Linearity tests of a multibeam echosounder

The backscatter information available from many modern multibeam echosounder systems (MBES) has been shown to be useful for a number of purposes such as habitat classification and bottom type classification. Linearity of the system response is posited to be an important requirement for many backscatter processing techniques. A procedure to measure the system linearity is developed for the Reson 7125. These measurements are performed both in a controlled test tank environment and with systems installed on operational platforms. The linearity of the system with respect to power, gain, and the returned signal level is evaluated. It is possible to drive the Reson 7125 to nonlinear behavior. The consequences of nonlinearity on both bathymetric measurements and backscatter intensity values are developed theoretically and tested against experimental observations. Nonlinear performance generally complicates and degrades both backscatter and bathymetric data products

Oceanographic Weather Maps: Using Oceanographic Models to Improve Seabed Mapping Planning and Acquisition

In a world of high precision sensors, one of the few remaining challenges in multibeam echosounding is that of refraction based uncertainty. A poor understanding of oceanographic variability can lead to inadequate sampling of the water mass and the uncertainties that result from this can dominate the uncertainty budget of even state-of-the-art echosounding systems. Though dramatic improvements have been made in sensor accuracies over the past few decades, survey accuracy and efficiency is still potentially limited by a poor understanding of the “underwater weather”. Advances in the sophistication of numerical oceanographic forecast modeling, combined with ever increasing computing power, allow for the timely operation and dissemination of oceanographic nowcast and forecast model systems on regional and global scales. These sources of information, when examined using sound speed uncertainty analysis techniques, have the potential to change the way hydrographers work by increasing our understanding of what to expect from the ocean and when to expect it. Sound speed analyses derived from ocean modeling system’s three-dimensional predictions could provide guidance for hydrographers during survey planning, acquisition and post-processing of hydrographic data. In this work, we examine techniques for processing and visualizing of predictions from global and regional operational oceanographic forecast models and climatological analyses from an ocean atlas to better understand how these data could best be put to use to in the field of hydrograph

Estimating oil concentration and flow rate with calibrated vessel-mounted acoustic echo sounders

As part of a larger program aimed at evaluating acoustic techniques for mapping the distribution of subsurface oil and gas associated with the Deepwater Horizon-Macondo oil spill, observations were made on June 24 and 25, 2010 using vessel-mounted calibrated single-beam echo sounders on the National Oceanic and Atmospheric Administration ship Thomas Jefferson. Coincident with visual observations of oil at the sea surface, the 200-kHz echo sounder showed anomalously high-volume scattering strength in the upper 200 m on the western side of the wellhead, more than 100 times higher than the surrounding waters at 1,800-m distance from the wellhead, and weakening with increasing distance out to 5,000 m. Similar high-volume scattering anomalies were not observed at 12 or 38 kHz, although observations of anomalously low-volume scattering strength were made in the deep scattering layer at these frequencies at approximately the same locations. Together with observations of ocean currents, the acoustic observations are consistent with a rising plume of small (\u3c 1-mm radius) oil droplets. Using simplistic but reasonable assumptions about the properties of the oil droplets, an estimate of the flow rate was made that is remarkably consistent with those made at the wellhead by other means. The uncertainty in this acoustically derived estimate is high due to lack of knowledge of the size distribution and rise speed of the oil droplets. If properly constrained, these types of acoustic measurements can be used to rapidly estimate the flow rate of oil reaching the surface over large temporal and spatial scales

Methods for Collecting and Using Backscatter Field Calibration Information for the Reson 7000 Series Multibeams

In support of Integrated Ocean and Coastal Mapping, the National Oceanic and Atmospheric Administration’s (NOAA) Office of Coast Survey collects meaningful acoustic backscatter as a ancillary product of its navigational charting mission. Many of NOAA’s field units have Reson 7000 series multibeam echosounders which have been shown to have decidedly non-linear response characteristics under certain high signal conditions. This non-linear behavior significantly increases the complexity of the radiometric corrections required to make use of backscatter under a variety of processing paradigms. Avoiding operating these systems in the non-linear operational domain is a simpler approach. However, the onset of non-linear behavior is not a simple function of the output signal level but instead depends on a number of tunable settings. Here we present a method for both determining the onset of non-linear behavior in any installed Reson 7000 series sonar and monitoring the system during real-time acquisition to ensure the system is operating in a linear fashion. In general this information improves the operator’s understanding of the system status and can lead to additional post processing advantages

Use of high resolution bathymetry and backscatter for mapping depositional environments on the New Hampshire continental shelf

The New Hampshire continental shelf is extremely heterogeneous and includes extensive bedrock outcrops, sand and gravel deposits and muddy basins. Many of the depositional features are glacial in origin and have been significantly modified by marine processes as sea level fluctuated since the end of the last major glaciation. Recent high resolution multibeam echosounder (MBES) bathymetric and backscatter surveys by the National Ocean Survey and University of New Hampshire Center for Coastal and Ocean Mapping/Joint Hydrographic Center has revealed features of the seafloor in exceptional detail that had not been previously described. Synthesis of the MBES bathymetry and backscatter, coupled with an extensive archived database consisting of subbottom seismics, bottom sediment grain size data and vibracores, is being used to develop new surficial geology maps and significantly improve our knowledge of the character and origin of the major depositional features of the New Hampshire shelf and vicinity (with support from the Bureau of Ocean Energy Management). Included are a number of large glacial features (e.g., drumlins) covering the bedrock that have been modified by marine processes (waves and currents). Some of the larger features were previously mapped (Birch, F.S. 1984. A geophysical survey of sedimentary deposits on the inner continental shelf of New Hampshire. Northeastern Geology 6:207-221), but the lack of high resolution bathymetry limited their characterization and interpretation. The new high resolution bathymetry and backscatter has resolved this limitation. Some of these deposits may represent significant sand and gravel deposits on the New Hampshire continental shelf that have the potential for future use for beach nourishment and other efforts to build coastal resiliency

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant