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

Evaluation of rockfish abundance in untrawlable habitat: combining acoustic and complementary sampling tools

Rockfishes (Sebastes spp.) are an important component of North Pacific marine ecosystems and commercial fisheries. Because the rocky, high-relief substrate that rockfishes often inhabit is inaccessible to standard survey trawls, population abundance assessments for many rockfish species are difficult. As part of a large study to classify substrate and compare complementary sampling tools, we investigated the feasibility of using an acoustic survey in conjunction with a lowered stereo-video camera, a remotely operated vehicle, and a modified bottom trawl to estimate rockfish biomass in untrawlable habitat. The Snakehead Bank south of Kodiak Island, Alaska, was surveyed repeatedly over 4 days and nights. Dusky rockfish (S. variabilis), northern rockfish (S. polyspinis), and harlequin rockfish (S. variegatus) were the most abundant species observed on the bank. Backscatter attributed to rockfish were collected primarily near the seafloor at a mean height off the bottom of 1.5 m. Total rockfish backscatter and the height of backscatter off the bottom did not differ among survey passes or between night and day. Biomass estimates for the 41 square nautical-mile area surveyed on this small, predominantly untrawlable bank were 2350 metric tons (t) of dusky rockfish, 331 t of northern rockfish, and 137 t of harlequin rockfish. These biomass estimates are 5–60 times the density estimated for these rockfish species by a regularly conducted bottom trawl survey covering the bank and the surrounding shelf. This finding shows that bottom trawl surveys can underestimate the abundance of rockfishes in untrawlable areas and, therefore, may underestimate overall population abundance for these species

Columbia River plume fronts. II. Distribution, abundance, and feeding ecology of juvenile salmon

Well-defined fronts develop at the seaward edge of riverine plumes where suspended materials and planktonic organisms are concentrated by convergent water flows. Riverine plume fronts have been hypothesized to be favorable fish habitats because they can lead to localized prey aggregations. We examined the spatial distribution of juvenile Pacific salmonids Oncorhynchus spp. in and around plankton-rich frontal regions of the Columbia River plume to test the hypothesis that juvenile salmonids aggregate at riverine plume fronts to feed. Juvenile salmonids tended to be abundant in the frontal and plume regions compared to the more marine shelf waters, but this pattern differed among species and was not consistent across the 2 study years. Stomach fullness tended to be higher in the more marine shelf waters than either the front or plume areas, which does not support the hypothesis that salmonids consistently ingest more prey at frontal regions. Many prey organisms were disproportionately abundant at these fronts, but salmon stomach-content analysis did not reveal higher stomach contents at fronts or identify prey groups indicative of feeding in the frontal areas. Although our results indicate that the Columbia River plume influences the distributions of juvenile salmon, our observations do not support the hypothesis that juvenile salmonids congregate to feed at fronts at the leading edge of the Columbia River plume. The short persistence time of these fronts may prevent juvenile salmon from exploiting these food-rich, but ephemeral, features.Keywords: Feeding habits, Distribution, Juvenile salmon, Frontal regions, Columbia River plumeKeywords: Feeding habits, Distribution, Juvenile salmon, Frontal regions, Columbia River plum

Expression of Transposable Elements in Neural Tissues during Xenopus Development

Transposable elements comprise a large proportion of animal genomes. Transposons can have detrimental effects on genome stability but also offer positive roles for genome evolution and gene expression regulation. Proper balance of the positive and deleterious effects of transposons is crucial for cell homeostasis and requires a mechanism that tightly regulates their expression. Herein we describe the expression of DNA transposons of the Tc1/mariner superfamily during Xenopus development. Sense and antisense transcripts containing complete Tc1-2_Xt were detected in Xenopus embryos. Both transcripts were found in zygotic stages and were mainly localized in Spemann's organizer and neural tissues. In addition, the Tc1-like elements Eagle, Froggy, Jumpy, Maya, Xeminos and TXr were also expressed in zygotic stages but not oocytes in X. tropicalis. Interestingly, although Tc1-2_Xt transcripts were not detected in Xenopus laevis embryos, transcripts from other two Tc1-like elements (TXr and TXz) presented a similar temporal and spatial pattern during X. laevis development. Deep sequencing analysis of Xenopus tropicalis gastrulae showed that PIWI-interacting RNAs (piRNAs) are specifically derived from several Tc1-like elements. The localized expression of Tc1-like elements in neural tissues suggests that they could play a role during the development of the Xenopus nervous system

Characterisation of irradiated thin silicon sensors for the CMS phase II pixel upgrade

The high luminosity upgrade of the Large Hadron Collider, foreseen for 2026, necessitates the replacement of the CMS experiment's silicon tracker. The innermost layer of the new pixel detector will be exposed to severe radiation, corresponding to a 1 MeV neutron equivalent fluence of up to Phi(eq) = 2x10(16) cm(-2), and an ionising dose of approximate to 5 MGy after an integrated luminosity of 3000 fb(-1). Thin, planar silicon sensors are good candidates for this application, since the degradation of the signal produced by traversing particles is less severe than for thicker devices. In this paper, the results obtained from the characterisation of 100 and 200 mu m thick p-bulk pad diodes and strip sensors irradiated up to fluences of Phi(eq) = 1.3 x 10(16) cm(-2) are shown.Peer reviewe

Fish avoidance of research vessels and the efficacy of noise-reduced vessels: a review

It has long been recognized that fish can avoid approaching vessels and that these behaviours can bias fishery surveys. Underwater noise is considered the primary stimulus, and standards for research vessel noise have been established to minimize fish reactions. We review the literature on fish reactions to vessels appearing since these recommendations were made, focusing on acoustic surveys, and compare how fish react to noise-reduced and conventional vessels. Reactions to approaching vessels are variable and difficult to predict. However, the behaviour can bias acoustic abundance measurements, and should be considered when performing acoustic surveys. The few comparisons of acoustic abundance measurements from noise-reduced and conventional vessels are contradictory, but demonstrate that the sound pressure level, on which the noise-reduction criterion is based, is insufficient to explain how fish react to survey vessels. Further research is needed to identify the stimuli fish perceive from approaching vessels and the factors affecting whether fish perceiving these stimuli will react before further recommendations to reduce vessel-avoidance reactions can be made. In the interim, measurement of the biases introduced by fish avoidance reactions during surveys, and timing of surveys when fish are in a less reactive state, may reduce errors introduced by vessel avoidance

Combining bottom trawls and acoustics in a diverse semipelagic environment: What is the contribution of walleye pollock (Gadus chalcogrammus) to near-bottom acoustic backscatter in the eastern Bering Sea?

The abundance of walleye pollock (Gadus chalcogrammus) in the eastern Bering Sea (EBS) is estimated through fisheries-independent acoustic trawl (AT) surveys, which currently use acoustic backscatter data down to 3 m above the bottom. A large portion of adult pollock are demersal and these estimates will become more accurate if the survey is extended closer to bottom. The purpose of this project was to assess the feasibility of extending the AT survey closer to the bottom by estimating the contributions of each fish species to observed acoustic backscatter in the highly diverse near-bottom region. This was accomplished by fitting a regression model to simultaneously collected acoustic backscatter and bottom trawl (BT) catch data. Pollock were the dominant source of acoustic backscatter among demersal species accounting for 85.9 ± 4.8 % of acoustic backscatter (mean ± standard deviation). A method was developed to extend the AT survey to within 0.5 m of the bottom and applied to the 1994-2014 surveys, pollock biomass increased by an average of 35 ± 12 %.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Experimental Evidence of Threat-Sensitive Collective Avoidance Responses in a Large Wild-Caught Herring School

Aggregation is commonly thought to improve animals' security. Within aquatic ecosystems, group-living prey can learn about immediate threats using cues perceived directly from predators, or from collective behaviours, for example, by reacting to the escape behaviours of companions. Combining cues from different modalities may improve the accuracy of prey antipredatory decisions. In this study, we explored the sensory modalities that mediate collective antipredatory responses of herring (Clupea harengus) when in a large school (approximately 60 000 individuals). By conducting a simulated predator encounter experiment in a semi-controlled environment (a sea cage), we tested the hypothesis that the collective responses of herring are threat-sensitive. We investigated whether cues from potential threats obtained visually or from the perception of water displacement, used independently or in an additive way, affected the strength of the collective avoidance reactions. We modified the sensory nature of the simulated threat by exposing the herring to 4 predator models differing in shape and transparency. The collective vertical avoidance response was observed and quantified using active acoustics. The combination of sensory cues elicited the strongest avoidance reactions, suggesting that collective antipredator responses in herring are mediated by the sensory modalities involved during threat detection in an additive fashion. Thus, this study provides evidence for magnitude-graded threat responses in a large school of wild-caught herring which is consistent with the “threat-sensitive hypothesis”

Can a bottom-moored echosounder array provide a survey-comparable index of abundance?

A small number of stationary echosounders have the potential to produce abundance indices where fish repeatedly occupy localized areas (e.g., spawning grounds). To investigate this possibility, we deployed three trawl-resistant moorings with a newly-designed autonomous echosounder for ~85 days during the walleye pollock spawning season in Shelikof Strait, Alaska. Backscatter observed from the moorings was highly correlated with ship-based acoustic surveys, suggesting that the mooring observations reflect abundance over much larger areas than the observation volume of the acoustic beam. A retrospective analysis of a 19-year time series of pre-spawning pollock surveys was used to select mooring locations and determine that 3-5 moorings can produce an index of pollock backscatter comparable to that produced by a ship-based survey covering ~18,000 km2 (mean prediction error ofThe accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author