Corneal topography reinterpretation through separate analysis of the projected rings

Póster presentado en SPIE Photonics Europe, Brussels, 16-19 April 2012.

Plant species, biomass and environmental characteristics of relevés along the North America Arctic bioclimate gradient

Question: How do interactions between the physical environment and biotic properties of vegetation influence the formation of small patterned-ground features along the Arctic bioclimate gradient? Location: At 68° to 78°N: six locations along the Dalton Highway in arctic Alaska and three in Canada (Banks Island, Prince Patrick Island and Ellef Ringnes Island). Methods: We analysed floristic and structural vegetation, biomass and abiotic data (soil chemical and physical parameters, the n-factor [a soil thermal index] and spectral information [NDVI, LAI]) on 147 microhabitat releves of zonalpatterned-ground features. Using mapping, table analysis (JUICE) and ordination techniques (NMDS). Results: Table analysis using JUICE and the phi-coefficient to identify diagnostic species revealed clear groups of diagnostic plant taxa in four of the five zonal vegetation complexes. Plant communities and zonal complexes were generally well separated in the NMDS ordination. The Alaska and Canada communities were spatially separated in the ordination because of different glacial histories and location in separate floristic provinces, but there was no single controlling environmental gradient. Vegetation structure, particularly that of bryophytes and total biomass, strongly affected thermal properties of the soils. Patterned-ground complexes with the largest thermal differential between the patterned-ground features and the surrounding vegetation exhibited the clearest patterned-ground morphologies.

Spectral analysis of seabed elevation from the Danish Wadden Sea

Bedforms both reflect and influence shallow water hydrodynamics and sediment dynamics. A correct characterization of their spatial distribution and dimensions is required for the understanding, assessment and prediction of numerous coastal processes. A method to parameterize geometrical characteristics using two-dimensional (2D) spectral analysis is presented and tested on seabed elevation data from the Knudedyb tidal inlet in the Danish Wadden Sea, where large compound bedforms are found. The bathymetric data were divided into 20x20 m areas on which a 2D spectral analysis was applied. The most energetic peak of the 2D spectrum was found and its energy, frequency and direction were calculated. A power-law was fitted to the average of slices taken through the 2D spectrum; its slope and y-intercept were calculated. Using these results the test area was morphologically classified into 4 distinct morphological regions. The most energetic peak and the slope and intercept of the power-law showed high values above the crest of the primary bedforms and scour holes, low values in areas without bedforms, and intermediate values in areas with secondary bedforms. The secondary bedform dimensions and orientations were calculated. An area of 700x700 m was used to determine the characteristics of the primary bedforms. However, they were less distinctively characterized compared to the secondary bedforms due to relatively large variations in their orientations and wavelengths. The method is thus appropriate for morphological classification of the seabed and for bedform characterization, being most efficient in areas characterized by bedforms with regular dimensions and directions.

SPECTRAL DOMAIN-OPTICAL COHERENCE TOMOGRAPHY IMAGE CONTRAST AND BACKGROUND COLOR SETTINGS INFLUENCE IDENTIFICATION OF RETINAL STRUCTURES.

PURPOSE To evaluate image contrast and color setting on assessment of retinal structures and morphology in spectral-domain optical coherence tomography. METHODS Two hundred and forty-eight Spectralis spectral-domain optical coherence tomography B-scans of 62 patients were analyzed by 4 readers. B-scans were extracted in 4 settings: W + N = white background with black image at normal contrast 9; W + H = white background with black image at maximum contrast 16; B + N = black background with white image at normal contrast 12; B + H = black background with white image at maximum contrast 16. Readers analyzed the images to identify morphologic features. Interreader correlation was calculated. Differences between Fleiss-kappa correlation coefficients were examined using bootstrap method. Any setting with significantly higher correlation coefficient was deemed superior for evaluating specific features. RESULTS Correlation coefficients differed among settings. No single setting was superior for all respective spectral-domain optical coherence tomography parameters (P = 0.3773). Some variables showed no differences among settings. Hard exudates and subretinal fluid were best seen with B + H (κ = 0.46, P = 0.0237 and κ = 0.78, P = 0.002). Microaneurysms were best seen with W + N (κ = 0.56, P = 0.025). Vitreomacular interface, enhanced transmission signal, and epiretinal membrane were best identified using all color/contrast settings together (κ = 0.44, P = 0.042, κ = 0.57, P = 0.01, and κ = 0.62, P ≤ 0.0001). CONCLUSION Contrast and background affect the evaluation of retinal structures on spectral-domain optical coherence tomography images. No single setting was superior for all features, though certain changes were best seen with specific settings.

Development of a Conceptual Site Model for Evaluating Seawater Intrusion under Sea Level Rise Scenarios Using Analytical Methods

Island County is located in the Puget Sound of Washington State and includes several islands, the largest of which is Whidbey Island. Central Whidbey Island was chosen as the project site, as residents use groundwater for their water supply and seawater intrusion near the coast is known to contaminate this resource. In 1989, Island County adopted a Saltwater Intrusion Policy and used chloride concentrations in existing wells in order to define and map “risk zones.” In 2005, this method of defining vulnerability was updated with the use of water level elevations in conjunction with chloride concentrations. The result of this work was a revised map of seawater intrusion vulnerability that is currently in use by Island County. This groundwater management strategy is defined as trigger-level management and is largely a reactive tool. In order to evaluate trends in the hydrogeologic processes at the site, including seawater intrusion under sea level rise scenarios, this report presents a workflow where groundwater flow and discharge to the sea are quantified using a revised conceptual site model. The revised conceptual site model used several simplifying assumptions that allow for first-order quantitative predictions of seawater intrusion using analytical methods. Data from water well reports included lithologic and well construction information, static water levels, and aquifer tests for specific capacity. Results from specific capacity tests define the relationship between discharge and drawdown and were input for a modified Theis equation to solve for transmissivity (Arihood, 2009). Components of the conceptual site model were created in ArcGIS and included interpolation of water level elevation, creation of groundwater basins, and the calculation of net recharge and groundwater discharge for each basin. The revised conceptual site model was then used to hypothesize regarding hydrogeologic processes based on observed trends in groundwater flow. Hypotheses used to explain a reduction in aquifer thickness and hydraulic gradient were: (1) A large increase in transmissivity occurring near the coast. (2) The reduced aquifer thickness and hydraulic gradient were the result of seawater intrusion. (3) Data used to create the conceptual site model were insufficient to resolve trends in groundwater flow. For Hypothesis 2, analytical solutions for groundwater flow under Dupuit assumptions were applied in order to evaluate seawater intrusion under projected sea level rise scenarios. Results indicated that a rise in sea level has little impact on the position of a saltwater wedge; however, a reduction in recharge has significant consequences. Future work should evaluate groundwater flow using an expanded monitoring well network and aquifer recharge should be promoted by reducing surface water runoff.

Method for determining reaction rate of mild steel containers during melting of magnesium-aluminium alloys and effect of aluminium content on directionally solidified microstructures

A magnesium alloy of eutectic composition (33 wt-'%Al) was directionally solidified in mild steel tubes at two growth rates, 32 and 580 mum s(-1,) in a temperature gradient between 10 and 20 K mm(-1). After directional solidification, the composition of each specimen varied dramatically, from 32'%Al in the region that had remained solid to 18%Al (32 mum s(-1) specimen) and 13%Al (580 mum s(-1) specimen) at the plane that had been quenched from the eutectic temperature. As the aluminium content decreased, the microstructure contained an increasing volume fraction of primary magnesium dendrites and the eutectic morphology gradually changed from lamellar to partially divorced. The reduction in aluminium content was caused by the growth of an Al-Fe phase ahead of the Mg-Al growth front. Most of the growth of the Al-Fe phase occurred during the remelting period before directional solidification. The thickness of the Al-Fe phase increased with increased temperature and time of contact with the molten Mg-Al alloy. (C) 2003 Maney Publishing.

A novel phantom and method for comprehensive 3-dimensional measurement and correction of geometric distortion in magnetic resonance imaging

A phantom that can be used for mapping geometric distortion in magnetic resonance imaging (MRI) is described. This phantom provides an array of densely distributed control points in three-dimensional (3D) space. These points form the basis of a comprehensive measurement method to correct for geometric distortion in MR images arising principally from gradient field non-linearity and magnet field inhomogeneity. The phantom was designed based on the concept that a point in space can be defined using three orthogonal planes. This novel design approach allows for as many control points as desired. Employing this novel design, a highly accurate method has been developed that enables the positions of the control points to be measured to sub-voxel accuracy. The phantom described in this paper was constructed to fit into a body coil of a MRI scanner, (external dimensions of the phantom were: 310 mm x 310 mm x 310 mm), and it contained 10,830 control points. With this phantom, the mean errors in the measured coordinates of the control points were on the order of 0.1 mm or less, which were less than one tenth of the voxel's dimensions of the phantom image. The calculated three-dimensional distortion map, i.e., the differences between the image positions and true positions of the control points, can then be used to compensate for geometric distortion for a full image restoration. It is anticipated that this novel method will have an impact on the applicability of MRI in both clinical and research settings. especially in areas where geometric accuracy is highly required, such as in MR neuro-imaging. (C) 2004 Elsevier Inc. All rights reserved.

An FDTD model for calculation of gradient-induced eddy currents in MRI system

In most magnetic resonance imaging (MRI) systems, pulsed magnetic gradient fields induce eddy currents in the conducting structures of the superconducting magnet. The eddy currents induced in structures within the cryostat are particularly problematic as they are characterized by long time constants by virtue of the low resistivity of the conductors. This paper presents a three-dimensional (3-D) finite-difference time-domain (FDTD) scheme in cylindrical coordinates for eddy-current calculation in conductors. This model is intended to be part of a complete FDTD model of an MRI system including all RF and low-frequency field generating units and electrical models of the patient. The singularity apparent in the governing equations is removed by using a series expansion method and the conductor-air boundary condition is handled using a variant of the surface impedance concept. The numerical difficulty due to the asymmetry of Maxwell equations for low-frequency eddy-current problems is circumvented by taking advantage of the known penetration behavior of the eddy-current fields. A perfectly matched layer absorbing boundary condition in 3-D cylindrical coordinates is also incorporated. The numerical method has been verified against analytical solutions for simple cases. Finally, the algorithm is illustrated by modeling a pulsed field gradient coil system within an MRI magnet system. The results demonstrate that the proposed FDTD scheme can be used to calculate large-scale eddy-current problems in materials with high conductivity at low frequencies.

Projected Gross-Pitaevskii equation for harmonically confined Bose gases at finite temperature

We extend the projected Gross-Pitaevskii equation formalism of Davis [Phys. Rev. Lett. 87, 160402 (2001)] to the experimentally relevant case of thermal Bose gases in harmonic potentials and outline a robust and accurate numerical scheme that can efficiently simulate this system. We apply this method to investigate the equilibrium properties of the harmonically trapped three-dimensional projected Gross-Pitaevskii equation at finite temperature and consider the dependence of condensate fraction, position, and momentum distributions and density fluctuations on temperature. We apply the scheme to simulate an evaporative cooling process in which the preferential removal of high-energy particles leads to the growth of a Bose-Einstein condensate. We show that a condensate fraction can be inferred during the dynamics even in this nonequilibrium situation.

A gradient descent algorithm for minimizing amino acid coupling reactions when synthesizing cyclic-peptide libraries

Combinatorial chemistry has become an invaluable tool in medicinal chemistry for the identification of new drug leads. For example, libraries of predetermined sequences and head-to-tail cyclized peptides are routinely synthesized in our laboratory using the IRORI approach. Such libraries are used as molecular toolkits that enable the development of pharmacophores that define activity and specificity at receptor targets. These libraries can be quite large and difficult to handle, due to physical and chemical constraints imposed by their size. Therefore, smaller sub-libraries are often targeted for synthesis. The number of coupling reactions required can be greatly reduced if the peptides having common amino acids are grouped into the same sub-library (batching). This paper describes a schedule optimizer to minimize the number of coupling reactions by rotating and aligning sequences while simultaneously batching. The gradient descent method thereby reduces the number of coupling reactions required for synthesizing cyclic peptide libraries. We show that the algorithm results in a 75% reduction in the number of coupling reactions for a typical cyclic peptide library.

A wave equation technique for designing compact gradient coils

A primary purpose of this research is to design a gradient coil that is planar in construction and can be inserted within existing infrastructure. The proposed wave equation method for the design of gradient coils is novel within the field. it is comprehensively shown how this method can be used to design the planar x-, y-, and z-gradient wire windings to produce the required magnetic fields within a certain domain. The solution for the cylindrical gradient coil set is also elucidated. The wave equation technique is compared with the well-known target held method to gauge the quality of resultant design. In the case of the planar gradient coil design, it is shown that using the new method, a set of compact gradient coils with large field of view can be produced. The final design is considerably smaller in dimension when compared with the design obtained using the target field method, and therefore the manufacturing costs and materials required are somewhat reduced.

A method for screening the temperature dependence of three-dimensional crystal formation

Temperature is an important parameter controlling protein crystal growth. A new temperature-screening system (Thermo-screen) is described consisting of a gradient thermocycler fitted with a special crystallization-plate adapter onto which a 192-well sitting-drop crystallization plate can be mounted (temperature range 277-372 K; maximum temperature gradient 20 K; interval precision 0.3 K). The system allows 16 different conditions to be monitored simultaneously over a range of 12 temperatures and is well suited to conduct wide (similar to 20 K) and fine (similar to 3 K) temperature-optimization screens. It can potentially aid in the determination of temperature phase diagrams and run more complex temperature-cycling experiments for seeding and crystal growth.

Analysis of transient eddy currents in MRI using a cylindrical FDTD method

Most magnetic resonance imaging (MRI) spatial encoding techniques employ low-frequency pulsed magnetic field gradients that undesirably induce multiexponentially decaying eddy currents in nearby conducting structures of the MRI system. The eddy currents degrade the switching performance of the gradient system, distort the MRI image, and introduce thermal loads in the cryostat vessel and superconducting MRI components. Heating of superconducting magnets due to induced eddy currents is particularly problematic as it offsets the superconducting operating point, which can cause a system quench. A numerical characterization of transient eddy current effects is vital for their compensation/control and further advancement of the MRI technology as a whole. However, transient eddy current calculations are particularly computationally intensive. In large-scale problems, such as gradient switching in MRI, conventional finite-element method (FEM)-based routines impose very large computational loads during generation/solving of the system equations. Therefore, other computational alternatives need to be explored. This paper outlines a three-dimensional finite-difference time-domain (FDTD) method in cylindrical coordinates for the modeling of low-frequency transient eddy currents in MRI, as an extension to the recently proposed time-harmonic scheme. The weakly coupled Maxwell's equations are adapted to the low-frequency regime by downscaling the speed of light constant, which permits the use of larger FDTD time steps while maintaining the validity of the Courant-Friedrich-Levy stability condition. The principal hypothesis of this work is that the modified FDTD routine can be employed to analyze pulsed-gradient-induced, transient eddy currents in superconducting MRI system models. The hypothesis is supported through a verification of the numerical scheme on a canonical problem and by analyzing undesired temporal eddy current effects such as the B-0-shift caused by actively shielded symmetric/asymmetric transverse x-gradient head and unshielded z-gradient whole-body coils operating in proximity to a superconducting MRI magnet.

Tailoring magnetic field gradient design to magnet cryostat geometry

Eddy currents induced within a magnetic resonance imaging (MRI) cryostat bore during pulsing of gradient coils can be applied constructively together with the gradient currents that generate them, to obtain good quality gradient uniformities within a specified imaging volume over time. This can be achieved by simultaneously optimizing the spatial distribution and temporal pre-emphasis of the gradient coil current, to account for the spatial and temporal variation of the secondary magnetic fields due to the induced eddy currents. This method allows the tailored design of gradient coil/magnet configurations and consequent engineering trade-offs. To compute the transient eddy currents within a realistic cryostat vessel, a low-frequency finite-difference time-domain (FDTD) method using total-field scattered-field (TFSF) scheme has been performed and validated

Monitoring the condition of savanna riparian zones in Northern Australia using high spatial resolution imagery and a field based rapid assessment method

Government agencies responsible for riparian environments are assessing the combined utility of field survey and remote sensing for mapping and monitoring indicators of riparian zone condition. The objective of this work was to compare the Tropical Rapid Appraisal of Riparian Condition (TRARC) method to a satellite image based approach. TRARC was developed for rapid assessment of the environmental condition of savanna riparian zones. The comparison assessed mapping accuracy, representativeness of TRARC assessment, cost-effectiveness, and suitability for multi-temporal analysis. Two multi-spectral QuickBird images captured in 2004 and 2005 and coincident field data covering sections of the Daly River in the Northern Territory, Australia were used in this work. Both field and image data were processed to map riparian health indicators (RHIs) including percentage canopy cover, organic litter, canopy continuity, stream bank stability, and extent of tree clearing. Spectral vegetation indices, image segmentation and supervised classification were used to produce RHI maps. QuickBird image data were used to examine if the spatial distribution of TRARC transects provided a representative sample of ground based RHI measurements. Results showed that TRARC transects were required to cover at least 3% of the study area to obtain a representative sample. The mapping accuracy and costs of the image based approach were compared to those of the ground based TRARC approach. Results proved that TRARC was more cost-effective at smaller scales (1-100km), while image based assessment becomes more feasible at regional scales (100-1000km). Finally, the ability to use both the image and field based approaches for multi-temporal analysis of RHIs was assessed. Change detection analysis demonstrated that image data can provide detailed information on gradual change, while the TRARC method was only able to identify more gross scale changes. In conclusion, results from both methods were considered to complement each other if used at appropriate spatial scales.