Acoustic scattering from density and sound speed gradients : modeling of oceanic pycnoclines

Author Posting. © Acoustical Society of America, 2012. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 131 (2012): EL54-EL60, doi:10.1121/1.3669394.A weak-scattering model that allows prediction of acoustic scattering from oceanic pycnoclines (and the accompanying sound speed gradients) based on hydrographic profiles is described. Model predictions, based on profiles from four locations, indicate that scattering from oceanic pycnoclines is measurable using standard scientific sonars operating at frequencies up to 200 kHz but generally only for pycnocline thicknesses less than 10 m. Accurate scattering models are key to assessing whether acoustic remote sensing can be used to map oceanic pycnoclines and for determining whether scattering from pycnoclines needs to be taken into account when estimating, for instance, zooplankton abundance from acoustic data

Orientation dependence of broadband acoustic backscattering from live squid

Author Posting. © Acoustical Society of America, 2012. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 131 (2012): 4461-4475, doi:10.1121/1.3701876.A controlled laboratory experiment of broadband acoustic backscattering from live squid (Loligo pealeii) was conducted using linear chirp signals (60–103 kHz) with data collected over the full 360° of orientation in the lateral plane, in <1° increments. The acoustic measurements were compared with an analytical prolate spheroid model and a three-dimensional numerical model with randomized squid shape, both based on the distorted-wave Born approximation formulation. The data were consistent with the hypothesized fluid-like scattering properties of squid. The contributions from the front and back interfaces of the squid were found to dominate the scattering at normal incidence, while the arms had a significant effect at other angles. The three-dimensional numerical model predictions out-performed the prolate spheroid model over a wide range of orientations. The predictions were found to be sensitive to the shape parameters, including the arms and the fins. Accurate predictions require setting these shape parameters to best describe the most probable squid shape for different applications. The understanding developed here serves as a basis for the accurate interpretation of in situ acoustic scattering measurements of squid.Funding for this research was provided by the Taiwan Merit Scholarship (NSC-095-SAF-I-564-021-TMS) and the Academic Program Office at WHOI

Use of the distorted wave Born approximation to predict scattering by inhomogeneous objects : application to squid

Author Posting. © Acoustical Society of America, 2009. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 125 (2009): 73-88, doi:10.1121/1.3021298.A new method has been developed to predict acoustic scattering by weakly scattering objects with three-dimensional variability in sound speed and density. This variability can take the form of inhomogeneities within the body of the scatterer and/or geometries where the acoustic wave passes through part of the scattering body, into the surrounding medium, and back into the body. This method applies the distorted wave Born approximation (DWBA) using a numerical approach that rigorously accounts for the phase changes within a scattering volume. Ranges of validity with respect to material properties and numerical considerations are first explored through comparisons with modal-series-based predictions of scattering by fluid-filled spherical and cylindrical fluid shells. The method is then applied to squid and incorporates high resolution spiral computerized tomography (SCT) scans of the complex morphology of the organism. Target strength predictions based on the SCT scans are compared with published backscattering data from live, freely swimming and tethered squid. The new method shows significant improvement for both single-orientation and orientation-averaged scattering predictions over the DWBA-homogeneous-prolate-spheroid model

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Curves+, a revised version of the Curves software for analyzing the conformation of nucleic acid structures, is now available as a web server. This version, which can be freely accessed at http://gbio-pbil.ibcp.fr/cgi/Curves_plus/, allows the user to upload a nucleic acid structure file, choose the nucleotides to be analyzed and after optionally setting a number of input variables, view the numerical and graphic results online or download files containing a set of helical, backbone and groove parameters that fully describe the structure. PDB format files are also provided for offline visualization of the helical axis and groove geometry

Exciton States of Dynamic DNA Double Helices: Alternating dCdG Sequences

The present communication deals with the excited states of the alternating DNA oligomer (dCdG)5·(dCdG)5 which correspond to the UV absorption band around 260 nm. Their properties are studied in the frame of the exciton theory, combining molecular dynamics simulations and quantum chemistry data. It is shown that the dipolar coupling undergoes important variations with the site and the helix geometry. In contrast, the energy of the monomer transitions within the double helix is not sensitive to the local environment. It is thus considered to be distributed over Gaussian curves whose maximum and width are derived from the experimental absorption spectra of nucleosides in aqueous solution. The influence of the spectral width on the excited state delocalization and the absorption spectra is much stronger than that of the oligomer plasticity. About half of the excited states are delocalized over at least two bases. Many of them result from the mixing of different monomer states and extend on both strands. The trends found in the simulated spectra, when going from non-interacting monomers to the duplex, are in agreement with experimental observations. Conformational changes enhance the diversity of the states which can be populated upon excitation at a given energy. The states with larger spatial extent are located close to the maximum of the absorption spectrum

Conformational analysis of nucleic acids revisited: Curves+

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamic

Frequency- and depth-dependent target strength measurements of individual mesopelagic scatterers

Author Posting. © Acoustical Society of America, 2020. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 148(2),(2020): EL153-EL158, doi:10.1121/10.0001745.Recent estimates based on shipboard echosounders suggest that 50% or more of global fish biomass may reside in the mesopelagic zone (depths of ∼200–1000 m). Nonetheless, little is known about the acoustic target strengths (TS) of mesopelagic animals because ship-based measurements cannot resolve individual targets. As a result, biomass estimates of mesopelagic organisms are poorly constrained. Using an instrumented tow-body, broadband (18–90 kHz) TS measurements were obtained at depths from 70 to 850 m. A comparison between TS measurements at-depth and values used in a recent global estimate of mesopelagic biomass suggests lower target densities at most depths.Development of Deep-See was funded by the National Science Foundation (Grant No. OCE MRI 1626087), field work was funded by NOAA, and ongoing support is provided by the WHOI Audacious/TED Project. Mike Jech (NOAA NWFSC) and WHOI collaborators Bob Pettit, Kaitlyn Tradd, Peter Weibe, and Joel Llopiz contributed to development and fieldwork

What's new in atopic eczema? An analysis of systematic reviews published in 2015. Part 2: prevention and treatment

This review forms part of a series of annual updates that summarize the evidence base for atopic eczema (AE), providing a succinct guide for clinicians and patients. It provides a summary of key findings from 26 systematic reviews that were published during 2015, and focuses on the treatment and prevention of AE. For systematic reviews on the epidemiology and methodological issues, see Part 1 of this update. Topical corticosteroid withdrawal syndrome, ‘steroid addiction’, has been evaluated in a high‐quality systematic review, which helps better define this entity and the risk factors for it. A Cochrane Review has not demonstrated any association between topical corticosteroid use in pregnancy and adverse outcomes, although very large quantities of potent/very potent topical corticosteroids may be associated with reduced birth weight. House dust mite avoidance strategies do not appear to prevent AE. Exposure to probiotics prenatally and in early infancy may help prevent AE, but there is no evidence that maternal diet or supplementation has a preventative effect