Toga Real Time Oceanography in the Pacific

2013 ◽  
pp. 127-135
Author(s):  
David Halpern
Keyword(s):  
Real Time ◽  
The Pacific

scholarly journals Real-Time Observations of the February 2010 Chile and March 2011 Japan Tsunamis Recorded in Honolulu by the Pacific Islands Ocean Observing System

Oceanography ◽  
2014 ◽  
Vol 27 (2) ◽  
Author(s):  
Julia Fiedler ◽  
Margaret McManus ◽  
Michael Tomlinson ◽  
Eric De Carlo ◽  
Geno Pawlak ◽  
...  
Keyword(s):  
Real Time ◽  
Pacific Islands ◽  
The Pacific ◽  
Ocean Observing

scholarly journals Exploring DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data

2013 ◽  
Author(s):  
Sterling Sawaya ◽  
James Boocock ◽  
Mik Black ◽  
Neil Gemmell
Keyword(s):  
Real Time ◽  
Dna Sequences ◽  
Double Helix ◽  
Dna Structure ◽  
R Package ◽  
Dna Structures ◽  
Pacific Biosciences ◽  
Tandem Repeat Sequences ◽  
The Pacific ◽  
Polymerase Pausing

Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA structure. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures. We have developed a new way to examine polymerase kinetics and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present. We discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.

A real-time PCR assay for detection of light leaf spot onBrassicacrops in the Pacific Northwest of the USA

2019 ◽  
Vol 41 (4) ◽  
pp. 566-575 ◽  
Author(s):  
William J. Thomas ◽  
Maryna Serdani ◽  
Briana Claassen ◽  
Morgan Schneider ◽  
Althea M. Hinds-Cook ◽  
...  
Keyword(s):  
Real Time ◽  
Pacific Northwest ◽  
Real Time Pcr ◽  
Leaf Spot ◽  
Pcr Assay ◽  
The Pacific ◽  
The Usa

Real-Time Tsunami Inundation Forecast for a Recurrence of 17thCentury Great Hokkaido Earthquake in Japan

2014 ◽  
Vol 9 (3) ◽  
pp. 358-364 ◽  
Author(s):  
Yuichiro Tanioka ◽  
◽  
Aditya Riadi Gusman ◽  
Kei Ioki ◽  
Yugo Nakamura
Keyword(s):  
Real Time ◽  
Pacific Coast ◽  
Great Earthquake ◽  
Tsunami Deposit ◽  
Fault Models ◽  
Fine Grid ◽  
Tsunami Inundation ◽  
Inundation Area ◽  
The Pacific ◽  
Tsunami Waveforms

Paleotsunami studies have shown that several large tsunamis hit the Pacific coast. Many tsunami deposit data were available for the 17thcentury tsunami. The most recent tsunami deposit study in 2013 indicated that the large slip of about 25 m along the plate interface near the Kurile trench would be necessary and the seismic moment of this 17thcentury earthquake was 1.7 × 1022Nm. If a great earthquake like the 17thcentury earthquake occurs off the Pacific coast of Hokkaido, the devastating disaster along the coast is expected. To minimize the tsunami disaster, a development of the real-time forecast of a tsunami inundation area is necessary. Estimating a tsunami inundation area requires tsunami numerical simulation with a very fine grid system of less than 1 arcsecond. There is not enough time to compute the tsunami inundation area after a large earthquake occurs. In this study, we develop a real-time tsunami inundation forecast method using a database including many tsunami inundation areas previously computed using various fault models. After great earthquakes, tsunamis are computed using linear long-wave equations for fault models estimated in real time. Simulating such tsunamis takes only 1-3 minutes on a typical PC, so it is potentially useful for forecasting tsunamis. Tsunami inundation areas computed numerically using various fault models and tsunami waveforms at several locations near the inundation area are stored in a database. Those computed tsunami waveforms are used to choose the most appropriate tsunami inundation area by comparing them to the tsunami waveforms computed in real time. This method is tested at Kushiro, a city in Hokkaido. We found that the method worked well enough to forecast the Kushiro’s tsunami inundation area.

Real-Time Simulation of the GOES-R ABI for User Readiness and Product Evaluation

2016 ◽  
Vol 97 (2) ◽  
pp. 245-261 ◽  
Author(s):  
Thomas J. Greenwald ◽  
R. Bradley Pierce ◽  
Todd Schaack ◽  
Jason Otkin ◽  
Marek Rogal ◽  
...  
Keyword(s):  
Real Time ◽  
Pacific Northwest ◽  
Prediction Models ◽  
Weather Prediction ◽  
Atmospheric Stability ◽  
Product Evaluation ◽  
Hurricane Sandy ◽  
Front Range ◽  
Test Bed ◽  
The Pacific

Abstract In support of the Geostationary Operational Environmental Satellite R series (GOES-R) program, the Cooperative Institute for Meteorological Satellite Studies (CIMSS) at the University of Wisconsin–Madison is generating high quality simulated Advanced Baseline Imager (ABI) radiances and derived products in real time over the continental United States. These data are mainly used for testing data-handling systems, evaluating ABI-derived products, and providing training material for forecasters participating in GOES-R Proving Ground test bed activities. The modeling system used to generate these datasets consists of advanced regional and global numerical weather prediction models in addition to state-of-the-art radiative transfer models, retrieval algorithms, and land surface datasets. The system and its generated products are evaluated for the 2014 Pacific Northwest wildfires; the 2013 Moore, Oklahoma, tornado; and Hurricane Sandy. Simulated aerosol optical depth over the Front Range of Colorado during the Pacific Northwest wildfires was validated using high-density Aerosol Robotic Network (AERONET) measurements. The aerosol, cloud, and meteorological modeling system used to generate ABI radiances was found to capture the transport of smoke from the Pacific wildfires into the Front Range of Colorado and true-color imagery created from these simulated radiances provided visualization of the smoke plumes. Evaluation of selected simulated ABI-derived products for the Moore tornado and Hurricane Sandy cases was done using real-time GOES sounder/imager products produced at CIMSS. Results show that simulated ABI moisture and atmospheric stability products, cloud products, and red–green–blue (RGB) airmass composite imagery are well suited as proxy ABI data for user preparedness.

scholarly journals Detection and Quantification of Pratylenchus thornei in DNA Extracted from Soil Using Real-Time PCR

2012 ◽  
Vol 102 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Guiping Yan ◽  
Richard W. Smiley ◽  
Patricia A. Okubara
Keyword(s):  
Real Time ◽  
Pacific Northwest ◽  
Real Time Pcr ◽  
Fungal Species ◽  
Internal Transcribed Spacer Region ◽  
Standard Curve ◽  
Pratylenchus Thornei ◽  
The Pacific ◽  
Greenhouse Soils ◽  
Positive Correlations

The root-lesion nematode Pratylenchus thornei is one of the most important pests restricting productivity of wheat in the Pacific Northwest (PNW). It is laborious and difficult to use microscopy to count and identify the nematodes in soils. A SYBR Green I-based real-time polymerase chain reaction (PCR) assay was developed to detect and quantify this species from DNA extracts of soil. A primer set, designed from the internal transcribed spacer region (ITS1) of rDNA, was highly specific to P. thornei and did not amplify DNA from 27 isolates of other Pratylenchus spp., other nematodes, and six fungal species present in PNW wheat fields. A standard curve relating threshold cycle and log values of nematode number was generated from artificially infested soils. The standard curve was supported by a high correlation between the numbers of P. thornei added to soil and the numbers quantified using real-time PCR. Examination of 15 PNW dryland field soils and 20 greenhouse samples revealed significant positive correlations between the numbers determined by real-time PCR and by the Whitehead tray and microscopic method. Real-time PCR is a rapid, sensitive alternative to time-consuming nematode extractions, microscopic identification, and counting of P. thornei from field and greenhouse soils.

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