Using Multibeam Echosounders for Hydrographic Surveying in the Water Column: Estimating Wreck Least Depths

Wreck superstructure can extend into the water column and pose a danger to navigation if the least depth is not accurately portrayed to mariners. NOAA has several methods available to acquire a wreck least depth: lead line, wire drag, diver investigation, side scan shadow length, single beam bathymetry, and multibeam bathymetry. Previous studies have demonstrated that the bottom detection algorithm can fail to locate a wreck mast that is evident in the water column data. Modern multibeam sonars can record water column data in addition to bottom detections. NOAA’s current Hydrographic Specifications do not require water column collection; the best practice is to collect additional bathymetry data during wreck developments. Several multibeam bathymetry and multibeam water column datasets collected by NOAA vessels are evaluated and the wreck least depth results are compared to previous international field trials. A workflow to extract filtered and sidelobe suppressed water column point clouds is presented using currently available software packages. This paper explores the challenges encountered with water column data collection and processing and finds that analysis of water column data provides an improvement to finding wreck least depths, in some cases

The Port Norfolk Project: Improved Raster Navigation Products From High Resolution Source Data

With increasing capabilities in technology, modern hydrographic surveys are comprised of similarly increasing amounts of data, only a minute fraction of which is currently available in the nautical charts produced by the NOAA Office of Coast Survey (OCS). Simultaneously, a tremendous amount of effort goes into the generalization and optimal cartographic representation of the hydrographic data onto raster products, from which the vector products are digitized. Preserving and maintaining a single database of high-resolution vector source data will retain— and make accessible—much more of the hydrographic data collected, alleviate the burden of generalization, and would allow for delivery of high-resolution vector products, as well as a very wide selection of raster products. From high-resolution source data, raster output could be generated at customer specifications. These “user-defined” raster products could be suitably tailored to meet anyone’s needs, regardless if they are a mariner, a scientist, a fisherman, a student, or a casual “common man” customer. The “user-defined” concept will ultimately improve our ability to meet the highly variable needs of our customers. This paper is intended as an exploratory endeavor, specifically, using the Paper Chart Editor component of CARIS HPD to create examples of the kinds of raster products one can create from high-resolution source data, how this process could optimize the current raster chart production workflow within OCS, while also providing a stronger focus on customer service. Finally, the capabilities and lessons learned from the experimentation with HPD will be applied toward the NOAA-wide implementation of Nautical Chart System II (NCSII)

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

Longer duration of epilepsy and earlier age at epilepsy onset correlate with impaired cognitive development in infancy.

We assessed the impact of age at onset of epilepsy and duration and frequency of seizures on cognitive development in children less than 3 years old. Retrospective analysis was conducted on clinical data and neuropsychological testing of 33 infants with epilepsy. Developmental quotients were calculated and were correlated with age at epilepsy onset, duration of epilepsy, seizure frequency, brain pathology, and types of seizures (with/without spasms) as potential predictors. Infants with longer duration and earlier onset of epilepsy performed worse on developmental neuropsychological testing. Regression analyses showed that age at epilepsy onset and percentage of life with epilepsy were both strongly associated (regression model

Single-molecule fluorescence detection of a tricyclic nucleoside analogue.

Fluorescent nucleobase surrogates capable of Watson-Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push-pull conjugated system and synthesized it in seven sequential steps. The resulting C-linked 8-(diethylamino)benzo[b][1,8]naphthyridin-2(1H)-one nucleoside, which we name ABN, exhibits ε 442 = 20 000 M-1 cm-1 and Φ em,540 = 0.39 in water, increasing to Φ em = 0.50-0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities

Genomic reconstruction of the SARS-CoV-2 epidemic in England

AbstractThe evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.</jats:p

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

AbstractWhole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.</jats:p

SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

Abstract Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals. </jats:sec