Depth and frequency dependence of geoacoustic properties on the New England Mud Patch from reflection coefficient inversiona).

Muddy sediments cover significant portions of continental shelves, but their physical properties remain poorly understood compared to sandy sediments. This paper presents a generally applicable model for sediment-column structure and variability on the New England Mud Patch (NEMP), based on trans-dimensional Bayesian inversion of wide-angle, broadband reflection-coefficient data in this work and in two previously published reflection-coefficient inversions at different sites on the NEMP. The data considered here include higher frequencies and larger bandwidth and cover lower reflection grazing angles than the previous studies, hence, resulting in geoacoustic profiles with significantly better structural resolution and smaller uncertainties. The general sediment-column structure model includes an upper mud layer in which sediment properties change slightly with depth due to near-surface processes, an intermediate mud layer with nearly uniform properties, and a geoacoustic transition layer where properties change rapidly with depth (porosity decreases and sound speed, density, and attenuation increase) due to increasing sand content in the mud above a sand layer. Over the full frequency band considered in the new and two previous data sets (400-3125 Hz), there is no significant sound-speed dispersion in the mud, and attenuation follows an approximately linear frequency dependence.

Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana.

Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN-FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear. Here, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze-fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains. Pharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell-wall components as well as connections between the cell wall and the plasma membrane. This study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems.

Durotropic Growth of Pollen Tubes.

To reach the female gametophyte, growing pollen tubes must penetrate different tissues within the pistil, the female reproductive organ of a flower. Past research has identified various chemotropic cues that guide pollen tubes through the transmitting tract of the pistil, which represents the longest segment of its growth path. In addition, physical mechanisms also play a role in pollen tube guidance; however, these processes remain poorly understood. Here we show that pollen tubes from plants with solid transmitting tracts actively respond to the stiffness of the environment. We found that pollen tubes from Nicotiana tabacum and other plant species with a solid or semisolid transmitting tract increase their growth rate in response to an increasing matrix stiffness. By contrast, pollen tubes from Lilium longiflorum and other plant species with a hollow transmitting tract decrease their growth rate with increasing matrix stiffness, even though the forces needed to maintain a constant growth rate remain far below the maximum penetration force these pollen tubes are able to generate. Moreover, when confronted with a transition from a softer to a stiffer matrix, pollen tubes from N. tabacum display a greater ability to penetrate into a stiffer matrix compared with pollen tubes from L. longiflorum, even though the maximum force generated by pollen tubes from N. tabacum (11 µN) is smaller than the maximum force generated by pollen tubes from L. longiflorum (36 µN). These findings demonstrate a mechano-sensitive growth behavior, termed here durotropic growth, that is only expressed in pollen tubes from plants with a solid or semisolid transmitting tract and thus may contribute to an effective pollen tube guidance within the pistil.

Tryptophan-dependent auxin biosynthesis is required for HD-ZIP III-mediated xylem patterning.

The development and growth of higher plants is highly dependent on the conduction of water and minerals throughout the plant by xylem vessels. In Arabidopsis roots the xylem is organized as an axis of cell files with two distinct cell fates: the central metaxylem and the peripheral protoxylem. During vascular development, high and low expression levels of the class III HD-ZIP transcription factors promote metaxylem and protoxylem identities, respectively. Protoxylem specification is determined by both mobile, ground tissue-emanating miRNA165/6 species, which downregulate, and auxin concentrated by polar transport, which promotes HD-ZIP III expression. However, the factors promoting high HD-ZIP III expression for metaxylem identity have remained elusive. We show here that auxin biosynthesis promotes HD-ZIP III expression and metaxylem specification. Several auxin biosynthesis genes are expressed in the outer layers surrounding the vascular tissue in Arabidopsis root and downregulation of HD-ZIP III expression accompanied by specific defects in metaxylem development is seen in auxin biosynthesis mutants, such as trp2-12, wei8 tar2 or a quintuple yucca mutant, and in plants treated with L-kynurenine, a pharmacological inhibitor of auxin biosynthesis. Some of the patterning defects can be suppressed by synthetically elevated HD-ZIP III expression. Taken together, our results indicate that polar auxin transport, which was earlier shown to be required for protoxylem formation, is not sufficient to establish a proper xylem axis but that root-based auxin biosynthesis is additionally required.

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.

A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.

Geoacoustic inversion for the seabed transition layer using a Bernstein polynomial model.

This paper develops an inversion method for the seabed transition layer at the water-sediment interface, often found in muddy sediments, which provides density and sound-speed profiles that were previously not resolvable. The resolution improvements are achieved by introducing a parametrization that captures general depth-dependent gradients in geoacoustic parameters with a small number of parameters. In particular, the gradients are represented by a sum of Bernstein basis functions, weighted by unknown coefficients. Compared to previous forms found in the literature, the Bernstein-based parametrization can represent a wider range of depth-dependent geoacoustic profiles using fewer parameters which leads to reduced uncertainty and improved resolution. In addition, the Bernstein basis is the most stable polynomial representation in that small perturbations to the unknown coefficients result in small, localized perturbations to the geoacoustic profile, thereby providing an efficient exploration of the parameter space using Markov-chain methods in nonlinear inversion. Geoacoustic profiles at four mud sites on the Malta Plateau are studied with the proposed approach. Results show exceptional resolution of density profiles, estimated with low uncertainty and clear sensitivity to sediment features of centimeter scale.

Bowhead whale localization using asynchronous hydrophones in the Chukchi Sea.

This paper estimates bowhead whale locations and uncertainties using non-linear Bayesian inversion of their modally-dispersed calls recorded on asynchronous recorders in the Chukchi Sea, Alaska. Bowhead calls were recorded on a cluster of 7 asynchronous ocean-bottom hydrophones that were separated by 0.5-9.2 km. A warping time-frequency analysis is used to extract relative mode arrival times as a function of frequency for nine frequency-modulated whale calls that dispersed in the shallow water environment. Each call was recorded on multiple hydrophones and the mode arrival times are inverted for: the whale location in the horizontal plane, source instantaneous frequency (IF), water sound-speed profile, seabed geoacoustic parameters, relative recorder clock drifts, and residual error standard deviations, all with estimated uncertainties. A simulation study shows that accurate prior environmental knowledge is not required for accurate localization as long as the inversion treats the environment as unknown. Joint inversion of multiple recorded calls is shown to substantially reduce uncertainties in location, source IF, and relative clock drift. Whale location uncertainties are estimated to be 30-160 m and relative clock drift uncertainties are 3-26 ms.

Efficient localization and spectral estimation of an unknown number of ocean acoustic sources using a graphics processing unit.

This paper develops a matched-field approach to localization and spectral estimation of an unknown number of ocean acoustic sources employing massively parallel implementation on a graphics processing unit (GPU) for real-time efficiency. A Bayesian formulation is developed in which the locations and complex spectra of multiple sources and noise variances are considered unknown random variables, and the Bayesian information criterion is minimized to estimate these parameters, as well as the number of sources present. Optimization is carried out using simulated annealing and includes steps that attempt to add/delete sources to/from the model. Closed-form maximum-likelihood (ML) solutions for source spectra and noise variances in terms of the source locations allow these parameters to be sampled implicitly, substantially reducing the dimensionality of the inversion. Source sampling, addition, and deletion are based on joint conditional probability distributions for source range and depth, which incorporate the ML spectral estimates. Computing these conditionals requires solving a very large number of systems of equations, which is carried out in parallel on a GPU, improving efficiency by 2 orders of magnitude. Simulated examples illustrate localizations and spectral estimation for a large number of sources (up to eight), and investigate mitigation of environmental mismatch via efficient multiple-frequency inversion.

Fast computation of seabed spherical-wave reflection coefficients in geoacoustic inversion.

This paper develops a fast numerical approach to computing spherical-wave reflection coefficients (SWRCs) for layered seabeds, which provides substantial savings in computation time when used as the forward model for geoacoustic inversion of broadband seabed reflectivity data. The approach exploits the Sommerfeld-integral representation of SWRCs as the Hankel transform of a function proportional to the plane-wave reflection coefficient (PWRC), and applies Levin integration to the rapidly oscillating integrand cast as the product of a (pre-computed) media-independent matrix and a vector involving PWRCs at a sparse sampling of integration angles. Compared to conventional Simpson's rule integration for computation of the SWRC, the Levin integration yields speed-up factors of an order of magnitude or more. Further, it results in reduced memory requirements for storage of pre-computed quantities, a desirable property when a graphics processing unit (GPU) is used for parallel computation of SWRCs. The paper applies trans-dimensional Bayesian inversion to investigate the impact of forward modeling in terms of PWRCs and SWRCs on the estimation of geoacoustic parameters and uncertainties. Model comparisons are quantified in simulated- and measured-data inversions by comparing the estimated geoacoustic parameters to the true parameters or core measurements, respectively, and by calculating the deviance information criterion for model selection.

Bayesian environmental inversion of airgun modal dispersion using a single hydrophone in the Chukchi Sea.

This paper presents estimated water-column and seabed parameters and uncertainties for a shallow-water site in the Chukchi Sea, Alaska, from trans-dimensional Bayesian inversion of the dispersion of water-column acoustic modes. Pulse waveforms were recorded at a single ocean-bottom hydrophone from a small, ship-towed airgun array during a seismic survey. A warping dispersion time-frequency analysis is used to extract relative mode arrival times as a function of frequency for source-receiver ranges of 3 and 4 km which are inverted for the water sound-speed profile (SSP) and subbottom geoacoustic properties. The SSP is modeled using an unknown number of sound-speed/depth nodes. The subbottom is modeled using an unknown number of homogeneous layers with unknown thickness, sound speed, and density, overlying a halfspace. A reversible-jump Markov-chain Monte Carlo algorithm samples the model parameterization in terms of the number of water-column nodes and subbottom interfaces that can be resolved by the data. The estimated SSP agrees well with a measured profile, and seafloor sound speed is consistent with an independent headwave arrival-time analysis. Environmental properties are required to model sound propagation in the Chukchi Sea for estimating sound exposure levels and environmental research associated with marine mammal localization.

Estimating seabed scattering mechanisms via Bayesian model selection.

A quantitative inversion procedure is developed and applied to determine the dominant scattering mechanism (surface roughness and/or volume scattering) from seabed scattering-strength data. The classification system is based on trans-dimensional Bayesian inversion with the deviance information criterion used to select the dominant scattering mechanism. Scattering is modeled using first-order perturbation theory as due to one of three mechanisms: Interface scattering from a rough seafloor, volume scattering from a heterogeneous sediment layer, or mixed scattering combining both interface and volume scattering. The classification system is applied to six simulated test cases where it correctly identifies the true dominant scattering mechanism as having greater support from the data in five cases; the remaining case is indecisive. The approach is also applied to measured backscatter-strength data where volume scattering is determined as the dominant scattering mechanism. Comparison of inversion results with core data indicates the method yields both a reasonable volume heterogeneity size distribution and a good estimate of the sub-bottom depths at which scatterers occur.

A trans-dimensional polynomial-spline parameterization for gradient-based geoacoustic inversion.

This paper presents a polynomial spline-based parameterization for trans-dimensional geoacoustic inversion. The parameterization is demonstrated for both simulated and measured data and shown to be an effective method of representing sediment geoacoustic profiles dominated by gradients, as typically occur, for example, in muddy seabeds. Specifically, the spline parameterization is compared using the deviance information criterion (DIC) to the standard stack-of-homogeneous layers parameterization for the inversion of bottom-loss data measured at a muddy seabed experiment site on the Malta Plateau. The DIC is an information criterion that is well suited to trans-D Bayesian inversion and is introduced to geoacoustics in this paper. Inversion results for both parameterizations are in good agreement with measurements on a sediment core extracted at the site. However, the spline parameterization more accurately resolves the power-law like structure of the core density profile and provides smaller overall uncertainties in geoacoustic parameters. In addition, the spline parameterization is found to be more parsimonious, and hence preferred, according to the DIC. The trans-dimensional polynomial spline approach is general, and applicable to any inverse problem for gradient-based profiles. [Work supported by ONR.].

In situ sediment dispersion estimates in the presence of discrete layers and gradients.

One of the difficulties in validating sediment models has been the lack of reliable low frequency dispersion measurements. A reflection method is presented that yields in situ dispersion without sediment disturbance over a broad range of frequencies and can explicitly disentangle frequency-dependent effects of vertical structure, e.g., layers and gradients. Measurements on the outer shelf from 300 to 3000 Hz show that dispersion is a strong function of depth in the sediment column. The depth and frequency-dependent results generally agree well with independent measurements on core data. Cohesive sediments in the upper few meters exhibit a nearly frequency-independent sound speed and a nearly linear frequency dependence of attenuation. In the lower part of the sediment column the sediments are more granular: the lowest layer exhibits an attenuation with a peak frequency at 1100 Hz, where its dependence below and above trends to f(2) and f(1/2), respectively. While Biot theory predicts this dependence, its underlying physical explanation, fluid flow through interstitial pores, does not seem plausible for this sediment due to the unreasonable permeability value required. Viscous grain shearing theory also predicts this dependence, but it is not known whether the parameter values are reasonable.

Probabilistic two-dimensional water-column and seabed inversion with self-adapting parameterizations.

This paper develops a probabilistic two-dimensional (2D) inversion for geoacoustic seabed and water-column parameters in a strongly range-dependent environment. Range-dependent environments in shelf and shelf-break regions are of increasing importance to the acoustical-oceanography community, and recent advances in nonlinear inverse theory and sampling methods are applied here for efficient probabilistic range-dependent inversion. The 2D seabed and water column are parameterized using highly efficient, self-adapting irregular grids which intrinsically match the local resolving power of the data and provide parsimonious solutions requiring few parameters to capture complex environments. The self-adapting parameterization is achieved by implementing the irregular grid as a trans-dimensional hierarchical Bayesian model with an unknown number of nodes which is sampled with the Metropolis-Hastings-Green algorithm. To improve sampling, population Monte Carlo is applied with a large number of interacting parallel Markov chains with adaptive proposal distributions. The inversion is applied to simulated data for a vertical-line array and several source locations to several kilometers range. Complex acoustic-pressure fields are computed using a parabolic equation model and results are considered in terms of 2D ensemble parameter estimates and credibility intervals.

Trans-dimensional joint inversion of seabed scattering and reflection data.

This paper examines joint inversion of acoustic scattering and reflection data to resolve seabed interface roughness parameters (spectral strength, exponent, and cutoff) and geoacoustic profiles. Trans-dimensional (trans-D) Bayesian sampling is applied with both the number of sediment layers and the order (zeroth or first) of auto-regressive parameters in the error model treated as unknowns. A prior distribution that allows fluid sediment layers over an elastic basement in a trans-D inversion is derived and implemented. Three cases are considered: Scattering-only inversion, joint scattering and reflection inversion, and joint inversion with the trans-D auto-regressive error model. Including reflection data improves the resolution of scattering and geoacoustic parameters. The trans-D auto-regressive model further improves scattering resolution and correctly differentiates between strongly and weakly correlated residual errors.

Seabed roughness parameters from joint backscatter and reflection inversion at the Malta Plateau.

This paper presents estimates of seabed roughness and geoacoustic parameters and uncertainties on the Malta Plateau, Mediterranean Sea, by joint Bayesian inversion of mono-static backscatter and spherical wave reflection-coefficient data. The data are modeled using homogeneous fluid sediment layers overlying an elastic basement. The scattering model assumes a randomly rough water-sediment interface with a von Karman roughness power spectrum. Scattering and reflection data are inverted simultaneously using a population of interacting Markov chains to sample roughness and geoacoustic parameters as well as residual error parameters. Trans-dimensional sampling is applied to treat the number of sediment layers and the order (zeroth or first) of an autoregressive error model (to represent potential residual correlation) as unknowns. Results are considered in terms of marginal posterior probability profiles and distributions, which quantify the effective data information content to resolve scattering/geoacoustic structure. Results indicate well-defined scattering (roughness) parameters in good agreement with existing measurements, and a multi-layer sediment profile over a high-speed (elastic) basement, consistent with independent knowledge of sand layers over limestone.

Trans-dimensional geoacoustic inversion of wind-driven ambient noise.

This letter applies trans-dimensional Bayesian geoacoustic inversion to quantify the uncertainty due to model selection when inverting bottom-loss data derived from wind-driven ambient-noise measurements. A partition model is used to represent the seabed, in which the number of layers, their thicknesses, and acoustic parameters are unknowns to be determined from the data. Exploration of the parameter space is implemented using the Metropolis-Hastings algorithm with parallel tempering, whereas jumps between parameterizations are controlled by a reversible-jump Markov chain Monte Carlo algorithm. Sediment uncertainty profiles from inversion of simulated and experimental data are presented.

Arabidopsis Lateral Root Development 3 is essential for early phloem development and function, and hence for normal root system development.

We have identified a gene, Lateral Root Development 3 (LRD3), that is important for maintaining a balance between primary and lateral root growth. The lrd3 mutant has decreased primary root growth and increased lateral root growth. We determined that the LRD3 gene encodes a LIM-domain protein of unknown function. LRD3 is expressed only in the phloem companion cells, which suggested a role in phloem function. Indeed, while phloem loading and export from the shoot appear to be normal, delivery of phloem to the primary root tip is limited severely in young seedlings. Abnormalities in phloem morphology in these seedlings indicate that LRD3 is essential for correct early phloem development. There is a subsequent spontaneous recovery of normal phloem morphology, which is correlated tightly with increased phloem delivery and growth of the primary root. The LRD3 gene is one of very few genes described to affect phloem development, and the only one that is specific to early phloem development. Continuous growth on auxin also leads to recovery of phloem development and function in lrd3, which demonstrates that auxin plays a key role in early phloem development. The root system architecture and the pattern of phloem allocation in the lrd3 root system suggested that there may be regulated mechanisms for selectively supporting certain lateral roots when the primary root is compromised. Therefore, this study provides new insights into phloem-mediated resource allocation and its effects on plant root system architecture.

Trans-dimensional matched-field geoacoustic inversion with hierarchical error models and interacting Markov chains.

This paper develops a trans-dimensional approach to matched-field geoacoustic inversion, including interacting Markov chains to improve efficiency and an autoregressive model to account for correlated errors. The trans-dimensional approach and hierarchical seabed model allows inversion without assuming any particular parametrization by relaxing model specification to a range of plausible seabed models (e.g., in this case, the number of sediment layers is an unknown parameter). Data errors are addressed by sampling statistical error-distribution parameters, including correlated errors (covariance), by applying a hierarchical autoregressive error model. The well-known difficulty of low acceptance rates for trans-dimensional jumps is addressed with interacting Markov chains, resulting in a substantial increase in efficiency. The trans-dimensional seabed model and the hierarchical error model relax the degree of prior assumptions required in the inversion, resulting in substantially improved (more realistic) uncertainty estimates and a more automated algorithm. In particular, the approach gives seabed parameter uncertainty estimates that account for uncertainty due to prior model choice (layering and data error statistics). The approach is applied to data measured on a vertical array in the Mediterranean Sea.

Resolving meso-scale seabed variability using reflection measurements from an autonomous underwater vehicle.

Seabed geoacoustic variability is driven by geological processes that occur over a wide spectrum of space-time scales. While the acoustics community has some understanding of horizontal fine-scale geoacoustic variability, less than O(10(0)) m, and large-scale variability, greater than O(10(3)) m, there is a paucity of data resolving the geoacoustic meso-scale O(10(0)-10(3)) m. Measurements of the meso-scale along an ostensibly "benign" portion of the outer shelf reveal three classes of variability. The first class was expected and is due to horizontal variability of layer thicknesses: this was the only class that could be directly tied to seismic reflection data. The second class is due to rapid changes in layer properties and/or boundaries, occurring over scales of meters to hundreds of meters. The third class was observed as rapid variations of the angle/frequency dependent reflection coefficient within a single observation and is suggestive of variability at scales of meter or less. Though generally assumed to be negligible in acoustic modeling, the second and third classes are indicative of strong horizontal geoacoustic variability within a given layer. The observations give early insight into possible effects of horizontal geoacoustic variability on long-range acoustic propagation and reverberation.