Acoustic micronektonic distribution and density is structured by macroscale oceanographic processes across 17-48° N latitudes in the North Atlantic Ocean.

This study investigates the large-scale distribution patterns of the acoustic scattering layers and micronekton density across the Northeast Atlantic Ocean during daylight hours. A research cruise on board R/V "Kronprins Haakon" was conducted during May 2019 from Cape Verde to Bay of Biscay. Hydrological data were obtained at 20 conductivity-temperature-depth sensor (CTD) stations. To estimate the micronekton densities in front of the trawl, an autonomous echo sounder (120 or 200 kHz) on the headrope of the macroplankton trawl was used. Acoustic data were also collected along the cruise track using ship-mounted multi-frequency echo sounders (backscatter at 18 and 38 kHz was analyzed). Acoustic observations (both at 18, 38 and 120/200 kHz) showed clear patterns in the horizontal distribution of the micronekton during daytime with higher backscatter and echo densities in the south of the study area (from 17 to 37° N), and the absence of high backscatter in the surface from 37 to 45° N. Backscatter and echo densities were found to be significantly influenced by: temperature, salinity, and oxygen, as well as depth and time of the day.

Two scales of distribution and biomass of Antarctic krill (Euphausia superba) in the eastern sector of the CCAMLR Division 58.4.2 (55°E to 80°E).

Regular monitoring is an important component of the successful management of pelagic animals of interest to commercial fisheries. Here we provide a biomass estimate for Antarctic krill (Euphausia superba) in the eastern sector of the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) Division 58.4.2 (55°E to 80°E; area = 775,732 km2) using data collected during an acoustic-trawl survey carried out in February and March 2021. Using acoustic data collected in day-time and trawl data, areal biomass density was estimated as 8.3 gm-2 giving a total areal krill biomass of 6.48 million tonnes, with a 28.9% coefficient of variation (CV). The inaccessibility of the East Antarctic makes fisheries-independent surveys of Antarctic krill expensive and time consuming, so we also assessed the efficacy of extrapolating smaller surveys to a wider area. During the large-scale survey a smaller scale survey (centre coordinates -66.28°S 63.35°E, area = 4,902 km2) was conducted. We examine how representative krill densities from the small-scale (Mawson box) survey were over a latitudinal range by comparing krill densities from the large-scale survey split into latitudinal bands. We found the small scale survey provided a good representation of the statistical distribution of krill densities within its latitudinal band (KS-test, D = 0.048, p-value = 0.98), as well as mean density (t-test p-value = 0.44), but not outside of the band. We recommend further in situ testing of this approach.

Nonlinear crosstalk in broadband multi-channel echosounders.

Distortion of acoustic wave caused by nonlinear propagation transfers acoustic energy into higher harmonics of the transmitted signal. When operating several broadband echosounders with non-overlapping frequency bands to cover a wide frequency range, higher harmonics generated by one band may interfere with the fundamental band of others. This interference (i.e., crosstalk) can adversely affect the measured backscattered amplitude frequency response and in some circumstances, appears as spurious targets above and/or below the main target in pulse-compressed echograms. The nonlinear propagation of frequency-modulated acoustic waves in a directional beam was modeled and used to assess methods to reduce the deleterious effects of harmonic components in the signal, and was also compared to field experiments using the seabed echo and a metallic target sphere, with good agreement. Two methods are shown to materially reduce crosstalk: (1) reduction in transmit power, which reduces crosstalk amplitude by a larger amount than the associated reduction in transmit power, and (2) selection of a proper Fourier window length in the processing stage. The effect of crosstalk was small (<0.4 dB or 10%) for area backscattering measurements, but could be several dB for target strength measurements at different frequencies, depending on the transmit signals and processing parameters.

Estimating target strength and physical characteristics of gas-bearing mesopelagic fish from wideband in situ echoes using a viscous-elastic scattering model.

Wideband (38 and 50-260 kHz) target strength of organisms were measured in situ using a towed platform in mesopelagic (200-1000 m depth) layers. Organisms with a gas-inclusion are strong scatterers of sound and acoustically distinct from organisms lacking one. In the mesopelagic zone, some of the fish species and physonect siphonophores have a gas-inclusion. Trawl and multinet biological sampling as well as photographic evidence indicate that in the study area (eastern mid-Atlantic Ocean) the majority of the gas-bearing organisms were fish. Subsequently, using a two-layer viscous-elastic spherical gas backscattering model, physical characteristics such as gas-bladder features and body flesh properties were deduced from the measured backscattering signal of individual gas-bearing fish. Acoustic techniques are non-extractive, can be used for the monitoring and quantification of marine organisms in a time- and cost-effective manner, and suit studies of the mesopelagic zone, which is logistically challenging. Vessel-mounted acoustics, widely used for epipelagic studies, has limitations for mesopelagic studies as the deep organisms are inaccessible to high-frequency (≳100 kHz) acoustic pulses transmitted from the surface due to absorption. Therefore, a towed platform equipped with wideband acoustics has several features that can be utilized for monitoring the mesopelagic dense scattering layers containing mixed species.

Field measurements of acoustic absorption in seawater from 38 to 360 kHz.

Accurate estimates of acoustic absorption in seawater are crucial to the acoustic estimation of aquatic biomass. Estimates of acoustic absorption were obtained via a "pulse-echo" method, implemented using commonly available scientific echosounders and spherical calibration targets over a range of discrete frequencies. Below about 200 kHz, the absorption estimates were not significantly different from those of existing formulas, but at around 333 kHz, the measured absorption was 15 dB km-1 higher than estimated from existing formulas. Measurement variability was about ±2 dB km-1 for all frequencies. This is consistent with an observed anomaly between modelled and measured frequency-dependent biological backscatter. Allowing for this deviation will avoid incorrect spectral-based classification of acoustic targets and improve uncertainty in aquatic biomass estimation.

Previously undescribed thyroid-specific miRNA sequences in papillary thyroid carcinoma.

Papillary thyroid carcinoma (PTC) is the most common thyroid malignancy, wherein diagnostic limitations and lack of accurate prognostic factors are important clinical challenges. In this study, we report the discovery of 234 novel miRNAs in non-neoplastic thyroid and PTC samples, obtained from publicly available small RNA sequencing datasets (TCGA and GEO). These sequences were observed to display similar molecular features compared to currently annotated miRNAs. These potentially novel miRNAs presented tissue-specificity and largely decreased expression in PTC compared to non-neoplastic samples. We showed that the disrupted novel miRNAs have diagnostic and prognostic potential, and were associated with BRAF mutation, a frequent alteration related to more aggressive PTC. In conclusion, our results expand the miRNA repertoire in thyroid tissues and highlight the potential biological role and clinical utility of previously unannotated miRNAs.

Genomics and Epigenetics of Malignant Mesothelioma.

Malignant mesothelioma is an aggressive and lethal asbestos-related disease. Diagnosis of malignant mesothelioma is particularly challenging and is further complicated by the lack of disease subtype-specific markers. As a result, it is especially difficult to distinguish malignant mesothelioma from benign reactive mesothelial proliferations or reactive fibrosis. Additionally, mesothelioma diagnoses can be confounded by other anatomically related tumors that can invade the pleural or peritoneal cavities, collectively resulting in delayed diagnoses and greatly affecting patient management. High-throughput analyses have uncovered key genomic and epigenomic alterations driving malignant mesothelioma. These molecular features have the potential to better our understanding of malignant mesothelioma biology as well as to improve disease diagnosis and patient prognosis. Genomic approaches have been instrumental in identifying molecular events frequently occurring in mesothelioma. As such, we review the discoveries made using high-throughput technologies, including novel insights obtained from the analysis of the non-coding transcriptome, and the clinical potential of these genetic and epigenetic findings in mesothelioma. Furthermore, we aim to highlight the potential of these technologies in the future clinical applications of the novel molecular features in malignant mesothelioma.

Investigating the Effect of Tones and Frequency Sweeps on the Collective Behavior of Penned Herring (Clupea harengus).

We experimentally played back tones and sweeps to captive herring (Clupea harengus) in a net pen and measured the collective response of a large and a small group of fish using a camera, echo sounder, and multibeam sonar. The playbacks ranged in frequency from 160 to 500 Hz and 131 to 147 dB re 1 µPa in received sound pressure level. Herring behavior was scored by a team that blindly evaluated the observations. Overall, the responses were modest. Stronger reactions were observed at higher source levels, lower frequencies, and smaller school sizes, but there was no effect on signal rise time.

Comparisons among ten models of acoustic backscattering used in aquatic ecosystem research.

Analytical and numerical scattering models with accompanying digital representations are used increasingly to predict acoustic backscatter by fish and zooplankton in research and ecosystem monitoring applications. Ten such models were applied to targets with simple geometric shapes and parameterized (e.g., size and material properties) to represent biological organisms such as zooplankton and fish, and their predictions of acoustic backscatter were compared to those from exact or approximate analytical models, i.e., benchmarks. These comparisons were made for a sphere, spherical shell, prolate spheroid, and finite cylinder, each with homogeneous composition. For each shape, four target boundary conditions were considered: rigid-fixed, pressure-release, gas-filled, and weakly scattering. Target strength (dB re 1 m(2)) was calculated as a function of insonifying frequency (f = 12 to 400 kHz) and angle of incidence (θ = 0° to 90°). In general, the numerical models (i.e., boundary- and finite-element) matched the benchmarks over the full range of simulation parameters. While inherent errors associated with the approximate analytical models were illustrated, so were the advantages as they are computationally efficient and in certain cases, outperformed the numerical models under conditions where the numerical models did not converge.

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".

Identification and target strength of orange roughy (Hoplostethus atlanticus) measured in situ.

It is often assumed that in situ target strength (TS) measurements from dispersed fish are representative of the surveyed schooling fish. For in situ TS measurements of orange roughy in deep water, it has been difficult to validate the target species, individual lengths, and tilt angles and how representative these are of schooling fish. These problems have been addressed by attaching an acoustic optical system (AOS) to a trawl net. The AOS enables in situ measurements of TS and volume backscattering strength (Sv) at 38 and 120 kHz with optical verification of species and stereo camera measurements of fish length and tilt angle. TS estimates believed representative of the schooling population were derived by (1) weighting the frequency-dependent TS values by the Sv frequency difference distribution of orange roughy schools and (2) weighting the in situ TS measurements with an assumed tilt angle distribution. The 120-kHz TS estimates were less sensitive to variations in frequency difference and tilt angle, suggesting that this frequency may be better for biomass estimates than 38 kHz, the traditional survey frequency. Computations performed with an anatomically detailed scattering model agree with measurements of TS at both frequencies over a range of tilt angles.

Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models.

The acoustic backscatter from pressure release prolate spheroids and a three-dimensional representation of a fish swimbladder (Chilean jack mackerel, Trachurus symmetricus murphyi) was calculated using four target strength models (Kirchhoff-approximation, Kirchhoff-ray-mode, finite element solution of the Helmholtz equation, and prolate-spheroid-modal-series). Smoothly varying errors were found in the Kirchhoff-approximation and Kirchhoff-ray-mode model results when compared to the other models, and provide objective criteria for constraining the use of the KA and KRM models. A generic correction technique is also proposed for the prolate spheroid estimates and tentatively tested on a jack mackerel swimbladder, resulting in improvements to the target strength estimates from the Kirchhoff-approximation and Kirchhoff-ray-mode models.

Mesoscale eddies are oases for higher trophic marine life.

Mesoscale eddies stimulate biological production in the ocean, but knowledge of energy transfers to higher trophic levels within eddies remains fragmented and not quantified. Increasing the knowledge base is constrained by the inability of traditional sampling methods to adequately sample biological processes at the spatio-temporal scales at which they occur. By combining satellite and acoustic observations over spatial scales of 10 s of km horizontally and 100 s of m vertically, supported by hydrographical and biological sampling we show that anticyclonic eddies shape distribution and density of marine life from the surface to bathyal depths. Fish feed along density structures of eddies, demonstrating that eddies catalyze energy transfer across trophic levels. Eddies create attractive pelagic habitats, analogous to oases in the desert, for higher trophic level aquatic organisms through enhanced 3-D motion that accumulates and redistributes biomass, contributing to overall bioproduction in the ocean. Integrating multidisciplinary observation methodologies promoted a new understanding of biophysical interaction in mesoscale eddies. Our findings emphasize the impact of eddies on the patchiness of biomass in the sea and demonstrate that they provide rich feeding habitat for higher trophic marine life.