ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Publication Date: 2015-08-11
    Description: The Special Supplemental Nutrition Program for Women, Infants and Children (WIC) Program is a key part of America's safety net, but its structure fails to incentivize participants to be cost-conscious in their purchases and may cause retailers to attach excessive markups to WIC products. We investigate cost containment in the WIC Program, with a focus on California. Results show that smaller vendors often charge considerably higher prices for WIC foods than their larger counterparts. However, larger vendors do not mark up WIC foods more or promote them less than comparable control products. Cost containment can be improved by targeting WIC Program sales to larger vendors when it is possible to do so without compromising participant access, and using large-vendor prices as a benchmark to limit prices set by smaller vendors.
    Keywords: D12 - Consumer Economics: Empirical Analysis, I38 - Government Policy ; Provision and Effects of Welfare Programs, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 2
    Publication Date: 2015-06-06
    Description: We describe a multihomogeneity theory for source-parameter estimation of potential fields. Similar to what happens for random source models, where the monofractal scaling-law has been generalized into a multifractal law, we propose to generalize the homogeneity law into a multihomogeneity law. This allows a theoretically correct approach to study real-world potential fields, which are inhomogeneous and so do not show scale invariance, except in the asymptotic regions (very near to or very far from their sources). Since the scaling properties of inhomogeneous fields change with the scale of observation, we show that they may be better studied at a set of scales than at a single scale and that a multihomogeneous model is needed to explain its complex scaling behaviour. In order to perform this task, we first introduce fractional-degree homogeneous fields, to show that: (i) homogeneous potential fields may have fractional or integer degree; (ii) the source-distributions for a fractional-degree are not confined in a bounded region, similarly to some integer-degree models, such as the infinite line mass and (iii) differently from the integer-degree case, the fractional-degree source distributions are no longer uniform density functions. Using this enlarged set of homogeneous fields, real-world anomaly fields are studied at different scales, by a simple search, at any local window W , for the best homogeneous field of either integer or fractional-degree, this yielding a multiscale set of local homogeneity-degrees and depth estimations which we call multihomogeneous model. It is so defined a new technique of source parameter estimation (Multi-HOmogeneity Depth Estimation, MHODE), permitting retrieval of the source parameters of complex sources. We test the method with inhomogeneous fields of finite sources, such as faults or cylinders, and show its effectiveness also in a real-case example. These applications show the usefulness of the new concepts, multihomogeneity and fractional homogeneity-degree, to obtain valid estimates of the source parameters in a consistent theoretical framework, so overcoming the limitations imposed by global-homogeneity to widespread methods, such as Euler deconvolution.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 3
    Publication Date: 2015-06-06
    Description: In this paper, two separate but related goals are tackled. The first one is to demonstrate that in some saturated rock textures the non-linear behaviour of induced polarization (IP) and the violation of Ohm's law not only are real phenomena, but they can also be satisfactorily predicted by a suitable physical-mathematical model, which is our second goal. This model is based on Fick's second law. As the model links the specific dependence of resistivity and chargeability of a laboratory sample to the injected current and this in turn to its pore size distribution, it is able to predict pore size distribution from laboratory measurements, in good agreement with mercury injection capillary pressure test results. This fact opens up the possibility for hydrogeophysical applications on a macro scale. Mathematical modelling shows that the chargeability acquired in the field under normal conditions, that is at low current, will always be very small and approximately proportional to the applied current. A suitable field test site for demonstrating the possible reliance of both resistivity and chargeability on current was selected and a specific measuring strategy was established. Two data sets were acquired using different injected current strengths, while keeping the charging time constant. Observed variations of resistivity and chargeability are in agreement with those predicted by the mathematical model. These field test data should however be considered preliminary. If confirmed by further evidence, these facts may lead to changing the procedure of acquiring field measurements in future, and perhaps may encourage the design and building of a new specific geo-resistivity meter. This paper also shows that the well-known Marshall and Madden's equations based on Fick's law cannot be solved without specific boundary conditions.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 4
    Publication Date: 2015-08-15
    Description: We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (~90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 5
    Publication Date: 2015-09-11
    Description: Iterative substitution of the coupled Marchenko equations is a novel methodology to retrieve the Green's functions from a source or receiver array at an acquisition surface to an arbitrary location in an acoustic medium. The methodology requires as input the single-sided reflection response at the acquisition surface and an initial focusing function, being the time-reversed direct wavefield from the acquisition surface to a specified location in the subsurface. We express the iterative scheme that is applied by this methodology explicitly as the successive actions of various linear operators, acting on an initial focusing function. These operators involve multidimensional crosscorrelations with the reflection data and truncations in time. We offer physical interpretations of the multidimensional crosscorrelations by subtracting traveltimes along common ray paths at the stationary points of the underlying integrals. This provides a clear understanding of how individual events are retrieved by the scheme. Our interpretation also exposes some of the scheme's limitations in terms of what can be retrieved in case of a finite recording aperture. Green's function retrieval is only successful if the relevant stationary points are sampled. As a consequence, internal multiples can only be retrieved at a subsurface location with a particular ray parameter if this location is illuminated by the direct wavefield with this specific ray parameter. Several assumptions are required to solve the Marchenko equations. We show that these assumptions are not always satisfied in arbitrary heterogeneous media, which can result in incomplete Green's function retrieval and the emergence of artefacts. Despite these limitations, accurate Green's functions can often be retrieved by the iterative scheme, which is highly relevant for seismic imaging and inversion of internal multiple reflections.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 6
    Publication Date: 2015-09-13
    Description: Employing dynamic reciprocity can be an effective tool to simplify the calculation of elastic wavefields for borehole problems and to check the results. We analytically obtain the reciprocity relations for the elastodynamic fields generated by multipole sources in a fluid–solid configuration: if the multipole sources are located in the fluid, the particle displacement due to a dipole source is reciprocal to the particle acceleration due to a single force; the fluid pressure due to a dipole source is reciprocal to the particle acceleration due to a monopole source; the particle displacement due to a quadrupole source is reciprocal to the spatial partial derivative of the particle acceleration due to a single force; the fluid pressure due to a quadrupole source is reciprocal to the spatial partial derivative of the particle acceleration due to a monopole source. These relations are tested by numerical experiments for different borehole problems, including acoustic logging, single-well imaging and vertical seismic profiling. A reciprocity test can be used as a quick check of a finite-difference algorithm and the implementation of the sources, although it cannot detect errors due to improper discretization of the interfaces.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 7
    Publication Date: 2015-09-19
    Description: Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 8
    Publication Date: 2015-09-26
    Description: The area of the 9.1-km-deep Continental Deep Drillhole (KTB) in Germany is used as a case study for a geothermal reservoir situated in folded and faulted metamorphic crystalline crust. The presented approach is based on the analysis of 3-D seismic reflection data combined with borehole data and hydrothermal numerical modelling. The KTB location exemplarily contains all elements that make seismic prospecting in crystalline environment often more difficult than in sedimentary units, basically complicated tectonics and fracturing and low-coherent strata. In a first step major rock units including two known nearly parallel fault zones are identified down to a depth of 12 km. These units form the basis of a gridded 3-D numerical model for investigating temperature and fluid flow. Conductive and advective heat transport takes place mainly in a metamorphic block composed of gneisses and metabasites that show considerable differences in thermal conductivity and heat production. Therefore, in a second step, the structure of this unit is investigated by seismic waveform modelling. The third step of interpretation consists of applying wavenumber filtering and log-Gabor-filtering for locating fractures. Since fracture networks are the major fluid pathways in the crystalline, we associate the fracture density distribution with distributions of relative porosity and permeability that can be calibrated by logging data and forward modelling of the temperature field. The resulting permeability distribution shows values between 10 –16 and 10 –19 m 2 and does not correlate with particular rock units. Once thermohydraulic rock properties are attributed to the numerical model, the differential equations for heat and fluid transport in porous media are solved numerically based on a finite difference approach. The hydraulic potential caused by topography and a heat flux of 54 mW m –2 were applied as boundary conditions at the top and bottom of the model. Fluid flow is generally slow and mainly occurring within the two fault zones. Thus, our model confirms the previous finding that diffusive heat transport is the dominant process at the KTB site. Fitting the observed temperature–depth profile requires a correction for palaeoclimate of about 4 K at 1 km depth. Modelled and observed temperature data fit well within 0.2 °C bounds. Whereas thermal conditions are suitable for geothermal energy production, hydraulic conditions are unfavourable without engineered stimulation.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 9
    Publication Date: 2015-05-29
    Description: Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 10
    Publication Date: 2015-05-31
    Description: This paper presents the results from the Deflo-hydroacoustic experiment in the Southern Indian Ocean using three autonomous underwater hydrophones, complemented by two permanent hydroacoustic stations. The array monitored for 14 months, from November 2006 to December 2007, a 3000 x 3000 km wide area, encompassing large segments of the three Indian spreading ridges that meet at the Indian Triple Junction. A catalogue of 11 105 acoustic events is derived from the recorded data, of which 55 per cent are located from three hydrophones, 38 per cent from 4, 6 per cent from five and less than 1 per cent by six hydrophones. From a comparison with land-based seismic catalogues, the smallest detected earthquakes are m b 2.6 in size, the range of recorded magnitudes is about twice that of land-based networks and the number of detected events is 5–16 times larger. Seismicity patterns vary between the three spreading ridges, with activity mainly focused on transform faults along the fast spreading Southeast Indian Ridge and more evenly distributed along spreading segments and transforms on the slow spreading Central and ultra-slow spreading Southwest Indian ridges; the Central Indian Ridge is the most active of the three with an average of 1.9 events/100 km/month. Along the Sunda Trench, acoustic events mostly radiate from the inner wall of the trench and show a 200-km-long seismic gap between 2 °S and the Equator. The array also detected more than 3600 cryogenic events, with different seasonal trends observed for events from the Antarctic margin, compared to those from drifting icebergs at lower (up to 50°S) latitudes. Vocalizations of five species and subspecies of large baleen whales were also observed and exhibit clear seasonal variability. On the three autonomous hydrophones, whale vocalizations dominate sound levels in the 20–30 and 100 Hz frequency bands, whereas earthquakes and ice tremor are a dominant source of ambient sound at frequencies 〈20 Hz.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 11
    Publication Date: 2015-05-31
    Description: Seismic reflections from the oceanic water column contain information about ocean temperature and salinity. Even though seismic waveform inversion is effective for studying oceanic structure, its application is limited in the absence of sufficient direct temperature/velocity measurements. Here, two methods are developed to invert pre-stack seismic waveform data for temperature and salinity when independent temperature/velocity data are sparse or unavailable, allowing estimation of water-column temperature/salinity from any marine seismic reflection data set. The first method combines a genetic algorithm (GA) with non-linear least squares inversion, and the second method is a parallel implementation of a GA. Both methods produce results to an accuracy between 0 and 0.1 °C in estimating temperature when applied to a field data set from the South China Sea. Although the second approach is superior, it is computationally demanding and requires large parallel computers. The first approach runs extremely fast on parallel computers and can even be run on much smaller machines to provide results in a reasonable runtime. While both methods are viable choices for estimating temperature and salinity, the choice of one over the other will largely depend upon the available computational resources and the time frame within which the inversion needs to be completed.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 12
    Publication Date: 2015-05-31
    Description: A new approach of seismoelectric imaging has been recently proposed to detect saturation fronts in which seismic waves are focused in the subsurface to scan its heterogeneous nature and determine saturation fronts. Such type of imaging requires however a complete modelling of the seismoelectric properties of porous media saturated by two immiscible fluid phases, one being usually electrically insulating (for instance water and oil). We combine an extension of Biot dynamic theory, valid for porous media containing two immiscible Newtonian fluids, with an extension of the electrokinetic theory based on the notion of effective volumetric charge densities dragged by the flow of each fluid phase. These effective charge densities can be related directly to the permeability and saturation of each fluid phase. The coupled partial differential equations are solved with the finite element method. We also derive analytically the transfer function connecting the macroscopic electrical field to the acceleration of the fast P wave (coseismic electrical field) and we study the influence of the water content on this coupling. We observe that the amplitude of the co-seismic electrical disturbance is very sensitive to the water content with an increase in amplitude with water saturation. We also investigate the seismoelectric conversions (interface effect) occurring at the water table. We show that the conversion response at the water table can be identifiable only when the saturation contrasts between the vadose and saturated zones are sharp enough. A relatively dry vadose zone represents the best condition to identify the water table through seismoelectric measurements. Indeed, in this case, the coseismic electrical disturbances are vanishingly small compared to the seismoelectric interface response.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 13
    Publication Date: 2015-05-26
    Description: With the enactment of Regulation (EC) No. 1924/2006, 20 December 2006, ‘ On nutrition and health claims made on foods ’ several health claims can no longer be used on food products in European markets. We simulate the overall impact of the regulation on consumers and producers using the Italian yogurt market as a case study, and data prior to the introduction of the policy. We quantify welfare losses incurred if accepted claims were false, and simulate scenarios where rejected truthful health claims are removed, considering also the case where the products carrying them exit the market. We find that consumers can incur large welfare losses if approved claims are untruthful; if truthful claims are instead denied both consumers and producers may incur losses, with consumers being penalised more than producers.
    Keywords: L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, M38 - Government Policy and Regulation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 14
    Publication Date: 2016-07-13
    Description: Rock permeability is an important parameter for the formation evaluation. In this paper, a new method with streaming current is proposed to determine the sample permeability based on the electrokinetic effects, and is proved by the experimental measurements. Corresponding to this method, we have designed an experimental setup and a test system, then performed the streaming current (potential) and electro-osmosis pressure experiments with 23 sandstone samples at 0.05 mol l –1 NaCl solution. The streaming current (potential) coefficient and electro-osmosis pressure coefficient are obtained, respectively, with the experimental data at low frequencies with AC lock-in technique. The electrokinetic permeabilities are further calculated with these coefficients. The results are consistent well with the gas permeability measured with Darcy's law, which verifies the current method for estimating rock permeability. Our measurements are also analysed and compared with previous measurements. The results indicate that our method can reflect the essence of electrokinetic effects better and simplify the electrokinetic measurements as well. In addition, we discuss the influences of experimental artefacts (core holder and confining pressure installation) on the electrokinetic data. The results show that the trough phenomenon, appeared in frequency curves of streaming current (potential) coefficients, is induced by the resonance of the core-holder/vibrator system. This is important for the design of electrokinetic setup and the analysis of low-frequency response of the electrokinetic coupling coefficients.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 15
    Publication Date: 2016-07-24
    Description: Multiparameter full waveform inversion (FWI) applied to an elastic orthorhombic model description of the subsurface requires in theory a nine-parameter representation of each pixel of the model. Even with optimal acquisition on the Earth surface that includes large offsets, full azimuth, and multicomponent sensors, the potential for trade-off between the elastic orthorhombic parameters are large. The first step to understanding such trade-off is analysing the scattering potential of each parameter, and specifically, its scattering radiation patterns. We investigate such radiation patterns for diffraction and for scattering from a horizontal reflector considering a background isotropic model. The radiation patterns show considerable potential for trade-off between the parameters and the potentially limited resolution in their recovery. The radiation patterns of C 11 , C 22 , and C 33 are well separated so that we expect to recover these parameters with limited trade-offs. However, the resolution of their recovery represented by recovered range of model wavenumbers varies between these parameters. We can only invert for the short wavelength components (reflection) of C 33 while we can mainly invert for the long wavelength components (transmission) of the elastic coefficients C 11 and C 22 if we have large enough offsets. The elastic coefficients C 13 , C 23 , and C 12 suffer from strong trade-offs with C 55 , C 44 , and C 66 , respectively. The trade-offs between C 13 and C 55 , as well as C 23 and C 44 , can be partially mitigated if we acquire P – SV and SV – SV waves. However, to reduce the trade-offs between C 12 and C 66 , we require credible SH – SH waves. The analytical radiation patterns of the elastic constants are supported by numerical gradients of these parameters.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 16
    Publication Date: 2016-07-25
    Description: Typically, seismic data are sparsely and irregularly sampled due to limitations in the survey environment and these cause problems for key seismic processing steps such as surface-related multiple elimination or wave-equation-based migration. Various interpolation techniques have been developed to alleviate the problems caused by sparse and irregular sampling. Among many interpolation techniques, matching pursuit interpolation is a robust tool to interpolate the regularly sampled data with large receiver separation such as crossline data in marine seismic acquisition when both pressure and particle velocity data are used. Multicomponent matching pursuit methods generally used the sinusoidal basis function, which have shown to be effective for interpolating multicomponent marine seismic data in the crossline direction. In this paper, we report the use of wavelet basis functions which further enhances the performance of matching pursuit methods for de-aliasing than sinusoidal basis functions. We also found that the range of the peak wavenumber of the wavelet is critical to the stability of the interpolation results and the de-aliasing performance and that the range should be determined based on Nyquist criteria. In addition, we reduced the computational cost by adopting the inner product of the wavelet and the input data to find the parameters of the wavelet basis function instead of using L-2 norm minimization. Using synthetic data, we illustrate that for aliased data, wavelet-based matching pursuit interpolation yields more stable results than sinusoidal function-based one when we use not only pressure data only but also both pressure and particle velocity together.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 17
    Publication Date: 2016-06-21
    Description: The goal of pathway analysis is to identify the pathways that are significantly impacted when a biological system is perturbed, e.g. by a disease or drug. Current methods treat pathways as independent entities. However, many signals are constantly sent from one pathway to another, essentially linking all pathways into a global, system-wide complex. In this work, we propose a set of three pathway analysis methods based on the impact analysis, that performs a system-level analysis by considering all signals between pathways, as well as their overlaps. Briefly, the global system is modeled in two ways: (i) considering the inter-pathway interaction exchange for each individual pathways, and (ii) combining all individual pathways to form a global, system-wide graph. The third analysis method is a hybrid of these two models. The new methods were compared with DAVID, GSEA, GSA, PathNet, Crosstalk and SPIA on 23 GEO data sets involving 19 tissues investigated in 12 conditions. The results show that both the ranking and the P -values of the target pathways are substantially improved when the analysis considers the system-wide dependencies and interactions between pathways.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 18
    Publication Date: 2016-06-23
    Description: Deep sea pockmarks underlain by chimney-like or pipe structures that contain methane hydrate are abundant along the Norwegian continental margin. In such hydrate provinces the interaction between hydrate formation and fluid flow has significance for benthic ecosystems and possibly climate change. The Nyegga region, situated on the western Norwegian continental slope, is characterized by an extensive pockmark field known to accommodate substantial methane gas hydrate deposits. The aim of this study is to detect and delineate both the gas hydrate and free gas reservoirs at one of Nyegga's pockmarks. In 2012, a marine controlled-source electromagnetic (CSEM) survey was performed at a pockmark in this region, where high-resolution 3-D seismic data were previously collected in 2006. 2-D CSEM inversions were computed using the data acquired by ocean bottom electrical field receivers. Our results, derived from unconstrained and seismically constrained CSEM inversions, suggest the presence of two distinctive resistivity anomalies beneath the pockmark: a shallow vertical anomaly at the underlying pipe structure, likely due to gas hydrate accumulation, and a laterally extensive anomaly attributed to a free gas zone below the base of the gas hydrate stability zone. This work contributes to a robust characterization of gas hydrate deposits within subseafloor fluid flow pipe structures.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 19
    Publication Date: 2016-05-06
    Description: One of the main applications of magnetic field measurements in boreholes is the detection of unexploded ordnance or buried utility structures like pipes or tiebacks. Even though the advantage of fully oriented magnetic vector measurements have long been recognized and could significantly reduce costs and risks, the tools used for those purposes typically measure only the total magnetic field, the vertical and horizontal components or gradients thereof. The Göttingen Bohrloch Magnetometer uses three fibre optic gyros to record its orientation and thus enables us to compute high-quality three-component magnetic vector data regardless of borehole orientation. The measurements described in this paper were run in the scientific borehole Cuxhaven Lüdingworth 1/1A, which was drilled as a part of the ‘Coastal Aquifer Test field’ project to study the dynamics of the saltwater/freshwater interface. As the drill string got stuck during drilling of the first borehole, a second hole was drilled in the immediate vicinity. The drill string lies at a depth between 80 and 114 m at a distance of only 2.5 m southeast of the borehole used for the measurements, making it an ideal target to demonstrate the benefits of vector magnetic surveys. Although the theories to calculate magnetic fields of objects with different shapes is well established and do not need to be tested, they almost exclusively include approximations of the geometry. It is not obvious whether these approximations are suited to describe real data, or whether additional effects or refinements have to be considered. We use both a simplified monopole model and a cylinder model to fit the data and are able to determine the position of the drill string within a statistical error of approximately 10 cm. Additionally, we show that the location of the drill string could not have been determined by measurements of the total field or its horizontal and vertical component alone and that those methods would require the drilling of additional boreholes to obtain an unambiguous result.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 20
    Publication Date: 2016-07-09
    Description: Bioinformatic analysis often produces large sets of genomic ranges that can be difficult to interpret in the absence of genomic context. Goldmine annotates genomic ranges from any source with gene model and feature contexts to facilitate global descriptions and candidate loci discovery. We demonstrate the value of genomic context by using Goldmine to elucidate context dynamics in transcription factor binding and to reveal differentially methylated regions (DMRs) with context-specific functional correlations. The open source R package and documentation for Goldmine are available at http://jeffbhasin.github.io/goldmine .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 21
    Publication Date: 2016-07-28
    Description: CCCTC-binding factor (CTCF) is a multi-functional protein that is assigned various, even contradictory roles in the genome. High-throughput sequencing-based technologies such as ChIP-seq and Hi-C provided us the opportunity to assess the multivalent functions of CTCF in the human genome. The location of CTCF-binding sites with respect to genomic features provides insights into the possible roles of this protein. Here we present the first genome-wide survey and characterization of three important functions of CTCF: enhancer insulator, chromatin barrier and enhancer linker. We developed a novel computational framework to discover the multivalent functions of CTCF based on chromatin state and three-dimensional chromatin architecture. We applied our method to five human cell lines and identified ~46 000 non-redundant CTCF sites related to the three functions. Disparate effects of these functions on gene expression were found and distinct genomic features of these CTCF sites were characterized in GM12878 cells. Finally, we investigated the cell-type specificities of CTCF sites related to these functions across five cell types. Our study provides new insights into the multivalent functions of CTCF in the human genome.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 22
    Publication Date: 2013-09-26
    Description: Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a collective signal composed of the aberrations of a mixed cell population of a tumor sample into its individual components are not available. We propose an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. We have developed an algorithm (TrAp) for solving this mixture problem. In silico analyses show that TrAp correctly deconvolves mixed subpopulations when the number of subpopulations and the measurement errors are moderate. We demonstrate the applicability of the method using tumor karyotypes and somatic hypermutation data sets. We applied TrAp to Exome-Seq experiment of a renal cell carcinoma tumor sample and compared the mutational profile of the inferred subpopulations to the mutational profiles of single cells of the same tumor. Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 23
    Publication Date: 2013-04-02
    Description: MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5' tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 24
    Publication Date: 2013-09-26
    Description: It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense–antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 25
    Publication Date: 2015-05-03
    Description: We analysed four newly retrieved tide gauge records of the 1998 July 17 Papua New Guinea (PNG) tsunami to study statistical and spectral properties of this tsunami. The four tide gauge records were from Lombrum (PNG), Rabaul (PNG), Malakal Island (Palau) and Yap Island (State of Yap) stations located 600–1450 km from the source. The tsunami registered a maximum trough-to-crest wave height of 3–9 cm at these gauges. Spectral analysis showed two dominant peaks at period bands of 2–4 and 6–20 min with a clear separation at the period of ~5 min. We interpreted these peak periods as belonging to the landslide and earthquake sources of the PNG tsunami, respectively. Analysis of the tsunami waveforms revealed 12–17 min delay in landslide generation compared to the origin time of the main shock. Numerical simulations including this delay fairly reproduced the observed tide gauge records. This is the first direct evidence of the delayed landslide source of the 1998 PNG tsunami which was previously indirectly estimated from acoustic T-phase records.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 26
    Publication Date: 2015-05-03
    Description: MicroRNAs (miRNAs) regulate gene expression by binding to partially complementary sequences on target mRNA transcripts, thereby causing their degradation, deadenylation, or inhibiting their translation. Genomic variants can alter miRNA regulation by modifying miRNA target sites, and multiple human disease phenotypes have been linked to such miRNA target site variants (miR-TSVs). However, systematic genome-wide identification of functional miR-TSVs is difficult due to high false positive rates; functional miRNA recognition sequences can be as short as six nucleotides, with the human genome encoding thousands of miRNAs. Furthermore, while large-scale clinical genomic data sets are becoming increasingly commonplace, existing miR-TSV prediction methods are not designed to analyze these data. Here, we present an open-source tool called SubmiRine that is designed to perform efficient miR-TSV prediction systematically on variants identified in novel clinical genomic data sets. Most importantly, SubmiRine allows for the prioritization of predicted miR-TSVs according to their relative probability of being functional. We present the results of SubmiRine using integrated clinical genomic data from a large-scale cohort study on chronic obstructive pulmonary disease (COPD), making a number of high-scoring, novel miR-TSV predictions. We also demonstrate SubmiRine's ability to predict and prioritize known miR-TSVs that have undergone experimental validation in previous studies.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 27
    Publication Date: 2015-05-10
    Description: For extensional wave propagation along a cylindrical pipe, there exists a natural stopband in the frequency range between the first and second modes. This study explores the feasibility and practicality of building a drill collar acoustic extensional-wave isolator by combining the stopbands of pipes of different thicknesses. Numerical modelling shows that this is indeed possible and a stopband of designated width can be obtained using an optimization procedure. Laboratory measurement on an optimized design further verified this concept. The result provides a viable approach for the acoustic isolation design of a logging while drilling acoustic tool.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 28
    Publication Date: 2015-05-12
    Description: China has long struggled to achieve food security. In the era of a planned economy, local self-sufficiency was dictated by policy. With China's transition to a market economy, however, different policy schemes have been utilized, with greater emphasis placed on the role of market forces, especially in conjunction with China's accession to the World Trade Organization in 2001. Nevertheless, self-sufficiency in grain production remains a deeply rooted goal, and interventionist measures geared towards its achievement are still viewed as the most direct and effective means of food security. This paper examines how the well-being of China's rural population, proxied by measures of food consumption, is affected by the promotion of grain production. Our findings suggest that targeted households bear a disproportionate burden of food security policy, as it is currently implemented.
    Keywords: O12 - Microeconomic Analyses of Economic Development, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 29
    Publication Date: 2015-05-12
    Description: Policymakers have dedicated increasing attention to whether Americans have access to healthful food. As a result, various methods for measuring food store access at the national level have been developed to identify areas that lack access. However, these methods face definitional, data, and methodological limitations. The focus on neighborhoods instead of individuals underestimates the barriers that some individuals face in accessing healthy food, and overestimates the problem in other neighborhoods. This paper reviews and critiques currently available national-level measures of food access. While multiple measures of food access are needed to understand the problem, we recommend greater attention be paid to individual measures of food store access.
    Keywords: I14 - Health and Inequality, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 30
    Publication Date: 2015-05-10
    Description: The Murray Ridge/Dalrymple Trough system forms the boundary between the Indian and Arabian plates in the northern Arabian Sea. Geodetic constraints from the surrounding continents suggest that this plate boundary is undergoing oblique extension at a rate of a few millimetres per year. We present wide-angle seismic data that constrains the composition of the Ridge and of adjacent lithosphere beneath the Indus Fan. We infer that Murray Ridge, like the adjacent Dalrymple Trough, is underlain by continental crust, while a thin crustal section beneath the Indus Fan represents thinned continental crust or exhumed serpentinized mantle that forms part of a magma-poor rifted margin. Changes in crustal structure across the Murray Ridge and Dalrymple Trough can explain short-wavelength gravity anomalies, but a long-wavelength anomaly must be attributed to deeper density contrasts that may result from a large age contrast across the plate boundary. The origin of this fragment of continental crust remains enigmatic, but the presence of basement fabrics to the south that are roughly parallel to Murray Ridge suggests that it separated from the India/Seychelles/Madagascar block by extension during early breakup of Gondwana.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 31
    Publication Date: 2015-05-12
    Description: The Canadian farm share for five crop-based products and seven livestock-based products from 1997 to 2010 is calculated using a supply chain IO analysis. Significant differences exist in farm shares across food commodities with higher farm shares for livestock products and lower farm shares for grain-based products. The decline in the Canadian farm share for food consumed at home is driven in large part by the food purchasing habits of consumers. This paper also addresses the hypothesis that the decline in the Canadian farm share could be partially driven by rising input costs in post-farmgate processes or rising input costs that have greater impact on downstream sectors than primary agricultural producers. Three experiments were conducted to assess the impact of an increase in the cost of corn, energy, and farm labor would have on commodity output prices, farm returns, food expenditure, and farm share. In all three cases, the overall farm share increases, albeit by a small amount, suggesting that these shocks have a larger relative impact on the prices of agricultural commodities than the prices of marketing commodities used in post-farmgate activities. A two-period comparison of these simulations shows that energy (corn and farm labour) price shocks would have had a greater (lower) impact on the farm share in 2007 than 1997.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 32
    Publication Date: 2015-05-12
    Description: Household food insecurity in the United States has reached its highest levels to date. As public and private initiatives have emerged to help improve diets by fostering access to food, the availability of more food stores may result in lower levels of food insecurity. In this article, we assess the relationship between adult food insecurity and food store density in metropolitan areas of the United States. We find that while small grocery/convenience stores show a mitigating effect on adult food insecurity across different samples of households, the effects of large supermarkets/grocery stores and supercenters vary. We also find that Supplemental Nutrition Assistance Program participation and food access can have a simultaneously beneficial effect in reducing adult food insecurity. Implications for policies aiming to improve food security by fostering access to food stores are discussed.
    Keywords: I14 - Health and Inequality, L81 - Retail and Wholesale Trade ; e-Commerce, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 33
    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 34
    Publication Date: 2015-01-24
    Description: Of the ~1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ~1300 Alu loci corresponding to detectable transcripts, with ~120 of them expressed in at least three cell lines. In vitro transcription of selected Alu s did not reflect their in vivo expression properties, and required the native 5'-flanking region in addition to internal promoter. We also identified a cluster of expressed Alu Ya5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu -unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alu s nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 35
    Publication Date: 2014-12-17
    Description: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 36
    Publication Date: 2015-04-12
    Description: In conventional marine seismic surveys, due to the time-delayed reflections from the sea surface on both source and receiver sides, ghosts present in recorded seismograms and lead to both phase and spectrum distortions (especially near certain frequency notches). To achieve a high-quality broad-band image/velocity model with conventional reverse time migration (RTM)/full waveform inversion (FWI) that adopts a synthetic zero-phase source wavelet and absorbing surface condition during wavefield modelling, marine seismic data have to be pre-processed to remove ghost effects. However, seismic deghosting is not a trivial task. Instead of employing an external deghosting process, we propose a strategy to compensate for ghost effects during FWI and RTM, which consists of two parts: first, to address phase distortions due to ghost effects by means of obtaining an accurate source wavelet estimation and adopting an appropriate surface boundary condition in both forward and backward wave propagation to appropriately generate ghosts; secondly, to build a compensation operator in the adjoint state computation to mitigate spectrum distortions caused by dominant ghost effects. To demonstrate the success and robustness of the proposed strategy, we present both synthetic experiments and field examples, which suggest that this strategy can lead to successful applications of FWI/RTM directly on marine seismic data without an extra deghosting process.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 37
    Publication Date: 2015-04-16
    Description: Seismic full waveform inversion (FWI) has been applied to simple elastic problems with certain symmetries, such as isotropic, transverse isotropic or vertical transversely isotropic media. In this study, the FWI concept is extended to the most general anisotropic case with 21 independent elastic material parameters and no symmetry plane (triclinic). Beside a short description of the 3-D finite-difference scheme to solve the forward problem and the FWI optimization algorithm, we present a sensitivity study for a simple anisotropic medium. This test problem consists of a homogenous triclinic anisotropic full space, which contains 21 spatially separated spheres. In each sphere one component of the elastic tensor deviates by 5 per cent from the background medium. The resolution of the different spheres, ambiguities between the different elastic parameters, as well as the effect of the acquisition geometry can be systematically investigated. Due to the high computational costs of the triclinic forward problem a few compromises have to be made regarding the acquisition geometries. Point sources are replaced by plane wave sources which lead to a limitation of incidence angles and therefore a strong decrease in resolution of the nondiagonal elastic tensor components. It is shown that, despite these limitations, a tomographic acquisition geometry would be able to resolve to some extent a monoclinic symmetry via FWI. Restricting the acquisition geometries (e.g. VSP combined with reflection seismic or reflection seismic only) significantly reduces the number of resolvable tensor elements in strict dependence of the covered incidence angles.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 38
    Publication Date: 2016-04-08
    Description: Existing methods for interpreting protein variation focus on annotating mutation pathogenicity rather than detailed interpretation of variant deleteriousness and frequently use only sequence-based or structure-based information. We present VIPUR, a computational framework that seamlessly integrates sequence analysis and structural modelling (using the Rosetta protein modelling suite) to identify and interpret deleterious protein variants. To train VIPUR, we collected 9477 protein variants with known effects on protein function from multiple organisms and curated structural models for each variant from crystal structures and homology models. VIPUR can be applied to mutations in any organism's proteome with improved generalized accuracy (AUROC .83) and interpretability (AUPR .87) compared to other methods. We demonstrate that VIPUR's predictions of deleteriousness match the biological phenotypes in ClinVar and provide a clear ranking of prediction confidence. We use VIPUR to interpret known mutations associated with inflammation and diabetes, demonstrating the structural diversity of disrupted functional sites and improved interpretation of mutations associated with human diseases. Lastly, we demonstrate VIPUR's ability to highlight candidate variants associated with human diseases by applying VIPUR to de novo variants associated with autism spectrum disorders.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 39
    Publication Date: 2015-12-29
    Description: This article empirically investigates the impact of trade barriers on the world wine trade focusing on trade costs impeding exports, including transport, tariffs, technical barriers and sanitary and phytosanitary (SPS) standards. A gravity model is estimated using data from the main importing and exporting countries for the years 1997–2010. The Poison pseudo-maximum likelihood estimator accounts for heteroskedasticity and the presence of zero trade flows. Our results identify which regulations can adversely affect trade providing useful information to policy-makers involved in negotiations on trade frictions. While SPS measures do not seem to obstruct exports, technical barriers have a varying impact on trade. A decreasing trend for tariffs has largely been compensated by more stringent technical barriers. The overall result is that frictions in the world wine trade have not changed during the past 15 years.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 40
    Publication Date: 2015-12-13
    Description: Non-linear resonant coupling of edge waves can occur with tsunamis generated by large-magnitude subduction zone earthquakes. Earthquake rupture zones that straddle beneath the coastline of continental margins are particularly efficient at generating tsunami edge waves. Using a stochastic model for earthquake slip, it is shown that a wide range of edge-wave modes and wavenumbers can be excited, depending on the variability of slip. If two modes are present that satisfy resonance conditions, then a third mode can gradually increase in amplitude over time, even if the earthquake did not originally excite that edge-wave mode. These three edge waves form a resonant triad that can cause unexpected variations in tsunami amplitude long after the first arrival. An M ~ 9, 1100 km-long continental subduction zone earthquake is considered as a test case. For the least-variable slip examined involving a Gaussian random variable, the dominant resonant triad includes a high-amplitude fundamental mode wave with wavenumber associated with the along-strike dimension of rupture. The two other waves that make up this triad include subharmonic waves, one of fundamental mode and the other of mode 2 or 3. For the most variable slip examined involving a Cauchy-distributed random variable, the dominant triads involve higher wavenumbers and modes because subevents, rather than the overall rupture dimension, control the excitation of edge waves. Calculation of the resonant period for energy transfer determines which cases resonant coupling may be instrumentally observed. For low-mode triads, the maximum transfer of energy occurs approximately 20–30 wave periods after the first arrival and thus may be observed prior to the tsunami coda being completely attenuated. Therefore, under certain circumstances the necessary ingredients for resonant coupling of tsunami edge waves exist, indicating that resonant triads may be observable and implicated in late, large-amplitude tsunami arrivals.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 41
    Publication Date: 2016-01-02
    Description: Although seismic attenuation measurements have great potential to enhance our knowledge of physical conditions and rock properties, their application is limited because robust methods for improving both the resolution and accuracy of attenuation estimates have not yet been established. We propose attenuation estimation methods for zero-offset vertical seismic profile (VSP) data by combining seismic interferometry (SI) and the modified median frequency shift (MMFS) method developed for attenuation estimation using sonic waveform data. The configuration of zero-offset VSP data is redatumed to that of the sonic logging measurement by adopting two types of SI: deconvolution interferometry and crosscorrelation interferometry (CCI). Then, we can apply the MMFS method to the redatumed VSP data. Although the amplitude information estimated from CCI is biased, we propose a correction method for this bias to correctly estimate attenuation. First, to investigate the performance both in resolution and accuracy, we apply different trace separations to synthetic data with random noise at different signal-to-noise ratio levels. Second, we estimate the influence of residual reflection events after wavefield separation on attenuation estimation. The proposed methods provide more stable attenuation estimates in comparison with the spectral ratio method because the mean-median procedure suppresses random events and characteristic features caused by residual reflection events in spectral domain. Our numerical experiments also imply that the proposed methods can estimate scattering attenuation values even if frequency components are not changed between the two receiver depths. Finally, by preliminarily applying the proposed methods to field VSP data, we demonstrate the advantages of the proposed method in the resolution and stability of attenuation estimates and these observations correlate with those of numerical tests.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 42
    Publication Date: 2015-06-17
    Description: One interpretation of a seismic image is the instantaneous scattered wave response of a colocated pseudo-source and pseudo-receiver at each point in the subsurface model. If there is no model perturbation at a point then there will be no instantaneous scattered wave so nothing will be imaged; if something is imaged then there must be a perturbation at that location. By extension, so-called extended images (EIs) represent the full spatio-temporal response between offset subsurface pseudo-sources and pseudo-receivers which can be used to constrain elastic properties around each image point. However, one-sided illumination of the subsurface (from the Earth's surface), errors in the initial velocity model estimate, and the use of a linearized, single-scattering assumption (as is usual in seismic imaging) cause errors in EI gathers such as missing events, incorrect amplitudes, and spurious energy. By creating elastic (P-to-P and P-to-S) EIs in a synthetic example of subsalt imaging, we demonstrate the advantages of incorporating multiply scattered waves correctly by non-linear imaging, and of including transmitted waves by using two-sided receiver arrays, and discuss how the recently developed autofocussing methods could provide us with the various required subsurface wavefields. Pre- and post-imaging f–k filtering procedures are introduced to further improve the quality of the EIs by (explicitly or implicitly) limiting the directions of waves arriving at the subsurface pseudo-source and receiver survey line. These filters suppress strong linear events that arise from the erroneous interaction of near-horizontally propagating waves which are not naturally accounted for due to the lack of sources and receivers on either side of the imaging target. Finally, we analyse the sensitivity of elastic P-to-P EIs to errors in the migration velocity models and show that events in the EI are shifted in opposite directions when constructed using reflection or transmission data. In other words, velocity errors are mapped into the EIs differently in the case of one-sided from two-sided illumination. This leads to the potential for new methods of migration velocity analysis when surface and borehole seismic data are jointly acquired.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 43
    Publication Date: 2015-08-08
    Description: Uncertainty estimation is a vital part of geophysical numerical modelling. There exist a variety of methods aimed at uncertainty estimation, which are often complicated and difficult to implement. We present an inversion technique that produces multiple solutions, based on bootstrap resampling, to create a qualitative uncertainty measure for 2-D magnetotelluric inversion models. The approach is easy to implement, can be used with almost any inversion code, and does not require access to the inversion software's source code. It is capable of detecting the effect of data uncertainties on the model result rather than just analysing the effect of model variations on the model response. To obtain uncertainty estimates for an inversion model, the original data set is resampled repeatedly and alternate data set realizations are created and inverted. This ensemble of solutions is then statistically analysed to determine the variability between the different solutions. The process yields interpretable uncertainty maps for the inversion model and we demonstrate its effectiveness to qualitatively quantify uncertainty in synthetic model tests and a case study.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 44
    Publication Date: 2015-08-30
    Description: Electromagnetic (EM) imaging methods are useful tools for monitoring subsurface changes in pore-fluid content and the associated changes in electrical permittivity and conductivity. The most common method for georadar tomography uses a high frequency ray-theoretic approximation that is valid when material variations are sufficiently small relative to the wavelength of the propagating wave. Georadar methods, however, often utilize EM waves that propagate within heterogeneous media at frequencies where ray theory may not be applicable. In this paper we describe EM wave propagation 3-D Fréchet sensitivity kernels that capture the data sensitivity to material perturbations for a given source–receiver combination. Various data functional types are formulated that consider all three components of the electric wavefield and incorporate near-, intermediate- and far-field contributions. We show that EM waves exhibit substantial variations for different relative source–receiver component orientations. The 3-D sensitivities also illustrate out of plane effects that are not captured in 2-D sensitivity kernels and can influence results obtained using 2-D inversion methods to image structures that are in reality 3-D.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 45
    Publication Date: 2015-10-22
    Description: This paper focuses on the modelling of fluid-filled poroelastic double porosity media under quasi-static and dynamic regimes. The double porosity model is derived from a two-scale homogenization procedure, by considering a medium locally characterized by blocks of poroelastic Biot microporous matrix and a surrounding system of fluid-filled macropores or fractures. The derived double porosity description is a two-pressure field poroelastic model with memory and viscoelastic effects. These effects result from the ‘time-dependent’ interaction between the pressure fields in the two pore networks. It is shown that this homogenized double porosity behaviour arises when the characteristic time of consolidation in the microporous domain is of the same order of magnitude as the macroscopic characteristic time of transient regime. Conversely, single porosity behaviours occur when both timescales are clearly distinct. Moreover, it is established that the phenomenological approaches that postulate the coexistence of two pressure fields in ‘instantaneous’ interaction only describe media with two pore networks separated by an interface flow barrier. Hence, they fail at predicting and reproducing the behaviour of usual double porosity media. Finally, the results are illustrated for the case of stratified media.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 46
    Publication Date: 2015-07-09
    Description: The Okavango Delta of northern Botswana is one of the world's largest inland deltas or megafans. To obtain information on the character of sediments and basement depths, audiomagnetotelluric (AMT), controlled-source audiomagnetotelluric (CSAMT) and central-loop transient electromagnetic (TEM) data were collected on the largest island within the delta. The data were inverted individually and jointly for 1-D models of electric resistivity. Distortion effects in the AMT and CSAMT data were accounted for by including galvanic distortion tensors as free parameters in the inversions. By employing Marquardt–Levenberg inversion, we found that a 3-layer model comprising a resistive layer overlying sequentially a conductive layer and a deeper resistive layer was sufficient to explain all of the electromagnetic data. However, the top of the basal resistive layer from electromagnetic-only inversions was much shallower than the well-determined basement depth observed in high-quality seismic reflection images and seismic refraction velocity tomograms. To resolve this discrepancy, we jointly inverted the electromagnetic data for 4-layer models by including seismic depths to an interface between sedimentary units and to basement as explicit a priori constraints. We have also estimated the interconnected porosities, clay contents and pore-fluid resistivities of the sedimentary units from their electrical resistivities and seismic P -wave velocities using appropriate petrophysical models. In the interpretation of our preferred model, a shallow ~40 m thick freshwater sandy aquifer with 85–100 m resistivity, 10–32 per cent interconnected porosity and 〈13 per cent clay content overlies a 105–115 m thick conductive sequence of clay and intercalated salt-water-saturated sands with 15–20 m total resistivity, 1–27 per cent interconnected porosity and 15–60 per cent clay content. A third ~60 m thick sandy layer with 40–50 m resistivity, 10–33 per cent interconnected porosity and 〈15 per cent clay content is underlain by the basement with 3200–4000 m total resistivity. According to an interpretation of helicopter TEM data that cover the entire Okavango Delta and borehole logs, the second and third layers may represent lacustrine sediments from Paleo Lake Makgadikgadi and a moderately resistive freshwater aquifer comprising sediments of the recently proposed Paleo Okavango Megafan, respectively.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 47
    Publication Date: 2015-07-10
    Description: In many developing countries, supermarkets are expanding rapidly. This affects farmers’ marketing options. Previous studies have analyzed welfare effects of smallholder participation in supermarket channels from a static perspective, using cross-section data. We develop a conceptual framework and use panel data to better understand participation and impact dynamics. The analysis focuses on vegetable producers in Kenya. Participation in supermarket channels is associated with income gains. However, many farmers have dropped out of the supermarket channel due to various constraints. The initial income gains cannot be sustained when returning to the traditional market. Organizational support may be needed to avoid widening income disparities.
    Keywords: L24 - Contracting Out ; Joint Ventures ; Technology Licensing, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 48
    Publication Date: 2015-07-15
    Description: Although the importance of diet quality for improving child health is widely recognized, the roles of environmental factors and the absorption of nutrients for children's physical growth and morbidity have not been adequately integrated into a policy framework. Moreover, nutrient intakes gradually affect child health, so it is helpful to use alternative tools to evaluate short-term interventions versus long-term food policies. This article emphasizes the role of diet quality reflected in the intake of nutrients such as protein, calcium, and iron for children's physical growth. Vitamins A and C are important for reducing morbidity. Children's growth and morbidity affect their cognitive development, which is critical for the future supply of skilled labor and economic growth. Evidence on these issues from countries such as Bangladesh, India, Kenya, the Philippines, and Tanzania is summarized. The supply of nutritious foods is appraised from the viewpoint of improving diet quality. Finally, the roles of educational campaigns and indirect taxes on unhealthy processed foods consumed by the affluent in developing countries are discussed.
    Keywords: O12 - Microeconomic Analyses of Economic Development, I15 - Health and Economic Development, I25 - Education and Economic Development, J10 - General, Q01 - Sustainable Development, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0257-3032
    Electronic ISSN: 1564-6971
    Topics: Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 49
    Publication Date: 2015-03-27
    Description: Interpolation and random noise removal is a pre-requisite for multichannel techniques because the irregularity and random noise in observed data can affect their performances. Projection Onto Convex Sets (POCS) method can better handle seismic data interpolation if the data's signal-to-noise ratio (SNR) is high, while it has difficulty in noisy situations because it inserts the noisy observed seismic data in each iteration. Weighted POCS method can weaken the noise effects, while the performance is affected by the choice of weight factors and is still unsatisfactory. Thus, a new weighted POCS method is derived through the Iterative Hard Threshold (IHT) view, and in order to eliminate random noise, a new adaptive method is proposed to achieve simultaneous seismic data interpolation and denoising based on dreamlet transform. Performances of the POCS method, the weighted POCS method and the proposed method are compared in simultaneous seismic data interpolation and denoising which demonstrate the validity of the proposed method. The recovered SNRs confirm that the proposed adaptive method is the most effective among the three methods. Numerical examples on synthetic and real data demonstrate the validity of the proposed adaptive method.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 50
    Publication Date: 2016-07-04
    Description: Capacitively Coupled Resistivity (CCR) is conventionally used to emulate DC resistivity measurements and may provide important information about the ice content of material in periglacial areas. The application of CCR theoretically enables the determination of both electrical parameters, that is, the resistivity and the electrical permittivity, by analysing magnitude and phase shift spectra. The electrical permittivity may dominate the impedance, especially in periglacial areas or regions of hydrogeological interest. However, previous theoretical work suggested that the phase shift may strongly depend on electrode height above ground, implying that electrode height must be known with great accuracy to determine electrical permittivity. Here, we demonstrate with laboratory test measurements, theoretical modelling and by analysing the Jacobian matrix of the inversion that the sensitivity towards electrode height is drastically reduced if the electrical permittivity is frequency dependent in a way that is typical for ice. For the first time, we used a novel broad-band CCR device ‘Chameleon’ for a field test located in one of the ridge galleries beneath the crest of Mount Zugspitze. A permanently ice covered bottom of a tunnel was examined. For the inversion of the measured spectra, the frequency dependence of the electrical parameters was parametrized in three different ways: A Debye Model for pure ices, a Cole–Cole Model for pure ices and a dual Cole–Cole Model including interfacial water additionally. The frequency-dependent resistivity and permittivity spectra obtained from the inversion, including low- and high-frequency limits, agree reasonably well with laboratory and field measurements reported in the literature.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 51
    Publication Date: 2016-07-06
    Description: We evaluate the applicability and the effectiveness of GPR attribute analysis for high-resolution glacier imaging and characterization, testing this approach on 4-D GPR multifrequency data collected in a small glacier in the Eastern Alps, by repeating the acquisition along the same profiles in four different periods of the year 2013. The main objectives are to image and characterize the glacier's inner structure and to quantitatively monitor the seasonal thawing of near-surface frozen materials (snow/firn). A multiattribute approach is used to characterize the subsurface through different attribute categories, including instantaneous and textural attributes considering not only amplitude-, phase- and frequency-related attributes, but also other more complex and integrated parameters. We combine information from more than one attribute into a single image with composite displays, using overlays or mixed displays. The results demonstrate that the developed GPR attribute analysis can provide significant improvements in the discrimination of GPR signals, and obtain enhanced and more constrained data interpretations.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 52
    Publication Date: 2016-08-27
    Description: Migration velocity analysis aims at automatically updating the large-scale components of the velocity model, called macromodel. Extended Common Image Gathers are panels used to evaluate focusing after imaging and are constructed as a function of a spatial shift introduced in the imaging condition. We investigate how transmitted waves can also be used in migration velocity analysis: instead of back-propagating the residuals associated with reflected waves, we propose to back-propagate the full wavefield. The image function, equivalent to the migrated section for reflected data, does not exhibit localized events in space along horizons but is still sensitive to the choice of the background velocity model and can thus be coupled to the same objective function defined in the image domain. In order to enhance the benefits of direct waves, we consider a cross-well configuration. Direct waves provide a large illumination between two vertical wells. Associated Common Image Gathers present different characteristics than the ones associated with reflected waves in surface acquisition. In particular, energy is spread over up to the maximum penetration depth. We invert cross-well seismic data along two lines. In the first case, the input data contain the full wavefield dominated by transmitted waves. It demonstrates the possibility to handle transmitted waves to determine the velocity model. It appears that the misfit in the data domain is largely reduced after inversion. In the second case, we use the same algorithm, but with reflected observed data only, as in a classical approach. Most of velocity updates are localized around the reflectivity, leading to an incorrect final model. This demonstrates the benefit of transmitted waves for migration velocity analysis in a cross-well configuration.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 53
    Publication Date: 2016-06-30
    Description: An integrated approach to interpret Self-Potential (SP) anomalies based on spectral analysis and tomographic methods is presented. The Maximum Entropy Method (MEM) is used for providing accurate estimates of the depth of the anomaly source. The 2-D tomographic inversion technique, based on the underground charge occurrence probability (COP) function, is, then, used to fully characterize the anomalous body, as the MEM is not helpful in delineating the shape of the anomaly source. The proposed integrated approach is applied for the inversion of synthetic SP data generated by geometrically simple anomalous bodies, such as cylinders and inclined sheets. This numerical study has allowed the determination of mathematical relationships between zero lines of the COP distributions, the polarization angles and the positions along the profile of the causative sources, which have been of great help for interpreting the related SP anomalies. Finally, the analysis of field examples shows the high potential applicability of the proposed integrated approach for SP data inversion.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 54
    Publication Date: 2016-07-03
    Description: Volcanic and tectonic events are the main processes involved in the generation of the oceanic crust and responsible for the seismicity associated with seafloor spreading. To monitor this activity, usually not or poorly detected by land-based seismological stations, we deployed from February 2012 to February 2013 a network of autonomous hydrophones to compare the behaviour of the ultraslow-spreading Southwest Indian ridge (SWIR) with that of the intermediate-spreading Southeast Indian ridge (SEIR). The rate of seismicity is similar for both ridges, suggesting that there is no systematic relationship between seismicity and spreading rates. The along-axis distribution of the seismic events, however, does differ, reflecting the rate dependence of accretion modes. Earthquakes are sparse and regularly spaced and scattered along the SWIR, reflecting prevailing tectonic processes. By contrast, along the SEIR, events are irregularly distributed and focus at ridge-segment ends and transforms faults, reflecting the ridge segmentation; only two swarms occurred at a segment centre and are probably caused by a magmatic event. This seismicity distribution thus looks controlled by segment-scale crustal heterogeneities along the SEIR and by regional-scale contrasting accretion processes along the SWIR, probably driven by different lithospheric and asthenospheric dynamics on either side of the Melville fracture zone. The comparison of hydroacoustic and teleseismic catalogues shows that, along these spreading ridges, the background seismicity observed in 1 yr by a hydroacoustic network is representative of the seismicity observed over two decades by land-based networks.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 55
    Publication Date: 2016-08-20
    Description: Concerns about the growing prevalence of obesity worldwide have led researchers and policy makers to investigate the potential health impact of fiscal policies such as taxes on unhealthy foods. A common instrument used to measure the relationship between food prices and food consumption is the price elasticity of demand. Using meta-regression analysis we assessed how differences in methodological approaches to estimating demand affected food price elasticities. Most methodological differences had a statistically significant impact on elasticity estimates, which stresses the importance of using meta-estimates or testing the sensitivity of simulation outcomes to a range of elasticity parameters before drawing policy conclusions.
    Keywords: D11 - Consumer Economics: Theory, H31 - Household, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 56
    Publication Date: 2015-09-30
    Description: Frequency-domain loop–loop electromagnetic (EM) methods are sensitive to the magnetic susceptibility of the Earth as well as its resistivity. Thus, inversion techniques have been used to simultaneously reconstruct both resistivity and susceptibility models from EM data. However, to take full advantage of inversion methods, calibration errors must be assessed and removed because ignoring them can result in misleading models. We present a multidimensional inversion method that jointly inverts EM and direct current (DC) resistivity data to derive offset errors as well as resistivity and susceptibility models, assuming that calibration errors can be represented by in-phase and quadrature offsets at each frequency. Addition of independent data such as DC data is effective for more accurately estimating the offsets, resulting in more reliable subsurface models. Synthetic examples involving small-loop EM data show that simultaneous inversion for resistivity and susceptibility is not stable, because of strong correlations between in-phase offset parameters and background susceptibility, but that the offsets are well determined when the data misfit is reduced rapidly in the early iteration step. Improvements achieved by joint inversion are mainly on the resistivity model. For airborne electromagnetic (AEM) data, the inversion process is stable, because AEM data are acquired using more loop–loop geometries and a wider range of frequencies. As a result, both the resistivity and susceptibility models are significantly improved by joint inversion.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 57
    Publication Date: 2015-10-15
    Description: Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro , are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein–protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 58
    Publication Date: 2015-10-22
    Description: We have developed an efficient numerical scheme for 3-D electromagnetic (EM) simulations using an exponential finite-difference (FD) method with non-uniform grids. The method uses the set of exponential basis functions {1, exp [ ± ( x x + y y + z z )]}, where the exponents x , y and z must be chosen carefully depending on the simulation frequency and local node conductivity. The method achieves an approximation of the oscillatory and exponentially decaying EM fields that is better than that obtained via the low-degree polynomial fitting from standard FDs—and hence also leads to more accurate results. An important property of the exponential FD method is that it tends to the standard FD method when the exponents x , y and z tend to zero. We applied the standard and exponential FD methods to three marine controlled-source EM modelling scenarios: deep-water, shallow-water and intermediate water depth. For the deep-water scenario, we found that the proposed exponential FD method gave two to three times more accurate results as compared to the standard FD method on the same grid. For the shallow-water and intermediate water depth scenarios, the exponential FD method improved the accuracy of the upgoing fields; it gave 2–2.5 times more accurate results for the upgoing fields than the standard FD method on the same grid. Consequently, the method can achieve the same accuracy with a coarser grid and hence is faster than the standard FD method, as demonstrated using a frequency-domain iterative solver.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 59
    Publication Date: 2015-10-22
    Description: Rocks in nature are multiphase composites of minerals and fluids with varying elastic properties. Predicting the effects that geochemical and geological processes, which lead to removal, alteration or substitution of one or more phases, have on seismic velocities is of considerable practical interest in geophysics. We present a new theory that quantifies the effect of replacing ‘one' or ‘more' phases (fluid or solid) on the elastic properties of multimineralic isotropic rocks. These new exact solutions relax the assumption of unchanging rock microstructure upon substitution of the pore-filling material. By developing equations that do not depend on this assumption, which is fundamental to conventional substitution theories, for example, Biot–Gassmann theory, we expand their range of applicability. Since the new exact solutions require usually unknown parameters, we also develop approximations that depend only on initial effective stiffness, elastic properties and volume fractions of constituents.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 60
    Publication Date: 2016-06-03
    Description: Geothermal well GRT-1 (Rittershoffen, Alsace) was drilled in 2012. Its open-hole section (extending down to a depth of 2.6 km) penetrated fractured sandstones and granite. In 2013, the well was subjected to Thermal, Chemical and Hydraulic (TCH) stimulation, which improved the injectivity index fivefold. The goal of the study was to assess the impact of the stimulation by comparing pre- and post-stimulation well-logging (acoustic and temperature [ T ] logs) and mud-logging data. This comparison revealed modifications of almost all the natural fractures. However, not all of these fractures are associated with permeability enhancement, and the post-stimulation T logs are important for characterizing this enhancement. Chemical alteration due to mechanical erosion at the tops and bottoms of the fractures was observed in the sandstones. These zones display indications of very small new permeability after the TCH stimulation. Because a major fault zone caved extensively where it crosses the borehole, it was not imaged in the acoustic logs. However, this originally permeable zone was enhanced as demonstrated by the T logs. Based on the natural injectivity of this fault zone, hydraulic erosion and thermal microcracking of its internal quartz veins are associated with this permeability enhancement. Although local changes in the borehole wall observed in the acoustic images cannot be directly linked to the improved injectivity index, the comparison of the acoustic image logs allows for identification of fracture zones impacted by the TCH stimulation.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 61
    Publication Date: 2016-06-03
    Description: We investigate the spatial coherence of underwater ambient noise using a yearlong time-series measured off Ascension Island. Qualitative agreement with observed cross-correlations is achieved using a simple range-dependent model, constrained by earlier, active tomographic studies in the area. In particular, the model correctly predicts the existence of two weakly dispersive normal modes in the microseism frequency range, with the group speed of one of the normal modes being smaller than the sound speed in water. The agreement justifies our interpretation of the peaks of the measured cross-correlation function of ambient noise as modal arrivals, with dispersion that is sensitive to crustal velocity structure. Our observations are consistent with Scholte to Moho head wave coupled propagation, with double mode conversion occurring due to the bathymetric variations between receivers. We thus demonstrate the feasibility of interrogating crustal properties using noise interferometry of moored hydrophone data at ranges in excess of 120 km.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 62
    Publication Date: 2016-06-03
    Description: Recent tectonic reconstructions of the South Atlantic have partitioned the ocean basin into several segments based upon one or more proposed intraplate South American deformation zones. In several of these reconstructions, opening of the southern segment(s) by seafloor spreading prior to Aptian-Albian time is accompanied by contemporaneous strike-slip motion along an intraplate boundary extending southeastward from the Andean Cochabamba—Santa Cruz bend to the Rio Grande Fracture Zone (RGFZ). We have examined new magnetic data over the Pelotas, Santos and Campos Basins, offshore Argentina and Brazil, acquired by ION-GXT in tandem with long-offset, long record seismic reflection data, and identified seafloor spreading anomalies M4, M3, M2 and M0 (~131, ~129, ~128 and ~125 Ma). Integrating these results with our earlier work, we have been able to correlate magnetochrons M4, M3, M2 and M0 north and south of the RGFZ on the South American margin, and north and south of the Walvis Ridge on the African side. Our results are therefore inconsistent with diachronous opening models that involve substantial continental strike-slip motion north of RGFZ during M4 to M0 time. Although the ocean basin may have opened from south to north, our results indicate that seafloor spreading began north of the RGFZ earlier than previously proposed.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 63
    Publication Date: 2016-06-03
    Description: The sequential chain of interactions altering the binary state of a biomolecule represents the ‘information flow’ within a cellular network that determines phenotypic properties. Given the lack of computational tools to dissect context-dependent networks and gene activities, we developed NetDecoder, a network biology platform that models context-dependent information flows using pairwise phenotypic comparative analyses of protein–protein interactions. Using breast cancer, dyslipidemia and Alzheimer's disease as case studies, we demonstrate NetDecoder dissects subnetworks to identify key players significantly impacting cell behaviour specific to a given disease context. We further show genes residing in disease-specific subnetworks are enriched in disease-related signalling pathways and information flow profiles, which drive the resulting disease phenotypes. We also devise a novel scoring scheme to quantify key genes—network routers, which influence many genes, key targets, which are influenced by many genes, and high impact genes, which experience a significant change in regulation. We show the robustness of our results against parameter changes. Our network biology platform includes freely available source code ( http://www.NetDecoder.org ) for researchers to explore genome-wide context-dependent information flow profiles and key genes, given a set of genes of particular interest and transcriptome data. More importantly, NetDecoder will enable researchers to uncover context-dependent drug targets.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 64
    Publication Date: 2016-08-20
    Description: This paper reviews the situation in the agricultural sector and food security in Cuba, and particularly the transformations that have (not) taken place since 1990. We compare the Cuban transition with transitions in other "transition countries" and show that Cuba does not easily fit into one of the transition patterns, and, in a way, has characteristics of "a bit of everything". To conclude, we discuss the (potential) effects of the recent policy changes and the new economic reforms that were announced.
    Keywords: O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, P21 - Planning, Coordination, and Reform, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 65
    Publication Date: 2016-08-21
    Description: Determining thin layer thickness is very important for reservoir characterization and CO 2 quantification. Given its high time–frequency resolution and robustness, the complex spectral decomposition method was applied on time-lapse 3-D seismic data from the Ketzin pilot site for CO 2 storage to evaluate the frequency-dependent characteristics of thin layers at the injection level. Higher temporal resolution and more stratigraphic details are seen in the all-frequency and monochromatic reflectivity amplitude sections obtained by complex spectral decomposition compared to the stacked sections. The mapped geologic discontinuities within the reservoir are consistent with the preferred orientation of CO 2 propagation. Tuning frequency mapping shows the thicknesses of the reservoir sandstone and gaseous CO 2 is consistent with the measured thickness of the sandstone unit from well logging. An attempt to discriminate between pressure effects and CO 2 saturation using the extracted tuning frequency indicates that CO 2 saturation is the main contributor to the amplitude anomaly at the Ketzin site. On the basis of determined thickness of gaseous CO 2 in the reservoir, quantitative analysis of the amount of CO 2 was performed and shows a discrepancy between the injected and calculated CO 2 mass. This may be explained by several uncertainties, like structural reservoir heterogeneity, a limited understanding of the complex subsurface conditions, error of determined tuning frequency, the presence of ambient noise and ongoing CO 2 dissolution.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 66
    Publication Date: 2016-07-09
    Description: If agricultural subsidies are largely capitalized into farmland values through their effect on rental rates, then expanding support for agriculture may not benefit farmers who rent the land they farm. Existing evidence on the incidence of subsidies on cash rental rates is mixed. Identification is obscured by unobserved or imprecisely measured factors that tend to be correlated with subsidies, especially land quality and time-varying factors like commodity prices and adverse weather events. A problem that has received less attention is the fact that subsidies and land quality on rented land may differ from owned land. Since most farms possess both rented and owned acreage, farm-level measures of subsidies, land values, and rental rates may bias estimated incidence. Using a new, field-level data set that, for the first time, precisely links subsidies to land parcels, we show that this bias is considerable: where farm-level estimates suggest an incidence of 42–49 cents of the marginal subsidy dollar, field-level estimates from the same farms indicate that landlords capture just 20–28 cents. The size of the farm and the duration of the rental arrangement have substantial effects. Incidence falls by 5–15 cents when doubling total operated acres, and the incidence falls by 0.1–0.8 cents with each additional year of the rental arrangement. Low incidence of subsidies on rents combined with the farm-size and duration effects suggest that farmers renting land have monopsony power.
    Keywords: H22 - Incidence, Q14 - Agricultural Finance, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 67
    Publication Date: 2016-07-09
    Description: Many countries adjust their trade policies counter-cyclically with food prices, to the extent that the use of restrictions by food-exporting countries has occasionally threatened the food security of food-importing countries. These trade policies are inconsistent with the terms-of-trade motivation often retained to characterize the payoff frontier of self-enforcing trade agreements, as they can worsen the terms of trade of the countries that apply them. This article analyzes trade policy coordination when trade policies are driven by terms-of-trade effects and a desire to reduce domestic food price volatility. This framework implies that importing and exporting countries have incentives to deviate from cooperation at different periods: the latter when prices are high and the former when prices are low. Since staple food prices tend to have asymmetric distributions, with more prices below than above the mean but with occasional spikes, a self-enforcing agreement generates asymmetric outcomes. Without cooperation, an importing country uses its trade policy more frequently because of the concentration of prices below the mean, but an exporting country has a greater incentive to deviate from a cooperative trade policy because positive deviations from the mean price are larger than negative ones. Thus, the asymmetry of the distribution of commodity prices can make it more difficult to discipline export taxes than tariffs in trade agreements.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 68
    Publication Date: 2016-06-25
    Description: Comprehensive analytical solutions to 3-D axisymmetric problems for static response of multilayered thermoelastic media subjected to surface loads and containing sources are presented in this study. The solution strategy employs Laplace and Hankel transforms to the field variables. The problem is formulated in cylindrical coordinate system and in this coordinate system vector surface harmonics and generalized propagator matrix are introduced to find the solution for the problem for the behaviour of thermoelastic multilayered media subject to surface loads and containing heat sources. A high-order adaptive Gaussian quadrature method with continued fraction expansions is employed to approximate the integral solutions expressed in terms of semi-infinite Hankel-type integrals. It is the first time to apply the proposed solution method to investigate the behaviour of repository for heat-emitting high-level nuclear waste (HLW) in a geological formation where the HLW can be regarded as a decaying with time point heat source.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 69
    Publication Date: 2016-07-09
    Description: We analyze the effects of the interactions that the two pillars of the European Union Common Agricultural Policy—market support and rural development—have on farmers’ uptake of organic farming practices. Special attention is given to the 2003 reform, which substantially altered the relative importance of the two types of support by decoupling direct agricultural payments from the production of a specific crop. In our empirical analysis we study the case of Sweden, making use of the variation in the timing of farmers’ decisions regarding participation in support programs. We estimate a dynamic non-linear unobserved effects probit model to account for unobserved individual heterogeneity and state dependence. Our results indicate the existence of a negative effect of the market support system in place when organic farming techniques were adopted before the 2003 reform. However, this effect is reversed by the introduction of decoupling. Furthermore, the effects of support differ between certified and non-certified organic production: both pillars have significant effects on non-certified organic farming, whereas certified organic farming is exclusively driven by agro-environmental subsidies.
    Keywords: C23 - Models with Panel Data, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 70
    Publication Date: 2015-04-19
    Description: We present 1D anisotropic inversion of magnetotelluric (MT) data as a potential tool for mapping structural permeability in sedimentary basins. Using 1D inversions of a 171 site, broadband MT data set from the Koroit region of the Otway Basin, Victoria, Australia, we have delineated an electrically anisotropic layer at approximately 2.5 to 3.5 km depth. The anisotropy strike is consistent between stations at approximately 160° east of north. The depth of anisotropy corresponds to the top depth of the Lower Cretaceous Crayfish Group, and the anisotropy factor increases from west to east. We interpret the anisotropy as resulting from north–northwest oriented, fluid-filled fractures resulting in enhanced electrical and hydraulic conductivity. This interpretation is consistent with permeability data from well formation tests. It is also consistent with the orientation of mapped faults in the area, which are optimally oriented for reactivation in the current stress field.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 71
    Publication Date: 2015-04-21
    Description: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 72
    Publication Date: 2015-05-20
    Description: A recent paper by Tarasov and Titov suggested that the Cole–Cole conductivity models should be preferred to the Pelton resistivity model in fitting induced polarization responses. Each model has four parameters: resistivity (or its inverse conductivity ), chargeability m , time parameter and frequency dependence c . Tarasov and Titov showed that in fitting experimental data, 3 of the parameters directly correspond across the two formulations, but that there is a difference between the Pelton and Cole–Cole model in that parameter is only the same at low frequency, but is an entangled function with m and c at high frequencies in the Pelton formulation. This claim of inconsistent was based on using the Pelton complex resistivity formulation and the Cole–Cole complex conductivity equation to analyse complex conductivity data as a function of frequency. However, if Pelton and Cole–Cole models are used to fit complex resistivity, rather than fitting conductivity, then it is the Cole–Cole model that has an entangled parameter at high chargeability m values. Simple testing shows that a Pelton model used to fit resistivity has all four model parameters directly corresponding with conductivity data fitted with a Cole–Cole model. The conclusion is that Cole–Cole and Pelton models in fact require identical independent parameters that can fit experimental or synthetic data, provided the Pelton resistivity formulation is restricted to fitting to resistivity data, and the Cole–Cole conductivity formulation is restricted to fitting conductivity results.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 73
    Publication Date: 2015-05-20
    Description: Stratum quality factors ( P -wave and S -wave quality factors, Q p and Q s ) have gradually been utilized in the study of physical state of crust and uppermost mantle, tectonic evolution, hydrogeololgy, gas hydrates, petroleum exploration, etc. Different opinions of the seismic attenuation mechanism result in various approaches to estimate the P -wave and S -wave quality factors. Considering the viscoelasticity of the underground medium, the constitutive matrix of the Earth medium is written as the superposition of homogeneous background medium, elastic perturbation medium and viscoelastic perturbation medium. Under the hypothesis of Born integral and stationary phase approximation, the seismic reflectivity is initially raised in terms of P -wave and S -wave moduli, density, P -wave and S -wave quality factors. Furthermore, incorporating the complex seismic traces with the seismic wavelets at different offsets, a two-step inversion approach is proposed to estimate the P -wave and S -wave quality factors. The AVO/AVA Bayesian inversion approach is suggested to estimate the P -wave modulus and S -wave modulus with the real component of the pre-stack seismic data initially. Taking the estimated P -wave and S -wave moduli as prior information, the P -wave and S -wave quality factors are further estimated with the imaginary component of the complex pre-stack seismic data, which is the quadrature of the original data. Finally, synthetic examples demonstrate that the proposed approach is able to estimate P -wave and S -wave quality factors stably and properly, and two field data examples demonstrate that the proposed approach may work as an efficient approach to fluid identification.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 74
    Publication Date: 2015-05-26
    Description: The European Union (EU) is the world's largest wine producer, as well as the world's most regulated wine market. In 2007, the EU decided on a major reform of its wine policy. A crucial element was the abolishment of a system of planting rights to limit the planting of vineyards. However, after intense lobbying by opponents of the liberalisation, this decision was reversed in 2013. Despite the importance of planting rights in European (and hence global) wine production, and despite the fierce debates surrounding the reforms, no model exists to study the effects of this policy. We develop the first theoretical model of planting rights, integrating the markets for land, planting rights and wine to analyse efficiency and distributional effects. We use the model to study the effects of differences among EU member states in restrictions on trade in planting rights, the role of government reserves and the impact of imperfect enforcement.
    Keywords: Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 75
    Publication Date: 2015-04-12
    Description: In this paper, we modelled the electrical transport behaviour of bimodal carbonate rocks from a reservoir in China using dual-pore networks. One basic assumption, generally supported by experimental data and microstructure observations in the reservoir samples, was that the low porosity, monomodal rocks had the same properties and structure as the microporous matrix of the high porosity, bimodal samples. We assumed that the matrix was homogeneous and always interconnected but that the connectivity and the pore size distribution of macropore system was randomly variable. Both pore systems were supposed to act locally as ‘in parallel’ electrical conductors, an approach previously used by Bauer et al. Hence, the effect of matrix properties, macropore size distribution and connectivity on electrical properties of bimodal rocks could be modelled and investigated. We simulated electrical current through 3-D, simple cubic and body-centred cubic networks with different coordination numbers, different pipe radius distributions of macropore system and different matrix properties. The main result was that the formation factor of dual-pore network obeyed a ‘universal’ scaling relationship (i.e. independent of lattice type). Based on this result, we extended the power-law model derived by Bernabé et al. for monomodal porous media. We developed methods for evaluating the scale-invariant pore structure parameters in the model using conventional core analysis and satisfactorily tested the proposed model against experimental data from the Chinese reservoir as well as some other previously published data sets.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 76
    Publication Date: 2015-04-12
    Description: Asymptotic expressions are derived for electromagnetic fields induced by arbitrarily oriented electric and magnetic dipoles in a laterally isotropic stratified medium. Considering that the leading terms, which describe the airwave, decay in accordance with the same geometric law whether the source is a horizontal electric or magnetic dipole, it is suggested to use a transmitter, which combines these sources. It is shown that the airwave greatly diminishes if the amplitudes and phases of the horizontal current and magnetic moments of this transmitter are chosen to minimize the far-zone vertical magnetic field. A properly tuned combined transmitter will induce the electromagnetic field with a relatively small transverse electric mode. Raw electromagnetic data acquired with the combined transmitter will be more sensitive to parameters of the resistive reservoir than data acquired using the traditional horizontal electric dipole type of the transmitter.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 77
    Publication Date: 2015-04-17
    Description: A Bayesian inversion methodology for identification of large-scale subsurface structures (strata) from controlled source electromagnetic data is developed. The Bayesian inverse problem is solved by sampling from the posterior probability distribution, using the ensemble Kalman filter. Prior knowledge is incorporated in the methodology by utilizing structural prior information from, for example, interpreted seismic data. A model-based, composite parametrization of the electric conductivity distribution is applied to represent the subsurface structures. The model-based representation also allows for estimation of variation of electric conductivity within each stratum. To enhance stability and reduce model nonlinearity, a reduced representation of structure boundaries and conductivity variation within each stratum is applied. Numerical experiments on various test cases show that the methodology is able to identify fairly complex subsurface conductivity distributions reasonably well, with and without a hydrocarbon reservoir present. These experiments included strata with weak conductivity contrast and the application of various prior probability distributions. Furthermore, the methodology shows the ability to (almost completely) remove a reservoir present in the prior model that is not present in the true model (‘false positive’).
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 78
    Publication Date: 2015-04-17
    Description: Non-linear inversion algorithms traverse a data misfit space over multiple iterations of trial models in search of either a global minimum or some target misfit contour. The success of the algorithm in reaching that objective depends upon the smoothness and predictability of the misfit space. For any given observation, there is no absolute form a datum must take, and therefore no absolute definition for the misfit space; in fact, there are many alternatives. However, not all misfit spaces are equal in terms of promoting the success of inversion. In this work, we appraise three common forms that complex data take in electromagnetic geophysical methods: real and imaginary components, a power of amplitude and phase, and logarithmic amplitude and phase. We find that the optimal form is logarithmic amplitude and phase. Single-parameter misfit curves of log-amplitude and phase data for both magnetotelluric and controlled-source electromagnetic methods are the smoothest of the three data forms and do not exhibit flattening at low model resistivities. Synthetic, multiparameter, 2-D inversions illustrate that log-amplitude and phase is the most robust data form, converging to the target misfit contour in the fewest steps regardless of starting model and the amount of noise added to the data; inversions using the other two data forms run slower or fail under various starting models and proportions of noise. It is observed that inversion with log-amplitude and phase data is nearly two times faster in converging to a solution than with other data types. We also assess the statistical consequences of transforming data in the ways discussed in this paper. With the exception of real and imaginary components, which are assumed to be Gaussian, all other data types do not produce an expected mean-squared misfit value of 1.00 at the true model (a common assumption) as the errors in the complex data become large. We recommend that real and imaginary data with errors larger than 10 per cent of the complex amplitude be withheld from a log-amplitude and phase inversion rather than retaining them with large error-bars.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 79
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2015-04-18
    Description: The prospects for plant variety protection to deliver improved varieties of self-pollinating crops is assessed using the experience of the Australian wheat breeding sector as a natural experiment. The analysis is based on detailed new data on the agronomic performance of all wheat varieties released by Australian breeders between 1976 and 2011. The results indicate that plant variety protection, and associated reforms, led to a substantial fall in breeder output. Qualitative evidence indicates that this was caused by a combination of fewer research spillovers, lower release standards, and a possible fall in total investment in breeding.
    Keywords: O34 - Intellectual Property Rights, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 80
    Publication Date: 2015-04-24
    Description: Seismic interferometry comprises a suite of methods to redatum recorded wavefields to those that would have been recorded if different sources (so-called virtual sources) had been activated. Seismic interferometry by cross-correlation has been formulated using either two-way (for full wavefields) or one-way (for directionally decomposed wavefields) representation theorems. To obtain improved Green's function estimates, the cross-correlation result can be deconvolved by a quantity that identifies the smearing of the virtual source in space and time, the so-called point-spread function. This type of interferometry, known as interferometry by multidimensional deconvolution (MDD), has so far been applied only to one-way directionally decomposed fields, requiring accurate wavefield decomposition from dual (e.g. pressure and velocity) recordings. Here we propose a form of interferometry by multidimensional deconvolution that uses full wavefields with two-way representations, and simultaneously invert for pressure and (normal) velocity Green's functions, rather than only velocity responses as for its one-way counterpart. Tests on synthetic data show that two-way MDD improves on results of interferometry by cross-correlation, and generally produces estimates of similar quality to those obtained by one-way MDD, suggesting that the preliminary decomposition into up- and downgoing components of the pressure field is not required if pressure and velocity data are jointly used in the deconvolution. We also show that constraints on the directionality of the Green's functions sought can be added directly into the MDD inversion process to further improve two-way multidimensional deconvolution. Finally, as a by-product of having pressure and particle velocity measurements, we adapt one- and two-way representation theorems to convert any particle velocity receiver into its corresponding virtual dipole/gradient source by means of MDD. Thus data recorded from standard monopolar (e.g. marine) pressure sources can be converted into data from dipolar (derivative) sources at no extra acquisition cost.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 81
    Publication Date: 2015-04-24
    Description: The primary objective of this study is to evaluate the applicability and the effectiveness of ground-penetrating radar (GPR) to identify a thin burnt soil layer, buried more than 2 m below the topographic surface at the Liangzhu Site, in Southeastern China. The site was chosen for its relatively challenging conditions of GPR techniques due to electrical conductivity and to the presence of peach tree roots that produced scattering. We completed the data acquisition by using 100 and 200 MHz antennas in TE and TM broadside and cross-polarized configurations. In the data processing and interpretation phase, we used GPR attribute analysis, including instantaneous phase and geometrical attributes. Validation analysis ground-truthing performed after the geophysical surveys, validated the GPR imaging, confirmed the electrical conductivity and relative dielectric permittivity (RDP) measurements performed at different depths, and allowed a reliable quantitative correlation between GPR results and subsurface physical properties. The research demonstrates that multiple antenna configurations in GPR data acquisition combined with attribute analysis can enhance the ability to characterize prehistoric archaeological remains even in complex subsurface conditions.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 82
    Publication Date: 2015-06-17
    Description: We critically examine the performance of sequential geostatistical resampling (SGR) as a model proposal mechanism for Bayesian Markov-chain-Monte-Carlo (MCMC) solutions to near-surface geophysical inverse problems. Focusing on a series of simple yet realistic synthetic crosshole georadar tomographic examples characterized by different numbers of data, levels of data error and degrees of model parameter spatial correlation, we investigate the efficiency of three different resampling strategies with regard to their ability to generate statistically independent realizations from the Bayesian posterior distribution. Quite importantly, our results show that, no matter what resampling strategy is employed, many of the examined test cases require an unreasonably high number of forward model runs to produce independent posterior samples, meaning that the SGR approach as currently implemented will not be computationally feasible for a wide range of problems. Although use of a novel gradual-deformation-based proposal method can help to alleviate these issues, it does not offer a full solution. Further, we find that the nature of the SGR is found to strongly influence MCMC performance; however no clear rule exists as to what set of inversion parameters and/or overall proposal acceptance rate will allow for the most efficient implementation. We conclude that although the SGR methodology is highly attractive as it allows for the consideration of complex geostatistical priors as well as conditioning to hard and soft data, further developments are necessary in the context of novel or hybrid MCMC approaches for it to be considered generally suitable for near-surface geophysical inversions.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 83
    Publication Date: 2015-06-28
    Description: The seismic properties of rocks are known to be sensitive to partial liquid or gas saturation, and to aligned fractures. P -wave anisotropy is widely used for fracture characterization and is known to be sensitive to the saturating fluid. However, studies combining the effect of multiphase saturation and aligned fractures are limited even though such conditions are common in the subsurface. An understanding of the effects of partial liquid or gas saturation on P -wave anisotropy could help improve seismic characterization of fractured, gas bearing reservoirs. Using octagonal-shaped synthetic sandstone samples, one containing aligned penny-shaped fractures and the other without fractures, we examined the influence of water saturation on P -wave anisotropy in fractured rocks. In the fractured rock, the saturation related stiffening effect at higher water saturation values is larger in the direction across the fractures than along the fractures. Consequently, the anisotropy parameter ‘ ’ decreases as a result of this fluid stiffening effect. These effects are frequency dependent as a result of wave-induced fluid flow mechanisms. Our observations can be explained by combining a frequency-dependent fractured rock model and a frequency-dependent partial saturation model.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 84
    Publication Date: 2015-06-28
    Description: Electrical resistivity tomography (ERT) has been widely used in environmental applications to study processes associated with subsurface contaminants and contaminant remediation. Anthropogenic alterations in subsurface electrical conductivity associated with contamination often originate from highly industrialized areas with significant amounts of buried metallic infrastructure. The deleterious influence of such infrastructure on imaging results generally limits the utility of ERT where it might otherwise prove useful for subsurface investigation and monitoring. In this manuscript we present a method of accurately modelling the effects of buried conductive infrastructure within the forward modelling algorithm, thereby removing them from the inversion results. The method is implemented in parallel using immersed interface boundary conditions, whereby the global solution is reconstructed from a series of well-conditioned partial solutions. Forward modelling accuracy is demonstrated by comparison with analytic solutions. Synthetic imaging examples are used to investigate imaging capabilities within a subsurface containing electrically conductive buried tanks, transfer piping, and well casing, using both well casings and vertical electrode arrays as current sources and potential measurement electrodes. Results show that, although accurate infrastructure modelling removes the dominating influence of buried metallic features, the presence of metallic infrastructure degrades imaging resolution compared to ERT imaging in the absence of infrastructure. However, it is possible to rectify this degradation in resolution through appropriate placement of electrodes.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 85
    Publication Date: 2015-06-06
    Description: Wells and boreholes are routinely steel-cased in oil and gas fields and geological storage sites. There have been a number of studies on the effects of a steel-cased well on various electrical and electromagnetic (EM) geophysical methods. In this paper, we examine the use of a steel-cased well as a virtual vertical electric source for sensing deep localized resistive (e.g. CO 2 , oil and gas) and conductive (e.g. conductive-proppant-filled fractures) targets when concentric electric sources are grounded around the collar of the well. To simulate the casing effects, we present a 3-D finite-element time-domain (FETD) algorithm with tetrahedral elements. The FETD algorithm is designed to reduce memory usage in adaptive time stepping by utilizing parallel direct and iterative solvers appropriately together. To avoid a larger number of tiny elements required for discretizing a thin wall of the casing, the hollow casing is approximated with a rectangular prism. By not discretizing the thin wall of and the curvature of the round casing, the approximation not only reduces the number of unknowns by an order of magnitude but also improves overall mesh qualities. We show that surface EM responses over the hollow casing and the prism are practically the same. Through FETD modelling of a rectangular prism as an approximation of a steel casing, we demonstrate that a steel casing can serve as a conduit through which a high concentration of electrical currents can flow downward from the surface, interact with deep localized reservoirs/fractures and produce a measurable perturbation in the surface EM fields. Concentric electric sources can further improve both the sensitivity to the deep targets and the overall magnitude of surface EM fields.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 86
    Publication Date: 2015-02-18
    Description: Protein sequences predicted from metagenomic datasets are annotated by identifying their homologs via sequence comparisons with reference or curated proteins. However, a majority of metagenomic protein sequences are partial-length, arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented. The fragmented nature of metagenomic protein predictions adversely impacts homology detection and, therefore, the quality of the overall annotation of the dataset. Here we present a novel algorithm called GRASP that accurately identifies the homologs of a given reference protein sequence from a database consisting of partial-length metagenomic proteins. Our homology detection strategy is guided by the reference sequence, and involves the simultaneous search and assembly of overlapping database sequences. GRASP was compared to three commonly used protein sequence search programs (BLASTP, PSI-BLAST and FASTM). Our evaluations using several simulated and real datasets show that GRASP has a significantly higher sensitivity than these programs while maintaining a very high specificity. GRASP can be a very useful program for detecting and quantifying taxonomic and protein family abundances in metagenomic datasets. GRASP is implemented in GNU C++, and is freely available at http://sourceforge.net/projects/grasp-release .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 87
    Publication Date: 2015-02-18
    Description: Genetic screens of an unprecedented scale have recently been made possible by the availability of high-complexity libraries of synthetic oligonucleotides designed to mediate either gene knockdown or gene knockout, coupled with next-generation sequencing. However, several sources of random noise and statistical biases complicate the interpretation of the resulting high-throughput data. We developed HiTSelect, a comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. We document the superior performance of HiTSelect using data from both genome-wide RNAi and CRISPR/Cas9 screens. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration. Binary executables are available at http://sourceforge.net/projects/hitselect/ , and the source code is available at https://github.com/diazlab/HiTSelect .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 88
    Publication Date: 2015-01-24
    Description: Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through data aggregation, integration and visualization. In this study, we demonstrated the utility of Epidaurus in validating hypotheses and generating novel biological insights. In particular, we described the use of Epidaurus to (i) integrate epigenetic data from prostate cancer cell lines to validate the activation function of EZH2 in castration-resistant prostate cancer and to (ii) study the mechanism of androgen receptor ( AR ) binding deregulation induced by the knockdown of FOXA1 . We found that EZH2 's noncanonical activation function was reaffirmed by its association with active histone markers and the lack of association with repressive markers. More importantly, we revealed that the binding of AR was selectively reprogramed to promoter regions, leading to the up-regulation of hundreds of cancer-associated genes including EGFR . The prebuilt epigenetic dataset from commonly used cell lines (LNCaP, VCaP, LNCaP-Abl, MCF7, GM12878, K562, HeLa-S3, A549, HePG2) makes Epidaurus a useful online resource for epigenetic research. As standalone software, Epidaurus is specifically designed to process user customized datasets with both efficiency and convenience.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 89
    Publication Date: 2015-02-11
    Description: Excess returns to producers insured by the Federal Crop Insurance Corporation can arise due to asymmetric information or from the design of the insurance programs themselves. Using unique, unit-level crop insurance contract data for major crops such as corn, soybeans, and wheat in five growing regions, we find evidence that producers in most regions may profit by selecting optional units, buy-up coverage, or by using transitional yields to participate in the federal crop insurance program. We also find evidence that advantages increase with land resource heterogeneity. However, the results do not support hypotheses that producers profit by selecting revenue insurance, nor that high levels of government "incompetence" exist in the design and administration of the crop insurance system.
    Keywords: Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 90
    Publication Date: 2015-02-11
    Description: We analyze the various welfare costs, transfers, trade, and employment consequences of the current U.S. sugar program for U.S. consumers, other sugar users, sugar refiners, cane and beet growing and processing industries, other associated agricultural sectors, and world markets. The removal of the sugar program would increase U.S. consumers' welfare by $2.9 to $3.5 billion each year and generate a modest job creation of 17,000 to 20,000 new jobs in food manufacturing and related industries. Imports of sugar containing products would fall dramatically, especially confectioneries substituting for domestic inputs under the sugar program. Sugar imports would rise substantially to 5–6 million short tons raw sugar equivalent. World sugar price increases would be minor, equivalent to about 1 cent per pound.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 91
    Publication Date: 2015-02-18
    Description: RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation. The experimental methods to solve RNA-protein interaction prediction problem remain expensive and time-consuming. Here, we present the RPI-Pred (RNA-protein interaction predictor), a new support-vector machine-based method, to predict protein-RNA interaction pairs, based on both the sequences and structures. The results show that RPI-Pred can correctly predict RNA-protein interaction pairs with ~94% prediction accuracy when using sequence and experimentally determined protein and RNA structures, and with ~83% when using sequences and predicted protein and RNA structures. Further, our proposed method RPI-Pred was superior to other existing ones by predicting more experimentally validated ncRNA-protein interaction pairs from different organisms. Motivated by the improved performance of RPI-Pred, we further applied our method for reliable construction of ncRNA-protein interaction networks. The RPI-Pred is publicly available at: http://ctsb.is.wfubmc.edu/projects/rpi-pred .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 92
    Publication Date: 2015-02-15
    Description: A strategy is presented to incorporate prior information from conceptual geological models in probabilistic inversion of geophysical data. The conceptual geological models are represented by multiple-point statistics training images (TIs) featuring the expected lithological units and structural patterns. Information from an ensemble of TI realizations is used in two different ways. First, dominant modes are identified by analysis of the frequency content in the realizations, which drastically reduces the model parameter space in the frequency-amplitude domain. Second, the distributions of global, summary metrics (e.g. model roughness) are used to formulate a prior probability density function. The inverse problem is formulated in a Bayesian framework and the posterior pdf is sampled using Markov chain Monte Carlo simulation. The usefulness and applicability of this method is demonstrated on two case studies in which synthetic crosshole ground-penetrating radar traveltime data are inverted to recover 2-D porosity fields. The use of prior information from TIs significantly enhances the reliability of the posterior models by removing inversion artefacts and improving individual parameter estimates. The proposed methodology reduces the ambiguity inherent in the inversion of high-dimensional parameter spaces, accommodates a wide range of summary statistics and geophysical forward problems.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 93
    Publication Date: 2015-02-18
    Description: Identifying conserved and divergent response patterns in gene networks is becoming increasingly important. A common approach is integrating expression information with gene association networks in order to find groups of connected genes that are activated or repressed. In many cases, researchers are also interested in comparisons across species (or conditions). Finding an active sub-network is a hard problem and applying it across species requires further considerations (e.g. orthology information, expression data and networks from different sources). To address these challenges we devised ModuleBlast, which uses both expression and network topology to search for highly relevant sub-networks. We have applied ModuleBlast to expression and interaction data from mouse, macaque and human to study immune response and aging. The immune response analysis identified several relevant modules, consistent with recent findings on apoptosis and NFB activation following infection. Temporal analysis of these data revealed cascades of modules that are dynamically activated within and across species. We have experimentally validated some of the novel hypotheses resulting from the analysis of the ModuleBlast results leading to new insights into the mechanisms used by a key mammalian aging protein.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 94
    Publication Date: 2015-02-18
    Description: Here we used discriminative training methods to uncover the chromatin, transcription factor (TF) binding and sequence features of enhancers underlying gene expression in individual cardiac cells. We used machine learning with TF motifs and ChIP data for a core set of cardiogenic TFs and histone modifications to classify Drosophila cell-type-specific cardiac enhancer activity. We show that the classifier models can be used to predict cardiac cell subtype cis -regulatory activities. Associating the predicted enhancers with an expression atlas of cardiac genes further uncovered clusters of genes with transcription and function limited to individual cardiac cell subtypes. Further, the cell-specific enhancer models revealed chromatin, TF binding and sequence features that distinguish enhancer activities in distinct subsets of heart cells. Collectively, our results show that computational modeling combined with empirical testing provides a powerful platform to uncover the enhancers, TF motifs and gene expression profiles which characterize individual cardiac cell fates.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 95
    Publication Date: 2015-02-19
    Description: Many rocks and layered/fractured sequences have a clearly expressed electrical anisotropy although it is rare in practice to incorporate anisotropy into resistivity inversion. In this contribution, we present a series of 2.5-D synthetic inversion experiments for various electrode configurations and 2-D anisotropic models. We examine and compare the image reconstructions obtained using the correct anisotropic inversion code with those obtained using the false but widely used isotropic assumption. Superior reconstruction in terms of reduced data misfit, true anomaly shape and position, and anisotropic background parameters were obtained when the correct anisotropic assumption was employed for medium to high coefficients of anisotropy. However, for low coefficient values the isotropic assumption produced better-quality results. When an erroneous isotropic inversion is performed on medium to high level anisotropic data, the images are dominated by patterns of banded artefacts and high data misfits. Various pole–pole, pole–dipole and dipole–dipole data sets were investigated and evaluated for the accuracy of the inversion result. The eigenvalue spectra of the pseudo-Hessian matrix and the formal resolution matrix were also computed to determine the information content and goodness of the results. We also present a data selection strategy based on high sensitivity measurements which drastically reduces the number of data to be inverted but still produces comparable results to that of the comprehensive data set. Inversion was carried out using transversely isotropic model parameters described in two different co-ordinate frames for the conductivity tensor, namely Cartesian versus natural or eigenframe. The Cartesian frame provided a more stable inversion product. This can be simply explained from inspection of the eigenspectra of the pseudo-Hessian matrix for the two model descriptions.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 96
    Publication Date: 2015-02-05
    Description: We studied artificial ore models that contained galena, pyrite, magnetite, graphite and cryptomelane with the time domain induced polarization technique. The models were mixtures of sand and metallic-type, electronically conductive mineral particles. We varied the volumetric content of the particles, their mineral composition and average grain size, as well as the pore water salinity. Based on the Debye decomposition approach, we obtained relaxation time distributions, which contained peaks. From these distributions, we obtained the total chargeability and the peak relaxation time. We correlated these parameters with the particle mineral composition, grain size, particle content and the pore solution resistivity. We also compared the experimental data with the Wong model prediction, which was unable to explain the entire data set. The above-mentioned correlations, in conjunction with some previously published data, allowed us to formulate a new, semi-empirical model that links (1) the total chargeability with the volumetric content of the particles and the total chargeability of the host matrix and (2) the time constant with the particle mineralogy, the particle radius and the pore solution resistivity.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 97
    Publication Date: 2015-02-05
    Description: Electrodes installed on active landslides and vulnerable earthworks to monitor changes in resistivity associated with moisture dynamics can be subject to movement. This affects the geoelectrical data and leads to errors in the resulting electrical resistivity tomography (ERT) images. This paper demonstrates the selection of appropriate ERT measurements to provide sensitivity to electrode displacements in both directions on a surface grid. Combinations of linear and equatorial dipole–dipole measurements are considered, which permit use on rectangular grids of any aspect ratio. A Gauss–Newton inversion scheme, initially based on simple homogeneous resistivity model calculations, is developed that allows for the incorporation of constraints based on the magnitude and direction of movement. The effects of the constraints are demonstrated with synthetic data, which are also used to show that displacement inversion can track electrodes positions during movement as a function of time. The conclusions of these simulations are subsequently confirmed by analogous experiments in a laboratory tank. The results show that tracking the positions of the electrodes is possible with sufficient accuracy, even in the presence of realistic subsurface resistivity structures, to correct the majority of distortions and resistivity anomalies caused by using the wrong electrode locations in ERT inversion. By incorporating estimates of the resistivity structure into the forward response modelling, the accuracy of the recovered displacements is improved. This also enables an iterative displacement and resistivity inversion to be developed that, for the first time, demonstrates the principle of using 3-D ERT data to monitor both subsurface geoelectrical properties and surface movements simultaneously.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 98
    Publication Date: 2015-01-24
    Description: Seismic waves propagating in a porous medium, under favourable conditions, generate measurable electromagnetic fields due to electrokinetic effects. It has been proposed, following experimental and numerical studies, that these so-called ‘seismoelectromagnetic’ couplings depend on pore fluid properties. The theoretical frame describing these phenomena are based on the original Biot's theory, assuming that pores are fluid-filled. We study here the impact of a partially saturated medium on amplitudes of those seismoelectric couplings by comparing experimental data to an effective fluid model. We have built a 1-m-length-scale experiment designed for imbibition and drainage of an homogeneous silica sand; the experimental set-up includes a seismic source, accelerometers, electric dipoles and capacitance probes in order to monitor seismic and seismoelectric fields during water saturation. Apparent velocities and frequency spectra (in the kiloHertz range) are derived from seismic and electrical measurements during experiments in varying saturation conditions. Amplitudes of seismic and seismoelectric waves and their ratios (i.e. transfer functions) are discussed using a spectral analysis performed by continuous wavelet transform. The experiments reveal that amplitude ratios of seismic to coseismic electric signals remain rather constant as a function of the water saturation in the S w  = [0.2–0.9] range, consistently with theoretically predicted transfer functions.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 99
    Publication Date: 2015-02-05
    Description: New marine geophysical data recorded across the Tonga-Kermadec subduction zone are used to image deformation and seismic velocity structures of the forearc and Pacific Plate where the Louisville Ridge seamount chain subducts. Due to the obliquity of the Louisville Ridge to the trench and the fast 128 mm yr –1 south–southwest migration of the ridge-trench collision zone, post-, current and pre-seamount subduction deformation can be investigated between 23°S and 28°S. We combine our interpretations from the collision zone with previous results from the post- and pre-collision zones to define the along-arc variation in deformation due to seamount subduction. In the pre-collision zone the lower-trench slope is steep, the mid-trench slope has ~3-km-thick stratified sediments and gravitational collapse of the trench slope is associated with basal erosion by subducting horst and graben structures on the Pacific Plate. This collapse indicates that tectonic erosion is a normal process affecting this generally sediment starved subduction system. In the collision zone the trench-slope decreases compared to the north and south, and rotation of the forearc is manifest as a steep plate boundary fault and arcward dipping sediment in a 12-km-wide, ~2-km-deep mid-slope basin. A ~3 km step increase in depth of the middle and lower crustal isovelocity contours below the basin indicates the extent of crustal deformation on the trench slope. At the leading edge of the overriding plate, upper crustal P -wave velocities are ~4.0 km s –1 and indicate the trench fill material is of seamount origin. Osbourn Seamount on the outer rise has extensional faulting on its western slope and mass wasting of the seamount provides the low V p material to the trench. In the post-collision zone to the north, the trench slope is smooth, the trench is deep, and the crystalline crust thins at the leading edge of the overriding plate where V p is low, ~5.5 km s –1 . These characteristics are attributed to a greater degree of extensional collapse of the forearc in the wake of seamount subduction. The northern end of a seismic gap lies at the transition from the smooth lower-trench slope of the post-collision zone, to the block faulted and elevated lower-trench slope in the collision zone, suggesting a causative link between the collapse of the forearc and seismogenesis. Along the forearc, the transient effects of a north-to-south progression of ridge subduction are preserved in the geomorphology, whereas longer-term effects may be recorded in the ~80 km offset in trench strike at the collision zone itself.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 100
    Publication Date: 2014-12-03
    Description: This study presents evidence from a survey and choice experiment on the preferences of Hispanic immigrants who entered the United States illegally for different immigration reform proposal attributes. Key components of the current competing US Senate and House immigration reform bills are considered including pathways to legal permanent residence, temporary work visas, family visitation rights, and access to medical care. The results quantify the value Hispanic immigrants place on different policy attributes and suggest that longer-term work visas are highly valued. Ability to legally work in the United States and a pathway to citizenship are substantially more valued than social services such as medical care and social security benefits.
    Keywords: J15 - Economics of Minorities and Races ; Non-labor Discrimination, K37 - Immigration Law, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...