological conditions in some parts of the investigated area, the fundamental resonance frequency of a site is difficult to estimate following standard criteria proposed by the SESAME consortium, suggesting that these are too restrictive under certain circumstances.

Strong Effects of Vs30 Heterogeneity on Physics-Based Scenario Ground-Shaking Computations

NASA Astrophysics Data System (ADS)

Louie, J. N.; Pullammanappallil, S. K.

2014-12-01

Hazard mapping and building codes worldwide use the vertically time-averaged shear-wave velocity between the surface and 30 meters depth, Vs30, as one predictor of earthquake ground shaking. Intensive field campaigns a decade ago in Reno, Los Angeles, and Las Vegas measured urban Vs30 transects with 0.3-km spacing. The Clark County, Nevada, Parcel Map includes urban Las Vegas and comprises over 10,000 site measurements over 1500 km2, completed in 2010. All of these data demonstrate fractal spatial statistics, with a fractal dimension of 1.5-1.8 at scale lengths from 0.5 km to 50 km. Vs measurements in boreholes up to 400 m deep show very similar statistics at 1 m to 200 m lengths. When included in physics-based earthquake-scenario ground-shaking computations, the highly heterogeneous Vs30 maps exhibit unexpectedly strong influence. In sensitivity tests (image below), low-frequency computations at 0.1 Hz display amplifications (as well as de-amplifications) of 20% due solely to Vs30. In 0.5-1.0 Hz computations, the amplifications are a factor of two or more. At 0.5 Hz and higher frequencies the amplifications can be larger than what the 1-d Building Code equations would predict from the Vs30 variations. Vs30 heterogeneities at one location have strong influence on amplifications at other locations, stretching out in the predominant direction of wave propagation for that scenario. The sensitivity tests show that shaking and amplifications are highly scenario-dependent. Animations of computed ground motions and how they evolve with time suggest that the fractal Vs30 variance acts to trap wave energy and increases the duration of shaking. Validations of the computations against recorded ground motions, possible in Las Vegas Valley due to the measurements of the Clark County Parcel Map, show that ground motion levels and amplifications match, while recorded shaking has longer duration than computed shaking. Several mechanisms may explain the amplification and increased duration of shaking in the presence of heterogeneous spatial distributions of Vs: conservation of wave energy across velocity changes; geometric focusing of waves by low-velocity lenses; vertical resonance and trapping; horizontal resonance and trapping; and multiple conversion of P- to S-wave energy.

On using surface-source downhole-receiver logging to determine seismic slownesses

USGS Publications Warehouse

Boore, D.M.; Thompson, E.M.

2007-01-01

We present a method to solve for slowness models from surface-source downhole-receiver seismic travel-times. The method estimates the slownesses in a single inversion of the travel-times from all receiver depths and accounts for refractions at layer boundaries. The number and location of layer interfaces in the model can be selected based on lithologic changes or linear trends in the travel-time data. The interfaces based on linear trends in the data can be picked manually or by an automated algorithm. We illustrate the method with example sites for which geologic descriptions of the subsurface materials and independent slowness measurements are available. At each site we present slowness models that result from different interpretations of the data. The examples were carefully selected to address the reliability of interface-selection and the ability of the inversion to identify thin layers, large slowness contrasts, and slowness gradients. Additionally, we compare the models in terms of ground-motion amplification. These plots illustrate the sensitivity of site amplifications to the uncertainties in the slowness model. We show that one-dimensional site amplifications are insensitive to thin layers in the slowness models; although slowness is variable over short ranges of depth, this variability has little affect on ground-motion amplification at frequencies up to 5 Hz.

SITE AMPLIFICATION OF EARTHQUAKE GROUND MOTION.

USGS Publications Warehouse

Hays, Walter W.

1986-01-01

When analyzing the patterns of damage in an earthquake, physical parameters of the total earthquake-site-structure system are correlated with the damage. Soil-structure interaction, the cause of damage in many earthquakes, involves the frequency-dependent response of both the soil-rock column and the structure. The response of the soil-rock column (called site amplification) is controversial because soil has strain-dependent properties that affect the way the soil column filters the input body and surface seismic waves, modifying the amplitude and phase spectra and the duration of the surface ground motion.

Molecular analysis of carbon monoxide-oxidizing bacteria associated with recent Hawaiian volcanic deposits.

PubMed

Dunfield, Kari E; King, Gary M

2004-07-01

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.

Molecular Analysis of Carbon Monoxide-Oxidizing Bacteria Associated with Recent Hawaiian Volcanic Deposits†

PubMed Central

Dunfield, Kari E.; King, Gary M.

2004-01-01

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity. PMID:15240307

On the Computation of H/V and its Application to Microzonation and Seismic Design

NASA Astrophysics Data System (ADS)

Perton, M.; Martínez, J. A.; Lermo, J. F.; Sanchez-Sesma, F. J.

2014-12-01

The H/V ratio is the square root of the ratio of horizontal to vertical energies of ground motion. It has been observed that the frequency of the main peak is well suited for the characterization of site effects and had been widely used for micro-zonation and seismic structural design. Historically that ratio was made from the average of individual H/V ratios obtained from noise autocorrelations. Nevertheless, it has been recently pointed out that the H/V ratio should be calculated differently as the ratio of the average of H over the average of V. This calculation is based on the relation between the directional energies (the imaginary part of Green's function) and the noise autocorrelations. In general, the average of ratios is different from the ratio of averages. Although the frequency of the main response was correctly obtained, the associated amplification factor has generally been badly predicted, having little matching with the amplification observed during strong earthquakes. The unexpected decay behavior of such ratios at high frequency and the lack of stability and reproducibility of the H/V ratios are other problems that face the method. These problems are addressed here from the point of view of normalization of noise correlations. In fact, several normalization techniques have already been proposed in order to correctly retrieve the Green's function. Some of them are well suited for the retrieval of the surface wave contribution, while others are more appropriate for bulk wave incidence. Since the H/V ratio may be used for various purposes like surface wave tomography, micro-zonation or seismic design, different normalizations are discussed in functions of the objectives. The H/V obtained from local historical earthquakes on top or far away from the subduction zone are also discussed. ACKNOWLEDGEMENT This research has been partially supported by DGAPA-UNAM under Project IN104712 and the AXA Research Fund.

Optimal-adaptive filters for modelling spectral shape, site amplification, and source scaling

USGS Publications Warehouse

Safak, Erdal

1989-01-01

This paper introduces some applications of optimal filtering techniques to earthquake engineering by using the so-called ARMAX models. Three applications are presented: (a) spectral modelling of ground accelerations, (b) site amplification (i.e., the relationship between two records obtained at different sites during an earthquake), and (c) source scaling (i.e., the relationship between two records obtained at a site during two different earthquakes). A numerical example for each application is presented by using recorded ground motions. The results show that the optimal filtering techniques provide elegant solutions to above problems, and can be a useful tool in earthquake engineering.

Prediction of maximum earthquake intensities for the San Francisco Bay region

USGS Publications Warehouse

Borcherdt, Roger D.; Gibbs, James F.

1975-01-01

The intensity data for the California earthquake of April 18, 1906, are strongly dependent on distance from the zone of surface faulting and the geological character of the ground. Considering only those sites (approximately one square city block in size) for which there is good evidence for the degree of ascribed intensity, the empirical relation derived between 1906 intensities and distance perpendicular to the fault for 917 sites underlain by rocks of the Franciscan Formation is: Intensity = 2.69 - 1.90 log (Distance) (km). For sites on other geologic units intensity increments, derived with respect to this empirical relation, correlate strongly with the Average Horizontal Spectral Amplifications (AHSA) determined from 99 three-component recordings of ground motion generated by nuclear explosions in Nevada. The resulting empirical relation is: Intensity Increment = 0.27 +2.70 log (AHSA), and average intensity increments for the various geologic units are -0.29 for granite, 0.19 for Franciscan Formation, 0.64 for the Great Valley Sequence, 0.82 for Santa Clara Formation, 1.34 for alluvium, 2.43 for bay mud. The maximum intensity map predicted from these empirical relations delineates areas in the San Francisco Bay region of potentially high intensity from future earthquakes on either the San Andreas fault or the Hazard fault.

Interfacial Polymerization for Colorimetric Labeling of Protein Expression in Cells

PubMed Central

Lilly, Jacob L.; Sheldon, Phillip R.; Hoversten, Liv J.; Romero, Gabriela; Balasubramaniam, Vivek; Berron, Brad J.

2014-01-01

Determining the location of rare proteins in cells typically requires the use of on-sample amplification. Antibody based recognition and enzymatic amplification is used to produce large amounts of visible label at the site of protein expression, but these techniques suffer from the presence of nonspecific reactivity in the biological sample and from poor spatial control over the label. Polymerization based amplification is a recently developed alternative means of creating an on-sample amplification for fluorescence applications, while not suffering from endogenous labels or loss of signal localization. This manuscript builds upon polymerization based amplification by developing a stable, archivable, and colorimetric mode of amplification termed Polymer Dye Labeling. The basic concept involves an interfacial polymer grown at the site of protein expression and subsequent staining of this polymer with an appropriate dye. The dyes Evans Blue and eosin were initially investigated for colorimetric response in a microarray setting, where both specifically stained polymer films on glass. The process was translated to the staining of protein expression in human dermal fibroblast cells, and Polymer Dye Labeling was specific to regions consistent with desired protein expression. The labeling is stable for over 200 days in ambient conditions and is also compatible with modern mounting medium. PMID:25536421

Optimizing direct amplification of forensic commercial kits for STR determination.

PubMed

Caputo, M; Bobillo, M C; Sala, A; Corach, D

2017-04-01

Direct DNA amplification in forensic genotyping reduces analytical time when large sample sets are being analyzed. The amplification success depends mainly upon two factors: on one hand, the PCR chemistry and, on the other, the type of solid substrate where the samples are deposited. We developed a workflow strategy aiming to optimize times and cost when starting from blood samples spotted onto diverse absorbent substrates. A set of 770 blood samples spotted onto Blood cards, Whatman ® 3 MM paper, FTA™ Classic cards, and Whatman ® Grade 1 was analyzed by a unified working strategy including a low-cost pre-treatment, a PCR amplification volume scale-down, and the use of the 3500 Genetic Analyzer as the analytical platform. Samples were analyzed using three different commercial multiplex STR direct amplification kits. The efficiency of the strategy was evidenced by a higher percentage of high-quality profiles obtained (over 94%), a reduced number of re-injections (average 3.2%), and a reduced amplification failure rate (lower than 5%). Average peak height ratio among different commercial kits was 0.91, and the intra-locus balance showed values ranging from 0.92 to 0.94. A comparison with previously reported results was performed demonstrating the efficiency of the proposed modifications. The protocol described herein showed high performance, producing optimal quality profiles, and being both time and cost effective. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Performance of MgO:PPLN, KTA, and KNbO₃ for mid-wave infrared broadband parametric amplification at high average power.

PubMed

Baudisch, M; Hemmer, M; Pires, H; Biegert, J

2014-10-15

The performance of potassium niobate (KNbO₃), MgO-doped periodically poled lithium niobate (MgO:PPLN), and potassium titanyl arsenate (KTA) were experimentally compared for broadband mid-wave infrared parametric amplification at a high repetition rate. The seed pulses, with an energy of 6.5 μJ, were amplified using 410 μJ pump energy at 1064 nm to a maximum pulse energy of 28.9 μJ at 3 μm wavelength and at a 160 kHz repetition rate in MgO:PPLN while supporting a transform limited duration of 73 fs. The high average powers of the interacting beams used in this study revealed average power-induced processes that limit the scaling of optical parametric amplification in MgO:PPLN; the pump peak intensity was limited to 3.8  GW/cm² due to nonpermanent beam reshaping, whereas in KNbO₃ an absorption-induced temperature gradient in the crystal led to permanent internal distortions in the crystal structure when operated above a pump peak intensity of 14.4  GW/cm².

Molecular Genetic Variability of Commercial and Wild Accessions of Passion Fruit (Passiflora spp.) Targeting ex Situ Conservation and Breeding

PubMed Central

Cerqueira-Silva, Carlos Bernard M.; Santos, Elisa S. L.; Jesus, Onildo N.; Vieira, João G. P.; Mori, Gustavo M.; Corrêa, Ronan X.; Souza, Anete P.

2014-01-01

Passiflora species are distributed throughout Latin America, and Brazil and Colombia serve as the centers of diversity for this genus. We performed cross-species amplification to evaluate 109 microsatellite loci in 14 Passiflora species and estimated the diversity and genetic structure of Passiflora cincinnata, Passiflora setaceae and Passiflora edulis. A total of 127 accessions, including 85 accessions of P. edulis, a commercial species, and 42 accessions of 13 wild species, were examined. The cross-species amplification was effective for obtaining microsatellite loci (average cross-amplification of 70%). The average number of alleles per locus (five) was relatively low, and the average diversity ranged from 0.52 in P. cincinnata to 0.32 in P. setacea. The Bayesian analyses indicated that the P. cincinnata and P. setacea accessions were distributed into two groups, and the P. edulis accessions were distributed into five groups. Private alleles were identified, and suggestions for core collections are presented. Further collections are necessary, and the information generated may be useful for breeding and conservation. PMID:25514245

Molecular genetic variability of commercial and wild accessions of passion fruit (Passiflora spp.) targeting ex situ conservation and breeding.

PubMed

Cerqueira-Silva, Carlos Bernard M; Santos, Elisa S L; Jesus, Onildo N; Vieira, João G P; Mori, Gustavo M; Corrêa, Ronan X; Souza, Anete P

2014-12-10

Passiflora species are distributed throughout Latin America, and Brazil and Colombia serve as the centers of diversity for this genus. We performed cross-species amplification to evaluate 109 microsatellite loci in 14 Passiflora species and estimated the diversity and genetic structure of Passiflora cincinnata, Passiflora setaceae and Passiflora edulis. A total of 127 accessions, including 85 accessions of P. edulis, a commercial species, and 42 accessions of 13 wild species, were examined. The cross-species amplification was effective for obtaining microsatellite loci (average cross-amplification of 70%). The average number of alleles per locus (five) was relatively low, and the average diversity ranged from 0.52 in P. cincinnata to 0.32 in P. setacea. The Bayesian analyses indicated that the P. cincinnata and P. setacea accessions were distributed into two groups, and the P. edulis accessions were distributed into five groups. Private alleles were identified, and suggestions for core collections are presented. Further collections are necessary, and the information generated may be useful for breeding and conservation.

Adjusting central and eastern North America ground‐motion intensity measures between sites with different reference‐rock site conditions

USGS Publications Warehouse

Boore, David; Campbell, Kenneth W.

2017-01-01

Adjustment factors are provided for converting ground‐motion intensity measures between central and eastern North America (CENA) sites with different reference‐rock site conditions (VS30=760, 2000, and 3000  m/s) for moment magnitudes ranging from 2 to 8, rupture distances ranging from 2 to 1200 km, Fourier amplitude spectra (FAS) for frequencies ranging from 0.01 to 100 Hz, response spectra for periods ranging from 0.01 to 10.0 s, peak ground acceleration, and peak ground velocity. The adjustment factors are given for a wide range of the site diminution parameters (κ0) for sites with VS30=760  m/s and for a κ0 of 0.006 s for two harder rock sites. Fourteen CENA velocity profiles with VS30 values within a factor of 1.1 of 760  m/s were used to derive average FAS amplification factors as a function of frequency, which were then used in simulations of peak ground‐motion parameters and response spectra to derive the adjustment factors. The amplification function differs from that used in western North America (e.g., Campbell and Boore, 2016) in having a peak near 9 Hz, due to the resonance of motions in the relatively thin low‐velocity material over hard rock that characterizes many CENA sites with VS30 near 760  m/s. We call these B/C sites, because this velocity marks the boundary between National Earthquake Hazards Reduction Program site classes B and C (Building Seismic Safety Council, 2004). The adjustments for short‐period motions are sensitive to the value of κ0, but there are very few if any determinations of κ0 for CENA B/C sites. For this reason, we determined κ0 from multiple recordings at Pinyon Flat Observatory (PFO), California, which has a velocity‐depth profile similar to those of CENA B/C sites. The PFO and other results from the literature suggest that appropriate values of κ0 for CENA B/C sites are expected to lie between 0.01 and 0.03 s.

Adjusting central and eastern North America ground-motion intensity measures between sites with different reference-rock site conditions

USGS Publications Warehouse

Boore, David; Campbell, Kenneth W.

2017-01-01

Adjustment factors are provided for converting ground‐motion intensity measures between central and eastern North America (CENA) sites with different reference‐rock site conditions (VS30=760, 2000, and 3000  m/s) for moment magnitudes ranging from 2 to 8, rupture distances ranging from 2 to 1200 km, Fourier amplitude spectra (FAS) for frequencies ranging from 0.01 to 100 Hz, response spectra for periods ranging from 0.01 to 10.0 s, peak ground acceleration, and peak ground velocity. The adjustment factors are given for a wide range of the site diminution parameters (κ0) for sites with VS30=760  m/s and for a κ0 of 0.006 s for two harder rock sites. Fourteen CENA velocity profiles with VS30 values within a factor of 1.1 of 760  m/s were used to derive average FAS amplification factors as a function of frequency, which were then used in simulations of peak ground‐motion parameters and response spectra to derive the adjustment factors. The amplification function differs from that used in western North America (e.g., Campbell and Boore, 2016) in having a peak near 9 Hz, due to the resonance of motions in the relatively thin low‐velocity material over hard rock that characterizes many CENA sites with VS30 near 760  m/s. We call these B/C sites, because this velocity marks the boundary between National Earthquake Hazards Reduction Program site classes B and C (Building Seismic Safety Council, 2004). The adjustments for short‐period motions are sensitive to the value of κ0, but there are very few if any determinations of κ0 for CENA B/C sites. For this reason, we determined κ0from multiple recordings at Pinyon Flat Observatory (PFO), California, which has a velocity‐depth profile similar to those of CENA B/C sites. The PFO and other results from the literature suggest that appropriate values of κ0 for CENA B/C sites are expected to lie between 0.01 and 0.03 s.

Regional comparisons of Vs30 and Spectral Ratio Methods

NASA Astrophysics Data System (ADS)

McNamara, D. E.; Gee, L. S.; Stephenson, W. J.; Odum, J. K.; Williams, R. A.; Hartzell, S.

2013-12-01

Earthquake damage is often increased due to local ground-motion amplification in soft soils and thick basin sediments with factors such as topographic effects and water saturation. Seismic hazard assessments depend on detailed information on local site response and many different methods have been developed to estimate site response. Based on numerous empirical studies, the average shear-wave velocity in the upper 30 m (Vs30) has become the most common means of classifying site conditions and has been adopted in the NEHRP design provisions for new buildings. In general, higher Vs30 values are associated with firm, dense rock and lower levels of ground shaking while lower Vs30 values are associated with softer soils and high site amplification. Vs30 is commonly computed by measuring the time it takes for shear-waves to travel from 30m depth to the surface using either active sources such as explosions or passive ambient noise microtremor sources. Since this approach is limited to locations where active measurements are undertaken, recent methods have sought to approximate Vs30 regionally, such as using topographic slope as a proxy. In this presentation, we compute a standard site response, horizontal-to-vertical spectral ratio (HVSR) using long-term power spectral density statistics of both ambient noise and earthquake signals at permanent and temporary seismic stations. We compare the HVSR results to surface observations of Vs30 and approximations using topographic slope in several different regions including the Eastern United States, St. Louis and the Los Angeles basin. In our comparison of the HVSR results to Vs30, we find that HVSR peak frequency can be used as a proxy for Vs30. Relationships between surface measured Vs30 and HVSR are less scattered than with Vs30 estimated using topographic approximations. In general, higher Vs30 is associated with higher HVSR peak frequency with variations in slope for different regions. We use these regional relationships to estimate NEHRP soil class at over 200 seismic stations in the US.

Evaluation of local site effect in the western side of the Suez Canal area by applying H/V and MASW techniques

NASA Astrophysics Data System (ADS)

Mohamed, Emad K.; Shokry, M. M. F.; Hassoup, Awad; Helal, A. M. A.

2016-11-01

The soft sediments are one of the most important factors responsible for the amplification of the seismic ground motion in an area of study. Three components, single-station microtremor measurements were performed at 61 sites along the Suez Canal to estimate the fundamental frequencies of the soil and corresponding H/V amplitude ratios by using the horizontal-to-vertical spectral ratio (HVSR) method. We have applied the investigations of the shear wave velocity for supplementing the existing seismic microzonation of the Suez Canal. The multichannel analysis of surface wave (MASW) tests were done along the Suez Canal in the three cities, Suez, Ismailia, and Port Said using 24 channels digital engineering seismograph with 4.5 Hz geophones from September 2014 to January 2015 to get the shear wave velocity VS30. The SeisImager/SW software was used for analyzing the data, and 1D-shear wave velocity model have achieved for each site. The HVSR curves show that the fundamental frequency values are ranging from 0.57 to 1.08 Hz, and H/V amplitude ratios are ranging from 4.05 to 6.46. The average values of VS30 are (548, 301), (241, 319), (194, 110, 238) for Suez, Ismailia, and Port Said respectively. The average of shear wave velocity up to 30 m depth is estimated and used for site classification based on the National Earthquake Hazard Reduction Program (NEHRP) classification. The majority of the sites was classified as Class D (stiff soil) except one site at Port Said city is classified as Class E (soft soils), and another site in the Suez city is classified as Class C (hard rock).

Seismic Wave Amplification in Las Vegas: Site Characterization Measurements and Response Models

NASA Astrophysics Data System (ADS)

Louie, J. N.; Anderson, J. G.; Luke, B.; Snelson, C.; Taylor, W.; Rodgers, A.; McCallen, D.; Tkalcic, H.; Wagoner, J.

2004-12-01

As part of a multidisciplinary effort to understand seismic wave amplification in Las Vegas Valley, we conducted geotechnical and seismic refraction field studies, geologic and lithologic interpretation, and geophysical model building. Frequency-dependent amplifications (site response) and peak ground motions strongly correlate with site conditions as characterized by the models. The models include basin depths and velocities, which also correlate against ground motions. Preliminary geologic models were constructed from detailed geologic and fault mapping, logs of over 500 wells penetrating greater than 200 m depth, gravity-inversion results from the USGS, and USDA soil maps. Valley-wide refraction studies we conducted in 2002 and 2003 were inverted for constraints on basin geometry, and deep basin and basement P velocities with some 3-d control to depths of 5 km. Surface-wave studies during 2002-2004 characterized more than 75 sites within the Valley for shear velocity to depths exceeding 100 m, including all the legacy sites where nuclear-blast ground motions were recorded. The SASW and refraction-microtremor surface-surveying techniques proved to provide complementary, and coordinating Rayleigh dispersion-curve data at a dozen sites. Borehole geotechnical studies at a half-dozen sites confirmed the shear-velocity profiles that we derived from surface-wave studies. We then correlated all the geotechnical data against a detailed stratigraphic model, derived from drilling logs, to create a Valley-wide model for shallow site conditions. This well-log-based model predicts site measurements better than do models based solely on geologic or soil mapping.

Variability of site response in the Los Angeles urban area

USGS Publications Warehouse

Hartzell, S.; Cranswick, E.; Frankel, A.; Carver, D.; Meremonte, M.

1997-01-01

This article addresses the variability of site response in the Los Angeles area and possible structural causes for the observations. Aftershock records from 231 sites in the San Fernando and Los Angeles basins and the surrounding mountains are used in this study. Spectral ratios, taken with respect to a low-amplitude reference site, are used to document the variation in site amplification in the frequency range 2 to 6 Hz, both spatially and with backazimuth to the source. At higher frequencies (6 to 10 Hz), spectral ratios are shown to have greater spatial variability. Interstation spectral ratios are used to measure the standard deviation among sources as a function of station separation. An increase in the variation in ground motion is shown to take place at a station separation of 1 km. Relative site-response estimates between nearby stations are used to demonstrate that preferred directions of motion can exist even in areas with no surface topographic effects. Significant variations in site response exist over short baselines (up to a factor of 2 over 200 m) that are not explained by differences in surficial geology or shallow shear-wave velocity. A variety of investigative approaches is used, including spectral ratios, arrival-time variations, 1D and 2D waveform modeling, and comparison with seismic reflection lines, to determine the most likely causes of these observations. A correlation is demonstrated between late arrival times of P and S waves and larger site amplification in Sherman Oaks and Northridge. This observation, in conjunction with waveform modeling and seismic reflection profiles, is used to infer that sedimentary structures in the upper 1 to 2 km and topography on the sediment-basement interface play an important role in determining site amplification. These structures, in the form of folds and buried basins, focus energy in spatially restricted areas at the surface. Comparison of displacement waveforms at nearby stations having disparate site amplifications, complemented by known shallow shear-wave velocities at selected sites, is used to support the argument that these structures, in some cases, can be the dominant factor in the modification of local ground motions.

A systematic analysis of directional site effects at stations of the Italian Seismic Network to test the role of local topography

NASA Astrophysics Data System (ADS)

Pischiutta, Marta; Cianfarra, Paola; Salvini, Francesco; Cara, Fabrizio; Vannoli, Paola

2018-03-01

Directional site effects observed at seismological stations on pronounced relief are analyzed. We investigate the ground motion properties calculating horizontal-to-vertical spectral ratios and horizontal polarization of both ambient vibrations and earthquake records using broadband seismograms of the Italian Seismic Network. We find that a subset of 47 stations with pronounced relief, results in a significant (>2) directional amplification of the horizontal component, with a well defined, site-specific direction of motion. However, the horizontal spectral response of sites is not uniform, varying from an isolated (resonant) frequency peak to a broadband amplification, interesting frequency bands as large as 1-10 Hz in many cases. Using the 47 selected stations, we have tried to establish a relation between directional amplification and topography geometry in a 2D-vision, when applicable, through a morphological analysis of the Digital Elevation Model using Geographic Information Systems. The procedure computes the parameters that characterize the geometry of topographic irregularities (size and slope), in combination with a principal component analysis that automatically yields the orientation of the elongated ridges. In seeking a relation between directional amplification and the surface morphology, we have found that it is impossible to fit the variety of observations with a resonant topography model as well as to identify common features in the ground motion behavior for stations with similar topography typologies. We conclude that, rather than the shape of the topography, local structural complexities and details of the near-surface structure must play a predominant role in controlling ground motion properties at sites with pronounced relief.

A systematic analysis of directional site effects at stations of the Italian seismic network to test the role of local topography

NASA Astrophysics Data System (ADS)

Pischiutta, Marta; Cianfarra, Paola; Salvini, Francesco; Cara, Fabrizio; Vannoli, Paola

2018-07-01

Directional site effects observed at seismological stations on pronounced relief are analysed. We investigate the ground motion properties calculating horizontal-to-vertical spectral ratios and horizontal polarization of both ambient vibrations and earthquake records using broad-band seismograms of the Italian seismic network. We find that a subset of 47 stations with pronounced relief results in a significant (>2) directional amplification of the horizontal component, with a well-defined, site-specific direction of motion. However, the horizontal spectral response of sites is not uniform, varying from an isolated (resonant) frequency peak to a broad-band amplification, interesting frequency bands as large as 1-10 Hz in many cases. Using 47 selected stations, we have tried to establish a relation between directional amplification and topography geometry in a 2-D vision, when applicable, through a morphological analysis of the digital elevation model using geographic information systems. The procedure computes the parameters that characterize the geometry of topographic irregularities (size and slope), in combination with a principal component analysis that automatically yields the orientation of the elongated ridges. In seeking a relation between directional amplification and the surface morphology, we have found that it is impossible to fit the variety of observations with a resonant topography model as well as to identify common features in the ground motion behaviour for stations with similar topography typologies. We conclude that, rather than the shape of the topography, local structural complexities and details of the near-surface structure must play a predominant role in controlling ground motion properties at sites with pronounced relief.

Miniaturized isothermal nucleic acid amplification, a review.

PubMed

Asiello, Peter J; Baeumner, Antje J

2011-04-21

Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.

Study of Site Response in the Seattle and Tacoma Basins, Washington, Using Spectral Ratio Methods

NASA Astrophysics Data System (ADS)

Keshvardoost, R.; Wolf, L. W.

2014-12-01

Sedimentary basins are known to have a pronounced influence on earthquake-generated ground motions, affecting both predominant frequencies and wave amplification. These site characteristics are important elements in estimating ground shaking and seismic hazard. In this study, we use three-component broadband and strong motion seismic data from three recent earthquakes to determine site response characteristics in the Seattle and Tacoma basins, Washington. Resonant frequencies and relative amplification of ground motions were determined using Fourier spectral ratios of velocity and acceleration records from the 2012 Mw 6.1 Vancouver Island earthquake, the 2012 Mw 7.8 Queen Charlotte Island earthquake, and the 2014 Mw 6.6 Vancouver Island earthquake. Recordings from sites within and adjacent to the Seattle and Tacoma basins were selected for the study based on their signal to noise ratios. Both the Standard Spectral Ratio (SSR) and the Horizontal-to-Vertical Spectral Ratio (HVSR) methods were used in the analysis, and results from each were compared to examine their agreement and their relation to local geology. Although 57% of the sites (27 out of 48) exhibited consistent results between the two methods, other sites varied considerably. In addition, we use data from the Seattle Liquefaction Array (SLA) to evaluate the site response at 4 different depths. Results indicate that resonant frequencies remain the same at different depths but amplification decreases significantly over the top 50 m.

Site-specific Seismic Hazard Assessment to Establish Elastic Design Properties for Oman Museum-Across Ages, Manah, Sultante of Oman

NASA Astrophysics Data System (ADS)

El Hussain, I. W.

2017-12-01

The current study provides a site specific deterministic seismic hazard assessment (DSHA) at the selected site for establishing the Oman Museum-Across Ages at Manah area, as a part of a comprehensive geotechnical and seismological plan to design the facilities accordingly. The DSHA first defines the seismic sources that might influence the site and assesses the maximum possible earthquake magnitude for each of them. By assuming each of these maximum earthquakes to occur at a location placing them at the closest distances to the site, the ground motion is predicted utilizing empirical ground motion prediction equations. The local site effects are performed by determining the fundamental frequency of the soft soil using HVSR technique and by estimating amplification spectra using the soil characteristics (mainly shear-wave velocity). Shear-wave velocity has been evaluated using the MASW technique. The maximum amplification value of 2.1 at spectral period 0.06 sec is observed at the ground surface, while the largest amplification value at the top of the conglomerate layer (at 5m depth) is 1.6 for a spectral period of 0.04 Sec. The maximum median 5% damped peak ground acceleration is found to be 0.263g at a spectral period of 0.1 sec. Keywords: DSHA; Site Effects; HVSR; MASW; PGA; Spectral Period

Horizontal localization and speech intelligibility with bilateral and unilateral hearing aid amplification.

PubMed

Köbler, S; Rosenhall, U

2002-10-01

Speech intelligibility and horizontal localization of 19 subjects with mild-to-moderate hearing loss were studied in order to evaluate the advantages and disadvantages of bilateral and unilateral hearing aid (HA) fittings. Eight loudspeakers were arranged in a circular array covering the horizontal plane around the subjects. Speech signals of a sentence test were delivered by one, randomly chosen, loudspeaker. At the same time, the other seven loudspeakers emitted noise with the same long-term average spectrum as the speech signals. The subjects were asked to repeat the speech signal and to point out the corresponding loudspeaker. Speech intelligibility was significantly improved by HAs, bilateral amplification being superior to unilateral. Horizontal localization could not be improved by HA amplification. However, bilateral HAs preserved the subjects' horizontal localization, whereas unilateral amplification decreased their horizontal localization abilities. Front-back confusions were common in the horizontal localization test. The results indicate that bilateral HA amplification has advantages compared with unilateral amplification.

A comparative study of noisy signal evolution in 2R all-optical regenerators with normal and anomalous average dispersions using an accelerated Multicanonical Monte Carlo method.

PubMed

Lakoba, Taras I; Vasilyev, Michael

2008-10-27

In [Opt. Express 15, 10061 (2007)] we proposed a new regime of multichannel all-optical regeneration that required anomalous average dispersion. This regime is superior to the previously studied normal-dispersion regime when signal distortions are deterministic in their temporal shape. However, there was a concern that the regenerator with anomalous average dispersion may be prone to noise amplification via modulational instability. Here, we show that this, in general, is not the case. Moreover, in the range of input powers that is of interest for multichannel regeneration, the device with anomalous average dispersion may even provide less noise amplification than the one with normal dispersion. These results are obtained with an improved version of the parallelized modification of the Multicanonical Monte Carlo method proposed in [IEEE J. Sel. Topics Quantum Electron. 14, 599 (2008)].

Analogous pleiotropic effects of insecticide resistance genotypes in peach-potato aphids and houseflies.

PubMed

Foster, S P; Young, S; Williamson, M S; Duce, I; Denholm, I; Devine, G J

2003-08-01

We show that single-point mutations conferring target-site resistance (kdr) to pyrethroids and DDT in aphids and houseflies, and gene amplification conferring metabolic resistance (carboxylesterase) to organophosphates and carbamates in aphids, can have deleterious pleiotropic effects on fitness. Behavioural studies on peach-potato aphids showed that a reduced response to alarm pheromone was associated with both gene amplification and the kdr target-site mutation. In this species, gene amplification was also associated with a decreased propensity to move from senescing leaves to fresh leaves at low temperature. Housefly genotypes possessing the identical kdr mutation were also shown to exhibit behavioural differences in comparison with susceptible insects. In this species, resistant individuals showed no positional preference along a temperature gradient while susceptible genotypes exhibited a strong preference for warmer temperatures.

Automated algorithm for mapping regions of cold-air pooling in complex terrain

NASA Astrophysics Data System (ADS)

Lundquist, Jessica D.; Pepin, Nicholas; Rochford, Caitlin

2008-11-01

In complex terrain, air in contact with the ground becomes cooled from radiative energy loss on a calm clear night and, being denser than the free atmosphere at the same elevation, sinks to valley bottoms. Cold-air pooling (CAP) occurs where this cooled air collects on the landscape. This article focuses on identifying locations on a landscape subject to considerably lower minimum temperatures than the regional average during conditions of clear skies and weak synoptic-scale winds, providing a simple automated method to map locations where cold air is likely to pool. Digital elevation models of regions of complex terrain were used to derive surfaces of local slope, curvature, and percentile elevation relative to surrounding terrain. Each pixel was classified as prone to CAP, not prone to CAP, or exhibiting no signal, based on the criterion that CAP occurs in regions with flat slopes in local depressions or valleys (negative curvature and low percentile). Along-valley changes in the topographic amplification factor (TAF) were then calculated to determine whether the cold air in the valley was likely to drain or pool. Results were checked against distributed temperature measurements in Loch Vale, Rocky Mountain National Park, Colorado; in the Eastern Pyrenees, France; and in Yosemite National Park, Sierra Nevada, California. Using CAP classification to interpolate temperatures across complex terrain resulted in improvements in root-mean-square errors compared to more basic interpolation techniques at most sites within the three areas examined, with average error reductions of up to 3°C at individual sites and about 1°C averaged over all sites in the study areas.

NEHRP soil classifications for estimating site-dependent seismic coefficients in the Upper Mississippi Embayment

USGS Publications Warehouse

Street, R.; Woolery, E.W.; Wang, Z.; Harris, J.B.

2001-01-01

Local soil conditions have a profound influence on the characteristics of ground shaking during an earthquake. Exceptionally deep soil deposits, on the order of 100-1000 m deep, are found in the Upper Mississippi Embayment of the central United States. Shear waves (SH) from earthquakes in the New Madrid seismic zone are expected to be strongly affected by the sharp impedance contrasts at the bedrock/sediment interface, attenuation of seismic waves in the soil column, and the SH-wave velocities of the more poorly consolidated near-surface (???50 m) soils. SH-wave velocities of the near-surface soils at nearly 400 sites in the Upper Mississippi Embayment were determined using conventional seismic SH-wave refraction and reflection techniques. Based on the average SH-wave velocities of the upper 30 m of the soils, sites in the Mississippi River floodplain portion of the study area are predominantly classified as Site Class D (180-360 m/s) in accordance with the 1997 NEHRP provisions. Sites away from the active floodplains in western Kentucky and western Tennessee, the SH-wave velocities of the upper 30 m of soils typically ranged from mid-200 to mid-300 m/s. Several sites in western Kentucky had averaged SH-wave velocities greater than 360 m/s, thereby qualifying them as Site Class C (360-760 m/s) in accordance with the 1997 NEHRP provisions. One dimensional site effects, including amplification and dynamic site period, were calculated for a representative suite of sites across the Upper Mississippi Embayment at latitude ?? 38.5??. Although seismic attenuation is greater in the Mississippi River floodplain (i.e. thicker, lower velocity material), the site effects tend to be greater than in the uplands of western Tennessee because of larger impedance contrasts within the near-surface soils. ?? 2001 Elsevier Science B.V. All rights reserved.

[Evaluating the Stability of Loop-Mediated Isothermal Amplification Reagents at Irregular Storage Temperatures for On-Site Diagnosis].

PubMed

Inoshima, Yasuo; Ishiguro, Naotaka

2015-01-01

Temperature-stability of loop-mediated isothermal amplification (LAMP) reagents was determined for their use in on-site diagnosis, such as in farms/pastures. Bst and Csa DNA polymerases and the reagents that were stored at different temperatures (4 or 25°C) for 1, 2, or 4 days were used for the LAMP assay to detect orf virus DNA as a model. After storage at 4 and 25°C for 2 days, the enzymes and reagents were found to retain sufficient activity to carry out successful DNA amplification. Visual diagnosis was also possible with the reagents (Loopamp Fluorescent Detection Reagent or hydroxy naphthol blue, as well as DNA amplification checker, D-Quick) that were stored for 2 days at different temperatures. Although the time taken to obtain the positive/negative results were delayed, the enzymes and reagents, stored at 25°C for 4 days, were active and had the ability to efficiently amplify DNA in less than 50 min. These results indicate that LAMP assay can be successfully utilized for the diagnosis of infectious diseases under non-clinical settings such as for on-site diagnosis in farms/pastures, owing to the fact that the relevant enzymes and reagents does not require restricted temperature storage.

RUNX1 Amplification Increases the Risk for Thrombosis in Children With B-cell Acute Lymphoblastic Leukemia.

PubMed

Boucher, Maria O; Smitherman, Andrew B; Pahl, Kristy S; Rao, Kathleen W; Deal, Allison M; Blatt, Julie

2016-04-01

RUNX1 (AML1) amplification in patients with B-cell acute lymphoblastic leukemia (B-ALL) has been associated with poor survival for unclear reasons. Our anecdotal experience suggests that children with B-ALL and RUNX1 amplification might be predisposed to thrombosis. We performed a retrospective cohort study of children with B-ALL treated from 2008 to 2014 at the North Carolina Children's Hospital. Patient demographics, cytogenetics, and diagnosis of thrombosis were extracted by blinded chart review. Analysis was performed examining the relationship between RUNX1 amplification and thrombosis. We identified 119 patients with B-ALL and a median age of 4.9 years (interquartile range, 2.9 to 8.6 y) at diagnosis. Four patients (3%) had RUNX1 amplification. The average number of RUNX1 copies among those with amplification was 5 (SD 0.81 [range, 4 to 6]). Eighteen thromboses were diagnosed within 6 months of starting treatment. These events were more likely among patients with RUNX1 amplification than in patients without amplification (75% vs. 13%; RR 5.75, 95% confidence interval, 2.75-12.01). RUNX1 amplification may predispose to early thrombotic events in children with B-ALL which could, in part, contribute to their poorer outcomes. Treatment implications, including possible prophylactic anticoagulation of patients with of RUNX1 amplification, justify larger studies to confirm these findings.

Lidar using the backscatter amplification effect

NASA Astrophysics Data System (ADS)

Razenkov, Igor A.; Banakh, Victor A.

2018-04-01

Experimental data proving the possibility of lidar measurement of the refractive turbulence strength based on the effect of backscatter amplification (BSA) are reported. It is shown that the values of the amplification factor correlate with the variance of random jitter of optical image of an incoherent light source depending on the value of the structure constant of the air refractive index turbulent fluctuations averaged over the probing path. This paper presents the results of measurements of the BSA factor in comparison with the simultaneous measurements of the BSA peak, which is very narrow and only occurs on the laser beam axis. It is constructed the range-time images of the derivative of the amplification factor gives a comprehensive picture of the location of turbulent zones and their temporal dynamics.

GAB2 amplifications refine molecular classification of melanoma.

PubMed

Chernoff, Karen A; Bordone, Lindsey; Horst, Basil; Simon, Katherine; Twadell, William; Lee, Keagan; Cohen, Jason A; Wang, Shuang; Silvers, David N; Brunner, Georg; Celebi, Julide Tok

2009-07-01

Gain-of-function mutations in BRAF, NRAS, or KIT are associated with distinct melanoma subtypes with KIT mutations and/or copy number changes frequently observed among melanomas arising from sun-protected sites, such as acral skin (palms, soles, and nail bed) and mucous membranes. GAB2 has recently been implicated in melanoma pathogenesis, and increased copy numbers are found in a subset of melanomas. We sought to determine the association of increased copy numbers of GAB2 among melanoma subtypes in the context of genetic alterations in BRAF, NRAS, and KIT. A total of 85 melanomas arising from sun-protected (n = 23) and sun-exposed sites (n = 62) were analyzed for copy number changes using array-based comparative genomic hybridization and for gain-of-function mutations in BRAF, NRAS, and KIT. GAB2 amplifications were found in 9% of the cases and were associated with melanomas arising from acral and mucosal sites (P = 0.005). Increased copy numbers of the KIT locus were observed in 6% of the cases. The overall mutation frequencies for BRAF and NRAS were 43.5% and 14%, respectively, and were mutually exclusive. Among the acral and mucosal melanomas studied, the genetic alteration frequency was 26% for GAB2, 13% for KIT, 30% for BRAF, and 4% for NRAS. Importantly, the majority of GAB2 amplifications occurred independent from genetic events in BRAF, NRAS, and KIT. GAB2 amplification is critical for melanomas arising from sun-protected sites. Genetic alterations in GAB2 will help refine the molecular classification of melanomas.

Ancient DNA in human bone remains from Pompeii archaeological site.

PubMed

Cipollaro, M; Di Bernardo, G; Galano, G; Galderisi, U; Guarino, F; Angelini, F; Cascino, A

1998-06-29

aDNA extraction and amplification procedures have been optimized for Pompeian human bone remains whose diagenesis has been determined by histological analysis. Single copy genes amplification (X and Y amelogenin loci and Y specific alphoid repeat sequences) have been performed and compared with anthropometric data on sexing.

[Prognostic significance of MYCN amplification in children neuroblastic tumors].

PubMed

Niu, Huilin; Xu, Tao; Wang, Fenghua; Chen, Zhengrong; Gao, Qiu; Yi, Peng; Xia, Jianqing

2015-02-01

To summarize the clinicopathologic features of neuroblastic tumors (NT), and to explore the prognostic significance of MYCN amplification in NT. The clinicopathologic data of 267 NT were reviewed. MYCN gene amplification was detected by fluorescence in situ hybridization (FISH) in 119 cases and the relationship with pathological characteristics and prognostic significance were analyzed. The study included 267 cases of children NT from patients aged from 1 day to 13 years (median 27 months). The male to female ratio was 1.43. There were 38 cases (14.2%), 43 cases (16.1%), 71 cases (26.6%), and 115 cases (43.1%) of INSS stages I, II, III and IV respectively.Favorable histology group had 157 cases (59.9%); unfavorable histology group had 110 cases (40.1%).Of the 119 NT cases with MYCN FISH performed, 18 cases (15.1%) showed amplification and the signal ratio of MYCN to CEP2 was 4.08-43.29. One hundred and one cases of non-amplified MYCN included MYCN gain in 79 cases (66.3%) and MYCN negative in 22 cases (18.5%). MYCN expression showed significant difference (P = 0.000) between ages, gender, NT type and MKI, but not INPC and clinical stage (P > 0.05).Of the 18 cases with MYCN amplification, 3 were undifferentiated, and 15 poorly differentiated; 17 had high MKI and one moderate MKI. All 18 cases were in unfavorable histology group; the overall survival rate was 3/18, with an average survival time of (17.9 ± 2.4) months.Of the 101 MYCN non-amplification cases, the overall survival rate was 68.3% (69/101), with an average survival time of (29.8 ± 1.3) months. Survival analysis showed the cases with MYCN amplification had worse prognosis (P < 0.05). NT were commonly diagnosed in early ages and easily to metastasize. Most of cases with favorable histology. The cases of MYCN amplification showed unfavorable histology, and the majority cases with high MKI; The patients with MYCN gene amplification had poor prognosis.

Optical Parametric Amplification of Single Photon: Statistical Properties and Quantum Interference

NASA Astrophysics Data System (ADS)

Xu, Xue-Xiang; Yuan, Hong-Chun

2014-05-01

By using phase space method, we theoretically investigate the quantum statistical properties and quantum interference of optical parametric amplification of single photon. The statistical properties, such as the Wigner function (WF), average photon number, photon number distribution and parity, are derived analytically for the fields of the two output ports. The results indicate that the fields in the output ports are multiphoton states rather than single photon state due to the amplification of the optical parametric amplifiers (OPA). In addition, the phase sensitivity is also examined by using the detection scheme of parity measurement.

The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification

USGS Publications Warehouse

Murphy, M.A.; Kendall, K.C.; Robinson, A.; Waits, L.P.

2007-01-01

To establish longevity of faecal DNA samples under varying summer field conditions, we collected 53 faeces from captive brown bears (Ursus arctos) on a restricted vegetation diet. Each faeces was divided, and one half was placed on a warm, dry field site while the other half was placed on a cool, wet field site on Moscow Mountain, Idaho, USA. Temperature, relative humidity, and dew point data were collected on each site, and faeces were sampled for DNA extraction at <1, 3, 6, 14, 30, 45, and 60 days. Faecal DNA sample viability was assessed by attempting PCR amplification of a mitochondrial DNA (mtDNA) locus (???150 bp) and a nuclear DNA (nDNA) microsatellite locus (180-200 bp). Time in the field, temperature, and dew point impacted mtDNA and nDNA amplification success with the greatest drop in success rates occurring between 1 and 3 days. In addition, genotyping errors significantly increased over time at both field sites. Based on these results, we recommend collecting samples at frequent transect intervals and focusing sampling efforts during drier portions of the year when possible. ?? 2007 Springer Science+Business Media, Inc.

Localized damage caused by topographic amplification during the 2010 M7.0 Haiti earthquake

USGS Publications Warehouse

Hough, S.E.; Altidor, J.R.; Anglade, D.; Given, D.; Janvier, M.G.; Maharrey, J.Z.; Meremonte, M.; Mildor, B.S.-L.; Prepetit, C.; Yong, A.

2010-01-01

Local geological conditions, including both near-surface sedimentary layers and topographic features, are known to significantly influence ground motions caused by earthquakes. Microzonation maps use local geological conditions to characterize seismic hazard, but commonly incorporate the effect of only sedimentary layers. Microzonation does not take into account local topography, because significant topographic amplification is assumed to be rare. Here we show that, although the extent of structural damage in the 2010 Haiti earthquake was primarily due to poor construction, topographic amplification contributed significantly to damage in the district of Petionville, south of central Port-au-Prince. A large number of substantial, relatively well-built structures situated along a foothill ridge in this district sustained serious damage or collapse. Using recordings of aftershocks, we calculate the ground motion response at two seismic stations along the topographic ridge and at two stations in the adjacent valley. Ground motions on the ridge are amplified relative to both sites in the valley and a hard-rock reference site, and thus cannot be explained by sediment-induced amplification. Instead, the amplitude and predominant frequencies of ground motion indicate the amplification of seismic waves by a narrow, steep ridge. We suggest that microzonation maps can potentially be significantly improved by incorporation of topographic effects. ?? 2010 Macmillan Publishers Limited. All rights reserved.

Detection of DNA Sequences Refractory to PCR Amplification Using a Biophysical SERRS Assay (Surface Enhanced Resonant Raman Spectroscopy)

PubMed Central

Feuillie, Cécile; Merheb, Maxime M.; Gillet, Benjamin; Montagnac, Gilles; Daniel, Isabelle; Hänni, Catherine

2014-01-01

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction – based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage. PMID:25502338

Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy).

PubMed

Feuillie, Cécile; Merheb, Maxime M; Gillet, Benjamin; Montagnac, Gilles; Daniel, Isabelle; Hänni, Catherine

2014-01-01

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction - based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage.

PDGFRA amplification is common in pediatric and adult high-grade astrocytomas and identifies a poor prognostic group in IDH1 mutant glioblastoma

PubMed Central

Phillips, Joanna J.; Aranda, Derick; Ellison, David W.; Judkins, Alexander R.; Croul, Sidney E.; Brat, Daniel J.; Ligon, Keith L.; Horbinski, Craig; Venneti, Sriram; Zadeh, Gelareh; Santi, Mariarita; Zhou, Shengmei; Appin, Christina L.; Sioletic, Stefano; Sullivan, Lisa M.; Martinez-Lage, Maria; Robinson, Aaron E.; Yong, William H.; Cloughesy, Timothy; Lai, Albert; Phillips, Heidi S.; Marshall, Roxanne; Mueller, Sabine; Haas-Kogan, Daphne A.; Molinaro, Annette M.; Perry, Arie

2013-01-01

High-grade astrocytomas (HGAs), corresponding to WHO grades III (AA) and IV (GBM), are biologically aggressive and their molecular classification is increasingly relevant to clinical management. PDGFRA amplification is common in HGAs, although its prognostic significance remains unclear. Using fluorescence in situ hybridization (FISH), the most sensitive technique for detecting PDGFRA copy number gains, we determined PDGFRA amplification status in 123 pediatric and 263 adult HGAs. A range of PDGFRA FISH patterns were identified and cases were scored as non-amplified (normal and polysomy) or amplified (low-level and high-level). PDGFRA amplification was frequent in pediatric (29.3%) and adult (20.9%) tumors. Amplification was not prognostic in pediatric HGAs. In adult tumors diagnosed initially as GBM, the presence of combined PDGFRA amplification and IDH1R132H mutation was a significant independent prognostic factor (p=0.01). In HGAs, PDGFRA amplification is common and can manifest as high-level and focal or low-level amplifications. Our data indicate that the latter is more prevalent than previously reported with copy number averaging techniques. To our knowledge, this is the largest survey of PDGFRA status in adult and pediatric HGAs and suggests PDGFRA amplification increases with grade and is associated with a less favorable prognosis in IDH1 mutant de novo GBMs. PMID:23438035

Tip-enhanced fluorescence with radially polarized illumination for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA

NASA Astrophysics Data System (ADS)

Wei, Shih-Chung; Chuang, Tsung-Liang; Wang, Da-Shin; Lu, Hui-Hsin; Gu, Frank X.; Sung, Kung-Bin; Lin, Chii-Wann

2015-02-01

A tip nanobiosensor for monitoring DNA replication was presented. The effects of excitation power and polarization on tip-enhanced fluorescence (TEF) were assessed with the tip immersed in fluorescein isothiocyanate solution first. The photon count rose on average fivefold with radially polarized illumination at 50 mW. We then used polymerase-functionalized tips for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA. The amplicon-SYBR Green I complex was detected and compared to real-time loop-mediated isothermal amplification. The signals of the reaction using 4 and 0.004 ng/μl templates were detected 10 and 30 min earlier, respectively. The results showed the potential of TEF in developing a nanobiosensor for real-time DNA amplification.

Hearing aid fitting for visual and hearing impaired patients with Usher syndrome type IIa.

PubMed

Hartel, B P; Agterberg, M J H; Snik, A F; Kunst, H P M; van Opstal, A J; Bosman, A J; Pennings, R J E

2017-08-01

Usher syndrome is the leading cause of hereditary deaf-blindness. Most patients with Usher syndrome type IIa start using hearing aids from a young age. A serious complaint refers to interference between sound localisation abilities and adaptive sound processing (compression), as present in today's hearing aids. The aim of this study was to investigate the effect of advanced signal processing on binaural hearing, including sound localisation. In this prospective study, patients were fitted with hearing aids with a nonlinear (compression) and linear amplification programs. Data logging was used to objectively evaluate the use of either program. Performance was evaluated with a speech-in-noise test, a sound localisation test and two questionnaires focussing on self-reported benefit. Data logging confirmed that the reported use of hearing aids was high. The linear program was used significantly more often (average use: 77%) than the nonlinear program (average use: 17%). The results for speech intelligibility in noise and sound localisation did not show a significant difference between type of amplification. However, the self-reported outcomes showed higher scores on 'ease of communication' and overall benefit, and significant lower scores on disability for the new hearing aids when compared to their previous hearing aids with compression amplification. Patients with Usher syndrome type IIa prefer a linear amplification over nonlinear amplification when fitted with novel hearing aids. Apart from a significantly higher logged use, no difference in speech in noise and sound localisation was observed between linear and nonlinear amplification with the currently used tests. Further research is needed to evaluate the reasons behind the preference for the linear settings. © 2016 The Authors. Clinical Otolaryngology Published by John Wiley & Sons Ltd.

Fibroblast growth factor receptor 1 gene amplification is associated with poor survival in patients with resected esophageal squamous cell carcinoma

PubMed Central

Kim, Dae Joon; Lee, Chang-Geol; Hur, Jin; Chung, Hyunsoo; Park, Jun Chul; Jung, Da Hyun; Shin, Sung Kwan; Lee, Sang Kil; Lee, Yong Chan; Kim, Hye Ryun; Moon, Yong Wha; Kim, Joo Hang; Shim, Young Mog; Jewell, Susan S.; Kim, Hyunki; Choi, Yoon-La; Cho, Byoung Chul

2015-01-01

To investigate the frequency and the prognostic impact of fibroblast growth factor receptor 1 (FGFR1) gene amplification in 526 curatively resected esophageal squamous cell carcinoma (ESCC). Using fluorescent in situ hybridization, high amplification was defined by an FGFR1/centromer 8 ratio is ≥ 2.0, or average number of FGFR1 signals/tumor cell nucleus ≥ 6.0, or percentage of tumor cells containing ≥ 15 FGFR1 signals or large cluster in ≥ 10%. Low amplification was defined by ≥ 5 FGFR1 signals in ≥ 50%. FGFR2 and FGFR3 mutations were assessed by direct sequencing in 388 cases and no mutation was detected. High and low amplification were detected in 8.6% and 1.1%, respectively. High FGFR1 amplification had significantly shorter disease-free survival (34.0 vs 158.5 months P=0.019) and overall survival (52.2 vs not reached P=0.022) than low/no amplification group. After adjusting for sex, smoking, stage, histology, and adjuvant treatment, high FGFR1 amplification had a greater risk of recurrence (adjusted hazard ratio [AHR], 1.6; P=0.029) and death (AHR, 1.53; P=0.050). High amplification was significantly higher in current smokers than former and never-smokers (Ptrend<0.001) and increased proportional to smoking dosage. High FGFR1 amplification is a frequent oncogenic alteration and an independent poor prognostic factor in resected ESCC. PMID:25537505

Evaluation of six NEHRP B/C crustal amplification models proposed for use in western North America

USGS Publications Warehouse

Boore, David; Campbell, Kenneth W.

2016-01-01

We evaluate six crustal amplification models based on National Earthquake Hazards Reduction Program (NEHRP) B/C crustal profiles proposed for use in western North America (WNA) and often used in other active crustal regions where crustal properties are unknown. One of the models is based on an interpolation of generic rock velocity profiles previously proposed for WNA and central and eastern North America (CENA), in conjunction with material densities based on an updated velocity–density relationship. A second model is based on the velocity profile used to develop amplification factors for the Next Generation Attenuation (NGA)‐West2 project. A third model is based on a near‐surface velocity profile developed from the NGA‐West2 site database. A fourth model is based on velocity and density profiles originally proposed for use in CENA but recently used to represent crustal properties in California. We propose two alternatives to this latter model that more closely represent WNA crustal properties. We adopt a value of site attenuation (κ0) for each model that is either recommended by the author of the model or proposed by us. Stochastic simulation is used to evaluate the Fourier amplification factors and their impact on response spectra associated with each model. Based on this evaluation, we conclude that among the available models evaluated in this study the NEHRP B/C amplification model of Boore (2016) best represents median crustal amplification in WNA, although the amplification models based on the crustal profiles of Kamai et al. (2013, 2016, unpublished manuscript, see Data and Resources) and Yenier and Atkinson (2015), the latter adjusted to WNA crustal properties, can be used to represent epistemic uncertainty.

Basin-edge generated Rayleigh waves in the Almaty basin and corresponding consequences for ground motion amplification

NASA Astrophysics Data System (ADS)

Pilz, Marco; Parolai, Stefano; Petrovic, Bojana; Silacheva, Natalya; Abakanov, Tanatkan; Orunbaev, Sagynbek; Moldobekov, Bolot

2018-04-01

During the past two centuries, several large earthquakes have caused extensive damages in the city of Almaty in Kazakhstan. Increasing the preparedness for future events, the definition of the optimal engineering designs for civil structures and the corresponding mitigation of earthquake risks involves the accomplishment of site response studies. To this regard, a temporary seismological network of 15 stations was installed in the city aiming at the accurate identification of local variations of site response at different locations. As the city is settled on a deep sediment-filled plain with laterally strongly varying thicknesses, bound to the south by the Tien-Shan mountain range, the city might face important site effects: large amplification and significant increase of shaking duration. In addition, surface waves in the low-frequency range around and slightly higher than the fundamental resonance frequency, which could be generated at the boundaries of the basin, can carry a large amount of energy. In turn, this will influence both the spatial distribution of the level of amplification and the temporal lengthening of ground motion significantly. For quantifying these effects, we apply complex trace analysis, which uses the instantaneous polarization characteristics of the seismic signal for separating waves arriving at a single site from different directions. In this way, secondary surface waves originating at various sites along the edge of the Almaty basin can be identified as well as their generation regions. After having assessed 1-D amplification effects with well-established techniques like the standard spectral ratio and the horizontal-to-vertical spectral ratio techniques, the results further indicate that thick layers of soft clay deposits and the 3-D structure of the basin give rise to lengthening of ground motion and high amplification values at low frequencies around 0.2 Hz. The steep structure of the sediment-bedrock interface at the southern edge of the Almaty basin can generate surface waves with distinct azimuths, meaning that the spatial variability of ground motion is not only related to a simple 1-D response but it can be strongly modified by secondary waves generated at the margin of the basin.

Seismic characterization and dynamic site response of a municipal solid waste landfill in Bangalore, India.

PubMed

Anbazhagan, P; SivakumarBabu, G L; Lakshmikanthan, P; VivekAnand, K S

2016-03-01

Seismic design of landfills requires an understanding of the dynamic properties of municipal solid waste (MSW) and the dynamic site response of landfill waste during seismic events. The dynamic response of the Mavallipura landfill situated in Bangalore, India, is investigated using field measurements, laboratory studies and recorded ground motions from the intraplate region. The dynamic shear modulus values for the MSW were established on the basis of field measurements of shear wave velocities. Cyclic triaxial testing was performed on reconstituted MSW samples and the shear modulus reduction and damping characteristics of MSW were studied. Ten ground motions were selected based on regional seismicity and site response parameters have been obtained considering one-dimensional non-linear analysis in the DEEPSOIL program. The surface spectral response varied from 0.6 to 2 g and persisted only for a period of 1 s for most of the ground motions. The maximum peak ground acceleration (PGA) obtained was 0.5 g and the minimum and maximum amplifications are 1.35 and 4.05. Amplification of the base acceleration was observed at the top surface of the landfill underlined by a composite soil layer and bedrock for all ground motions. Dynamic seismic properties with amplification and site response parameters for MSW landfill in Bangalore, India, are presented in this paper. This study shows that MSW has less shear stiffness and more amplification due to loose filling and damping, which need to be accounted for seismic design of MSW landfills in India. © The Author(s) 2016.

Investigation on earthquake ground motions observed along a north-south survey line in the Kumamoto Plain, during the aftershocks of 2016 Kumamoto earthquake

NASA Astrophysics Data System (ADS)

Tsuno, S.; Korenaga, M.; Okamoto, K.; Chimoto, K.; Yamanaka, H.; Yamada, N.; Matsushima, T.

2017-12-01

To evaluate local site effects in the Kumamoto Plain, we installed 15 temporary seismic stations along the north-south survey line, after the 2016 Kumamoto earthquake foreshock (Mj 6.4). In this report, to investigate earthquake ground motions observed along the north-south survey line, we estimated site amplification factors from weak ground motion data and estimated S-wave velocity structures by array microtremor observations at temporary seismic stations. We installed 15 temporary seismic stations at an interval of 300m to 2.5km along the north-south survey line. We estimated site amplification factors, with a station at Mt. Kinbo as a reference. Site amplification factors at the middle part and the southern part along the survey line, located in the alluvial lowland, were dominated in the frequency of 1-2Hz. On the other hand, site amplification factors at the northern part along the survey line were dominated in the frequency of 2-5Hz. It suggests that the ground profiles near the surface are complicate along this north-south survey line in the Kumamoto Plain. Therefore, we performed array microtremor observations at the temporary seismic stations, to estimate S-wave velocity structures along the north-south survey line. We obtained phase velocities of Rayleigh waves by the SPAC method and estimated S-wave velocity structures by applying the Genetic Algorism to those phase velocity. The low velocity layer with a thickness of around 15m was deposited on the surface at sites located in the alluvial lowland. Finally, we compared the distribution of PGAs observed along the north-south survey line to AVs30 estimated by S-wave velocity structures. As a result, PGAs along the survey line were strongly concerned by AVs30. We concluded that earthquake ground motions in the frequency of more than 1Hz observed in this north-south survey line were excited by the low velocity layer near the surface.

Sediment-induced amplification and the collapse of the Nimitz Freeway

USGS Publications Warehouse

Hough, S.E.; Friberg, P.A.; Busby, R.; Field, E.F.; Jacob, K.H.; Borcherdt, R.D.

1990-01-01

THE amplification of ground motion by low-seismic-velocity surface sediments is an important factor in determining the seismic hazard specific to a given site. The Ms = 7.1 Loma Prieta earthquake of 17 October 1989 was the largest event in the contiguous United States in 37 years, and yielded an unparalleled volume of seismic data from the main shock and aftershock sequence1. These data can be used to image the seismic source, to study detailed Earth structure, and to study the propagation of seismic waves both through bedrock at depth and through sediment layers near the surface. Near the edge of San Francisco Bay, site conditions vary considerably on scales of hundreds of metres. The collapsed section of the two-tiered Nimitz Freeway in Oakland was built on San Francisco Bay mud, whereas stiffer alluvial sediments underlie a southern section that was damaged but did not collapse. Here we analyse high-quality, digital aftershock recordings from several sites near the Nimitz Freeway, and conclude that soil conditions and resulting ground-motion amplification may have contributed significantly to the failure of the structure.

Variation in Ground Shaking on the Fraser River Delta (Greater Vancouver, Canada)

NASA Astrophysics Data System (ADS)

Cassidy, J. F.; Rogers, G. R.

2003-04-01

The thick, soft soils of the Fraser River delta, just south of Vancouver, Canada, are home to critical infrastructure such as one of North America's busiest port facilities, Canada's second busiest airport, and key transportation and power-transmission facilities for 2-3 million people. This area is also one of the most seismically active regions in Canada. We have utilised recent three-component, digital records of recent moderate (1996 M=5.1 at 200 km distance, 1997 M=4.3 at 40 km distance) and large (2001 M=6.8 at 300 km distance) earthquakes to examine the response to seismic shaking in the greater Vancouver, region, with an emphasis on the site response of the Fraser River delta. These suites of accelerograms have relatively low amplitudes (maximums of 0.015g for the 1996 records, 0.024g for the 1997 records, and 0.035g for the 2001 records). The 1997 data set is significant as it contains the first three-component recordings made on bedrock in greater Vancouver, and the 2001 data set is significant as it contains long-period signal (1-10 second energy). Using the method of spectral ratios, we estimate the site response for each of the strong motion instrument soil sites. Our results show frequency-dependent amplification, with factors of up to 12 times (relative to competent bedrock) near the edge of the delta. Here, the amplification is observed over a relatively narrow frequency range of 1.5-4 Hz (0.25-0.67 s period). Near the centre of the delta(where the soft soils are thickest) peak amplification of 4-10 times(relative to competent bedrock) is measured. Relative to firm soil, the peak amplification ranges from 2-5 for the thick soil delta centre sites, and 2-6 for the delta edge sites. At higher frequencies, little or no amplification, and in many cases slight attenuation is observed. The more distant earthquakes (200-300 km) present a simpler and more predictable picture of ground motion variation than that of the 1997 earthquake (40 km distant). The Geological Survey of Canada is currently deploying a demonstration dense urban seismograph network (~1km spacing) which crosses the northern edge of the Fraser delta in the greater Vancouver area to address varying site response in more detail.

Strong nonlinear dependence of the spectral amplification factors of deep Vrancea earthquakes magnitude

NASA Astrophysics Data System (ADS)

Marmureanu, Gheorghe; Ortanza Cioflan, Carmen; Marmureanu, Alexandru

2010-05-01

Nonlinear effects in ground motion during large earthquakes have long been a controversial issue between seismologists and geotechnical engineers. Aki wrote in 1993:"Nonlinear amplification at sediments sites appears to be more pervasive than seismologists used to think…Any attempt at seismic zonation must take into account the local site condition and this nonlinear amplification( Local site effects on weak and strong ground motion, Tectonophysics,218,93-111). In other words, the seismological detection of the nonlinear site effects requires a simultaneous understanding of the effects of earthquake source, propagation path and local geological site conditions. The difficulty for seismologists in demonstrating the nonlinear site effects has been due to the effect being overshadowed by the overall patterns of shock generation and path propagation. The researchers from National Institute for Earth Physics ,in order to make quantitative evidence of large nonlinear effects, introduced the spectral amplification factor (SAF) as ratio between maximum spectral absolute acceleration (Sa), relative velocity (Sv) , relative displacement (Sd) from response spectra for a fraction of critical damping at fundamental period and peak values of acceleration(a-max),velocity (v-max) and displacement (d-max),respectively, from processed strong motion record and pointed out that there is a strong nonlinear dependence on earthquake magnitude and site conditions.The spectral amplification factors(SAF) are finally computed for absolute accelerations at 5% fraction of critical damping (β=5%) in five seismic stations: Bucharest-INCERC(soft soils, quaternary layers with a total thickness of 800 m);Bucharest-Magurele (dense sand and loess on 350m); Cernavoda Nuclear Power Plant site (marl, loess, limestone on 270 m) Bacau(gravel and loess on 20m) and Iassy (loess, sand, clay, gravel on 60 m) for last strong and deep Vrancea earthquakes: March 4,1977 (MGR =7.2 and h=95 km);August 30,1986(MGR =7.0 and h=130 km);May 30,1990 (MGR =6.7 and h=90 km) and May 31,1990 (MGR =6.1 and h=87 km). With a view to understand the characteristics of nonlinear soil behavior and the nonlinearity in the seismology and the influence to hazard and risk assessment ,this study examined the ways that nonlinearity would expected to appear on strong motion records made on Romania territory during to last Vrancea earthquake. The effect on nonlinearity is very large. For example, if we maintain the same amplification factor (SAF=5.8942) as for relatively strong earthquake on May 31,1990 with magnitude Ms =6,1 then at Bacau seismic station for earthquake on May 30,1990 (MGR =6.7) the peak acceleration has to be a*max =0.154g( +14.16%) and the actual recorded was only, a max =0.135g. Also, for Vrancea earthquake on August 30,1986, the peak acceleration has to be a*max=0.107g (+45,57%), instead of real value of 0.0736 g recorded at Bacau seismic station. More, the spectral amplification factors(SAF) are function of earthquake magnitude and there is a strong nonlinear dependence of the SAF of earthquake magnitude. The median values of SAF of the last strong Vrancea earthquakes for damping 5% are: 4.16; 3.63 and 3.26 corresponding to May 31,1990 Vrancea earthquake (Ms=6.1),May 30,1990 Vrancea earthquake(Ms=6.7),respectively, August 30,1986 Vrancea one(Ms=7.0). At the same seismic station, for example at Bacau, for 5% damping, SAF for accelerations is 5.22 for May 31,1990 earthquake (Ms =6.1);4.32 for May 30,1990 earthquake (Ms =6.7) and 3,94 for August 30,1986 one (Ms=7.0) etc. Finally, it will be made a comment in connection to U.S. Atomic Energy Commission-Regulatory Guide 1.60 on "Design Response Spectra for seismic design of nuclear power plants " to see spectral amplification factors for deep Vrancea earthquakes are larger and different.

Uncertainty in Vs30-based site response

USGS Publications Warehouse

Thompson, Eric M.; Wald, David J.

2016-01-01

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 (VS30) and basin depth parameters. Because VS30 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 VS30 has been measured to address effects of VS30 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 VS30 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.

Surface seismic measurements of near-surface P-and S-wave seismic velocities at earthquake recording stations, Seattle, Washington

USGS Publications Warehouse

Williams, R.A.; Stephenson, W.J.; Frankel, A.D.; Odum, J.K.

1999-01-01

We measured P-and S-wave seismic velocities to about 40-m depth using seismic-refraction/reflection data on the ground surface at 13 sites in the Seattle, Washington, urban area, where portable digital seismographs recently recorded earthquakes. Sites with the lowest measured Vs correlate with highest ground motion amplification. These sites, such as at Harbor Island and in the Duwamish River industrial area (DRIA) south of the Kingdome, have an average Vs in the upper 30 m (V??s30) of 150 to 170 m/s. These values of V??s30 place these sites in soil profile type E (V??s30 < 180 m/s). A "rock" site, located at Seward Park on Tertiary sedimentary deposits, has a V??S30 of 433 m/s, which is soil type C (V??s30: 360 to 760 m/s). The Seward Park site V??s30 is about equal to, or up to 200 m/s slower than sites that were located on till or glacial outwash. High-amplitude P-and S-wave seismic reflections at several locations appear to correspond to strong resonances observed in earthquake spectra. An S-wave reflector at the Kingdome at about 17 to 22 m depth probably causes strong 2-Hz resonance that is observed in the earthquake data near the Kingdome.

Study of the Pan-ERBB Inhibitor Neratinib Given in Combination With Everolimus, Palbociclib or Trametinib in Advanced Cancer Subjects With EGFR Mutation/Amplification, HER2 Mutation/Amplification or HER3/4 Mutation

ClinicalTrials.gov

2018-03-26

Malignant Neoplasm of Breast; Malignant Neoplasms of Digestive Organs; Malignant Neoplasms of Female Genital Organs; Malignant Neoplasms of Ill-defined Secondary and Unspecified Sites; Malignant Neoplasms of Independent (Primary) Multiple Sites; Malignant Neoplasms of Lip Oral Cavity and Pharynx; Malignant Neoplasms of Mesothelial and Soft Tissue; Malignant Neoplasms of Respiratory and Intrathoracic Organs; Malignant Neoplasms of Thyroid and Other Endocrine Glands; Malignant Neoplasms of Urinary Tract; Neoplasms of Uncertain or Unknown Behavior

Ferrocenemonocarboxylic-HRP@Pt nanoparticles labeled RCA for multiple amplification of electro-immunosensing.

PubMed

Su, Huilan; Yuan, Ruo; Chai, Yaqin; Mao, Li; Zhuo, Ying

2011-07-15

A multiple amplification immunoassay was proposed to detect alpha-fetoprotein (AFP), which was based on ferrocenemonocarboxylic-HRP conjugated on Pt nanoparticles as labels for rolling circle amplification (RCA). Firstly, the capture antibody (anti-AFP) was immobilized on glass carbon electrode (GCE) deposited nano-sized gold particles. After a typical immuno-sandwich protocol, primary DNA was immobilized by labeling secondary antibody, which acted as a precursor to initiate RCA. The products of RCA provide large amount of sites to link detection DNAs, which were labeled by signal probes (ferrocenemonocarboxylic) and horseradish peroxidase (HRP). Moreover, the enzymatic amplification signals could be produced by the catalysis of HRP and Pt nanoparticles with the addition of H₂O₂. These lead to multiple amplification signals monitoring by electrochemical instrument and further resulted in high sensitivity of the immunoassay with the detection limit of 1.7 pg/mL. Copyright © 2011 Elsevier B.V. All rights reserved.

Signal amplification strategies for DNA and protein detection based on polymeric nanocomposites and polymerization: A review.

PubMed

Zhou, Shaohong; Yuan, Liang; Hua, Xin; Xu, Lingling; Liu, Songqin

2015-06-02

Demand is increasing for ultrasensitive bioassays for disease diagnosis, environmental monitoring and other research areas. This requires novel signal amplification strategies to maximize the signal output. In this review, we focus on a series of significant signal amplification strategies based on polymeric nanocomposites and polymerization. Some common polymers are used as carriers to increase the local concentration of signal probes and/or biomolecules on their surfaces or in their interiors. Some polymers with special fluorescence and optical properties can efficiently transfer the excitation energy from a single site to the whole polymer backbone. This results in superior fluorescence signal amplification due to the resulting collective effort (integration of signal). Recent polymerization-based signal amplification strategies that employ atom transfer radical polymerization (ATRP) and photo-initiated polymerization are also summarized. Several distinctive applications of polymers in ultrasensitive bioanalysis are highlighted. Copyright © 2015 Elsevier B.V. All rights reserved.

Directional Site Amplification Effect on Tarzana Hill, California

NASA Astrophysics Data System (ADS)

Graizer, V.; Shakal, A.

2003-12-01

Significantly amplified ground accelerations at the Tarzana Hill station were recorded during the 1987 Mw 5.9 Whittier Narrows and the 1994 Mw 6.7 Northridge earthquakes. Peak horizontal ground acceleration at the Tarzana station during the 1999 Mw 7.1 Hector Mine earthquake was almost twice as large as the accelerations recorded at nearby stations. The Tarzana site was drilled to a depth of 100 m. A low shear-wave velocity near the surface of 100 m/sec increasing to near 750 m/sec at 100 m depth was measured. The 20 m high hill was found to be well drained with a water table near 17 m. Modelo formation (extremely weathered at the surface to fresh at depth) underlies the hill. The subsurface geology and velocities obtained allow classification of this location as a soft-rock site. After the Northridge earthquake the California Strong Motion Instrumentation Program significantly increased instrumentation at Tarzana to study the unusual site amplification effect. Current instrumentation at Tarzana consists of an accelerograph at the top of Tarzana hill (Tarzana - Cedar Hill B), a downhole instrument at 60 m depth, and an accelerograph at the foot of the hill (Tarzana - Clubhouse), 180 m from the Cedar Hill B station. The original station, Tarzana - Cedar Hill Nursery A, was lost in 1999 due to construction. More than twenty events, including the Hector Mine earthquake, were recorded by all these instruments at Tarzana. Comparison of recordings and response spectra demonstrates strong directional resonance on the top of the hill in a direction perpendicular to the strike of the hill in the period range from 0.04 to 0.8 sec (1.2 to 25 Hz). There is practically no amplification from the bottom to the top of the hill for the component parallel to the strike of the hill. In contrast to accelerations recorded during the Hector Mine earthquake (high frequency part of seismic signal), displacements (relatively low frequency part of seismic signal) demonstrate almost no site amplification from the bottom of the hole to the surface at periods greater than 1.5 sec, in either direction. The directional effect at Tarzana hill seems to be azimuth dependent. Relatively higher amplification at the perpendicular component is produced for the earthquake sources located north of the station. We were not able to see any differences in hill response before and after development (a relatively small part of the hill was developed). The source of the site amplification that produces large motions at Tarzana is still under investigation with "the usual suspects" like topography and shear wave velocity profile not providing the explanation. New data recorded at Tarzana in recent years clearly show that the Tarzana effect is a very localized high-frequency effect observed only at the top of the hill. Drilling at Tarzana was co-funded by CSMIP and by the National Science Foundation through the Resolution of Site Response Issues from the Northridge Earthquake Project (ROSRINE).

Epistemic Uncertainty and Limitations of the Kappa0 model for Near-surface Attenuation at Hard Rock Sites

NASA Astrophysics Data System (ADS)

Edwards, Benjamin

2016-04-01

The determination of near-surface attenuation for hard rock sites is an important issue in a wide range of seismological applications, particularly seismic hazard analysis. In this article we choose six hard to very-hard rock sites (Vs30 1030 to 3000 m/s) and apply a range of analysis methods to measure the observed attenuation at distance based on a simple exponential decay model with whole-path attenuation operator κ. The κ values are subsequently decoupled from path attenuation (Q) so as to obtain estimates of near-surface attenuation (κ0). Five methods are employed to measure κ which can be split into two groups: broadband methods and high-frequency methods. Each of the applied methods has advantages and disadvantages, which are explored and discussed through the comparison of results from common datasets. In our first step we examine the variability of the individual measured κ values. Some variation between methods is expected due to simplifications of source, path, and site effects. However, we find that significant differences arise between attenuation measured on individual recordings, depending on the method employed or the modelling decisions made during a particular approach. Some of the differences can be explained through site amplification effects: although usually weak at rock sites, amplification may still lead to bias of the measured κ due to the chosen fitting frequency bandwidth, which often varies between methods. At some sites the observed high-frequency spectral shape was clearly different to the typical κ attenuation model, with curved or bi-linear rather than linear decay at high frequencies. In addition to amplification effects this could be related to frequency-dependent attenuation effects (e.g., Q(f)): since the κ model is implicitly frequency independent, κ will in this case be dependent on the selected analysis bandwidth. In our second step, using the whole-path κ datasets from the five approaches, we investigate the robustness of the near-surface attenuation parameter κ0 and the influence of constraints, such as assuming a value for the regional crustal attenuation (Q). We do this by using a variety of fitting methods: least-squares, absolute amplitude, and regressions with and without fixing Q to an a priori value. We find that the value to which we fix Q strongly influences the near-surface attenuation term κ0. Differences in Q derived from the data at the six sites under investigation could not be reconciled with the average values found previously over the wider Swiss region. This led to starkly different κ0 values, depending on whether we allowed for a data-driven Q, or whether we forced Q to be consistent with existing simulation models or GMPEs valid for the wider region. Considering all the possible approaches we found that the contribution to epistemic uncertainty for κ0 determination at the six hard-rock sites in Switzerland could be represented by a normal distribution with standard deviation σκ0=0.0083±0.0014 s.

Selective amyloid β oligomer assay based on abasic site-containing molecular beacon and enzyme-free amplification.

PubMed

Zhu, Linling; Zhang, Junying; Wang, Fengyang; Wang, Ya; Lu, Linlin; Feng, Chongchong; Xu, Zhiai; Zhang, Wen

2016-04-15

Amyloid-beta (Aβ) oligomers are highly toxic species in the process of Aβ aggregation and are regarded as potent therapeutic targets and diagnostic markers for Alzheimer's disease (AD). Herein, a label-free molecular beacon (MB) system integrated with enzyme-free amplification strategy was developed for simple and highly selective assay of Aβ oligomers. The MB system was constructed with abasic site (AP site)-containing stem-loop DNA and a fluorescent ligand 2-amino-5,6,7-trimethyl-1,8-naphyridine (ATMND), of which the fluorescence was quenched upon binding to the AP site in DNA stem. Enzyme-free amplification was realized by target-triggered continuous opening of two delicately designed MBs (MB1 and MB2). Target DNA hybridization with MB1 and then MB2 resulted in the release of two ATMND molecules in one binding event. Subsequent target recycling could greatly amplify the detection sensitivity due to the greatly enhanced turn-on emission of ATMND fluorescence. Combining with Aβ oligomers aptamers, the strategy was applied to analyze Aβ oligomers and the results showed that it could quantify Aβ oligomers with high selectivity and monitor the Aβ aggregation process. This novel method may be conducive to improve the diagnosis and pathogenic study of Alzheimer's disease. Copyright © 2015 Elsevier B.V. All rights reserved.

Probabilistic and Scenario Seismic and Liquefaction Hazard Analysis of the Mississippi Embayment Incorporating Nonlinear Site Effects

NASA Astrophysics Data System (ADS)

Cramer, C. H.; Dhar, M. S.

2017-12-01

The influence of deep sediment deposits of the Mississippi Embayment (ME) on the propagation of seismic waves is poorly understood and remains a major source of uncertainty for site response analysis. Many researchers have studied the effects of these deposits on seismic hazard of the area using available information at the time. In this study, we have used updated and newly available resources for seismic and liquefaction hazard analyses of the ME. We have developed an improved 3D geological model. Additionally, we used surface geological maps from Cupples and Van Arsdale (2013) to prepare liquefaction hazard maps. Both equivalent linear and nonlinear site response codes were used to develop site amplification distributions for use in generating hazard maps. The site amplification distributions are created using the Monte Carlo approach of Cramer et al. (2004, 2006) on a 0.1-degree grid. The 2014 National Seismic Hazard model and attenuation relations (Petersen et al., 2014) are used to prepare seismic hazard maps. Then liquefaction hazard maps are generated using liquefaction probability curves from Holzer (2011) and Cramer et al. (2015). Equivalent linear response (w/ increased precision, restricted nonlinear behavior with depth) shows similar hazard for the ME compared to nonlinear analysis (w/o pore pressure) results. At short periods nonlinear deamplification dominates the hazard, but at long periods resonance amplification dominates. The liquefaction hazard tends to be high in Holocene and late Pleistocene lowland sediments, even with lowered ground water levels, and low in Pleistocene loess of the uplands. Considering pore pressure effects in nonlinear site response analysis at a test site on the lowlands shows amplification of ground motion at short periods. PGA estimates from ME liquefaction and MMI observations are in the 0.25 to 0.4 g range. Our estimated M7.5 PGA hazard within 10 km of the fault can exceed this. Ground motion observations from liquefaction sites in New Zealand and Japan support PGAs below 0.4 g, except at sites within 20 km exhibiting pore-pressure induced acceleration spikes due to cyclic mobility where PGA ranges from 0.5 to 1.5 g. This study is being extended to more detailed seismic and liquefaction hazard studies in five western Tennessee counties under a five year grant from HUD.

High power industrial picosecond laser from IR to UV

NASA Astrophysics Data System (ADS)

Saby, Julien; Sangla, Damien; Pierrot, Simonette; Deslandes, Pierre; Salin, François

2013-02-01

Many industrial applications such as glass cutting, ceramic micro-machining or photovoltaic processes require high average and high peak power Picosecond pulses. The main limitation for the expansion of the picosecond market is the cost of high power picosecond laser sources, which is due to the complexity of the architecture used for picosecond pulse amplification, and the difficulty to keep an excellent beam quality at high average power. Amplification with fibers is a good technology to achieve high power in picosecond regime but, because of its tight confinement over long distances, light undergoes dramatic non linearities while propagating in fibers. One way to avoid strong non linearities is to increase fiber's mode area. Nineteen missing holes fibers offering core diameter larger than 80μm have been used over the past few years [1-3] but it has been shown that mode instabilities occur at approximately 100W average output power in these fibers [4]. Recently a new fiber design has been introduced, in which HOMs are delocalized from the core to the clad, preventing from HOMs amplification [5]. In these so-called Large Pitch Fibers, threshold for mode instabilities is increased to 294W offering robust single-mode operation below this power level [6]. We have demonstrated a high power-high efficiency industrial picosecond source using single-mode Large Pitch rod-type fibers doped with Ytterbium. Large Pitch Rod type fibers can offer a unique combination of single-mode output with a very large mode area from 40 μm up to 100μm and very high gain. This enables to directly amplify a low power-low energy Mode Locked Fiber laser with a simple amplification architecture, achieving very high power together with singlemode output independent of power level or repetition rate.

Instant, Visual, and Instrument-Free Method for On-Site Screening of GTS 40-3-2 Soybean Based on Body-Heat Triggered Recombinase Polymerase Amplification.

PubMed

Wang, Rui; Zhang, Fang; Wang, Liu; Qian, Wenjuan; Qian, Cheng; Wu, Jian; Ying, Yibin

2017-04-18

On-site monitoring the plantation of genetically modified (GM) crops is of critical importance in agriculture industry throughout the world. In this paper, a simple, visual and instrument-free method for instant on-site detection of GTS 40-3-2 soybean has been developed. It is based on body-heat recombinase polymerase amplification (RPA) and followed with naked-eye detection via fluorescent DNA dye. Combining with extremely simplified sample preparation, the whole detection process can be accomplished within 10 min and the fluorescent results can be photographed by an accompanied smart phone. Results demonstrated a 100% detection rate for screening of practical GTS 40-3-2 soybean samples by 20 volunteers under different ambient temperatures. This method is not only suitable for on-site detection of GM crops but also demonstrates great potential to be applied in other fields.

Local site effect of soil slope based on microtremor measurement in Samigaluh, Kulon Progo Yogyakarta

NASA Astrophysics Data System (ADS)

Prabowo, U. N.; Amalia, A. F.; Wiranata, F. E.

2018-03-01

This paper investigated soil slope-local site effect of earthquake inducing landslide by using microtremor Horizontal to Vertical Spectral Ratio (HVSR) method. Microtremor measurements of 15 sites which were recorded for 45 minutes at each site were carried out in Ngargosari village, Samigaluh, Kulon Progo-Indonesia. Microtremor analysis using HVSR method was performed using Geopsy software. HVSR method resulted in predominant frequency values that ranges between 2,77 to 13,82 Hz and amplification factors varied from 0,46 to 5,70. The predominant frequency is associated with the depth of bedrock and the amplification factor reflects the geological condition of soil (sedimentary layer). The soil vulnerability index (Kg) varied from 0,08 to 5,77 and the higher value (Kg>3,4) in the south of the research area was identified as the weak zone of earthquake inducing landslide.

A novel restriction endonuclease GlaI for rapid and highly sensitive detection of DNA methylation coupled with isothermal exponential amplification reaction.

PubMed

Sun, Yueying; Sun, Yuanyuan; Tian, Weimin; Liu, Chenghui; Gao, Kejian; Li, Zhengping

2018-02-07

Sensitive and accurate detection of site-specific DNA methylation is of critical significance for early diagnosis of human diseases, especially cancers. Herein, for the first time we employ a novel methylation-dependent restriction endonuclease GlaI to detect site-specific DNA methylation in a highly specific and sensitive way by coupling with isothermal exponential amplification reaction (EXPAR). GlaI can only cut the methylated target site with excellent selectivity but leave the unmethylated DNA intact. Then the newly exposed end fragments of methylated DNA can trigger EXPAR for highly efficient signal amplification while the intact unmethylated DNA will not initiate EXPAR at all. As such, only the methylated DNA is quantitatively and faithfully reflected by the real-time fluorescence signal of the GlaI-EXPAR system, and the potential false positive interference from unmethylated DNA can be effectively eliminated. Therefore, by integrating the unique features of GlaI for highly specific methylation discrimination and EXPAR for rapid and powerful signal amplification, the elegant GlaI-EXPAR assay allows the direct quantification of methylated DNA with ultrahigh sensitivity and accuracy. The detection limit of methylated DNA target has been pushed down to the aM level and the whole detection process of GlaI-EXPAR can be accomplished within a short time of 2 h. More importantly, ultrahigh specificity is achieved and as low as 0.01% methylated DNA can be clearly identified in the presence of a large excess of unmethylated DNA. This GlaI-EXPAR is also demonstrated to be capable of determining site-specific DNA methylations in real genomic DNA samples. Sharing the distinct advantages of ultrahigh sensitivity, outstanding specificity and facile operation, this new GlaI-EXPAR strategy may provide a robust and reliable platform for the detection of site-specific DNA methylations with low abundances.

Amplification and spectral shifts of vocalizations inside burrows of the frog Eupsophus calcaratus (Leptodactylidae)

NASA Astrophysics Data System (ADS)

Penna, Mario

2004-08-01

A variety of animals that communicate by sound emit signals from sites favoring their propagation, thereby increasing the range over which these sounds convey information. A different significance of calling sites has been reported for burrowing frogs Eupsophus emiliopugini from southern Chile: the cavities from which these frogs vocalize amplify conspecific vocalizations generated externally, thus providing a means to enhance the reception of neighbor's vocalizations in chorusing aggregations. In the current study the amplification of vocalizations of a related species, E. calcaratus, is investigated, to explore the extent of sound enhancement reported previously. Advertisement calls broadcast through a loudspeaker placed in the vicinity of a burrow, monitored with small microphones, are amplified by up to 18 dB inside cavities relative to outside. The fundamental resonant frequency of burrows, measured with broadcast noise and pure tones, ranges from 842 to 1836 Hz and is significantly correlated with the burrow's length. Burrows change the spectral envelope of incoming calls by increasing the amplitude of lower relative to higher harmonics. The call amplification effect inside burrows of E. calcaratus parallels the effect reported previously for E. emiliopugini, and indicates that the acoustic properties of calling sites may affect signal reception by burrowing animals.

Amplification and spectral shifts of vocalizations inside burrows of the frog Eupsophus calcaratus (Leptodactylidae).

PubMed

Penna, Mario

2004-08-01

A variety of animals that communicate by sound emit signals from sites favoring their propagation, thereby increasing the range over which these sounds convey information. A different significance of calling sites has been reported for burrowing frogs Eupsophus emiliopugini from southern Chile: the cavities from which these frogs vocalize amplify conspecific vocalizations generated externally, thus providing a means to enhance the reception of neighbor's vocalizations in chorusing aggregations. In the current study the amplification of vocalizations of a related species, E. calcaratus, is investigated, to explore the extent of sound enhancement reported previously. Advertisement calls broadcast through a loudspeaker placed in the vicinity of a burrow, monitored with small microphones, are amplified by up to 18 dB inside cavities relative to outside. The fundamental resonant frequency of burrows, measured with broadcast noise and pure tones, ranges from 842 to 1836 Hz and is significantly correlated with the burrow's length. Burrows change the spectral envelope of incoming calls by increasing the amplitude of lower relative to higher harmonics. The call amplification effect inside burrows of E. calcaratus parallels the effect reported previously for E. emiliopugini, and indicates that the acoustic properties of calling sites may affect signal reception by burrowing animals.

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

PubMed Central

Zhao, Hongjuan; Hastie, Trevor; Whitfield, Michael L; Børresen-Dale, Anne-Lise; Jeffrey, Stefanie S

2002-01-01

Background T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. Results Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3–3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. Conclusion T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays. PMID:12445333

Origins of DNA Replication and Amplification in the Breast Cancer Genome

DTIC Science & Technology

2011-09-01

AD_________________ Award Number: W81XWH-10-1-0463 TITLE: Origins of DNA Replication and...hypothesis we need to map origins of DNA replication in the genome and ask which of these coincide with sites of DNA amplification and with ER...Spring Harbor DNA Replication meetings this summer/earlyfall. Figures from the posters and also the abstracts are attached. The samples have been

Seismic loading due to mining: Wave amplification and vibration of structures

NASA Astrophysics Data System (ADS)

Lokmane, N.; Semblat, J.-F.; Bonnet, G.; Driad, L.; Duval, A.-M.

2003-04-01

A vibration induced by the ground motion, whatever its source is, can in certain cases damage surface structures. The scientific works allowing the analysis of this phenomenon are numerous and well established. However, they generally concern dynamic motion from real earthquakes. The goal of this work is to analyse the impact of shaking induced by mining on the structures located on the surface. The methods allowing to assess the consequences of earthquakes of strong amplitude are well established, when the methodology to estimate the consequences of moderate but frequent dynamic loadings is not well defined. The mining such as the "Houillères de Bassin du Centre et du Midi" (HBCM) involves vibrations which are regularly felt on the surface. An extracting work of coal generates shaking similar to those caused by earthquakes (standard waves and laws of propagation) but of rather low magnitude. On the other hand, their recurrent feature makes the vibrations more harmful. A three-dimensional modeling of standard structure of the site was carried out. The first results show that the fundamental frequencies of this structure are compatible with the amplification measurements carried out on site. The motion amplification in the surface soil layers is then analyzed. The modeling works are performed on the surface soil layers of Gardanne (Provence), where measurements of microtremors were performed. The analysis of H/V spectral ratio (horizontal on vertical component) indeed makes it possible to characterize the fundamental frequencies of the surface soil layers. This experiment also allows to characterize local evolution of amplification induced by the topmost soil layers. The numerical methods we consider to model seismic wave propagation and amplification in the site, is the Boundary Element Methode (BEM) The main advantage of the boundary element method is to get rid of artificial truncations of the mesh (as in Finite Element Method) in the case of infinite medium. For dynamic problems, these truncations lead to spurious wave reflections giving a numerical error in the solution. The experimental and numerical (BEM) results on surface motion amplification are then compared in terms of both amplitude and frequency range.

Amplification in the rehabilitation of unilateral deafness: speech in noise and directional hearing effects with bone-anchored hearing and contralateral routing of signal amplification.

PubMed

Lin, Li-Mei; Bowditch, Stephen; Anderson, Michael J; May, Bradford; Cox, Kenneth M; Niparko, John K

2006-02-01

Vibromechanical stimulation with a semi-implantable bone conductor (Entific BAHA device) overcomes some of the head-shadow effects in unilateral deafness. What specific rehabilitative benefits are observed when the functional ear exhibits normal hearing versus moderate sensorineural hearing loss (SNHL)? The authors conducted a prospective trial of subjects with unilateral deafness in a tertiary care center. This study comprised adults with unilateral deafness (pure-tone average [PTA] > 90 dB; Sp.D. < 20%) and either normal monaural hearing (n = 18) or moderate SNHL (PTA = 25-50 dB: Sp.D. > 75%) in the contralateral functional ear (n = 5). Subjects were fit with contralateral routing of signal (CROS) devices for 1 month and tested before (mastoid) implantation, fitting, and testing with a bone-anchored hearing aid (BAHA). Outcome measures were: 1) subjective benefit; 2) source localization tests (Source Azimuth Identification in Noise Test [SAINT]); 3) speech discrimination in quiet and in noise assessed with Hearing In Noise Test (HINT) protocols. There was consistent satisfaction with BAHA amplification and poor acceptance of CROS amplification. General directional hearing decreased with CROS use and was unchanged by BAHA and directional microphone aids. Relative to baseline and CROS, BAHA produced significantly better speech recognition in noise. Twenty-two of 23 subjects followed up in this study continue to use their BAHA device over an average follow-up period of 30.24 months (range, 51-12 months). BAHA amplification on the side of a deaf ear yields greater benefit in subjects with monaural hearing than does CROS amplification. Advantages likely related to averting the interference of speech signals delivered to the better ear, as occurs with conventional CROS amplification, while alleviating the negative head-shadow effects of unilateral deafness. The advantages of head-shadow reduction in enhancing speech recognition with noise in the hearing ear outweigh disadvantages inherent in head-shadow reduction that can occur by introducing noise from the deaf side. The level of hearing impairment correlates with incremental benefit provided by the BAHA. Patients with a moderate SNHL in the functioning ear perceived greater increments in benefit, especially in background noise, and demonstrated greater improvements in speech understanding with BAHA amplification.

Vs30 and spectral response from collocated shallow, active- and passive-source Vs data at 27 sites in Puerto Rico

USGS Publications Warehouse

Odum, Jack K.; Stephenson, William J.; Williams, Robert A.; von Hillebrandt-Andrade, Christa

2013-01-01

Shear‐wave velocity (VS) and time‐averaged shear‐wave velocity to 30 m depth (VS30) are the key parameters used in seismic site response modeling and earthquake engineering design. Where VS data are limited, available data are often used to develop and refine map‐based proxy models of VS30 for predicting ground‐motion intensities. In this paper, we present shallow VS data from 27 sites in Puerto Rico. These data were acquired using a multimethod acquisition approach consisting of noninvasive, collocated, active‐source body‐wave (refraction/reflection), active‐source surface wave at nine sites, and passive‐source surface‐wave refraction microtremor (ReMi) techniques. VS‐versus‐depth models are constructed and used to calculate spectral response plots for each site. Factors affecting method reliability are analyzed with respect to site‐specific differences in bedrock VS and spectral response. At many but not all sites, body‐ and surface‐wave methods generally determine similar depths to bedrock, and it is the difference in bedrock VS that influences site amplification. The predicted resonant frequencies for the majority of the sites are observed to be within a relatively narrow bandwidth of 1–3.5 Hz. For a first‐order comparison of peak frequency position, predictive spectral response plots from eight sites are plotted along with seismograph instrument spectra derived from the time series of the 16 May 2010 Puerto Rico earthquake. We show how a multimethod acquisition approach using collocated arrays compliments and corroborates VS results, thus adding confidence that reliable site characterization information has been obtained.

Site correction of a high-frequency strong-ground-motion simulation based on an empirical transfer function

NASA Astrophysics Data System (ADS)

Huang, Jyun-Yan; Wen, Kuo-Liang; Lin, Che-Min; Kuo, Chun-Hsiang; Chen, Chun-Te; Chang, Shuen-Chiang

2017-05-01

In this study, an empirical transfer function (ETF), which is the spectrum difference in Fourier amplitude spectra between observed strong ground motion and synthetic motion obtained by a stochastic point-source simulation technique, is constructed for the Taipei Basin, Taiwan. The basis stochastic point-source simulations can be treated as reference rock site conditions in order to consider site effects. The parameters of the stochastic point-source approach related to source and path effects are collected from previous well-verified studies. A database of shallow, small-magnitude earthquakes is selected to construct the ETFs so that the point-source approach for synthetic motions might be more widely applicable. The high-frequency synthetic motion obtained from the ETF procedure is site-corrected in the strong site-response area of the Taipei Basin. The site-response characteristics of the ETF show similar responses as in previous studies, which indicates that the base synthetic model is suitable for the reference rock conditions in the Taipei Basin. The dominant frequency contour corresponds to the shape of the bottom of the geological basement (the top of the Tertiary period), which is the Sungshan formation. Two clear high-amplification areas are identified in the deepest region of the Sungshan formation, as shown by an amplification contour of 0.5 Hz. Meanwhile, a high-amplification area was shifted to the basin's edge, as shown by an amplification contour of 2.0 Hz. Three target earthquakes with different kinds of source conditions, including shallow small-magnitude events, shallow and relatively large-magnitude events, and deep small-magnitude events relative to the ETF database, are tested to verify site correction. The results indicate that ETF-based site correction is effective for shallow earthquakes, even those with higher magnitudes, but is not suitable for deep earthquakes. Finally, one of the most significant shallow large-magnitude earthquakes (the 1999 Chi-Chi earthquake in Taiwan) is verified in this study. A finite fault stochastic simulation technique is applied, owing to the complexity of the fault rupture process for the Chi-Chi earthquake, and the ETF-based site-correction function is multiplied to obtain a precise simulation of high-frequency (up to 10 Hz) strong motions. The high-frequency prediction has good agreement in both time and frequency domain in this study, and the prediction level is the same as that predicted by the site-corrected ground motion prediction equation.

Improving 1D Site Specific Velocity Profiles for the Kik-Net Network

NASA Astrophysics Data System (ADS)

Holt, James; Edwards, Benjamin; Pilz, Marco; Fäh, Donat; Rietbrock, Andreas

2017-04-01

Ground motion predication equations (GMPEs) form the cornerstone of modern seismic hazard assessments. When produced to a high standard they provide reliable estimates of ground motion/spectral acceleration for a given site and earthquake scenario. This information is crucial for engineers to optimise design and for regulators who enforce legal minimum safe design capacities. Classically, GMPEs were built upon the assumption that variability around the median model could be treated as aleatory. As understanding improved, it was noted that the propagation could be segregated into the response of the average path from the source and the response of the site. This is because the heterogeneity of the near-surface lithology is significantly different from that of the bulk path. It was then suggested that the semi-ergodic approach could be taken if the site response could be determined, moving uncertainty away from aleatory to epistemic. The determination of reliable site-specific response models is therefore becoming increasingly critical for ground motion models used in engineering practice. Today it is common practice to include proxies for site response within the scope of a GMPE, such as Vs30 or site classification, in an effort to reduce the overall uncertainty of the predication at a given site. However, these proxies are not always reliable enough to give confident ground motion estimates, due to the complexity of the near-surface. Other approaches of quantifying the response of the site include detailed numerical simulations (1/2/3D - linear, EQL, non-linear etc.). However, in order to be reliable, they require highly detailed and accurate velocity and, for non-linear analyses, material property models. It is possible to obtain this information through invasive methods, but is expensive, and not feasible for most projects. Here we propose an alternative method to derive reliable velocity profiles (and their uncertainty), calibrated using almost 20 years of recorded data from the Kik-Net network. First, using a reliable subset of sites, the empirical surface to borehole (S/B) ratio is calculated in the frequency domain using all events recorded at that site. In a subsequent step, we use numerical simulation to produce 1D SH transfer function curves using a suite of stochastic velocity models. Comparing the resulting amplification with the empirical S/B ratio we find optimal 1D velocity models and their uncertainty. The method will be tested to determine the level of initial information required to obtain a reliable Vs profile (e.g., starting Vs model, only Vs30, site-class, H/V ratio etc.) and then applied and tested against data from other regions using site-to-reference or empirical spectral model amplification.

Effect of soil conditions on predicted ground motion: Case study from Western Anatolia, Turkey

NASA Astrophysics Data System (ADS)

Gok, Elcin; Chávez-García, Francisco J.; Polat, Orhan

2014-04-01

We present a site effect study for the city of Izmir, Western Anatolia, Turkey. Local amplification was evaluated using state-of-practice tools. Ten earthquakes recorded at 16 sites were analysed using spectral ratios relative to a reference site, horizontal-to-vertical spectral ratios, and an inversion scheme of the Fourier amplitude spectra of the recorded S-waves. Seismic noise records were also used to estimate site effects. The different estimates are in good agreement among them, although a basic uncertainty of a factor of 2 seems difficult to decrease. We used our site effect estimates to predict ground motion in Izmir for a possible M6.5 earthquake close to the city using stochastic modelling. Site effects have a large impact on PSV (pseudospectral velocity), where local amplification increases amplitudes by almost a factor of 9 at 1 Hz relative to the firm ground condition. Our results allow identifying the neighbourhoods of Izmir where hazard mitigation measurements are a priority task and will also be useful for planning urban development.

Factors affecting genotyping success in giant panda fecal samples.

PubMed

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong; Zhang, He-Min

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH -20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at -20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates ( P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.

Factors affecting genotyping success in giant panda fecal samples

PubMed Central

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies. PMID:28560107

Outbreak or illusion: consequences of 'improved' diagnostics for gonorrhoea.

PubMed

Bennett, Amy; Jeffery, Katie; O'Neill, Eunan; Sherrard, Jackie

2017-06-01

The sexual health service in Oxford introduced gonorrhoea nucleic amplification acid testing using the BD Viper XTR™ System. For practical reasons, a confirmatory nucleic amplification acid testing using a different platform was not used initially. Following the introduction of nucleic amplification acid testing, the rates of gonorrhoea increased threefold. Concerns were raised that this increase represented an outbreak. A retrospective review of cases over six months suggested that there may have been a number of false-positive results. A prospective study was then undertaken over six months, where all gonorrhoea positive samples were sent for confirmatory testing. This evaluation of all gonorrhoea cases in an English county found that the overall presumptive false-positive rates for gonorrhoea nucleic amplification acid testing using BD Viper XTR™ in our population are significant at 27% of female samples, 13.2% of heterosexual male samples, 3.5% of anogenital multiple site men who have sex with men samples and 62.8% of pharyngeal only men who have sex with men samples. The data demonstrate the need for confirmatory testing using a second nucleic acid target, as per BASHH/Public Health England guidelines, especially in low-prevalence settings and extragenital sites, due to cross-reactivity with commensal Neisseria species and low positive predictive values.

Clinical significance of Anoctamin-1 gene at 11q13 in the development and progression of head and neck squamous cell carcinomas

PubMed Central

Rodrigo, Juan P.; Menéndez, Sofía Tirados; Hermida-Prado, Francisco; Álvarez-Teijeiro, Saúl; Villaronga, M. Ángeles; Alonso-Durán, Laura; Vallina, Aitana; Martínez-Camblor, Pablo; Astudillo, Aurora; Suárez, Carlos; María García-Pedrero, Juana

2015-01-01

This study investigates the clinical significance of Anoctamin-1 gene mapping at 11q13 amplicon in both the development and progression of head and neck squamous cell carcinomas (HNSCC). ANO1 protein expression was evaluated by immunohistochemistry in a cohort of 372 surgically treated HNSCC patients and also in 35 laryngeal precancerous lesions. ANO1 gene amplification was determined by real-time PCR in all the laryngeal premalignancies and 60 of the HNSCCs, and molecular data correlated with clinical outcome. ANO1 gene amplification was frequently detected in both premalignant lesions (63%) and HNSCC tumours (58%), whereas concomitant ANO1 expression occurred at a much lower frequency (20 and 22%). Interestingly, laryngeal dysplasias harbouring ANO1 gene amplification showed a higher risk of malignant transformation (HR = 3.62; 95% CI 0.79–16.57; P = 0.097; Cox regression). ANO1 expression and gene amplification showed no significant associations with clinicopathological parameters in HNSCC. However, remarkably ANO1 expression differentially influenced patient survival depending on the tumour site. Collectively, this study provides original evidence demonstrating the distinctive impact of ANO1 expression on HNSCC prognosis depending on the tumour site. PMID:26498851

Improved Performance of Loop-Mediated Isothermal Amplification Assays via Swarm Priming.

PubMed

Martineau, Rhett L; Murray, Sarah A; Ci, Shufang; Gao, Weimin; Chao, Shih-Hui; Meldrum, Deirdre R

2017-01-03

This work describes an enhancement to the loop-mediated isothermal amplification (LAMP) reaction which results in improved performance. Enhancement is achieved by adding a new set of primers to conventional LAMP reactions. These primers are termed "swarm primers" based on their relatively high concentration and their ability to create new amplicons despite the theoretical lack of single-stranded annealing sites. The primers target a region upstream of the FIP/BIP primer recognition sequences on opposite strands, substantially overlapping F1/B1 sites. Thus, despite the addition of a new primer set to an already complex assay, no significant increase in assay complexity is incurred. Swarm priming is presented for three DNA templates: Lambda phage, Synechocystis sp. PCC 6803 rbcL gene, and human HFE. The results of adding swarm primers to conventional LAMP reactions include increased amplification speed, increased indicator contrast, and increased reaction products. For at least one template, minor improvements in assay repeatability are also shown. In addition, swarm priming is shown to be effective at increasing the reaction speed for RNA amplification via RT-LAMP. Collectively, these results suggest that the addition of swarm primers will likely benefit most if not all existing LAMP assays based on state-of-the-art, six-primer reactions.

A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples.

PubMed

Sun, Yi; Quyen, Than Linh; Hung, Tran Quang; Chin, Wai Hoe; Wolff, Anders; Bang, Dang Duong

2015-04-21

Foodborne disease is a major public health threat worldwide. Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture or molecular-based methods are time consuming and usually take a few hours to days to complete. In response to the demand for rapid on line or on site detection of pathogens, in this study, we describe for the first time an eight-chamber lab-on-a-chip (LOC) system with integrated magnetic bead-based sample preparation and loop-mediated isothermal amplification (LAMP) for rapid and quantitative detection of Salmonella spp. in food samples. The whole diagnostic procedures including DNA isolation, isothermal amplification, and real-time detection were accomplished in a single chamber. Up to eight samples could be handled simultaneously and the system was capable to detect Salmonella at concentration of 50 cells per test within 40 min. The simple design, together with high level of integration, isothermal amplification, and quantitative analysis of multiple samples in short time, will greatly enhance the practical applicability of the LOC system for rapid on-site screening of Salmonella for applications in food safety control, environmental surveillance, and clinical diagnostics.

The effect of working memory capacity limitations on the intuitive assessment of correlation: amplification, attenuation, or both?

PubMed

Cahan, Sorel; Mor, Yaniv

2007-03-01

This article challenges Yaakov Kareev's (1995a, 2000) argument regarding the positive bias of intuitive correlation estimates due to working memory capacity limitations and its adaptive value. The authors show that, under narrow window theory's primacy effect assumption, there is a considerable between-individual variability of the effects of capacity limitations on the intuitive assessment of correlation, in terms of both sign and magnitude: Limited capacity acts as an amplifier for some individuals and as a silencer for others. Furthermore, the average amount of attenuation exceeds the average amount of amplification, and the more so, the smaller the capacity. Implications regarding the applicability and contribution of the bias notion in this context and the evaluation of the adaptive value of capacity limitations are discussed.

Non-Invasive Seismic Methods for Earthquake Site Classification Applied to Ontario Bridge Sites

NASA Astrophysics Data System (ADS)

Bilson Darko, A.; Molnar, S.; Sadrekarimi, A.

2017-12-01

How a site responds to earthquake shaking and its corresponding damage is largely influenced by the underlying ground conditions through which it propagates. The effects of site conditions on propagating seismic waves can be predicted from measurements of the shear wave velocity (Vs) of the soil layer(s) and the impedance ratio between bedrock and soil. Currently the seismic design of new buildings and bridges (2015 Canadian building and bridge codes) requires determination of the time-averaged shear-wave velocity of the upper 30 metres (Vs30) of a given site. In this study, two in situ Vs profiling methods; Multichannel Analysis of Surface Waves (MASW) and Ambient Vibration Array (AVA) methods are used to determine Vs30 at chosen bridge sites in Ontario, Canada. Both active-source (MASW) and passive-source (AVA) surface wave methods are used at each bridge site to obtain Rayleigh-wave phase velocities over a wide frequency bandwidth. The dispersion curve is jointly inverted with each site's amplification function (microtremor horizontal-to-vertical spectral ratio) to obtain shear-wave velocity profile(s). We apply our non-invasive testing at three major infrastructure projects, e.g., five bridge sites along the Rt. Hon. Herb Gray Parkway in Windsor, Ontario. Our non-invasive testing is co-located with previous invasive testing, including Standard Penetration Test (SPT), Cone Penetration Test and downhole Vs data. Correlations between SPT blowcount and Vs are developed for the different soil types sampled at our Ontario bridge sites. A robust earthquake site classification procedure (reliable Vs30 estimates) for bridge sites across Ontario is evaluated from available combinations of invasive and non-invasive site characterization methods.

The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification.

PubMed

Jevtuševskaja, Jekaterina; Krõlov, Katrin; Tulp, Indrek; Langel, Ülo

2017-04-01

The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification Results: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.

Experimental approach for estimating seismic amplification effects at the top of a ridge and their implication on ground motion predictions: the case of Narni (Central Italy).

NASA Astrophysics Data System (ADS)

Lovati, Sara; Bakavoli, Mohammad; Massa, Marco; Ferretti, Gabriele; Pacor, Francesca; Paolucci, Roberto

2010-05-01

From March to September 2009 a dense velocimetric network was installed in correspondence of Narni, a little village in central Italy, built on the top of a massive limestone ridge. The network was planned with the aim to investigate possible local site effects due to the morphology of the ridge, characterized by slopes ranging from 22° to 35° and a maximum difference of quota between top and bottom of 230 m. Three stations were installed at the base of the hill and other 7 monitored the crest. A remarkable dataset was obtained, composed by about 700 earthquakes, the great amount of which occurred after the 06th April 2009, Mw 6.3, L'Aquila earthquake. Site amplifications related to the ridge morphological features were investigated through empirical techniques with and without reference site, computing Spectral Standard Ratio, SSR and Horizontal to Vertical spectral ratio, HVSR. Directional spectral analyses were also performed . The agreement between the results coming from HVSR and SSR techniques allows us to assess with reliability a clear amplification effect for frequencies ranging between 3 and 5 Hz for all stations installed on the crest: in particular, SSR results show an amplification level with respect to the reference station up to 4.5. The highest amplification level (almost double) were observed when the direction perpendicular to the main elongation of the ridge is taken into account. Finally, considering the L'Aquila events with Mw > 4.5 and merging the information coming from the reference and non-reference site techniques, it was possible to recognize further amplification effects, at frequency lower than 1 Hz, probably related not to the morphology of the area but to source and/or polarization effects. Bidimensional numerical simulations were then computed in order to compare the results coming from the experiment with those obtained through numerical modeling. A hybrid finite-boundary element method based on code named HYBRID has been used for modeling. The model has been excited by SV and P Ricker wavelet in order to extract transform functions. The medium assumed to have a linear elastic constitutive behavior. All calculations were performed in time domain using direct boundary element method. The amplification patterns both in time and frequency domain were derived and similarities and discrepancies between the results were discussed. At last, considering only local events (epicentral distance R <= 30 km), empirical ground motion predictive equations, calibrated for maximum horizontal peak ground acceleration, PGA, velocity, PGV, and acceleration response spectra (SA, 5% damping) up to 1s, were carried out with the only aim to estimate topographical corrective coefficients. The results show significant corrective term values (between 0.35 and 0.48 in logarithmic scale) for the spectral ordinates between 0.2 s and 0.3 s. These results, in agreement to those obtained from the spectral analyses, suggest that the introduction of a topographic site class in the calculation of predictive models might probably reduce the inter-station variability for stations installed in correspondence of topographic irregularities, often included in reference-rock classes.

Optimization and validation of a fast amplification protocol for AmpFlSTR® Profiler Plus® for rapid forensic human identification.

PubMed

Laurin, Nancy; Frégeau, Chantal

2012-01-01

The goal of this work was to optimize and validate a fast amplification protocol for the multiplex amplification of the STR loci included in AmpFlSTR(®) Profiler Plus(®) to expedite human DNA identification. By modifying the cycling conditions and by combining the use of a DNA polymerase optimized for high speed PCR (SpeedSTAR™ HS) and a more efficient thermal cycler instrument (Bio-RAD C1000™), we were able to reduce the amplification process from 4h to 26 min. No modification to the commercial AmpFlSTR(®) Profiler Plus(®) primer mix was required. When compared to the current Royal Canadian Mounted Police (RCMP) amplification protocol, no differences with regards to specificity, sensitivity, heterozygote peak height ratios and overall profile balance were noted. Moreover, complete concordance was obtained with profiles previously generated with the standard amplification protocol and minor alleles in mixture samples were reliably typed. An increase in n-4 stutter ratios (2.2% on average for all loci) was observed for profiles amplified with the fast protocol compared to the current procedure. Our results document the robustness of this rapid amplification protocol for STR profiling using the AmpFlSTR(®) Profiler Plus(®) primer set and demonstrate that comparable data can be obtained in substantially less time. This new approach could provide an alternative option to current multiplex STR typing amplification protocols in order to increase throughput or expedite time-sensitive cases. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Urban seismology - Northridge aftershocks recorded by multi-scale arrays of portable digital seismographs

USGS Publications Warehouse

Meremonte, M.; Frankel, A.; Cranswick, E.; Carver, D.; Worley, D.

1996-01-01

We deployed portable digital seismographs in the San Fernando Valley (SFV), the Los Angeles basin (LAB), and surrounding hills to record aftershocks of the 17 January 1994 Northridge California earthquake. The purpose of the deployment was to investigate factors relevant to seismic zonation in urban areas, such as site amplification, sedimentary basin effects, and the variability of ground motion over short baselines. We placed seismographs at 47 sites (not all concurrently) and recorded about 290 earthquakes with magnitudes up to 5.1 at five stations or more. We deployed widely spaced stations for profiles across the San Fernando Valley, as well as five dense arrays (apertures of 200 to 500 m) in areas of high damage, such as the collapsed Interstate 10 overpass, Sherman Oaks, and the collapsed parking garage at CalState Northridge. Aftershock data analysis indicates a correlation of site amplification with mainshock damage. We found several cases where the site amplification depended on the azimuth of the aftershock, possibly indicating focusing from basin structures. For the parking garage array, we found large ground-motion variabilities (a factor of 2) over 200-m distances for sites on the same mapped soil unit. Array analysis of the aftershock seismograms demonstrates that sizable arrivals after the direct 5 waves consist of surface waves traveling from the same azimuth as that of the epicenter. These surface waves increase the duration of motions and can have frequencies as high as about 4 Hz. For the events studied here, we do not observe large arrivals reflected from the southern edge of the San Fernando Valley.

Overview of topographic effects based on experimental observations: meaning, causes and possible interpretations

NASA Astrophysics Data System (ADS)

Massa, Marco; Barani, Simone; Lovati, Sara

2014-06-01

The paper presents an extensive review of topographic effects in seismology taking into account the knowledge of 40 yr of scientific literature. An overview of topographic effects based on experimental observations and numerical modelling is presented with the aim of highlighting meaning and causes of these phenomena as well as possible correlations between site response (fundamental frequency, amplification level) and geometrical (width and shape ratio of a relief) parameters. After a thorough summary of topographic effects, the paper focuses on five Italian sites whose seismic response is potentially affected by local morphology, as already evidenced by previous studies. In this study, seismic data recorded at these sites are analysed computing directional spectral ratios both in terms of horizontal to vertical spectral ratios (HVSRs) and, wherever possible, in terms of standard spectral ratios (SSRs). The analysis lead to the conclusion that wavefield tends to be polarized along a direction perpendicular to the main axis of a topographic irregularity, direction along which ground motion amplification is maximum. The final section of the article compares and contrasts different spectral ratio techniques in order to examine their effectiveness and reliability in detecting topographic effects. The examples discussed in the paper show that site responses based on HVSRs rather than SSR measurements could lead to misinterpretation of ground response results, both as concerns the definition of the site fundamental frequency and amplification level. Results and findings of this work will be used as starting point to discuss the influence of topographic effects on ground motion prediction equations and regulations for design. These topics will be discussed in the companion article.

Strand Invasion Based Amplification (SIBA®): a novel isothermal DNA amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte.

PubMed

Hoser, Mark J; Mansukoski, Hannu K; Morrical, Scott W; Eboigbodin, Kevin E

2014-01-01

Isothermal nucleic acid amplification technologies offer significant advantages over polymerase chain reaction (PCR) in that they do not require thermal cycling or sophisticated laboratory equipment. However, non-target-dependent amplification has limited the sensitivity of isothermal technologies and complex probes are usually required to distinguish between non-specific and target-dependent amplification. Here, we report a novel isothermal nucleic acid amplification technology, Strand Invasion Based Amplification (SIBA). SIBA technology is resistant to non-specific amplification, is able to detect a single molecule of target analyte, and does not require target-specific probes. The technology relies on the recombinase-dependent insertion of an invasion oligonucleotide (IO) into the double-stranded target nucleic acid. The duplex regions peripheral to the IO insertion site dissociate, thereby enabling target-specific primers to bind. A polymerase then extends the primers onto the target nucleic acid leading to exponential amplification of the target. The primers are not substrates for the recombinase and are, therefore unable to extend the target template in the absence of the IO. The inclusion of 2'-O-methyl RNA to the IO ensures that it is not extendible and that it does not take part in the extension of the target template. These characteristics ensure that the technology is resistant to non-specific amplification since primer dimers or mis-priming are unable to exponentially amplify. Consequently, SIBA is highly specific and able to distinguish closely-related species with single molecule sensitivity in the absence of complex probes or sophisticated laboratory equipment. Here, we describe this technology in detail and demonstrate its use for the detection of Salmonella.

Detection of Low-Copy-Number Genomic DNA Sequences in Individual Bacterial Cells by Using Peptide Nucleic Acid-Assisted Rolling-Circle Amplification and Fluorescence In Situ Hybridization▿ †

PubMed Central

Smolina, Irina; Lee, Charles; Frank-Kamenetskii, Maxim

2007-01-01

An approach is proposed for in situ detection of short signature DNA sequences present in single copies per bacterial genome. The site is locally opened by peptide nucleic acids, and a circular oligonucleotide is assembled. The amplicon generated by rolling circle amplification is detected by hybridization with fluorescently labeled decorator probes. PMID:17293504

Noiseless intensity amplification of repetitive signals by coherent addition using the temporal Talbot effect

PubMed Central

Maram, Reza; Van Howe, James; Li, Ming; Azaña, José

2014-01-01

Amplification of signal intensity is essential for initiating physical processes, diagnostics, sensing, communications and measurement. During traditional amplification, the signal is amplified by multiplying the signal carriers through an active gain process, requiring the use of an external power source. In addition, the signal is degraded by noise and distortions that typically accompany active gain processes. We show noiseless intensity amplification of repetitive optical pulse waveforms with gain from 2 to ~20 without using active gain. The proposed method uses a dispersion-induced temporal self-imaging (Talbot) effect to redistribute and coherently accumulate energy of the original repetitive waveforms into fewer replica waveforms. In addition, we show how our passive amplifier performs a real-time average of the wave-train to reduce its original noise fluctuation, as well as enhances the extinction ratio of pulses to stand above the noise floor. Our technique is applicable to repetitive waveforms in any spectral region or wave system. PMID:25319207

Computation of ground motion amplification in Kolkata megacity (India) using finite-difference method for seismic microzonation

NASA Astrophysics Data System (ADS)

Shiuly, Amit; Kumar, Vinay; Narayan, Jay

2014-06-01

This paper presents the ground motion amplification scenario along with fundamental frequency (F 0) of sedimentary deposit for the seismic microzonation of Kolkata City, situated on the world's largest delta island with very soft soil deposit. A 4th order accurate SH-wave viscoelastic finite-difference algorithm is used for computation of response of 1D model for each borehole location. Different maps, such as for F 0, amplification at F 0, average spectral amplification (ASA) in the different frequency bandwidth of earthquake engineering interest are developed for a variety of end-users communities. The obtained ASA of the order of 3-6 at most of the borehole locations in a frequency range of 0.25-10.0 Hz reveals that Kolkata City may suffer severe damage even during a moderate earthquake. Further, unexpected severe damage to collapse of multi-storey buildings may occur in localities near Hoogly River and Salt Lake area due to double resonance effects during distant large earthquakes.

Applicability of the site fundamental frequency as a VS30 proxy for Central and Eastern North America

NASA Astrophysics Data System (ADS)

Hassani, B.; Atkinson, G. M.

2015-12-01

One of the most important issues in developing accurate ground-motion prediction equations (GMPEs) is the effective use of limited regional site information in developing a site effects model. In modern empirical GMPE models site effects are usually characterized by simplified parameters that describe the overall near-surface effects on input ground-motion shaking. The most common site effects parameter is the time-averaged shear-wave velocity in the upper 30 m (VS30), which has been used in the Next Generation Attenuation-West (NGA-West) and NGA-East GMPEs, and is widely used in building code applications. For the NGA-East GMPE database, only 6% of the stations have measured VS30 values, while the rest have proxy-based VS30 values. Proxy-based VS30 values are derived from a weighted average of different proxies' estimates such as topographic slope and surface geology proxies. For the proxy-based approaches, the uncertainty in the estimation of Vs30 is significantly higher (~0.25, log10 units) than that for stations with measured VS30(0.04, log10 units); this translates into error in site amplification and hence increased ground motion variability. We introduce a new VS30 proxy as a function of the site fundamental frequency (fpeak) using the NGA-East database, and show that fpeak is a particularly effective proxy for sites in central and eastern North America We first use horizontal to vertical spectra ratios (H/V) of 5%-damped pseudo spectral acceleration (PSA) to find the fpeak values for the recording stations. We develop an fpeak-based VS30 proxy by correlating the measured VS30 values with the corresponding fpeak value. The uncertainty of the VS30 estimate using the fpeak-based model is much lower (0.14, log10 units) than that for the proxy-based methods used in the NGA-East database (0.25 log10 units). The results of this study can be used to recalculate the VS30 values more accurately for stations with known fpeak values (23% of the stations), and potentially reduce the overall variability of the developed NGA-East GMPE models.

Characterization of site conditions for selected seismic stations in eastern part of Romania

NASA Astrophysics Data System (ADS)

Grecu, B.; Zaharia, B.; Diaconescu, M.; Bala, A.; Nastase, E.; Constantinescu, E.; Tataru, D.

2018-02-01

Strong motion data are essential for seismic hazard assessment. To correctly understand and use this kind of data is necessary to have a good knowledge of local site conditions. Romania has one of the largest strong motion networks in Europe with 134 real-time stations. In this work, we aim to do a comprehensive site characterization for eight of these stations located in the eastern part of Romania. We make use of a various seismological dataset and we perform ambient noise and earthquake-based investigations to estimate the background noise level, the resonance frequencies and amplification of each site. We also derive the Vs30 parameter from the surface shear-wave velocity profiles obtained through the inversion of the Rayleigh waves recorded in active seismic measurements. Our analyses indicate similar results for seven stations: high noise levels for frequencies larger than 1 Hz, well defined fundamental resonance at low frequencies (0.15-0.29 Hz), moderate amplification levels (up to 4 units) for frequencies between 0.15 and 5-7 Hz and same soil class (type C) according to the estimated Vs30 and Eurocode 8. In contrast, the eighth station for which the soil class is evaluated of type B exhibits a very good noise level for a wide range of frequencies (0.01-20 Hz), a broader fundamental resonance at high frequencies ( 8 Hz) and a flat amplification curve between 0.1 and 3-4 Hz.

Masking Release in Children and Adults With Hearing Loss When Using Amplification

PubMed Central

McCreery, Ryan; Kopun, Judy; Lewis, Dawna; Alexander, Joshua; Stelmachowicz, Patricia

2016-01-01

Purpose This study compared masking release for adults and children with normal hearing and hearing loss. For the participants with hearing loss, masking release using simulated hearing aid amplification with 2 different compression speeds (slow, fast) was compared. Method Sentence recognition in unmodulated noise was compared with recognition in modulated noise (masking release). Recognition was measured for participants with hearing loss using individualized amplification via the hearing-aid simulator. Results Adults with hearing loss showed greater masking release than the children with hearing loss. Average masking release was small (1 dB) and did not depend on hearing status. Masking release was comparable for slow and fast compression. Conclusions The use of amplification in this study contrasts with previous studies that did not use amplification. The results suggest that when differences in audibility are reduced, participants with hearing loss may be able to take advantage of dips in the noise levels, similar to participants with normal hearing. Although children required a more favorable signal-to-noise ratio than adults for both unmodulated and modulated noise, masking release was not statistically different. However, the ability to detect a difference may have been limited by the small amount of masking release observed. PMID:26540194

Site Effect Analysis in the Izmit Basin of Turkey: Preliminary Results from the Wave Propagation Simulation using the Spectral Element Method

NASA Astrophysics Data System (ADS)

Firtana Elcomert, Karolin; Kocaoglu, Argun

2014-05-01

Sedimentary basins affect the propagation characteristics of the seismic waves and cause significant ground motion amplification during an earthquake. While the impedance contrast between the sedimentary layer and bedrock predominantly controls the resonance frequencies and their amplitudes (seismic amplification), surface waves generated within the basin, make the waveforms more complex and longer in duration. When a dense network of weak and/or strong motion sensors is available, site effect or more specifically sedimentary basin amplification can be directly estimated experimentally provided that significant earthquakes occur during the period of study. Alternatively, site effect can be investigated through simulation of ground motion. The objective of this study is to investigate the 2-D site effect in the Izmit Basin located in the eastern Marmara region of Turkey, using the currently available bedrock topography and shear-wave velocity data. The Izmit Basin was formed in Plio-Quaternary period and is known to be a pull-apart basin controlled by the northern branch of the North Anatolian Fault Zone (Şengör et al. 2005). A thorough analysis of seismic hazard is important since the city of Izmit and its metropolitan area is located in this region. Using a spectral element code, SPECFEM2D (Komatitsch et al. 1998), this work presents some of the preliminary results of the 2-D seismic wave propagation simulations for the Izmit basin. The spectral-element method allows accurate and efficient simulation of seismic wave propagation due to its advantages over the other numerical modeling techniques by means of representation of the wavefield and the computational mesh. The preliminary results of this study suggest that seismic wave propagation simulations give some insight into the site amplification phenomena in the Izmit basin. Comparison of seismograms recorded on the top of sedimentary layer with those recorded on the bedrock show more complex waveforms with higher amplitudes on seismograms recorded at the free surface. Furthermore, modeling reveals that observed seismograms include surface waves whose excitation is clearly related to the basin geometry.

Microsatellite DNA markers for assessing phylogeographic and population structure in Preble's meadow jumping mice (Zapus hudsonius preblei) and cross-amplification among neighbouring taxa

USGS Publications Warehouse

King, T.L.; Eackles, M.S.; Young, C.

2006-01-01

We document the isolation and characterization of 14 tetranucleotide microsatellite DNA markers in Preble's meadow jumping mouse (Zapus hudsonius preblei). The identified markers displayed moderate levels of allelic diversity (averaging 4.9 alleles per locus) and heterozygosity (averaging 55.1%). Genotypic and allelic frequencies in a collection of 30 individuals conformed to Hardy-Weinberg equilibrium expectations and indicated no linkage disequilibrium. High levels of cross-amplification (95% overall) among neighbouring subspecies and two congeners (Zapus princeps and Zapus trinotatus) were observed. Multilocus genotypes resulting from these markers appear to provide ample genetic diversity for studies assessing individual- and population-level ecological interactions within Z. h. preblei and evolutionary relationships among neighbouring subspecies (Z. h. campestris, Z. h. intermedius, Z. h. pallidus and Z. h. luteus). ?? 2006 The Authors.

VS Characterization of Hard-Rock DAM Sites in British Columbia

NASA Astrophysics Data System (ADS)

Addo, K. O.; Catchings, R.; Yong, A.; Goldman, M.; Chan, J. H.; Martin, A. J.

2017-12-01

We present results consisting of shear-wave velocity (VS) profiles and the time-averaged VS in the uppermost 30 m (VS30) measured with multiple noninvasive seismic methods and acquired at five hydro dam locations in British Columbia, Canada. VS30 is typically the main parameter used to account for site amplification in ground motion models (GMMs), including models for western (WNA) and central/eastern North America (CENA). As VS30 quantifies soil shear stiffness, which affects frequency content and damping within shallow sediments, it correlates with the shallow-crustal damping parameter, kappa (k), and particularly the site component of kappa (k0). The upper limit on k0-VS30-scaling is in the range of 1100 to 1500 m/s (or less) and the lack of data from stiffer sites reflects the scarcity of direct VS measurements for such site conditions in North America. Hard-rock sites (VS30 > 1500 m/s) are of great engineering interest, but the lack of such measurements increases epistemic uncertainties in the GMMs. Moreover, it is currently not possible to correlate site-to-site variations in k0 with VS30 for such conditions because most hard-rock sites are assigned a generic VS30 of 2000 m/s, due to the lack of measured VS30 values. For the British Columbia sites, our preliminary analysis of field records indicates near-surface shear-wave velocities in excess of 2500 m/s in the upper few meters. Additional analysis of body- and surface-waves will include: refraction tomography, multi-channel analysis of surface waves (MASW), reflection, extended-spatial-autocorrelation, horizontal-to-vertical spectral ratio, and multi-spectral analysis of surface waves

MDM2 copy numbers in well-differentiated and dedifferentiated liposarcoma: characterizing progression to high-grade tumors.

PubMed

Ware, Patrick L; Snow, Anthony N; Gvalani, Maya; Pettenati, Mark J; Qasem, Shadi A

2014-03-01

MDM2 gene amplification is associated with well-differentiated (WDL) and dedifferentiated liposarcomas (DDL). Using fluorescent in situ hybridization (FISH), we sought to characterize various patterns of MDM2 amplification among the morphologic spectrum of liposarcoma. Forty-six cases of liposarcoma in various sites were examined and included 22 WDLs, 14 DLLs, and 10 negative control subjects. The MDM2 amplification ratio (MDM2/CEP12) was lower in WDL (10.2) compared with DDL (18.3) cases (P = .0000002). An amplification ratio of 16 showed optimal sensitivity (0.86) and specificity (0.96) as a cutoff point for progression to DDL. Borderline areas, defined as tumors with increased cellularity and atypia but with preserved lipomatous differentiation, showed a significantly higher MDM2 ratio (17.5; P = .0007) compared with WDL. Central (retroperitoneal and intra-abdominal) tumors also showed a significantly higher MDM2 ratio than peripheral ones (P = .02). Differences in MDM2 amplification profiles among liposarcomas could help further define and predict progression to high-grade neoplasia.

Fidelity criterion for quantum-domain transmission and storage of coherent states beyond the unit-gain constraint.

PubMed

Namiki, Ryo; Koashi, Masato; Imoto, Nobuyuki

2008-09-05

We generalize the experimental success criterion for quantum teleportation (memory) in continuous-variable quantum systems to be suitable for a non-unit-gain condition by considering attenuation (amplification) of the coherent-state amplitude. The new criterion can be used for a nonideal quantum memory and long distance quantum communication as well as quantum devices with amplification process. It is also shown that the framework to measure the average fidelity is capable of detecting all Gaussian channels in the quantum domain.

Physical principles of the amplification of electromagnetic radiation due to negative electron masses in a semiconductor superlattice

NASA Astrophysics Data System (ADS)

Shorokhov, A. V.; Pyataev, M. A.; Khvastunov, N. N.; Hyart, T.; Kusmartsev, F. V.; Alekseev, K. N.

2015-02-01

In a superlattice placed in crossed static electric and magnetic fields, under certain conditions, the inversion of electron population can appear at which the average energy of electrons is above the middle of the mini-band and the effective mass of the electron is negative. This is the implementation of the negative effective mass amplifier and generator (NEMAG) in the superlattice. It can result in the amplification and generation of terahertz radiation even in the absence of negative differential conductivity.

Improved amplification results following episodes of failure to amplify at the Amelogenin Locus using PowerPlex® ESI 16 Fast System.

PubMed

Berlyne, Sigal; Oz, Carla; Einot, Naftaly; Avraham, Shlomit; Ram, Tanya; Goldberg, Miri D; Gafny, Ron

2017-07-01

In 2012 the Israel Police DNA Casework laboratory adopted the 16 STR PowerPlex ® ESI kit for routine use. The Promega Company updated this kit and developed the PowerPlex ® ESI 16 Fast System in which all autosomal primer pairs remained identical to the original set, except at the amelogenin site. The master mix was improved and optimized which allowed for direct, faster and more robust amplification. Prior to implementing the PowerPlex ® ESI 16 Fast System in our lab, we conducted a preliminary assay where 213 casework samples were amplified using the new kit. These samples had previously been extracted by one of two extraction kits employed by our lab. (the PrepFiler ExpressTM and PrepFiler BTATM Forensic DNA Extraction Kits). The amplification results from these samples were compared to samples amplified using the original PowerPlex ® ESI 16 kit. Multiple incidents of failure to amplify at the amelogenin locus were noted using the new system with the recommended protocol at a rate of 13% (28 of 213 samples). Experiments were performed to understand whether these amplification failures could be a result of primer binding site mutations, extraction method reagents and/or inhibitors. The conclusions reached following these experiments, in conjunction with consultation with the manufacturer, led to the trial of a modified amplification protocol where the suggested annealing temperature was reduced by 2 degrees. To evaluate the efficiency of this altered protocol, a comparison study was undertaken where 88 additional casework samples were chosen and amplified using both the modified 58°C and the recommended 60°C annealing temperatures. We concluded that the most effective method in our laboratory for achieving a consistent and balanced amplification at the amelogenin locus was to reduce the annealing temperature from the manufacturer's recommended 60°C to 58°C. This modification resulted in a reduction of the failure to amplify at the amelogenin locus from 13% (28/213) to 1.1% (1/88) without any observed changes to the autosomal STR amplification results. Copyright © 2017 Elsevier B.V. All rights reserved.

Direct duplex real-time loop mediated isothermal amplification assay for the simultaneous detection of cow and goat species origin of milk and yogurt products for field use.

PubMed

Kim, Mi-Ju; Kim, Hae-Yeong

2018-04-25

A multiple loop-mediated isothermal amplification (LAMP) method was developed to detect cow and goat milk in the field using a portable fluorescence device. For rapid on-site detection, this duplex LAMP assay was used in combination with direct amplification, without DNA extraction. The cow- and goat-specific LAMP primer sets were designed based on the mitochondrial cytochrome b gene, and showed specificity against 13 other animal species in the reactions. The sensitivity of the duplex LAMP assay for cow and goat was 0.1 and 1 pg, respectively. The detection limit for both target species in milk mixtures was 2%. This assay successfully amplified and identified the two target species in 24 samples of commercial milk and yogurt products, with 30 min sampling-to-result analysis time. Therefore, this direct duplex real-time LAMP assay is useful for on-site simultaneous detection of cow and goat milk in commercial products, a capability needed to confirm accurate labeling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Long-period amplification in deep alluvial basins and consequences for site-specific probabilistic seismic-hazard: the case of Castelleone in the Po Plain (Northern Italy)

NASA Astrophysics Data System (ADS)

Barani, S.; Mascandola, C.; Massa, M.; Spallarossa, D.

2017-12-01

The recent Emilia seismic sequence (Northern Italy) occurred at the end of the first half of 2012 with main shock of Mw6.1 highlighted the importance of studying site effects in the Po Plain, the larger and deeper sedimentary basin in Italy. As has long been known, long-period amplification related to deep sedimentary basins can significantly affect the characteristics of the ground-motion induced by strong earthquakes. It follows that the effects of deep sedimentary deposits on ground shaking require special attention during the definition of the design seismic action. The work presented here analyzes the impact of deep-soil discontinuities on ground-motion amplification, with particular focus on long-period probabilistic seismic-hazard assessment. The study focuses on the site of Castelleone, where a seismic station of the Italian National Seismic Network has been recording since 2009. Our study includes both experimental and numerical site response analyses. Specifically, extensive active and passive geophysical measurements were carried out in order to define a detailed shear-wave velocity (VS) model to be used in the numerical analyses. These latter are needed to assess the site-specific ground-motion hazard. Besides classical seismic refraction profiles and multichannel analysis of surface waves, we analyzed ambient vibration measurements in both single and array configurations. The VS profile was determined via joint inversion of the experimental phase-velocity dispersion curve with the ellipticity curve derived from horizontal-to-vertical spectral ratios. The profile shows two main discontinuities at depths of around 160 and 1350 m, respectively. The probabilistic site-specific hazard was assessed in terms of both spectral acceleration and displacement. A partially non-ergodic approach was adopted. We have found that the spectral acceleration hazard is barely sensitive to long-period (up to 10 s) amplification related to the deeper discontinuity whereas the displacement hazard is strongly affected. Our results show that neglecting the effects of the deeper discontinuity implies an underestimation of the hazard of up to about 49% for a mean return period (MRP) of 475 years and 57% for an MRP of 2475 years, with possible consequences on the design of very tall buildings and large bridges.

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification

PubMed Central

Schouten, Jan P.; McElgunn, Cathal J.; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-01-01

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down’s syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50–70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences. PMID:12060695

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification.

PubMed

Schouten, Jan P; McElgunn, Cathal J; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-06-15

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down's syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50-70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences.

Optical frequency transfer via a 660 km underground fiber link using a remote Brillouin amplifier.

PubMed

Raupach, S M F; Koczwara, A; Grosche, G

2014-11-03

In long-distance, optical continuous-wave frequency transfer via fiber, remote bidirectional Er³ ⁺ -doped fiber amplifiers are commonly used to mitigate signal attenuation. We demonstrate for the first time the ultrastable transfer of an optical frequency using a remote fiber Brillouin amplifier, placed in a server room along the link. Using it as the only means of remote amplification, on a 660 km loop of installed underground fiber we bridge distances of 250 km and 160 km between amplifications. Over several days of uninterrupted measurement, we find an instability of the frequency transfer (Allan deviation of Λ-weighted data with 1 s gate time) of around 1 × 10(-19) and less for averaging times longer than 3000 s. The modified Allan deviation reaches 3 × 10(-19) at an averaging time of 100 s. Beyond 100 s it follows the interferometer noise floor, and for averaging times longer than 1000 s the modified Allan deviation is in the 10(-20) range. A conservative value of the overall accuracy is 1 × 10(-19)

PCR-mediated site-directed mutagenesis.

PubMed

Carey, Michael F; Peterson, Craig L; Smale, Stephen T

2013-08-01

Unlike traditional site-directed mutagenesis, this protocol requires only a single PCR step using full plasmid amplification to generate point mutants. The method can introduce small mutations into promoter sites and is even better suited for introducing single or double mutations into proteins. It is elegant in its simplicity and can be applied quite easily in any laboratory using standard protein expression vectors and commercially available reagents.

Site response, shallow shear-wave velocity, and wave propagation at the San Jose, California, dense seismic array

USGS Publications Warehouse

Hartzell, S.; Carver, D.; Williams, R.A.; Harmsen, S.; Zerva, A.

2003-01-01

Ground-motion records from a 52-element dense seismic array near San Jose, California, are analyzed to obtain site response, shallow shear-wave velocity, and plane-wave propagation characteristics. The array, located on the eastern side of the Santa Clara Valley south of the San Francisco Bay, is sited over the Evergreen basin, a 7-km-deep depression with Miocene and younger deposits. Site response values below 4 Hz are up to a factor of 2 greater when larger, regional records are included in the analysis, due to strong surface-wave development within the Santa Clara Valley. The pattern of site amplification is the same, however, with local or regional events. Site amplification increases away from the eastern edge of the Santa Clara Valley, reaching a maximum over the western edge of the Evergreen basin, where the pre-Cenozoic basement shallows rapidly. Amplification then decreases further to the west. This pattern may be caused by lower shallow shear-wave velocities and thicker Quaternary deposits further from the edge of the Santa Clara Valley and generation/trapping of surface waves above the shallowing basement of the western Evergreen basin. Shear-wave velocities from the inversion of site response spectra based on smaller, local earthquakes compare well with those obtained independently from our seismic reflection/refraction measurements. Velocities from the inversion of site spectra that include larger, regional records do not compare well with these measurements. A mix of local and regional events, however, is appropriate for determination of site response to be used in seismic hazard evaluation, since large damaging events would excite both body and surface waves with a wide range in ray parameters. Frequency-wavenumber, plane-wave analysis is used to determine the backazimuth and apparent velocity of coherent phases at the array. Conventional, high-resolution, and multiple signal characterization f-k power spectra and stacked slowness power spectra are compared. These spectra show surface waves generated/ scattered at the edges of the Santa Clara Valley and possibly within the valley at the western edge of the Evergreen basin.

Polymorphic microsatellite markers for the endangered fish, the slender shiner Pseudopungtungia tenuicorpa and cross-species amplification across five related species.

PubMed

Kim, K S; Moon, S J; Han, S H; Kim, K Y; Bang, I C

2016-09-02

The slender shiner Pseudopungtungia tenuicorpa (Cypriniformes; Cyprinidae; Gobioninae) is an endangered freshwater fish species endemic to Korea. The current strategies for its conservation involve the study of population genetic characters and identification of management units. These strategies require suitable molecular markers to study genetic diversity and genetic structure. Here, we developed nine polymorphic microsatellite markers for P. tenuicorpa for the first time by applying an enrichment method from a size-selected genomic library. The developed microsatellite markers produced a total of 101 alleles (average 11.2). The observed and expected heterozygosities averaged 0.805 and 0.835, respectively. Among the nine identified markers, five markers showed successful amplification across five related Korean Gobioninae species. Thus, the microsatellite markers developed in this study will be useful to establish conservation strategies for both P. tenuicorpa and other related species.

High repetition rate tunable femtosecond pulses and broadband amplification from fiber laser pumped parametric amplifier.

PubMed

Andersen, T V; Schmidt, O; Bruchmann, C; Limpert, J; Aguergaray, C; Cormier, E; Tünnermann, A

2006-05-29

We report on the generation of high energy femtosecond pulses at 1 MHz repetition rate from a fiber laser pumped optical parametric amplifier (OPA). Nonlinear bandwidth enhancement in fibers provides the intrinsically synchronized signal for the parametric amplifier. We demonstrate large tunability extending from 700 nm to 1500 nm of femtosecond pulses with pulse energies as high as 1.2 muJ when the OPA is seeded by a supercontinuum generated in a photonic crystal fiber. Broadband amplification over more than 85 nm is achieved at a fixed wavelength. Subsequent compression in a prism sequence resulted in 46 fs pulses. With an average power of 0.5 W these pulses have a peak-power above 10 MW. In particular, the average power and pulse energy scalability of both involved concepts, the fiber laser and the parametric amplifier, will enable easy up-scaling to higher powers.

A unique dual recognition hairpin probe mediated fluorescence amplification method for sensitive detection of uracil-DNA glycosylase and endonuclease IV activities.

PubMed

Wu, Yushu; Yan, Ping; Xu, Xiaowen; Jiang, Wei

2016-03-07

Uracil-DNA glycosylase (UDG) and endonuclease IV (Endo IV) play cooperative roles in uracil base-excision repair (UBER) and inactivity of either will interrupt the UBER to cause disease. Detection of UDG and Endo IV activities is crucial to evaluate the UBER process in fundamental research and diagnostic application. Here, a unique dual recognition hairpin probe mediated fluorescence amplification method was developed for sensitively and selectively detecting UDG and Endo IV activities. For detecting UDG activity, the uracil base in the probe was excised by the target enzyme to generate an apurinic/apyrimidinic (AP) site, achieving the UDG recognition. Then, the AP site was cleaved by a tool enzyme Endo IV, releasing a primer to trigger rolling circle amplification (RCA) reaction. Finally, the RCA reaction produced numerous repeated G-quadruplex sequences, which interacted with N-methyl-mesoporphyrin IX to generate an enhanced fluorescence signal. Alternatively, for detecting Endo IV activity, the uracil base in the probe was first converted into an AP site by a tool enzyme UDG. Next, the AP site was cleaved by the target enzyme, achieving the Endo IV recognition. The signal was then generated and amplified in the same way as those in the UDG activity assay. The detection limits were as low as 0.00017 U mL(-1) for UDG and 0.11 U mL(-1) for Endo IV, respectively. Moreover, UDG and Endo IV can be well distinguished from their analogs. This method is beneficial for properly evaluating the UBER process in function studies and disease prognoses.

De novo amplification within a silent human cholinesterase gene in a family subjected to prolonged exposure to organophosphorus insecticides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prody, C.A.; Dreyfus, P.; Soreq, H.

1989-01-01

A 100-fold DNA amplification in the CHE gene, coding for serum butyrylcholinesterase (BtChoEase), was found in a farmer expressing silent CHE phenotype. Individuals homozygous for this gene display a defective serum BtChoEase and are particularly vulnerable to poisoning by agricultural organophosphorus insecticides, to which all members of this family had long been exposed. DNA blot hybridization with regional BtChoEase cDNA probes suggested that the amplification was most intense in regions encoding central sequences within BtChoEase cDNA, whereas distal sequences were amplified to a much lower extent. This is in agreement with the onion skin model, based on amplification of genesmore » in cultured cells and primary tumors. The amplification was absent in the grandparents but present at the same extent in one of their sons and in a grandson, with similar DNA blot hybridization patterns. In situ hybridization experiments localized the amplified sequences to the long arm of chromosome 3, close to the site where the authors previously mapped the CHE gene. Altogether, these observations suggest that the initial amplification event occurred early in embryogenesis, spermatogenesis, or oogenesis, where the CHE gene is intensely active and where cholinergic functioning was indicated to be physiologically necessary. These findings demonstrate a de novo amplification in apparently healthy individuals within an autosomal gene producing a target protein to an inhibitor.« less

The 2006 Bahía Asunción Earthquake Swarm: Seismic Evidence of Active Deformation Along the Western Margin of Baja California Sur, Mexico

NASA Astrophysics Data System (ADS)

Munguía, Luis; Mayer, Sergio; Aguirre, Alfredo; Méndez, Ignacio; González-Escobar, Mario; Luna, Manuel

2016-10-01

The study of the Bahía Asunción earthquake swarm is important for two reasons. First, the earthquakes are clear evidence of present activity along the zone of deformation on the Pacific margin of Baja California. The swarm, with earthquakes of magnitude M w of up to 5.0, occurred on the coastline of the peninsula, showing that the Tosco-Abreojos zone of deformation is wider than previously thought. Second, the larger earthquakes in the swarm caused some damage and much concern in Bahía Asunción, a small town located in the zone of epicenters. We relocated the larger earthquakes with regional and/or local seismic data. Our results put the earthquake sources below the urban area of Bahía Asunción, at 40-50 km to the north of the teleseismically determined epicenters. In addition, these new locations are in the area of epicenters of many smaller events that were located with data from local temporary stations. This area trends in an E-W direction and has dimensions of approximately 15 km by 10 km. Most earthquakes had sources at depths that are between 4 and 9 km. A composite focal mechanism for the smaller earthquakes indicated right-lateral strike-slip motion and pure-normal faulting occurred during this swarm. Interestingly, the ANSS earthquake catalog of the United States Geological Survey (USGS) reported each one of these faulting styles for two large events of the swarm, with one of these earthquakes occurring 2 days before the other one. We associate the earthquake with strike-slip mechanism with the San Roque Fault, and the earthquake with the normal faulting style with the Asunción Fault. However, there is need of further study to verify this possible relation between the faults and the earthquakes. In addition, we recorded peak accelerations of up to 0.63 g with an accelerometer installed in Bahía Asunción. At this site, an earthquake of M w 4.9 produced those high values at a distance of 4.1 km. We also used the acceleration dataset from this site to estimate the linear response of sediments lying beneath the station. The resulting average amplification function has a fundamental resonance frequency of about 5 Hz and shows amplification factors of 2-4 for motions at frequencies in the range 2-8 Hz. A comparison of this amplification function with the response of soils to shaking from larger events shows that above 20 Hz the amplification of motion in the larger events decreases relative to the weak-motion response.

Erbium:ytterbium fiber-laser system delivering watt-level femtosecond pulses using divided pulse amplification

NASA Astrophysics Data System (ADS)

Herda, Robert; Zach, Armin

2015-03-01

We present an Erbium:Ytterbium codoped fiber-amplifer system based on Divided-Pulses-Amplification (DPA) for ultrashort pulses. The output from a saturable-absorber mode-locked polarization-maintaining (PM) fiber oscillator is amplified in a PM normal-dispersion Erbium-doped fiber. After this stage the pulses are positively chirped and have a duration of 2.0 ps at an average power of 93 mW. A stack of 5 birefringent Yttrium-Vanadate crystals divides these pulses 32 times. We amplify these pulses using a double-clad Erbium:Ytterbium codoped fiber pumped through a multimode fiber combiner. The pulses double pass the amplifier and recombine in the crystals using non-reciprocal polarization 90° rotation by a Faraday rotating mirror. Pulses with a duration of 144 fs are obtained after separation from the input beam using a polarizing beam splitter cube. These pulses have an average power of 1.85 W at a repetition rate of 80 MHz. The generation of femtosecond pulses directly from the amplifier was enabled by a positively chirped seed pulse, normally dispersive Yttrium-Vanadate crystals, and anomalously dispersive amplifier fibers. Efficient frequency doubling to 780 nm with an average power of 725 mW and a pulse duration of 156 fs is demonstrated. In summary we show a DPA setup that enables the generation of femtosecond pulses at watt-level at 1560 nm without the need for further external dechirping and demonstrate a good pulse quality by efficient frequency doubling. Due to the use of PM fiber components and a Faraday rotator the setup is environmentally stable.

Changes in teachers' voice quality during a working day with and without electric sound amplification.

PubMed

Jónsdottir, Valdis; Laukkanen, Anne-Maria; Siikki, Ilona

2003-01-01

The present study investigated changes in the voice quality of teachers during a working day (a). in ordinary conditions and (b). when using electrical sound amplification while teaching. Classroom speech of 5 teachers was recorded with a portable DAT recorder and a head-mounted microphone during the first and the last lesson of a hard working day first in ordinary conditions and the following week using amplification. Long-term average spectrum and sound pressure level (SPL) analyses were made. The subjects' comments were gathered by questionnaire. Voice quality was evaluated by 2 speech trainers. With amplification, SPL was lower and the spectrum more tilted. Voice quality was evaluated to be better. The subjects reported less fatigue in the vocal mechanism. Spectral tilt decreased and SPL increased during the day. There was a tendency for perceived asthenia to decrease. No significant changes were observed in ordinary conditions. The acoustic changes seem to reflect a positive adaptation to vocal loading. Their absence may be a sign of vocal fatigue. Copyright 2003 S. Karger AG, Basel

'Mitominis': multiplex PCR analysis of reduced size amplicons for compound sequence analysis of the entire mtDNA control region in highly degraded samples.

PubMed

Eichmann, Cordula; Parson, Walther

2008-09-01

The traditional protocol for forensic mitochondrial DNA (mtDNA) analyses involves the amplification and sequencing of the two hypervariable segments HVS-I and HVS-II of the mtDNA control region. The primers usually span fragment sizes of 300-400 bp each region, which may result in weak or failed amplification in highly degraded samples. Here we introduce an improved and more stable approach using shortened amplicons in the fragment range between 144 and 237 bp. Ten such amplicons were required to produce overlapping fragments that cover the entire human mtDNA control region. These were co-amplified in two multiplex polymerase chain reactions and sequenced with the individual amplification primers. The primers were carefully selected to minimize binding on homoplasic and haplogroup-specific sites that would otherwise result in loss of amplification due to mis-priming. The multiplexes have successfully been applied to ancient and forensic samples such as bones and teeth that showed a high degree of degradation.

High energy, high average power solid state green or UV laser

DOEpatents

Hackel, Lloyd A.; Norton, Mary; Dane, C. Brent

2004-03-02

A system for producing a green or UV output beam for illuminating a large area with relatively high beam fluence. A Nd:glass laser produces a near-infrared output by means of an oscillator that generates a high quality but low power output and then multi-pass through and amplification in a zig-zag slab amplifier and wavefront correction in a phase conjugator at the midway point of the multi-pass amplification. The green or UV output is generated by means of conversion crystals that follow final propagation through the zig-zag slab amplifier.

High-power ultrashort fiber laser for solar cells micromachining

NASA Astrophysics Data System (ADS)

Lecourt, J.-B.; Duterte, C.; Liegeois, F.; Lekime, D.; Hernandez, Y.; Giannone, D.

2012-02-01

We report on a high-power ultra-short fiber laser for thin film solar cells micromachining. The laser is based on Chirped Pulse Amplification (CPA) scheme. The pulses are stretched to hundreds of picoseconds prior to amplification and can be compressed down to picosecond at high energy. The repetition rate is adjustable from 100 kHz to 1 MHz and the optical average output power is close to 13 W (before compression). The whole setup is fully fibred, except the compressor achieved with bulk gratings, resulting on a compact and reliable solution for cold ablation.

An exact solution for effects of topography on free Rayleigh waves

USGS Publications Warehouse

Savage, W.Z.

2004-01-01

An exact solution for the effects of topography on Rayleigh wave amplification is presented. The solution is obtained by incorporating conformal mapping into complex-variable stress functions developed for free Rayleigh wave propagation in an elastic half-space with a flat upper surface. Results are presented for free Rayleigh wave propagation across isolated symmetric ridges and valleys. It is found for wavelengths that are comparable to ridge widths that horizontal Rayleigh wave amplitudes are amplified at ridge crests and that vertical amplitudes are strongly reduced near ridge crests relative to horizontal and vertical amplitudes of free Rayleigh waves in the flat case. Horizontal amplitudes are strongly deamplified at valley bottoms relative to those for the flat case for Rayleigh wavelengths comparable to valley widths. Wave amplitudes in the symmetric ridges and valleys asymptotically approach those for the flat case with increased wavelengths, increased ridge and valley widths, and with horizontal distance from and depth below the isolated ridges and valleys. Also, prograde particle motion is predicted near crests of narrow ridges and near the bottoms of narrow valleys. Finally, application of the theory at two sites known for topographic wave amplification gives a predicted surface wave amplification ratio of 3.80 at the ridge center for a frequency of 1.0 Hz at Robinwood Ridge in northern California and a predicted surface wave amplification ratio of 1.67 at the ridge center for the same frequency at the Cedar Hill Nursery site at Tarzana in southern California.

Ligation with Nucleic Acid Sequence–Based Amplification

PubMed Central

Ong, Carmichael; Tai, Warren; Sarma, Aartik; Opal, Steven M.; Artenstein, Andrew W.; Tripathi, Anubhav

2012-01-01

This work presents a novel method for detecting nucleic acid targets using a ligation step along with an isothermal, exponential amplification step. We use an engineered ssDNA with two variable regions on the ends, allowing us to design the probe for optimal reaction kinetics and primer binding. This two-part probe is ligated by T4 DNA Ligase only when both parts bind adjacently to the target. The assay demonstrates that the expected 72-nt RNA product appears only when the synthetic target, T4 ligase, and both probe fragments are present during the ligation step. An extraneous 38-nt RNA product also appears due to linear amplification of unligated probe (P3), but its presence does not cause a false-positive result. In addition, 40 mmol/L KCl in the final amplification mix was found to be optimal. It was also found that increasing P5 in excess of P3 helped with ligation and reduced the extraneous 38-nt RNA product. The assay was also tested with a single nucleotide polymorphism target, changing one base at the ligation site. The assay was able to yield a negative signal despite only a single-base change. Finally, using P3 and P5 with longer binding sites results in increased overall sensitivity of the reaction, showing that increasing ligation efficiency can improve the assay overall. We believe that this method can be used effectively for a number of diagnostic assays. PMID:22449695

Seismically induced rock slope failures resulting from topographic amplification of strong ground motions: The case of Pacoima Canyon, California

USGS Publications Warehouse

Sepulveda, S.A.; Murphy, W.; Jibson, R.W.; Petley, D.N.

2005-01-01

The 1994 Northridge earthquake (Mw = 6.7) triggered extensive rock slope failures in Pacoima Canyon, immediately north of Los Angeles, California. Pacoima Canyon is a narrow and steep canyon incised in gneissic and granitic rocks. Peak accelerations of nearly 1.6 g were recorded at a ridge that forms the left abutment of Pacoima Dam; peak accelerations at the bottom of the canyon were less than 0.5 g, suggesting the occurrence of topographic amplification. Topographic effects have been previously suggested to explain similarly high ground motions at the site during the 1971 (Mw = 6.7) San Fernando earthquake. Furthermore, high landslide concentrations observed in the area have been attributed to unusually strong ground motions rather than higher susceptibility to sliding compared with nearby zones. We conducted field investigations and slope stability back-analyses to confirm the impact of topographic amplification on the triggering of landslides during the 1994 earthquake. Our results suggest that the observed extensive rock sliding and falling would have not been possible under unamplified seismic conditions, which would have generated a significantly lower number of areas affected by landslides. In contrast, modelling slope stability using amplified ground shaking predicts slope failure distributions matching what occurred in 1994. This observation confirms a significant role for topographic amplification on the triggering of landslides at the site, and emphasises the need to select carefully the inputs for seismic slope stability analyses. ?? 2005 Elsevier B.V. All rights reserved.

Genetic diversity analysis of tree peony germplasm using iPBS markers.

PubMed

Duan, Y B; Guo, D L; Guo, L L; Wei, D F; Hou, X G

2015-07-06

We examined the genetic diversity of 10 wild species (populations) and 55 varieties of tree peony using inter-primer binding site (iPBS) markers. From a total of 36 iPBS primers, 16 were selected based on polymorphic amplification. The number of bands amplified by each primer ranged from 9 to 19, with an average of 12.88 bands per primer. The length of bands ranged from 100 to 2000 bp, concentrated at 200 to 1800 bp. Sixteen primers amplified 206 bands in total, of which 173 bands were polymorphic with a polymorphism ratio of 83.98%. Each primer amplified 10.81 polymorphic bands on average. The data were then used to construct a phylogenetic tree using unweighted pair group method with arithmetic mean methods. Clustering analysis showed that the genetic relationships among the varieties were not only related to the genetic background or geographic origin, but also to the flowering phase, flower color, and flower type. Our data also indicated that iPBS markers were useful tools for classifying tree peony germplasms and for tree peony breeding, and the specific bands were helpful for molecular identification of tree peony varieties.

Detection of the CLOCK/BMAL1 heterodimer using a nucleic acid probe with cycling probe technology.

PubMed

Nakagawa, Kazuhiro; Yamamoto, Takuro; Yasuda, Akio

2010-09-15

An isothermal signal amplification technique for specific DNA sequences, known as cycling probe technology (CPT), has enabled rapid acquisition of genomic information. Here we report an analogous technique for the detection of an activated transcription factor, a transcription element-binding assay with fluorescent amplification by apurinic/apyrimidinic (AP) site lysis cycle (TEFAL). This simple amplification assay can detect activated transcription factors by using a unique nucleic acid probe containing a consensus binding sequence and an AP site, which enables the CPT reaction with AP endonuclease. In this article, we demonstrate that this method detects the functional CLOCK/BMAL1 heterodimer via the TEFAL probe containing the E-box consensus sequence to which the CLOCK/BMAL1 heterodimer binds. Using TEFAL combined with immunoassays, we measured oscillations in the amount of CLOCK/BMAL1 heterodimer in serum-stimulated HeLa cells. Furthermore, we succeeded in measuring the circadian accumulation of the functional CLOCK/BMAL1 heterodimer in human buccal mucosa cells. TEFAL contributes greatly to the study of transcription factor activation in mammalian tissues and cell extracts and is a powerful tool for less invasive investigation of human circadian rhythms. 2010 Elsevier Inc. All rights reserved.

An experimental topographic amplification study at Los Alamos National Laboratory using ambient vibrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stolte, Andrew C.; Cox, Brady R.; Lee, Richard C.

An experimental study aimed at investigating potential topographic amplification of seismic waves was conducted on a 50-m-tall and 185-m-wide soft-rock ridge located at Los Alamos National Laboratory near Los Alamos, New Mexico. Ten portable broadband seismograph stations were placed in arrays across the ridge and left to record ambient vibration data for ~9 hours. Clear evidence of topographic amplification was observed by comparing spectral ratios calculated from ambient noise recordings at the toe, slope, and crest of the instrumented ridge. The inferred resonance frequency of the ridge obtained from the experimental recordings was found to agree well with several simplemore » estimates of the theoretical resonance frequency based on its geometry and stiffness. Results support the feasibility of quantifying the frequency range of topographic amplification solely using ambient vibrations, rather than strong or weak ground motions. Additionally, comparisons have been made between a number of widely used experimental methods for quantifying topographic effects, such as the standard spectral ratio, median reference method, and horizontal-to-vertical spectral ratio. As a result, differences in the amplification and frequency range of topographic effects indicated by these methods highlight the importance of choosing a reference condition that is appropriate for the site-specific conditions and goals associated with an experimental topographic amplification study.« less

An experimental topographic amplification study at Los Alamos National Laboratory using ambient vibrations

DOE PAGES

Stolte, Andrew C.; Cox, Brady R.; Lee, Richard C.

2017-03-14

An experimental study aimed at investigating potential topographic amplification of seismic waves was conducted on a 50-m-tall and 185-m-wide soft-rock ridge located at Los Alamos National Laboratory near Los Alamos, New Mexico. Ten portable broadband seismograph stations were placed in arrays across the ridge and left to record ambient vibration data for ~9 hours. Clear evidence of topographic amplification was observed by comparing spectral ratios calculated from ambient noise recordings at the toe, slope, and crest of the instrumented ridge. The inferred resonance frequency of the ridge obtained from the experimental recordings was found to agree well with several simplemore » estimates of the theoretical resonance frequency based on its geometry and stiffness. Results support the feasibility of quantifying the frequency range of topographic amplification solely using ambient vibrations, rather than strong or weak ground motions. Additionally, comparisons have been made between a number of widely used experimental methods for quantifying topographic effects, such as the standard spectral ratio, median reference method, and horizontal-to-vertical spectral ratio. As a result, differences in the amplification and frequency range of topographic effects indicated by these methods highlight the importance of choosing a reference condition that is appropriate for the site-specific conditions and goals associated with an experimental topographic amplification study.« less

A comparative study on seismic response of two unstable rock slopes within same tectonic setting but different activity level

NASA Astrophysics Data System (ADS)

Kleinbrod, Ulrike; Burjánek, Jan; Hugentobler, Marc; Amann, Florian; Fäh, Donat

2017-12-01

In this study, the seismic response of two slope instabilities is investigated with seismic ambient vibration analysis. Two similar sites have been chosen: an active deep-seated slope instability at Cuolm da Vi and the geologically, structurally and morphologically similar, but presently not moving Alp Caschlè slope. Both slopes are located at the upper Vorderrheintal (Canton Graubünden, Switzerland). Ambient vibrations were recorded on both slopes and processed by time-frequency polarization and site-to-reference spectral ratio analysis. The data interpretation shows correlations between degree of disintegration of the rock mass and amplification. However, the ambient vibration analysis conducted, does not allow retrieving a resonance frequency that can be related to the total depth of the instability of Cuolm da Vi. Even though seismic waves can be hardly traced in rock instabilities containing open fractures, it was possible to retrieve a dispersion curve and a velocity profile from the array measurement at Cuolm da Vi due to the high level of disintegration of the rock material down to a depth of about 100 m. From the similar amplification pattern at the two sites, we expect a similar structure, indicating that also the slope at Alp Caschlè was active in the past in a similar manner as Cuolm da Vi. However, a smoother increase of amplification with frequency is observed at Alp Caschlè, which might indicate less disintegration of the rock mass in a particular depth range at this site, when comparing to Cuolm da Vi where a high level of disintegration is observed, resulting from the high activity at the slope. From the frequency-dependent amplification, we can distinguish between two parts within both instabilities, one part showing decreasing disintegration of the rock mass with increasing depth, for the other parts less-fractured blocks are observed. Since the block structures are found in the lower part of the instabilities, they might contribute to the stability of the slopes. Using the velocity profiles, it was possible to estimate the depth of the two largest open fractures (i.e. tension cracks) at Cuolm da Vi.

Ground motion amplification at rock sites: the competing role of topography and fractured rocks in the San Giovanni fault, central Italy

NASA Astrophysics Data System (ADS)

Pischiutta, M.; Cara, F.; Di Giulio, G.; Vassallo, M.; Cultrera, G.

2017-12-01

Amplification at rock sites in areas of high topographic relief has been increasingly observed in the last years, with unexpected level of damage after strong earthquakes. In regions affected by recent tectonic activity, topographic irregularities can include fault damage zones. In such conditions, seismic waves can be locally amplified as a double effect of wave focusing along the topography and /or the presence of fractures/joints or locally weakened rocks. The role of topography vs. geological complexities in controlling the ground motion amplification at rock sites is a newly debated issue in the seismological community. The most crucial questions regard what is the real contribution of the topography shape and fracturing, and how to parameterize such effects for their inclusion in the seismic design codes. In this framework, the EMERSITO INGV task force installed 7 seismic stations across the San Giovanni fault, after the Amatrice mainshock of the 2016 sequence in Central Italy. This active normal fault is located in the area of the Montereale intermountain basin (Abruzzi region, Italy) and bounds the southwestern slope of Mt. Mozzano, a roughly 2D-shaped, up to 1450 m high pronounced topography. Moreover, this fault has been recently studied by several authors who performed detailed geological and geophysical surveys. Our stations recorded more than 100 earthquakes with magnitude ranging from 2.5 to 3.9 as well as a 4.4 M earthquake with hypocenter in Capitignano district, few kilometres far. We have analyzed in detail the recorded signals calculating the traditional spectral ratios at single station (HVSRs) and using the reference site (SSRs) using both ambient noise and earthquakes. In order to obtain a robust estimate of the site amplification effect at each station, we have investigated the influence of backazimuth and epicentral distance. We have also applied the time-domain covariance matrix analysis and the frequency domain polarization analysis. We have found that, in spite of the complexity of the seismic data, the observed polarization pattern is generally oriented orthogonal to the ridge elongation, as well as to the fault strike, suggesting the existence of a high angle relation between ground motion polarization and fracture systems.

Quantification of HIV-1 DNA using real-time recombinase polymerase amplification.

PubMed

Crannell, Zachary Austin; Rohrman, Brittany; Richards-Kortum, Rebecca

2014-06-17

Although recombinase polymerase amplification (RPA) has many advantages for the detection of pathogenic nucleic acids in point-of-care applications, RPA has not yet been implemented to quantify sample concentration using a standard curve. Here, we describe a real-time RPA assay with an internal positive control and an algorithm that analyzes real-time fluorescence data to quantify HIV-1 DNA. We show that DNA concentration and the onset of detectable amplification are correlated by an exponential standard curve. In a set of experiments in which the standard curve and algorithm were used to analyze and quantify additional DNA samples, the algorithm predicted an average concentration within 1 order of magnitude of the correct concentration for all HIV-1 DNA concentrations tested. These results suggest that quantitative RPA (qRPA) may serve as a powerful tool for quantifying nucleic acids and may be adapted for use in single-sample point-of-care diagnostic systems.

Improving Mobile Phone Speech Recognition by Personalized Amplification: Application in People with Normal Hearing and Mild-to-Moderate Hearing Loss.

PubMed

Kam, Anna Chi Shan; Sung, John Ka Keung; Lee, Tan; Wong, Terence Ka Cheong; van Hasselt, Andrew

In this study, the authors evaluated the effect of personalized amplification on mobile phone speech recognition in people with and without hearing loss. This prospective study used double-blind, within-subjects, repeated measures, controlled trials to evaluate the effectiveness of applying personalized amplification based on the hearing level captured on the mobile device. The personalized amplification settings were created using modified one-third gain targets. The participants in this study included 100 adults of age between 20 and 78 years (60 with age-adjusted normal hearing and 40 with hearing loss). The performance of the participants with personalized amplification and standard settings was compared using both subjective and speech-perception measures. Speech recognition was measured in quiet and in noise using Cantonese disyllabic words. Subjective ratings on the quality, clarity, and comfortableness of the mobile signals were measured with an 11-point visual analog scale. Subjective preferences of the settings were also obtained by a paired-comparison procedure. The personalized amplification application provided better speech recognition via the mobile phone both in quiet and in noise for people with hearing impairment (improved 8 to 10%) and people with normal hearing (improved 1 to 4%). The improvement in speech recognition was significantly better for people with hearing impairment. When the average device output level was matched, more participants preferred to have the individualized gain than not to have it. The personalized amplification application has the potential to improve speech recognition for people with mild-to-moderate hearing loss, as well as people with normal hearing, in particular when listening in noisy environments.

152 W average power Tm-doped fiber CPA system.

PubMed

Stutzki, Fabian; Gaida, Christian; Gebhardt, Martin; Jansen, Florian; Wienke, Andreas; Zeitner, Uwe; Fuchs, Frank; Jauregui, Cesar; Wandt, Dieter; Kracht, Dietmar; Limpert, Jens; Tünnermann, Andreas

2014-08-15

A high-power thulium (Tm)-doped fiber chirped-pulse amplification system emitting a record compressed average output power of 152 W and 4 MW peak power is demonstrated. This result is enabled by utilizing Tm-doped photonic crystal fibers with mode-field diameters of 35 μm, which mitigate detrimental nonlinearities, exhibit slope efficiencies of more than 50%, and allow for reaching a pump-power-limited average output power of 241 W. The high-compression efficiency has been achieved by using multilayer dielectric gratings with diffraction efficiencies higher than 98%.

Microtremor Measurements Over a Non-Producing Reservoir in Dhahran, Saudi Arabia

NASA Astrophysics Data System (ADS)

Popoola, A. K.; Kaka, S. I.

2011-12-01

As part of National Science, Technology and Innovation Plan of the King Abdulaziz City for Science and Technology (KACST) program, we are conducting a small-scale pilot passive seismic experiment over a non-producing reservoir to better understand and characterize the origin of various near-surface noises. In this paper, we present the results obtained so far from five stations distributed at various locations of interest over the Dammam Dome structure, which is where the first discovery of oil in Saudi Arabia is situated. One of our stations is located on a concrete foundation structure that used to house the old seismic station at KFUPM. The remaining four stations are situated within the Dammam Dome structure at KFUPM where both middle and upper Rus Formations are exposed. Continuous data was collected at all stations with a Geospace Seismic Recording system manufactured by the OYO Geospace. We systematically selected recordings at all stations at different times of the day in order to check the diurnal variations and site dependences. We analyzed time series data and performed spectral analysis at various frequency range of interest between 0.1-30 Hz. We also looked at microtremor signals between 2 to 3 Hz to see whether or not there exists the correlation between low-frequency microtremors and hydrocarbon bearing structures under the subsurface as reported by various researchers in the region. The results obtained so far show no clear signals between 2-3 Hz. We hope that our ongoing experiment will likely contribute in resolving the ongoing debate on the use of microtremor signals as a direct hydrocarbon indicator by bringing new data and experimental results. Meanwhile, strong signals were consistently observed between 23-25 Hz, specifically at stations located on open grounds. We observed microtremor signals due to site amplifications at frequency < 3Hz with periodic peaks at an average frequency of about10 Hz before the amplification disappears. We also noticed spectral spikes that have likely originated from heavy machinery working at construction sites at a distance which disappear at night.

Developing Vs30 site-condition maps by combining observations with geologic and topographic constraints

USGS Publications Warehouse

Thompson, E.M.; Wald, D.J.

2012-01-01

Despite obvious limitations as a proxy for site amplification, the use of time-averaged shear-wave velocity over the top 30 m (VS30) remains widely practiced, most notably through its use as an explanatory variable in ground motion prediction equations (and thus hazard maps and ShakeMaps, among other applications). As such, we are developing an improved strategy for producing VS30 maps given the common observational constraints. Using the abundant VS30 measurements in Taiwan, we compare alternative mapping methods that combine topographic slope, surface geology, and spatial correlation structure. The different VS30 mapping algorithms are distinguished by the way that slope and geology are combined to define a spatial model of VS30. We consider the globally applicable slope-only model as a baseline to which we compare two methods of combining both slope and geology. For both hybrid approaches, we model spatial correlation structure of the residuals using the kriging-with-a-trend technique, which brings the map into closer agreement with the observations. Cross validation indicates that we can reduce the uncertainty of the VS30 map by up to 16% relative to the slope-only approach.

Implications of the Mw9.0 Tohoku-Oki earthquake for ground motion scaling with source, path, and site parameters

USGS Publications Warehouse

Stewart, Jonathan P.; Midorikawa, Saburoh; Graves, Robert W.; Khodaverdi, Khatareh; Kishida, Tadahiro; Miura, Hiroyuki; Bozorgnia, Yousef; Campbell, Kenneth W.

2013-01-01

The Mw9.0 Tohoku-oki Japan earthquake produced approximately 2,000 ground motion recordings. We consider 1,238 three-component accelerograms corrected with component-specific low-cut filters. The recordings have rupture distances between 44 km and 1,000 km, time-averaged shear wave velocities of VS30 = 90 m/s to 1,900 m/s, and usable response spectral periods of 0.01 sec to >10 sec. The data support the notion that the increase of ground motions with magnitude saturates at large magnitudes. High-frequency ground motions demonstrate faster attenuation with distance in backarc than in forearc regions, which is only captured by one of the four considered ground motion prediction equations for subduction earthquakes. Recordings within 100 km of the fault are used to estimate event terms, which are generally positive (indicating model underprediction) at short periods and zero or negative (overprediction) at long periods. We find site amplification to scale minimally with VS30 at high frequencies, in contrast with other active tectonic regions, but to scale strongly with VS30 at low frequencies.

Earthquake site response in Santa Cruz, California

USGS Publications Warehouse

Carver, D.; Hartzell, S.H.

1996-01-01

Aftershocks of the 1989 Loma Prieta, California, earthquake are used to estimate site response in a 12-km2 area centered on downtown Santa Cruz. A total of 258 S-wave records from 36 aftershocks recorded at 33 sites are used in a linear inversion for site-response spectra. The inversion scheme takes advantage of the redundancy of the large data set for which several aftershocks are recorded at each site. The scheme decomposes the observed spectra into source, path, and site terms. The path term is specified before the inversion. The undetermined degree of freedom in the decomposition into source and site spectra is removed by specifying the site-response factor to be approximately 1.0 at two sites on crystalline bedrock. The S-wave site responses correlate well with the surficial geology and observed damage pattern of the mainshock. The site-response spectra of the floodplain sites, which include the heavily damaged downtown area, exhibit significant peaks. The largest peaks are between 1 and 4 Hz. Five floodplain sites have amplification factors of 10 or greater. Most of the floodplain site-response spectra also have a smaller secondary peak between 6 and 8 Hz. Residential areas built on marine terraces above the flood-plain experienced much less severe damage. Site-response spectra for these areas also have their largest peaks between 1 and 4 Hz, but the amplification is generally below 6. Several of these sites also have a secondary peak between 6 and 8 Hz. The response peaks seen at nearly all sites between 1 and 4 Hz are probably caused by the natural resonance of the sedimentary rock column. The higher amplifications at floodplain sites may be caused by surface waves generated at the basin margins. The secondary peak between 6 and 8 Hz at many sites may be a harmonic of the 1- to 4-Hz peaks. We used waveforms from a seven-station approximately linear array located on the floodplain to calculate the apparent velocity and azimuth of propagation of coherent arrivals within moving windows of the S-wave codas. The initial windows give results that are consistent with direct S-wave arrivals. The apparent velocities are high (greater than 4.0 km/sec), and azimuths are from the source. Waves arriving later than 2 sec after the direct S waves have apparent velocities of less than 1 km/ sec, indicating that they are surface waves, and arrive from divergent azimuths. This analysis indicates that after the direct S-wave arrival, long-duration shaking comes from surface waves that are generated at the basin margin and reverberate in the floodplain sediments.

Uniform amplification of phage display libraries in monodisperse emulsions.

PubMed

Matochko, Wadim L; Ng, Simon; Jafari, Mohammad R; Romaniuk, Joseph; Tang, Sindy K Y; Derda, Ratmir

2012-09-01

In this paper, we describe a complete experimental setup for the uniform amplification of libraries of phage. Uniform amplification, which multiplies every phage clone by the same amount irrespective of the growth rate of the clone is essential for phage-display screening. Amplification of phage libraries in a common solution is often non-uniform: it favors fast-growing clones and eliminates those that grow slower. This competition leads to elimination of many useful binding clones, and it is a major barrier to identification of ligands for targets with multiple binding sites such as cells, tissues, or mixtures of proteins. Uniform amplification is achieved by encapsulating individual phage clones into isolated compartments (droplets) of identical volume. Each droplet contains culture medium and an excess of host (Escherichia coli). Here, we describe microfluidics devices that generate mono-disperse droplet-based compartments, and optimal conditions for amplification of libraries of different size. We also describe the detailed synthesis of a perfluoro surfactant, which gives droplets exceptional stability. Droplets stabilized by this compound do not coalesce after many hours in shaking culture. We identified a commercially available compound (Krytox), which destabilizes these droplets to recover the amplified libraries. Overall, uniform amplification is a sequence of three simple steps: (1) encapsulation of mixture of phage and bacteria in droplets using microfluidics; (2) incubation of droplets in a shaking culture; (3) destabilization of droplets to harvest the amplified phage. We anticipate that this procedure can be easily adapted in any academic or industrial laboratory that uses phage display. Copyright © 2012 Elsevier Inc. All rights reserved.

Shear-wave velocity and site-amplification factors for 50 Australian sites determined by the spectral analysis of surface waves method

USGS Publications Warehouse

Kayen, Robert E.; Carkin, Bradley A.; Allen, Trevor; Collins, Clive; McPherson, Andrew; Minasian, Diane L.

2015-01-01

One-dimensional shear-wave velocity (VS ) profiles are presented at 50 strong motion sites in New South Wales and Victoria, Australia. The VS profiles are estimated with the spectral analysis of surface waves (SASW) method. The SASW method is a noninvasive method that indirectly estimates the VS at depth from variations in the Rayleigh wave phase velocity at the surface.

A simulation of Earthquake Loss Estimation in Southeastern Korea using HAZUS and the local site classification Map

NASA Astrophysics Data System (ADS)

Kang, S.; Kim, K.

2013-12-01

Regionally varying seismic hazards can be estimated using an earthquake loss estimation system (e.g. HAZUS-MH). The estimations for actual earthquakes help federal and local authorities develop rapid, effective recovery measures. Estimates for scenario earthquakes help in designing a comprehensive earthquake hazard mitigation plan. Local site characteristics influence the ground motion. Although direct measurements are desirable to construct a site-amplification map, such data are expensive and time consuming to collect. Thus we derived a site classification map of the southern Korean Peninsula using geologic and geomorphologic data, which are readily available for the entire southern Korean Peninsula. Class B sites (mainly rock) are predominant in the area, although localized areas of softer soils are found along major rivers and seashores. The site classification map is compared with independent site classification studies to confirm our site classification map effectively represents the local behavior of site amplification during an earthquake. We then estimated the losses due to a magnitude 6.7 scenario earthquake in Gyeongju, southeastern Korea, with and without the site classification map. Significant differences in loss estimates were observed. The loss without the site classification map decreased without variation with increasing epicentral distance, while the loss with the site classification map varied from region to region, due to both the epicentral distance and local site effects. The major cause of the large loss expected in Gyeongju is the short epicentral distance. Pohang Nam-Gu is located farther from the earthquake source region. Nonetheless, the loss estimates in the remote city are as large as those in Gyeongju and are attributed to the site effect of soft soil found widely in the area.

Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (suborder: Mysticeti).

PubMed

Baker, C S; Vant, M D; Dalebout, M L; Lento, G M; O'Brien, S J; Yuhki, N

2006-05-01

The molecular diversity and phylogenetic relationships of two class II genes of the baleen whale major histocompatibility complex were investigated and compared to toothed whales and out-groups. Amplification of the DQB exon 2 provided sequences showing high within-species and between-species nucleotide diversity and uninterrupted reading frames consistent with functional class II loci found in related mammals (e.g., ruminants). Cloning of amplified products indicated gene duplication in the humpback whale and triplication in the southern right whale, with average nucleotide diversity of 5.9 and 6.3%, respectively, for alleles of each species. Significantly higher nonsynonymous divergence at sites coding for peptide binding (32% for humpback and 40% for southern right) suggested that these loci were subject to positive (overdominant) selection. A population survey of humpback whales detected 23 alleles, differing by up to 21% of their inferred amino acid sequences. Amplification of the DRB exon 2 resulted in two groups of sequences. One was most similar to the DRB3 of the cow and present in all whales screened to date, including toothed whales. The second was most similar to the DRB2 of the cow and was found only in the bowhead and right whales. Both loci showed low diversity among species and apparent loss of function or altered function including interruption of reading frames. Finally, comparison of inferred protein sequence of the DRB3-like locus suggested convergence with the DQB, perhaps resulting from intergenic conversion or recombination.

Towards sub-100 fs multi-GW pulses directly emitted from a Thulium-doped fiber CPA system

NASA Astrophysics Data System (ADS)

Gaida, C.; Gebhardt, M.; Stutzki, F.; Jauregui, C.; Limpert, J.; Tünnermann, A.

2017-02-01

Experimental demonstrations of Tm-doped fiber amplifiers (typically in CW- or narrow-band pulsed operation) span a wavelength range going from about 1700 nm to well beyond 2000 nm. Thus, it should be possible to obtain a bandwidth of more than 100 nm, which would enable sub-100 fs pulse duration in an efficient, linear amplification scheme. In fact, this would allow the emission of pulses with less than 20 optical cycles directly from a Tm-doped fiber system, something that seems to be extremely challenging for other dopants in a fused silica fiber. In this contribution, we summarize the current development of our Thulium-doped fiber CPA system, demonstrate preliminary experiments for further scaling and discuss important design factors for the next steps. The current single-channel laser system presented herein delivers a pulse-peak power of 2 GW and a nearly transform-limited pulse duration of 200 fs in combination with 28.7 W of average power. Special care has been taken to reduce the detrimental impact of water vapor absorption by placing the whole system in a dry atmosphere housing (<0.1% rel. humidity) and by using a sufficiently long wavelength (1920-1980 nm). The utilization of a low-pressure chamber in the future will allow for the extension of the amplification bandwidth. Preliminary experiments demonstrating a broader amplification bandwidth that supports almost 100 fs pulse duration and average power scaling to < 100W have already been performed. Based on these results, a Tm-doped fiber CPA with sub-100 fs pulse duration, multi-GW pulse peak power and >100 W average power can be expected in the near future.

Comparison of shear-wave slowness profiles at 10 strong-motion sites from noninvasive SASW measurements and measurements made in boreholes

USGS Publications Warehouse

Brown, L.T.; Boore, D.M.; Stokoe, K.H.

2002-01-01

The spectral-analysis-of-surface-waves (SASW) method is a relatively new in situ method for determining shear-wave slownesses. All measurements are made on the ground surface, making it much less costly than methods that require boreholes. The SASW method uses a number of active sources (ranging from a commercial Vibroseis truck to a small handheld hammer for the study conducted here) and different receiver spacings to map a curve of apparent phase velocity versus frequency. With the simplifying assumption that the phase velocities correspond to fundamental mode surface waves, forward modeling yields an estimate of the sub-surface shear-wave slownesses. To establish the reliability of this indirect technique, we conducted a blind evaluation of the SASW method. SASW testing was performed at 10 strong-motion stations at which borehole seismic measurements were previously or subsequently made; if previously made, the borehole results were not used for the interpretation of the SASW data, and vice-versa. Comparisons of the shear-wave slownesses from the SASW and borehole measurements are generally very good. The differences in predicted ground-motion amplifications are less than about 15% for most frequencies. In addition, both methods gave the same NEHRP site classification for seven of the sites. For the other three sites the average velocities from the downhole measurements were only 5-13 m/sec larger than the velocity defining the class C/D boundary. This study demonstrates that in many situations the SASW method can provide subsurface information suitable for site response predictions.

Compressed 6 ps pulse in nonlinear amplification of a Q-switched microchip laser

NASA Astrophysics Data System (ADS)

Diao, Ruxin; Liu, Zuosheng; Niu, Fuzeng; Wang, Aimin; Taira, Takunori; Zhang, Zhigang

2017-02-01

We present a passively Q-switched Nd:YVO4 crystal microchip laser with a 6 ps pulse width, which is based on SPM-induced spectral broadening and pulse compression. The passive Q-switching is obtained by a semiconductor saturable absorber mirror. The laser’s seed source centered at 1064 nm pulses with a duration of 80 ps, at a repetition rate of 600 kHz corresponding to an average output power of 10 mW. After amplification and compression, the pulses were compressed to 6 ps with a maximum pulse energy of 0.5 µJ.

Method of artificial DNA splicing by directed ligation (SDL).

PubMed Central

Lebedenko, E N; Birikh, K R; Plutalov, O V; Berlin YuA

1991-01-01

An approach to directed genetic recombination in vitro has been devised, which allows for joining together, in a predetermined way, a series of DNA segments to give a precisely spliced polynucleotide sequence (DNA splicing by directed ligation, SDL). The approach makes use of amplification, by means of several polymerase chain reactions (PCR), of a chosen set of DNA segments. Primers for the amplifications contain recognition sites of the class IIS restriction endonucleases, which transform blunt ends of the amplification products into protruding ends of unique primary structures, the ends to be used for joining segments together being mutually complementary. Ligation of the mixture of the segments so synthesized gives the desired sequence in an unambiguous way. The suggested approach has been exemplified by the synthesis of a totally processed (intronless) gene encoding human mature interleukin-1 alpha. Images PMID:1662363

Zygotic amplification of secondary piRNAs during silkworm embryogenesis

PubMed Central

Kawaoka, Shinpei; Arai, Yuji; Kadota, Koji; Suzuki, Yutaka; Hara, Kahori; Sugano, Sumio; Shimizu, Kentaro; Tomari, Yukihide; Shimada, Toru; Katsuma, Susumu

2011-01-01

PIWI-interacting RNAs (piRNAs) are 23–30-nucleotide-long small RNAs that act as sequence-specific silencers of transposable elements in animal gonads. In flies, genetics and deep sequencing data have led to a hypothesis for piRNA biogenesis called the ping-pong cycle, where antisense primary piRNAs initiate an amplification loop to generate sense secondary piRNAs. However, to date, the process of the ping-pong cycle has never been monitored at work. Here, by large-scale profiling of piRNAs from silkworm ovary and embryos of different developmental stages, we demonstrate that maternally inherited antisense-biased piRNAs trigger acute amplification of secondary sense piRNA production in zygotes, at a time coinciding with zygotic transcription of sense transposon mRNAs. These results provide on-site evidence for the ping-pong cycle. PMID:21628432

Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification

PubMed Central

Cain-Hom, Carol; Splinter, Erik; van Min, Max; Simonis, Marieke; van de Heijning, Monique; Martinez, Maria; Asghari, Vida

2017-01-01

Abstract Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used targeted locus amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic lines. In all lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven lines the exact integration site and breakpoint sequences were identified. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the TLA method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events. PMID:28053125

Quinone Methide Signal Amplification: Covalent Reporter Labeling of Cancer Epitopes using Alkaline Phosphatase Substrates.

PubMed

Polaske, Nathan W; Kelly, Brian D; Ashworth-Sharpe, Julia; Bieniarz, Christopher

2016-03-16

Diagnostic assays with the sensitivity required to improve cancer therapeutics depend on the development of new signal amplification technologies. Herein, we report the development and application of a novel amplification system which utilizes latent quinone methides (QMs) activated by alkaline phosphatase (AP) for signal amplification in solid-phase immunohistochemical (IHC) assays. Phosphate-protected QM precursor substrates were prepared and conjugated to either biotin or a fluorophore through an amine-functionalized linker group. Upon reaction with AP, the phosphate group is cleaved, followed by elimination of the leaving group and formation of the highly reactive and short-lived QM. The QMs either react with tissue nucleophiles in close proximity to their site of generation, or are quenched by nucleophiles in the reaction media. The reporter molecules that covalently bind to the tissue were then detected visually by fluorescence microscopy in the case of fluorophore reporters, or brightfield microscopy using diaminobenzidine (DAB) in the case of biotin reporters. With multiple reporters deposited per enzyme, significant signal amplification was observed utilizing QM precursor substrates containing either benzyl difluoro or benzyl monofluoro leaving group functionalities. However, the benzyl monofluoro leaving group gave superior results with respect to both signal intensity and discretion, the latter of which was found to be imperative for use in diagnostic IHC assays.

Ultrasensitive electrochemical aptasensor for ochratoxin A based on two-level cascaded signal amplification strategy.

PubMed

Yang, Xingwang; Qian, Jing; Jiang, Ling; Yan, Yuting; Wang, Kan; Liu, Qian; Wang, Kun

2014-04-01

Ochratoxin A (OTA) has a number of toxic effects to both humans and animals, so developing sensitive detection method is of great importance. Herein, we describe an ultrasensitive electrochemical aptasensor for OTA based on the two-level cascaded signal amplification strategy with methylene blue (MB) as a redox indicator. In this method, capture DNA, aptamers, and reporter DNA functionalized-gold nanoparticles (GNPs) were immobilized on the electrode accordingly, where GNPs were used as the first-level signal enhancer. To receive the more sensitive response, a larger number of guanine (G)-rich DNA was bound to the GNPs' surface to provide abundant anchoring sites for MB to achieve the second-level signal amplification. By employing this novel strategy, an ~8.5 (±0.3) fold amplification in signal intensity was obtained. Afterward, OTA was added to force partial GNPs/G-rich DNA to release from the sensing interface and thus decreased the electrochemical response. An effective sensing range from 2.5pM to 2.5nM was received with an extremely low detection limit of 0.75 (±0.12) pM. This amplification strategy has the potential to be the main technology for aptamer-based electrochemical biosensor in a variety of fields. Copyright © 2013 Elsevier B.V. All rights reserved.

Spectral amplification models for response spectrum addressing the directivity effect

NASA Astrophysics Data System (ADS)

Moghimi, Saed; Akkar, Sinan

2017-04-01

Ground motions with forward directivity effects are known with their significantly large spectral ordinates in medium-to-long periods. The large spectral ordinates stem from the impulsive characteristics of the forward directivity ground motions. The quantification of these spectral amplifications requires the identification of major seismological parameters that play a role in their generation. After running a suite of probabilistic seismic hazard analysis, Moghimi and Akkar (2016) have shown that fault slip rate, fault characteristic magnitude, fault-site geometry as well as mean annual exceedance rate are important parameters that determine the level of spectral amplification due to directivity. These parameters are considered to develop two separate spectral amplification equations in this study. The proposed equations rely on Shahi and Baker (SHB11; 2011) and Chiou and Spudich (CHS13; Spudic et al., 2013) narrow-band forward directivity models. The presented equations only focus on the estimation of maximum spectral amplifications that occur at the ends of the fault segments. This way we eliminate the fault-site parameter in our equations for simplification. The proposed equations show different trends due to differences in the narrow-band directivity models of SHB11 and CHS13. The equations given in this study can form bases for describing forward directivity effects in seismic design codes. REFERENCES Shahi. S., Baker, J.W. (2011), "An Empirically Calibrated Framework for Including the Effects of Near-Fault Directivity in Probabilistic Seismic Hazard Analysis", Bulletin of the Seismological Society of America, 101(2): 742-755. Spudich, P., Watson-Lamprey, J., Somerville, P., Bayless, J., Shahi, S. K., Baker, J. W., Rowshandel, B., and Chiou, B. (2013), "Final Report of the NGA-West2 Directivity Working Group", PEER Report 2013/09. Moghimi. S., Akkar, S. (2016), "Implications of Forward Directivity Effects on Design Ground Motions", Seismological Society of America, Annual meeting, 2016, Reno, Nevada, 87:2B Pg. 464

Opposing effects of pericentrin and microcephalin on the pericentriolar material regulate CHK1 activation in the DNA damage response.

PubMed

Antonczak, A K; Mullee, L I; Wang, Y; Comartin, D; Inoue, T; Pelletier, L; Morrison, C G

2016-04-14

Genotoxic stresses lead to centrosome amplification, a frequently-observed feature in cancer that may contribute to genome instability and to tumour cell invasion. Here we have explored how the centrosome controls DNA damage responses. For most of the cell cycle, centrosomes consist of two centrioles embedded in the proteinaceous pericentriolar material (PCM). Recent data indicate that the PCM is not an amorphous assembly of proteins, but actually a highly organised scaffold around the centrioles. The large coiled-coil protein, pericentrin, participates in PCM assembly and has been implicated in the control of DNA damage responses (DDRs) through its interactions with checkpoint kinase 1 (CHK1) and microcephalin (MCPH1). CHK1 is required for DNA damage-induced centrosome amplification, whereas MCPH1 deficiency greatly increases the amplification seen after DNA damage. We found that the PCM showed a marked expansion in volume and a noticeable change in higher-order organisation after ionising radiation treatment. PCM expansion was dependent on CHK1 kinase activity and was potentiated by MCPH1 deficiency. Furthermore, pericentrin deficiency or mutation of a separase cleavage site blocked DNA damage-induced PCM expansion. The extent of nuclear CHK1 activation after DNA damage reflected the level of PCM expansion, with a reduction in pericentrin-deficient or separase cleavage site mutant-expressing cells, and an increase in MCPH1-deficient cells that was suppressed by the loss of pericentrin. Deletion of the nuclear export signal of CHK1 led to its hyperphosphorylation after irradiation and reduced centrosome amplification. Deletion of the nuclear localisation signal led to low CHK1 activation and low centrosome amplification. From these data, we propose a feedback loop from the PCM to the nuclear DDR in which CHK1 regulates pericentrin-dependent PCM expansion to control its own activation.

Site Effect and Expected Seismic Performance of Buildings in Palestine- Case Study: Nablus City

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Dabbeek, Jalal N.; El-Kelani, Radwan J.

2008-07-08

The effects of local geology on ground-motion amplification and building damage were studied in Palestine-West Bank. Nakamura's method of microtremor analysis was applied in this study. The measurements showed significantly higher amplification in the frequency range of building vulnerability in different parts of Nablus city. This finding is consistent with the distribution of the earthquake damage grades in the urban areas struck by the 11 February 2004 earthquake (ML = 5.2) with a focal depth of 17 km beneath the northeastern part of the Dead Sea Basin. Quite large differences in amplification between around 1 and 9 were computed betweenmore » the eastern and western rims of the city. The downtown built in the central part of the city on soft clay, marl and valley deposits, whereas the northern and southern parts of urban areas in Nablus city lying on mountains consist of consolidated carbonates bedrock. In the central part of the city and at the rims, where the thickness of fluvial deposits and soft formations is about 15 m, amplifications between 6.74 and 8.67 for dominant natural period range of 0.8-1.1 sec were obtained. On the southern and northern mountains, which are located on limestone rocks covered with a thin layer of soil, the amplification in the same frequency range was low. Calculating the natural period of the existing common buildings (T{sub b}) in the studied area (buildings with 10-12 stories), by using the dynamic analysis method. The values of T{sub b} obtained were much closed to the site dominant natural period (Ts). The findings of this study indicate that the expected differences in damage grades for urban areas in Nablus city could be attributed to variations in the thickness and physical properties of Tertiary-Quaternary sediments, which appear to be rather heterogeneous.« less

Site Effect and Expected Seismic Performance of Buildings in Palestine- Case Study: Nablus City

NASA Astrophysics Data System (ADS)

Al-Dabbeek, Jalal N.; El-Kelani, Radwan J.

2008-07-01

The effects of local geology on ground-motion amplification and building damage were studied in Palestine-West Bank. Nakamura's method of microtremor analysis was applied in this study. The measurements showed significantly higher amplification in the frequency range of building vulnerability in different parts of Nablus city. This finding is consistent with the distribution of the earthquake damage grades in the urban areas struck by the 11 February 2004 earthquake (ML = 5.2) with a focal depth of 17 km beneath the northeastern part of the Dead Sea Basin. Quite large differences in amplification between around 1 and 9 were computed between the eastern and western rims of the city. The downtown built in the central part of the city on soft clay, marl and valley deposits, whereas the northern and southern parts of urban areas in Nablus city lying on mountains consist of consolidated carbonates bedrock. In the central part of the city and at the rims, where the thickness of fluvial deposits and soft formations is about 15 m, amplifications between 6.74 and 8.67 for dominant natural period range of 0.8-1.1 sec were obtained. On the southern and northern mountains, which are located on limestone rocks covered with a thin layer of soil, the amplification in the same frequency range was low. Calculating the natural period of the existing common buildings (Tb) in the studied area (buildings with 10-12 stories), by using the dynamic analysis method. The values of Tb obtained were much closed to the site dominant natural period (Ts). The findings of this study indicate that the expected differences in damage grades for urban areas in Nablus city could be attributed to variations in the thickness and physical properties of Tertiary-Quaternary sediments, which appear to be rather heterogeneous.

Site-specific Microzonation Study in Delhi Metropolitan City by 2-D Modelling of SH and P-SV Waves

NASA Astrophysics Data System (ADS)

Parvez, Imtiyaz A.; Vaccari, F.; Panza, G. F.

Delhi - the capital of India lies on a severe earthquake hazard threat not only from local earthquakes but also from Himalayan events just 200-250 km apart. The seismic ground motion in a part of Delhi City is computed with a hybrid technique based on the modal summation and the finite-difference scheme for site-specific strong ground motion modelling. Complete realistic SH and #E5/E5#-SV wave seismograms are computed along two geological cross sections, (1) north-south, from Inter State Bus Terminal (ISBT) to Sewanagar and (2) east-west, from Tilak Bridge to Punjabi Bagh. Two real earthquake sources of July 15, 1720 (MMI=IX, M=7.4) and August 27, 1960 (M=6.0) have been used in modelling. The response spectra ratio (RSR), i.e. the response spectra computed from the signals synthesized along the laterally varying section and normalized by the response spectra computed from the corresponding signals, synthesized for the bedrock reference regional model, have been determined. As expected, the sedimentary cover causes an increase of the signal amplitude, particularly in the radial and transverse components. To further check the site-effects, we reversed the source location to the other side of the cross section and recomputed the site amplifications. There are only a few sites where a large amplification is invariant with respect to the two source locations considered. The RSR ranges between 5 to 10 in the frequency range from 2.8 to 3.7 Hz for the radial and transverse components of motion along the NS cross section. Along the EW cross section RSR varies between 3.5 to 7.5 in the frequency range from 3.5 to 4.1 Hz. The amplification of the vertical component is considerable at high frequency (>4 Hz.) whereas it is negligible in lower frequency range.

All-fiber high-power monolithic femtosecond laser at 1.59 µm with 63-fs pulse width

NASA Astrophysics Data System (ADS)

Hekmat, M. J.; Omoomi, M.; Gholami, A.; Yazdabadi, A. Bagheri; Abdollahi, M.; Hamidnejad, E.; Ebrahimi, A.; Normohamadi, H.

2018-01-01

In this research, by adopting an alternative novel approach to ultra-short giant pulse generation which basically originated from difficulties with traditional employed methods, an optimized Er/Yb co-doped double-clad fiber amplifier is applied to boost output average power of single-mode output pulses to a high level of 2-W at 1.59-µm central wavelength. Output pulses of approximately 63-fs pulse width at 52-MHz repetition rate are obtained in an all-fiber monolithic laser configuration. The idea of employing parabolic pulse amplification for stretching output pulses together with high-power pulse amplification using Er/Yb co-doped active fibers for compressing and boosting output average power plays crucial role in obtaining desired results. The proposed configuration enjoys massive advantages over previously reported literature which make it well-suited for high-power precision applications such as medical surgery. Detailed dynamics of pulse stretching and compressing in active fibers with different GVD parameters are numerically and experimentally investigated.

Influence of atmospheric energy transport on amplification of winter warming in the Arctic

NASA Astrophysics Data System (ADS)

Alekseev, Genrikh; Kuzmina, Svetlana; Urazgildeeva, Aleksandra; Bobylev, Leonid

2016-04-01

The study was performed on base reanalysis ERA/Interim to discover the link between amplified warming in the high Arctic and the atmospheric transport of heat and water vapor through the 70 ° N. The partitioning transports across the Atlantic and Pacific "gates" is established the link between variations of atmospheric flux through the "gates" and a larger part of the variability of the average surface air temperature, water vapor content and its trends in the winter 1980-2014. Influence of winter (December-February) atmospheric transport across the Atlantic "gate" at the 1000 hPa on variability of average for January-February surface air temperature to north 70° N is estimated correlation coefficient 0.75 and contribution to the temperature trend 40%. These results for the first time denote the leading role of increasing atmospheric transport on the amplification of winter warming in the high Arctic. The investigation is supported with RFBR project 15-05-03512.

Diagnostic performance of a novel loop-mediated isothermal amplification (LAMP) assay targeting the apicoplast genome for malaria diagnosis in a field setting in sub-Saharan Africa.

PubMed

Oriero, Eniyou C; Okebe, Joseph; Jacobs, Jan; Van Geertruyden, Jean-Pierre; Nwakanma, Davis; D'Alessandro, Umberto

2015-10-09

New diagnostic tools to detect reliably and rapidly asymptomatic and low-density malaria infections are needed as their treatment could interrupt transmission. Isothermal amplification techniques are being explored for field diagnosis of malaria. In this study, a novel molecular tool (loop-mediated isothermal amplification-LAMP) targeting the apicoplast genome of Plasmodium falciparum was evaluated for the detection of asymptomatic malaria-infected individuals in a rural setting in The Gambia. A blood was collected from 341 subjects (median age 9 years, range 1-68 years) screened for malaria. On site, a rapid diagnostic test (RDT, SD Bioline Malaria Antigen P.f) was performed, thick blood films (TBF) slides for microscopy were prepared and dry blood spots (DBS) were collected on Whatman(®) 903 Specimen collection paper. The TBF and DBS were transported to the field laboratory where microscopy and LAMP testing were performed. The latter was done on DNA extracted from the DBS using a crude (methanol/heating) extraction method. A laboratory-based PCR amplification was done on all the samples using DNA extracted with the Qiagen kit and its results were taken as reference for all the other tests. Plasmodium falciparum malaria prevalence was 37 % (127/341) as detected by LAMP, 30 % (104/341) by microscopy and 37 % (126/341) by RDT. Compared to the reference PCR method, sensitivity was 92 % for LAMP, 78 % for microscopy, and 76 % for RDT; specificity was 97 % for LAMP, 99 % for microscopy, and 88 % for RDT. Area under the receiver operating characteristic (ROC) curve in comparison with the reference standard was 0.94 for LAMP, 0.88 for microscopy and 0.81 for RDT. Turn-around time for the entire LAMP assay was approximately 3 h and 30 min for an average of 27 ± 9.5 samples collected per day, compared to a minimum of 10 samples an hour per operator by RDT and over 8 h by microscopy. The LAMP assay could produce reliable results the same day of the screening. It could detect a higher proportion of low density malaria infections than the other methods tested and may be used for large campaigns of systematic screening and treatment.

Visual Biopsy by Hydrogen Peroxide-Induced Signal Amplification.

PubMed

Zhao, Wenjie; Yang, Sheng; Yang, Jinfeng; Li, Jishan; Zheng, Jing; Qing, Zhihe; Yang, Ronghua

2016-11-01

Visual biopsy has attracted special interest by surgeons due to its simplicity and practicality; however, the limited sensitivity of the technology makes it difficult to achieve an early diagnosis. To circumvent this problem, herein, we report a visual signal amplification strategy for establishing a marker-recognizable biopsy that enables early cancer diagnosis. In our proposed approach, hydrogen peroxide (H 2 O 2 ) was selected as a potential underlying marker for its compact relationship in cancer progression. For selective recognition of H 2 O 2 in the process of visual biopsy, a benzylbenzeneboronic acid pinacol ester-decorated copolymer, namely, PMPC-Bpe, was synthesized, affording the final formation of the H 2 O 2 -responsive micelles in which amylose was trapped. The presence of H 2 O 2 activates the boronate ester recognition site and induces it releasing abundant indicator amylose, leading to signal amplification. The indicator came across the solution of KI/I 2 added to the sample, and the formative amylose-KI/I 2 complex has a distinct blue color at 574 nm for visual amplification detection. The feasibility of the proposed method is demonstrated by visualizing the H 2 O 2 content of cancer at different stages and three kinds of actual cancerous samples. As far as we know, this is the first paradigm to rationally design a signaling amplification-based molecular recognizable biopsy for visual and sensitive disease identification, which will extend new possibilities for marker-recognition and signal amplification-based biopsy in disease progressing.

The real evidence of effects from source to freefield as base for nonlinear seismology

NASA Astrophysics Data System (ADS)

Marmureanu, Gheorghe; Marmureanu, Alexandru; Ortanza Cioflan, Carmen-; -Florinela Manea, Elena

2014-05-01

Authors developed in last time the concept of "Nonlinear Seismology-The Seismology of the XXI Century". Prof. P. M. Shearer, California Univ. in last book:(i) Strong ground accelerations from large earthquakes can produce a non-linear response in shallow soils; (ii) The shaking from large earthquakes cannot be predicted by simple scaling of records from small earthquakes; (iii) This is an active area of research in strong motion and engineering seismology. Aki: Nonlinear amplification at sediments sites appears to be more pervasive than seismologists used to think. Any attempt at seismic zonation must take into account the local site condition and this nonlinear amplification (Tectonophysics, 218, 93-111, 1993). The difficulty to seismologists in demonstrating the nonlinear site effects has been due to the effect being overshadowed by the overall patterns of shock generation and propagation. In other words, the seismological detection of the nonlinear site effects requires a simultaneous understanding and splitting up (if it is possible…and if it is necessary!) the effects of earthquake source, propagation path and local geological site conditions. To see the actual influence of nonlinearity of the whole system (seismic source-path propagation-local geological structure) the authors used to study the free field response spectra which are the last in this chain and they are the ones who are taken into account in seismic design of all structures. Soils from last part of this system(source-freefield) exhibit a strong nonlinear behaviour under cyclic loading conditions and although have many common mechanical properties require the use of different models to describe behavior differences. Sands typically have low rheological properties and can be modeled with an acceptable linear elastic model and clays which frequently presents significant changes over time can be modeled by a nonlinear viscoelastic model The real evidence of site effects from source to freefield analysis was conducted by using spectral amplification factors for last strong and deep Vrancea earthquakes (March 04,1977;MW =7.5;h=94.5 km; August 30,1986;MW=7.1;h=134.5 km; May 30 1009;MW=6.0;h=90.9 km; May 31, 1990; MW=6.4 ;h=86.9 km).The amplification factors decrease with increasing the magnitudes of strong Vrancea earthquakes and these values are far of that given by Regulatory Guide 1.60 of the U. S. Atomic Energy Commission and IAEA Vienna. The concept was used for last Stress Test asked by IAEA Vienna for Romanian Cernavoda Nuclear Power Plant.. The spectral amplification factors were: SAF= 4.07 (MW =7.1); 4.74(MW=6.9) and 5.78 (MW=6.4), unction of earthquake magnitude. The analysis indicates that the effect of nonlinearity could be very important and if the analysis is made for peak accelerations, it is 48.87% smaller assuming that response of soil to earthquake with MW=6.4, it is still in elastic domain. In other 25 seismic stations here are values between 14.2% and 55.4%. The authors are coming with new quantitative real and recorded data in extra-Carpathian area with large alluvial deposits / sediments, thick Quaternary layers etc.

Effects of topographic position and geology on shaking damage to residential wood-framed structures during the 2003 San Simeon earthquake, western San Luis obispo county, California

USGS Publications Warehouse

McCrink, T.P.; Wills, C.J.; Real, C.R.; Manson, M.W.

2010-01-01

A statistical evaluation of shaking damage to wood-framed houses caused by the 2003 M6.5 San Simeon earthquake indicates that both the rate and severity of damage, independent of structure type, are significantly greater on hilltops compared to hill slopes when underlain by Cretaceous or Tertiary sedimentary rocks. This increase in damage is interpreted to be the result of topographic amplification. An increase in the damage rate is found for all structures built on Plio-Pleistocene rocks independent of topographic position, and this is interpreted to be the result of amplified shaking caused by geologic site response. Damage rate and severity to houses built on Tertiary rocks suggest that amplification due to both topographic position and geologic site response may be occurring in these rocks, but effects from other topographic parameters cannot be ruled out. For all geologic and topographic conditions, houses with raised foundations are more frequently damaged than those with slab foundations. However, the severity of damage to houses on raised foundations is only significantly greater for those on hill slopes underlain by Tertiary rocks. Structures with some damage-resistant characteristics experienced greater damage severity on hilltops, suggesting a spectral response to topographic amplification. ?? 2010, Earthquake Engineering Research Institute.

Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight.

PubMed

Bühlmann, Andreas; Pothier, Joël F; Rezzonico, Fabio; Smits, Theo H M; Andreou, Michael; Boonham, Neil; Duffy, Brion; Frey, Jürg E

2013-03-01

Several molecular methods have been developed for the detection of Erwinia amylovora, the causal agent of fire blight in pear and apple, but none are truly applicable for on-site use in the field. We developed a fast, reliable and field applicable detection method using a novel target on the E. amylovora chromosome that we identified by applying a comparative genomic pipeline. The target coding sequences (CDSs) are both uniquely specific for and all-inclusive of E. amylovora genotypes. This avoids potential false negatives that can occur with most commonly used methods based on amplification of plasmid gene targets, which can vary among strains. Loop-mediated isothermal AMPlification (LAMP) with OptiGene Genie II chemistry and instrumentation proved to be an exceptionally rapid (under 15 min) and robust method for detecting E. amylovora in orchards, as well as simple to use in the plant diagnostic laboratory. Comparative validation results using plant samples from inoculated greenhouse trials and from natural field infections (of regional and temporal diverse origin) showed that our LAMP had an equivalent or greater performance regarding sensitivity, specificity, speed and simplicity than real-time PCR (TaqMan), other LAMP assays, immunoassays and plating, demonstrating its utility for routine testing. Copyright © 2012 Elsevier B.V. All rights reserved.

RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection.

PubMed

Takahashi, Hirokazu; Ohkawachi, Masahiko; Horio, Kyohei; Kobori, Toshiro; Aki, Tsunehiro; Matsumura, Yukihiko; Nakashimada, Yutaka; Okamura, Yoshiko

2018-05-17

RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3'-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes. When padlock probes are hybridized to the target RNA molecule, they are converted to the circular form by SplintR ligase. Subsequently, RNase H creates nick sites only in the hybridized RNA sequence, and single-stranded DNA is finally synthesized from the nick site by phi29 DNA polymerase. This method could specifically detect at least 10 fmol of the target RNA molecule without reverse transcription. Moreover, this method detected GFP mRNA present in 10 ng of total RNA isolated from Escherichia coli without background DNA amplification. Therefore, this method can potentially detect almost all types of RNA molecules without reverse transcription and reveal full-length sequence information.

Dynamo-driven plasmoid formation from a current-sheet instability

DOE PAGES

Ebrahimi, F.

2016-12-15

Axisymmetric current-carrying plasmoids are formed in the presence of nonaxisymmetric fluctuations during nonlinear three-dimensional resistive MHD simulations in a global toroidal geometry. In this study, we utilize the helicity injection technique to form an initial poloidal flux in the presence of a toroidal guide field. As helicity is injected, two types of current sheets are formed from the oppositely directed field lines in the injector region (primary reconnecting current sheet), and the poloidal flux compression near the plasma edge (edge current sheet). We first find that nonaxisymmetric fluctuations arising from the current-sheet instability isolated near the plasma edge have tearingmore » parity but can nevertheless grow fast (on the poloidal Alfven time scale). These modes saturate by breaking up the current sheet. Second, for the first time, a dynamo poloidal flux amplification is observed at the reconnection site (in the region of the oppositely directed magnetic field). This fluctuation-induced flux amplification increases the local Lundquist number, which then triggers a plasmoid instability and breaks the primary current sheet at the reconnection site. Finally, the plasmoids formation driven by large-scale flux amplification, i.e., a large-scale dynamo, observed here has strong implications for astrophysical reconnection as well as fast reconnection events in laboratory plasmas.« less

Is it time to move to nucleic acid amplification tests screening for pharyngeal and rectal gonorrhoea in men who have sex with men to improve gonorrhoea control?

PubMed

Fairley, Christopher K; Chen, Marcus Y; Bradshaw, Catriona S; Tabrizi, Sepehr N

2011-03-01

The use of nucleic acid amplification tests (NAAT), as well as or in preference to culture for non-genital sites is now recommended both in Australia and overseas because of their greater sensitivity and improved specificity. A survey of 22 Australian sexual health clinics who each year test over 14500 men who have sex with men (MSM) show that culture remains the predominate method for detecting gonorrhoea at pharyngeal (64%) and rectal (73%) sites. This editorial discusses the potential disadvantages of using culture over NAAT in relation to optimal gonorrhoea control among MSM and advocates that significantly improved control would be achieved by moving to NAAT with the proviso that culture samples are taken wherever possible on NAAT-positive samples and from clients with urethritis to ensure continued surveillance for antimicrobial resistance.

Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP).

PubMed

Peraza-Echeverria, S; Herrera-Valencia, V A.; Kay, A -J.

2001-07-01

The extent of DNA methylation polymorphisms was evaluated in micropropagated banana (Musa AAA cv. 'Grand Naine') derived from either the vegetative apex of the sucker or the floral apex of the male inflorescence using the methylation-sensitive amplification polymorphism (MSAP) technique. In all, 465 fragments, each representing a recognition site cleaved by either or both of the isoschizomers were amplified using eight combinations of primers. A total of 107 sites (23%) were found to be methylated at cytosine in the genome of micropropagated banana plants. In plants micropropagated from the male inflorescence explant 14 (3%) DNA methylation events were polymorphic, while plants micropropagated from the sucker explant produced 8 (1.7%) polymorphisms. No DNA methylation polymorphisms were detected in conventionally propagated banana plants. These results demonstrated the usefulness of MSAP to detect DNA methylation events in micropropagated banana plants and indicate that DNA methylation polymorphisms are associated with micropropagation.

ASC filament formation serves as a signal amplification mechanism for inflammasomes

PubMed Central

Dick, Mathias S.; Sborgi, Lorenzo; Rühl, Sebastian; Hiller, Sebastian; Broz, Petr

2016-01-01

A hallmark of inflammasome activation is the ASC speck, a micrometre-sized structure formed by the inflammasome adaptor protein ASC (apoptosis-associated speck-like protein containing a CARD), which consists of a pyrin domain (PYD) and a caspase recruitment domain (CARD). Here we show that assembly of the ASC speck involves oligomerization of ASCPYD into filaments and cross-linking of these filaments by ASCCARD. ASC mutants with a non-functional CARD only assemble filaments but not specks, and moreover disrupt endogenous specks in primary macrophages. Systematic site-directed mutagenesis of ASCPYD is used to identify oligomerization-deficient ASC mutants and demonstrate that ASC speck formation is required for efficient processing of IL-1β, but dispensable for gasdermin-D cleavage and pyroptosis induction. Our results suggest that the oligomerization of ASC creates a multitude of potential caspase-1 activation sites, thus serving as a signal amplification mechanism for inflammasome-mediated cytokine production. PMID:27329339

A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification.

PubMed

Park, Jung Hun; Jang, Hyowon; Jung, Yun Kyung; Jung, Ye Lim; Shin, Inkyung; Cho, Dae-Yeon; Park, Hyun Gyu

2017-05-15

We herein describe a new mass spectrometry-based method for multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification (SDA) reaction. In this method, allele-specific ligation is first performed to discriminate base sequence variations at the SNP site within the PCR-amplified target DNA. The primary ligation probe is extended by a universal primer annealing site while the secondary ligation probe has base sequences as an overhang with a nicking enzyme recognition site and complementary mass marker sequence. The ligation probe pairs are ligated by DNA ligase only at specific allele in the target DNA and the resulting ligated product serves as a template to promote the SDA reaction using a universal primer. This process isothermally amplifies short DNA fragments, called mass markers, to be analyzed by mass spectrometry. By varying the sizes of the mass markers, we successfully demonstrated the multiplex SNP genotyping capability of this method by reliably identifying several BRCA mutations in a multiplex manner with mass spectrometry. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of three methods of DNA extraction from peripheral blood mononuclear cells and lung fragments of equines.

PubMed

Santos, E M; Paula, J F R; Motta, P M C; Heinemann, M B; Leite, R C; Haddad, J P A; Del Puerto, H L; Reis, J K P

2010-08-17

We compared three different protocols for DNA extraction from horse peripheral blood mononuclear cells (PBMC) and lung fragments, determining average final DNA concentration, purity, percentage of PCR amplification using beta-actin, and cost. Thirty-four samples from PBMC, and 33 samples from lung fragments were submitted to DNA extraction by three different protocols. Protocol A consisted of a phenol-chloroform and isoamylic alcohol extraction, Protocol B used alkaline extraction with NaOH, and Protocol C used the DNAzol((R)) reagent kit. Protocol A was the best option for DNA extraction from lung fragments, producing high DNA concentrations, with high sensitivity in PCR amplification (100%), followed by Protocols C and B. On the other hand, for PBMC samples, Protocol B gave the highest sensitivity in PCR amplification (100%), followed by Protocols C and A. We conclude that Protocol A should be used for PCR diagnosis from lung fragment samples, while Protocol B should be used for PBMC.

Dynamical amplification of Arctic and global warming

NASA Astrophysics Data System (ADS)

Alekseev, Genrikh; Ivanov, Nikolai; Kharlanenkova, Natalia; Kuzmina, Svetlana; Bobylev, Leonid; Gnatiuk, Natalia; Urazgildeeva, Aleksandra

2015-04-01

The Arctic is coupled with global climate system by the atmosphere and ocean circulation that provides a major contribution to the Arctic energy budget. Therefore increase of meridional heat transport under global warming can impact on its Arctic amplification. Contribution of heat transport to the recent warming in the Arctic, Northern Hemisphere and the globe are estimated on base of reanalysis data, global climate model data and proposed special index. It is shown that significant part of linear trend during last four decades in average surface air temperature in these areas can be attributed to dynamical amplification. This attribution keeps until 400 mb height with progressive decreasing. The Arctic warming is amplified also due to an increase of humidity and cloudiness in the Arctic atmosphere that follow meridional transport gain. From October to January the Arctic warming trends are amplified as a result of ice edge retreat from the Siberian and Alaska coast and the heating of expanded volume of sea water. This investigation is supported with RFBR project 15-05-03512.

Amplification of terahertz pulses in gases beyond thermodynamic equilibrium

NASA Astrophysics Data System (ADS)

Schwaab, G. W.; Schroeck, K.; Havenith, M.

2007-03-01

In Ebbinghaus [Plasma Sources Sci. Technol. 15, 72 (2006)] we reported terahertz time-domain spectroscopy in a plasma at low pressure, we observed a simultaneous absorption and amplification process within each single rotational transition. Here we show that this observation is a direct consequence of the short interaction time of the pulsed terahertz radiation with the plasma, which is shorter than the average collision time between the molecules. Thus, during the measurement time the molecular states may be considered entangled. Solution of the time-dependent Schrödinger equation yields a linear term that may be neglected for long observation times, large frequencies, or nonentangled states. We determine the restrictions for the observation of this effect and calculate the spectrum of a simple diatomic molecule. Using this model we are able to explain the spectral features showing a change from emission to absorption as observed previously. In addition we find that the amplification and absorption do not follow the typical Lambert-Beer exponential law but an approximate square law.

Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq.

PubMed

Faherty, Sheena L; Campbell, C Ryan; Larsen, Peter A; Yoder, Anne D

2015-07-30

RNA-Seq has enabled high-throughput gene expression profiling to provide insight into the functional link between genotype and phenotype. Low quantities of starting RNA can be a severe hindrance for studies that aim to utilize RNA-Seq. To mitigate this bottleneck, whole transcriptome amplification (WTA) technologies have been developed to generate sufficient sequencing targets from minute amounts of RNA. Successful WTA requires accurate replication of transcript abundance without the loss or distortion of specific mRNAs. Here, we test the efficacy of NuGEN's Ovation RNA-Seq V2 system, which uses linear isothermal amplification with a unique chimeric primer for amplification, using white adipose tissue from standard laboratory rats (Rattus norvegicus). Our goal was to investigate potential biological artifacts introduced through WTA approaches by establishing comparisons between matched raw and amplified RNA libraries derived from biological replicates. We found that 93% of expressed genes were identical between all unamplified versus matched amplified comparisons, also finding that gene density is similar across all comparisons. Our sequencing experiment and downstream bioinformatic analyses using the Tuxedo analysis pipeline resulted in the assembly of 25,543 high-quality transcripts. Libraries constructed from raw RNA and WTA samples averaged 15,298 and 15,253 expressed genes, respectively. Although significant differentially expressed genes (P < 0.05) were identified in all matched samples, each of these represents less than 0.15% of all shared genes for each comparison. Transcriptome amplification is efficient at maintaining relative transcript frequencies with no significant bias when using this NuGEN linear isothermal amplification kit under ideal laboratory conditions as presented in this study. This methodology has broad applications, from clinical and diagnostic, to field-based studies when sample acquisition, or sample preservation, methods prove challenging.

Vertical structure of recent Arctic warming.

PubMed

Graversen, Rune G; Mauritsen, Thorsten; Tjernström, Michael; Källén, Erland; Svensson, Gunilla

2008-01-03

Near-surface warming in the Arctic has been almost twice as large as the global average over recent decades-a phenomenon that is known as the 'Arctic amplification'. The underlying causes of this temperature amplification remain uncertain. The reduction in snow and ice cover that has occurred over recent decades may have played a role. Climate model experiments indicate that when global temperature rises, Arctic snow and ice cover retreats, causing excessive polar warming. Reduction of the snow and ice cover causes albedo changes, and increased refreezing of sea ice during the cold season and decreases in sea-ice thickness both increase heat flux from the ocean to the atmosphere. Changes in oceanic and atmospheric circulation, as well as cloud cover, have also been proposed to cause Arctic temperature amplification. Here we examine the vertical structure of temperature change in the Arctic during the late twentieth century using reanalysis data. We find evidence for temperature amplification well above the surface. Snow and ice feedbacks cannot be the main cause of the warming aloft during the greater part of the year, because these feedbacks are expected to primarily affect temperatures in the lowermost part of the atmosphere, resulting in a pattern of warming that we only observe in spring. A significant proportion of the observed temperature amplification must therefore be explained by mechanisms that induce warming above the lowermost part of the atmosphere. We regress the Arctic temperature field on the atmospheric energy transport into the Arctic and find that, in the summer half-year, a significant proportion of the vertical structure of warming can be explained by changes in this variable. We conclude that changes in atmospheric heat transport may be an important cause of the recent Arctic temperature amplification.

Voice amplification as a means of reducing vocal load for elementary music teachers.

PubMed

Morrow, Sharon L; Connor, Nadine P

2011-07-01

Music teachers are over four times more likely than classroom teachers to develop voice disorders and greater than eight times more likely to have voice-related problems than the general public. Research has shown that individual voice-use parameters of phonation time, fundamental frequency and vocal intensity, as well as vocal load as calculated by cycle dose and distance dose are significantly higher for music teachers than their classroom teacher counterparts. Finding effective and inexpensive prophylactic measures to decrease vocal load for music teachers is an important aspect for voice preservation for this group of professional voice users. The purpose of this study was to determine the effects of voice amplification on vocal intensity and vocal load in the workplace as measured using a KayPENTAX Ambulatory Phonation Monitor (APM) (KayPENTAX, Lincoln Park, NJ). Seven music teachers were monitored for 1 workweek using an APM to determine average vocal intensity (dB sound pressure level [SPL]) and vocal load as calculated by cycle dose and distance dose. Participants were monitored a second week while using a voice amplification unit (Asyst ChatterVox; Asyst Communications Company, Inc., Indian Creek, IL). Significant decreases in mean vocal intensity of 7.00-dB SPL (P<0.001) were found using amplification, along with significant decreases (P=0.001) in cycle dose and distance dose. In addition, mean phonation time was found to decrease using amplification (P=0.023). These data suggest that voice amplification may be an effective intervention to decrease the potentially damaging vocal loads experienced by elementary music teachers in the classroom. Copyright © 2011 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Apparatus and method for enabling quantum-defect-limited conversion efficiency in cladding-pumped Raman fiber lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heebner, John E.; Sridharan, Arun K.; Dawson, Jay Walter

Cladding-pumped Raman fiber lasers and amplifiers provide high-efficiency conversion efficiency at high brightness enhancement. Differential loss is applied to both single-pass configurations appropriate for pulsed amplification and laser oscillator configurations applied to high average power cw source generation.

Effects of plasma flows on particle diffusion in stochastic magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlad, M.; Spineanu, F.; Misguich, J.H.

1996-07-01

The study of collisional test particle diffusion in stochastic magnetic fields is extended to include the effects of the macroscopic flows of the plasma (drifts). We show that a substantial amplification of the diffusion coefficient can be obtained. This effect is produced by the combined action of the parallel collisional velocity and of the average drifts. The perpendicular collisional velocity influences the effective diffusion only in the limit of small average drifts. {copyright} {ital 1996 The American Physical Society.}

Development of Local Amplification Factors in the NEAM Region for Production of Regional Tsunami Hazard Maps

NASA Astrophysics Data System (ADS)

Harbitz, C. B.; Glimsdal, S.; Løvholt, F.; Orefice, S.; Romano, F.; Brizuela, B.; Lorito, S.; Hoechner, A.; Babeyko, A. Y.

2016-12-01

The standard way of estimating tsunami inundation is by applying numerical depth-averaged shallow-water run-up models. However, for a regional Probabilistic Tsunami Hazard Assessment (PTHA), applying such inundation models may be too time-consuming. A faster, yet less accurate procedure, is to relate the near-shore surface elevations at offshore points to maximum shoreline water levels by using a set of amplification factors based on the characteristics of the incident wave and the bathymetric slope. The surface elevation at the shoreline then acts as a rough approximation for the maximum inundation height or run-up height along the shoreline. An amplification-factor procedure based on a limited set of idealized broken shoreline segments has previously been applied to estimate the maximum inundation heights globally. Here, we present a study where this technique is developed further, by taking into account the local bathymetric profiles. We extract a large number of local bathymetric transects over a significant part of the North East Atlantic, the Mediterranean and connected seas (NEAM) region. For each bathymetric transect, we compute the wave amplification from an offshore control point to points close to the shoreline using a linear shallow-water model for waves of different period and polarity with a sinusoidal pulse wave as input. The amplification factors are then tabulated. We present maximum water levels from the amplification factor method, and compare these with results from conventional inundation models. Finally, we demonstrate how the amplification factor method can be convolved with PTHA results to provide regional tsunami hazard maps. This work has been supported by the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement 603839 (Project ASTARTE), and the TSUMAPS-NEAM Project (http://www.tsumapsneam.eu/), co-financed by the European Union Civil Protection Mechanism, Agreement Number: ECHO/SUB/2015/718568/PREV26.

Development of Local Amplification Factors in the NEAM Region for Production of Regional Tsunami Hazard Maps

NASA Astrophysics Data System (ADS)

Glimsdal, Sylfest; Løvholt, Finn; Bonnevie Harbitz, Carl; Orefice, Simone; Romano, Fabrizio; Brizuela, Beatriz; Lorito, Stefano; Hoechner, Andreas; Babeyko, Andrey

2017-04-01

The standard way of estimating tsunami inundation is by applying numerical depth-averaged shallow-water run-up models. However, for a regional Probabilistic Tsunami Hazard Assessment (PTHA), applying such inundation models may be too time-consuming. A faster, yet less accurate procedure, is to relate the near-shore surface elevations at offshore points to maximum shoreline water levels by using a set of amplification factors based on the characteristics of the incident wave and the bathymetric slope. The surface elevation at the shoreline then acts as a rough approximation for the maximum inundation height or run-up height along the shoreline. An amplification-factor procedure based on a limited set of idealized broken shoreline segments has previously been applied to estimate the maximum inundation heights globally. Here, we present a study where this technique is developed further, by taking into account the local bathymetric profiles. We extract a large number of local bathymetric transects over a significant part of the North East Atlantic, the Mediterranean and connected seas (NEAM region). For each bathymetric transect, we compute the wave amplification from an offshore control point to points close to the shoreline using a linear shallow-water model for waves of different period and polarity with a sinusoidal pulse wave as input. The amplification factors are then tabulated. We present maximum water levels from the amplification factor method, and compare these with results from conventional inundation models. Finally, we demonstrate how the amplification factor method can be convolved with PTHA results to provide regional tsunami hazard maps. This work has been supported by the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement 603839 (Project ASTARTE), and the TSUMAPS-NEAM Project (http://www.tsumapsneam.eu/), co-financed by the European Union Civil Protection Mechanism, Agreement Number: ECHO/SUB/2015/718568/PREV26.

Pre-chirp managed nonlinear amplification in fibers delivering 100  W, 60  fs pulses.

PubMed

Liu, Wei; Schimpf, Damian N; Eidam, Tino; Limpert, Jens; Tünnermann, Andreas; Kärtner, Franz X; Chang, Guoqing

2015-01-15

We demonstrate a pre-chirp managed Yb-doped fiber laser system that outputs 75 MHz, 130 W spectrally broadened pulses, which are compressed by a diffraction-grating pair to 60 fs with average powers as high as 100 W. Fine tuning the pulse chirp prior to amplification leads to high-quality compressed pulses. Detailed experiments and numerical simulation reveal that the optimum pre-chirp group-delay dispersion increases from negative to positive with increasing output power for rod-type high-power fiber amplifiers. The resulting laser parameters are suitable for extreme nonlinear optics applications such as frequency conversion in femtosecond enhancement cavities.

Impact of pumping configuration on all-fibered femtosecond chirped pulse amplification

NASA Astrophysics Data System (ADS)

Lecourt, Jean-Bernard; Duterte, Charles; Bertrand, Anthony; Liégeois, Flavien; Hernandez, Yves; Giannone, Domenico

2008-04-01

We experimentally compared the co- and counter-propagative pumping scheme for the amplification of ultra-short optical pulses. According to pumping direction we show that optical pulses with a duration of 75 fs and 100mW of average output power can be obtained for co-propagative pumping, while pulse duration is never shorter than 400 fs for the counter-propagative case. We show that the impact of non-linear effects on pulse propagation is different for the two pumping configurations. We assume that Self Phase Modulation (SPM) is the main effect in the copropagative case, whereas the impact of Stimulated Raman Scattering is bigger for the counter-propagative case.

DNA barcoding Indian freshwater fishes.

PubMed

Lakra, Wazir Singh; Singh, M; Goswami, Mukunda; Gopalakrishnan, A; Lal, K K; Mohindra, V; Sarkar, U K; Punia, P P; Singh, K V; Bhatt, J P; Ayyappan, S

2016-11-01

DNA barcoding is a promising technique for species identification using a short mitochondrial DNA sequence of cytochrome c oxidase I (COI) gene. In the present study, DNA barcodes were generated from 72 species of freshwater fish covering the Orders Cypriniformes, Siluriformes, Perciformes, Synbranchiformes, and Osteoglossiformes representing 50 genera and 19 families. All the samples were collected from diverse sites except the species endemic to a particular location. Species were represented by multiple specimens in the great majority of the barcoded species. A total of 284 COI sequences were generated. After amplification and sequencing of 700 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.40%, 9.60%, 13.10%, and 17.16%, respectively. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.

Liquefaction-induced lateral spreading in Oceano, California, during the 2003 San Simeon Earthquake

USGS Publications Warehouse

Holzer, Thomas L.; Noce, Thomas E.; Bennett, Michael J.; Di Alessandro, Carola; Boatwright, John; Tinsley, John C.; Sell, Russell W.; Rosenberg, Lewis I.

2004-01-01

The December 22, 2003, San Simeon, California, (M6.5) earthquake caused damage to houses, road surfaces, and underground utilities in Oceano, California. The community of Oceano is approximately 50 miles (80 km) from the earthquake epicenter. Damage at this distance from a M6.5 earthquake is unusual. To understand the causes of this damage, the U.S. Geological Survey conducted extensive subsurface exploration and monitoring of aftershocks in the months after the earthquake. The investigation included 37 seismic cone penetration tests, 5 soil borings, and aftershock monitoring from January 28 to March 7, 2004. The USGS investigation identified two earthquake hazards in Oceano that explain the San Simeon earthquake damage?site amplification and liquefaction. Site amplification is a phenomenon observed in many earthquakes where the strength of the shaking increases abnormally in areas where the seismic-wave velocity of shallow geologic layers is low. As a result, earthquake shaking is felt more strongly than in surrounding areas without similar geologic conditions. Site amplification in Oceano is indicated by the physical properties of the geologic layers beneath Oceano and was confirmed by monitoring aftershocks. Liquefaction, which is also commonly observed during earthquakes, is a phenomenon where saturated sands lose their strength during an earthquake and become fluid-like and mobile. As a result, the ground may undergo large permanent displacements that can damage underground utilities and well-built surface structures. The type of displacement of major concern associated with liquefaction is lateral spreading because it involves displacement of large blocks of ground down gentle slopes or towards stream channels. The USGS investigation indicates that the shallow geologic units beneath Oceano are very susceptible to liquefaction. They include young sand dunes and clean sandy artificial fill that was used to bury and convert marshes into developable lots. Most of the 2003 damage was caused by lateral spreading in two separate areas, one near Norswing Drive and the other near Juanita Avenue. The areas coincided with areas with the highest liquefaction potential found in Oceano. Areas with site amplification conditions similar to those in Oceano are particularly vulnerable to earthquakes. Site amplification may cause shaking from distant earthquakes, which normally would not cause damage, to increase locally to damaging levels. The vulnerability in Oceano is compounded by the widespread distribution of highly liquefiable soils that will reliquefy when ground shaking is amplified as it was during the San Simeon earthquake. The experience in Oceano can be expected to repeat because the region has many active faults capable of generating large earthquakes. In addition, liquefaction and lateral spreading will be more extensive for moderate-size earthquakes that are closer to Oceano than was the 2003 San Simeon earthquake. Site amplification and liquefaction can be mitigated. Shaking is typically mitigated in California by adopting and enforcing up-to-date building codes. Although not a guarantee of safety, application of these codes ensures that the best practice is used in construction. Building codes, however, do not always require the upgrading of older structures to new code requirements. Consequently, many older structures may not be as resistant to earthquake shaking as new ones. For older structures, retrofitting is required to bring them up to code. Seismic provisions in codes also generally do not apply to nonstructural elements such as drywall, heating systems, and shelving. Frequently, nonstructural damage dominates the earthquake loss. Mitigation of potential liquefaction in Oceano presently is voluntary for existing buildings, but required by San Luis Obispo County for new construction. Multiple mitigation procedures are available to individual property owners. These procedures typically involve either

Strong ground motion in Port-au-Prince, Haiti, during the M7.0 12 January 2010 Haiti earthquake

USGS Publications Warehouse

Hough, Susan E; Given, Doug; Taniguchi, Tomoyo; Altidor, J.R.; Anglade, Dieuseul; Mildor, S-L.

2011-01-01

No strong motion records are available for the 12 January 2010 M7.0 Haiti earthquake. We use aftershock recordings as well as detailed considerations of damage to estimate the severity and distribution of mainshock shaking in Port-au-Prince. Relative to ground motions at a hard - rock reference site, peak accelerations are amplified by a factor of approximately 2 at sites on low-lying deposits in central Port-au-Prince and by a factor of 2.5 - 3.5 on a steep foothill ridge in the southern Port-au-Prince metropolitan region. The observed amplification along the ridge cannot be explained by sediment - induced amplification , but is consistent with predicted topographic amplification by a steep, narrow ridge. Although damage was largely a consequence of poor construction , the damage pattern inferred from analysis of remote sensing imagery provides evidence for a correspondence between small-scale (0.1 - 1.0 km) topographic relief and high damage. Mainshock shaking intensity can be estimated crudely from a consideration of macroseismic effects . We further present detailed, quantitative analysis of the marks left on a tile floor by an industrial battery rack displaced during the mainshock, at the location where we observed the highest weak motion amplifications. Results of this analysis indicate that mainshock shaking was significantly higher at this location (~0.5 g , MMI VIII) relative to the shaking in parts of Port-au-Prince that experienced light damage. Our results further illustrate how observations of rigid body horizontal displacement during earthquakes can be used to estimate peak ground accelerations in the absence of instrumental data .

Spectroscopic analysis of a novel Nd3+-activated barium borate glass for broadband laser amplification

NASA Astrophysics Data System (ADS)

Vázquez, G. V.; Muñoz H., G.; Camarillo, I.; Falcony, C.; Caldiño, U.; Lira, A.

2015-08-01

Spectroscopic parameters of a novel Nd3+-activated barium borate (BBONd) glass have been analyzed for broadband laser amplification. The Judd-Ofelt (JO) intensity parameters were determined through a systematic analysis of the absorption spectrum of Nd3+ ions in the BBONd glass. High values of the JO intensity parameters reveal a great centro-symmetrical loss of the Nd3+ sites and high covalency degree of the ligand field. The very high Ω6 intensity parameter value makes evident both a great structural distortion of the Nd3+ sites and a strong electron-phonon coupling between Nd3+ and free OH- ions, which is consistent with the phonon energy maximum (3442.1 cm-1) recorded by Raman spectroscopy. This strong electron-phonon coupling favors high effective bandwidth and gain bandwidth values of the laser emission (4F3/2 → 4I11/2) of Nd3+ ions. The electric-dipole oscillator strengths of all the Nd3+ absorption transitions, and in particular that of the hypersensitive transition (4I9/2 → 4G5/2), are enhanced by this great structural distortion of the host. Broadband laser amplification of the 4F3/2 → 4I11/2 emission (1062 nm) of Nd3+ ions in the BBONd glass pumped at 805 nm (4I9/2 → 4F5/2 + 2H9/2) is evaluated through the main fluorescent parameters in competition with non-radiative processes. In general, the BBONd glass exhibits spectroscopic parameters comparable with those reported in the literature for broadband laser amplification into the IR region.

Excision Repair-Initiated Enzyme-Assisted Bicyclic Cascade Signal Amplification for Ultrasensitive Detection of Uracil-DNA Glycosylase.

PubMed

Wang, Li-Juan; Ren, Ming; Zhang, Qianyi; Tang, Bo; Zhang, Chun-Yang

2017-04-18

Uracil-DNA glycosylase (UDG) is an important base excision repair (BER) enzyme responsible for the repair of uracil-induced DNA lesion and the maintenance of genomic integrity, while the aberrant expression of UDG is associated with a variety of cancers. Thus, the accurate detection of UDG activity is essential to biomedical research and clinical diagnosis. Here, we develop a fluorescent method for ultrasensitive detection of UDG activity using excision repair-initiated enzyme-assisted bicyclic cascade signal amplification. This assay involves (1) UDG-actuated uracil-excision repair, (2) excision repair-initiated nicking enzyme-mediated isothermal exponential amplification, (3) ribonuclease H (RNase H)-induced hydrolysis of signal probes for generating fluorescence signal. The presence of UDG enables the removal of uracil from U·A pairs and generates an apurinic/apyrimidinic (AP) site. Endonuclease IV (Endo IV) subsequently cleaves the AP site, resulting in the break of DNA substrate. The cleaved DNA substrate functions as both a primer and a template to initiate isothermal exponential amplification, producing a large number of triggers. The resultant trigger may selectively hybridize with the signal probe which is modified with FAM and BHQ1, forming a RNA-DNA heterogeneous duplex. The subsequent hydrolysis of RNA-DNA duplex by RNase H leads to the generation of fluorescence signal. This assay exhibits ultrahigh sensitivity with a detection limit of 0.0001 U/mL, and it can even measure UDG activity at the single-cell level. Moreover, this method can be applied for the measurement of kinetic parameters and the screening of inhibitors, thereby providing a powerful tool for DNA repair enzyme-related biomedical research and clinical diagnosis.

Determination of EGFR mutations in single cells microdissected from enriched lung tumor cells in peripheral blood.

PubMed

Ran, Ran; Li, Longyun; Wang, Mengzhao; Wang, Shulan; Zheng, Zhi; Lin, Peter Ping

2013-09-01

A minimally invasive and repeatable approach for real-time epidermal growth factor receptor (EGFR) mutation surveillance would be highly beneficial for individualized therapy of late stage lung cancer patients whose surgical specimens are often not available. We aim to develop a viable method to detect EGFR mutations in single circulating tumor cells (CTCs). Using a model CTC system of spiked tumor cells in whole blood, we evaluated EGFR mutation determination in single tumor cells enriched from blood. We used magnetic beads labeled with antibody against leukocyte surface antigens to deplete leukocytes and enrich native CTCs independent of epithelial marker expression level. We then used laser cell microdissection (LCM) to isolate individual CTCs, followed by whole-genome amplification of the DNA for exon 19 microdeletion, L858R and T790M mutation detection by PCR sequencing. EGFR mutations were successfully measured in individual spiked tumor cells enriched from 7.5 ml whole blood. Whole-genome amplification provided sufficient DNA for mutation determination at multiple sites. Ninety-five percent of the single CTCs microdissected by LCM (19/20) yielded PCR amplicons for at least one of the three mutation sites. The amplification success rates were 55 % (11/20) for exon 19 deletion, 45 % (9/20) for T790M, and 85 % (17/20) for L858R. Sequencing of the amplicons showed allele dropout in the amplification reactions, but mutations were correctly identified in 80 % of the amplicons. EGFR mutation determination from single captured tumor cells from blood is feasible with the approach described here. However, to overcome allele dropout and to obtain reliable information about the tumor's EGFR status, multiple individual tumor cells should be assayed.

High amplification of FGFR1 gene is a delayed poor prognostic factor in early stage ESCC patients

PubMed Central

Song, Qi; Liu, Yalan; Jiang, Dongxian; Wang, Haixing; Huang, Jie; Xu, Yifan; Sujie, Akesu; Zeng, Haiying; Xu, Chen; Hou, Yingyong

2017-01-01

Amplification of the fibroblast growth factor receptor 1 (FGFR1) is believed to predict response to FGFR inhibitors. The aim of this study was to investigate the frequency and the prognostic impact of FGFR1 amplification in patients with resected esophageal squamous cell carcinoma (ESCC) by using fluorescent in situ hybridization. Microarrayed paraffin embedded blocks were constructed, and the cohort of tissues came from 506 patients with ESCC. FGFR1 high amplification (FGFR1high) was defined by an FGFR1/centromere 8 ratio of ≥ 2.0, or average number of FGFR1 signals/tumor cell nucleus ≥ 6.0, or percentage of tumor cells containing ≥ 15 FGFR1 signals, or large cluster in ≥ 10% of cancer cells. FGFR1 low amplification was defined by ≥ 5 FGFR1 signals in ≥ 50% of cancer cells. Kaplan-Meier curves with log-rank tests and Cox proportional hazards model were used to analyze patients’ survival. Among 506 patients, high amplification, low amplification, and disomy were detected in 8.7%, 3.6% and 87.7%, respectively. In general, the FGFR1high group trended towards worse disease-free survival (DFS) and overall survival (OS) compared to the FGFR1 low amplification/disomy (FGFR1low/disomy) group (DFS, P=0.108; OS, P=0.112), but this trend was amplified for patients with DFS ≥ 30 months (DFS, P=0.009; OS, P=0.007). Furthermore, when patients were stratified into stage I-II and stage III-IV, the FGFR1high group directly presented with adverse DFS and OS than the FGFR1low/disomy group in stage I-II patients (DFS, P=0.019; OS, P=0.034), especially with DFS ≥ 30 months (DFS, P=0.002; OS, P=0.001). However, for patients in stage III-IV, FGFR1high had no effect on prognosis regardless of DFS time. FGFR1high occurs in a minority of ESCC, and it predicts delayed poor prognosis in stage I and II ESCC patients. PMID:29088806

Clinical significance of MYCN amplification in patients with high-risk neuroblastoma.

PubMed

Lee, Ji Won; Son, Meong Hi; Cho, Hee Won; Ma, Young Eun; Yoo, Keon Hee; Sung, Ki Woong; Koo, Hong Hoe

2018-05-24

This study investigated the clinical significance of MYCN amplification within high-risk neuroblastoma (NB). Medical records of 135 patients who were diagnosed with high-risk NB from 2004 to 2016 were reviewed. Fifty-one (38%) patients had MYCN amplified tumors, and the remaining 84 (62%) had nonamplified tumors. MYCN amplification was associated with abdominal primary site, less differentiated pathology, higher levels of lactate dehydrogenase and neuron-specific enolase (NSE), lower vanillylmandelic acid level, and larger primary tumor volume at diagnosis. MYCN amplification was associated with a better early response (faster reduction of primary tumor volume and NSE level). The proportion of patients in complete response or very good partial response after induction treatment was relatively higher in MYCN amplified tumors than in nonamplified tumors; however, all progressions during induction treatment occurred only in MYCN amplified tumors (P = 0.007). The time to progression was shorter (median 1.5 years vs. 1.9 years, P = 0.037) and survival after relapse/progression was worse in MYCN amplified tumors (3 year overall survival: 7.7 ± 7.4% vs. 20.5 ± 8.8%, P = 0.046). There was no difference in event-free survival and overall survival between MYCN amplified and nonamplified tumors. MYCN amplification was associated with more aggressive features at diagnosis and a better early response, but a higher progression rate during induction treatment and lower chance of survival after relapse/progression. There was no difference in survival rates according to MYCN amplification in patients with high-risk NB. © 2018 Wiley Periodicals, Inc.

Highly sensitive and selective microRNA detection based on DNA-bio-bar-code and enzyme-assisted strand cycle exponential signal amplification.

PubMed

Dong, Haifeng; Meng, Xiangdan; Dai, Wenhao; Cao, Yu; Lu, Huiting; Zhou, Shufeng; Zhang, Xueji

2015-04-21

Herein, a highly sensitive and selective microRNA (miRNA) detection strategy using DNA-bio-bar-code amplification (BCA) and Nb·BbvCI nicking enzyme-assisted strand cycle for exponential signal amplification was designed. The DNA-BCA system contains a locked nucleic acid (LNA) modified DNA probe for improving hybridization efficiency, while a signal reported molecular beacon (MB) with an endonuclease recognition site was designed for strand cycle amplification. In the presence of target miRNA, the oligonucleotides functionalized magnetic nanoprobe (MNP-DNA) and gold nanoprobe (AuNP-DNA) with numerous reported probes (RP) can hybridize with target miRNA, respectively, to form a sandwich structure. After sandwich structures were separated from the solution by the magnetic field, the RP were released under high temperature to recognize the MB and cleaved the hairpin DNA to induce the dissociation of RP. The dissociated RP then triggered the next strand cycle to produce exponential fluorescent signal amplification for miRNA detection. Under optimized conditions, the exponential signal amplification system shows a good linear range of 6 orders of magnitude (from 0.3 pM to 3 aM) with limit of detection (LOD) down to 52.5 zM, while the sandwich structure renders the system with high selectivity. Meanwhile, the feasibility of the proposed strategy for cell miRNA detection was confirmed by analyzing miRNA-21 in HeLa lysates. Given the high-performance for miRNA analysis, the strategy has a promising application in biological detection and in clinical diagnosis.

Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes.

PubMed

Fujita, Hiroto; Kataoka, Yuka; Tobita, Seiji; Kuwahara, Masayasu; Sugimoto, Naoki

2016-07-19

We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.

Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome.

PubMed

Gorshkova, Natalya V; Lobanova, Juliya S; Tokmakova, Irina L; Smirnov, Sergey V; Akhverdyan, Valerii Z; Krylov, Alexander A; Mashko, Sergey V

2018-03-01

A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10 -4 per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition-amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.

Strand displacement amplification as an in vitro model for rolling-circle replication: deletion formation and evolution during serial transfer.

PubMed Central

Walter, N G; Strunk, G

1994-01-01

Strand displacement amplification is an isothermal DNA amplification reaction based on a restriction endonuclease nicking its recognition site and a polymerase extending the nick at its 3' end, displacing the downstream strand. The reaction resembles rolling-circle replication of single-stranded phages and small plasmids. The displaced sense strand serves as target for an antisense reaction and vice versa, resulting in exponential growth and the autocatalytic nature of this in vitro reaction as long as the template is the limiting agent. We describe the optimization of strand displacement amplification for in vitro evolution experiments under serial transfer conditions. The reaction was followed and controlled by use of the fluorescent dye thiazole orange binding to the amplified DNA. We were able to maintain exponential growth conditions with a doubling time of 3.0 min throughout 100 transfers or approximately 350 molecular generations by using an automatic handling device. Homology of in vitro amplification with rolling-circle replication was mirrored by the occurring evolutionary processes. Deletion events most likely caused by a slipped mispairing mechanism as postulated for in vivo replication took place. Under our conditions, the mutation rate was high and a molecular quasi-species formed with a mutant lacking internal hairpin formation ability and thus outgrowing all other species under dGTP/dCTP deficiency. Images PMID:8058737

High average/peak power linearly polarized all-fiber picosecond MOPA seeded by mode-locked noise-like pulses

NASA Astrophysics Data System (ADS)

Yu, H. L.; Ma, P. F.; Tao, R. M.; Wang, X. L.; Zhou, P.; Chen, J. B.

2015-06-01

The characteristics of mode-locked noise-like pulses generated from a passively mode-locked fiber oscillator are experimentally investigated. By carefully adjusting the two polarization controllers, stable mode-locked noise-like pulse emission with a high radio frequency signal/noise ratio of  >55 dB is successfully achieved, ensuring the safety and possibility of high power amplification. To investigate the amplification characteristics of such pulses, one all-fiber master oscillator power amplifier (MOPA) is built to boost the power and energy of such pulses. Amplified noise-like pulses with average output power of 423 W, repetition rate of 18.71 MHz, pulse energy of 22.61 μJ, pulse duration of 72.1 ps and peak power of 314 kW are obtained. Near diffraction-limited beam is also demonstrated with M2 factor measured at full power operation of ~1.2 in the X and Y directions. The polarization extinction ratio at output power of 183 W is measured to be ~13 dB. To the best of our knowledge, this is the first demonstration of high-power amplification of noise-like pulses and the highest peak power ever reported in all-fiber picosecond MOPAs. The temporal self-compression process of such pulses and high peak power when amplified make it an ideal pump source for generation of high-power supercontinuum. Other potential applications, such as material processing and optical coherent tomography, could also be foreseen.

Prediction of earthquake ground motion at rock sites in Japan: evaluation of empirical and stochastic approaches for the PEGASOS Refinement Project

NASA Astrophysics Data System (ADS)

Edwards, Benjamin; Fäh, Donat

2017-11-01

Strong ground-motion databases used to develop ground-motion prediction equations (GMPEs) and calibrate stochastic simulation models generally include relatively few recordings on what can be considered as engineering rock or hard rock. Ground-motion predictions for such sites are therefore susceptible to uncertainty and bias, which can then propagate into site-specific hazard and risk estimates. In order to explore this issue we present a study investigating the prediction of ground motion at rock sites in Japan, where a wide range of recording-site types (from soil to very hard rock) are available for analysis. We employ two approaches: empirical GMPEs and stochastic simulations. The study is undertaken in the context of the PEGASOS Refinement Project (PRP), a Senior Seismic Hazard Analysis Committee (SSHAC) Level 4 probabilistic seismic hazard analysis of Swiss nuclear power plants, commissioned by swissnuclear and running from 2008 to 2013. In order to reduce the impact of site-to-site variability and expand the available data set for rock and hard-rock sites we adjusted Japanese ground-motion data (recorded at sites with 110 m s-1 < Vs30 < 2100 m s-1) to a common hard-rock reference. This was done through deconvolution of: (i) empirically derived amplification functions and (ii) the theoretical 1-D SH amplification between the bedrock and surface. Initial comparison of a Japanese GMPE's predictions with data recorded at rock and hard-rock sites showed systematic overestimation of ground motion. A further investigation of five global GMPEs' prediction residuals as a function of quarter-wavelength velocity showed that they all presented systematic misfit trends, leading to overestimation of median ground motions at rock and hard-rock sites in Japan. In an alternative approach, a stochastic simulation method was tested, allowing the direct incorporation of site-specific Fourier amplification information in forward simulations. We use an adjusted version of the model developed for Switzerland during the PRP. The median simulation prediction at true rock and hard-rock sites (Vs30 > 800 m s-1) was found to be comparable (within expected levels of epistemic uncertainty) to predictions using an empirical GMPE, with reduced residual misfit. As expected, due to including site-specific information in the simulations, the reduction in misfit could be isolated to a reduction in the site-related within-event uncertainty. The results of this study support the use of finite or pseudo-finite fault stochastic simulation methods in estimating strong ground motions in regions of weak and moderate seismicity, such as central and northern Europe. Furthermore, it indicates that weak-motion data has the potential to allow estimation of between- and within-site variability in ground motion, which is a critical issue in site-specific seismic hazard analysis, particularly for safety critical structures.

Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification.

PubMed

Cain-Hom, Carol; Splinter, Erik; van Min, Max; Simonis, Marieke; van de Heijning, Monique; Martinez, Maria; Asghari, Vida; Cox, J Colin; Warming, Søren

2017-05-05

Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used targeted locus amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic lines. In all lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven lines the exact integration site and breakpoint sequences were identified. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the TLA method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development and significance of a fetal electrocardiogram recorded by signal-averaged high-amplification electrocardiography.

PubMed

Hayashi, Risa; Nakai, Kenji; Fukushima, Akimune; Itoh, Manabu; Sugiyama, Toru

2009-03-01

Although ultrasonic diagnostic imaging and fetal heart monitors have undergone great technological improvements, the development and use of fetal electrocardiograms to evaluate fetal arrhythmias and autonomic nervous activity have not been fully established. We verified the clinical significance of the novel signal-averaged vector-projected high amplification ECG (SAVP-ECG) method in fetuses from 48 gravidas at 32-41 weeks of gestation and in 34 neonates. SAVP-ECGs from fetuses and newborns were recorded using a modified XYZ-leads system. Once noise and maternal QRS waves were removed, the P, QRS, and T wave intervals were measured from the signal-averaged fetal ECGs. We also compared fetal and neonatal heart rates (HRs), coefficients of variation of heart rate variability (CV) as a parasympathetic nervous activity, and the ratio of low to high frequency (LF/HF ratio) as a sympathetic nervous activity. The rate of detection of a fetal ECG by SAVP-ECG was 72.9%, and the fetal and neonatal QRS and QTc intervals were not significantly different. The neonatal CVs and LF/HF ratios were significantly increased compared with those in the fetus. In conclusion, we have developed a fetal ECG recording method using the SAVP-ECG system, which we used to evaluate autonomic nervous system development.

Low frequency amplification in deep alluvial basins: an example in the Po Plain (Northern Italy) and consequences for site specific SHA

NASA Astrophysics Data System (ADS)

Mascandola, Claudia; Massa, Marco; Barani, Simone; Lovati, Sara; Santulin, Marco

2016-04-01

This work deals with the problem of long period seismic site amplification that potentially might involve large and deep alluvial basins in case of strong earthquakes. In particular, it is here presented a case study in the Po Plain (Northern Italy), one of the most extended and deep sedimentary basin worldwide. Even if the studied area shows a low annul seismicity rate with rare strong events (Mw>6.0) and it is characterized by low to medium seismic hazard conditions, the seismic risk is significant for the high density of civil and strategic infrastructures (i.e. high degree of exposition) and the unfavourable geological conditions. The aim of this work is to provide general considerations about the seismic site response of the Po Plain, with particular attention on deep discontinuities (i.e. geological bedrock), in terms of potential low frequency amplification and their incidence on the PSHA. The current results were obtained through active and passive geophysical investigations performed near Castelleone, a site where a seismic station, which is part of the INGV (National Institute for Geophysics and Volcanology) Seismic National Network, is installed from 2009. In particular, the active analyses consisted in a MASW and a refraction survey, whereas the passive ones consisted in seismic ambient noise acquisitions with single stations and arrays of increasing aperture. The results in terms of noise HVSR indicate two main peaks, the first around 0.17 Hz and the second, as already stated in the recent literature, around 0.7 Hz. In order to correlate the amplified frequencies with the geological discontinuities, the array acquisitions were processed to obtain a shear waves velocity profile, computed with a joint inversion, considering the experimental dispersion curves and the HVSR results. The obtained velocity profile shows two main discontinuities: the shallower at ~165 m of depth, which can be correlated to the seismic bedrock (i.e. Vs > 800 m/) and the deeper at ~1350 m of depth, properly associable to the geological bedrock, considering the transition between the pliocenic loose sediments and the miocenic marls observable from the available stratigraphy. Numerical 1D analyses, computed to obtain the theoretical Transfer Function at the site, support the correlation between the experimental amplification peak around 0.17 Hz and the hypothesized geological bedrock. In terms of site specific SHA, the UHS expressed in displacement (MRP: 475 years) shows a significant increase if the seismic input is located at the geological bedrock (~1350 m) instead of the seismic bedrock (~165 m). Even if this increase is not relevant for the studied site, since the seismic hazard is low, it could be significant in other part of the Po Plain, where the seismic hazard is medium-high. According to the HVSR results, obtained for other available Po Plain broadband stations, the considerations of this work could represent a warning for future seismic hazard investigations in other areas of the basin.

A Simple Method for the Extraction, PCR-amplification, Cloning, and Sequencing of Pasteuria 16S rDNA from Small Numbers of Endospores.

PubMed

Atibalentja, N; Noel, G R; Ciancio, A

2004-03-01

For many years the taxonomy of the genus Pasteuria has been marred with confusion because the bacterium could not be cultured in vitro and, therefore, descriptions were based solely on morphological, developmental, and pathological characteristics. The current study sought to devise a simple method for PCR-amplification, cloning, and sequencing of Pasteuria 16S rDNA from small numbers of endospores, with no need for prior DNA purification. Results show that DNA extracts from plain glass bead-beating of crude suspensions containing 10,000 endospores at 0.2 x 10 endospores ml(-1) were sufficient for PCR-amplification of Pasteuria 16S rDNA, when used in conjunction with specific primers. These results imply that for P. penetrans and P. nishizawae only one parasitized female of Meloidogyne spp. and Heterodera glycines, respectively, should be sufficient, and as few as eight cadavers of Belonolaimus longicaudatus with an average number of 1,250 endospores of "Candidatus Pasteuria usgae" are needed for PCR-amplification of Pasteuria 16S rDNA. The method described in this paper should facilitate the sequencing of the 16S rDNA of the many Pasteuria isolates that have been reported on nematodes and, consequently, expedite the classification of those isolates through comparative sequence analysis.

Impediments to predicting site response: Seismic property estimation and modeling simplifications

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Guzina, B.B.

2009-01-01

We compare estimates of the empirical transfer function (ETF) to the plane SH-wave theoretical transfer function (TTF) within a laterally constant medium for invasive and noninvasive estimates of the seismic shear-wave slownesses at 13 Kiban-Kyoshin network stations throughout Japan. The difference between the ETF and either of the TTFs is substantially larger than the difference between the two TTFs computed from different estimates of the seismic properties. We show that the plane SH-wave TTF through a laterally homogeneous medium at vertical incidence inadequately models observed amplifications at most sites for both slowness estimates, obtained via downhole measurements and the spectral analysis of surface waves. Strategies to improve the predictions can be separated into two broad categories: improving the measurement of soil properties and improving the theory that maps the 1D soil profile onto spectral amplification. Using an example site where the 1D plane SH-wave formulation poorly predicts the ETF, we find a more satisfactory fit to the ETF by modeling the full wavefield and incorporating spatially correlated variability of the seismic properties. We conclude that our ability to model the observed site response transfer function is limited largely by the assumptions of the theoretical formulation rather than the uncertainty of the soil property estimates.

The impacts of intense moisture transport on the deep and marginal sea-ice zones of the Arctic during winter

NASA Astrophysics Data System (ADS)

Woods, Cian; Caballero, Rodrigo

2015-04-01

Over the past few decades observations have shown that the Arctic is warming at a much faster rate than the global average; a phenomenon know as polar amplification. This tendency for the high latitudes to warm at a disproportionate rate compared to the global average is also a robust feature of global climate model simulations and highlights the importance of climate research in this region. The most often cited mechanism explaining polar amplification is the ice-albedo feed-back; a mechanism by which the surface albedo decreases as sea ice retreats in response to a warming climate. This in turn leads to a higher absorption of insolation and the melting of more ice. In recent years the role of the ice-albedo feedback mechanism as the main cause of polar amplification has been brought into question. GCM studies show a slight reduction of the total poleward energy transport in a warming climate; with the dry static component decreasing at a much faster rate than the moist component. This repartitioning of the poleward energy transport has implications for the formation of clouds in the Arctic, which induce a secondary warming by trapping escaping OLR. These cloud processes in the atmosphere can explain at least part of the recent temperature amplification in the Arctic; and indeed even aquaplanet model studies with zero sea-ice reproduce the polar amplification phenomenon. Directionally, the ice-albedo feedback is a "bottom-up" process; inducing warming in the atmosphere from an increasing surface heat source i.e. more open ocean. The opening of more ocean surface is also consistent with the bottom amplified structure of warming in the Arctic. Here we present evidence for a mechanism in the atmosphere that matches with observations, but in fact acts the opposite direction i.e. "top-down", whereby moist air masses from lower latitudes, termed "moisture intrusions", travelling over the sea-ice increase the longwave down radiation and in turn induce a bottom amplified warming at the surface. There are an average of 14 such events that enter the polar cap each winter, driving about 50% of the seasonal variation in surface temperature over the deep Arctic. We show that, over the last 30 years, the marginal ice-zones in the Barents, Labrador and Chukchi Seas have experienced roughly a doubling in the frequency of these intense moisture intrusion events during winter. Interestingly, these are the regions that have experienced the most rapid wintertime ice loss in the Arctic, raising the question: to what extent has the recent Arctic warming been driven by local vs. interannual/remote processes?

Sedimentary basin effects in Seattle, Washington: Ground-motion observations and 3D simulations

USGS Publications Warehouse

Frankel, Arthur; Stephenson, William; Carver, David

2009-01-01

Seismograms of local earthquakes recorded in Seattle exhibit surface waves in the Seattle basin and basin-edge focusing of S waves. Spectral ratios of Swaves and later arrivals at 1 Hz for stiff-soil sites in the Seattle basin show a dependence on the direction to the earthquake, with earthquakes to the south and southwest producing higher average amplification. Earthquakes to the southwest typically produce larger basin surface waves relative to S waves than earthquakes to the north and northwest, probably because of the velocity contrast across the Seattle fault along the southern margin of the Seattle basin. S to P conversions are observed for some events and are likely converted at the bottom of the Seattle basin. We model five earthquakes, including the M 6.8 Nisqually earthquake, using 3D finite-difference simulations accurate up to 1 Hz. The simulations reproduce the observed dependence of amplification on the direction to the earthquake. The simulations generally match the timing and character of basin surface waves observed for many events. The 3D simulation for the Nisqually earth-quake produces focusing of S waves along the southern margin of the Seattle basin near the area in west Seattle that experienced increased chimney damage from the earthquake, similar to the results of the higher-frequency 2D simulation reported by Stephenson et al. (2006). Waveforms from the 3D simulations show reasonable agreement with the data at low frequencies (0.2-0.4 Hz) for the Nisqually earthquake and an M 4.8 deep earthquake west of Seattle.

How long time will we go with linear seismology?

NASA Astrophysics Data System (ADS)

Marmureanu, Gheorghe; Cioflan, Carmen; Marmureanu, Alexandru; Apostol, Bogdan

2013-04-01

Motto: The nonlinear seismology is the rule, The linear seismology is the exception. Paraphrasing Tullio Levi-Civita The leading question is: how many cities, villages, metropolitan areas etc. in seismic regions are constructed on rock sites? Most of them are located on alluvial deposits/ sediments, on Quaternary layers or in river valleys. In last book written by Peter M. Shearer, Professor of Geophysics at University of California, we can find, in total, only 12 rows about non-linear seismology(page 176).Among others are the following conclusions:(i)-Strong ground accelerations from large earthquakes can produce a non-linear response in shallow soils; (ii)-When a non-linear site response is present, then the shaking from large earthquakes cannot be predicted by simple scaling of records from small earthquakes; (iii)-This is an active area of research in strong motion and engineering seismology. On the other hand, Aki wrote: Nonlinear amplification at sediments sites appears to be more pervasive than seismologists used to think…Any attempt at seismic zonation must take into account the local site condition and this nonlinear amplification(Aki, A., Local Site Effects on Weak and Strong Ground Motion, Tectonophysics,218,93-111,1993). The difficulty to seismologists in demonstrating the nonlinear site effects has been due to the effect being overshadowed by the overall patterns of shock generation and propagation. In other words, the seismological detection of the nonlinear site effects requires a simultaneous understanding and separating of the effects of earthquake source, propagation path and local geological site conditions. To see the actual influence of nonlinearity of the whole system (seismic source-path propagation-local geological structure) the authors used to study the response spectra because they are the last in this chain and, of course, that they are the ones who are taken into account in seismic design of all structures Stress-strain relationships for soils are usually nonlinear, soil stiffness decreases and internal damping increases with increasing shear strain during of strong earthquakes. There is a strong nonlinear dependence of the spectral amplification factors(SAF) on earthquake magnitude for all seismic stations on Romanian territory on extra-Carpathian area (Iasi, Bacau, Focsani, Bucharest etc.). Median values of SAF for last strong Vrancea earthquakes are decreasing from 4.16(May 31,1990;Mw=6.4),to 3.63 (May 30,1990;Mw=6.9) and to 3.26 (August 30, 1986; Mw=7.1) .The novelty and the complexity degree comes from the fact that for first time, the final decision for NPP Cernavoda site was also based on local strong nonlinear spectral amplifications for strong earthquakes and used in last "STRESS TEST" asked by IAEA Vienna in 2011. The present analysis indicates that the effect of nonlinearity could be very important and if the analysis is made for peak accelerations, it is 48.87% and for stronger earthquakes it will be bigger. The authors are coming with new recorded data which will open up a new challenge for seismologists studying nonlinear site effects in 2-D and 3-D irregular geological structures, leading them to a fascinating research subject in earth physics(Aki,1993, p.108,idem),in nonlinear seismology and,finally, in a real evaluation of earthquake risk and loss estimates.

Site-specific seismic ground motion analyses for transportation infrastructure in the New Madrid seismic zone.

DOT National Transportation Integrated Search

2012-11-01

Generic, code-based design procedures cannot account for the anticipated short-period attenuation and long-period amplification of earthquake ground motions in the deep, soft sediments of the Mississippi Embayment within the New Madrid Seismic Zone (...

Electroacoustic Performance of Direct-Input Hearing Aids with FM Amplification Systems.

ERIC Educational Resources Information Center

Thibodeau, Linda M.

1990-01-01

The electroacoustic performance of 18 direct-input and two inductive-coupling hearing aids was compared when operating with two different frequency modulation (FM) systems. The most significant differences occurred in full-on gain, equivalent-input noise, and frequency response, as opposed to high frequency average saturation sound pressure level…

Amplification and dampening of soil respiration by changes in temperature variability

Treesearch

C.A. Sierra; M.E. Harmon; E.A. Thomann; S.S. Perakis; H.W. Loescher

2011-01-01

Accelerated release of carbon from soils is one of the most important feedbacks related to anthropogenically induced climate change. Studies addressing the mechanisms for soil carbon release through organic matter decomposition have focused on the effect of changes in the average temperature, with little attention to changes in temperature variability. Anthropogenic...

Coastal Amplification Laws for the French Tsunami Warning Center: Numerical Modeling and Fast Estimate of Tsunami Wave Heights Along the French Riviera

NASA Astrophysics Data System (ADS)

Gailler, A.; Hébert, H.; Schindelé, F.; Reymond, D.

2017-11-01

Tsunami modeling tools in the French tsunami Warning Center operational context provide rapidly derived warning levels with a dimensionless variable at basin scale. A new forecast method based on coastal amplification laws has been tested to estimate the tsunami onshore height, with a focus on the French Riviera test-site (Nice area). This fast prediction tool provides a coastal tsunami height distribution, calculated from the numerical simulation of the deep ocean tsunami amplitude and using a transfer function derived from the Green's law. Due to a lack of tsunami observations in the western Mediterranean basin, coastal amplification parameters are here defined regarding high resolution nested grids simulations. The preliminary results for the Nice test site on the basis of nine historical and synthetic sources show a good agreement with the time-consuming high resolution modeling: the linear approximation is obtained within 1 min in general and provides estimates within a factor of two in amplitude, although the resonance effects in harbors and bays are not reproduced. In Nice harbor especially, variation in tsunami amplitude is something that cannot be really assessed because of the magnitude range and maximum energy azimuth of possible events to account for. However, this method is well suited for a fast first estimate of the coastal tsunami threat forecast.

Coastal amplification laws for the French tsunami Warning Center: numerical modeling and fast estimate of tsunami wave heights along the French Riviera

NASA Astrophysics Data System (ADS)

Gailler, A.; Schindelé, F.; Hebert, H.; Reymond, D.

2017-12-01

Tsunami modeling tools in the French tsunami Warning Center operational context provide for now warning levels with a no dimension scale, and at basin scale. A new forecast method based on coastal amplification laws has been tested to estimate the tsunami onshore height, with a focus on the French Riviera test-site (Nice area). This fast prediction tool provides a coastal tsunami height distribution, calculated from the numerical simulation of the deep ocean tsunami amplitude and using a transfer function derived from the Green's law. Due to a lack of tsunami observation in the western Mediterranean basin, coastal amplification parameters are here defined regarding high resolution nested grids simulations. The first encouraging results for the Nice test site on the basis of 9 historical and fake sources show a good agreement with the time-consuming high resolution modeling: the linear approximation provides within in general 1 minute estimates less a factor of 2 in amplitude, although the resonance effects in harbors and bays are not reproduced. In Nice harbor especially, variation in tsunami amplitude is something that cannot be really appreciated because of the magnitude range and maximum energy azimuth of possible events to account for. However, this method suits well for a fast first estimate of the coastal tsunami threat forecast.

Coastal Amplification Laws for the French Tsunami Warning Center: Numerical Modeling and Fast Estimate of Tsunami Wave Heights Along the French Riviera

NASA Astrophysics Data System (ADS)

Gailler, A.; Hébert, H.; Schindelé, F.; Reymond, D.

2018-04-01

Tsunami modeling tools in the French tsunami Warning Center operational context provide rapidly derived warning levels with a dimensionless variable at basin scale. A new forecast method based on coastal amplification laws has been tested to estimate the tsunami onshore height, with a focus on the French Riviera test-site (Nice area). This fast prediction tool provides a coastal tsunami height distribution, calculated from the numerical simulation of the deep ocean tsunami amplitude and using a transfer function derived from the Green's law. Due to a lack of tsunami observations in the western Mediterranean basin, coastal amplification parameters are here defined regarding high resolution nested grids simulations. The preliminary results for the Nice test site on the basis of nine historical and synthetic sources show a good agreement with the time-consuming high resolution modeling: the linear approximation is obtained within 1 min in general and provides estimates within a factor of two in amplitude, although the resonance effects in harbors and bays are not reproduced. In Nice harbor especially, variation in tsunami amplitude is something that cannot be really assessed because of the magnitude range and maximum energy azimuth of possible events to account for. However, this method is well suited for a fast first estimate of the coastal tsunami threat forecast.

Characterizing the Kathmandu Valley sediment response through strong motion recordings of the 2015 Gorkha earthquake sequence

USGS Publications Warehouse

Rajaure, S.; Asimaki, Domniki; Thompson, Eric M.; Hough, Susan E.; Martin, Stacey; Ampuero, J.P.; Dhital, M.R.; Inbal, A; Takai, N; Shigefuji, M.; Bijukchhen, S; Ichiyanagi, M; Sasatani, T; Paudel, L

2017-01-01

We analyze strong motion records and high-rate GPS measurements of the M 7.8 Gorkha mainshock, M 7.3 Dolakha, and two moderate aftershock events recorded at four stations on the Kathmandu basin sediments, and one on rock-outcrop. Recordings on soil from all four events show systematic amplification relative to the rock site at multiple frequencies in the 0.1–2.5 Hz frequency range, and de-amplification of higher frequencies ( >2.5–10 Hz). The soil-to-rock amplification ratios for the M 7.8 and M 7.3 events have lower amplitude and frequency peaks relative to the ratios of the two moderate events, effects that could be suggestive of nonlinear site response. Further, comparisons to ground motion prediction equations show that 1) both soil and rock mainshock recordings were severely depleted of high frequencies, and 2) the depletion at high frequencies is not present in the aftershocks. These observations indicate that the high frequency deamplification is additionally related to characteristics of the source that are not captured by simplified ground motion prediction equations, and allude to seismic hazard analysis models being revised – possibly by treating isolated high frequency radiation sources separately from long period components to capture large magnitude near-source events such as the 2015 Gorkha mainshock.

Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia1[W][OPEN

PubMed Central

Jugulam, Mithila; Niehues, Kindsey; Godar, Amar S.; Koo, Dal-Hoe; Danilova, Tatiana; Friebe, Bernd; Sehgal, Sunish; Varanasi, Vijay K.; Wiersma, Andrew; Westra, Philip; Stahlman, Phillip W.; Gill, Bikram S.

2014-01-01

Recent rapid evolution and spread of resistance to the most extensively used herbicide, glyphosate, is a major threat to global crop production. Genetic mechanisms by which weeds evolve resistance to herbicides largely determine the level of resistance and the rate of evolution of resistance. In a previous study, we determined that glyphosate resistance in Kochia scoparia is due to the amplification of the 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) gene, the enzyme target of glyphosate. Here, we investigated the genomic organization of the amplified EPSPS copies using fluorescence in situ hybridization (FISH) and extended DNA fiber (Fiber FISH) on K. scoparia chromosomes. In both glyphosate-resistant K. scoparia populations tested (GR1 and GR2), FISH results displayed a single and prominent hybridization site of the EPSPS gene localized on the distal end of one pair of homologous metaphase chromosomes compared with a faint hybridization site in glyphosate-susceptible samples (GS1 and GS2). Fiber FISH displayed 10 copies of the EPSPS gene (approximately 5 kb) arranged in tandem configuration approximately 40 to 70 kb apart, with one copy in an inverted orientation in GR2. In agreement with FISH results, segregation of EPSPS copies followed single-locus inheritance in GR1 population. This is the first report of tandem target gene amplification conferring field-evolved herbicide resistance in weed populations. PMID:25037215

Development of an efficient signal amplification strategy for label-free enzyme immunoassay using two site-specific biotinylated recombinant proteins.

PubMed

Tang, Jin-Bao; Tang, Ying; Yang, Hong-Ming

2015-02-15

Constructing a recombinant protein between a reporter enzyme and a detector protein to produce a homogeneous immunological reagent is advantageous over random chemical conjugation. However, the approach hardly recombines multiple enzymes in a difunctional fusion protein, which results in insufficient amplification of the enzymatic signal, thereby limiting its application in further enhancement of analytical signal. In this study, two site-specific biotinylated recombinant proteins, namely, divalent biotinylated alkaline phosphatase (AP) and monovalent biotinylated ZZ domain, were produced by employing the Avitag-BirA system. Through the high streptavidin (SA)-biotin interaction, the divalent biotinylated APs were clustered in the SA-biotin complex and then incorporated with the biotinylated ZZ. This incorporation results in the formation of a functional macromolecule that involves numerous APs, thereby enhancing the enzymatic signal, and in the production of several ZZ molecules for the interaction with immunoglobulin G (IgG) antibody. The advantage of this signal amplification strategy is demonstrated through ELISA, in which the analytical signal was substantially enhanced, with a 32-fold increase in the detection sensitivity compared with the ZZ-AP fusion protein approach. The proposed immunoassay without chemical modification can be an alternative strategy to enhance the analytical signals in various applications involving immunosensors and diagnostic chips, given that the label-free IgG antibody is suitable for the ZZ protein. Copyright © 2014 Elsevier B.V. All rights reserved.

EzyAmp signal amplification cascade enables isothermal detection of nucleic acid and protein targets.

PubMed

Linardy, Evelyn M; Erskine, Simon M; Lima, Nicole E; Lonergan, Tina; Mokany, Elisa; Todd, Alison V

2016-01-15

Advancements in molecular biology have improved the ability to characterize disease-related nucleic acids and proteins. Recently, there has been an increasing desire for tests that can be performed outside of centralised laboratories. This study describes a novel isothermal signal amplification cascade called EzyAmp (enzymatic signal amplification) that is being developed for detection of targets at the point of care. EzyAmp exploits the ability of some restriction endonucleases to cleave substrates containing nicks within their recognition sites. EzyAmp uses two oligonucleotide duplexes (partial complexes 1 and 2) which are initially cleavage-resistant as they lack a complete recognition site. The recognition site of partial complex 1 can be completed by hybridization of a triggering oligonucleotide (Driver Fragment 1) that is generated by a target-specific initiation event. Binding of Driver Fragment 1 generates a completed complex 1, which upon cleavage, releases Driver Fragment 2. In turn, binding of Driver Fragment 2 to partial complex 2 creates completed complex 2 which when cleaved releases additional Driver Fragment 1. Each cleavage event separates fluorophore quencher pairs resulting in an increase in fluorescence. At this stage a cascade of signal production becomes independent of further target-specific initiation events. This study demonstrated that the EzyAmp cascade can facilitate detection and quantification of nucleic acid targets with sensitivity down to aM concentration. Further, the same cascade detected VEGF protein with a sensitivity of 20nM showing that this universal method for amplifying signal may be linked to the detection of different types of analytes in an isothermal format. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Site Effects on Regional Seismograms Recorded in the Vicinity of Weston Observatory

DTIC Science & Technology

1993-09-30

flanks of the active volcanoes of Mauna Loa and Kilauea . The distances between the sites ranged from a few km to over 100 km. Although there is little...on the island of Hawaii using S-wave coda spectral ratios for frequencies between 1.5 and 15-Hz. They used 40 vertical I-Hz seismometers, and recorded...for the island of Hawaii , Bull. Seis Soc. Am-, 12 No- 3 1151-1185. Mayeda, K., S. Koyanagi, and K. Aki (1991). Site amplification from S-wave coda in

Sin Nombre Virus and Rodent Species Diversity: A Test of the Dilution and Amplification Hypotheses

PubMed Central

Clay, Christine A.; Lehmer, Erin M.; Jeor, Stephen St.; Dearing, M. Denise

2009-01-01

Background Species diversity is proposed to greatly impact the prevalence of pathogens. Two predominant hypotheses, the “Dilution Effect” and the “Amplification Effect”, predict divergent outcomes with respect to the impact of species diversity. The Dilution Effect predicts that pathogen prevalence will be negatively correlated with increased species diversity, while the Amplification Effect predicts that pathogen prevalence will be positively correlated with diversity. For many host-pathogen systems, the relationship between diversity and pathogen prevalence has not be empirically examined. Methodology/Principal Findings We tested the Dilution and Amplification Effect hypotheses by examining the prevalence of Sin Nombre virus (SNV) with respect to diversity of the nocturnal rodent community. SNV is directly transmitted primarily between deer mice (Peromyscus maniculatus). Using mark-recapture sampling in the Spring and Fall of 2003–2005, we measured SNV prevalence in deer mice at 16 landscape level sites (3.1 hectares each) that varied in rodent species diversity. We explored several mechanisms by which species diversity may affect SNV prevalence, including reduced host density, reduced host persistence, the presence of secondary reservoirs and community composition. We found a negative relationship between species diversity and SNV prevalence in deer mice, thereby supporting the Dilution Effect hypothesis. Deer mouse density and persistence were lower at sites with greater species diversity; however, only deer mouse persistence was positively correlated with SNV prevalence. Pinyon mice (P. truei) may serve as dilution agents, having a negative effect on prevalence, while kangaroo rats (Dipodomys ordii), may have a positive effect on the prevalence of SNV, perhaps through effects on deer mouse behavior. Conclusions/Significance While previous studies on host-pathogen systems have found patterns of diversity consistent with either the Dilution or Amplification Effects, the mechanisms by which species diversity influences prevalence have not been investigated. Our study indicates that changes in host persistence, coupled with interspecific interactions, are important mechanisms through which diversity may influence patterns of pathogens. Our results reveal the complexity of rodent community interactions with respect to SNV dynamics. PMID:19649283

Estimation of 1-D velocity models beneath strong-motion observation sites in the Kathmandu Valley using strong-motion records from moderate-sized earthquakes

NASA Astrophysics Data System (ADS)

Bijukchhen, Subeg M.; Takai, Nobuo; Shigefuji, Michiko; Ichiyanagi, Masayoshi; Sasatani, Tsutomu; Sugimura, Yokito

2017-07-01

The Himalayan collision zone experiences many seismic activities with large earthquakes occurring at certain time intervals. The damming of the proto-Bagmati River as a result of rapid mountain-building processes created a lake in the Kathmandu Valley that eventually dried out, leaving thick unconsolidated lacustrine deposits. Previous studies have shown that the sediments are 600 m thick in the center. A location in a seismically active region, and the possible amplification of seismic waves due to thick sediments, have made Kathmandu Valley seismically vulnerable. It has suffered devastation due to earthquakes several times in the past. The development of the Kathmandu Valley into the largest urban agglomerate in Nepal has exposed a large population to seismic hazards. This vulnerability was apparent during the Gorkha Earthquake (Mw7.8) on April 25, 2015, when the main shock and ensuing aftershocks claimed more than 1700 lives and nearly 13% of buildings inside the valley were completely damaged. Preparing safe and up-to-date building codes to reduce seismic risk requires a thorough study of ground motion amplification. Characterizing subsurface velocity structure is a step toward achieving that goal. We used the records from an array of strong-motion accelerometers installed by Hokkaido University and Tribhuvan University to construct 1-D velocity models of station sites by forward modeling of low-frequency S-waves. Filtered records (0.1-0.5 Hz) from one of the accelerometers installed at a rock site during a moderate-sized (mb4.9) earthquake on August 30, 2013, and three moderate-sized (Mw5.1, Mw5.1, and Mw5.5) aftershocks of the 2015 Gorkha Earthquake were used as input motion for modeling of low-frequency S-waves. We consulted available geological maps, cross-sections, and borehole data as the basis for initial models for the sediment sites. This study shows that the basin has an undulating topography and sediment sites have deposits of varying thicknesses, from 155 to 440 m. These models also show high velocity contrast at the bedrock depth which results in significant wave amplification.[Figure not available: see fulltext.

Synchronous digitization for high dynamic range lock-in amplification in beam-scanning microscopy

PubMed Central

Muir, Ryan D.; Sullivan, Shane Z.; Oglesbee, Robert A.; Simpson, Garth J.

2014-01-01

Digital lock-in amplification (LIA) with synchronous digitization (SD) is shown to provide significant signal to noise (S/N) and linear dynamic range advantages in beam-scanning microscopy measurements using pulsed laser sources. Direct comparisons between SD-LIA and conventional LIA in homodyne second harmonic generation measurements resulted in S/N enhancements consistent with theoretical models. SD-LIA provided notably larger S/N enhancements in the limit of low light intensities, through the smooth transition between photon counting and signal averaging developed in previous work. Rapid beam scanning instrumentation with up to video rate acquisition speeds minimized photo-induced sample damage. The corresponding increased allowance for higher laser power without sample damage is advantageous for increasing the observed signal content. PMID:24689588

Amplification and noise properties of an erbium-doped multicore fiber amplifier.

PubMed

Abedin, K S; Taunay, T F; Fishteyn, M; Yan, M F; Zhu, B; Fini, J M; Monberg, E M; Dimarcello, F V; Wisk, P W

2011-08-15

A multicore erbium-doped fiber (MC-EDF) amplifier for simultaneous amplification in the 7-cores has been developed, and the gain and noise properties of individual cores have been studied. The pump and signal radiation were coupled to individual cores of MC-EDF using two tapered fiber bundled (TFB) couplers with low insertion loss. For a pump power of 146 mW, the average gain achieved in the MC-EDF fiber was 30 dB, and noise figure was less than 4 dB. The net useful gain from the multicore-amplifier, after taking into consideration of all the passive losses, was about 23-27 dB. Pump induced ASE noise transfer between the neighboring channel was negligible. © 2011 Optical Society of America

Profiling In Situ Microbial Community Structure with an Amplification Microarray

PubMed Central

Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

2013-01-01

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

CD274 (PDL1) and JAK2 genomic amplifications in pulmonary squamous-cell and adenocarcinoma patients.

PubMed

Clavé, Sergi; Pijuan, Lara; Casadevall, David; Taus, Álvaro; Gimeno, Javier; Hernández-Llodrà, Silvia; Rodríguez-Rivera, María; Lorenzo, Marta; Menéndez, Silvia; Albanell, Joan; Espinet, Blanca; Arriola, Edurne; Salido, Marta

2018-01-01

CD274 (PDL1) and JAK2 (9p24.1) gene amplifications have been recently described in pulmonary carcinomas in association with programmed death-ligand 1 (PD-L1) expression. Furthermore, PTEN loss has been explored preclinically in relation to PD-L1 expression. Our aim was to determine whether these genomic alterations affect PD-L1 expression levels in non-small-cell lung cancer. PD-L1 and PTEN expression determined by immunohistochemistry (IHC), and CD274, JAK2 and PTEN copy number alterations (CNAs) determined by fluorescence in-situ hybridisation, were studied in 171 pulmonary carcinoma specimens. PD-L1 expression was positive in 40 cases (23.3%), and CD274 amplification was present in 14 tumours (8.8%). Concordance between both events was found in 12 of 14 amplified cases (P = 0.0001). We found nine JAK2-amplified cases (5.7%), seven with PD-L1 expression (P = 0.0006). Moreover, six of the seven cases had JAK2 and CD274 coamplification (9p24.1 genomic amplification). Remarkably, the average PD-L1 IHC score was higher in these amplified cases (230 versus 80; P = 0.001). Non-statistical associations were observed between PD-L1 expression and PTEN loss and PTEN deletions. We describe a subset of patients (8.2%) who had 9p24.1 amplifications resulting in high expression of PD-L1. Our results provide evidence for genomic up-regulation of PD-L1 expression in non-small-cell lung cancer. © 2017 John Wiley & Sons Ltd.

Numerical Simulation of Strong Ground Motion at Mexico City:A Hybrid Approach for Efficient Evaluation of Site Amplification and Path Effects for Different Types of Earthquakes

NASA Astrophysics Data System (ADS)

Cruz, H.; Furumura, T.; Chavez-Garcia, F. J.

2002-12-01

The estimation of scenarios of the strong ground motions caused by future great earthquakes is an important problem in strong motion seismology. This was pointed out by the great 1985 Michoacan earthquake, which caused a great damage in Mexico City, 300 km away from the epicenter. Since the seismic wavefield is characterized by the source, path and site effects, the pattern of strong motion damage from different types of earthquakes should differ significantly. In this study, the scenarios for intermediate-depth normal-faulting, shallow-interplate thrust faulting, and crustal earthquakes have been estimated using a hybrid simulation technique. The character of the seismic wavefield propagating from the source to Mexico City for each earthquake was first calculated using the pseudospectral method for 2D SH waves. The site amplifications in the shallow structure of Mexico City are then calculated using the multiple SH wave reverberation theory. The scenarios of maximum ground motion for both inslab and interplate earthquakes obtained by the simulation show a good agreement with the observations. This indicates the effectiveness of the hybrid simulation approach to investigate the strong motion damage for future earthquakes.

Methylation-sensitive amplification polymorphism analysis of fat and muscle tissues in pigs.

PubMed

Ma, J D; Li, M Z; Zhou, S L; Zhou, C W; Li, X W

2012-09-26

DNA methylation may be involved in regulating the expression of protein-coding genes, resulting in different fat and muscle phenotypes. Using a methylation-sensitive amplified polymorphism approach, we obtained 7423 bands by selective amplification of genomic DNA from six different fat depots and two heterogeneous muscle types from Duroc/Landrace/Yorkshire cross-bred pigs. The degrees of DNA methylation, determined by the percentages of hemi- and fully methylated sites relative to the total number of CCGG sites, were similar in male and female pigs for each specific tissue [χ(2) test; P (two-tailed) > 0.05]. Gender bias was therefore ignored. There were significant differences in the degree of DNA methylation among the eight tissue types [χ(2) test; P(total) (two-tailed) = 0.009]. However, similar degrees of methylation were observed among the six fat depots [χ(2) test; P(fat) (two-tailed) = 0.24 > 0.05]and between the two muscle types [χ(2) test; P(muscle) (two-tailed) = 0.76 > 0.05]. We conclude that the degree of DNA methylation differs between porcine fat and muscle tissue, but that the methylation status of a particular tissue type is similar, despite being deposited at different body sites.

ChIP-chip.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein-DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein-DNA interactions. © 2018 Cold Spring Harbor Laboratory Press.

Potential for an Arctic-breeding migratory bird to adjust spring migration phenology to Arctic amplification.

PubMed

Lameris, Thomas K; Scholten, Ilse; Bauer, Silke; Cobben, Marleen M P; Ens, Bruno J; Nolet, Bart A

2017-10-01

Arctic amplification, the accelerated climate warming in the polar regions, is causing a more rapid advancement of the onset of spring in the Arctic than in temperate regions. Consequently, the arrival of many migratory birds in the Arctic is thought to become increasingly mismatched with the onset of local spring, consequently reducing individual fitness and potentially even population levels. We used a dynamic state variable model to study whether Arctic long-distance migrants can advance their migratory schedules under climate warming scenarios which include Arctic amplification, and whether such an advancement is constrained by fuel accumulation or the ability to anticipate climatic changes. Our model predicts that barnacle geese Branta leucopsis suffer from considerably reduced reproductive success with increasing Arctic amplification through mistimed arrival, when they cannot anticipate a more rapid progress of Arctic spring from their wintering grounds. When geese are able to anticipate a more rapid progress of Arctic spring, they are predicted to advance their spring arrival under Arctic amplification up to 44 days without any reproductive costs in terms of optimal condition or timing of breeding. Negative effects of mistimed arrival on reproduction are predicted to be somewhat mitigated by increasing summer length under warming in the Arctic, as late arriving geese can still breed successfully. We conclude that adaptation to Arctic amplification may rather be constrained by the (un)predictability of changes in the Arctic spring than by the time available for fuel accumulation. Social migrants like geese tend to have a high behavioural plasticity regarding stopover site choice and migration schedule, giving them the potential to adapt to future climate changes on their flyway. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Development of loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Penicillium nordicum in dry-cured meat products.

PubMed

Ferrara, M; Perrone, G; Gallo, A; Epifani, F; Visconti, A; Susca, A

2015-06-02

The need of powerful diagnostic tools for rapid, simple, and cost-effective detection of food-borne fungi has become very important in the area of food safety. Currently, several isothermal nucleic acid amplification methods have been developed as an alternative to PCR-based analyses. Loop-mediated isothermal amplification (LAMP) is one of these innovative methods; it requires neither gel electrophoresis to separate and visualize the products nor expensive laboratory equipment and it has been applied already for detection of pathogenic organisms. In the current study, we developed a LAMP assay for the specific detection of Penicillium nordicum, the major causative agent of ochratoxin A contamination in protein-rich food, especially dry-cured meat products. The assay was based on targeting otapksPN gene, a key gene in the biosynthesis of ochratoxin A (OTA) in P. nordicum. Amplification of DNA during the reaction was detected directly in-tube by color transition of hydroxynaphthol blue from violet to sky blue, visible to the naked eye, avoiding further post amplification analyses. Only DNAs isolated from several P. nordicum strains led to positive results and no amplification was observed from non-target OTA and non OTA-producing strains. The assay was able to detect down to 100 fg of purified targeted genomic DNA or 10(2) conidia/reaction within 60 min. The LAMP assay for detection and identification of P. nordicum was combined with a rapid DNA extraction method set up on serially diluted conidia, providing an alternative rapid, specific and sensitive DNA-based method suitable for application directly "on-site", notably in key steps of dry-cured meat production. Copyright © 2015 Elsevier B.V. All rights reserved.

Confirmation and calibration of computer modeling of tsunamis produced by Augustine volcano, Alaska

USGS Publications Warehouse

Beget, James E.; Kowalik, Zygmunt

2006-01-01

Numerical modeling has been used to calculate the characteristics of a tsunami generated by a landslide into Cook Inlet from Augustine Volcano. The modeling predicts travel times of ca. 50-75 minutes to the nearest populated areas, and indicates that significant wave amplification occurs near Mt. Iliamna on the western side of Cook Inlet, and near the Nanwelak and the Homer-Anchor Point areas on the east side of Cook Inlet. Augustine volcano last produced a tsunami during an eruption in 1883, and field evidence of the extent and height of the 1883 tsunamis can be used to test and constrain the results of the computer modeling. Tsunami deposits on Augustine Island indicate waves near the landslide source were more than 19 m high, while 1883 tsunami deposits in distal sites record waves 6-8 m high. Paleotsunami deposits were found at sites along the coast near Mt. Iliamna, Nanwelak, and Homer, consistent with numerical modeling indicating significant tsunami wave amplification occurs in these areas. 

A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification

PubMed Central

Florio, Marta; Namba, Takashi; Pääbo, Svante; Hiller, Michael; Huttner, Wieland B.

2016-01-01

The gene ARHGAP11B promotes basal progenitor amplification and is implicated in neocortex expansion. It arose on the human evolutionary lineage by partial duplication of ARHGAP11A, which encodes a Rho guanosine triphosphatase–activating protein (RhoGAP). However, a lack of 55 nucleotides in ARHGAP11B mRNA leads to loss of RhoGAP activity by GAP domain truncation and addition of a human-specific carboxy-terminal amino acid sequence. We show that these 55 nucleotides are deleted by mRNA splicing due to a single C→G substitution that creates a novel splice donor site. We reconstructed an ancestral ARHGAP11B complementary DNA without this substitution. Ancestral ARHGAP11B exhibits RhoGAP activity but has no ability to increase basal progenitors during neocortex development. Hence, a single nucleotide substitution underlies the specific properties of ARHGAP11B that likely contributed to the evolutionary expansion of the human neocortex. PMID:27957544

KSHV cell attachment sites revealed by ultra sensitive tyramide signal amplification (TSA) localize to membrane microdomains that are up-regulated on mitotic cells.

PubMed

Garrigues, H Jacques; Rubinchikova, Yelena E; Rose, Timothy M

2014-03-01

Cell surface structures initiating attachment of Kaposi's sarcoma-associated herpesvirus (KSHV) were characterized using purified hapten-labeled virions visualized by confocal microscopy with a sensitive fluorescent enhancement using tyramide signal amplification (TSA). KSHV attachment sites were present in specific cellular domains, including actin-based filopodia, lamellipodia, ruffled membranes, microvilli and intercellular junctions. Isolated microdomains were identified on the dorsal surface, which were heterogeneous in size with a variable distribution that depended on cellular confluence and cell cycle stage. KSHV binding domains ranged from scarce on interphase cells to dense and continuous on mitotic cells, and quantitation of bound virus revealed a significant increase on mitotic compared to interphase cells. KSHV also bound to a supranuclear domain that was distinct from microdomains in confluent and interphase cells. These results suggest that rearrangement of the cellular membrane during mitosis induces changes in cell surface receptors implicated in the initial attachment stage of KSHV entry. Copyright © 2014 Elsevier Inc. All rights reserved.

Pitfalls using tyramide signal amplification (TSA) in the mouse gastrointestinal tract: endogenous streptavidin-binding sites lead to false positive staining.

PubMed

Horling, L; Neuhuber, W L; Raab, M

2012-02-15

Highly sensitive immunohistochemical detection systems such as tyramide signal amplification (TSA) are widely used, since they allow using two primary antibodies raised in the same species. Most of them are based on the streptavidin-biotin-peroxidase system and include streptavidin-coupled secondary antibodies. Using TSA in cryostat-sectioned tissues of mouse esophagus, we were puzzled by negative controls with unexpected staining mostly in the ganglionic areas. This prompted us to search for the causing agent and to include also other parts of the mouse gastrointestinal tract for comparison. Streptavidin-coupled antibodies bound to endogenous binding sites yet to be characterized, which are present throughout the mouse intestines. Staining was mainly localized around neuronal cell bodies of enteric ganglia. Thus, caution is warranted when applying streptavidin-coupled antibodies in the mouse gastrointestinal tract. The use of endogenous biotin-blocking kits combined with a prolonged post-fixation time could significantly reduce unintentional staining. Copyright © 2011 Elsevier B.V. All rights reserved.

Rapid screening method for male DNA by using the loop-mediated isothermal amplification assay.

PubMed

Kitamura, Masashi; Kubo, Seiji; Tanaka, Jin; Adachi, Tatsushi

2017-08-12

Screening for male-derived biological material from collected samples plays an important role in criminal investigations, especially those involving sexual assaults. We have developed a loop-mediated isothermal amplification (LAMP) assay targeting multi-repeat sequences of the Y chromosome for detecting male DNA. Successful amplification occurred with 0.5 ng of male DNA under isothermal conditions of 61 to 67 °C, but no amplification occurred with up to 10 ng of female DNA. Under the optimized conditions, the LAMP reaction initiated amplification within 10 min and amplified for 20 min. The LAMP reaction was sensitive at levels as low as 1-pg male DNA, and a quantitative LAMP assay could be developed because of the strong correlation between the reaction time and the amount of template DNA in the range of 10 pg to 10 ng. Furthermore, to apply the LAMP assay to on-site screening for male-derived samples, we evaluated a protocol using a simple DNA extraction method and a colorimetric intercalating dye that allows detection of the LAMP reaction by evaluating the change in color of the solution. Using this protocol, samples of male-derived blood and saliva stains were processed in approximately 30 min from DNA extraction to detection. Because our protocol does not require much hands-on time or special equipment, this LAMP assay promises to become a rapid and simple screening method for male-derived samples in forensic investigations.

The role of local soil-induced amplification in the 27 July 1980 northeastern Kentucky earthquake

USGS Publications Warehouse

Woolery, E.W.; Lin, T.-L.; Wang, Z.; Shi, B.

2008-01-01

Amplification of earthquake ground motions by near-surface soil deposits was believed to have occurred in Maysville, Kentucky, U.S.A. during the northeast Kentucky (Sharpsburg) earthquake (mb,Lg 5.3) of July 27, 1980. The city of Maysville, founded on approximately 30 m of Late Quaternary Ohio River flood plain alluvium, was 52 km from the epicenter, but experienced equivalent or higher Modified Mercalli Intensity (MMI) VII, compared with the epicentral area of the earthquake (i.e., MMI VI-VII). In this study, dynamic soil properties were obtained at 10 sites in Maysville using seismic P-wave and S-wave (SH-mode) refraction and reflection methods. Synthetically generated composite time histories and limited geotechnical information, along with the measured dynamic properties, were used to perform one-dimensional linear-equivalent amplification analyses. The results indicated the soils generated ground-motion amplification factors between 3.0 and 6.0 and at a frequency range between 2.0 and 5.0 Hz (0.2 to 0.5 s). The building damage in Maysville from the Sharpsburg earthquake was predominantly found in one- to three-story masonry structures. The estimated fundamental period for one- to three-story masonry buildings is approximately 0.11 to 0.26 s (3.8 to 9 Hz). These correlations suggest the elevated ground motion intensity in Maysville can be accounted for by near-surface soil-amplification effects and resonance of the ground motion by the buildings (i.e., double resonance).

Seismic Hazard Assessment for the Baku City and Absheron Peninsula, Azerbaijan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Babayev, Gulam R.

2006-03-23

This paper deals with the seismic hazard assessment for Baku and the Absheron peninsula. The assessment is based on the information on the features of earthquake ground motion excitation, seismic wave propagation (attenuation), and site effect. I analyze active faults, seismicity, soil and rock properties, geological cross-sections, the borehole data of measured shear-wave velocity, lithology, amplification factor of each geological unit, geomorphology, topography, and basic rock and surface ground motions. To estimate peak ground acceleration (PGA) at the surface, PGA at the basic rock is multiplied by the amplification parameter of each surface layers. Quaternary soft deposits, representing a highmore » risk due to increasing PGA values at surface, are studied in detail. For a near-zone target earthquake PGA values are compared to intensity at MSK-64 scale for the Absheron peninsula. The amplification factor for the Baku city is assessed and provides estimations for a level of a seismic motion and seismic intensity of the studied area.« less

The Location of the Cochlear Amplifier: Spatial Representation of a Single Tone on the Guinea Pig Basilar Membrane

NASA Astrophysics Data System (ADS)

Russell, I. J.; Nilsen, K. E.

1997-03-01

Acoustic stimulation vibrates the cochlear basilar membrane, initiating a wave of displacement that travels toward the apex and reaches a peak over a restricted region according to the stimulus frequency. In this characteristic frequency region, a tone at the characteristic frequency maximally excites the sensory hair cells of the organ of Corti, which transduce it into electrical signals to produce maximum activity in the auditory nerve. Saturating, nonlinear, feedback from the motile outer hair cells is thought to provide electromechanical amplification of the travelling wave. However, neither the location nor the extent of the source of amplification, in relation to the characteristic frequency, are known. We have used a laser--diode interferometer to measure in vivo the distribution along the basilar membrane of nonlinear, saturating vibrations to 15 kHz tones. We estimate that the site of amplification for the 15 kHz region is restricted to a 1.25 mm length of basilar membrane centered on the 15 kHz place.

Gain-switched laser diode seeded Yb-doped fiber amplifier delivering 11-ps pulses at repetition rates up to 40-MHz

NASA Astrophysics Data System (ADS)

Ryser, Manuel; Neff, Martin; Pilz, Soenke; Burn, Andreas; Romano, Valerio

2012-02-01

Here, we demonstrate all-fiber direct amplification of 11 picosecond pulses from a gain-switched laser diode at 1063 nm. The diode was driven at a repetition rate of 40 MHz and delivered 13 μW of fiber-coupled average output power. For the low output pulse energy of 0.33 pJ we have designed a multi-stage core pumped preamplifier based on single clad Yb-doped fibers in order to keep the contribution of undesired amplified spontaneous emission as low as possible and to minimize temporal and spectral broadening. After the preamplifier we reduced the 40 MHz repetition rate to 1 MHz using a fiber coupled pulse-picker. The final amplification was done with a cladding pumped Yb-doped large mode area fiber and a subsequent Yb-doped rod-type fiber. With our setup we achieved amplification of 72 dBs to an output pulse energy of 5.7 μJ, pulse duration of 11 ps and peak power of >0.6 MW.

SEISMIC SITE RESPONSE ESTIMATION IN THE NEAR SOURCE REGION OF THE 2009 L’AQUILA, ITALY, EARTHQUAKE

NASA Astrophysics Data System (ADS)

Bertrand, E.; Azzara, R.; Bergamashi, F.; Bordoni, P.; Cara, F.; Cogliano, R.; Cultrera, G.; di Giulio, G.; Duval, A.; Fodarella, A.; Milana, G.; Pucillo, S.; Régnier, J.; Riccio, G.; Salichon, J.

2009-12-01

The 6th of April 2009, at 3:32 local time, a Mw 6.3 earthquake hit the Abruzzo region (central Italy) causing more than 300 casualties. The epicenter of the earthquake was 95km NE of Rome and 10km from the center of the city of L’Aquila, the administrative capital of the Abruzzo region. This city has a population of about 70,000 and was severely damaged by the earthquake, the total cost of the buildings damage being estimated around 3 Bn €. Historical masonry buildings particularly suffered from the seismic shaking, but some reinforced concrete structures from more modern construction were also heavily damaged. To better estimate the seismic solicitation of these structures during the earthquake, we deployed temporary arrays in the near source region. Downtown L’Aquila, as well as a rural quarter composed of ancient dwelling-centers located western L’Aquila (Roio area), have been instrumented. The array set up downtown consisted of nearly 25 stations including velocimetric and accelerometric sensors. In the Roio area, 6 stations operated for almost one month. The data has been processed in order to study the spectral ratios of the horizontal component of ground motion at the soil site and at a reference site, as well as the spectral ratio of the horizontal and the vertical movement at a single recording site. Downtown L’Aquila is set on a Quaternary fluvial terrace (breccias with limestone boulders and clasts in a marly matrix), which forms the left bank of the Aterno River and slopes down in the southwest direction towards the Aterno River. The alluvial are lying on lacustrine sediments reaching their maximum thickness (about 250m) in the center of L’Aquila. After De Luca et al. (2005), these quaternary deposits seem to lead in an important amplification factor in the low frequency range (0.5-0.6 Hz). However, the level of amplification varies strongly from one point to the other in the center of the city. This new experimentation allows new and more detailed investigation of site effects in L’Aquila. The Roio area is located 5km away from downtown L’Aquila, directly above the epicenter of the April 6th earthquake. It forms a little quaternary basin almost 300m above the city center, on the right bank of the Aterno river. The seismological stations were set up on different hard soil sites surrounding the basin, and on soft soil in the middle of the basin, recording more than 400 aftershocks from a magnitude Ml 1.5 to 4.9. Both ambient vibration and aftershock recordings exhibit a strong amplification in the center of the valley between 2Hz and 5Hz. The stations located at the edge of cliffs also present some important amplification, even if they are installed on rocky soil.

A Study on Empirical Site Response at Bodrum Peninsula, Turkey

NASA Astrophysics Data System (ADS)

Alcik, H. A.; Tanircan, G.

2016-12-01

The Bodrum Peninsula with a population of one million in summer season is one of the most populated touristic centers of the southwest coast of Turkey. The region is located at the eastern part of the Volcanic Arc and Hellenic Arc-Trench System at the Aegean Sea. It is also surrounded by several offshore Aegean Graben systems. All of those systems have capability of producing large magnitude (M7+) earthquakes. Such tectonic entities pose a great threat to settlements around the region. Enrichment in ground motion arrays is an indispensable tool to investigate ground motion characteristics as well as behavior of shallow site profiles at such seismically active urban regions. Hence, Boğaziçi University Kandilli Observatory and Earthquake Research Institute (KOERI) Earthquake Engineering Department deployed a strong motion network at the Peninsula in June 2015. Three out of five stations (B1, B2, B3) are on an Alluvium sediment. The rests are on Limestone (B4) and Volcanic rock (B5). Soil profiles of the sites are not currently available. The network recorded more than 100 earthquakes in the last year. In the present study 15 events with magnitudes (Ml) from 3.4-5.4 occurred within 170 km epicentral distances were selected for calculation. PGA variations among stations were compared. B2 and B3 stations show consistently greater PGA values than others. Fundamental resonant frequencies of the sites were estimated by the H/V technique and relative amplifications were calculated by the Standard Spectral Ratio (SSR) technique. Based on fundamental resonant frequencies, B5 station was selected as the reference station for calculation of SSR spectra.Examining the earthquake data it was found out that (1) Predominant frequencies change between 2.0 - 3.7 Hz for soft soils, where it is 6 Hz for the reference site. The lowest frequency was observed at site B2; (2) Relative amplifications are in the range of 3 to 8. Even though B1, B2 and B3 stations rest on similar geological units, B1 gives the lowest relative amplification. It has been known that the building housing B1 station has a pile foundation and station may not be representative of free field conditions. Structural behaviors could be one of the reasons of such effect; (3) Spectral shapes obtained from SSR are similar to those obtained from H/V.

High average power scaling of optical parametric amplification through cascaded difference-frequency generators

DOEpatents

Jovanovic, Igor; Comaskey, Brian J.

2004-09-14

A first pump pulse and a signal pulse are injected into a first optical parametric amplifier. This produces a first amplified signal pulse. At least one additional pump pulse and the first amplified signal pulse are injected into at least one additional optical parametric amplifier producing an increased power coherent optical pulse.

Estimation of slip scenarios of mega-thrust earthquakes and strong motion simulations for Central Andes, Peru

NASA Astrophysics Data System (ADS)

Pulido, N.; Tavera, H.; Aguilar, Z.; Chlieh, M.; Calderon, D.; Sekiguchi, T.; Nakai, S.; Yamazaki, F.

2012-12-01

We have developed a methodology for the estimation of slip scenarios for megathrust earthquakes based on a model of interseismic coupling (ISC) distribution in subduction margins obtained from geodetic data, as well as information of recurrence of historical earthquakes. This geodetic slip model (GSM) delineates the long wavelength asperities within the megathrust. For the simulation of strong ground motion it becomes necessary to introduce short wavelength heterogeneities to the source slip to be able to efficiently simulate high frequency ground motions. To achieve this purpose we elaborate "broadband" source models constructed by combining the GSM with several short wavelength slip distributions obtained from a Von Karman PSD function with random phases. Our application of the method to Central Andes in Peru, show that this region has presently the potential of generating an earthquake with moment magnitude of 8.9, with a peak slip of 17 m and a source area of approximately 500 km along strike and 165 km along dip. For the strong motion simulations we constructed 12 broadband slip models, and consider 9 possible hypocenter locations for each model. We performed strong motion simulations for the whole central Andes region (Peru), spanning an area from the Nazca ridge (16^o S) to the Mendana fracture (9^o S). For this purpose we use the hybrid strong motion simulation method of Pulido et al. (2004), improved to handle a general slip distribution. Our simulated PGA and PGV distributions indicate that a region of at least 500 km along the coast of central Andes is subjected to a MMI intensity of approximately 8, for the slip model that yielded the largest ground motions among the 12 slip models considered, averaged for all assumed hypocenter locations. This result is in agreement with the macroseismic intensity distribution estimated for the great 1746 earthquake (M~9) in central Andes (Dorbath et al. 1990). Our results indicate that the simulated PGA and PGV for all scenario slips for central Andes, and for an average soil condition, exhibit similar amplitudes and attenuation characteristics with distance as the PGA and PGV values observed during the 2010 Maule (Mw 8.8), and 2011 Tohoku-oki (Mw 9.0) earthquakes. Our results clearly indicate that the simulated ground motions for scenarios with deep rupture nucleations (~40 km) are consistently smaller than the ground motions obtained for shallower rupture nucleations. We also performed strong ground motion simulations in metropolitan Lima by using the aforementioned slip scenarios, and incorporating site amplifications obtained from several microtremors array surveys conducted at representative geotechnical zones in this city. Our simulated PGA and PGV in Lima reach values of 1000 cm/s^2 and 80 cm/s. Our results show that the largest values of PGA (at Puente Piedra district, Northern Lima) are related with short period site effects, whereas the largest values of PGV are related with large site amplifications for periods from 1s to 1.5s (at Callao, Villa el Salvador and La Molina districts). Our results also indicate that the simulated PGA and PGV in central Lima (Parque de la Reserva) are in average 2~3 times larger than the values recorded by a strong motion instrument installed at this location, during the 1974 (Mw8.0) and 1966 (Mw8.0) earthquakes off-shore Lima.

Mode-locked Yb:YAG thin-disk oscillator with 41 µJ pulse energy at 145 W average infrared power and high power frequency conversion.

PubMed

Bauer, Dominik; Zawischa, Ivo; Sutter, Dirk H; Killi, Alexander; Dekorsy, Thomas

2012-04-23

We demonstrate the generation of 1.1 ps pulses containing more than 41 µJ of energy directly out of an Yb:YAG thin-disk without any additional amplification stages. The laser oscillator operates in ambient atmosphere with a 3.5 MHz repetition rate and 145 W of average output power at a fundamental wavelength of 1030 nm. An average output power of 91.5 W at 515 nm was obtained by frequency doubling with a conversion efficiency exceeding 65%. Third harmonic generation resulted in 34 W at 343 nm at 34% efficiency. © 2012 Optical Society of America

Virus-like attachment sites as structural landmarks of plants retrotransposons.

PubMed

Ochoa Cruz, Edgar Andres; Cruz, Guilherme Marcello Queiroga; Vieira, Andréia Prata; Van Sluys, Marie-Anne

2016-01-01

The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. Recently it has been found that Del lineage, an LTR-RT of Gypsy superfamily, has putative virus-like attachment (vl-att) sites. This signature, originally described for retroviruses, is recognized by retroviral integrase conferring specificity to the integration process. Here we retrieved 26,092 putative complete LTR-RTs from 10 lineages found in 10 fully sequenced angiosperm genomes and found putative vl-att sites that are a conserved structural landmark across these genomes. Furthermore, we reveal that each plant genome has a distinguishable LTR-RT lineage amplification pattern that could be related to the vl-att sites diversity. We used these patterns to generate a specific quick-response (QR) code for each genome that could be used as a barcode of identification of plants in the future. The universal distribution of vl-att sites represents a new structural feature common to plant LTR-RTs and retroviruses. This is an important finding that expands the information about the structural similarity between LTR-RT and retroviruses. We speculate that the sequence diversity of vl-att sites could be important for the life cycle of retrotransposons, as it was shown for retroviruses. All the structural vl-att site signatures are strong candidates for further functional studies. Moreover, this is the first identification of specific LTR-RT content and their amplification patterns in a large dataset of LTR-RT lineages and angiosperm genomes. These distribution patterns could be used in the future with biotechnological identification purposes.

Seismic response of soft deposits due to landslide: The Mission Peak, California, landslide

USGS Publications Warehouse

Hartzell, Stephen; Leeds, Alena L.; Jibson, Randall W.

2017-01-01

The seismic response of active and intermittently active landslides is an important issue to resolve to determine if such landslides present an elevated hazard in future earthquakes. To study the response of landslide deposits, seismographs were placed on the Mission Peak landslide in the eastern San Francisco Bay region for a period of one year. Numerous local and near‐regional earthquakes were recorded that reveal a complexity of seismic response phenomena using the horizontal‐to‐vertical spectral ratio method. At lower frequencies, a clear spectral peak is observed at 0.5 Hz common to all four stations in the array and is attributed to a surface topographic effect. At higher frequencies, other spectral peaks occur that are interpreted in terms of local deposits and structures. Site amplification from the standard reference site method shows the minimum amplification with a factor of 2, comparing a site on and off the landslide. A site located on relatively homogeneous deposits of loose soils shows a clear spectral peak associated with the thickness of the deposit. Another site on a talus‐filled graben near the headscarp shows possible 2D or 3D effects from subsurface topography or scattering within and between buried sandstone blocks. A third site on a massive partially detached block below the crown of the headscarp shows indications of resonance caused by the reverberation of shear waves within the block. The varied seismic response of different parts of this complex landslide is consistent with other studies which found that, although landslide response is commonly enhanced in the downslope direction of landslide movement, such a response does not occur uniformly or consistently. When it does occur, enhanced site response parallel to the direction of landslide movement would contribute to landslide reactivation during significant earthquakes.

Development of a molecular diagnostic system to discriminate Dreissena polymorpha (zebra mussel) and Dreissena bugensis (quagga mussel)

USGS Publications Warehouse

Hoy, M.S.; Kelly, K.; Rodriguez, R.J.

2010-01-01

A 3-primer PCR system was developed to discriminate invasive zebra (Dreissena polymorpha) and quagga (Dreissena bugensis) mussel. The system is based on: 1) universal primers that amplifies a region of the nuclear 28s rDNA gene from both species and 2) a species-specific primer complementary to either zebra or quagga mussel. The species-specific primers bind to sequences between the binding sites for the universal primers resulting in the amplification of two products from the target species and one product from the nontarget species. Therefore, nontarget products are positive amplification controls. The 3-primer system accurately discriminated zebra and quagga mussels from seven geographically distinct populations.

Directional topographic site response at Tarzana observed in aftershocks of the 1994 Northridge, California, earthquake: Implications for mainshock motions

USGS Publications Warehouse

Spudich, P.; Hellweg, M.; Lee, W.H.K.

1996-01-01

The Northridge earthquake caused 1.78 g acceleration in the east-west direction at a site in Tarzana, California, located about 6 km south of the mainshock epicenter. The accelerograph was located atop a hill about 15-m high, 500-m long, and 130-m wide, striking about N78??E. During the aftershock sequence, a temporary array of 21 three-component geophones was deployed in six radial lines centered on the accelerograph, with an average sensor spacing of 35 m. Station COO was located about 2 m from the accelerograph. We inverted aftershock spectra to obtain average relative site response at each station as a function of direction of ground motion. We identified a 3.2-Hz resonance that is a transverse oscillation of the hill (a directional topographic effect). The top/base amplification ratio at 3.2 Hz is about 4.5 for horizontal ground motions oriented approximately perpendicular to the long axis of the hill and about 2 for motions parallel to the hill. This resonance is seen most strongly within 50 m of COO. Other resonant frequencies were also observed. A strong lateral variation in attenuation, probably associated with a fault, caused substantially lower motion at frequencies above 6 Hz at the east end of the hill. There may be some additional scattered waves associated with the fault zone and seen at both the base and top of the hill, causing particle motions (not spectral ratios) at the top of the hill to be rotated about 20?? away from the direction transverse to the hill. The resonant frequency, but not the amplitude, of our observed topographic resonance agrees well with theory, even for such a low hill. Comparisons of our observations with theoretical results indicate that the 3D shape of the hill and its internal structure are important factors affecting its response. The strong transverse resonance of the hill does not account for the large east-west mainshock motions. Assuming linear soil response, mainshock east-west motions at the Tarzana accelerograph were amplified by a factor of about 2 or less compared with sites at the base of the hill. Probable variations in surficial shear-wave velocity do not account for the observed differences among mainshock acceleration observed at Tarzana and at two different sites within 2 km of Tarzana.

Optimization of ultrahigh-speed multiplex PCR for forensic analysis.

PubMed

Gibson-Daw, Georgiana; Crenshaw, Karin; McCord, Bruce

2018-01-01

In this paper, we demonstrate the design and optimization of an ultrafast PCR amplification technique, used with a seven-locus multiplex that is compatible with conventional capillary electrophoresis systems as well as newer microfluidic chip devices. The procedure involves the use of a high-speed polymerase and a rapid cycling protocol to permit multiplex PCR amplification of forensic short tandem repeat loci in 6.5 min. We describe the selection and optimization of master mix reagents such as enzyme, buffer, MgCl 2 , and dNTPs, as well as primer ratios, total volume, and cycle conditions, in order to get the best profile in the shortest time possible. Sensitivity and reproducibility studies are also described. The amplification process utilizes a small high-speed thermocycler and compact laptop, making it portable and potentially useful for rapid, inexpensive on-site genotyping. The seven loci of the multiplex were taken from conventional STR genotyping kits and selected for their size and lack of overlap. Analysis was performed using conventional capillary electrophoresis and microfluidics with fluorescent detection. Overall, this technique provides a more rapid method for rapid sample screening of suspects and victims. Graphical abstract Rapid amplification of forensic DNA using high speed thermal cycling followed by capillary or microfluidic electrophoresis.

Assessment of primer/template mismatch effects on real-time PCR amplification of target taxa for GMO quantification.

PubMed

Ghedira, Rim; Papazova, Nina; Vuylsteke, Marnik; Ruttink, Tom; Taverniers, Isabel; De Loose, Marc

2009-10-28

GMO quantification, based on real-time PCR, relies on the amplification of an event-specific transgene assay and a species-specific reference assay. The uniformity of the nucleotide sequences targeted by both assays across various transgenic varieties is an important prerequisite for correct quantification. Single nucleotide polymorphisms (SNPs) frequently occur in the maize genome and might lead to nucleotide variation in regions used to design primers and probes for reference assays. Further, they may affect the annealing of the primer to the template and reduce the efficiency of DNA amplification. We assessed the effect of a minor DNA template modification, such as a single base pair mismatch in the primer attachment site, on real-time PCR quantification. A model system was used based on the introduction of artificial mismatches between the forward primer and the DNA template in the reference assay targeting the maize starch synthase (SSIIb) gene. The results show that the presence of a mismatch between the primer and the DNA template causes partial to complete failure of the amplification of the initial DNA template depending on the type and location of the nucleotide mismatch. With this study, we show that the presence of a primer/template mismatch affects the estimated total DNA quantity to a varying degree.

Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification.

PubMed

Tzvetkov, Mladen V; Becker, Christian; Kulle, Bettina; Nürnberg, Peter; Brockmöller, Jürgen; Wojnowski, Leszek

2005-02-01

Whole-genome DNA amplification by multiple displacement (MD-WGA) is a promising tool to obtain sufficient DNA amounts from samples of limited quantity. Using Affymetrix' GeneChip Human Mapping 10K Arrays, we investigated the accuracy and allele amplification bias in DNA samples subjected to MD-WGA. We observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. This concordance was only 0.01% lower than the intra-assay reproducibility of the genotyping technique used. However, MD-WGA failed to amplify an estimated 7% of polymorphic loci. Due to the algorithm used to call genotypes, this was detected only for heterozygous loci. We achieved a 4.3-fold reduction of noncalled SNPs by combining the results from two independent MD-WGA reactions. This indicated that inter-reaction variations rather than specific chromosomal loci reduced the efficiency of MD-WGA. Consistently, we detected no regions of reduced amplification, with the exception of several SNPs located near chromosomal ends. Altogether, despite a substantial loss of polymorphic sites, MD-WGA appears to be the current method of choice to amplify genomic DNA for array-based SNP analyses. The number of nonamplified loci can be substantially reduced by amplifying each DNA sample in duplicate.

Trifunctional molecular beacon-mediated quadratic amplification for highly sensitive and rapid detection of mercury(II) ion with tunable dynamic range.

PubMed

Zhao, Yue; Liu, Huaqing; Chen, Feng; Bai, Min; Zhao, Junwu; Zhao, Yongxi

2016-12-15

Analyses of target with low abundance or concentration varying over many orders of magnitude are severe challenges faced by numerous assay methods due to their modest sensitivity and limited dynamic range. Here, we introduce a homogeneous and rapid quadratic polynomial amplification strategy through rational design of a trifunctional molecular beacon, which serves as not only a reporter molecule but also a bridge to couple two stage amplification modules without adding any reaction components or process other than basic linear amplification. As a test bed for our studies, we took mercury(II) ion as an example and obtained a high sensitivity with detection limit down to 200 pM within 30min. In order to create a tunable dynamic range, homotropic allostery is employed to modulate the target specific binding. When the number of metal binding site varies from 1 to 3, signal response is programmed accordingly with useful dynamic range spanning 50, 25 and 10 folds, respectively. Furthermore, the applicability of the proposed method in river water and biological samples are successfully verified with good recovery and reproducibility, indicating considerable potential for its practicality in complex real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Topographic Slope as a Proxy for Seismic Site-Conditions (VS30) and Amplification Around the Globe

USGS Publications Warehouse

Allen, Trevor I.; Wald, David J.

2007-01-01

Executive Summary It is well-known that large global earthquakes can have a dramatic effect on local communities and the built environment. Moreover, ground motions amplified by surficial materials can exacerbate the situation, often making the difference between minor and major damage. For a real-time earthquake impact alert system, such as Prompt Assessment of Global Earthquakes for Response (PAGER) (Wald and others, 2006), we seek to rapidly evaluate potential ground shaking in the source region and subsequently provide an estimate of the population exposure to potentially fatal levels of ground shaking in any region of the world. The contribution of surficial geology (particularly soft sediments) to the amplification of ground shaking is an important component in predicting the levels of ground motion observed at any site. Unfortunately, the availability of information regarding seismic siteconditions is only available at a few sites around the globe. Herein, we describe a methodology for deriving maps of seismic site-conditions anywhere in the world using topographic slope as a proxy. Average shear-velocity down to 30 m (or VS30) measurements are correlated against topographic slope to develop two sets of coefficients for predicting VS30: one for active tectonic regions that possess dynamic topographic relief, and one for stable continental regions where changes in topography are more subdued. These coefficients have been applied to the continental United States, in addition to other regions around the world. They are subsequently compared to existing site-condition maps based on geology and observed VS30 measurements, where available. The application of the topographic slope method in regions with abundant VS30 measurements (for example California, Memphis, and Taiwan) indicates that this method provides site condition-maps of similar quality, or in some cases, maps superior to those developed from more traditional techniques. Having a first-order assessment of seismic site-conditions anywhere in the world provides a valuable tool to rapidly estimate ground motions following any global earthquake, the primary motivation for this research. These VS30 maps will enable us to better quantify possible ground shaking and rapidly deliver these predictions to emergency managers and responders. In addition, the VS30 maps for the globe will also have practical applications for numerous related probabilistic- and scenario-based studies. To date, several researchers have requested maps or have used the approach outlined herein for their own applications (for example Cagnan and Kariptas, written commun., 2007; Harmandar and others, 2007). Given that we anticipate a significant demand for these products, we have developed an internet delivery service so that users can download maps and grids of seismic site-conditions for specified regions. To some extent, these grids can also be customized by the user if they disagree with the predefined correlations derived using the methodologies described within this report. Finally, this report represents a more comprehensive account of this technique and provides a more fully illustrated global description of results than that given in Wald and Allen (2007), which has been accepted for publication in the Bulletin of the Seismological Society of America.

Newly-Identified Fragile Sites Push Stressed Cells toward Cancer | Center for Cancer Research

Cancer.gov

The genomes of cancer cells are often riddled with chromosomal alterations such as amplifications, deletions, and even translocations, where a piece of one chromosome breaks off and attaches to another. Understanding how these changes arise can give researchers new insights into the process of cancer development.

NGA West 2 | Pacific Earthquake Engineering Research Center

Science.gov Websites

, multi-year research program to improve Next Generation Attenuation models for active tectonic regions earthquake engineering, including modeling of directivity and directionality; verification of NGA-West models epistemic uncertainty; and evaluation of soil amplification factors in NGA models versus NEHRP site factors

Estimating Bodywave Arrivals and Attenuation from Seismic Noise

DTIC Science & Technology

2009-09-30

power) and Figure 3d the standardized site amplification terms from Savage and Helmberger (2004) who used the Pnl ratio of vertical to radial energy...incident Pnl waves, Bull. Seismol. Soc. Am. 94: 357-362. Shearer, P. (1997). Improving local earthquake locations using the LI norm and waveform

Genomic DNA sequence and cytosine methylation changes of adult rice leaves after seeds space flight

NASA Astrophysics Data System (ADS)

Shi, Jinming

In this study, cytosine methylation on CCGG site and genomic DNA sequence changes of adult leaves of rice after seeds space flight were detected by methylation-sensitive amplification polymorphism (MSAP) and Amplified fragment length polymorphism (AFLP) technique respectively. Rice seeds were planted in the trial field after 4 days space flight on the shenzhou-6 Spaceship of China. Adult leaves of space-treated rice including 8 plants chosen randomly and 2 plants with phenotypic mutation were used for AFLP and MSAP analysis. Polymorphism of both DNA sequence and cytosine methylation were detected. For MSAP analysis, the average polymorphic frequency of the on-ground controls, space-treated plants and mutants are 1.3%, 3.1% and 11% respectively. For AFLP analysis, the average polymorphic frequencies are 1.4%, 2.9%and 8%respectively. Total 27 and 22 polymorphic fragments were cloned sequenced from MSAP and AFLP analysis respectively. Nine of the 27 fragments from MSAP analysis show homology to coding sequence. For the 22 polymorphic fragments from AFLP analysis, no one shows homology to mRNA sequence and eight fragments show homology to repeat region or retrotransposon sequence. These results suggest that although both genomic DNA sequence and cytosine methylation status can be effected by space flight, the genomic region homology to the fragments from genome DNA and cytosine methylation analysis were different.

Transcription Factor Stat5, A Novel Therapeutic Protein, Inhibits Metastatic Potential and Invasive Characteristics of Human Breast Cancer Cells

DTIC Science & Technology

2004-10-01

digestion and cloned into pLoxpNeo upstream of the PGK-neomycin cassette. A 1.3 kb fragment with the first coding exon was amplified by Pfx polymerase ...introducing a XhoI site on the 5’-end of the amplification product. The PCR fragment was cloned blunt into the HinDIII(blunt) site 5’ of the single...functionality of each of the loxP sites was tested in AM-1 cells (Invitrogen) that express Cre recombinase . Step 2: Gene targeting in embryonic stem

Microsatellite markers for Vellozia gigantea (Velloziaceae), a narrowly endemic species to the Brazilian campos rupestres.

PubMed

Martins, Ana Paula V; Proite, Karina; Kalapothakis, Evanguedes; Santos, Fabrício R; Chaves, Anderson V; Borba, Eduardo L

2012-07-01

Microsatellite primers were developed for the first time in Velloziaceae, in the endangered species Vellozia gigantea. Using two different protocols, seven primer sets were characterized in three populations of V. gigantea. The primers amplified di- and trinucleotide repeats with six to 12 alleles per locus. These revealed high levels of genetic variation, presenting an average observed heterozygosity of 0.508 in V. gigantea. The seven primers were tested for cross-amplification in three Vellozia species. All primers successfully amplified in V. auriculata. Six primers amplified in V. compacta and three in V. hirsuta. The new marker set described here will be useful for studies of population genetics of V. gigantea. The cross-amplification results indicate the utility of primers for studies in other Vellozia species.

Characterization of a 21-Story Reinforced Building in the Valley of Mexico Using MEMS Accelerometers.

NASA Astrophysics Data System (ADS)

Husker, A. L.; Dominguez, L. A.; Becerril, A.; Espejo, L.; Cochran, E. S.

2014-12-01

Low cost MEMS accelerometers are becoming increasingly higher resolution making them useful in strong motion studies. Here we present a building response analysis in the lakebed zone of the Valley of Mexico. The Valley of Mexico represents one of the highest seismic risk locations in the world and incorporates Mexico City and part of Mexico State. More than 20 million people live there and it is the political and economic center of Mexico. In addition the valley has very high site effects with amplifications 100 - 500 times that of sites outside of the basin (Singh et al., 1988; Singh et al., 1995). We instrumented a 21-story building with MEMS accelerometers as part of the Quake Catcher Network or Red Atrapa Sismos as it is called in Mexico. The building known as the Centro Cultural de Tlateloco is located in an important historical and political area as well as a zone with some of the highest amplifications in the Valley of Mexico that had some of the worst destruction after the 1985 M8.1 Michoacan earthquake. During the earthquake most of the buildings that failed were between 7 - 18 stories tall. The peak accelerations near Tlateloco were at periods of 2 seconds. Since the earthquake the building has been retrofitted with N-S crossing supports to help withstand another earthquake. We present the measurements of frequencies and amplifications between floors for the length of the building.

The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans

PubMed Central

Yang, Huan; Vallandingham, Jim; Shiu, Philip; Li, Hua; Hunter, Craig P.; Mak, Ho Yi

2014-01-01

Summary RNA interference (RNAi) is a potent mechanism for down-regulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi and other eukaryotes [1–3]. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary siRNAs [4–6]. Exogenous double stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis [7, 8]. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear if the sub-cellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively [9–11]. We report that RDE-12, a conserved FG domain containing DEAD-box helicase, localizes in P-granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA targeted mRNA in distinct cytoplasmic compartments. PMID:24684930

The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans.

PubMed

Yang, Huan; Vallandingham, Jim; Shiu, Philip; Li, Hua; Hunter, Craig P; Mak, Ho Yi

2014-04-14

RNAi is a potent mechanism for downregulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi, and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary small interfering RNAs (siRNAs). Exogenous double-stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA-dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear whether the subcellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved phenylalanine-glycine (FG) domain-containing DEAD box helicase, localizes in P granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA-targeted mRNA in distinct cytoplasmic compartments. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sensitivity of ground motion parameters to local site effects for areas characterised by a thick buried low-velocity layer.

NASA Astrophysics Data System (ADS)

Farrugia, Daniela; Galea, Pauline; D'Amico, Sebastiano; Paolucci, Enrico

2016-04-01

It is well known that earthquake damage at a particular site depends on the source, the path that the waves travel through and the local geology. The latter is capable of amplifying and changing the frequency content of the incoming seismic waves. In regions of sparse or no strong ground motion records, like Malta (Central Mediterranean), ground motion simulations are used to obtain parameters for purposes of seismic design and analysis. As an input to ground motion simulations, amplification functions related to the shallow subsurface are required. Shear-wave velocity profiles of several sites on the Maltese islands were obtained using the Horizontal-to-Vertical Spectral Ratio (H/V), the Extended Spatial Auto-Correlation (ESAC) technique and the Genetic Algorithm. The sites chosen were all characterised by a layer of Blue Clay, which can be up to 75 m thick, underlying the Upper Coralline Limestone, a fossiliferous coarse grained limestone. This situation gives rise to a velocity inversion. Available borehole data generally extends down till the top of the Blue Clay layer therefore the only way to check the validity of the modelled shear-wave velocity profile is through the thickness of the topmost layer. Surface wave methods are characterised by uncertainties related to the measurements and the model used for interpretation. Moreover the inversion procedure is also highly non-unique. Such uncertainties are not commonly included in site response analysis. Yet, the propagation of uncertainties from the extracted dispersion curves to inversion solutions can lead to significant differences in the simulations (Boaga et al., 2011). In this study, a series of sensitivity analyses will be presented with the aim of better identifying those stratigraphic properties which can perturb the ground motion simulation results. The stochastic one-dimensional site response analysis algorithm, Extended Source Simulation (EXSIM; Motazedian and Atkinson, 2005), was used to perform these analyses. The amplification functions were extracted using the programme SITE_AMP (Boore, 2003), which computes amplifications based on the square root of the effective seismic impedance. Sensitivity indices were obtained by changing two parameters (thickness and shear-wave velocity) of the different layers while keeping the others constant. Additional analyses were carried out by producing various profiles within specified boundaries which are able to fit the experimental data. The analyses also show the important role that the shear-wave velocity profiles play in ground motion simulations. The results obtained highlight the importance of the correct knowledge of both the properties of the Upper Coralline Limestone and the Blue Clay, especially the Blue Clay thickness.

Intensity noise reduction of a high-power nonlinear femtosecond fiber amplifier based on spectral-breathing self-similar parabolic pulse evolution

NASA Astrophysics Data System (ADS)

Wang, Sijia; Liu, Bowen; Song, Youjian; Hu, Minglie

2016-04-01

We report on a simple passive scheme to reduce the intensity noise of high-power nonlinear fiber amplifiers by use of the spectral-breathing parabolic evolution of the pulse amplification with an optimized negative initial chirp. In this way, the influences of amplified spontaneous emission (ASE) on the amplifier intensity noise can be efficiently suppressed, owing to the lower overall pulse chirp, shorter spectral broadening distance, as well as the asymptotic attractive nature of self-similar pulse amplification. Systematic characterizations of the relative intensity noise (RIN) of a free-running nonlinear Yb-doped fiber amplifier are performed over a series of initial pulse parameters. Experiments show that the measured amplifier RIN increases respect to the decreased input pulse energy, due to the increased amount of ASE noise. For pulse amplification with a proper negative initial chirp, the increase of RIN is found to be smaller than with a positive initial chirp, confirming the ASE noise tolerance of the proposed spectral-breathing parabolic amplification scheme. At the maximum output average power of 27W (25-dB amplification gain), the incorporation of an optimum negative initial chirp (-0.84 chirp parameter) leads to a considerable amplifier root-mean-square (rms) RIN reduction of ~20.5% (integrated from 10 Hz to 10 MHz Fourier frequency). The minimum amplifier rms RIN of 0.025% (integrated from 1 kHz to 5 MHz Fourier frequency) is obtained along with the transform-limited compressed pulse duration of 55fs. To our knowledge, the demonstrated intensity noise performance is the lowest RIN level measured from highpower free-running femtosecond fiber amplifiers.

Forensic DNA methylation profiling from minimal traces: How low can we go?

PubMed

Naue, Jana; Hoefsloot, Huub C J; Kloosterman, Ate D; Verschure, Pernette J

2018-03-01

Analysis of human DNA methylation (DNAm) can provide additional investigative leads in crime cases, e.g. the type of tissue or body fluid, the chronological age of an individual, and differentiation between identical twins. In contrast to the genetic profile, the DNAm level is not the same in every cell. At the single cell level, DNAm represents a binary event at a defined CpG site (methylated versus non-methylated). The DNAm level from a DNA extract however represents the average level of methylation of the CpG of interest of all molecules in the forensic sample. The variance of DNAm levels between replicates is often attributed to technological issues, i.e. degradation of DNA due to bisulfite treatment, preferential amplification of DNA, and amplification failure. On the other hand, we show that stochastic variations can lead to gross fluctuation in the analysis of methylation levels in samples with low DNA levels. This stochasticity in DNAm results is relevant since low DNA amounts (1pg - 1ng) is rather the norm than the exception when analyzing forensic DNA samples. This study describes a conceptual analysis of DNAm profiling and its dependence on the amount of input DNA. We took a close look at the variation of DNAm analysis due to DNA input and its consequences for different DNAm-based forensic applications. As can be expected, the 95%-confidence interval of measured DNAm becomes narrower with increasing amounts of DNA. We compared this aspect for two different DNAm-based forensic applications: body fluid identification and chronological age determination. Our study shows that DNA amount should be well considered when using DNAm for forensic applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Application of plant DNA markers in forensic botany: genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites.

PubMed

Craft, Kathleen J; Owens, Jeffrey D; Ashley, Mary V

2007-01-05

As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.

Genetic Analysis of Aedes aegypti Using Random Amplified Polymorphic DNA (RAPD) Markers from Dengue Outbreaks in Pakistan.

PubMed

Ashraf, Hafiz Muhammad; Zahoor, Muhammad Kashif; Nasir, Shabab; Majeed, Humara Naz; Zahoor, Sarwat

2016-12-01

Keeping in view the havoc situation of dengue fever in Pakistan, the current study was designed to demonstrate the genetic variations, gene flow and rate of migration from Lahore and Faisalabad. The larvae were collected from both natural and artificial breeding places from each collection site. The adult mosquitoes were collected by means of sweep net and battery-operated aspirator. DNA extraction was performed using TNE buffer method. Ten GeneLink-A series RAPD primers were used for PCR amplification and the data was analyzed through POPGENE. The number of amplification products produced per primer varied from 8-12, ranging from 200 to 2000 bp with an average of 10.0 bands per primer. The percentage of polymorphic loci amplified by each primer varied from 22.5 to 51%. The UPGMA dendrogram demonstrates two distinct groups from Faisalabad and Lahore populations. The genetic diversity ranged from 0.260 in Faisalabad to 0.294 in Lahore with a total heterozygosity of 0.379. The G ST value for nine populations within Lahore was 0.131 (Nm= 3.317), whereas for nine populations in Faisalabad G ST value was 0.117 (Nm= 3.773). The overall genetic variation among eighteen populations showed G ST = 0.341 and Nm= 1.966. The genetic relatedness and Nm value show that Ae . aegypti populations exhibit intra-population gene flow both in Faisalabad and Lahore. Although, both cities show a distinct pattern of genetic structure; however, few areas from both the cities show genetic similarity. The gene flow and the genetic relatedness in few populations of Lahore and Faisalabad cities need further investigation.

MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene.

PubMed

Kim, Jisun; Geyer, Felipe C; Martelotto, Luciano G; Ng, Charlotte Ky; Lim, Raymond S; Selenica, Pier; Li, Anqi; Pareja, Fresia; Fusco, Nicola; Edelweiss, Marcia; Kumar, Rahul; Gularte-Merida, Rodrigo; Forbes, Andre N; Khurana, Ekta; Mariani, Odette; Badve, Sunil; Vincent-Salomon, Anne; Norton, Larry; Reis-Filho, Jorge S; Weigelt, Britta

2018-02-01

Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer, has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangements, have been reported in MYB-NFIB-negative salivary gland AdCCs. Here we report on the molecular characterization by massively parallel sequencing of four breast AdCCs lacking the MYB-NFIB fusion gene. In two cases, we identified MYBL1 rearrangements (MYBL1-ACTN1 and MYBL1-NFIB), which were associated with MYBL1 overexpression. A third AdCC harboured a high-level MYB amplification, which resulted in MYB overexpression at the mRNA and protein levels. RNA-sequencing and whole-genome sequencing revealed no definite alternative driver in the fourth AdCC studied, despite high levels of MYB expression and the activation of pathways similar to those activated in MYB-NFIB-positive AdCCs. In this case, a deletion encompassing the last intron and part of exon 15 of MYB, including the binding site of ERG-1, a transcription factor that may downregulate MYB, and the exon 15 splice site, was detected. In conclusion, we demonstrate that MYBL1 rearrangements and MYB amplification probably constitute alternative genetic drivers of breast AdCCs, functioning through MYBL1 or MYB overexpression. These observations emphasize that breast AdCCs probably constitute a convergent phenotype, whereby activation of MYB and MYBL1 and their downstream targets can be driven by the MYB-NFIB fusion gene, MYBL1 rearrangements, MYB amplification, or other yet to be identified mechanisms. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches

PubMed Central

Green, Stefan J.; Venkatramanan, Raghavee; Naqib, Ankur

2015-01-01

The polymerase chain reaction (PCR) is sensitive to mismatches between primer and template, and mismatches can lead to inefficient amplification of targeted regions of DNA template. In PCRs in which a degenerate primer pool is employed, each primer can behave differently. Therefore, inefficiencies due to different primer melting temperatures within a degenerate primer pool, in addition to mismatches between primer binding sites and primers, can lead to a distortion of the true relative abundance of targets in the original DNA pool. A theoretical analysis indicated that a combination of primer-template and primer-amplicon interactions during PCR cycles 3–12 is potentially responsible for this distortion. To test this hypothesis, we developed a novel amplification strategy, entitled “Polymerase-exonuclease (PEX) PCR”, in which primer-template interactions and primer-amplicon interactions are separated. The PEX PCR method substantially and significantly improved the evenness of recovery of sequences from a mock community of known composition, and allowed for amplification of templates with introduced mismatches near the 3’ end of the primer annealing sites. When the PEX PCR method was applied to genomic DNA extracted from complex environmental samples, a significant shift in the observed microbial community was detected. Furthermore, the PEX PCR method provides a mechanism to identify which primers in a primer pool are annealing to target gDNA. Primer utilization patterns revealed that at high annealing temperatures in the PEX PCR method, perfect match annealing predominates, while at lower annealing temperatures, primers with up to four mismatches with templates can contribute substantially to amplification. The PEX PCR method is simple to perform, is limited to PCR mixes and a single exonuclease step which can be performed without reaction cleanup, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and template are possible. PMID:25996930

Label-Free Sensitive Detection of DNA Methyltransferase by Target-Induced Hyperbranched Amplification with Zero Background Signal.

PubMed

Zhang, Yan; Wang, Xin-Yan; Zhang, Qianyi; Zhang, Chun-Yang

2017-11-21

DNA methyltransferases (MTases) may specifically recognize the short palindromic sequences and transfer a methyl group from S-adenosyl-l-methionine to target cytosine/adenine. The aberrant DNA methylation is linked to the abnormal DNA MTase activity, and some DNA MTases have become promising targets of anticancer/antimicrobial drugs. However, the reported DNA MTase assays often involve laborious operation, expensive instruments, and radio-labeled substrates. Here, we develop a simple and label-free fluorescent method to sensitively detect DNA adenine methyltransferase (Dam) on the basis of terminal deoxynucleotidyl transferase (TdT)-activated Endonuclease IV (Endo IV)-assisted hyperbranched amplification. We design a hairpin probe with a palindromic sequence in the stem as the substrate and a NH 2 -modified 3' end for the prevention of nonspecific amplification. The substrate may be methylated by Dam and subsequently cleaved by DpnI, producing three single-stranded DNAs, two of which with 3'-OH termini may be amplified by hyperbranched amplification to generate a distinct fluorescence signal. Because high exactitude of TdT enables the amplification only in the presence of free 3'-OH termini and Endo IV only hydrolyzes the intact apurinic/apyrimidinic sites in double-stranded DNAs, zero background signal can be achieved. This method exhibits excellent selectivity and high sensitivity with a limit of detection of 0.003 U/mL for pure Dam and 9.61 × 10 -6 mg/mL for Dam in E. coli cells. Moreover, it can be used to screen the Dam inhibitors, holding great potentials in disease diagnosis and drug development.

Nonenzymatic catalytic signal amplification for nucleic acid hybridization assays

NASA Technical Reports Server (NTRS)

Fan, Wenhong (Inventor); Han, Jie (Inventor); Cassell, Alan M. (Inventor)

2006-01-01

Devices, methods, and kits for amplifying the signal from hybridization reactions between nucleic acid probes and their cognate targets are presented. The devices provide partially-duplexed, immobilized probe complexes, spatially separate from and separately addressable from immobilized docking strands. Cognate target acts catalytically to transfer probe from the site of probe complex immobilization to the site of immobilized docking strand, generating a detectable signal. The methods and kits of the present invention may be used to identify the presence of cognate target in a fluid sample.

Clinical, Biologic, and Prognostic Differences on the Basis of Primary Tumor Site in Neuroblastoma: A Report From the International Neuroblastoma Risk Group Project

PubMed Central

Vo, Kieuhoa T.; Matthay, Katherine K.; Neuhaus, John; London, Wendy B.; Hero, Barbara; Ambros, Peter F.; Nakagawara, Akira; Miniati, Doug; Wheeler, Kate; Pearson, Andrew D.J.; Cohn, Susan L.; DuBois, Steven G.

2014-01-01

Purpose Neuroblastoma (NB) is a heterogeneous tumor arising from sympathetic tissues. The impact of primary tumor site in influencing the heterogeneity of NB remains unclear. Patients and Methods Children younger than age 21 years diagnosed with NB or ganglioneuroblastoma between 1990 and 2002 and with known primary site were identified from the International Neuroblastoma Risk Group database. Data were compared between sites with respect to clinical and biologic features, as well as event-free survival (EFS) and overall survival (OS). Results Among 8,369 children, 47% had adrenal tumors. All evaluated clinical and biologic variables differed statistically between primary sites. The features that were > 10% discrepant between sites were stage 4 disease, MYCN amplification, elevated ferritin, elevated lactate dehydrogenase, and segmental chromosomal aberrations, all of which were more frequent in adrenal versus nonadrenal tumors (P < .001). Adrenal tumors were more likely than nonadrenal tumors (adjusted odds ratio, 2.09; 95% CI, 1.67 to 2.63; P < .001) and thoracic tumors were less likely than nonthoracic tumors (adjusted odds ratio, 0.20; 95% CI, 0.11 to 0.39; P < .001) to have MYCN amplification after controlling for age, stage, and histologic grade. EFS and OS differed significantly according to the primary site (P < .001 for both comparisons). After controlling for age, MYCN status, and stage, patients with adrenal tumors had higher risk for events (hazard ratio, 1.13 compared with nonadrenal tumors; 95% CI, 1.03 to 1.23; P = .008), and patients with thoracic tumors had lower risk for events (HR, 0.79 compared with nonthoracic; 95% CI, 0.67 to 0.92; P = .003). Conclusion Clinical and biologic features show important differences by NB primary site, with adrenal and thoracic sites associated with inferior and superior survival, respectively. Future studies will need to investigate the biologic origin of these differences. PMID:25154816

Using Ambient Noise for Investigating Cultural Heritage Sites and Evaluating Seismic Site Response

NASA Astrophysics Data System (ADS)

D'Amico, S.; Farrugia, D.; Galea, P. M.; Ruben, B. P., Sr.

2016-12-01

Recordings of ambient noise as well as use of the HVSR technique represent a common tool for evaluating seismic site response. In this study we applied such techniques to several cultural heritage sites located on the Maltese archipelago (Central Mediterranean). In particular, two of the Maltese watchtowers, built by the Knights of St. John between 1637 and 1659, were investigated together with the megalithic temple site of Mnajdra. Array data were acquired using the Micromed SoilSpy Rosina™ equipped with 4.5 Hz vertical geophones, setting the array in an L-shaped configuration. The Extended Spatial Autocorrelation (ESAC) technique was used to extract Rayleigh-wave dispersion curves. Moreover, single-station data close to the array was collected using a Tromino 3-component seismograph (www.tromino.eu), and the H/V curves were extracted. The dispersion curves and the H/V curves were jointly inverted using the Genetic Algorithm (GA) to obtain the shear-wave velocity profile. A fixed number of layers was used in the inversion and ranges for the layer thickness, P-wave and S-wave velocity, and density were specified. The obtained velocity profiles were used to compute the amplification function for the site based on the square root of the effective seismic impedance, also known as the quarter-wavelength approximation. This was used in the simulation of ground motion parameters at the site for various earthquakes using the stochastic one-dimensional site response analysis algorithm, Extended Source Simulation (EXSIM). In addition, the fundamental period and the damping ratio of the watchtowers was obtained by recording ambient vibrations. In the megalithic temples we were also able to evaluate the coverage of the soil deposits within the structure, comparing our results with previous study that used different geophysical techniques. In conclusion, this study enables us to map the seismic amplification hazard and provides primary data on the seismic risk assessment of each cultural heritage site.

Pathways of Prion Spread during Early Chronic Wasting Disease in Deer

PubMed Central

Hoover, Clare E.; Davenport, Kristen A.; Henderson, Davin M.; Denkers, Nathaniel D.; Mathiason, Candace K.; Soto, Claudio; Zabel, Mark D.

2017-01-01

ABSTRACT Among prion infections, two scenarios of prion spread are generally observed: (i) early lymphoid tissue replication or (ii) direct neuroinvasion without substantial antecedent lymphoid amplification. In nature, cervids are infected with chronic wasting disease (CWD) prions by oral and nasal mucosal exposure, and studies of early CWD pathogenesis have implicated pharyngeal lymphoid tissue as the earliest sites of prion accumulation. However, knowledge of chronological events in prion spread during early infection remains incomplete. To investigate this knowledge gap in early CWD pathogenesis, we exposed white-tailed deer to CWD prions by mucosal routes and performed serial necropsies to assess PrPCWD tissue distribution by real-time quaking-induced conversion (RT-QuIC) and tyramide signal amplification immunohistochemistry (TSA-IHC). Although PrPCWD was not detected by either method in the initial days (1 and 3) postexposure, we observed PrPCWD seeding activity and follicular immunoreactivity in oropharyngeal lymphoid tissues at 1 and 2 months postexposure (MPE). At 3 MPE, PrPCWD replication had expanded to all systemic lymphoid tissues. By 4 MPE, the PrPCWD burden in all lymphoid tissues had increased and approached levels observed in terminal disease, yet there was no evidence of nervous system invasion. These results indicate the first site of CWD prion entry is in the oropharynx, and the initial phase of prion amplification occurs in the oropharyngeal lymphoid tissues followed by rapid dissemination to systemic lymphoid tissues. This lymphoid replication phase appears to precede neuroinvasion. IMPORTANCE Chronic wasting disease (CWD) is a universally fatal transmissible spongiform encephalopathy affecting cervids, and natural infection occurs through oral and nasal mucosal exposure to infectious prions. Terminal disease is characterized by PrPCWD accumulation in the brain and lymphoid tissues of affected animals. However, the initial sites of prion accumulation and pathways of prion spread during early CWD infection remain unknown. To investigate the chronological events of early prion pathogenesis, we exposed deer to CWD prions and monitored the tissue distribution of PrPCWD over the first 4 months of infection. We show CWD uptake occurs in the oropharynx with initial prion replication in the draining oropharyngeal lymphoid tissues, rapidly followed by dissemination to systemic lymphoid tissues without evidence of neuroinvasion. These data highlight the two phases of CWD infection: a robust prion amplification in systemic lymphoid tissues prior to neuroinvasion and establishment of a carrier state. PMID:28250130

Site Response for Micro-Zonation from Small Earthquakes

NASA Astrophysics Data System (ADS)

Gospe, T. B.; Hutchings, L.; Liou, I. Y. W.; Jarpe, S.

2017-12-01

We have developed a method to obtain absolute geologic site response from small earthquakes using inexpensive instrumentation that enables us to perform micro-zonation inexpensively and in a short amount of time. We record small earthquakes (M<3) at several sites simultaneously and perform inversion to obtain actual absolute site response. The key to the inversion is that recordings at several stations from an earthquake have the same moment, source corner frequency and whole path Q effect on their spectra, but have individual Kappa and spectral amplification as a function of frequency. When these source and path effects are removed and corrections for different propagation distances are performed, we are left with actual site response. We develop site response functions from 0.5 to 25.0 Hz. Cities situated near active and dangerous faults experience small earthquakes on a regular basis. We typically record at least ten small earthquakes over time to stabilize the uncertainly. Of course, dynamic soil modeling is necessary to scale our linear site response to non-linear regime for large earthquakes. Our instrumentation is very inexpensive and virtually disposable, and can be placed throughout a city at a high density. Operation only requires turning on a switch, and data processing is automated to minimize human labor. We have installed a test network and implemented our full methodology in upper Napa Valley, California where there is variable geology and nearby rock outcrop sites, and a supply of small earthquakes from the nearby Geysers development area. We test several methbods of obtaining site response. We found that rock sites have a site response of their own and distort the site response estimate based upon spectral ratios with soil sites. Also, rock sites may not even be available near all sites throughout a city. Further, H/V site response estimates from earthquakes are marginally better, but vertical motion also has a site response of its own. H/V spectral ratios of noise don't provide accurate site response estimates either. Vs30 only provides one amplification number and doesn't account for the variable three-dimensional structure beneath sites. We conclude that absolute site response obtained directly from earthquakes is the best, and possibly, the only way to get accurate site response estimates.

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

PubMed

Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

2015-12-08

Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

Development and characterization of fourteen novel microsatellite markers for the chestnut short-tailed fruit bat (Carollia castanea), and cross-amplification to related species.

PubMed

Cleary, Katherine A; Waits, Lisette P; Hohenlohe, Paul A

2016-01-01

Rapid anthropogenic land use change threatens the primary habitat of the Chestnut short-tailed bat (Carollia castanea) throughout much of its range. Information on population genetic structure can inform management strategies for this widespread frugivorous bat, and effective protection of C. castanea will also benefit the more than 20 mutualistic plant species of which this bat is the primary seed disperser. To facilitate understanding of population genetic structure in this species, fourteen novel microsatellite markers were developed using restriction-site-associated DNA libraries and Illumina sequencing and tested on 28 individuals from 13 locations in Costa Rica. These are the first microsatellite markers developed for C. castanea. All loci were polymorphic, with number of alleles ranging from 2-11 and average observed heterozygosity of 0.631. Markers were also cross-amplified in three additional frugivorous bat species threatened by habitat loss and fragmentation: Sowell's short-tailed bat (Carollia sowelli), Seba's short-tailed bat (Carollia perspicillata), and the Jamaican fruit bat (Artibeus jamaicensis), and 10, 11, and 8 were polymorphic, respectively.

A rapid real-time PCR method to differentiate between mottled skate (Beringraja pulchra) and other skate and ray species.

PubMed

Kim, Mi-Ra; Kwon, Kisung; Jung, Yoo-Kyung; Kang, Tae Sun

2018-07-30

Skates and rays are commercially important fish in South Korea, and among them, Beringraja pulchra has the highest economic value. However, the similar morphological traits among skates and rays are often exploited for seafood fraud. Here, we designed both Beringraja pulchra-specific and skate-universal primer sets, capable of detecting short sequences in the cytochrome oxidase subunit I gene, and developed highly sensitive and reliable quantitative real-time PCR (qPCR) assays to differentiate between Beringraja pulchra and other skate and ray species. AΔCq method based on differences in the amplification efficiency was developed, validated, and then used to confirm the presence of Beringraja pulchra in twenty-six commercial skate products. The averageΔCq value obtained for other skate species (18.94 ± 3.46) was significantly higher than that of Beringraja pulchra (1.18 ± 0.15). For on-site applications, we developed an ultra-fast qPCR assay, allowing for completion of the entire analytical procedure within 30 min. Copyright © 2018 Elsevier Ltd. All rights reserved.

Power scaling of supercontinuum seeded megahertz-repetition rate optical parametric chirped pulse amplifiers.

PubMed

Riedel, R; Stephanides, A; Prandolini, M J; Gronloh, B; Jungbluth, B; Mans, T; Tavella, F

2014-03-15

Optical parametric chirped-pulse amplifiers with high average power are possible with novel high-power Yb:YAG amplifiers with kW-level output powers. We demonstrate a compact wavelength-tunable sub-30-fs amplifier with 11.4 W average power with 20.7% pump-to-signal conversion efficiency. For parametric amplification, a beta-barium borate crystal is pumped by a 140 W, 1 ps Yb:YAG InnoSlab amplifier at 3.25 MHz repetition rate. The broadband seed is generated via supercontinuum generation in a YAG crystal.

160 W 800 fs Yb:YAG single crystal fiber amplifier without CPA.

PubMed

Markovic, Vesna; Rohrbacher, Andreas; Hofmann, Peter; Pallmann, Wolfgang; Pierrot, Simonette; Resan, Bojan

2015-10-05

We demonstrate a compact and simple two-stage Yb:YAG single crystal fiber amplifier which delivers 160 W average power, 800 fs pulses without chirped pulse amplification. This is the highest average power of femtosecond laser based on SCF. Additionally, we demonstrate the highest small signal gain of 32.5 dB from the SCF in the first stage and the highest extraction efficiency of 42% in the second stage. The excellent performance of the second stage was obtained using the bidirectional pumping scheme, which is applied to SCF for the first time.

Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater.

PubMed

Kanitkar, Yogendra H; Stedtfeld, Robert D; Hatzinger, Paul B; Hashsham, Syed A; Cupples, Alison M

2017-06-01

TaqMan probe-based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes is a widely accepted molecular biological tool (MBT) for determining the abundance of Dehalococcoides sp. in groundwater samples from chlorinated solvent-contaminated sites. However, there are significant costs associated with this MBT. In this study, we describe an approach that requires only low-cost laboratory equipment (a bench top centrifuge and a water bath) and requires less time and resources compared to qPCR. The method involves the concentration of biomass from groundwater, without DNA extraction, and loop-mediated isothermal amplification (LAMP) of the cell templates. The amplification products are detected by a simple visual color change (orange/green). The detection limits of the assay were determined using groundwater from a contaminated site. In addition, the assay was tested with groundwater from three additional contaminated sites. The final approach to detect RDase genes, without DNA extraction or a thermal cycler, was successful to 1.8 × 10 5  gene copies per L for vcrA and 1.3 × 10 5  gene copies per L for tceA. Both values are below the threshold recommended for effective in situ dechlorination.

Linking Surface and Subsurface Processes: Implications for Seismic Hazards in Southern California

NASA Astrophysics Data System (ADS)

Lin, J. C.; Moon, S.; Yong, A.; Meng, L.; Martin, A. J.; Davis, P. M.

2017-12-01

Earth's surface and subsurface processes such as bedrock weathering, soil production, and river incision can influence and be influenced by spatial variations in the mechanical strength of surface material. Mechanically weakened rocks tend to have reduced seismic velocity, which can result in larger ground-motion amplification and greater potential for earthquake-induced damages. However, the influence and extent of surface and subsurface processes on the mechanical strength of surface material and seismic site conditions in southern California remain unclear. In this study, we examine whether physics-based models of surface and subsurface processes can explain the spatial variability and non-linearity of near-surface seismic velocity in southern California. We use geophysical measurements (Yong et al., 2013; Ancheta et al., 2014), consisting of shear-wave velocity (Vs) tomography data, Vs profiles, and the time-averaged Vs in the upper 30 m of the crust (Vs30) to infer lateral and vertical variations of surface material properties. Then, we compare Vs30 values with geologic and topographic attributes such as rock type, slope, elevation, and local relief, as well as metrics for surface processes such as soil production and bedrock weathering from topographic stress, frost cracking, chemical reactions, and vegetation presence. Results from this study will improve our understanding of physical processes that control subsurface material properties and their influences on local variability in seismic site conditions.

[Expression and purification of a novel thermophilic bacterial single-stranded DNA-binding protein and enhancement the synthesis of DNA and cDNA].

PubMed

Jia, Xiao-Wei; Zhang, Guo-Hui; Shi, Hai-Yan

2012-12-01

Express a novel species of single-stranded DNA-binding protein (SSB) derived from Thermococcus kodakarensis KOD1, abbreviated kod-ssb. And evaluate the effect of kod-ssb on PCR-based DNA amplification and reverse transcription. We express kod-ssb with the Transrtta (DE3), and kod-ssb was purified by affinity chromatography on a Ni2+ Sepharose column, detected by SDS-PAGE. To evaluate the effect of kod-ssb on PCR-based DNA amplification, the human beta globin gene was used as template to amplify a 5-kb, 9-kb and 13-kb. And to detect the effect of kod-ssb on reverse transcription, we used RNA from flu cell culture supernatant extraction as templates to implement qRT-PCR reaction. The plasmid pET11a-kod was transformed into Transetta (DE3) and the recombinant strain Transetta (pET11 a-kod) was obtained. The kod-ssb was highly expressed when the recombinant strain Transetta(pET11a-kod) was induced by IPTG. The specific protein was detected by SDS-PAGE. To confirm that kod-ssb can enhance target DNA synthesis and reduce PCR by-products, 5-, 9-, and 13-kb human beta globin gene fragments were used as templates for PCR. When PCR reactions did not include SSB proteins, the specific PCR product was contaminated with non-specific products. When kod -ssb was added, kod-ssb significantly enhanced amplification of the 5-, 9-and 13-kb target product and minimised the non-specific PCR products. To confirm that kod-ssb can enhance target cDNA synthesis, RNA from flu cell culture supernatant extraction was used as templates for qRT-PCR reaction. The results was that when kod-ssb was added, kod-ssb significantly enhanced the synthesis of cDNA, average Ct value is 19.42, and the average Ct value without kod-ssb is 22.15. kod-ssb may in future be used to enhance DNA and cDNA amplification.

How might Australian rainforest cloud interception respond to climate change?

NASA Astrophysics Data System (ADS)

Wallace, Jim; McJannet, Dave

2013-02-01

SummaryThe lower and upper montane rainforests in northern Queensland receive significant amounts of cloud interception that affect both in situ canopy wetness and downstream runoff. Cloud interception contributes 5-30% of the annual water input to the canopy and this increases to 40-70% of the monthly water input during the dry season. This occult water is therefore an important input to the canopy, sustaining the epiphytes, mosses and other species that depend on wet canopy conditions. The potential effect of climate change on cloud interception was examined using the relationship between cloud interception and cloud frequency derived from measurements made at four different rainforest locations. Any given change in cloud frequency produces a greater change in cloud interception and this 'amplification' increases from 1.1 to 1.7 as cloud frequency increases from 5% to 70%. This means that any changes in cloud frequency will have the greatest relative effects at the higher altitude sites where cloud interception is greatest. As cloud frequency is also a major factor affecting canopy wetness, any given change in cloud frequency will therefore have a greater impact on canopy wetness at the higher altitude sites. These changes in wetness duration will augment those due to changes in rainfall and may have important implications for the fauna and flora that depend on wet canopy conditions. We also found that the Australian rainforests may be more efficient (by ˜50% on average) in intercepting cloud water than American coniferous forests, which may be due to differences in canopy structure and exposure at the different sites.

Direct RNA detection without nucleic acid purification and PCR: Combining sandwich hybridization with signal amplification based on branched hybridization chain reaction.

PubMed

Xu, Yao; Zheng, Zhi

2016-05-15

We have developed a convenient, robust and low-cost RNA detection system suitable for high-throughput applications. This system uses a highly specific sandwich hybridization to capture target RNA directly onto solid support, followed by on-site signal amplification via 2-dimensional, branched hybridizing chain polymerization through toehold-mediated strand displacement reaction. The assay uses SYBR Green to detect targets at concentrations as low as 1 pM, without involving nucleic acid purification or any enzymatic reaction, using ordinary oligonucleotides without modification or labeling. The system was demonstrated in the detection of malaria RNA in blood and GAPDH gene expression in cell lysate. Copyright © 2015 Elsevier B.V. All rights reserved.

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

2001-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

1999-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

Rapid and Quantitative Detection of Vibrio parahemolyticus by the Mixed-Dye-Based Loop-Mediated Isothermal Amplification Assay on a Self-Priming Compartmentalization Microfluidic Chip.

PubMed

Pang, Bo; Ding, Xiong; Wang, Guoping; Zhao, Chao; Xu, Yanan; Fu, Kaiyue; Sun, Jingjing; Song, Xiuling; Wu, Wenshuai; Liu, Yushen; Song, Qi; Hu, Jiumei; Li, Juan; Mu, Ying

2017-12-27

Vibrio parahemolyticus (VP) mostly isolated from aquatic products is one of the major causes of bacterial food-poisoning events worldwide, which could be reduced using a promising on-site detection method. Herein, a rapid and quantitative method for VP detection was developed by applying a mixed-dye-loaded loop-mediated isothermal amplification (LAMP) assay on a self-priming compartmentalization (SPC) microfluidic chip, termed on-chip mixed-dye-based LAMP (CMD-LAMP). In comparison to conventional approaches, CMD-LAMP was advantageous on the limit of detection, which reached down to 1 × 10 3 CFU/mL in food-contaminated samples without the pre-enrichment of bacteria. Additionally, as a result of the use of a mixed dye and SPC chip, the quantitative result could be easily acquired, avoiding the requirement of sophisticated instruments and tedious operation. Also, CMD-LAMP was rapid and cost-effective. Conclusively, CMD-LAMP has great potential in realizing the on-site quantitative analysis of VP for food safety.

Ducted whistler-mode signals received at two widely spaced locations

NASA Astrophysics Data System (ADS)

Clilverd, M. A.; Thomson, N. R.; Smith, A. J.

1996-06-01

Whistler-mode signals from a single VLF transmitter that have propagated in the same duct, have been observed simultaneously at Faraday, Antarctica (65°S, 64°W) and Dunedin, New Zealand (46°S, 171°E). The signals received have group-delay times that differ in the order of 10 ms, which can be explained by the differences in southern-hemisphere sub-ionospheric propagation time from duct exit region to receiver for the two sites. This difference has been used to determine the location of the duct exit region, with confirmation provided by arrival-bearing information from both sites. The whistler-mode signals typically occur one or two days after geomagnetic activity, with Kpgeq5. The sub-ionospheric-propagation model, LWPC, is used to estimate the whistler-mode power radiated from the duct exit region. These results are then combined with estimated loss values for ionospheric and ducted transmission to investigate the role of wave-particle amplification or absorption. On at least half of the events studied, plasmaspheric amplification of the signals appears to be needed to explain the observed whistler-mode signal strengths.

Apolipoprotein E genotyping by multiplex tetra-primer amplification refractory mutation system PCR in single reaction tube.

PubMed

Yang, Young Geun; Kim, Jong Yeol; Park, Su Jeong; Kim, Suhng Wook; Jeon, Ok-Hee; Kim, Doo-Sik

2007-08-31

Apolipoprotein E (APOE) plays a critical role in lipoprotein metabolism by binding to both low-density lipoprotein and APOE receptors. The APOE gene has three allelic forms, epsilon2, epsilon3, and epsilon4, which encode different isoforms of the APOE protein. In this study, we have developed a new genotyping method for APOE. Our multiplex tetra-primer amplification refractory mutation system (multiplex T-ARMS) polymerase chain reaction (PCR) was performed in a single reaction tube with six primers consisting of two common primers and two specific primers for each of two single nucleotide polymorphism (SNP) sites. We obtained definitive electropherograms that showed three (epsilon2/epsilon2, epsilon3/epsilon3, and epsilon4/epsilon4), four (epsilon2/epsilon3 and epsilon3/epsilon4), and five (epsilon2/epsilon4) amplicons by multiplex T-ARMS PCR in a single reaction tube. Multiplex T-ARMS PCR for APOE genotyping is a simple and accurate method that requires only a single PCR reaction, without any another treatments or expensive instrumentation, to simultaneously identify two sites of single nucleotide polymorphisms.

Uncertainties in evaluation of hazard and seismic risk

NASA Astrophysics Data System (ADS)

Marmureanu, Gheorghe; Marmureanu, Alexandru; Ortanza Cioflan, Carmen; Manea, Elena-Florinela

2015-04-01

Two methods are commonly used for seismic hazard assessment: probabilistic (PSHA) and deterministic(DSHA) seismic hazard analysis.Selection of a ground motion for engineering design requires a clear understanding of seismic hazard and risk among stakeholders, seismologists and engineers. What is wrong with traditional PSHA or DSHA ? PSHA common used in engineering is using four assumptions developed by Cornell in 1968:(1)-Constant-in-time average occurrence rate of earthquakes; (2)-Single point source; (3).Variability of ground motion at a site is independent;(4)-Poisson(or "memory - less") behavior of earthquake occurrences. It is a probabilistic method and "when the causality dies, its place is taken by probability, prestigious term meant to define the inability of us to predict the course of nature"(Nils Bohr). DSHA method was used for the original design of Fukushima Daichii, but Japanese authorities moved to probabilistic assessment methods and the probability of exceeding of the design basis acceleration was expected to be 10-4-10-6 . It was exceeded and it was a violation of the principles of deterministic hazard analysis (ignoring historical events)(Klügel,J,U, EGU,2014, ISSO). PSHA was developed from mathematical statistics and is not based on earthquake science(invalid physical models- point source and Poisson distribution; invalid mathematics; misinterpretation of annual probability of exceeding or return period etc.) and become a pure numerical "creation" (Wang, PAGEOPH.168(2011),11-25). An uncertainty which is a key component for seismic hazard assessment including both PSHA and DSHA is the ground motion attenuation relationship or the so-called ground motion prediction equation (GMPE) which describes a relationship between a ground motion parameter (i.e., PGA,MMI etc.), earthquake magnitude M, source to site distance R, and an uncertainty. So far, no one is taking into consideration strong nonlinear behavior of soils during of strong earthquakes. But, how many cities, villages, metropolitan areas etc. in seismic regions are constructed on rock? Most of them are located on soil deposits? A soil is of basic type sand or gravel (termed coarse soils), silt or clay (termed fine soils) etc. The effect on nonlinearity is very large. For example, if we maintain the same spectral amplification factor (SAF=5.8942) as for relatively strong earthquake on May 3,1990(MW=6.4),then at Bacǎu seismic station for Vrancea earthquake on May 30,1990 (MW =6.9) the peak acceleration has to be a*max =0.154g and the actual recorded was only, amax =0.135g(-14.16%). Also, for Vrancea earthquake on August 30,1986(MW=7.1),the peak acceleration has to be a*max = 0.107g instead of real value recorded of 0.0736 g(- 45.57%). There are many data for more than 60 seismic stations. There is a strong nonlinear dependence of SAF with earthquake magnitude in each site. The authors are coming with an alternative approach called "real spectral amplification factors" instead of GMPE for all extra-Carpathian area where all cities and villages are located on soil deposits. Key words: Probabilistic Seismic Hazard; Uncertainties; Nonlinear seismology; Spectral amplification factors(SAF).

A combined source and site-effect study of ground motions generated by an earthquake in Port au Prince (Haiti)

NASA Astrophysics Data System (ADS)

St Fleur, Sadrac; Courboulex, Francoise; Bertrand, Etienne; Deschamps, Anne; Mercier de Lepinay, Bernard; Prepetit, Claude; Hough, Suzan

2013-04-01

We present the preliminary results of a study with the aim of understanding how some combinations of source and site effects can generate extreme ground motions in the city of Port au Prince. For this study, we have used the recordings of several tens of earthquakes with magnitude larger than 3.0 at 3 to 14 stations from three networks: 3 stations of the Canadian Broad-band network (RNCan), 2 stations of the educational French network (SaE) and 9 stations of the accelerometric network (Bureau des Mines et de l'Energie of Port au Prince and US Geological survey). In order to estimate site effects under each station, we have applied classical spectral ratio methods: The H/V (Horizontal/Vertical) method was first used to select a reference station, which was itself used in a site/reference method. Because a true reference station was not available, we have used successively stations HCEA, then station PAPH, then an average value of 3 stations. In the frequency range studied (0.5 - 20 Hz), we found a site-to-reference ratio up to 3 to 8. However, these values present a large variability, depending on the earthquake recordings. This may indicate that the observed amplification from one station to the other depends not only from the local site effect but also from the source. We then used the same earthquake recordings as Empirical Green's Functions (EGF) in order to simulate the ground motions generated by a virtual earthquake. For this simulation, we have used a stochastic EGF summation method. We have worked on the simulation of a magnitude Mw=6.8 using successively 2 smaller events that occurred on the Leogane fault as EGF. The results obtained using the two events are surprisingly very different. Using the first EGF, we obtained almost the same ground motion values at each station in Port au Prince, whereas with the second EGF, the results highlight large differences. The large variability obtained in the results indicates that a particular combination of site and source effects may be responsible of large ground motions, especially at some given sites.

Linear nicking endonuclease-mediated strand-displacement DNA amplification.

PubMed

Joneja, Aric; Huang, Xiaohua

2011-07-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to 5000 nucleotides can be linearly amplified using a nicking endonuclease with 7-bp recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length is linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. Copyright © 2011 Elsevier Inc. All rights reserved.

Self-powered integrated microfluidic point-of-care low-cost enabling (SIMPLE) chip

PubMed Central

Yeh, Erh-Chia; Fu, Chi-Cheng; Hu, Lucy; Thakur, Rohan; Feng, Jeffrey; Lee, Luke P.

2017-01-01

Portable, low-cost, and quantitative nucleic acid detection is desirable for point-of-care diagnostics; however, current polymerase chain reaction testing often requires time-consuming multiple steps and costly equipment. We report an integrated microfluidic diagnostic device capable of on-site quantitative nucleic acid detection directly from the blood without separate sample preparation steps. First, we prepatterned the amplification initiator [magnesium acetate (MgOAc)] on the chip to enable digital nucleic acid amplification. Second, a simplified sample preparation step is demonstrated, where the plasma is separated autonomously into 224 microwells (100 nl per well) without any hemolysis. Furthermore, self-powered microfluidic pumping without any external pumps, controllers, or power sources is accomplished by an integrated vacuum battery on the chip. This simple chip allows rapid quantitative digital nucleic acid detection directly from human blood samples (10 to 105 copies of methicillin-resistant Staphylococcus aureus DNA per microliter, ~30 min, via isothermal recombinase polymerase amplification). These autonomous, portable, lab-on-chip technologies provide promising foundations for future low-cost molecular diagnostic assays. PMID:28345028

Stress-induced rearrangement of Fusarium retrotransposon sequences.

PubMed

Anaya, N; Roncero, M I

1996-11-27

Rearrangement of fusarium oxysporum retrotransposon skippy was induced by growth in the presence of potassium chlorate. Three fungal strains, one sensitive to chlorate (Co60) and two resistant to chlorate and deficient for nitrate reductase (Co65 and Co94), were studied by Southern analysis of their genomic DNA. Polymorphism was detected in their hybridization banding pattern, relative to the wild type grown in the absence of chlorate, using various enzymes with or without restriction sites within the retrotransposon. Results were consistent with the assumption that three different events had occurred in strain Co60: genomic amplification of skippy yielding tandem arrays of the element, generation of new skippy sequences, and deletion of skippy sequences. Amplification of Co60 genomic DNA using the polymerase chain reaction and divergent primers derived from the retrotransposon generated a new band, corresponding to one long terminal repeat plus flanking sequences, that was not present in the wild-type strain. Molecular analysis of nitrate reductase-deficient mutants showed that generation and deletion of skippy sequences, but not genomic amplification in tandem repeats, had occurred in their genomes.

Linear nicking endonuclease-mediated strand displacement DNA amplification

PubMed Central

Joneja, Aric; Huang, Xiaohua

2011-01-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to five thousand nucleotides can be linearly amplified using a nicking endonuclease with seven base-pair recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length are linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. PMID:21342654

Stellar feedback strongly alters the amplification and morphology of galactic magnetic fields

NASA Astrophysics Data System (ADS)

Su, Kung-Yi; Hayward, Christopher C.; Hopkins, Philip F.; Quataert, Eliot; Faucher-Giguère, Claude-André; Kereš, Dušan

2018-01-01

Using high-resolution magnetohydrodynamic simulations of idealized, non-cosmological galaxies, we investigate how cooling, star formation and stellar feedback affect galactic magnetic fields. We find that the amplification histories, saturation values and morphologies of the magnetic fields vary considerably depending on the baryonic physics employed, primarily because of differences in the gas density distribution. In particular, adiabatic runs and runs with a subgrid (effective equation of state) stellar feedback model yield lower saturation values and morphologies that exhibit greater large-scale order compared with runs that adopt explicit stellar feedback and runs with cooling and star formation but no feedback. The discrepancies mostly lie in gas denser than the galactic average, which requires cooling and explicit fragmentation to capture. Independent of the baryonic physics included, the magnetic field strength scales with gas density as B ∝ n2/3, suggesting isotropic flux freezing or equipartition between the magnetic and gravitational energies during the field amplification. We conclude that accurate treatments of cooling, star formation and stellar feedback are crucial for obtaining the correct magnetic field strength and morphology in dense gas, which, in turn, is essential for properly modelling other physical processes that depend on the magnetic field, such as cosmic ray feedback.

SOX2 amplification is a common event in squamous cell carcinomas of different organ sites.

PubMed

Maier, Sebastian; Wilbertz, Theresia; Braun, Martin; Scheble, Veit; Reischl, Markus; Mikut, Ralf; Menon, Roopika; Nikolov, Pavel; Petersen, Karen; Beschorner, Christine; Moch, Holger; Kakies, Christoph; Protzel, Chris; Bauer, Jürgen; Soltermann, Alex; Fend, Falko; Staebler, Annette; Lengerke, Claudia; Perner, Sven

2011-08-01

Acquired chromosomal aberrations, including gene copy number alterations, are involved in the development and progression of human malignancies. SOX2, a transcription factor-coding gene located at 3q26.33, is known to be recurrently and specifically amplified in squamous cell carcinomas of the lung, the esophagus, and the oral cavity. In these organs, the SOX2 protein plays an important role in tumorigenesis and tumor survival. The aim of this study was to determine whether SOX2 amplification is also found in squamous cell carcinomas in other organs commonly affected by this tumor entity. In addition, we examined a large spectrum of lung cancer entities with neuroendocrine differentiation (ie, small cell cancers, large cell cancers, typical and atypical carcinoids) for SOX2 and TTF1 copy number gains to reveal potential molecular ties to squamous cell carcinomas or adenocarcinomas of the lung. Applying fluorescence in situ hybridization, we assessed squamous cell carcinomas of the cervix uteri (n = 47), the skin (n = 57), and the penis (n = 53) for SOX2 copy number alterations and detected amplifications in 28%, 28%, and 32% of tumors, respectively. Furthermore, we performed immunohistochemical SOX2 staining and found that SOX2 amplification is significantly associated with overexpression of the corresponding protein in squamous cell carcinomas (P < .001). Of the lung cancer entities with neuroendocrine differentiation, only small cell cancers and large cell cancers exhibited SOX2 or TTF1 amplifications at significant frequencies, indicating that at least a subset of these might be dedifferentiated forms of squamous cell carcinomas or adenocarcinomas of the lung. We conclude that SOX2 amplification and consequent SOX2 protein overexpression may represent important mechanisms of tumor initiation and progression in a considerable subset of squamous cell carcinomas. Copyright © 2011 Elsevier Inc. All rights reserved.

Novel Degenerate PCR Method for Whole-Genome Amplification Applied to Peru Margin (ODP Leg 201) Subsurface Samples

PubMed Central

Martino, Amanda J.; Rhodes, Matthew E.; Biddle, Jennifer F.; Brandt, Leah D.; Tomsho, Lynn P.; House, Christopher H.

2011-01-01

A degenerate polymerase chain reaction (PCR)-based method of whole-genome amplification, designed to work fluidly with 454 sequencing technology, was developed and tested for use on deep marine subsurface DNA samples. While optimized here for use with Roche 454 technology, the general framework presented may be applicable to other next generation sequencing systems as well (e.g., Illumina, Ion Torrent). The method, which we have called random amplification metagenomic PCR (RAMP), involves the use of specific primers from Roche 454 amplicon sequencing, modified by the addition of a degenerate region at the 3′ end. It utilizes a PCR reaction, which resulted in no amplification from blanks, even after 50 cycles of PCR. After efforts to optimize experimental conditions, the method was tested with DNA extracted from cultured E. coli cells, and genome coverage was estimated after sequencing on three different occasions. Coverage did not vary greatly with the different experimental conditions tested, and was around 62% with a sequencing effort equivalent to a theoretical genome coverage of 14.10×. The GC content of the sequenced amplification product was within 2% of the predicted values for this strain of E. coli. The method was also applied to DNA extracted from marine subsurface samples from ODP Leg 201 site 1229 (Peru Margin), and results of a taxonomic analysis revealed microbial communities dominated by Proteobacteria, Chloroflexi, Firmicutes, Euryarchaeota, and Crenarchaeota, among others. These results were similar to those obtained previously for those samples; however, variations in the proportions of taxa identified illustrates well the generally accepted view that community analysis is sensitive to both the amplification technique used and the method of assigning sequences to taxonomic groups. Overall, we find that RAMP represents a valid methodology for amplifying metagenomes from low-biomass samples. PMID:22319519

MemStar: a one-shot Escherichia coli-based approach for high-level bacterial membrane protein production.

PubMed

Lee, Chiara; Kang, Hae Joo; Hjelm, Anna; Qureshi, Abdul Aziz; Nji, Emmanuel; Choudhury, Hassanul; Beis, Konstantinos; de Gier, Jan-Willem; Drew, David

2014-10-16

Optimising membrane protein production yields in Escherichiacoli can be time- and resource-consuming. Here, we present a simple and effective Membrane protein Single shot amplification recipe: MemStar. This one-shot amplification recipe is based on the E. coli strain Lemo21(DE3), the PASM-5052 auto-induction medium and, contradictorily, an IPTG induction step. Using MemStar, production yields for most bacterial membrane proteins tested were improved to reach an average of 5 mg L(-1) per OD600 unit, which is significantly higher than yields obtained with other common production strategies. With MemStar, we have been able to obtain new structural information for several transporters, including the sodium/proton antiporter NapA. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Statistical mechanics of self-driven Carnot cycles.

PubMed

Smith, E

1999-10-01

The spontaneous generation and finite-amplitude saturation of sound, in a traveling-wave thermoacoustic engine, are derived as properties of a second-order phase transition. It has previously been argued that this dynamical phase transition, called "onset," has an equivalent equilibrium representation, but the saturation mechanism and scaling were not computed. In this work, the sound modes implementing the engine cycle are coarse-grained and statistically averaged, in a partition function derived from microscopic dynamics on criteria of scale invariance. Self-amplification performed by the engine cycle is introduced through higher-order modal interactions. Stationary points and fluctuations of the resulting phenomenological Lagrangian are analyzed and related to background dynamical currents. The scaling of the stable sound amplitude near the critical point is derived and shown to arise universally from the interaction of finite-temperature disorder, with the order induced by self-amplification.

Projected Changes in Persistent Extreme Warm-Season Weather Events: The Role of Quasi-Resonant Amplification

NASA Astrophysics Data System (ADS)

Mann, M. E.; Rahmstorf, S.; Kornhuber, K.; Steinman, B. A.; Miller, S. K.; Coumou, D.

2017-12-01

Persistent episodes of extreme weather in the Northern Hemisphere summer are typically associated with high-amplitude quasi-stationary atmospheric Rossby waves with zonal wavenumbers. Such disturbances are favoured by the phenomenon of Quasi-Resonant Amplification (QRA). A fingerprint for the occurrence of QRA can be defined in terms of the zonally-averaged surface temperature field. Examining future state-of-the-art (CMIP5) climate model projections we find that such events are likely to increase by 50% over the next century under business-as-usual carbon emissions, but there is considerable variation among climate models, with some models predicting a near tripling of QRA events by the end of the century. These results are strongly dependent on assumptions regarding the prominence of changes in radiative forcing associated with anthropogenic aerosols over the next century.

The role of complex site and basin response in Wellington city, New Zealand, during the 2016 Mw 7.8 Kaikōura earthquake and other recent earthquake sequences.

NASA Astrophysics Data System (ADS)

Kaiser, A. E.; McVerry, G.; Wotherspoon, L.; Bradley, B.; Gerstenberger, M.; Benites, R. A.; Bruce, Z.; Bourguignon, S.; Giallini, S.; Hill, M.

2017-12-01

We present analysis of ground motion and complex amplification characteristics in Wellington during recent earthquake sequences and an overview of the 3D basin characterization and ongoing work to update site parameters for seismic design. Significant damage was observed in central Wellington, New Zealand's capital city, following the 2016 Mw7.8 Kaikōura earthquake. Damage was concentrated in mid-rise structures (5 - 15 storeys) and was clearly exacerbated by the particular characteristics of ground motion and the presence of basin effects. Due to the distance of the source (50 - 60km) from the central city, peak ground accelerations were moderate (up to 0.28g) and well within ultimate limit state (ULS) design levels. However, spectral accelerations within the 1 -2 s period range, exceeded 1 in 500 year design level spectra (ULS) in deeper parts of the basin. Amplification with respect to rock at these locations reached factors of up to 7, and was also observed with factors up to at least three across all central city soil recording sites. The ground motions in Wellington were the strongest recorded in the modern era of instrumentation. While similar amplification was observed during the 2013 Mw 6.6 Cook Strait and Grassmere earthquakes, which struck close to the termination of the Kaikōura earthquake rupture, these sources were not sufficiently large to excite significant long-period motions. However, other M7.2+ sources in the region that dominate the seismic hazard, e.g. Wellington Fault, Hikurangi subduction interface and other large proximal crustal faults, are also potentially capable of exciting significant long-period basin response in Wellington. These observations and the expectation of ongoing heightened seismicity have prompted re-evaluation of the current seismic demand levels. Additional field campaigns have also been undertaken to update geotechnical properties and the 3D basin model, in order to inform ongoing research and seismic design practice.

Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9

PubMed Central

Kanitkar, Yogendra H.; Stedtfeld, Robert D.; Steffan, Robert J.; Hashsham, Syed A.

2016-01-01

Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures. PMID:26746711

Biologically relevant effects of mRNA amplification on gene expression profiles.

PubMed

van Haaften, Rachel I M; Schroen, Blanche; Janssen, Ben J A; van Erk, Arie; Debets, Jacques J M; Smeets, Hubert J M; Smits, Jos F M; van den Wijngaard, Arthur; Pinto, Yigal M; Evelo, Chris T A

2006-04-11

Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results. In the present study we compared microarray data obtained from amplified mRNA derived from biopsies of rat cardiac left ventricle and non-amplified mRNA derived from the same organ. Biopsies were linearly amplified to acquire enough material for a microarray experiment. Both amplified and unamplified samples were hybridized to the Rat Expression Set 230 Array of Affymetrix. Analysis of the microarray data showed that unamplified material of two different left ventricles had 99.6% identical gene expression. Gene expression patterns of two biopsies obtained from the same parental organ were 96.3% identical. Similarly, gene expression pattern of two biopsies from dissimilar organs were 92.8% identical to each other.Twenty-one percent of reporters called present in parental left ventricular tissue disappeared after amplification in the biopsies. Those reporters were predominantly seen in the low intensity range. Sequence analysis showed that reporters that disappeared after amplification had a GC-content of 53.7+/-4.0%, while reporters called present in biopsy- and whole LV-samples had an average GC content of 47.8+/-5.5% (P <0.001). Those reporters were also predicted to form significantly more (0.76+/-0.07 versus 0.38+/-0.1) and longer (9.4+/-0.3 versus 8.4+/-0.4) hairpins as compared to representative control reporters present before and after amplification. This study establishes that the gene expression profile obtained after amplification of mRNA of left ventricular biopsies is representative for the whole left ventricle of the rat heart. However, specific gene transcripts present in parental tissues were undetectable in the minute left ventricular biopsies. Transcripts that were lost due to the amplification process were not randomly distributed, but had higher GC-content and hairpins in the sequence and were mainly found in the lower intensity range which includes many transcription factors from specific signalling pathways.

Biologically relevant effects of mRNA amplification on gene expression profiles

PubMed Central

van Haaften, Rachel IM; Schroen, Blanche; Janssen, Ben JA; van Erk, Arie; Debets, Jacques JM; Smeets, Hubert JM; Smits, Jos FM; van den Wijngaard, Arthur; Pinto, Yigal M; Evelo, Chris TA

2006-01-01

Background Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results. In the present study we compared microarray data obtained from amplified mRNA derived from biopsies of rat cardiac left ventricle and non-amplified mRNA derived from the same organ. Biopsies were linearly amplified to acquire enough material for a microarray experiment. Both amplified and unamplified samples were hybridized to the Rat Expression Set 230 Array of Affymetrix. Results Analysis of the microarray data showed that unamplified material of two different left ventricles had 99.6% identical gene expression. Gene expression patterns of two biopsies obtained from the same parental organ were 96.3% identical. Similarly, gene expression pattern of two biopsies from dissimilar organs were 92.8% identical to each other. Twenty-one percent of reporters called present in parental left ventricular tissue disappeared after amplification in the biopsies. Those reporters were predominantly seen in the low intensity range. Sequence analysis showed that reporters that disappeared after amplification had a GC-content of 53.7+/-4.0%, while reporters called present in biopsy- and whole LV-samples had an average GC content of 47.8+/-5.5% (P <0.001). Those reporters were also predicted to form significantly more (0.76+/-0.07 versus 0.38+/-0.1) and longer (9.4+/-0.3 versus 8.4+/-0.4) hairpins as compared to representative control reporters present before and after amplification. Conclusion This study establishes that the gene expression profile obtained after amplification of mRNA of left ventricular biopsies is representative for the whole left ventricle of the rat heart. However, specific gene transcripts present in parental tissues were undetectable in the minute left ventricular biopsies. Transcripts that were lost due to the amplification process were not randomly distributed, but had higher GC-content and hairpins in the sequence and were mainly found in the lower intensity range which includes many transcription factors from specific signalling pathways. PMID:16608515

Markers and mapping revisited: finding your gene.

PubMed

Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

2009-01-01

This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science.

Multifunctional reduced graphene oxide trigged chemiluminescence resonance energy transfer: Novel signal amplification strategy for photoelectrochemical immunoassay of squamous cell carcinoma antigen.

PubMed

Zhang, Yan; Sun, Guoqiang; Yang, Hongmei; Yu, Jinghua; Yan, Mei; Song, Xianrang

2016-05-15

Herein, a photoelectrochemical (PEC) immunoassay is constructed for squamous cell carcinoma antigen (SCCA) detection using zinc oxide nanoflower-bismuth sulfide (Bi2S3) composites as photoactive materials and reduced graphene oxide (rGO) as signal labels. Horseradish peroxidase is used to block sites against nonspecific binding, and then participated in luminol-based chemiluminescence (CL) system. The induced CL emission is acted as an inner light source to excite photoactive materials, simplifying the instrument. A novel signal amplification strategy is stem from rGO because of the rGO acts as an energy acceptor, while luminol serves as a donor to rGO, triggering the CL resonance energy transfer phenomenon between luminol and rGO. Thus, the efficient CL emission to photoactive materials decreases. Furthermore, the signal amplification caused by rGO labeled signal antibodies is related to photogenerated electron-hole pairs: perfect matching of energy levels between rGO and Bi2S3 makes rGO a sink to capture photogenerated electrons from Bi2S3; the increased steric hindrance hinders the electron donor to the surface of Bi2S3 for reaction with the photogenerated holes. On the basis of the novel signal amplification strategy, the proposed immunosensor exhibits excellent analytical performance for PEC detection of SCCA, ranging from 0.8 pg mL(-1) to 80 ng mL(-1) with a low detection limit of 0.21 pg mL(-1). Meanwhile, the designed signal amplification strategy provides a general format for future development of PEC assays. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of site effects on ground motions based on equivalent linear site response analysis and liquefaction potential in Chennai, south India

NASA Astrophysics Data System (ADS)

Nampally, Subhadra; Padhy, Simanchal; Trupti, S.; Prabhakar Prasad, P.; Seshunarayana, T.

2018-05-01

We study local site effects with detailed geotechnical and geophysical site characterization to evaluate the site-specific seismic hazard for the seismic microzonation of the Chennai city in South India. A Maximum Credible Earthquake (MCE) of magnitude 6.0 is considered based on the available seismotectonic and geological information of the study area. We synthesized strong ground motion records for this target event using stochastic finite-fault technique, based on a dynamic corner frequency approach, at different sites in the city, with the model parameters for the source, site, and path (attenuation) most appropriately selected for this region. We tested the influence of several model parameters on the characteristics of ground motion through simulations and found that stress drop largely influences both the amplitude and frequency of ground motion. To minimize its influence, we estimated stress drop after finite bandwidth correction, as expected from an M6 earthquake in Indian peninsula shield for accurately predicting the level of ground motion. Estimates of shear wave velocity averaged over the top 30 m of soil (V S30) are obtained from multichannel analysis of surface wave (MASW) at 210 sites at depths of 30 to 60 m below the ground surface. Using these V S30 values, along with the available geotechnical information and synthetic ground motion database obtained, equivalent linear one-dimensional site response analysis that approximates the nonlinear soil behavior within the linear analysis framework was performed using the computer program SHAKE2000. Fundamental natural frequency, Peak Ground Acceleration (PGA) at surface and rock levels, response spectrum at surface level for different damping coefficients, and amplification factors are presented at different sites of the city. Liquefaction study was done based on the V S30 and PGA values obtained. The major findings suggest show that the northeast part of the city is characterized by (i) low V S30 values (< 200 m/s) associated with alluvial deposits, (ii) relatively high PGA value, at the surface, of about 0.24 g, and (iii) factor of safety and liquefaction below unity at three sites (no. 12, no. 37, and no. 70). Thus, this part of the city is expected to experience damage for the expected M6 target event.

Assessing the New American Society of Clinical Oncology/College of American Pathologists Guidelines for HER2 Testing by Fluorescence In Situ Hybridization: Experience of an Academic Consultation Practice.

PubMed

Press, Michael F; Villalobos, Ivonne; Santiago, Angela; Guzman, Roberta; Cervantes, Monica; Gasparyan, Armen; Campeau, Anaamika; Ma, Yanling; Tsao-Wei, Denice D; Groshen, Susan

2016-04-15

Context .- Evaluation of HER2 gene amplification by fluorescence in situ hybridization (FISH) was changed by recent American Society of Clinical Oncology/College of American Pathologists (ASCO-CAP) guidelines. Objective . -To determine frequencies and assess patterns of HER2 protein expression for each ASCO-CAP guideline FISH category among 7526 breast cancers accrued to our consultation practice. Design .- We retrospectively reevaluated the HER2 FISH status of breast cancers in our consultation practice according to ASCO-CAP FISH guidelines, and documented HER2 protein levels in each category. Results . -According to new guidelines, 17.7% of our consultation breast cancers were "ISH-positive" with HER2:CEP17 FISH ratios ≥2.0 and average HER2 gene copies per cell ≥4.0 (group 1); 0.4% were "ISH-positive" with ratios ≥2.0 and average copies <4.0 (group 2); 0.6% were "ISH-positive" with ratios <2.0 and average copies ≥6.0 (group 3); 4.6% were "ISH-equivocal" with ratios <2.0 and average copies ≥4.0 and <6.0 (group 4); and 76.7% were "ISH-negative" with ratios <2.0 and average copies <4.0 (group 5). However, only groups 1 (HER2 amplified) and 5 (HER2 not amplified) agreed with our previously reported status, and only these groups demonstrated the expected immunohistochemistry status, overexpression and low expression, respectively. Groups 2 and 4 breast cancers lacked overexpression, whereas group 3 was not significantly associated with either increased or decreased HER2 expression. Conclusions .- Although the status of approximately 95% of our cases (groups 1 and 5) is not affected by the new guidelines, those of the other 5% (groups 2-4) conflict with previous HER2 gene amplification status and with HER2 status by immunohistochemistry.

Isolation and characterization of 10 microsatellite loci in Callicarpa subpubescens (Verbenaceae), an endemic species of the Bonin Islands.

PubMed

Mori, K; Kaneko, S; Isagi, Y; Murakami, N; Kato, H

2008-11-01

Ten microsatellite loci were isolated and characterized for Callicarpa subpubescens (Verbenaceae), an endemic tree species of the Bonin Islands. The observed number of alleles at each locus ranged from two to eight with an average of 4.9, and the expected heterozygosity ranged from 0.238 to 0.690 with an average of 0.483. All 10 loci were screened in cross-amplification tests for two other endemic Callicarpa species that also inhabit the Bonin Islands. All loci were successfully amplified in these species. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Propensity to spending of an average consumer over a brief period

NASA Astrophysics Data System (ADS)

De Luca, Roberto; Di Mauro, Marco; Falzarano, Angelo; Naddeo, Adele

2016-08-01

Understanding consumption dynamics and its impact on the whole economy and welfare within the present economic crisis is not an easy task. Indeed the level of consumer demand for different goods varies with the prices, consumer incomes and demographic factors. Furthermore crisis may trigger different behaviors which result in distortions and amplification effects. In the present work we propose a simple model to quantitatively describe the time evolution over a brief period of the amount of money an average consumer decides to spend, depending on his/her available budget. A simple hydrodynamical analog of the model is discussed. Finally, perspectives of this work are briefly outlined.

Development of a distance-to-roadway proximity metric to compare near-road pollutant levels to a central site monitor

NASA Astrophysics Data System (ADS)

Barzyk, Timothy M.; George, Barbara Jane; Vette, Alan F.; Williams, Ronald W.; Croghan, Carry W.; Stevens, Carvin D.

The primary objective of the Detroit Exposure and Aerosol Research Study (DEARS) was to compare air pollutant concentrations measured at various neighborhoods, or exposure monitoring areas (EMAs), throughout a major metropolitan area to levels measured at a central site or community monitor. One of the EMAs was located near a busy freeway (annual average daily traffic (AADT) of ˜130,000) so that impacts of mobile sources could be examined. Air pollution concentrations from the roadway-proximate sites were compared to the central site monitor. The volatile organic compounds (VOCs) selected (benzene, toluene, ethylbenzene, m,p- and o-xylene, 1,3 butadiene, 1,3,5-trimethylbenzene and 4-ethyltoluene) are typically associated with mobile sources. Gradients were also evident that demonstrated the amplification of pollutant levels near the roadway compared to the community monitor. A novel distance-to-roadway proximity metric was developed to plot the measurements and model these gradients. Effective distance represents the actual distance an air parcel travels from the middle of a roadway to a site and varies as a function of wind direction, whereas perpendicular distance is a fixed distance oriented normal to the roadway. Perpendicular distance is often used as a proxy for exposures to traffic emissions in epidemiological studies. Elevated concentrations of all the compounds were found for both a summer and winter season. Effective distance was found to be a statistically significant ( p < 0.05) univariate predictor for concentrations of toluene, ethylbenzene, m,p-xylene and o-xylene for summer 2005. For each of these pollutants, effective distance yielded lower p-values than the corresponding perpendicular distance models, and model fit improved. Results demonstrate that this near-road EMA had elevated levels of traffic-related VOCs compared to the community monitor, and that effective distance was a more accurate predictor of the degree to which they were elevated as a function of distance. Effective distance produced a range of distance-to-roadway values for a single site based on wind direction, thus increasing the number and range of values that could be used to plot and predict relative differences in pollutant concentrations between two sites.

Rolling Circle Amplification For Spatially Directed Synthesis Of A Solid Phase Anchored Single-Stranded DNA Molecule

NASA Astrophysics Data System (ADS)

Reiß, Edda; Hölzel, Ralph; von Nickisch-Rosenegk, Markus; Bier, Frank F.

2006-09-01

In this article the usefulness of the enzyme phi29 DNA polymerase and the principle of rolling circle amplification (RCA) for creating single-stranded DNA (ssDNA) nanostructures is described. Currently we are working on the spatial orientation of a growing ssDNA molecule during its RCA-based synthesis by the application of a hydrodynamic force. Starting at an immobilized primer at single molecule level, the aim is to construct a nanostructure of known location and orientation, providing multiple repeating binding sites that can be addressed via complementary base-pairing. Proof-of-principle experiments demonstrate the potential of the enzymatic reaction. ssDNA molecules of more than 20 μm length were created at an immobilized primer and detected by means of fluorescence microscopy.

On the significance of germline cytogenetic rearrangements at MYCN locus in neuroblastoma

PubMed Central

2013-01-01

Background MYCN oncogene amplification is the most important prognostic factor in neuroblastoma. 25% neuroblastoma tumors have somatic amplifications at this locus but little is known about its constitutional aberrations and their potential role in carcinogenesis. Here, we have performed an array-CGH and qPCR characterization of two patients with constitutional partial 2p trisomy including MYCN genomic region. Results One of the patients had congenital neuroblastoma and showed presence of minute areas of gains and losses within the common fragile site FRA2C at 2p24 encompassing MYCN. The link between 2p24 germline rearrangements and neuroblastoma development was reassessed by reviewing similar cases in the literature. Conclusions It appears that constitutional rearrangements involving chromosome 2p24 may play role in NB development. PMID:24131700

Early Site Permit Demonstration Program: Guidelines for determining design basis ground motions. Volume 2, Appendices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

This report develops and applies a methodology for estimating strong earthquake ground motion. The motivation was to develop a much needed tool for use in developing the seismic requirements for structural designs. An earthquake`s ground motion is a function of the earthquake`s magnitude, and the physical properties of the earth through which the seismic waves travel from the earthquake fault to the site of interest. The emphasis of this study is on ground motion estimation in Eastern North America (east of the Rocky Mountains), with particular emphasis on the Eastern United States and southeastern Canada. Eastern North America is amore » stable continental region, having sparse earthquake activity with rare occurrences of large earthquakes. While large earthquakes are of interest for assessing seismic hazard, little data exists from the region to empirically quantify their effects. The focus of the report is on the attributes of ground motion in Eastern North America that are of interest for the design of facilities such as nuclear power plants. This document, Volume II, contains Appendices 2, 3, 5, 6, and 7 covering the following topics: Eastern North American Empirical Ground Motion Data; Examination of Variance of Seismographic Network Data; Soil Amplification and Vertical-to-Horizontal Ratios from Analysis of Strong Motion Data From Active Tectonic Regions; Revision and Calibration of Ou and Herrmann Method; Generalized Ray Procedure for Modeling Ground Motion Attenuation; Crustal Models for Velocity Regionalization; Depth Distribution Models; Development of Generic Site Effects Model; Validation and Comparison of One-Dimensional Site Response Methodologies; Plots of Amplification Factors; Assessment of Coupling Between Vertical & Horizontal Motions in Nonlinear Site Response Analysis; and Modeling of Dynamic Soil Properties.« less

Variable anelastic attenuation and site effect in estimating source parameters of various major earthquakes including M w 7.8 Nepal and M w 7.5 Hindu kush earthquake by using far-field strong-motion data

NASA Astrophysics Data System (ADS)

Kumar, Naresh; Kumar, Parveen; Chauhan, Vishal; Hazarika, Devajit

2017-10-01

Strong-motion records of recent Gorkha Nepal earthquake ( M w 7.8), its strong aftershocks and seismic events of Hindu kush region have been analysed for estimation of source parameters. The M w 7.8 Gorkha Nepal earthquake of 25 April 2015 and its six aftershocks of magnitude range 5.3-7.3 are recorded at Multi-Parametric Geophysical Observatory, Ghuttu, Garhwal Himalaya (India) >600 km west from the epicentre of main shock of Gorkha earthquake. The acceleration data of eight earthquakes occurred in the Hindu kush region also recorded at this observatory which is located >1000 km east from the epicentre of M w 7.5 Hindu kush earthquake on 26 October 2015. The shear wave spectra of acceleration record are corrected for the possible effects of anelastic attenuation at both source and recording site as well as for site amplification. The strong-motion data of six local earthquakes are used to estimate the site amplification and the shear wave quality factor ( Q β) at recording site. The frequency-dependent Q β( f) = 124 f 0.98 is computed at Ghuttu station by using inversion technique. The corrected spectrum is compared with theoretical spectrum obtained from Brune's circular model for the horizontal components using grid search algorithm. Computed seismic moment, stress drop and source radius of the earthquakes used in this work range 8.20 × 1016-5.72 × 1020 Nm, 7.1-50.6 bars and 3.55-36.70 km, respectively. The results match with the available values obtained by other agencies.

Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

PubMed

Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

2018-01-01

Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

Polarity of recombination in transformation of Streptococcus pneumoniae

PubMed Central

Pasta, Franck; Sicard, Michel A.

1999-01-01

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5′- and 3′-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami− transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5′ to the deletion, showing that, in vivo, the 5′ side is strongly favored by recombination. Further results suggest that exchanges occurring from 5′ to 3′ relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5′ preference. PMID:10077616

Polarity of recombination in transformation of Streptococcus pneumoniae.

PubMed

Pasta, F; Sicard, M A

1999-03-16

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5'- and 3'-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami- transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5' to the deletion, showing that, in vivo, the 5' side is strongly favored by recombination. Further results suggest that exchanges occurring from 5' to 3' relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5' preference.

Blind shear-wave velocity comparison of ReMi and MASW results with boreholes to 200 m in Santa Clara Valley: Implications for earthquake ground-motion assessment

USGS Publications Warehouse

Stephenson, W.J.; Louie, J.N.; Pullammanappallil, S.; Williams, R.A.; Odum, J.K.

2005-01-01

Multichannel analysis of surface waves (MASW) and refraction microtremor (ReMi) are two of the most recently developed surface acquisition techniques for determining shallow shear-wave velocity. We conducted a blind comparison of MASW and ReMi results with four boreholes logged to at least 260 m for shear velocity in Santa Clara Valley, California, to determine how closely these surface methods match the downhole measurements. Average shear-wave velocity estimates to depths of 30, 50, and 100 m demonstrate that the surface methods as implemented in this study can generally match borehole results to within 15% to these depths. At two of the boreholes, the average to 100 m depth was within 3%. Spectral amplifications predicted from the respective borehole velocity profiles similarly compare to within 15 % or better from 1 to 10 Hz with both the MASW and ReMi surface-method velocity profiles. Overall, neither surface method was consistently better at matching the borehole velocity profiles or amplifications. Our results suggest MASW and ReMi surface acquisition methods can both be appropriate choices for estimating shearwave velocity and can be complementary to each other in urban settings for hazards assessment.

Genetic variability of citrinin-producing Penicillium citrinum strains as occupational health hazards in northern Iran.

PubMed

Khosravi, Ali Reza; Sheikhkarami, Mojgan; Shokri, Hojjatollah; Sabokbar, Azar

2012-12-01

We evaluated the ability of randomly amplified polymorphic DNA (RAPD) to type citrinin-producing Penicillium citrinum (P. citrinum) strains recovered from the forest's air in northern Iran. A total of 12 P. citrinum strains (P1-P12) were characterised by citrinin production and random amplification of polymorphic DNA (RAPD) technique. All the strains produced citrinin with levels ranging from 1.5 μg mL(-1) to 39.6 μg mL(-1) (average value: 12.68 μg mL(-1)). Of 11 primers tested, eight primers produced polymorphic amplification patterns. These primers generated a total of 105 reproducible RAPD bands, averaging to 13.1 bands per primer. Dendrogram for each primer indicating the distance of the strains to each other was constructed. RAPD results showed that the collected strains constituted four different clusters. The first cluster included two isolates (P1 and P3). The second cluster included seven isolates (P2, P4, P5, P6, P7, P8, and P10). The third and fourth clusters included one isolate (P9) and two isolates (P11 and P12), respectively. We concluded that RAPD analysis might be used in providing genotypic characters for toxigenic P. citrinum strains typing in epidemiological investigations and public health related risk assessment.

Phase estimation of coherent states with a noiseless linear amplifier

NASA Astrophysics Data System (ADS)

Assad, Syed M.; Bradshaw, Mark; Lam, Ping Koy

Amplification of quantum states is inevitably accompanied with the introduction of noise at the output. For protocols that are probabilistic with heralded success, noiseless linear amplification in theory may still be possible. When the protocol is successful, it can lead to an output that is a noiselessly amplified copy of the input. When the protocol is unsuccessful, the output state is degraded and is usually discarded. Probabilistic protocols may improve the performance of some quantum information protocols, but not for metrology if the whole statistics is taken into consideration. We calculate the precision limits on estimating the phase of coherent states using a noiseless linear amplifier by computing its quantum Fisher information and we show that on average, the noiseless linear amplifier does not improve the phase estimate. We also discuss the case where abstention from measurement can reduce the cost for estimation.

An expanded nuclear phylogenomic PCR toolkit for Sapindales1

PubMed Central

Collins, Elizabeth S.; Gostel, Morgan R.; Weeks, Andrea

2016-01-01

Premise of the study: We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). Methods and Results: Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16–90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon. Conclusions: Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation. PMID:28101434

Pathways of Prion Spread during Early Chronic Wasting Disease in Deer.

PubMed

Hoover, Clare E; Davenport, Kristen A; Henderson, Davin M; Denkers, Nathaniel D; Mathiason, Candace K; Soto, Claudio; Zabel, Mark D; Hoover, Edward A

2017-05-15

Among prion infections, two scenarios of prion spread are generally observed: (i) early lymphoid tissue replication or (ii) direct neuroinvasion without substantial antecedent lymphoid amplification. In nature, cervids are infected with chronic wasting disease (CWD) prions by oral and nasal mucosal exposure, and studies of early CWD pathogenesis have implicated pharyngeal lymphoid tissue as the earliest sites of prion accumulation. However, knowledge of chronological events in prion spread during early infection remains incomplete. To investigate this knowledge gap in early CWD pathogenesis, we exposed white-tailed deer to CWD prions by mucosal routes and performed serial necropsies to assess PrP CWD tissue distribution by real-time quaking-induced conversion (RT-QuIC) and tyramide signal amplification immunohistochemistry (TSA-IHC). Although PrP CWD was not detected by either method in the initial days (1 and 3) postexposure, we observed PrP CWD seeding activity and follicular immunoreactivity in oropharyngeal lymphoid tissues at 1 and 2 months postexposure (MPE). At 3 MPE, PrP CWD replication had expanded to all systemic lymphoid tissues. By 4 MPE, the PrP CWD burden in all lymphoid tissues had increased and approached levels observed in terminal disease, yet there was no evidence of nervous system invasion. These results indicate the first site of CWD prion entry is in the oropharynx, and the initial phase of prion amplification occurs in the oropharyngeal lymphoid tissues followed by rapid dissemination to systemic lymphoid tissues. This lymphoid replication phase appears to precede neuroinvasion. IMPORTANCE Chronic wasting disease (CWD) is a universally fatal transmissible spongiform encephalopathy affecting cervids, and natural infection occurs through oral and nasal mucosal exposure to infectious prions. Terminal disease is characterized by PrP CWD accumulation in the brain and lymphoid tissues of affected animals. However, the initial sites of prion accumulation and pathways of prion spread during early CWD infection remain unknown. To investigate the chronological events of early prion pathogenesis, we exposed deer to CWD prions and monitored the tissue distribution of PrP CWD over the first 4 months of infection. We show CWD uptake occurs in the oropharynx with initial prion replication in the draining oropharyngeal lymphoid tissues, rapidly followed by dissemination to systemic lymphoid tissues without evidence of neuroinvasion. These data highlight the two phases of CWD infection: a robust prion amplification in systemic lymphoid tissues prior to neuroinvasion and establishment of a carrier state. Copyright © 2017 American Society for Microbiology.

Does the Arctic Amplification peak this decade?

NASA Astrophysics Data System (ADS)

Martin, Torge; Haine, Thomas W. N.

2017-04-01

Temperatures rise faster in the Arctic than on global average, a phenomenon known as Arctic Amplification. While this is well established from observations and model simulations, projections of future climate (here: RCP8.5) with models of the Coupled Model Intercomparison Project phase 5 (CMIP5) also indicate that the Arctic Amplification has a maximum. We show this by means of an Arctic Amplification factor (AAF), which we define as the ratio of Arctic mean to global mean surface air temperature (SAT) anomalies. The SAT anomalies are referenced to the period 1960-1980 and smoothed by a 30-year running mean. For October, the multi-model ensemble-mean AAF reaches a maximum in 2017. The maximum moves however to later years as Arctic winter progresses: for the autumn mean SAT (September to November) the maximum AAF is found in 2028 and for winter (December to February) in 2060. Arctic Amplification is driven, amongst others, by the ice-albedo feedback (IAF) as part of the more general surface albedo feedback (involving clouds, snow cover, vegetation changes) and temperature effects (Planck and lapse-rate feedbacks). We note that sea ice retreat and the associated warming of the summer Arctic Ocean are not only an integral part of the IAF but are also involved in the other drivers. In the CMIP5 simulations, the timing of the AAF maximum coincides with the period of fastest ice retreat for the respective month. Presence of at least some sea ice is crucial for the IAF to be effective because of the contrast in surface albedo between ice and open water and the need to turn ocean warming into ice melt. Once large areas of the Arctic Ocean are ice-free, the IAF should be less effective. We thus hypothesize that the ice retreat significantly affects AAF variability and forces a decline of its magnitude after at least half of the Arctic Ocean is ice-free and the ice cover becomes basically seasonal.

Gene amplification confers glyphosate resistance in Amaranthus palmeri

PubMed Central

Gaines, Todd A.; Zhang, Wenli; Wang, Dafu; Bukun, Bekir; Chisholm, Stephen T.; Shaner, Dale L.; Nissen, Scott J.; Patzoldt, William L.; Tranel, Patrick J.; Culpepper, A. Stanley; Grey, Timothy L.; Webster, Theodore M.; Vencill, William K.; Sammons, R. Douglas; Jiang, Jiming; Preston, Christopher; Leach, Jan E.; Westra, Philip

2009-01-01

The herbicide glyphosate became widely used in the United States and other parts of the world after the commercialization of glyphosate-resistant crops. These crops have constitutive overexpression of a glyphosate-insensitive form of the herbicide target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Increased use of glyphosate over multiple years imposes selective genetic pressure on weed populations. We investigated recently discovered glyphosate-resistant Amaranthus palmeri populations from Georgia, in comparison with normally sensitive populations. EPSPS enzyme activity from resistant and susceptible plants was equally inhibited by glyphosate, which led us to use quantitative PCR to measure relative copy numbers of the EPSPS gene. Genomes of resistant plants contained from 5-fold to more than 160-fold more copies of the EPSPS gene than did genomes of susceptible plants. Quantitative RT-PCR on cDNA revealed that EPSPS expression was positively correlated with genomic EPSPS relative copy number. Immunoblot analyses showed that increased EPSPS protein level also correlated with EPSPS genomic copy number. EPSPS gene amplification was heritable, correlated with resistance in pseudo-F2 populations, and is proposed to be the molecular basis of glyphosate resistance. FISH revealed that EPSPS genes were present on every chromosome and, therefore, gene amplification was likely not caused by unequal chromosome crossing over. This occurrence of gene amplification as an herbicide resistance mechanism in a naturally occurring weed population is particularly significant because it could threaten the sustainable use of glyphosate-resistant crop technology. PMID:20018685

Exploration of S-wave velocity profiles at strong motion stations in Eskisehir, Turkey, using microtremor phase velocity and S-wave amplification

NASA Astrophysics Data System (ADS)

Yamanaka, Hiroaki; Özmen, Ögur Tuna; Chimoto, Kosuke; Alkan, Mehmet Akif; Tün, Muammer; Pekkan, Emrah; Özel, Oguz; Polat, Derya; Nurlu, Murat

2018-05-01

We have explored 1D S-wave velocity profiles of shallow and deep soil layers over a basement at strong motion stations in Eskisehir Province, Turkey. Microtremor array explorations were conducted at eight strong motion stations in the area to know shallow 1D S-wave velocity models. Rayleigh wave phase velocity at a frequency range from 3 to 30 Hz was estimated with the spatial autocorrelation analysis of array records of vertical microtremors at each station. Individual phase velocity was inverted to a shallow S-wave velocity profile. Low-velocity layers were identified at the stations in the basin. Site amplification factors from S-wave parts of earthquake records that had been estimated at the strong motion stations by Yamanaka et al. (2017) were inverted to the S-wave velocities and Q-values of the sedimentary layers. The depths to the basement with an S-wave velocity of 2.2 km/s are about 1 km in the central part of the basin, while the basement becomes shallow as 0.3 km in the marginal part of the basin. We finally discussed the effects of the shallow and deep sedimentary layers on the 1D S-wave amplification characteristics using the revealed profiles. It is found that the shallow soil layers have no significant effects in the amplification at a frequency range lower than 3 Hz in the area.

Stochastic finite-fault simulation of ground motion from the August 11, 2012, M w 6.4 Ahar earthquake, northwestern Iran

NASA Astrophysics Data System (ADS)

Heidari, Reza

2016-04-01

In this study, the 11 August 2012 M w 6.4 Ahar earthquake is investigated using the ground motion simulation based on the stochastic finite-fault model. The earthquake occurred in northwestern Iran and causing extensive damage in the city of Ahar and surrounding areas. A network consisting of 58 acceleration stations recorded the earthquake within 8-217 km of the epicenter. Strong ground motion records from six significant well-recorded stations close to the epicenter have been simulated. These stations are installed in areas which experienced significant structural damage and humanity loss during the earthquake. The simulation is carried out using the dynamic corner frequency model of rupture propagation by extended fault simulation program (EXSIM). For this purpose, the propagation features of shear-wave including {Q}_s value, kappa value {k}_0 , and soil amplification coefficients at each site are required. The kappa values are obtained from the slope of smoothed amplitude of Fourier spectra of acceleration at higher frequencies. The determined kappa values for vertical and horizontal components are 0.02 and 0.05 s, respectively. Furthermore, an anelastic attenuation parameter is derived from energy decay of a seismic wave by using continuous wavelet transform (CWT) for each station. The average frequency-dependent relation estimated for the region is Q=(122± 38){f}^{(1.40± 0.16)}. Moreover, the horizontal to vertical spectral ratio H/V is applied to estimate the site effects at stations. Spectral analysis of the data indicates that the best match between the observed and simulated spectra occurs for an average stress drop of 70 bars. Finally, the simulated and observed results are compared with pseudo acceleration spectra and peak ground motions. The comparison of time series spectra shows good agreement between the observed and the simulated waveforms at frequencies of engineering interest.

Earthquake scenario ground motions for the urban area of Evansville, Indiana

USGS Publications Warehouse

Haase, Jennifer S.; Nowack, Robert L.; Cramer, Chris H.; Boyd, Oliver S.; Bauer, Robert A.

2011-01-01

The Wabash Valley seismic zone and the New Madrid seismic zone are the closest large earthquake source zones to Evansville, Indiana. The New Madrid earthquakes of 1811-1812, over 180 kilometers (km) from Evansville, produced ground motions with a Modified Mercalli Intensity of VII near Evansville, the highest intensity observed in Indiana. Liquefaction evidence has been documented less than 40 km away from Evansville resulting from two large earthquakes in the past 12,000 years in the Wabash Valley. Two earthquake scenarios are described in this paper that demonstrate the expected ground motions for a 33×42-km region around Evansville based on a repeat earthquake from each of these source regions. We perform a one-dimensional analysis for a grid of sites that takes into account the amplification or deamplification of ground motion in the unconsolidated soil layer using a new three-dimensional model of seismic velocity and bedrock depth. There are significant differences in the calculated amplification from that expected for National Earthquake Hazard Reduction Program site class D conditions, with deamplification at many locations within the ancient bedrock valley underlying Evansville. Ground motions relative to the acceleration of gravity (g) in the Evansville area from a simulation of a magnitude (M) 7.7 New Madrid earthquake range from 0.15 to 0.25 g for peak ground acceleration, 0.14 to 0.7 g for 0.2-second (s) spectral acceleration, and 0.05 to 0.25 g for 1.0-s spectral acceleration. Ground motions from a M6.8 Wabash Valley earthquake centered 40 km northwest of the city produce ground motions that decrease with distance from 1.5 to 0.3 g for 0.2-s spectral acceleration when they reach the main part of Evansville, but then increase in amplitude from 0.3 to 0.6 g south of the city and the Ohio River. The densest urbanization in Evansville and Henderson, Ky., is within the area of preferential amplification at 1.0-s period for both scenarios, but the area experiences relatively less amplification than surrounding areas at 0.2 s, consistent with expected resonance periods based on the soil profiles.

Highly sensitive fluorescence assay of DNA methyltransferase activity by methylation-sensitive cleavage-based primer generation exponential isothermal amplification-induced G-quadruplex formation.

PubMed

Xue, Qingwang; Lv, Yanqin; Xu, Shuling; Zhang, Yuanfu; Wang, Lei; Li, Rui; Yue, Qiaoli; Li, Haibo; Gu, Xiaohong; Zhang, Shuqiu; Liu, Jifeng

2015-04-15

Site-specific identification of DNA methylation and assay of MTase activity are imperative for determining specific cancer types, provide insights into the mechanism of gene repression, and develop novel drugs to treat methylation-related diseases. Herein, we developed a highly sensitive fluorescence assay of DNA methyltransferase by methylation-sensitive cleavage-based primer generation exponential isothermal amplification (PG-EXPA) coupled with supramolecular fluorescent Zinc(II)-protoporphyrin IX (ZnPPIX)/G-quadruplex. In the presence of DNA adenine methylation (Dam) MTase, the methylation-responsive sequence of hairpin probe is methylated and cleaved by the methylation-sensitive restriction endonuclease Dpn I. The cleaved hairpin probe then functions as a signal primer to initiate the exponential isothermal amplification reaction (EXPAR) by hybridizing with a unimolecular DNA containing three functional domains as the amplification template, producing a large number of G-quadruplex nanostructures by utilizing polymerases and nicking enzymes as mechanical activators. The G-quadruplex nanostructures act as host for ZnPPIX that lead to supramolecular complexes ZnPPIX/G-quadruplex, which provides optical labels for amplified fluorescence detection of Dam MTase. While in the absence of Dam MTase, neither methylation/cleavage nor PG-EXPA reaction can be initiated and no fluorescence signal is observed. The proposed method exhibits a wide dynamic range from 0.0002 to 20U/mL and an extremely low detection limit of 8.6×10(-5)U/mL, which is superior to most conventional approaches for the MTase assay. Owing to the specific site recognition of MTase toward its substrate, the proposed sensing system was able to readily discriminate Dam MTase from other MTase such as M.SssI and even detect the target in a complex biological matrix. Furthermore, the application of the proposed sensing strategy for screening Dam MTase inhibitors was also demonstrated with satisfactory results. This novel method not only provides a promising platform for monitoring activity and inhibition of DNA MTases, but also shows great potentials in biological process researches, drugs discovery and clinical diagnostics. Copyright © 2014 Elsevier B.V. All rights reserved.

HPV16 and 18 genome amplification show different E4-dependence, with 16E4 enhancing E1 nuclear accumulation and replicative efficiency via its cell cycle arrest and kinase activation functions

PubMed Central

Jackson, Deborah; Mahmood, Radma

2017-01-01

To clarify E1^E4’s role during high-risk HPV infection, the E4 proteins of HPV16 and 18 were compared side by side using an isogenic keratinocyte differentiation model. While no effect on cell proliferation or viral genome copy number was observed during the early phase of either virus life cycle, time-course experiments showed that viral genome amplification and L1 expression were differently affected upon differentiation, with HPV16 showing a much clearer E4 dependency. Although E4 loss never completely abolished genome amplification, its more obvious contribution in HPV16 focused our efforts on 16E4. As previously suggested, in the context of the virus life cycle, 16E4s G2-arrest capability was found to contribute to both genome amplification success and L1 accumulation. Loss of 16E4 also lead to a reduced maintenance of ERK, JNK and p38MAPK activity throughout the genome amplifying cell layers, with 16E4 (but not 18E4) co-localizing precisely with activated cytoplasmic JNK in both wild type raft tissue, and HPV16-induced patient biopsy tissue. When 16E1 was co-expressed with E4, as occurs during genome amplification in vivo, the E1 replication helicase accumulated preferentially in the nucleus, and in transient replication assays, E4 stimulated viral genome amplification. Interestingly, a 16E1 mutant deficient in its regulatory phosphorylation sites no longer accumulated in the nucleus following E4 co-expression. E4-mediated stabilisation of 16E2 was also apparent, with E2 levels declining in organotypic raft culture when 16E4 was absent. These results suggest that 16E4-mediated enhancement of genome amplification involves its cell cycle inhibition and cellular kinase activation functions, with E4 modifying the activity and function of viral replication proteins including E1. These activities of 16E4, and the different kinase patterns seen here with HPV18, 31 and 45, may reflect natural differences in the biology and tropisms of these viruses, as well as differences in E4 function. PMID:28306742

Attenuation of the S+Lg+Surface Wave Group out to 600 km in Northeastern North America: A Baseline Study?

NASA Astrophysics Data System (ADS)

Boatwright, J.; Seekins, L. C.

2009-12-01

We analyze the S+Lg+surface wave groups radiated out to 600 km by four moderate (4 ≤ M ≤ 5) earthquakes in Quebec, New York, and Maine: the 1997 Cap Rouge, 2002 Ausable Forks, 2005 Rivière du Loup, and 2006 Bar Harbor earthquakes. The raypaths predominately sample the Appalacian Province, and the crustal velocity structure is roughly homogeneous across the study area. We compute spectra using 20-60 s windows of the horizontal broadband components. We restrict our analysis to hard-rock (Vs > 1500 m/s) and soft-rock (Vs > 700 m/s) sites, avoiding resonant sedimentary sites; we model site amplification using average 1D impedance functions (Boore and Joyner, 1997). We use ro = 50 km instead of ro = 100 km for the crossover distance in the Street et al. (1975) function for geometrical spreading: this distance adjusts the corrected spectra at 10 s to the moment tensor estimates. This simple correction scheme allows us to regress for Q directly as a function of frequency: the source spectral shape is entirely unconstrained. Fitting a Qo f q function to the Q estimates from 0.2 to 25 Hz yields Q = 410 f 0.5 for a group velocity of 3.5 km/s. This attenuation is stronger than the Lg attenuation of 650 f 0.36 obtained by Erickson et al. (2004). The Q estimates are consistent for individual events. For f > 20 Hz, the Q estimates increase more rapidly than f 0.5: this deviation from the Qo f q form appears characteristic. To gauge how these Q estimates depend on the distance limit, we will rerun the analysis using broadband data out to 1000 km, adding 30% more recordings to the dataset.

Rapid microfluidic analysis of a Y-STR multiplex for screening of forensic samples.

PubMed

Gibson-Daw, Georgiana; Albani, Patricia; Gassmann, Marcus; McCord, Bruce

2017-02-01

In this paper, we demonstrate a rapid analysis procedure for use with a small set of rapidly mutating Y chromosomal short tandem repeat (Y-STR) loci that combines both rapid polymerase chain reaction (PCR) and microfluidic separation elements. The procedure involves a high-speed polymerase and a rapid cycling protocol to permit PCR amplification in 16 min. The resultant amplified sample is next analysed using a short 1.8-cm microfluidic electrophoresis system that permits a four-locus Y-STR genotype to be produced in 80 s. The entire procedure takes less than 25 min from sample collection to result. This paper describes the rapid amplification protocol as well as studies of the reproducibility and sensitivity of the procedure and its optimisation. The amplification process utilises a small high-speed thermocycler, microfluidic device and compact laptop, making it portable and potentially useful for rapid, inexpensive on-site genotyping. The four loci used for the multiplex were selected due to their rapid mutation rates and should proved useful in preliminary screening of samples and suspects. Overall, this technique provides a method for rapid sample screening of suspect and crime scene samples in forensic casework. Graphical abstract ᅟ.

Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence

PubMed Central

Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

2016-01-01

Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided. PMID:27146605

Long-period effects of the Denali earthquake on water bodies in the Puget Lowland: Observations and modeling

USGS Publications Warehouse

Barberopoulou, A.; Qamar, A.; Pratt, T.L.; Steele, W.P.

2006-01-01

Analysis of strong-motion instrument recordings in Seattle, Washington, resulting from the 2002 Mw 7.9 Denali, Alaska, earthquake reveals that amplification in the 0.2-to 1.0-Hz frequency band is largely governed by the shallow sediments both inside and outside the sedimentary basins beneath the Puget Lowland. Sites above the deep sedimentary strata show additional seismic-wave amplification in the 0.04- to 0.2-Hz frequency range. Surface waves generated by the Mw 7.9 Denali, Alaska, earthquake of 3 November 2002 produced pronounced water waves across Washington state. The largest water waves coincided with the area of largest seismic-wave amplification underlain by the Seattle basin. In the current work, we present reports that show Lakes Union and Washington, both located on the Seattle basin, are susceptible to large water waves generated by large local earthquakes and teleseisms. A simple model of a water body is adopted to explain the generation of waves in water basins. This model provides reasonable estimates for the water-wave amplitudes in swimming pools during the Denali earthquake but appears to underestimate the waves observed in Lake Union.

Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence.

PubMed

Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

2016-05-05

Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided.

Evidence-based guidelines for recommending cochlear implantation for young children: Audiological criteria and optimizing age at implantation.

PubMed

Leigh, Jaime R; Dettman, Shani J; Dowell, Richard C

2016-01-01

Establish up-to-date evidence-based guidelines for recommending cochlear implantation for young children. Speech perception results for early-implanted children were compared to children using traditional amplification. Equivalent pure-tone average (PTA) hearing loss for cochlear implant (CI) users was established. Language of early-implanted children was assessed over six years and compared to hearing peers. Seventy-eight children using CIs and 62 children using traditional amplification with hearing losses ranging 25-120 dB HL PTA (speech perception study). Thirty-two children who received a CI before 2.5 years of age (language study). Speech perception outcomes suggested that children with a PTA greater than 60 dB HL have a 75% chance of benefit over traditional amplification. More conservative criteria applied to the data suggested that children with PTA greater than 82 dB HL have a 95% chance of benefit. Children implanted under 2.5 years with no significant cognitive deficits made normal language progress but retained a delay approximately equal to their age at implantation. Hearing-impaired children under three years of age may benefit from cochlear implantation if their PTA exceeds 60 dB HL bilaterally. Implantation as young as possible should minimize any language delay resulting from an initial period of auditory deprivation.

Finite Element Modelling of the Indo-Gangetic Basin to Study Site Amplification

NASA Astrophysics Data System (ADS)

Sivasubramonian, J.; Jaya, D.; Raghukanth, S. T. G.; Mai, P. M.

2017-12-01

We have developed a finite-element model of the 3D velocity structure of the Indo-Gangetic basin (IG basin) to quantify site amplifications due to seismic waves emanated from regional earthquakes. Estimating seismic wave amplifications is difficult in case of limited instrumentation, thus motivating us to propose a new simulation-based approach. The input required for the finite-element model include the spatial coordinates and the material properties (density, P-wave and S-wave velocities, Q factor) of the basin. Recent studies in the basin demarcate sediment layers of varying thickness, reaching down to a depth of 6 km and S-wave velocities ranging from 0.4-2.4 km/s (Srinivas et al., 2013). In the present study, our regional model has dimensions 900 x 900 x 80 km in x, y and z directions, discretized into 320 x 320 x 53 hexahedral elements. The top 6 km of the IG basin is divided into 8 different sediment layers with varying material properties. We use kinematic rupture models for the earthquake sources to simulate past as well as hypothetical future events. Two past earthquakes (Mw4.9, Delhi; Mw5.2, Chamoli) and two hypothetical earthquakes (Mw7.1; Mw8.5) are considered in our study. The rupture plane dimensions (L and W) and the slip distribution are estimated using the method of Mai and Beroza (2002). Based on focal-mechanism solutions and the depths of seismicity, we define the strike (580, 3090), the dip (650, 210), the rake (160, 770), and the depth of top edge of fault (5 km, 19 km) for the two large hypothetical earthquakes. Based on these parameters, the Centroid Moment Tensor (CMT) solution of the source is obtained. Ground motions are then simulated by solving the three-dimensional wave equation using the spectral element method (Komatitsch and Tromp, 1999). The key observations from our results are: 1) basin amplification factors for Peak Ground Velocity (PGV) are twice as high as Peak Ground Displacement (PGD) 2) PGV amplifications are as high as a factor of 6 for earthquakes occurring inside the basin, and a factor of 4 for Himalayan earthquakes (to the north of the study region) 3) The simulated shake maps of PGV and PGD show directivity. Based on the above observations, we conclude that it is important to include our model into low-frequency ground-motion estimation for seismic hazard analysis.

Random whole metagenomic sequencing for forensic discrimination of soils.

PubMed

Khodakova, Anastasia S; Smith, Renee J; Burgoyne, Leigh; Abarno, Damien; Linacre, Adrian

2014-01-01

Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.

Search for methylation-sensitive amplification polymorphisms associated with the mantled variant phenotype in oil palm (Elaeis guineensis Jacq).

PubMed

Jaligot, E; Beulé, T; Baurens, F-C; Billotte, N; Rival, A

2004-02-01

The methylation-sensitive amplification polymorphism (MSAP) technique has been employed on somatic embryo-derived oil palms (Elaeis guineensis Jacq.) to identify methylation polymorphisms correlated with the "mantled" somaclonal variation. The variant phenotype displays an unstable feminization of male organs in both male and female flowers. Using MSAP, the methylation status of CCGG sites was compared in three normal versus three mantled regenerants sampled in clonal populations obtained through somatic embryogenesis from four genotypically distinct mother palms. Overall, 64 selective primer combinations were used and they have amplified 23 markers exhibiting a differential methylation pattern between the two phenotypes. Our results indicate that CCGG sites are poorly affected by the considerable decrease in global DNA methylation that has been previously associated with the mantled phenotype. Each of the 23 markers isolated in the present study could discriminate between the two phenotypes only when they were from the same genetic origin. This result hampers at the moment the direct use of MSAP markers for the early detection of variants, even though valuable information on putative target sequences will be obtained from a further characterization of these polymorphic markers.

Surface invasive cleavage assay on a maskless light-directed diamond DNA microarray for genome-wide human SNP mapping.

PubMed

Nie, Bei; Yang, Min; Fu, Weiling; Liang, Zhiqing

2015-07-07

The surface invasive cleavage assay, because of its innate accuracy and ability for self-signal amplification, provides a potential route for the mapping of hundreds of thousands of human SNP sites. However, its performance on a high density DNA array has not yet been established, due to the unusual "hairpin" probe design on the microarray and the lack of chemical stability of commercially available substrates. Here we present an applicable method to implement a nanocrystalline diamond thin film as an alternative substrate for fabricating an addressable DNA array using maskless light-directed photochemistry, producing the most chemically stable and biocompatible system for genetic analysis and enzymatic reactions. The surface invasive cleavage reaction, followed by degenerated primer ligation and post-rolling circle amplification is consecutively performed on the addressable diamond DNA array, accurately mapping SNP sites from PCR-amplified human genomic target DNA. Furthermore, a specially-designed DNA array containing dual probes in the same pixel is fabricated by following a reverse light-directed DNA synthesis protocol. This essentially enables us to decipher thousands of SNP alleles in a single-pot reaction by the simple addition of enzyme, target and reaction buffers.

Anomalous concentrations of seismically triggered rock falls in Pacoima Canyon: Are they caused by highly susceptible slopes or local amplification of seismic shaking?

USGS Publications Warehouse

Harp, Edwin L.; Jibson, Randall W.

2002-01-01

Anomalously high concentrations of rock falls were triggered in Pacoima Canyon (Los Angeles, California) during the 1994 Northridge earthquake. Similar concentrations were also documented from the 1971 San Fernando earthquake. Using an engineering rock-mass classification that evaluates the susceptibility of rock slopes to seismic failure based on the fracture properties of a rock mass (in terms of a numerical "Q-value" that describes rock quality), the rock slopes in Pacoima Canyon were compared with rock slopes in sorrounding areas where topography and lithology are similar, but rock-fall concentrations from the earthquakes were much lower. A statistical comparison of Q-values from five sites surrounding Pacoima Canyon indicates that seismic susceptibilities are similar to those within Pacoima Canyon; differences in the characteristics of rock slopes between these sites are not sufficient to account for the relatively high concentrations of rock falls within Pacoima Canyon as compared to low concentrations elsewhere. By eliminating susceptibility differences as a cause, the most likely explanations for the differences in rock-fall concentrations is anomalously high shaking levels in Pacoima Canyon, possibly resulting from topographic amplification within the canyon.

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes.

PubMed

Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

2017-01-01

Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare . However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

PubMed Central

Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

2017-01-01

Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes. PMID:29250096

High-resolution mapping of the 11q13 amplicon and identification of a gene, TAOS1, that is amplified and overexpressed in oral cancer cells

PubMed Central

Huang, Xin; Gollin, Susanne M.; Raja, Siva; Godfrey, Tony E.

2002-01-01

Amplification of chromosomal band 11q13 is a common event in human cancer. It has been reported in about 45% of head and neck carcinomas and in other cancers including esophageal, breast, liver, lung, and bladder cancer. To understand the mechanism of 11q13 amplification and to identify the potential oncogene(s) driving it, we have fine-mapped the structure of the amplicon in oral squamous cell carcinoma cell lines and localized the proximal and distal breakpoints. A 5-Mb physical map of the region has been prepared from which sequence is available. We quantified copy number of sequence-tagged site markers at 42–550 kb intervals along the length of the amplicon and defined the amplicon core and breakpoints by using TaqMan-based quantitative microsatellite analysis. The core of the amplicon maps to a 1.5-Mb region. The proximal breakpoint localizes to two intervals between sequence-tagged site markers, 550 kb and 160 kb in size, and the distal breakpoint maps to a 250 kb interval. The cyclin D1 gene maps to the amplicon core, as do two new expressed sequence tag clusters. We have analyzed one of these expressed sequence tag clusters and now report that it contains a previously uncharacterized gene, TAOS1 (tumor amplified and overexpressed sequence 1), which is both amplified and overexpressed in oral cancer cells. The data suggest that TAOS1 may be an amplification-dependent candidate oncogene with a role in the development and/or progression of human tumors, including oral squamous cell carcinomas. The approach described here should be useful for characterizing amplified genomic regions in a wide variety of tumors. PMID:12172009

Real-time estimation system for seismic-intensity exposed-population

NASA Astrophysics Data System (ADS)

Aoi, S.; Nakamura, H.; Kunugi, T.; Suzuki, W.; Fujiwara, H.

2013-12-01

For an appropriate first-action to an earthquake, risk (damage) information evaluated in real-time are important as well as hazard (ground motion) information. To meet this need, we are developing real-time estimation system (J-RISQ) for exposed population and earthquake damage on buildings. We plan to open the web page of estimated exposed population to the public from autumn. When an earthquake occurs, seismic intensities are calculated at each observation station and sent to the DMC (Data Management Center) in different timing. For rapid estimation, the system does not wait for the data from all the stations but begins the first estimation when the number of the stations observing the seismic intensity of 2.5 or larger exceeds the threshold amount. Estimations are updated several times using all the available data at that moment. Spatial distribution of seismic intensity in 250 m meshes is estimated by the site amplification factor of surface layers and the observed data. By using this intensity distribution, the exposed population is estimated using population data of each mesh. The exposed populations for municipalities and prefectures are estimated by summing-up the exposures of included meshes for the area and are appropriately rounded taking estimation precision into consideration. The estimated intensities for major cities are shown by the histograms, which indicate the variation of the estimated values in the city together with the observed maximum intensity. The variation is mainly caused by the difference of the site amplification factors. The intensities estimated for meshes with large amplification factor are sometimes larger than the maximum value observed in the city. The estimated results are seen on the web site just after the earthquake. The results of the past earthquakes can be easily searched by keywords such as date, magnitudes, seismic intensities and source areas. The summary of the results in the one-page report of Portable Document Format is also available. This system has been experimentally operated since 2010 and has performed the estimations in real-time for more than 670 earthquakes by July of 2012. For about 75 % of these earthquakes, it takes less than one minute to send the e-mail of first estimation after receiving data from the first triggered station, and therefore, the rapidity of the system is satisfactory. To upload a PDF report form to the web site, it takes approximately additional 30 second.

Along-Arc and Back-Arc Attenuation, Site Response, and Source Spectrum for the Intermediate-Depth 8 January 2006 M 6.7 Kythera, Greece, Earthquake

USGS Publications Warehouse

Boore, David M.; Skarlatoudis, A.A.; Margaris, B.N.; Costas, B.P.; Ventouzi, C.

2009-01-01

An M 6.7 intermediate-depth (66 km), in-slab earthquake occurring near the island of Kythera in Greece on 8 January 2006 was well recorded on networks of stations equipped with acceleration sensors and with broadband velocity sensors. All data were recorded digitally using recording instruments with resolutions ranging from almost 11 to 24 bits. We use data from these networks to study the distance dependence of the horizontal-component Fourier acceleration spectra (FAS) and horizontal-component pseudoabsolute response spectral acceleration (PSA). For purposes of simulating motions in the future, we parameterize the distance decay using several forms of the geometrical-spreading function, for each of which we derive Q as a function of frequency. By extrapolating the distance decay back to 1 km, we obtain a reference spectrum that can be used in future simulations. This spectrum requires a more complicated spectral shape than the classic single-corner-frequency model; in particular, there appears to be an enhancement of motion around 0.2-0.3 Hz that may be due to the radiation of a 3-5 sec pulse from the source. We infer a ??0 value of about 0.055 sec for rock stations and a stress parameter in the range of 400-600 bars. We also find distinctive differences in the site response of stations on soft soil and soil; both the FAS and the 5% damped PSA amplifications have similar peak amplitudes (about 2 and 4 for soil and soft-soil sites, respectively, relative to the rock sites) at similar frequencies (between about 0.4 and 2.0 Hz, with the soft-soil amplifications peaking at somewhat lower frequencies than the soil amplifications). One of the most distinctive features of the data is the clear difference in the motions for along-arc and back-arc stations, with the former being significantly higher than the latter over a broad range of frequencies at distances beyond about 250 km. The motions from the Kythera earthquake are roughly comparable to those from intermediate-depth earthquakes elsewhere, but they appear to be significantly higher than those from recordings of shallow earthquakes in Greece of comparable magnitude and hypocentral distance.

DNA-based techniques for authentication of processed food and food supplements.

PubMed

Lo, Yat-Tung; Shaw, Pang-Chui

2018-02-01

Authentication of food or food supplements with medicinal values is important to avoid adverse toxic effects, provide consumer rights, as well as for certification purpose. Compared to morphological and spectrometric techniques, molecular authentication is found to be accurate, sensitive and reliable. However, DNA degradation and inclusion of inhibitors may lead to failure in PCR amplification. This paper reviews on the existing DNA extraction and PCR protocols, and the use of small size DNA markers with sufficient discriminative power for molecular authentication. Various emerging new molecular techniques such as isothermal amplification for on-site diagnosis, next-generation sequencing for high-throughput species identification, high resolution melting analysis for quick species differentiation, DNA array techniques for rapid detection and quantitative determination in food products are also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

DNA Hydrogel with Tunable pH-Responsive Properties Produced by Rolling Circle Amplification.

PubMed

Xu, Wanlin; Huang, Yishun; Zhao, Haoran; Li, Pan; Liu, Guoyuan; Li, Jing; Zhu, Chengshen; Tian, Leilei

2017-12-22

Recently, smart DNA hydrogels, which are generally formed by the self-assembly of oligonucleotides or through the cross-linking of oligonucleotide-polymer hybrids, have attracted tremendous attention. However, the difficulties of fabricating DNA hydrogels limit their practical applications. We report herein a novel method for producing pH-responsive hydrogels by rolling circle amplification (RCA). In this method, pH-sensitive cross-linking sites were introduced into the polymeric DNA chains during DNA synthesis. As the DNA sequence can be precisely defined by its template, the properties of such hydrogels can be finely tuned in a very facile way through template design. We have investigated the process of hydrogel formation and pH-responsiveness to provide rationales for functional hydrogel design based on the RCA reaction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid amplification of 5' complementary DNA ends (5' RACE).

PubMed

2005-08-01

This method is used to extend partial cDNA clones by amplifying the 5' sequences of the corresponding mRNAs 1-3. The technique requires knowledge of only a small region of sequence within the partial cDNA clone. During PCR, the thermostable DNA polymerase is directed to the appropriate target RNA by a single primer derived from the region of known sequence; the second primer required for PCR is complementary to a general feature of the target-in the case of 5' RACE, to a homopolymeric tail added (via terminal transferase) to the 3' termini of cDNAs transcribed from a preparation of mRNA. This synthetic tail provides a primer-binding site upstream of the unknown 5' sequence of the target mRNA. The products of the amplification reaction are cloned into a plasmid vector for sequencing and subsequent manipulation.

MLL duplication in a pediatric patient with B-cell lymphoblastic lymphoma.

PubMed

Mater, David Van; Goodman, Barbara K; Wang, Endi; Gaca, Ana M; Wechsler, Daniel S

2012-04-01

Lymphoblastic lymphoma is the second most common type of non-Hodgkin lymphoma seen in children. Approximately, 90% of lymphoblastic lymphomas arise from T cells, with the remaining 10% being B-cell-lineage derived. Although T-cell lymphoblastic lymphoma most frequently occurs in the anterior mediastinum (thymus), B-cell lymphoblastic lymphoma (B-LBL) predominates in extranodal sites such as skin and bone. Here, we describe a pediatric B-LBL patient who presented with extensive abdominal involvement and whose lymphoma cells displayed segmental duplication of the mixed lineage leukemia (MLL) gene. MLL duplication/amplification has been described primarily in acute myeloid leukemia and myelodysplastic syndrome with no published reports of discrete MLL duplication/amplification events in B-LBL. The MLL gene duplication noted in this case may represent a novel mechanism for tumorigenesis in B-LBL.

Multiple scattering of waves in random media: Application to the study of the city-site effect in Mexico City area.

NASA Astrophysics Data System (ADS)

Ishizawa, O. A.; Clouteau, D.

2007-12-01

Long-duration, amplifications and spatial response's variability of the seismic records registered in Mexico City during the September 1985 earthquake cannot only be explained by the soil velocity model. We will try to explain these phenomena by studying the extent of the effect of buildings' diffracted wave fields during an earthquake. The main question is whether the presence of a large number of buildings can significantly modify the seismic wave field. We are interested in the interaction between the incident wave field propagating in a stratified half- space and a large number of structures at the free surface, i.e., the coupled city-site effect. We study and characterize the seismic wave propagation regimes in a city using the theory of wave propagation in random media. In the coupled city-site system, the buildings are modeled as resonant scatterers uniformly distributed at the surface of a deterministic, horizontally layered elastic half-space representing the soil. Based on the mean-field and the field correlation equations, we build a theoretical model which takes into account the multiple scattering of seismic waves and allows us to describe the coupled city-site system behavior in a simple and rapid way. The results obtained for the configurationally averaged field quantities are validated by means of 3D results for the seismic response of a deterministic model. The numerical simulations of this model are computed with MISS3D code based on classical Soil-Structure Interaction techniques and on a variational coupling between Boundary Integral Equations for a layered soil and a modal Finite Element approach for the buildings. This work proposes a detailed numerical and a theoretical analysis of the city-site interaction (CSI) in Mexico City area. The principal parameters in the study of the CSI are the buildings resonant frequency distribution, the soil characteristics of the site, the urban density and position of the buildings in the city, as well as the type of incident wave. The main results of the theoretical and numerical models allow us to characterize the seismic movement in urban areas.

Sensitivity Tests Between Vs30 and Detailed Shear Wave Profiles Using 1D and 3D Site Response Analysis, Las Vegas Valley

NASA Astrophysics Data System (ADS)

West, Loyd Travis

Site characterization is an essential aspect of hazard analysis and the time-averaged shear-wave velocity to 30 m depth "Vs30" for site-class has become a critical parameter in site-specific and probabilistic hazard analysis. Yet, the general applicability of Vs30 can be ambiguous and much debate and research surround its application. In 2007, in part to mitigate the uncertainty associated with the use of Vs30 in Las Vegas Valley, the Clark County Building Department (CCBD) in collaboration with the Nevada System of Higher Education (NSHE) embarked on an endeavor to map Vs30 using a geophysical methods approach for a site-class microzonation map of over 500 square miles (1500 km2) in southern Nevada. The resulting dataset, described by Pancha et al. (2017), contains over 10,700 1D shear-wave-velocity-depth profiles (SWVP) that constitute a rich database of 3D shear-wave velocity structure that is both laterally and vertical heterogenous. This study capitalizes on the uniquely detailed and spatially dense CCBD database to carry out sensitivity tests on the detailed shear-wave-velocity-profiles and the Vs30 utilizing 1D and 3D site-response approaches. Sensitivity tests are derived from the 1D oscillator response of a single-degree-of-freedom-oscillator and from 3D finite-difference deterministic simulations up to 15 Hz frequency using similar model parameters. Results demonstrate that the detailed SWVP are amplifying ground motions by roughly 50% over the simple Vs30 models, above 4.6 Hz frequency. Numerical simulations also depict significant lateral resonance, focusing, and scattering from seismic energy attributed to the 3D small-scale heterogeneities of the shear-wave-velocity profiles that result in a 70% increase in peak ground velocity. Additionally, PGV ratio maps clearly establish that the increased amplification from the detailed SWVPs is consistent throughout the model space. As a corollary, this study demonstrates the use of finite-differencing numerical based methods to simulate ground motions at high frequencies, up to 15 Hz.

What do data used to develop ground-motion prediction equations tell us about motions near faults?

USGS Publications Warehouse

Boore, David M.

2014-01-01

A large database of ground motions from shallow earthquakes occurring in active tectonic regions around the world, recently developed in the Pacific Earthquake Engineering Center’s NGA-West2 project, has been used to investigate what such a database can say about the properties and processes of crustal fault zones. There are a relatively small number of near-rupture records, implying that few recordings in the database are within crustal fault zones, but the records that do exist emphasize the complexity of ground-motion amplitudes and polarization close to individual faults. On average over the whole data set, however, the scaling of ground motions with magnitude at a fixed distance, and the distance dependence of the ground motions, seem to be largely consistent with simple seismological models of source scaling, path propagation effects, and local site amplification. The data show that ground motions close to large faults, as measured by elastic response spectra, tend to saturate and become essentially constant for short periods. This saturation seems to be primarily a geometrical effect, due to the increasing size of the rupture surface with magnitude, and not due to a breakdown in self similarity.

What Do Data Used to Develop Ground-Motion Prediction Equations Tell Us About Motions Near Faults?

NASA Astrophysics Data System (ADS)

Boore, David M.

2014-11-01

A large database of ground motions from shallow earthquakes occurring in active tectonic regions around the world, recently developed in the Pacific Earthquake Engineering Center's NGA-West2 project, has been used to investigate what such a database can say about the properties and processes of crustal fault zones. There are a relatively small number of near-rupture records, implying that few recordings in the database are within crustal fault zones, but the records that do exist emphasize the complexity of ground-motion amplitudes and polarization close to individual faults. On average over the whole data set, however, the scaling of ground motions with magnitude at a fixed distance, and the distance dependence of the ground motions, seem to be largely consistent with simple seismological models of source scaling, path propagation effects, and local site amplification. The data show that ground motions close to large faults, as measured by elastic response spectra, tend to saturate and become essentially constant for short periods. This saturation seems to be primarily a geometrical effect, due to the increasing size of the rupture surface with magnitude, and not due to a breakdown in self similarity.

Nucleic acid amplification using modular branched primers

DOEpatents

Ulanovsky, Levy; Raja, Mugasimangalam C.

2001-01-01

Methods and compositions expand the options for making primers for use in amplifying nucleic acid segments. The invention eliminates the step of custom synthesis of primers for Polymerase Chain Reactions (PCR). Instead of being custom-synthesized, a primer is replaced by a combination of several oligonucleotide modules selected from a pre-synthesized library. A modular combination of just a few oligonucleotides essentially mimics the performance of a conventional, custom-made primer by matching the sequence of the priming site in the template. Each oligonucleotide module has a segment that matches one of the stretches within the priming site.

Comparisons of shear-wave slowness in the Santa Clara Valley, California using blind interpretations of data from invasive and noninvasive methods

USGS Publications Warehouse

Boore, D.M.; Asten, M.W.

2008-01-01

Many groups contributed to a blind interpretation exercise for the determination of shear-wave slowness beneath the Santa Clara Valley. The methods included invasive methods in deep boreholes as well as noninvasive methods using active and passive sources, at six sites within the valley (with most investigations being conducted at a pair of closely spaced sites near the center of the valley). Although significant variability exists between the models, the slownesses from the various methods are similar enough that linear site amplifications estimated in several ways are generally within 20% of one another. The methods were able to derive slownesses that increase systematically with distance from the valley edge, corresponding to a tendency for the sites to be underlain by finer-grained materials away from the valley edge. This variation is in agreement with measurements made in the boreholes at the sites.

Selection of the simplest RNA that binds isoleucine

PubMed Central

LOZUPONE, CATHERINE; CHANGAYIL, SHANKAR; MAJERFELD, IRENE; YARUS, MICHAEL

2003-01-01

We have identified the simplest RNA binding site for isoleucine using selection-amplification (SELEX), by shrinking the size of the randomized region until affinity selection is extinguished. Such a protocol can be useful because selection does not necessarily make the simplest active motif most prominent, as is often assumed. We find an isoleucine binding site that behaves exactly as predicted for the site that requires fewest nucleotides. This UAUU motif (16 highly conserved positions; 27 total), is also the most abundant site in successful selections on short random tracts. The UAUU site, now isolated independently at least 63 times, is a small asymmetric internal loop. Conserved loop sequences include isoleucine codon and anticodon triplets, whose nucleotides are required for amino acid binding. This reproducible association between isoleucine and its coding sequences supports the idea that the genetic code is, at least in part, a stereochemical residue of the most easily isolated RNA–amino acid binding structures. PMID:14561881

Predicting Strong Ground-Motion Seismograms for Magnitude 9 Cascadia Earthquakes Using 3D Simulations with High Stress Drop Sub-Events

NASA Astrophysics Data System (ADS)

Frankel, A. D.; Wirth, E. A.; Stephenson, W. J.; Moschetti, M. P.; Ramirez-Guzman, L.

2015-12-01

We have produced broadband (0-10 Hz) synthetic seismograms for magnitude 9.0 earthquakes on the Cascadia subduction zone by combining synthetics from simulations with a 3D velocity model at low frequencies (≤ 1 Hz) with stochastic synthetics at high frequencies (≥ 1 Hz). We use a compound rupture model consisting of a set of M8 high stress drop sub-events superimposed on a background slip distribution of up to 20m that builds relatively slowly. The 3D simulations were conducted using a finite difference program and the finite element program Hercules. The high-frequency (≥ 1 Hz) energy in this rupture model is primarily generated in the portion of the rupture with the M8 sub-events. In our initial runs, we included four M7.9-8.2 sub-events similar to those that we used to successfully model the strong ground motions recorded from the 2010 M8.8 Maule, Chile earthquake. At periods of 2-10 s, the 3D synthetics exhibit substantial amplification (about a factor of 2) for sites in the Puget Lowland and even more amplification (up to a factor of 5) for sites in the Seattle and Tacoma sedimentary basins, compared to rock sites outside of the Puget Lowland. This regional and more localized basin amplification found from the simulations is supported by observations from local earthquakes. There are substantial variations in the simulated M9 time histories and response spectra caused by differences in the hypocenter location, slip distribution, down-dip extent of rupture, coherence of the rupture front, and location of sub-events. We examined the sensitivity of the 3D synthetics to the velocity model of the Seattle basin. We found significant differences in S-wave focusing and surface wave conversions between a 3D model of the basin from a spatially-smoothed tomographic inversion of Rayleigh-wave phase velocities and a model that has an abrupt southern edge of the Seattle basin, as observed in seismic reflection profiles.

Three-Level De-Multiplexed Dual-Branch Complex Delta-Sigma Transmitter.

PubMed

Arfi, Anis Ben; Elsayed, Fahmi; Aflaki, Pouya M; Morris, Brad; Ghannouchi, Fadhel M

2018-02-20

In this paper, a dual-branch topology driven by a Delta-Sigma Modulator (DSM) with a complex quantizer, also known as the Complex Delta Sigma Modulator (CxDSM), with a 3-level quantized output signal is proposed. By de-multiplexing the 3-level Delta-Sigma-quantized signal into two bi-level streams, an efficiency enhancement over the operational frequency range is achieved. The de-multiplexed signals drive a dual-branch amplification block composed of two switch-mode back-to-back power amplifiers working at peak power. A signal processing technique known as quantization noise reduction with In-band Filtering (QNRIF) is applied to each of the de-multiplexed streams to boost the overall performances; particularly the Adjacent Channel Leakage Ratio (ACLR). After amplification, the two branches are combined using a non-isolated combiner, preserving the efficiency of the transmitter. A comprehensive study on the operation of this topology and signal characteristics used to drive the dual-branch Switch-Mode Power Amplifiers (SMPAs) was established. Moreover, this work proposes a highly efficient design of the amplification block based on a back-to-back power topology performing a dynamic load modulation exploiting the non-overlapping properties of the de-multiplexed Complex DSM signal. For experimental validation, the proposed de-multiplexed 3-level Delta-Sigma topology was implemented on the BEEcube™ platform followed by the back-to-back Class-E switch-mode power amplification block. The full transceiver is assessed using a 4th-Generation mobile communications standard LTE (Long Term Evolution) standard 1.4 MHz signal with a peak to average power ratio (PAPR) of 8 dB. The dual-branch topology exhibited a good linearity and a coding efficiency of the transmitter chain higher than 72% across the band of frequency from 1.8 GHz to 2.7 GHz.

Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients

NASA Astrophysics Data System (ADS)

Ruiz, Carmen; Li, Julia; Luttgen, Madelyn S.; Kolatkar, Anand; Kendall, Jude T.; Flores, Edna; Topp, Zheng; Samlowski, Wolfram E.; McClay, Edward; Bethel, Kelly; Ferrone, Soldano; Hicks, James; Kuhn, Peter

2015-02-01

Purpose. Circulating melanoma cells (CMCs) constitute a potentially important representation of time-resolved tumor biology in patients. To date, genomic characterization of CMCs has been limited due to the lack of a robust methodology capable of identifying them in a format suitable for downstream characterization. Here, we have developed a methodology to detect intact CMCs that enables phenotypic, morphometric and genomic analysis at the single cell level. Experimental design. Blood samples from 40 metastatic melanoma patients and 10 normal blood donors were prospectively collected. A panel of 7 chondroitin sulfate proteoglycan 4 (CSPG4)-specific monoclonal antibodies (mAbs) was used to immunocytochemically label CMCs. Detection was performed by automated digital fluorescence microscopy and multi-parametric computational analysis. Individual CMCs were captured by micromanipulation for whole genome amplification and copy number variation (CNV) analysis. Results. Based on CSPG4 expression and nuclear size, 1-250 CMCs were detected in 22 (55%) of 40 metastatic melanoma patients (0.5-371.5 CMCs ml-1). Morphometric analysis revealed that CMCs have a broad spectrum of morphologies and sizes but exhibit a relatively homogeneous nuclear size that was on average 1.5-fold larger than that of surrounding PBMCs. CNV analysis of single CMCs identified deletions of CDKN2A and PTEN, and amplification(s) of TERT, BRAF, KRAS and MDM2. Furthermore, novel chromosomal amplifications in chr12, 17 and 19 were also found. Conclusions. Our findings show that CSPG4 expressing CMCs can be found in the majority of advanced melanoma patients. High content analysis of this cell population may contribute to the design of effective personalized therapies in patients with melanoma.

Future ocean hypercapnia driven by anthropogenic amplification of the natural CO2 cycle

NASA Astrophysics Data System (ADS)

McNeil, B.

2016-02-01

Elevated carbon dioxide concentrations in seawater (hypercapnia) can induce neurological, physiological and behavioural deficiencies in marine animals. Prediction of the onset and evolution of hypercapnia in the ocean requires a good understanding of annual oceanic carbon dioxide variability, but relevant global observational data are sparse. Here we diagnose global ocean patterns of monthly carbon variability based on observations that allow us to examine the evolution of surface ocean CO2 levels over the entire annual cycle under increasing atmospheric CO2 concentrations. We find that some oceanic regions undergo an up to 10-fold amplification of the natural cycle of CO2 by 2100, if atmospheric carbon dioxide concentrations continue to rise throughout this century (RCP8.5). Projections from a suite of Earth System Climate Models are broadly consistent with the findings from our data based approach. Our predicted amplification in the annual CO2 cycle displays distinct global patterns that may expose major fisheries in the Southern, Pacific and North Atlantic Oceans to high CO2 events many decades earlier than expected from average atmospheric CO2 concentrations. We suggest that these ocean 'CO2 hotspots' evolve as a combination of the strong seasonal dynamics of CO2 and the long-term effective storage of anthropogenic CO2 that lowers the buffer capacity in those regions, causing a non-linear CO2 amplification over the annual cycle. The onset of ocean hypercapnia events (pCO2 >1000 µatm) is forecast for atmospheric CO2 concentrations that exceed 650 ppm, with hypercapnia spreading to up to one half of the surface ocean by the year 2100 under a high-emissions scenario (RCP8.5) with potential implications for fisheries over the coming century.

CPT site characterization for seismic hazards in the New Madrid seismic zone

USGS Publications Warehouse

Liao, T.; Mayne, P.W.; Tuttle, M.P.; Schweig, E.S.; Van Arsdale, R.B.

2002-01-01

A series of cone penetration tests (CPTs) were conducted in the vicinity of the New Madrid seismic zone in central USA for quantifying seismic hazards, obtaining geotechnical soil properties, and conducting studies at liquefaction sites related to the 1811-1812 and prehistoric New Madrid earthquakes. The seismic piezocone provides four independent measurements for delineating the stratigraphy, liquefaction potential, and site amplification parameters. At the same location, two independent assessments of soil liquefaction susceptibility can be made using both the normalized tip resistance (qc1N) and shear wave velocity (Vs1). In lieu of traditional deterministic approaches, the CPT data can be processed using probability curves to assess the level and likelihood of future liquefaction occurrence. ?? 2002 Elsevier Science Ltd. All rights reserved.

DNA polymerase preference determines PCR priming efficiency.

PubMed

Pan, Wenjing; Byrne-Steele, Miranda; Wang, Chunlin; Lu, Stanley; Clemmons, Scott; Zahorchak, Robert J; Han, Jian

2014-01-30

Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3' hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3' end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially available DNA polymerases. The results suggest that the interaction of the DNA polymerase with the primer:template junction during the initiation of DNA polymerization is very important in terms of overall amplification bias and has broader implications for both the primer design process and multiplex PCR.

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

PubMed Central

Ullrich, Thomas; Ermantraut, Eugen; Schulz, Torsten; Steinmetzer, Katrin

2012-01-01

Background State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a single assay and to perform the assay on simple and robust instrumentation is a prerequisite for the development of novel molecular point of care tests. PMID:22539973

ENSO and hydrologic extremes in the western United States

USGS Publications Warehouse

Cayan, D.R.; Redmond, K.T.; Riddle, L.G.

1999-01-01

Frequency distributions of daily precipitation in winter and daily stream flow from late winter to early summer, at several hundred sites in the western United States, exhibit strong and systematic responses to the two phases of ENSO. Most of the stream flows considered are driven by snowmelt. The Southern Oscillation index (SOI) is used as the ENSO phase indicator. Both modest (median) and larger (90th percentile) events were considered. In years with negative SOI values (El Nino), days with high daily precipitation and stream flow are more frequent than average over the Southwest and less frequent over the Northwest. During years with positive SOI values (La Nina), a nearly opposite pattern is seen. A more pronounced increase is seen in the number of days exceeding climatological 90th percentile values than in the number exceeding climatological 50th percentile values, for both precipitation and stream flow. Stream flow responses to ENSO extremes are accentuated over precipitation responses. Evidence suggests that the mechanism for this amplification involves ENSO-phase differences in the persistence and duration of wet episodes, affecting the efficiency of the process by which precipitation is converted to runoff. The SOI leads the precipitation events by several months, and hydrologic lags (mostly through snowmelt) dealy the stream flow response by several more months. The combined 6-12 month predictive aspect of this relationship should be of significant benefit in responding to flood (or drought) risk and in improving overall water management in the western states.Frequency distributions of daily precipitation in winter and daily stream flow from late winter to early summer, at several hundred sites in the western United States, exhibit strong and systematic responses to the two phases of ENSO. Most of the stream flows considered are driven by snowmelt. The Southern Oscillation index (SOI) is used as the ENSO phase indicator. Both modest (median) and larger (90th percentile) events were considered. In years with negative SOI values (El Nino), days with high daily precipitation and stream flow are more frequent than average over the Southwest and less frequent over the Northwest. During years with positive SOI values (La Nina), a nearly opposite pattern is seen. A more pronounced increase is seen in the number of days exceeding climatological 90th percentile values than in the number exceeding climatological 50th percentile values, for both precipitation and stream flow. Stream flow responses to ENSO extremes are accentuated over precipitation responses. Evidence suggests that the mechanism for this amplification involves ENSO-phase differences in the persistence and duration of wet episodes, affecting the efficiency of the process by which precipitation is converted to runoff. The SOI leads the precipitation events by several months, and hydrologic lags (mostly through snowmelt) delay the stream flow response by several more months. The combined 6-12-month predictive aspect of this relationship should be of significant benefit in responding to flood (or drought) risk and in improving overall water management in the western states.

The stability of H/V spectral ratios from noise measurements in Armutlu Peninsula (Turkey)

NASA Astrophysics Data System (ADS)

Livaoǧlu, Hamdullah; Irmak, T. Serkan; Caka, Deniz; Yavuz, Evrim; Lühr, B. G.; Woith, H.; Tunç, B.; Baris, S.

2016-04-01

The horizontal to vertical spectral ratio (H/V) method has been successfully using in order to estimate the fundamental resonance frequency of the sedimentary cover, its thickness and amplification factor since at least 3 decades. There are numerous studies have been carried out on the stability of the H/V spectral ratios. Almost all studies showed that fundamental frequency is stable even measurements are repeated at different times. From this point of view, the results will show us an approach whether the stations are suitable for accurate estimate of earthquake studies and engineering purposes or not. Also we want to see if any effects of the amplification factor changing on the seismograms for Armutlu Seismic Network (ARNET) even though seismic stations are established far away from cultural noise and located on hard rock sites. It has been selected one hour recorded data of all stations during the most stationary times. The amplification and resonant frequency variations of H/V ratio were calculated to investigate temporal stability in time. There is a total harmony in fundamental frequencies values and H/V spectral ratio values in time-lagged periods. Some stations shows secondary minor peaks in high frequency band due to a shallow formation effect or cultural noises around. In the east side of the area ILYS station shows amplitude peak in lower fundamental frequency band from expected. This could compose a high amplification in lower frequencies and so that yield less reliable results in local earthquakes studies. By the experimental results from ambient noise analysis, it could be worked up for relocation of one station.

Muscle RAS oncogene homolog (MRAS) recurrent mutation in Borrmann type IV gastric cancer.

PubMed

Yasumoto, Makiko; Sakamoto, Etsuko; Ogasawara, Sachiko; Isobe, Taro; Kizaki, Junya; Sumi, Akiko; Kusano, Hironori; Akiba, Jun; Torimura, Takuji; Akagi, Yoshito; Itadani, Hiraku; Kobayashi, Tsutomu; Hasako, Shinichi; Kumazaki, Masafumi; Mizuarai, Shinji; Oie, Shinji; Yano, Hirohisa

2017-01-01

The prognosis of patients with Borrmann type IV gastric cancer (Type IV) is extremely poor. Thus, there is an urgent need to elucidate the molecular mechanisms underlying the oncogenesis of Type IV and to identify new therapeutic targets. Although previous studies using whole-exome and whole-genome sequencing have elucidated genomic alterations in gastric cancer, none has focused on comprehensive genetic analysis of Type IV. To discover cancer-relevant genes in Type IV, we performed whole-exome sequencing and genome-wide copy number analysis on 13 patients with Type IV. Exome sequencing identified 178 somatic mutations in protein-coding sequences or at splice sites. Among the mutations, we found a mutation in muscle RAS oncogene homolog (MRAS), which is predicted to cause molecular dysfunction. MRAS belongs to the Ras subgroup of small G proteins, which includes the prototypic RAS oncogenes. We analyzed an additional 46 Type IV samples to investigate the frequency of MRAS mutation. There were eight nonsynonymous mutations (mutation frequency, 17%), showing that MRAS is recurrently mutated in Type IV. Copy number analysis identified six focal amplifications and one homozygous deletion, including insulin-like growth factor 1 receptor (IGF1R) amplification. The samples with IGF1R amplification had remarkably higher IGF1R mRNA and protein expression levels compared with the other samples. This is the first report of MRAS recurrent mutation in human tumor samples. Our results suggest that MRAS mutation and IGF1R amplification could drive tumorigenesis of Type IV and could be new therapeutic targets. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Viability and Burden of Leishmania in Extralesional Sites during Human Dermal Leishmaniasis

PubMed Central

Romero, Ibeth; Téllez, Jair; Suárez, Yazmín; Cardona, Maria; Figueroa, Roger; Zelazny, Adrian; Gore Saravia, Nancy

2010-01-01

Background The clinical and epidemiological significance of Leishmania DNA in extralesional sites is obscured by uncertainty of whether the DNA derives from viable parasites. To examine dissemination of Leishmania during active disease and the potential participation of human infection in transmission, Leishmania 7SLRNA was exploited to establish viability and estimate parasite burden in extralesional sites of dermal leishmaniasis patients. Methods The feasibility of discriminating parasite viability by PCR of Leishmania 7SLRNA was evaluated in relation with luciferase activity of luc transfected intracellular amastigotes in dose-response assays of Glucantime cytotoxicity. Monocytes, tonsil swabs, aspirates of normal skin and lesions of 28 cutaneous and 2 mucocutaneous leishmaniasis patients were screened by kDNA amplification/Southern blot. Positive samples were analyzed by quantitative PCR of Leishmania 7SLRNA genes and transcripts. Results 7SLRNA amplification coincided with luciferase activity, confirming discrimination of parasite viability. Of 22 patients presenting kDNA in extralesional samples, Leishmania 7SLRNA genes or transcripts were detected in one or more kDNA positive samples in 100% and 73% of patients, respectively. Gene and transcript copy number amplified from extralesional tissues were comparable to lesions. 7SLRNA transcripts were detected in 13/19 (68%) monocyte samples, 5/12 (42%) tonsil swabs, 4/11 (36%) normal skin aspirates, and 22/25 (88%) lesions; genes were quantifiable in 15/19 (79%) monocyte samples, 12/13 (92%) tonsil swabs, 8/11 (73%) normal skin aspirates. Conclusion Viable parasites are present in extralesional sites, including blood monocytes, tonsils and normal skin of dermal leishmaniasis patients. Leishmania 7SLRNA is an informative target for clinical and epidemiologic investigations of human leishmaniasis. PMID:20856851

Probabilistic seismic hazard estimates incorporating site effects - An example from Indiana, U.S.A

USGS Publications Warehouse

Hasse, J.S.; Park, C.H.; Nowack, R.L.; Hill, J.R.

2010-01-01

The U.S. Geological Survey (USGS) has published probabilistic earthquake hazard maps for the United States based on current knowledge of past earthquake activity and geological constraints on earthquake potential. These maps for the central and eastern United States assume standard site conditions with Swave velocities of 760 m/s in the top 30 m. For urban and infrastructure planning and long-term budgeting, the public is interested in similar probabilistic seismic hazard maps that take into account near-surface geological materials. We have implemented a probabilistic method for incorporating site effects into the USGS seismic hazard analysis that takes into account the first-order effects of the surface geologic conditions. The thicknesses of sediments, which play a large role in amplification, were derived from a P-wave refraction database with over 13, 000 profiles, and a preliminary geology-based velocity model was constructed from available information on S-wave velocities. An interesting feature of the preliminary hazard maps incorporating site effects is the approximate factor of two increases in the 1-Hz spectral acceleration with 2 percent probability of exceedance in 50 years for parts of the greater Indianapolis metropolitan region and surrounding parts of central Indiana. This effect is primarily due to the relatively thick sequence of sediments infilling ancient bedrock topography that has been deposited since the Pleistocene Epoch. As expected, the Late Pleistocene and Holocene depositional systems of the Wabash and Ohio Rivers produce additional amplification in the southwestern part of Indiana. Ground motions decrease, as would be expected, toward the bedrock units in south-central Indiana, where motions are significantly lower than the values on the USGS maps.

Analysis of Site Effect in the Izmit Basin of Turkey by Wave Propagation Simulation Using the Spectral Element Method: Preliminary Results

NASA Astrophysics Data System (ADS)

Firtana Elcomert, K.; Kocaoglu, A. H.

2013-12-01

Sedimentary basins generally cause significant ground motion amplification during an earthquake. Along with the resonance controlled by the impedance contrast between the sedimentary cover and bedrock, surface waves generated within the basin make the waveforms more complex and longer in duration. When a dense network of weak and/or strong motion sensors is available, site effect or more specifically sedimentary basin amplification can be directly estimated experimentally provided that significant earthquakes occur during the period of study. Alternatively, site effect can be investigated through simulation of ground motion. The objective of this study is to investigate the 2-D and/or 3-D site effect in the Izmit Basin located in the eastern Marmara region of Turkey, using the currently available bedrock topography and shear-wave velocity data. The Izmit Basin was formed in Plio-Quaternary period and is known to be controlled by the northern branch of the North Anatolian Fault Zone. A thorough analysis of seismic hazard is important since the city of Izmit and its metropolitan area is located in this region. This work presents some of the preliminary results obtained from 2-D and 3-D seismic wave propagation simulations using the spectral element method, which is based on high order polynomial approximation of the weak formulation of the wave equation. In this study, the numerical simulations were carried out with SPECFEM2D/3D program. Comparison of seismograms recorded on the top of sedimentary layer with those recorded on the bedrock show more complex waveforms with higher amplitudes on seismograms recorded at the free surface. Furthermore, modeling clearly reveals that observed seismograms include surface waves whose excitation is clearly related with the basin geometry.

Modelling of Earthquake Ground Response in the Maltese Islands Using Results from Geophysical Investigations

NASA Astrophysics Data System (ADS)

Farrugia, D.; Galea, P. M.; D'Amico, S.

2016-12-01

The Maltese archipelago is characterised by a four layer sequence of limestones and clays. The Lower Coralline Limestone is the oldest exposed layer, overlain by the Globigerina Limestone. Some parts of the islands are characterised by Upper Coralline Limestone plateaus and hillcaps covering a soft Blue Clay layer which can be up to 75 m thick. The BC layer introduces a velocity inversion in the stratigraphy, and makes the Vs30 parameter not always suitable for seismic microzonation purposes. Such a layer may still produce amplification effects, however would not contribute to the numerical mean of Vs in the upper 30m. In this study, site response analysis for the Maltese islands is conducted, with particular attention being given to sites described above. Array and single-station measurements of ambient noise were first carried out at numerous sites in Malta. Surface wave dispersion and H/V curves were jointly inverted using a genetic algorithm, so that the Vs profiles were obtained. The stochastic extended-fault algorithm EXSIM was used to simulate historical and recent earthquakes at the bedrock. These were used in conjunction with the equivalent-linear programme SHAKE2000 to carry out the site-specific response analysis, using the derived geophysical models. Maps of ground motion parameters, such as peak ground acceleration and spectral accelerations, confirm that the clay, even when buried under a hard outcropping layer can still produce significant amplifications at frequencies which are of engineering interest when considering the recent urbanisation patterns. The results of this project will give important, and previously unavailable information and predictions about the behaviour of local lithotypes in response to earthquake ground shaking while also contributing knowledge about the issue of buried low velocity layers.

Development of a High-Average-Power Compton Gamma Source for Lepton Colliders

NASA Astrophysics Data System (ADS)

Pogorelsky, Igor; Polyanskiy, Mikhail N.; Yakimenko, Vitaliy; Platonenko, Viktor T.

2009-01-01

Gamma- (γ-) ray beams of high average power and peak brightness are of demand for a number of applications in high-energy physics, material processing, medicine, etc. One of such examples is gamma conversion into polarized positrons and muons that is under consideration for projected lepton colliders. A γ-source based on the Compton backscattering from the relativistic electron beam is a promising candidate for this application. Our approach to the high-repetition γ-source assumes placing the Compton interaction point inside a CO2 laser cavity. A laser pulse interacts with periodical electron bunches on each round-trip inside the laser cavity producing the corresponding train of γ-pulses. The round-trip optical losses can be compensated by amplification in the active laser medium. The major challenge for this approach is in maintaining stable amplification rate for a picosecond CO2-laser pulse during multiple resonator round-trips without significant deterioration of its temporal and transverse profiles. Addressing this task, we elaborated on a computer code that allows identifying the directions and priorities in the development of such a multi-pass picosecond CO2 laser. Proof-of-principle experiments help to verify the model and show the viability of the concept. In these tests we demonstrated extended trains of picosecond CO2 laser pulses circulating inside the cavity that incorporates the Compton interaction point.

Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing

PubMed Central

Wang, Jinjin; Yu, Xiaomu; Zhao, Kai; Zhang, Yaoguang; Tong, Jingou; Peng, Zuogang

2012-01-01

Megalobrama pellegrini is an endemic fish species found in the upper Yangtze River basin in China. This species has become endangered due to the construction of the Three Gorges Dam and overfishing. However, the available genetic data for this species is limited. Here, we developed 26 polymorphic microsatellite markers from the M. pellegrini genome using next-generation sequencing techniques. A total of 257,497 raw reads were obtained from a quarter-plate run on 454 GS-FLX titanium platforms and 49,811 unique sequences were generated with an average length of 404 bp; 24,522 (49.2%) sequences contained microsatellite repeats. Of the 53 loci screened, 33 were amplified successfully and 26 were polymorphic. The genetic diversity in M. pellegrini was moderate, with an average of 3.08 alleles per locus, and the mean observed and expected heterozygosity were 0.47 and 0.51, respectively. In addition, we tested cross-species amplification for all 33 loci in four additional breams: M. amblycephala, M. skolkovii, M. terminalis, and Sinibrama wui. The cross-species amplification showed a significant high level of transferability (79%–97%), which might be due to their dramatically close genetic relationships. The polymorphic microsatellites developed in the current study will not only contribute to further conservation genetic studies and parentage analyses of this endangered species, but also facilitate future work on the other closely related species. PMID:22489139

Site effects in the city of Port au Prince (Haiti) : A combined use of spectral ratio methods and empirical Greens functions simulations

NASA Astrophysics Data System (ADS)

St Fleur, S.; Courboulex, F.; Bertrand, E.; Deschamps, A.; Mercier de Lepinay, B.; Prepetit, C.; Hough, S. E.

2013-12-01

Haiti was struck in January 2010 by a strong Mw=7 earthquake that caused extensive damages in the city of Port au Prince. At this time, very few seismological stations were working in Haiti and the only one that recorded the mainshock in Port au Prince was saturated. Thus, there were no direct measurements of the ground motion produced by this large event. Quickly after the 2010 event, several permanent accelerometric stations were installed by the USGS (U.S. Geological Survey) and the BME (Bureau des Mines et de l'Energie d'Haiti) as well as broad-band stations by the GSC (Geological Survey of Canada). Since their installation, these stations recorded several tens of aftershocks. The aim of our work is to take advantage of this new dataset to better understand the ground motions generated by earthquakes in the city of Port au Prince. We have used first spectral ratio methods to obtain the transfer function of each station, and then an empirical Green's Function simulation approach to combine source and site effects. In order to estimate site effects under each station, we have used classical spectral ratio methods. In a first step, the H/V (Horizontal/Vertical) method was used to select a reference station (in Port au Prince) that should be ideally a station without any site effects. We selected two stations, HCEA and PAPH, as reference stations, as even if the shape of their H/V curves is not always equal to 1 in the entire frequency band. In a second step, we computed the transfer function at each station by a ratio between the spectra of each earthquake at each station and the spectra obtained at the reference station (we use successively HCEA, PAPH and a combination of both). The results were kept only for the frequencies where the signal to noise was larger than 3. In the frequency range 1 to 20 Hz, we found site/reference ratios that reach values from 3 to 8 and a large variability from one station to another one. In the low frequency band 0.5 to 1 Hz a peak is present at almost all the stations in Port au Prince, which may indicate an amplification due to a deep interface. However, these values have a large variability from one earthquake recording to the other. This may indicate that the observed amplification depends not only on the effect of local site, but also on the source or the propagation direction. We then used the recordings of two earthquakes (Mw 4.3 and Mw 4.4) that occurred on the Leogane fault as Empirical Green's Functions (EGF) in order to simulate the ground motions generated by a virtual Mw 6.8 earthquake. For this simulation a stochastic EGF summation method was used. The results obtained using the two events are surprisingly very different. Using the first EGF, nearly the same ground motion was obtained at each station in Port-au-Prince, whereas with the second EGF, the results highlight large differences. Finally, the estimated site response (site/reference) was used in combination with a direct estimation of the rock site motion (HCEA simulation) in order to reproduce the ground motions which were compared to the EGF simulation method. The comparison confirms the large variability in the modeled ground shaking which can be due to both site and source effects and the low frequency amplification on the plain of Port-au-Prince.

Protocol for the use of a rapid real-time PCR method for the detection of HIV-1 proviral DNA using double-stranded primer.

PubMed

Pau, Chou-Pong; Wells, Susan K; Granade, Timothy C

2012-01-01

This chapter describes a real-time PCR method for the detection of HIV-1 proviral DNA in whole blood samples using a novel double-stranded primer system. The assay utilizes a simple commercially available DNA extraction method and a rapid and easy-to-perform real-time PCR protocol to consistently detect a minimum of four copies of HIV-1 group M proviral DNA in as little as 90 min after sample (whole blood) collection. Co-amplification of the human RNase P gene serves as an internal control to monitor the efficiency of both the DNA extraction and amplification. Once the assay is validated properly, it may be suitable as an alternative confirmation test for HIV-1 infections in a variety of HIV testing venues including the mother-to-child transmission testing sites, clinics, and diagnostic testing centers.

Seismic hazard analysis for Jayapura city, Papua

NASA Astrophysics Data System (ADS)

Robiana, R.; Cipta, A.

2015-04-01

Jayapura city had destructive earthquake which occurred on June 25, 1976 with the maximum intensity VII MMI scale. Probabilistic methods are used to determine the earthquake hazard by considering all possible earthquakes that can occur in this region. Earthquake source models using three types of source models are subduction model; comes from the New Guinea Trench subduction zone (North Papuan Thrust), fault models; derived from fault Yapen, TareraAiduna, Wamena, Memberamo, Waipago, Jayapura, and Jayawijaya, and 7 background models to accommodate unknown earthquakes. Amplification factor using geomorphological approaches are corrected by the measurement data. This data is related to rock type and depth of soft soil. Site class in Jayapura city can be grouped into classes B, C, D and E, with the amplification between 0.5 - 6. Hazard maps are presented with a 10% probability of earthquake occurrence within a period of 500 years for the dominant periods of 0.0, 0.2, and 1.0 seconds.

Successful application of preimplantation genetic diagnosis for Leigh syndrome.

PubMed

Unsal, Evrim; Aktaş, Yasemin; Uner, Ozge; BaltacI, Aysun; Ozcan, Sarp; Turhan, Feriba; Baltaci, Volkan

2008-11-01

To perform preimplantation genetic diagnosis (PGD) for a SURF1 gene mutation of the Leigh syndrome to transfer unaffected or carrier embryo/embryos. Case report. Clinical IVF laboratory. A couple carrying an nt769 G/A mutation that is associated with Leigh syndrome. Oocytes were fertilized by means of intracytoplasmic sperm injection. The resulting embryos were biopsied 3 days after fertilization. One blastomere was taken and whole-genome amplification was performed. Amplification of the mutation site was achieved by polymerase chain reaction (PCR) and restriction digestion was completed. Gel Imager was used to measure the digests of normal and mutant load. Embryo testing by means of PGD-PCR and pregnancy. Successful preimplantation genetic diagnosis for a SURF1 gene mutation and transfer of healthy or carrier embryos. Successful singleton pregnancy resulting in the delivery of healthy baby girl. We report the first case of successful PGD for Leigh syndrome resulting in delivery of a healthy newborn.

Serological Investigation of Heartland Virus (Bunyaviridae: Phlebovirus) Exposure in Wild and Domestic Animals Adjacent to Human Case Sites in Missouri 2012–2013

PubMed Central

Bosco-Lauth, Angela M.; Panella, Nicholas A.; Root, J. Jeffrey; Gidlewski, Tom; Lash, R. Ryan; Harmon, Jessica R.; Burkhalter, Kristen L.; Godsey, Marvin S.; Savage, Harry M.; Nicholson, William L.; Komar, Nicholas; Brault, Aaron C.

2015-01-01

Heartland virus (HRTV; Bunyaviridae: Phlebovirus) has recently emerged as a causative agent of human disease characterized by thrombocytopenia and leukopenia in the United States. The lone star tick (Amblyomma americanum L.) has been implicated as a vector. To identify candidate vertebrate amplification hosts associated with enzootic maintenance of the virus, sera and ticks were sampled from 160 mammals (8 species) and 139 birds (26 species) captured near 2 human case residences in Andrew and Nodaway Counties in northwest Missouri. HRTV-specific neutralizing antibodies were identified in northern raccoons (42.6%), horses (17.4%), white-tailed deer (14.3%), dogs (7.7%), and Virginia opossums (3.8%), but not in birds. Virus isolation attempts from sera and ticks failed to detect HRTV. The high antibody prevalence coupled with local abundance of white-tailed deer and raccoons identifies these species as candidate amplification hosts. PMID:25870419

Cross-amplified microsatellites in the European cherry fly, Rhagoletis cerasi: medium polymorphic-highly informative markers.

PubMed

Augustinos, A A; Asimakopoulou, A K; Papadopoulos, N T; Bourtzis, K

2011-02-01

The European cherry fruit fly, Rhagoletis cerasi (Diptera: Tephritidae), is a major pest of cherries in Europe and parts of Asia. Despite its big economic significance, there is a lack of studies on the genetic structure of its natural populations. Knowledge about an insect pest on molecular, genetic and population levels facilitates the development of environmentally friendly control methods. In this study, we present the development of 13 microsatellite markers for R. cerasi, through cross-species amplification. These markers have been used for the genotyping of 130 individuals from five different sampling sites in Greece. Our results indicate that (i) cross-species amplification is a versatile and rapid tool for developing microsatellite markers in Rhagoletis spp., (ii) the microsatellite markers presented here constitute an important tool for population studies on this pest, and (iii) there is clear structuring of natural European cherry fly populations.

Rapid Authentication of Ginkgo biloba Herbal Products Using the Recombinase Polymerase Amplification Assay.

PubMed

Liu, Yang; Wang, Xiao-Yue; Wei, Xue-Min; Gao, Zi-Tong; Han, Jian-Ping

2018-05-22

Species adulteration in herbal products (HPs) exposes consumers to health risks. Chemical and morphological methods have their own deficiencies when dealing with the detection of species containing the same active compounds in HPs. In this study, we developed a rapid identification method using the recombinase polymerase amplification (RPA) assay to detect two species, Ginkgo biloba and Sophora japonica (as adulteration), in Ginkgo biloba HPs. Among 36 Ginkgo biloba HP samples, 34 were found to have Ginkgo biloba sequences, and 9 were found to have Sophora japonica sequences. During the authentication process, the RPA-LFS assay showed a higher specificity, sensitivity and efficiency than PCR-based methods. We initially applied the RPA-LSF technique to detect plant species in HPs, demonstrating that this assay can be developed into an efficient tool for the rapid on-site authentication of plant species in Ginkgo biloba HPs.

Entangled quantum key distribution over two free-space optical links.

PubMed

Erven, C; Couteau, C; Laflamme, R; Weihs, G

2008-10-13

We report on the first real-time implementation of a quantum key distribution (QKD) system using entangled photon pairs that are sent over two free-space optical telescope links. The entangled photon pairs are produced with a type-II spontaneous parametric down-conversion source placed in a central, potentially untrusted, location. The two free-space links cover a distance of 435 m and 1,325 m respectively, producing a total separation of 1,575 m. The system relies on passive polarization analysis units, GPS timing receivers for synchronization, and custom written software to perform the complete QKD protocol including error correction and privacy amplification. Over 6.5 hours during the night, we observed an average raw key generation rate of 565 bits/s, an average quantum bit error rate (QBER) of 4.92%, and an average secure key generation rate of 85 bits/s.

Mapping NEHRP VS30 site classes

USGS Publications Warehouse

Holzer, T.L.; Padovani, A.C.; Bennett, M.J.; Noce, T.E.; Tinsley, J. C.

2005-01-01

Site-amplification potential in a 140-km2 area on the eastern shore of San Francisco Bay, California, was mapped with data from 210 seismic cone penetration test (SCPT) soundings. NEHRP VS30 values were computed on a 50-m grid by both taking into account the thickness and using mean values of locally measured shear-wave velocities of shallow geologic units. The resulting map of NEHRP VS30 site classes differs from other published maps that (1) do not include unit thickness and (2) are based on regional compilations of velocity. Although much of the area in the new map is now classified as NEHRP Site Class D, the velocities of the geologic deposits within this area are either near the upper or lower VS30 boundary of Class D. If maps of NEHRP site classes are to be based on geologic maps, velocity distributions of geologic units may need to be considered in the definition of VS30 boundaries of NEHRP site classes. ?? 2005, Earthquake Engineering Research Institute.

Instantaneous polarization analysis of ambient noise recordings in site response investigations

NASA Astrophysics Data System (ADS)

Del Gaudio, Vincenzo

2017-07-01

A new procedure is proposed for analyses of ambient noise aimed at investigating complex cases of site response to seismic shaking. Information on site response characterized by several resonance frequencies and by amplifications varying with direction can be obtained by analysing instantaneous polarization properties of ambient noise recordings. Through this kind of analysis, it is possible to identify Rayleigh wave packets emerging from incoherent background noise for very short intervals. Analysing noise recordings passed through narrow-band filters with different central frequencies, variations of Rayleigh wave properties depending on frequencies can be estimated. In particular, one can calculate: (i) the instantaneous ratios H/V between the amplitudes of horizontal and vertical components of the elliptical particle motion and (ii) the azimuthal direction of the vertical plane containing such a motion. These can be determined on a large number of recording samples, providing the basis for statistical estimates. A preferential concentration of H/V peak values at site-specific frequencies and directions can reveal directional resonance phenomena. Furthermore, peak amplitudes can be related to site amplification factors and provide constraints for subsurface velocity modelling. Some tests, carried out on data acquired at sites with known response properties, gave indications on how to select the parameters of the analysis that optimize its implementation. In particular, preliminary trials, conducted on a limited number of frequencies, allow the selection of the parameters that, while providing a large number of instantaneous H/V estimates for Rayleigh waves, minimize their scattering. The analysis can then be refined and an H/V curve as function of frequency can be obtained with a higher spectral resolution. First tests showed that cases of directional resonance can be more effectively recognized with this technique and more details can be revealed on its properties (e.g. secondary peaks) in comparison to the Nakamura's method currently employed for ordinary noise analysis. For sites characterized by isotropic response or by differently oriented directional maxima, however, the presence of noise sources with an anisotropic spatial distribution, which excite signals with inhomogeneous distribution of energy through the examined spectral band, can make the correct interpretation of data more difficult.

Successful isolation and PCR amplification of DNA from National Institute of Standards and Technology herbal dietary supplement standard reference material powders and extracts.

PubMed

Cimino, Matthew T

2010-03-01

Twenty-four herbal dietary supplement powder and extract reference standards provided by the National Institute of Standards and Technology (NIST) were investigated using three different commercially available DNA extraction kits to evaluate DNA availability for downstream nucleotide-based applications. The material included samples of Camellia, Citrus, Ephedra, Ginkgo, Hypericum, Serenoa, And Vaccinium. Protocols from Qiagen, MoBio, and Phytopure were used to isolate and purify DNA from the NIST standards. The resulting DNA concentration was quantified using SYBR Green fluorometry. Each of the 24 samples yielded DNA, though the concentration of DNA from each approach was notably different. The Phytopure method consistently yielded more DNA. The average yield ratio was 22 : 3 : 1 (ng/microL; Phytopure : Qiagen : MoBio). Amplification of the internal transcribed spacer II region using PCR was ultimately successful in 22 of the 24 samples. Direct sequencing chromatograms of the amplified material suggested that most of the samples were comprised of mixtures. However, the sequencing chromatograms of 12 of the 24 samples were sufficient to confirm the identity of the target material. The successful extraction, amplification, and sequencing of DNA from these herbal dietary supplement extracts and powders supports a continued effort to explore nucleotide sequence-based tools for the authentication and identification of plants in dietary supplements. (c) Georg Thieme Verlag KG Stuttgart . New York.

Rapid DNA Amplification Using a Battery-Powered Thin-Film Resistive Thermocycler

PubMed Central

Herold, Keith E.; Sergeev, Nikolay; Matviyenko, Andriy; Rasooly, Avraham

2010-01-01

Summary A prototype handheld, compact, rapid thermocycler was developed for multiplex analysis of nucleic acids in an inexpensive, portable configuration. Instead of the commonly used Peltier heating/cooling element, electric thin-film resistive heater and a miniature fan enable rapid heating and cooling of glass capillaries leading to a simple, low-cost Thin-Film Resistive Thermocycler (TFRT). Computer-based pulse width modulation control yields heating rates of 6–7 K/s and cooling rates of 5 K/s. The four capillaries are closely coupled to the heater, resulting in low power consumption. The energy required by a nominal PCR cycle (20 s at each temperature) was found to be 57 ± 2 J yielding an average power of approximately 1.0 W (not including the computer and the control system). Thus the device can be powered by a standard 9 V alkaline battery (or other 9 V power supply). The prototype TFRT was demonstrated (in a benchtop configuration) for detection of three important food pathogens (E. coli ETEC, Shigella dysenteriae, and Salmonella enterica). PCR amplicons were analyzed by gel electrophoresis. The 35 cycle PCR protocol using a single channel was completed in less then 18 min. Simple and efficient heating/cooling, low cost, rapid amplification, and low power consumption make the device suitable for portable DNA amplification applications including clinical point of care diagnostics and field use. PMID:19159110

Tone-excited jet: Theory and experiments

NASA Technical Reports Server (NTRS)

Ahuja, K. K.; Lepicovsky, J.; Tam, C. K. W.; Morris, P. J.; Burrin, R. H.

1982-01-01

A detailed study to understand the phenomenon of broadband jet-noise amplification produced by upstream discrete-tone sound excitation has been carried out. This has been achieved by simultaneous acquisition of the acoustic, mean velocity, turbulence intensities, and instability-wave pressure data. A 5.08 cm diameter jet has been tested for this purpose under static and also flight-simulation conditions. An open-jet wind tunnel has been used to simulate the flight effects. Limited data on heated jets have also been obtained. To improve the physical understanding of the flow modifications brought about by the upstream discrete-tone excitation, ensemble-averaged schlieren photographs of the jets have also been taken. Parallel to the experimental study, a mathematical model of the processes that lead to broadband-noise amplification by upstream tones has been developed. Excitation of large-scale turbulence by upstream tones is first calculated. A model to predict the changes in small-scale turbulence is then developed. By numerically integrating the resultant set of equations, the enhanced small-scale turbulence distribution in a jet under various excitation conditions is obtained. The resulting changes in small-scale turbulence have been attributed to broadband amplification of jet noise. Excellent agreement has been found between the theory and the experiments. It has also shown that the relative velocity effects are the same for the excited and the unexcited jets.

Dynamics of the Coupled Human-climate System Resulting from Closed-loop Control of Solar Geoengineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacMartin, Douglas; Kravitz, Benjamin S.; Keith, David

2014-07-08

If solar radiation management (SRM) were ever implemented, feedback of the observed climate state might be used to adjust the radiative forcing of SRM, in order to compensate for uncertainty in either the forcing or the climate response; this would also compensate for unexpected changes in the system, e.g. a nonlinear change in climate sensitivity. This feedback creates an emergent coupled human-climate system, with entirely new dynamics. In addition to the intended response to greenhouse-gas induced changes, the use of feedback would also result in a geoengineering response to natural climate variability. We use a simple box-diffusion dynamic model tomore » understand how changing feedback-control parameters and time delay affect the behavior of this coupled natural-human system, and verify these predictions using the HadCM3L general circulation model. In particular, some amplification of natural variability is unavoidable; any time delay (e.g., to average out natural variability, or due to decision-making) exacerbates this amplification, with oscillatory behavior possible if there is a desire for rapid correction (high feedback gain), but a delayed response needed for decision making. Conversely, the need for feedback to compensate for uncertainty, combined with a desire to avoid excessive amplification, results in a limit on how rapidly SRM could respond to uncertain changes.« less

High Phosphohistone H3 Expression Correlates with Adverse Clinical, Biological, and Pathological Factors in Neuroblastomas

PubMed Central

Ramani, Pramila; Taylor, Scott; Miller, Elizabeth; Sowa-Avugrah, Emile; May, Margaret T.

2015-01-01

Phosphohistone H3 (pHH3), a biomarker of the late G2- and M-phase of the cell cycle, provides a powerful indication of the proliferative state of many cancers. We investigated the prognostic significance of pHH3 by immunostaining 80 neuroblastomas and counting the average number of strongly stained nuclei and mitotic figures. The median and 75th percentile pHH3 proliferation indices (PIs) were 0.54% and 1.06% (range, 0.01% to 2.23%) respectively. pHH3 expression was significantly higher in neuroblastomas from patients with adverse clinical characteristics, all unfavorable pathological factors including high mitosis karyorrhexis index (MKI), and adverse biological factors including MYCN oncogene amplification. High pHH3-PIs, at 1% threshold, were significantly associated with a shorter overall survival (OS) and event-free survival (EFS) in the univariable Cox regression analyses. In the multivariable models, high pHH3 counts were significantly associated with worse OS after adjustment for age but were not independent of either high MKI or MYCN amplification. In children less than 18 months of age, high MKIs and high PHH3-PIs were associated with significantly worse OS and EFS. In conclusion, high pHH3 expression correlates strongly with high MKI and MYCN amplification and indicates poor prognosis in neuroblastomas. PMID:25711230

Sensitive Immunofluorescent Staining of Cells via Generation of Fluorescent Nanoscale Polymer Films in Response to Biorecognition

PubMed Central

Avens, Heather J.; Berron, Brad J.; May, Allison M.; Voigt, Katerina R.; Seedorf, Gregory J.; Balasubramaniam, Vivek; Bowman, Christopher N.

2011-01-01

Immunofluorescent staining is central to nearly all cell-based research, yet only a few fluorescent signal amplification approaches for cell staining exist, each with distinct limitations. Here, the authors present a novel, fluorescent polymerization-based amplification (FPBA) method that is shown to enable similar signal intensities as the highly sensitive, enzyme-based tyramide signal amplification (TSA) approach. Being non-enzymatic, FPBA is not expected to suffer from nonspecific staining of endogenous enzymes, as occurs with enzyme-based approaches. FPBA employs probes labeled with photopolymerization initiators, which lead to the controlled formation of fluorescent polymer films only at targeted biorecognition sites. Nuclear pore complex proteins (NPCs; in membranes), vimentin (in filaments), and von Willebrand factor (in granules) were all successfully immunostained by FPBA. Also, FPBA was demonstrated to be capable of multicolor immunostaining of multiple antigens. To assess relative sensitivity, decreasing concentrations of anti-NPC antibody were used, indicating that both FPBA and TSA stained NPC down to a 1:100,000 dilution. Nonspecific, cytoplasmic signal resulting from NPC staining was found to be reduced up to 5.5-fold in FPBA as compared to TSA, demonstrating better signal localization with FPBA. FPBA’s unique approach affords a combination of preferred attributes, including high sensitivity and specificity not otherwise available with current techniques. PMID:21339175

An electrochemical biosensor for double-stranded Wnt7B gene detection based on enzymatic isothermal amplification.

PubMed

Li, Junlong; Chen, Zhongping; Xiang, Yu; Zhou, Lili; Wang, Ting; Zhang, Zhang; Sun, Kexin; Yin, Dan; Li, Yi; Xie, Guoming

2016-12-15

Wnt7B gene plays an important role in the development and progression of breast cancer, gastric cancer, esophageal cancer and pancreatic cancer. While, the natural state of DNA is double stranded, which makes it difficult to be directly detected. Here, we develop an electrochemical biosensor method for Wnt7B gene detection without the need to denature the target. This method firstly used nicking enzyme for exploiting in the double-stranded DNA (dsDNA). Then, long single-stranded DNA (ssDNA) was generated from the cutting site through polymerase extension reaction. Whereafter, the long ssDNA triggered a hairpin self-assembly recycling reaction, which gave rise to another isothermal amplification reaction. Last, short ssDNA was formed after the this amplification process, which could hybridize with the capture probe immobilized on Au electrode and result in signal variation. This method showed excellent analytical performance for dsDNA, of which the linear range was 2fM to 500pM and the detection limit was 1.6fM (S/N=3). It also showed an good results when applied to the real sample of Wnt7B gene detection. Copyright © 2016 Elsevier B.V. All rights reserved.

Role of the RS1 sequence of the cholera vibrio in amplification of the segment of plasmid DNA carrying the gene of resistance to tetracycline and the genes of cholera toxin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fil'kova, S.L.; Il'ina, T.S.; Gintsburg, A.L.

1988-11-01

The hybrid plasmid pCO107, representing cointegrate 14(2)-5(2) of two plasmids, an F-derivative (pOX38) and a PBR322-derivative (pCT105) with an RS1 sequence of the cholera vibrio cloned in its makeup, contains two copes of RS1 at the sites of union of the two plasmids. Using a tetracycline resistance marker (Tc/sup R/) of the plasmid pCT105, clones were isolated which have an elevated level of resistance to tetracycline (an increase of from 4- to 30-fold). Using restriction analysis and the Southern blot method of hybridization it was shown that the increase in the level of resistance of tetracycline is associated with themore » amplification of pCT105 portion of the cointegrate, and that the process of amplification is governed by the presence of direct repeats of the RS1 sequence at its ends. The increase in the number of copies of the pCT105 segment, which contains in its composition the genes of cholera toxin (vct), is accompanied by an increase in toxin production.« less

Development and application of loop-mediated isothermal amplification (LAMP) for detection of Plasmopara viticola

PubMed Central

Kong, Xiangjiu; Qin, Wentao; Huang, Xiaoqing; Kong, Fanfang; Schoen, Cor D.; Feng, Jie; Wang, Zhongyue; Zhang, Hao

2016-01-01

A rapid LAMP (loop-mediated isothermal amplification) detection method was developed on the basis of the ITS sequence of P. viticola, the major causal agent of grape downy mildew. Among the 38 fungal and oomycete species tested, DNA isolated exclusively from P. viticola resulted in a specific product after LAMP amplification. This assay had high sensitivity and was able to detect the presence of less than 33 fg of genomic DNA per 25-μL reaction within 30 min. The infected leaves may produce sporangia that serve as a secondary inoculum. The developed LAMP assay is efficient for estimating the latent infection of grape leaves by P. viticola. When combined with the rapid and simple DNA extraction method, this assay’s total detection time is shortened to approximately one hour; therefore it is suitable for on-site detection of latent infection in the field. The sporangia levels in the air are strongly associated with disease severity. The LAMP method was also demonstrated to be able to estimate the level of sporangia released in the air in a certain period. This assay should make disease forecasting more accurate and rapid and should be helpful in decision-making regarding the control of grape downy mildew. PMID:27363943

Nuclemeter: A Reaction-Diffusion Column for Quantifying Nucleic Acids Undergoing Enzymatic Amplification

NASA Astrophysics Data System (ADS)

Bau, Haim; Liu, Changchun; Killawala, Chitvan; Sadik, Mohamed; Mauk, Michael

2014-11-01

Real-time amplification and quantification of specific nucleic acid sequences plays a major role in many medical and biotechnological applications. In the case of infectious diseases, quantification of the pathogen-load in patient specimens is critical to assessing disease progression, effectiveness of drug therapy, and emergence of drug-resistance. Typically, nucleic acid quantification requires sophisticated and expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low resource settings. We describe a simple, low-cost, reactiondiffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. We model the process with the Fisher Kolmogoroff Petrovskii Piscounoff (FKPP) Equation and compare theoretical predictions with experimental observations. The proposed method is suitable for nucleic acid quantification at the point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. C.L. was supported by NIH/NIAID K25AI099160; M.S. was supported by the Pennsylvania Ben Franklin Technology Development Authority; C.K. and H.B. were funded, in part, by NIH/NIAID 1R41AI104418-01A1.

Documentation for Initial Seismic Hazard Maps for Haiti

USGS Publications Warehouse

Frankel, Arthur; Harmsen, Stephen; Mueller, Charles; Calais, Eric; Haase, Jennifer

2010-01-01

In response to the urgent need for earthquake-hazard information after the tragic disaster caused by the moment magnitude (M) 7.0 January 12, 2010, earthquake, we have constructed initial probabilistic seismic hazard maps for Haiti. These maps are based on the current information we have on fault slip rates and historical and instrumental seismicity. These initial maps will be revised and improved as more data become available. In the short term, more extensive logic trees will be developed to better capture the uncertainty in key parameters. In the longer term, we will incorporate new information on fault parameters and previous large earthquakes obtained from geologic fieldwork. These seismic hazard maps are important for the management of the current crisis and the development of building codes and standards for the rebuilding effort. The boundary between the Caribbean and North American Plates in the Hispaniola region is a complex zone of deformation. The highly oblique ~20 mm/yr convergence between the two plates (DeMets and others, 2000) is partitioned between subduction zones off of the northern and southeastern coasts of Hispaniola and strike-slip faults that transect the northern and southern portions of the island. There are also thrust faults within the island that reflect the compressional component of motion caused by the geometry of the plate boundary. We follow the general methodology developed for the 1996 U.S. national seismic hazard maps and also as implemented in the 2002 and 2008 updates. This procedure consists of adding the seismic hazard calculated from crustal faults, subduction zones, and spatially smoothed seismicity for shallow earthquakes and Wadati-Benioff-zone earthquakes. Each one of these source classes will be described below. The lack of information on faults in Haiti requires many assumptions to be made. These assumptions will need to be revisited and reevaluated as more fieldwork and research are accomplished. We made two sets of maps using different assumptions about site conditions. One set of maps is for a firm-rock site condition (30-m averaged shear-wave velocity, Vs30, of 760 m/s). We also developed hazard maps that contain site amplification based on a grid of Vs30 values estimated from topographic slope. These maps take into account amplification from soils. We stress that these new maps are designed to quantify the hazard for Haiti; they do not consider all the sources of earthquake hazard that affect the Dominican Republic and therefore should not be considered as complete hazard maps for eastern Hispaniola. For example, we have not included hazard from earthquakes in the Mona Passage nor from large earthquakes on the subduction zone interface north of Puerto Rico. Furthermore, they do not capture all the earthquake hazards for eastern Cuba.

Hypsometric Amplification of Greenland Ice Sheet Meltwater Release

NASA Astrophysics Data System (ADS)

van As, D.; Hasholt, B.; Mikkelsen, A. B.; Holtegaard Nielsen, M.; Box, J.; Claesson Liljedahl, L.; Lindback, K.; Pitcher, L. H.

2017-12-01

Proglacial discharge monitoring provides valuable insights in Greenland ice sheet meltwater release. We use a 2006-2016 discharge time series from the Watson River draining 12000 km2 of the ice sheet in southwest Greenland to investigate the large variability in catchment-total meltwater production. An observationally-constrained reconstruction of past discharge shows that meltwater release has on average increased by a factor of 1.5 since 2003 compared to the 1949-2002 period, and that interannual variability has disproportionally increased by a factor of 2.1, suggesting that melt amplifiers are at play. We derive a hypsometric amplification factor of 1.6, which is the result of the exponential melt area increase with rising temperature. Peak meltwater discharge events such as during the July 2012 flooding are due to this and other melt amplifiers, but also require intense melting over a period exceeding the multi-day transit time for high-elevation meltwater to pass through the glacial drainage system.

Chirped pulse Raman amplification in warm plasma: towards controlling saturation

PubMed Central

Yang, X.; Vieux, G.; Brunetti, E.; Ersfeld, B.; Farmer, J. P.; Hur, M. S.; Issac, R. C.; Raj, G.; Wiggins, S. M.; Welsh, G. H.; Yoffe, S. R.; Jaroszynski, D. A.

2015-01-01

Stimulated Raman backscattering in plasma is potentially an efficient method of amplifying laser pulses to reach exawatt powers because plasma is fully broken down and withstands extremely high electric fields. Plasma also has unique nonlinear optical properties that allow simultaneous compression of optical pulses to ultra-short durations. However, current measured efficiencies are limited to several percent. Here we investigate Raman amplification of short duration seed pulses with different chirp rates using a chirped pump pulse in a preformed plasma waveguide. We identify electron trapping and wavebreaking as the main saturation mechanisms, which lead to spectral broadening and gain saturation when the seed reaches several millijoules for durations of 10’s – 100’s fs for 250 ps, 800 nm chirped pump pulses. We show that this prevents access to the nonlinear regime and limits the efficiency, and interpret the experimental results using slowly-varying-amplitude, current-averaged particle-in-cell simulations. We also propose methods for achieving higher efficiencies. PMID:26290153

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beresnyak, Andrey; Li, Hui

Nonresonant current instability was identified by Bell as an important mechanism for magnetic field amplification in supernova remnants. In this paper we focus on studying the nonlinear stage of this instability using the incompressible MHD formulation. We demonstrate that the evolution of magnetic turbulence driven by the Bell instability resembles turbulence driven on large scales. More importantly, we demonstrate that the energy-containing scale for magnetic fields is proportional to the square root of the magnetic energy density. Given the observational constraints of the possible field amplification, this new relation allows us to directly estimate the maximum energy of particles scatteredmore » by such fields, and this estimate is normally below the average particle energy. This implies that, without taking into account the feedback to cosmic rays (CRs), the typical scales of Bell fields, in either the linear or nonlinear regime, will be too small to affect high-energy particle acceleration. We mention several scenarios of back reaction to CRs that could be important.« less

500 MW peak power degenerated optical parametric amplifier delivering 52 fs pulses at 97 kHz repetition rate.

PubMed

Rothhardt, J; Hädrich, S; Röser, F; Limpert, J; Tünnermann, A

2008-06-09

We present a high peak power degenerated parametric amplifier operating at 1030 nm and 97 kHz repetition rate. Pulses of a state-of-the art fiber chirped-pulse amplification (FCPA) system with 840 fs pulse duration and 410 microJ pulse energy are used as pump and seed source for a two stage optical parametric amplifier. Additional spectral broadening of the seed signal in a photonic crystal fiber creates enough bandwidth for ultrashort pulse generation. Subsequent amplification of the broadband seed signal in two 1 mm BBO crystals results in 41 microJ output pulse energy. Compression in a SF 11 prism compressor yields 37 microJ pulses as short as 52 fs. Thus, pulse shortening of more than one order of magnitude is achieved. Further scaling in terms of average power and pulse energy seems possible and will be discussed, since both concepts involved, the fiber laser and the parametric amplifier have the reputation to be immune against thermo-optical effects.

Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats.

PubMed

Poissant, J; Shafer, A B A; Davis, C S; Mainguy, J; Hogg, J T; Côté, S D; Coltman, D W

2009-07-01

We tested for cross-species amplification of microsatellite loci located throughout the domestic sheep (Ovis aries) genome in two north American mountain ungulates (bighorn sheep, Ovis canadensis, and mountain goats, Oreamnos americanus). We identified 247 new polymorphic markers in bighorn sheep (≥ 3 alleles in one of two study populations) and 149 in mountain goats (≥ 2 alleles in a single study population) using 648 and 576 primer pairs, respectively. Our efforts increased the number of available polymorphic microsatellite markers to 327 for bighorn sheep and 180 for mountain goats. The average distance between successive polymorphic bighorn sheep and mountain goat markers inferred from the Australian domestic sheep genome linkage map (mean ± 1 SD) was 11.9 ± 9.2 and 15.8 ± 13.8 centimorgans, respectively. The development of genomic resources in these wildlife species enables future studies of the genetic architecture of trait variation. © 2009 Blackwell Publishing Ltd.

Disaster risk management in prospect mining area Blitar district, East Java, using microtremor analysis and ANP (analytical network processing) approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parwatiningtyas, Diyan, E-mail: diane.tyas@gmail.com, E-mail: erlinunindra@gmail.com; Ambarsari, Erlin Windia, E-mail: diane.tyas@gmail.com, E-mail: erlinunindra@gmail.com; Marlina, Dwi, E-mail: diane.tyas@gmail.com, E-mail: erlinunindra@gmail.com

Indonesia has a wealth of natural assets is so large to be managed and utilized, either from its own local government and local communities, especially in the mining sector. However, mining activities can change the state of the surface layer of the earth that have a high impact disaster risk. This could threaten the safety and disrupt human life, environmental damage, loss of property, and the psychological impact, sulking to the rule of law no 24 of 2007. That's why we strive to manage and minimize the risk of mine disasters in the region, how to use the method ofmore » calculation of Amplification Factor (AF) from the analysis based microtremor sulking Kanai and Nakamura, and decision systems were tested by analysis of ANP. Based on the amplification factor and Analytical Network Processing (ANP) obtained, some points showed instability in the surface layer of a mining area include the site of the TP-7, TP-8, TP-9, TP-10, (Birowo2). If in terms of structure, location indicated unstable due to have a sloping surface layer, resulting in the occurrence of landslides and earthquake risk is high. In the meantime, other areas of the mine site can be said to be a stable area.« less

Eocene greenhouse climate revealed by coupled clumped isotope-Mg/Ca thermometry.

PubMed

Evans, David; Sagoo, Navjit; Renema, Willem; Cotton, Laura J; Müller, Wolfgang; Todd, Jonathan A; Saraswati, Pratul Kumar; Stassen, Peter; Ziegler, Martin; Pearson, Paul N; Valdes, Paul J; Affek, Hagit P

2018-02-06

Past greenhouse periods with elevated atmospheric CO 2 were characterized by globally warmer sea-surface temperatures (SST). However, the extent to which the high latitudes warmed to a greater degree than the tropics (polar amplification) remains poorly constrained, in particular because there are only a few temperature reconstructions from the tropics. Consequently, the relationship between increased CO 2 , the degree of tropical warming, and the resulting latitudinal SST gradient is not well known. Here, we present coupled clumped isotope (Δ 47 )-Mg/Ca measurements of foraminifera from a set of globally distributed sites in the tropics and midlatitudes. Δ 47 is insensitive to seawater chemistry and therefore provides a robust constraint on tropical SST. Crucially, coupling these data with Mg/Ca measurements allows the precise reconstruction of Mg/Ca sw throughout the Eocene, enabling the reinterpretation of all planktonic foraminifera Mg/Ca data. The combined dataset constrains the range in Eocene tropical SST to 30-36 °C (from sites in all basins). We compare these accurate tropical SST to deep-ocean temperatures, serving as a minimum constraint on high-latitude SST. This results in a robust conservative reconstruction of the early Eocene latitudinal gradient, which was reduced by at least 32 ± 10% compared with present day, demonstrating greater polar amplification than captured by most climate models.

Disaster risk management in prospect mining area Blitar district, East Java, using microtremor analysis and ANP (analytical network processing) approach

NASA Astrophysics Data System (ADS)

Parwatiningtyas, Diyan; Ambarsari, Erlin Windia; Marlina, Dwi; Wiratomo, Yogi

2014-03-01

Indonesia has a wealth of natural assets is so large to be managed and utilized, either from its own local government and local communities, especially in the mining sector. However, mining activities can change the state of the surface layer of the earth that have a high impact disaster risk. This could threaten the safety and disrupt human life, environmental damage, loss of property, and the psychological impact, sulking to the rule of law no 24 of 2007. That's why we strive to manage and minimize the risk of mine disasters in the region, how to use the method of calculation of Amplification Factor (AF) from the analysis based microtremor sulking Kanai and Nakamura, and decision systems were tested by analysis of ANP. Based on the amplification factor and Analytical Network Processing (ANP) obtained, some points showed instability in the surface layer of a mining area include the site of the TP-7, TP-8, TP-9, TP-10, (Birowo2). If in terms of structure, location indicated unstable due to have a sloping surface layer, resulting in the occurrence of landslides and earthquake risk is high. In the meantime, other areas of the mine site can be said to be a stable area.

Amplification Factors for Spectral Acceleration Using Borehole Seismic Array in Taiwan

NASA Astrophysics Data System (ADS)

Lai, T. S.; Yih-Min, W.; Chao, W. A.; Chang, C. H.

2017-12-01

In order to reduce the noise from surface to get the high-quality seismic recordings, there are 54 borehole seismic arrays have been installed in Taiwan deployed by Central Weather Bureau (CWB) until the end of 2016. Each array includes two force balance accelerometers, one at the surface and other inside the borehole, as well as one broadband seismometer inside the borehole. The downhole instruments are placed at a depth between 120 and 400 m. The background noise level are lower at the borehole stations, but the amplitudes recorded by borehole stations are smaller than surface stations for the same earthquake due to the different geology conditions. Therefore, the earthquake magnitude estimated by borehole station is smaller than surface station. So far, CWB only use the surface stations in the magnitude determination due to this situation. In this study, we investigate the site effects between surface and downhole for borehole seismic arrays. Using the spectral ratio derived by the two-station spectral method as the transfer function, simulated the waveform recorded by borehole stations to the surface stations. In the future, through the transfer function, the borehole stations will be included in the estimation of earthquake magnitude and the results of amplification factors can provide the information of near-surface site effects for the ground motion simulation applications.

Potential of cross-priming amplification and DNA-based lateral-flow strip biosensor for rapid on-site GMO screening.

PubMed

Huang, Xin; Zhai, Congcong; You, Qimin; Chen, Hongjun

2014-07-01

The requirement to monitor the presence of genetically modified organisms (GMO) in a variety of marked products has generated an increasing demand for reliable, rapid, and time and cost-effective analytical methods. Here we report an on-site method for rapid detection of cauliflower mosaic virus promoter (CaMV 35S), a common element present in most GMO, using cross-priming amplification (CPA) technology. Detection was achieved using a DNA-based contamination-proof strip biosensor. The limit of detection was 30 copies for the pBI121 plasmid containing the CaMV 35S gene. The certified reference sample of GM maize line MON810 was detectable even at the low relative mass concentration of 0.05%. The developed CPA method had high specificity for the CaMV 35S gene, as compared with other GM lines not containing this gene and non-GM products. The method was further validated using nine real-world samples, and the results were confirmed by real-time PCR analysis. Because of its simplicity, rapidity, and high sensitivity, this method of detecting the CaMV 35S gene has great commercial prospects for rapid GMO screening of high-consumption food and agriculture products.

DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila

PubMed Central

Liu, Jun; Zimmer, Kurt; Rusch, Douglas B.; Paranjape, Neha; Podicheti, Ram; Tang, Haixu; Calvi, Brian R.

2015-01-01

Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC. PMID:26227968

Infrequent transposition of Ac in lettuce, Lactuca sativa.

PubMed

Yang, C H; Ellis, J G; Michelmore, R W

1993-08-01

The maize transposable element Activator (Ac) is being used to develop a transposon mutagenesis system in lettuce, Lactuca sativa. Two constructs containing the complete Ac from the waxy-m7 locus of maize were introduced into lettuce and monitored for activity using Southern analysis and PCR amplification of the excision site. No transposition of Ac was detected in over 32 transgenic R1 plants, although these constructs were known to provide frequent transposition in other species. Also, no transposition was observed in later generations. In subsequent experiments, transposition was detected in lettuce calli using constructs that allowed selection for excision events. In these constructs, the neomycin phosphotransferase II gene was interrupted by either Ac or Ds. Excision was detected as the ability of callus to grow on kanamycin. Synthesis of the transposase from the cDNA of Ac expressed from the T-DNA 2' promoter resulted in more frequent excision of Ds than was observed with the wild-type Ac. No excision was observed with Ds in the absence of the transposase. The excision events were confirmed by amplification of the excision site by PCR followed by DNA sequencing. Excision and reintegration were also confirmed by Southern analysis. Ac/Ds is therefore capable of transposition in at least calli of lettuce.

Very broad bandwidth klystron amplifiers

NASA Astrophysics Data System (ADS)

Faillon, G.; Egloff, G.; Farvet, C.

Large surveillance radars use transmitters at peak power levels of around one MW and average levels of a few kW, and possibly several tens of kW, in S band, or even C band. In general, the amplification stage of these transmitters is a microwave power tube, frequently a klystron. Although designers often turn to klystrons because of their good peak and average power capabilities, they still see them as narrow band amplifiers, undoubtedly because of their resonant cavities which, at first sight, would seem highly selective. But, with the progress of recent years, it has now become quite feasible to use these tubes in installations requiring bandwidths in excess of 10 - 12 percent, and even 15 percent, at 1 MW peak for example, in S-band.

Measurements of aerosol absorption and scattering in the Mexico City Metropolitan Area during the MILAGRO field campaign: a comparison of results from the T0 and T1 sites

NASA Astrophysics Data System (ADS)

Marley, N. A.; Gaffney, J. S.; Castro, T.; Salcido, A.; Frederick, J.

2008-07-01

Measurements of aerosol absorption and scattering were obtained in Mexico City during the MILAGRO (Megacity Initiative: Local and Global Research Observations) field campaign in March 2006. A comparison of aerosol absorption and scattering was obtained in Mexico City at site T0 located in the northern part of Mexico City at the Instituto Mexicano del Petróleo Laboratories and at site T1 located at the Universidad Tecnológica de Tecamac, 18 miles northwest of T0. Hourly averages of aerosol absorption were similar at both sites, ranging from 6 93 Mm-1 with an average of 31 Mm-1 at T0; and from 2 104 Mm-1 with an average of 19 Mm-1 at T1. Aerosol scattering at T0 ranged from 16 344 Mm-1 with an average of 105 Mm-1; while the scattering values at T1 were lower than T0 ranging from 2 136 with an average of 53 Mm-1. Aerosol single scattering albedos (SSAs) were determined at both sites using these data. SSAs at T1 ranged from 0.44 0.90 with an average 0.75 as compared to hose at T0, range 0.51 0.93 with an average of 0.77. Broadband UV-B intensity was found to be higher at site T0, with an average of 64 μW/cm2 at solar noon, than at site T1, which had an average of 54 μW/cm2 at solar noon. Comparisons of clear-sky modeled UV-B intensities with the simultaneous UV-B measurements obtained at site T0 and at site T1 for cloudless days indicate a larger diffuse radiation field at site T0 than at site T1. The determination of aerosol scattering Ångstrom coefficient at T0 suggests the larger diffuse radiation is due to the predominance of submicron aerosols at T0 with aerosol scattering of UV-B radiation peaked in the forward direction, leading to the enhancement observed at ground level.

Developments in ambient noise analysis for the characterization of dynamic response of slopes to seismic shaking

NASA Astrophysics Data System (ADS)

Del Gaudio, Vincenzo; Wasowski, Janusz

2016-04-01

In the last few decades, we have witnessed a growing awareness of the role of site dynamic response to seismic shaking in slope failures during earthquakes. Considering the time and costs involved in acquiring accelerometer data on landslide prone slopes, the analysis of ambient noise offers a profitable investigative alternative. Standard procedures of ambient noise analysis, according to the technique known as HVNR or Nakamura's method, were originally devised to interpret data under simple site conditions similar to 1D layering (flat horizontal layering infinitely extended). In such cases, conditions of site amplification, characterized by a strong impedance contrast between a soft surface layer and a stiff bedrock, result in a single pronounced isotropic maximum of spectral ratios between horizontal and vertical component of ambient noise. However, previous studies have shown that the dynamic response of slopes affected by landslides is rather complex, being characterized by multiple resonance peaks with directional variability, thus, the use of standard techniques can encounter difficulties in providing reliable information. A new approach of data analysis has recently been proposed to exploit the potential of information content of Rayleigh waves present in ambient noise, with regard to the identification of frequency and orientation of directional resonance. By exploiting ground motion ellipticity this approach can also provide information on vertical distribution of S-wave velocity, which controls site amplification factors. The method, based on the identification of Rayleigh wave packets from instantaneous polarization properties of ambient noise, was first tested using synthetic signals in order to optimize the data processing system. Then the improved processing scheme is adopted to re-process and re-interpret the ambient noise data acquired on landslide prone slopes around Caramanico Terme (central Italy), at sites monitored also with accelerometer stations. The comparison of ambient noise analysis results with the outcomes of accelerometer monitoring reveals potential and limits of the new method for the investigations on slope dynamic response.

Strain-guided mineralization in the bone–PDL–cementum complex of a rat periodontium

DOE PAGES

Grandfield, Kathryn; Herber, Ralf -Peter; Chen, Ling; ...

2015-04-18

Objective: The objective of this study was to investigate the effect of mechanical strain by mapping physicochemical properties at periodontal ligament (PDL)–bone and PDL–cementum attachment sites and within the tissues per se. Design: Accentuated mechanical strain was induced by applying a unidirectional force of 0.06 N for 14 days on molars in a rat model. The associated changes in functional space between the tooth and bone, mineral forming and resorbing events at the PDL–bone and PDL–cementum attachment sites were identified by using micro-X-ray computed tomography (micro-XCT), atomic force microscopy (AFM), dynamic histomorphometry, Raman microspectroscopy, and AFM-based nanoindentation technique. Results frommore » these analytical techniques were correlated with histochemical strains specific to low and high molecular weight GAGs, including biglycan, and osteoclast distribution through tartrate resistant acid phosphatase (TRAP) staining. Results: Unique chemical and mechanical qualities including heterogeneous bony fingers with hygroscopic Sharpey's fibers contributing to a higher organic (amide III — 1240 cm⁻¹) to inorganic (phosphate — 960 cm⁻¹) ratio, with lower average elastic modulus of 8 GPa versus 12 GPa in unadapted regions were identified. Furthermore, an increased presence of elemental Zn in cement lines and mineralizing fronts of PDL–bone was observed. Adapted regions containing bony fingers exhibited woven bone-like architecture and these regions rich in biglycan (BGN) and bone sialoprotein (BSP) also contained high-molecular weight polysaccharides predominantly at the site of polarized bone growth. Conclusions: From a fundamental science perspective the shift in local properties due to strain amplification at the soft–hard tissue attachment sites is governed by semiautonomous cellular events at the PDL–bone and PDL–cementum sites. Over time, these strain-mediated events can alter the physicochemical properties of tissues per se, and consequently the overall biomechanics of the bone–PDL–tooth complex. From a clinical perspective, the shifts in magnitude and duration of forces on the periodontal ligament can prompt a shift in physiologic mineral apposition in cementum and alveolar bone albeit of an adapted quality owing to the rapid mechanical translation of the tooth.« less

Strain-guided mineralization in the bone–PDL–cementum complex of a rat periodontium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grandfield, Kathryn; Herber, Ralf -Peter; Chen, Ling

Objective: The objective of this study was to investigate the effect of mechanical strain by mapping physicochemical properties at periodontal ligament (PDL)–bone and PDL–cementum attachment sites and within the tissues per se. Design: Accentuated mechanical strain was induced by applying a unidirectional force of 0.06 N for 14 days on molars in a rat model. The associated changes in functional space between the tooth and bone, mineral forming and resorbing events at the PDL–bone and PDL–cementum attachment sites were identified by using micro-X-ray computed tomography (micro-XCT), atomic force microscopy (AFM), dynamic histomorphometry, Raman microspectroscopy, and AFM-based nanoindentation technique. Results frommore » these analytical techniques were correlated with histochemical strains specific to low and high molecular weight GAGs, including biglycan, and osteoclast distribution through tartrate resistant acid phosphatase (TRAP) staining. Results: Unique chemical and mechanical qualities including heterogeneous bony fingers with hygroscopic Sharpey's fibers contributing to a higher organic (amide III — 1240 cm⁻¹) to inorganic (phosphate — 960 cm⁻¹) ratio, with lower average elastic modulus of 8 GPa versus 12 GPa in unadapted regions were identified. Furthermore, an increased presence of elemental Zn in cement lines and mineralizing fronts of PDL–bone was observed. Adapted regions containing bony fingers exhibited woven bone-like architecture and these regions rich in biglycan (BGN) and bone sialoprotein (BSP) also contained high-molecular weight polysaccharides predominantly at the site of polarized bone growth. Conclusions: From a fundamental science perspective the shift in local properties due to strain amplification at the soft–hard tissue attachment sites is governed by semiautonomous cellular events at the PDL–bone and PDL–cementum sites. Over time, these strain-mediated events can alter the physicochemical properties of tissues per se, and consequently the overall biomechanics of the bone–PDL–tooth complex. From a clinical perspective, the shifts in magnitude and duration of forces on the periodontal ligament can prompt a shift in physiologic mineral apposition in cementum and alveolar bone albeit of an adapted quality owing to the rapid mechanical translation of the tooth.« less

Paraxial Stage of the Spatiotemporal Dynamics of Loop Solitons

NASA Astrophysics Data System (ADS)

Sazonov, Sergey V.

2018-03-01

Using the averaged Lagrangian method, an analytic study of the spatiotemporal dynamics of extremely short loop solitons of the generalized Vakhnenko-Schäfer-Wayne equation is carried out. The conditions under which soliton propagation occurs in the modes of defocusing and self-focusing are determined. It is shown that transverse defocusing is accompanied by a temporal compression of the soliton and a decrease in its amplitude. At the same time, with transverse self-focusing, its temporal broadening and peak amplification occur.

News and views in discontinuous phase transitions

NASA Astrophysics Data System (ADS)

Nagler, Jan

2014-03-01

Recent progress in the theory of discontinuous percolation allow us to better understand the the sudden emergence of large-scale connectedness both in networked systems and on the lattice. We analytically study mechanisms for the amplification of critical fluctuations at the phase transition point, non-self-averaging and power law fluctuations. A single event analysis allow to establish criteria for discontinuous percolation transitions, even on the high-dimensional lattice. Some applications such as salad bowl percolation, and inverse fragmentation are discussed.

Activation and quenching of the phototransduction cascade in retinal cones as inferred from electrophysiology and mathematical modeling

PubMed Central

Astakhova, Luba; Firsov, Michael

2015-01-01

Purpose To experimentally identify and quantify factors responsible for the lower sensitivity of retinal cones compared to rods. Methods Electrical responses of frog rods and fish (Carassius) cones to short flashes of light were recorded using the suction pipette technique. A fast solution changer was used to apply a solution that fixed intracellular Ca2+ concentration at the prestimulus level, thereby disabling Ca2+ feedback, to the outer segment (OS). The results were analyzed with a specially designed mathematical model of phototransduction. The model included all basic processes of activation and quenching of the phototransduction cascade but omitted unnecessary mechanistic details of each step. Results Judging from the response versus intensity curves, Carassius cones were two to three orders of magnitude less sensitive than frog rods. There was a large scatter in sensitivity among individual cones, with red-sensitive cones being on average approximately two times less sensitive than green-sensitive ones. The scatter was mostly due to different signal amplification, since the kinetic parameters of the responses among cones were far less variable than sensitivity. We argue that the generally accepted definition of the biochemical amplification in phototransduction cannot be used for comparing amplification in rods and cones, since it depends on an irrelevant factor, that is, the cell’s volume. We also show that the routinely used simplified parabolic curve fitting to an initial phase of the response leads to a few-fold underestimate of the amplification. We suggest a new definition of the amplification that only includes molecular parameters of the cascade activation, and show how it can be derived from experimental data. We found that the mathematical model with unrestrained parameters can yield an excellent fit to experimental responses. However, the fits with wildly different sets of parameters can be virtually indistinguishable, and therefore cannot provide meaningful data on underlying mechanisms. Based on results of Ca2+-clamp experiments, we developed an approach to strongly constrain the values of many key parameters that set the time course and sensitivity of the photoresponse (such as the dark turnover rate of cGMP, rates of turnoffs of the photoactivated visual pigment and phosphodiesterase, and kinetics of Ca2+ feedback). We show that applying these constraints to our mathematical model enables accurate determination of the biochemical amplification in phototransduction. It appeared that, contrary to many suggestions, maximum biochemical amplification derived for “best” Carassius cones was as high as in frog rods. On the other hand, all turnoff and recovery reactions in cones proceeded approximately 10 times faster than in rods. Conclusions The main cause of the differing sensitivity of rods and cones is cones’ ability to terminate their photoresponse faster. PMID:25866462

Children with Auditory Neuropathy Spectrum Disorder Fitted with Hearing Aids Applying the American Academy of Audiology Pediatric Amplification Guideline: Current Practice and Outcomes.

PubMed

Walker, Elizabeth; McCreery, Ryan; Spratford, Meredith; Roush, Patricia

2016-03-01

Up to 15% of children with permanent hearing loss (HL) have auditory neuropathy spectrum disorder (ANSD), which involves normal outer hair cell function and disordered afferent neural activity in the auditory nerve or brainstem. Given the varying presentations of ANSD in children, there is a need for more evidence-based research on appropriate clinical interventions for this population. This study compared the speech production, speech perception, and language outcomes of children with ANSD, who are hard of hearing, to children with similar degrees of mild-to-moderately severe sensorineural hearing loss (SNHL), all of whom were fitted with bilateral hearing aids (HAs) based on the American Academy of Audiology pediatric amplification guidelines. Speech perception and communication outcomes data were gathered in a prospective accelerated longitudinal design, with entry into the study between six mo and seven yr of age. Three sites were involved in participant recruitment: Boys Town National Research Hospital, the University of North Carolina at Chapel Hill, and the University of Iowa. The sample consisted of 12 children with ANSD and 22 children with SNHL. The groups were matched based on better-ear pure-tone average, better-ear aided speech intelligibility index, gender, maternal education level, and newborn hearing screening result (i.e., pass or refer). Children and their families participated in an initial baseline visit, followed by visits twice a year for children <2 yr of age and once a yr for children >2 yr of age. Paired-sample t-tests were used to compare children with ANSD to children with SNHL. Paired t-tests indicated no significant differences between the ANSD and SNHL groups on language and articulation measures. Children with ANSD displayed functional speech perception skills in quiet. Although the number of participants was too small to conduct statistical analyses for speech perception testing, there appeared to be a trend in which the ANSD group performed more poorly in background noise with HAs, compared to the SNHL group. The American Academy of Audiology Pediatric Amplification Guidelines recommend that children with ANSD receive an HA trial if their behavioral thresholds are sufficiently high enough to impede speech perception at conversational levels. For children with ANSD in the mild-to-severe HL range, the current results support this recommendation, as children with ANSD can achieve functional outcomes similar to peers with SNHL. American Academy of Audiology.

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation

PubMed Central

Veal, Colin D.; Xu, Hang; Reekie, Katherine; Free, Robert; Hardwick, Robert J.; McVey, David; Brookes, Anthony J.; Hollox, Edward J.; Talbot, Christopher J.

2013-01-01

Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design. Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT. Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org). Contact: cjt14@le.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23742985

The stability of H/V spectral ratios from noise measurements in Armutlu Peninsula (Turkey)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Livaoğlu, Hamdullah, E-mail: hamdullah.livaoglu@kocaeli.edu.tr; Irmak, T. Serkan; Caka, Deniz

The horizontal to vertical spectral ratio (H/V) method has been successfully using in order to estimate the fundamental resonance frequency of the sedimentary cover, its thickness and amplification factor since at least 3 decades. There are numerous studies have been carried out on the stability of the H/V spectral ratios. Almost all studies showed that fundamental frequency is stable even measurements are repeated at different times. From this point of view, the results will show us an approach whether the stations are suitable for accurate estimate of earthquake studies and engineering purposes or not. Also we want to see ifmore » any effects of the amplification factor changing on the seismograms for Armutlu Seismic Network (ARNET) even though seismic stations are established far away from cultural noise and located on hard rock sites. It has been selected one hour recorded data of all stations during the most stationary times. The amplification and resonant frequency variations of H/V ratio were calculated to investigate temporal stability in time. There is a total harmony in fundamental frequencies values and H/V spectral ratio values in time-lagged periods. Some stations shows secondary minor peaks in high frequency band due to a shallow formation effect or cultural noises around. In the east side of the area ILYS station shows amplitude peak in lower fundamental frequency band from expected. This could compose a high amplification in lower frequencies and so that yield less reliable results in local earthquakes studies. By the experimental results from ambient noise analysis, it could be worked up for relocation of one station.« less

Imatinib for melanomas harboring mutationally activated or amplified KIT arising on mucosal, acral, and chronically sun-damaged skin.

PubMed

Hodi, F Stephen; Corless, Christopher L; Giobbie-Hurder, Anita; Fletcher, Jonathan A; Zhu, Meijun; Marino-Enriquez, Adrian; Friedlander, Philip; Gonzalez, Rene; Weber, Jeffrey S; Gajewski, Thomas F; O'Day, Steven J; Kim, Kevin B; Lawrence, Donald; Flaherty, Keith T; Luke, Jason J; Collichio, Frances A; Ernstoff, Marc S; Heinrich, Michael C; Beadling, Carol; Zukotynski, Katherine A; Yap, Jeffrey T; Van den Abbeele, Annick D; Demetri, George D; Fisher, David E

2013-09-10

Amplifications and mutations in the KIT proto-oncogene in subsets of melanomas provide therapeutic opportunities. We conducted a multicenter phase II trial of imatinib in metastatic mucosal, acral, or chronically sun-damaged (CSD) melanoma with KIT amplifications and/or mutations. Patients received imatinib 400 mg once per day or 400 mg twice per day if there was no initial response. Dose reductions were permitted for treatment-related toxicities. Additional oncogene mutation screening was performed by mass spectroscopy. Twenty-five patients were enrolled (24 evaluable). Eight patients (33%) had tumors with KIT mutations, 11 (46%) with KIT amplifications, and five (21%) with both. Median follow-up was 10.6 months (range, 3.7 to 27.1 months). Best overall response rate (BORR) was 29% (21% excluding nonconfirmed responses) with a two-stage 95% CI of 13% to 51%. BORR was significantly greater than the hypothesized null of 5% and statistically significantly different by mutation status (7 of 13 or 54% KIT mutated v 0% KIT amplified only). There were no statistical differences in rates of progression or survival by mutation status or by melanoma site. The overall disease control rate was 50% but varied significantly by KIT mutation status (77% mutated v 18% amplified). Four patients harbored pretreatment NRAS mutations, and one patient acquired increased KIT amplification after treatment. Melanomas that arise on mucosal, acral, or CSD skin should be assessed for KIT mutations. Imatinib can be effective when tumors harbor KIT mutations, but not if KIT is amplified only. NRAS mutations and KIT copy number gain may be mechanisms of therapeutic resistance to imatinib.

G-quadruplex based Exo III-assisted signal amplification aptasensor for the colorimetric detection of adenosine.

PubMed

Xu, Lei; Shen, Xin; Li, Bingzhi; Zhu, Chunhong; Zhou, Xuemin

2017-08-08

Adenosine is an endogenous nucleotide pivotally involved in nucleic acid and energy metabolism. Its excessive existence may indicate tumorigenesis, typically lung cancer. Encouraged by its significance as the clinical biomarker, sensitive assay methods towards adenosine have been popularized, with high cost and tedious procedures as the inevitable defects. Herein, we report a label-free aptamer-based exonuclease III (Exo III) amplification colorimetric aptasensor for the highly sensitive and cost-effective detection of adenosine. The strategy employed two unlabeled hairpin DNA oligonucleotides (HP1 and HP2), where HP1 contained the aptamer towards adenosine and HP2 embedded the guanine-rich sequence (GRS). In the presence of adenosine, hairpin HP1 could form specific binding with adenosine and trigger the unfolding of HP1's hairpin structure. The resulting adenosine-HP1 complex could hybridize with HP2, generating the Exo III recognition site. After Exo III-assisted degradation, the GRS was released from HP2, and the adenosine-HP1 was released back to the solution to combine another HP2, inducing the cycling amplification. After multiple circulations, the released ample GRSs were induced to form G-quadruplex, further catalyzing the oxidation of TMB, yielding a color change which was finally mirrored in the absorbance change. On the contrary, the absence of adenosine failed to unfold HP1, remaining color unchanged eventually. Thanks to the amplification strategy, the limit of detection was lowered to 17 nM with a broad linear range from 50 nM to 6 μM. The proposed method was successfully applied to the detection of adenosine in biological samples and satisfying recoveries were acquired. Copyright © 2017 Elsevier B.V. All rights reserved.

Stand age and climate drive forest carbon balance recovery

NASA Astrophysics Data System (ADS)

Besnard, Simon; Carvalhais, Nuno; Clevers, Jan; Herold, Martin; Jung, Martin; Reichstein, Markus

2016-04-01

Forests play an essential role in the terrestrial carbon (C) cycle, especially in the C exchanges between the terrestrial biosphere and the atmosphere. Ecological disturbances and forest management are drivers of forest dynamics and strongly impact the forest C budget. However, there is a lack of knowledge on the exogenous and endogenous factors driving forest C recovery. Our analysis includes 68 forest sites in different climate zones to determine the relative influence of stand age and climate conditions on the forest carbon balance recovery. In this study, we only included forest regrowth after clear-cut stand replacement (e.g. harvest, fire), and afforestation/reforestation processes. We synthesized net ecosystem production (NEP), gross primary production (GPP), ecosystem respiration (Re), the photosynthetic respiratory ratio (GPP to Re ratio), the ecosystem carbon use efficiency (CUE), that is NEP to GPP ratio, and CUEclimax, where GPP is derived from the climate conditions. We implemented a non-linear regression analysis in order to identify the best model representing the C flux patterns with stand age. Furthermore, we showed that each C flux have a non-linear relationship with stand age, annual precipitation (P) and mean annual temperature (MAT), therefore, we proposed to use non-linear transformations of the covariates for C fluxes'estimates. Non-linear stand age and climate models were, therefore, used to establish multiple linear regressions for C flux predictions and for determining the contribution of stand age and climate in forest carbon recovery. Our findings depicted that a coupled stand age-climate model explained 33% (44%, average site), 62% (76%, average site), 56% (71%, average site), 41% (59%, average site), 50% (65%, average site) and 36% (50%, average site) of the variance of annual NEP, GPP, Re, photosynthetic respiratory ratio, CUE and CUEclimax across sites, respectively. In addition, we showed that gross fluxes (e.g. GPP and Re) are mainly climatically driven with 54.2% (68.4%, average site) and 54.1% (71.0%, average site) of GPP and Re variability, respectively, explained by the sum of MAT and P. However, annual NEP, GPP to Re ratio and CUEclimax are affected by both forest stand age and climate conditions, in particular MAT. The key result is that forest stand age plays a crucial role in determining CUE (36.4% and 48.2% for all years per site and average site, respectively), while climate conditions have less effect on CUE (13.6% and 15.4% for all years per site and average site, respectively). These findings are relevant for the implementation of Earth system models and imply that information both on forest stand age and climate conditions are critical to improve the accuracy of global terrestrial C models's estimates.

Estimating seismic site response in Christchurch City (New Zealand) from dense low-cost aftershock arrays

USGS Publications Warehouse

Kaiser, Anna E.; Benites, Rafael A.; Chung, Angela I.; Haines, A. John; Cochran, Elizabeth S.; Fry, Bill

2011-01-01

The Mw 7.1 September 2010 Darfield earthquake, New Zealand, produced widespread damage and liquefaction ~40 km from the epicentre in Christchurch city. It was followed by the even more destructive Mw 6.2 February 2011 Christchurch aftershock directly beneath the city’s southern suburbs. Seismic data recorded during the two large events suggest that site effects contributed to the variations in ground motion observed throughout Christchurch city. We use densely-spaced aftershock recordings of the Darfield earthquake to investigate variations in local seismic site response within the Christchurch urban area. Following the Darfield main shock we deployed a temporary array of ~180 low-cost 14-bit MEMS accelerometers linked to the global Quake-Catcher Network (QCN). These instruments provided dense station coverage (spacing ~2 km) to complement existing New Zealand national network strong motion stations (GeoNet) within Christchurch city. Well-constrained standard spectral ratios were derived for GeoNet stations using a reference station on Miocene basalt rock in the south of the city. For noisier QCN stations, the method was adapted to find a maximum likelihood estimate of spectral ratio amplitude taking into account the variance of noise at the respective stations. Spectral ratios for QCN stations are similar to nearby GeoNet stations when the maximum likelihood method is used. Our study suggests dense low-cost accelerometer aftershock arrays can provide useful information on local-scale ground motion properties for use in microzonation. Preliminary results indicate higher amplifications north of the city centre and strong high-frequency amplification in the small, shallower basin of Heathcote Valley.

Instrument Correction and Dynamic Site Profile Validation at the Central United States Seismic Observatory, New Madrid Seismic Zone

NASA Astrophysics Data System (ADS)

Brengman, C.; Woolery, E. W.; Wang, Z.; Carpenter, S.

2016-12-01

The Central United States Seismic Observatory (CUSSO) is a vertical seismic array located in southwestern Kentucky within the New Madrid seismic zone. It is intended to describe the effects of local geology, including thick sediment overburden, on seismic-wave propagation, particularly strong-motion. The three-borehole array at CUSSO is composed of seismic sensors placed on the surface, and in the bedrock at various depths within the 585 m thick sediment overburden. The array's deep borehole provided a unique opportunity in the northern Mississippi embayment for the direct geological description and geophysical measurement of the complete late Cretaceous-Quaternary sediment column. A seven layer, intra-sediment velocity model is interpreted from the complex, inhomogeneous stratigraphy. The S- and P-wave sediment velocities range between 160 and 875 m/s and between 1000 and 2300 m/s, respectively, with bedrock velocities of 1452 and 3775 m/s, respectively. Cross-correlation and direct comparisons were used to filter out the instrument response and determine the instrument orientation, making CUSSO data ready for analysis, and making CUSSO a viable calibration site for other free-field sensors in the area. The corrected bedrock motions were numerically propagated through the CUSSO soil profile (transfer function) and compared, in terms of both peak acceleration and amplitude spectra, to the recorded surface observations. Initial observations reveal a complex spectral mix of amplification and de-amplification across the array, indicating the site effect in this deep sediment setting is not simply generated by the shallowest layers.

High-frequency ground motion amplification during the 2011 Tohoku earthquake explained by soil dilatancy

NASA Astrophysics Data System (ADS)

Roten, D.; Fäh, D.; Bonilla, L. F.

2013-05-01

Ground motions of the 2011 Tohoku earthquake recorded at Onahama port (Iwaki, Fukushima prefecture) rank among the highest accelerations ever observed, with the peak amplitude of the 3-D acceleration vector approaching 2g. The response of the site was distinctively non-linear, as indicated by the presence of horizontal acceleration spikes which have been linked to cyclic mobility during similar observations. Compared to records of weak ground motions, the response of the site during the Mw 9.1 earthquake was characterized by increased amplification at frequencies above 10 Hz and in peak ground acceleration. This behaviour contrasts with the more common non-linear response encountered at non-liquefiable sites, which results in deamplification at higher frequencies. We simulate propagation of SH waves through the dense sand deposit using a non-linear finite difference code that is capable of modelling the development of excess pore water pressure. Dynamic soil parameters are calibrated using a direct search method that minimizes the difference between observed and simulated acceleration envelopes and response spectra. The finite difference simulations yield surface acceleration time-series that are consistent with the observations in shape and amplitude, pointing towards soil dilatancy as a likely explanation for the high-frequency pulses recorded at Onahama port. The simulations also suggest that the occurrence of high-frequency spikes coincided with a rapid increase in pore water pressure in the upper part of the sand deposit between 145 and 170 s. This sudden increase is possibly linked to a burst of high-frequency energy from a large slip patch below the Iwaki region.

Surface-seismic imaging for nehrp soil profile classifications and earthquake hazards in urban areas

USGS Publications Warehouse

Williams, R.A.; Stephenson, W.J.; Odum, J.K.

1998-01-01

We acquired high-resolution seismic-refraction data on the ground surface in selected areas of the San Fernando Valley (SFV) to help explain the earthquake damage patterns and the variation in ground motion caused by the 17 January 1994 magnitude 6.7 Northridge earthquake. We used these data to determine the compressional- and shear-wave velocities (Vp and Vs) at 20 aftershock recording sites to 30-m depth ( V??s30, and V??p30). Two other sites, located next to boreholes with downhole Vp and Vs data, show that we imaged very similar seismic-vefocity structures in the upper 40 m. Overall, high site response appears to be associated with tow Vs in the near surface, but there can be a wide rangepf site amplifications for a given NEHRP soil type. The data suggest that for the SFV, if the V??s30 is known, we can determine whether the earthquake ground motion will be amplified above a factor of 2 relative to a local rock site.

Characterization of the Aerobic Oxidation of cis-Dichloroethene and Vinyl Chloride in Support of Bioremediation of Chloroethene-Contaminated Sites

DTIC Science & Technology

2004-11-05

perchloroethylene) PCR polymerase chain reaction SERDP Strategic Environmental Research and Development Program TCE trichloroethene VC vinyl chloride iv...from one of the enrichments, which was inoculated with activated carbon from a pump-and-treat plant (Dortmund, Germany) processing chloroethene...dependent enzyme activity in extracts from VC and ethene-grown cells 8 (Coleman and Spain, 2003a). PCR amplifications using primers targeted at

Radial Growth and Physiological Response of Coniferous Trees to Arctic Amplification

NASA Astrophysics Data System (ADS)

Tei, Shunsuke; Sugimoto, Atsuko; Liang, Maochang; Yonenobu, Hitoshi; Matsuura, Yojiro; Osawa, Akira; Sato, Hisashi; Fujinuma, Junichi; Maximov, Trofim

2017-11-01

We describe the physiological responses of boreal conifers to climate change for the past 112 years using ring-width and carbon isotope ratio (δ13C) chronologies at six forest sites in northern Eurasia and Canada. Responses differed among regions, depending on their climatic and/or geographic characteristics. Tree radial growth decreased over the past 52 years in central eastern Siberia with the higher rate of summer temperature increase than other regions, as indicated by the negative correlation between radial growth and summer temperature, but increased in northern Europe and Canada. Changes in tree-ring δ13C indicated that recent climatic conditions have induced stronger drought stress for trees from central eastern Siberia than for those from other regions. The observed tree growth trends were compared to those simulated using a dynamic global vegetation model. Although the modeled annual net primary production (NPP) for trees generally exhibited similar decadal variation to radial growth, simulations did not show a recent decrease in tree growth, even in central eastern Siberia. This was probably due to an overestimation of the sensitivity of modeled tree NPP to precipitation. Our results suggest that the tree NPP forecasted under the expected future increases in temperature and average precipitation might be overestimated, especially in severely dry regions such as central eastern Siberia.

Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Sorcidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus

USGS Publications Warehouse

Sonsthagen, Sarah A.; Sage, G. Kevin; Fowler, Megan C.; Hope, Andrew G.; Cook, J.A.; Talbot, Sandra L.

2013-01-01

We used next generation shotgun sequencing to develop 21 novel microsatellite markers for the barren-ground shrew (Sorex ugyunak), which were polymorphic among individuals from northern Alaska. The loci displayed moderate allelic diversity (averaging 6.81 alleles per locus) and heterozygosity (averaging 70 %). Two loci deviated from Hardy–Weinberg equilibrium (HWE) due to heterozygote deficiency. While the population did not deviate from HWE overall, it showed significant linkage disequilibrium suggesting this population is not in mutation-drift equilibrium. Nineteen of 21 loci were polymorphic in masked shrews (S. cinereus) from interior Alaska and exhibited linkage equilibrium and HWE overall. All loci yielded sufficient variability for use in population studies.

Integrated monitoring of hydrogeomorphic, vegetative, and edaphic conditions in riparian ecosystems of Great Basin National Park, Nevada

USGS Publications Warehouse

Beever, Erik A.; Pyke, D.A.

2004-01-01

In contrast to the more incised riparian channels of central Nevada, we observed knickzones, downcutting, and incision only rarely and usually with limited extent in the walking surveys. Downcutting occurred most frequently and extensively in Strawberry and Snake creeks, due in part to their more erodible soils. According to a hydrogeomorphologist with extensive experience in Great Basin riparian systems, the sediment-delivery and hydrologic systems appeared relatively undisturbed in most reaches, with respect to grazing animals and other types of anthropogenic alteration. Site elevation of the 31 transects ranged from 1,950-2,987 m, and stream slope (i.e., gradient) was relatively steep (mean = 9.3%, range 3-16%). Strawberry Creek averaged the lowest maximum water depth, and correspondingly had greatest width/depth ratios. Baker Creek sites averaged the smallest amount of tree-canopy gaps, whereas Snake Creek sites on average had the largest proportion of gaps in understory vegetation. Sites in terrace-bound valley types averaged the lowest slope in the channel as well as the least cover of trees, litter, and vegetation overall, whereas alluviated, boulder-bed canyon sites averaged the greatest widths of the active channel. Sites in Lehman Creek averaged nearly twice as much coarse woody debris as sites from any other creek, whereas Baker Creek sites averaged greatest tree cover (mean = 67%, range 40 – 96%) and species richness (mean = 17.3 species). Multivariate ordinations suggested that sites in leveed outwash valleys and alluvial-fan-influenced valleys had the greatest inter-site heterogeneity in plant composition, whereas sites in incised moraine-filled valleys appeared most homogeneous. Differences among homogeneity of sites within vegetation types were less pronounced, but sites dominated by either aspen and Woodsʼ rose or narrow-leaved cottonwood had the most similar plant communities among sites of the same vegetation type. A number of species were faithful indicators of various valley and vegetation types, using either set of plant-frequency data. We estimate that all 31 sites could be subsequently re-sampled in 14-18 field days by individuals possessing familiarity of the riparian flora of the southern Snake Range. As with any research, monitoring-focused investigations must balance the concerns for number of ecosystem attributes measured, extensiveness in time and space of sampling periods and locations, and the time and cost of sampling.

Alternative (G-16v2) Ground Motion Prediction Equations for the Central and Eastern North America

NASA Astrophysics Data System (ADS)

Graizer, V.

2016-12-01

Introduced is the ground motion prediction equations model for the Central and Eastern North America that represents an alternative more physically justified approach to ground motion attenuation modeling then previous Graizer (2016) G-16 model. The new model has a bilinear slope of R-1 within 70 km from the fault with a slope of R-0.5 at larger distances corresponding to the geometrical spreading of body and surface waves. The new (G-16v2) model is based in part on the NGA-East database for the horizontal peak ground acceleration and 5%-damped pseudo spectral acceleration (SA) and also on comparisons with the Western U.S. data and ground motion simulations. Based on data, I estimated the average slope of the distance attenuation within the 50-70 km distance from the fault to be -1.0 at most of the frequencies supporting regular geometrical spreading of body waves. Multiple inversions are performed to estimate apparent (combined intrinsic and scattering) attenuation of SA amplitudes from the NGA-East database for incorporation into the model. These estimates demonstrate a difference between seismological Q(f) and the above mentioned attenuation factor that I recommend calling QSA(f). I adjusted previously developed site correction which was based on multiple runs of representative VS30 (time-averaged shear-wave velocity in the upper 30 m) profiles through SHAKE-type equivalent-linear codes. Site amplifications are calculated relative to the hard rock definition used in nuclear industry (VS=2800 m/s). These improvements resulted in a modest reduction in standard deviation in the new G-16v2 relative to the G-16 model. The number of model predictors is limited to a few measurable parameters: moment magnitude M, closest distance to fault rupture plane Rrup, VS30, and apparent attenuation factor QSA(f). The model is applicable for the stable continental regions and covers the following range: 4.0≤M≤8.5, 0≤Rrup≤1000 km, 450≤VS30≤2800 m/s and frequencies 0.1≤f≤100 Hz.

Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis.

PubMed

Jain, A; Bhatia, S; Banga, S S; Prakash, S; Lakshmikumaran, M

1994-04-01

RAPD assays were performed, using 34 arbitrary decamer oligonucleotide primers and six combinations of two primers, to detect inherent variations and genetic relationships among 12 Indian and 11 exotic B. juncea genotypes. Of 595 amplification products identified, 500 of them were polymorphic across all genotypes. A low level of genetic variability was detected among the Indian genotypes, while considerable polymorphism was present among the exotic ones. Based on the pair-wise comparisons of amplification products the genetic similarity was calculated using Jaccard's similarity coefficients and a dendrogram was constructed using an unweighted pair group method was arithmetical averages (UPGMA). On the basis of this analysis the genotypes were clustered into two groups, A and B. Group A comprised only exotic genotypes, whereas all the Indian genotypes and four of the exotic genotypes were clustered in group B. Almost similar genotypic rankings could also be established by computing as few as 200 amplification products. In general, a high per cent of heterosis was recorded in crosses involving Indian x exotic genotypes. On the other hand, when crosses were made amongst Indian or exotic genotypes, about 80% of them exhibited negative heterosis. Results from this study indicate that, despite the lack of direct correlation between the genetic distance and the degree of heterosis, genetic diversity forms a very useful guide not only for investigating the relationships among Brassica genotypes but also in the selection of parents for heterotic hybrid combinations.

Ca2+-induced Ca2+ Release Phenomena in Mammalian Sympathetic Neurons Are Critically Dependent on the Rate of Rise of Trigger Ca2+

PubMed Central

Hernández-Cruz, Arturo; Escobar, Ariel L.; Jiménez, Nicolás

1997-01-01

The role of ryanodine-sensitive intracellular Ca2+ stores present in nonmuscular cells is not yet completely understood. Here we examine the physiological parameters determining the dynamics of caffeine-induced Ca2+ release in individual fura-2–loaded sympathetic neurons. Two ryanodine-sensitive release components were distinguished: an early, transient release (TR) and a delayed, persistent release (PR). The TR component shows refractoriness, depends on the filling status of the store, and requires caffeine concentrations ≥10 mM. Furthermore, it is selectively suppressed by tetracaine and intracellular BAPTA, which interfere with Ca2+-mediated feedback loops, suggesting that it constitutes a Ca2+-induced Ca2+-release phenomenon. The dynamics of release is markedly affected when Sr2+ substitutes for Ca2+, indicating that Sr2+ release may operate with lower feedback gain than Ca2+ release. Our data indicate that when the initial release occurs at an adequately fast rate, Ca2+ triggers further release, producing a regenerative response, which is interrupted by depletion of releasable Ca2+ and Ca2+-dependent inactivation. A compartmentalized linear diffusion model can reproduce caffeine responses: When the Ca2+ reservoir is full, the rapid initial Ca2+ rise determines a faster occupation of the ryanodine receptor Ca2+ activation site giving rise to a regenerative release. With the store only partially loaded, the slower initial Ca2+ rise allows the inactivating site of the release channel to become occupied nearly as quickly as the activating site, thereby suppressing the initial fast release. The PR component is less dependent on the store's Ca2+ content. This study suggests that transmembrane Ca2+ influx in rat sympathetic neurons does not evoke widespread amplification by CICR because of its inability to raise [Ca2+] near the Ca2+ release channels sufficiently fast to overcome their Ca2+-dependent inactivation. Conversely, caffeine-induced Ca2+ release can undergo considerable amplification especially when Ca2+ stores are full. We propose that the primary function of ryanodine-sensitive stores in neurons and perhaps in other nonmuscular cells, is to emphasize subcellular Ca2+ gradients resulting from agonist-induced intracellular release. The amplification gain is dependent both on the agonist concentration and on the filling status of intracellular Ca2+ stores. PMID:9041445

Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies.

PubMed

Haag, Taiana; Santos, Anelisie S; De Angelo, Carlos; Srbek-Araujo, Ana Carolina; Sana, Dênis A; Morato, Ronaldo G; Salzano, Francisco M; Eizirik, Eduardo

2009-07-01

The elusive nature and endangered status of most carnivore species imply that efficient approaches for their non-invasive sampling are required to allow for genetic and ecological studies. Faecal samples are a major potential source of information, and reliable approaches are needed to foster their application in this field, particularly in areas where few studies have been conducted. A major obstacle to the reliable use of faecal samples is their uncertain species-level identification in the field, an issue that can be addressed with DNA-based assays. In this study we describe a sequence-based approach that efficiently distinguishes jaguar versus puma scats, and that presents several desirable properties: (1) considerably high amplification and sequencing rates; (2) multiple diagnostic sites reliably differentiating the two focal species; (3) high information content that allows for future application in other carnivores; (4) no evidence of amplification of prey DNA; and (5) no evidence of amplification of a nuclear mitochondrial DNA insertion known to occur in the jaguar. We demonstrate the reliability and usefulness of this approach by evaluating 55 field-collected samples from four locations in the highly fragmented Atlantic Forest biome of Brazil and Argentina, and document the presence of one or both of these endangered felids in each of these areas.

A modified Trastuzumab antibody for the immunohistochemical detection of HER-2 overexpression in breast cancer

PubMed Central

Bussolati, G; Montemurro, F; Righi, L; Donadio, M; Aglietta, M; Sapino, A

2005-01-01

The immunohistochemical determination of HER-2 to identify patients with advanced breast cancer candidates for Trastuzumab treatment proved neither accurate nor fully reliable, possibly because none of the current reagents detects the specific antigenic site target of Trastuzumab. To circumvent this problem, we conjugated the NH2 groups of Trastuzumab with biotin, and the compound obtained, designated BiotHER, was added directly to tissue sections. Biotin-labelling was revealed with horseradish peroxidase-conjugated streptavidin. Specificity and sensitivity of BiotHER immunostaining with respect to HER-2 amplification were tested on 164 breast carcinoma samples. BiotHER staining was detected on the tumour cell membrane of 12% of all specimens and in 49% specimens with gene amplification, while absent in nonamplified tumours. Predictivity of BiotHER status with respect to the clinical outcome was analysed in 54 patients with HER-2 amplified advanced breast cancer treated with Trastuzumab plus chemotherapy. BiotHER staining, detected in 50% of tumours with HER-2 amplification, was an independent predictor of clinical outcome. In fact, BiotHER positivity was independently associated with increased likelihood of tumour response and reduced risk of tumour progression and death. Biotinylated Trastuzumab can thus be used for immunohistochemical detection of HER-2 overexpression in breast cancer, and has the potential to identify patients likely to benefit from Trastuzumab treatment. PMID:15812476

Ultrasensitive electrochemical sensing platform based on graphene wrapping SnO2 nanocorals and autonomous cascade DNA duplication strategy.

PubMed

Chen, Ying-Xu; Huang, Ke-Jing; Lin, Feng; Fang, Lin-Xia

2017-12-01

In this work, a sensitive, universal and reusable electrochemical biosensor based on stannic oxide nanocorals-graphene hybrids (SnO 2 NCs-Gr) is developed for target DNA detection by using two kinds of DNA enzymes for signal amplification through an autonomous cascade DNA duplication strategy. A hairpin probe is designed composing of a projecting part at the 3'-end as identification sequence for target, a recognition site for nicking endonuclease, and an 18-carbon shim to stop polymerization process. The designed DNA duplication-incision-replacement process is handled by KF polymerase and endonuclease, then combining with gold nanoparticles as signal carrier for further signal amplification. In the detection system, the electrochemical-chemical-chemical procedure, which uses ferrocene methanol, tris(2-carboxyethyl)phosphine and l-ascorbic acid 2-phosphate as oxidoreduction neurogen, deoxidizer and zymolyte, separately, is applied to amplify detection signal. Benefiting from the multiple signal amplification mechanism, the proposed sensor reveals a good linear connection between the peak current and logarithm of analyte concentration in range of 0.0001-1 × 10 -11 molL -1 with a detection limit of 1.25 × 10 -17 molL -1 (S/N=3). This assay also opens one promising strategy for ultrasensitive determination of other biological molecules for bioanalysis and biomedicine diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.