Anomalous thresholds and edge singularities in Electrical Impedance Tomography

Studies of models of current flow behaviour in Electrical Impedance Tomography (EIT) have shown that the current density distribution varies extremely rapidly near the edge of the electrodes used in the technique. This behaviour imposes severe restrictions on the numerical techniques used in image reconstruction algorithms. In this paper we have considered a simple two dimensional case and we have shown how the theory of end point/pinch singularities which was developed for studying the anomalous thresholds encountered in elementary particle physics can be used to give a complete description of the analytic structure of the current density near to the edge of the electrodes. As a byproduct of this study it was possible to give a complete description of the Riemann sheet manifold of the eigenfunctions of the logarithmic kernel. These methods can be readily extended to other weakly singular kernels.Comment: Correction of a misprint which occurred in the unnumbered formula preceding Eq. (14), LaTeX file as an uuencoded file, 40 pages with 12 figures, uses epsf.st

A three-dimensional image reconstruction algorithm for electrical impedance tomography using planar electrode arrays

We present a three-dimensional non-iterative reconstruction algorithm developed for conductivity imaging with real data collected on a planar rectangular array of electrodes. Such an electrode configuration as well as the proposed imaging technique is intended to be used for breast cancer detection. The algorithm is based on linearizing the conductivity about a constant value and allows real-time reconstructions. The performance of the algorithm was tested on numerically simulated data and we successfully detected small inclusions with conductivities three or four times the background lying beneath the data collection surface. The results were fairly stable with respect to the noise level in the data and displayed very good spatial resolution in the plane of electrodes

A regularized solution for the inverse conductivity problem using mollifiers

In this article, we present a reconstruction method for the inverse conductivity problem suitable for smooth conductivity distributions. The inverse problem is reformulated in terms of a pair of coupled integral equations, one of which is of the first kind which we regularize using mollifier methods. An interesting feature of this method is that the kernel of this integral equation is not given, but can be modified for the choice of mollifier. We are able to obtain conductivity reconstructions rapidly and without relying on accurate a priori information

Modular decomposition of metabolic systems via null space analysis

We describe a method by which the reactions in a metabolic system may be grouped hierarchically into sets of modules to form a metabolic reaction tree. In contrast to previous approaches, the method described here takes into account the fact that, in a viable network, reactions must be capable of sustaining a steady-state flux. In order to achieve this decomposition we introduce a new concept—the reaction correlation coefficient, φ, and show that this is a logical extension of the concept of enzyme (or reaction) subsets. In addition to their application to modular decomposition, reaction correlation coefficients have a number of other interesting properties, including a convenient means for identifying disconnected subnetworks in a system and potential applications to metabolic engineering. The method computes reaction correlation coefficients from an orthonormal basis of the null-space of the stoichiometry matrix. We show that reaction correlation coefficients are uniquely defined, even though the basis of the null-space is not. Once a complete set of reaction correlation coefficients is calculated, a metabolic reaction tree can be determined through the application of standard programming techniques. Computation of the reaction correlation coefficients, and the subsequent construction of the metabolic reaction tree is readily achievable for genome-scale models using a commodity desk-top PC

Quantifying mesoscale-driven nitrate supply: a case study

The supply of nitrate to surface waters plays a crucial role in maintaining marine life. Physical processes at the mesoscale (~10-100?km) and smaller have been advocated to provide a major fraction of the global supply. Whilst observational studies have focussed on well-defined features, such as isolated eddies, the vertical circulation and nutrient supply in a typical 100-200?km square of ocean will involve a turbulent spectrum of interacting, evolving and decaying features. A crucial step in closing the ocean nitrogen budget is to be able to rank the importance of mesoscale fluxes against other sources of nitrate for surface waters for a representative area of open ocean. While this has been done using models, the vital observational equivalent is still lacking.To illustrate the difficulties that prevent us from putting a global estimate on the significance of the mesoscale observationally, we use data from a cruise in the Iceland Basin where vertical velocity and nitrate observations were made simultaneously at the same high spatial resolution. Local mesoscale nitrate flux is found to be an order of magnitude greater than that due to small-scale vertical mixing and exceeds coincident nitrate uptake rates and estimates of nitrate supply due to winter convection. However, a non-zero net vertical velocity for the region introduces a significant bias in regional estimates of the mesoscale vertical nitrate transport. The need for synopticity means that a more accurate estimate can not be simply found by using a larger survey area. It is argued that time-series, rather than spatial surveys, may be the best means to quantify the contribution of mesoscale processes to the nitrate budget of the surface ocean

Surface dosimetry for breast radiotherapy in the presence of immobilization cast material

Curative breast radiotherapy typically leaves patients with varying degrees of cosmetic damage. One problem interfering with cosmetically acceptable breast radiotherapy is the external contour for large pendulous breasts which often results in high doses to skin folds. Thermoplastic casts are often employed to secure the breasts to maintain setup reproducibility and limit the presence of skin folds. This paper aims to determine changes in surface dose that can be attributed to the use of thermoplastic immobilization casts. Skin dose for a clinical hybrid conformal/IMRT breast plan was measured using radiochromic film and MOSFET detectors at a range ofwater equivalent depths representative of the different skin layers. The radiochromic film was used as an integrating dosimeter, while the MOSFETs were used for real-time dosimetry to isolate the contribution of skin dose from individual IMRT segments. Strips of film were placed at various locations on the breast and the MOSFETs were used to measure skin dose at 16 positions spaced along the film strips for comparison of data. The results showed an increase in skin dose in the presence of the immobilization cast of up to 45.7% and 62.3% of the skin dose without the immobilization cast present as measured with Gafchromic EBT film and MOSFETs, respectively. The increase in skin dose due to the immobilization cast varied with the angle of beam incidence and was greatest when the beam was normally incident on the phantom. The increase in surface dose with the immobilization cast was greater under entrance dose conditions compared to exit dose conditions

Estimates of new and total productivity in central Long Island Sound from in situ measurements of nitrate and dissolved oxygen

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Estuaries and Coasts 36 (2013): 74-97, doi:10.1007/s12237-012-9560-5.Biogeochemical cycles in estuaries are regulated by a diverse set of physical and biological variables that operate over a variety of time scales. Using in situ optical sensors, we conducted a high-frequency time-series study of several biogeochemical parameters at a mooring in central Long Island Sound from May to August 2010. During this period, we documented well-defined diel cycles in nitrate concentration that were correlated to dissolved oxygen, wind stress, tidal mixing, and irradiance. By filtering the data to separate the nitrate time series into various signal components, we estimated the amount of variation that could be ascribed to each process. Primary production and surface wind stress explained 59% and 19%, respectively, of the variation in nitrate concentrations. Less frequent physical forcings, including large-magnitude wind events and spring tides, served to decouple the relationship between oxygen, nitrate, and sunlight on about one-quarter of study days. Daytime nitrate minima and dissolved oxygen maxima occurred nearly simultaneously on the majority (> 80%) of days during the study period; both were strongly correlated with the daily peak in irradiance. Nighttime nitrate maxima reflected a pattern in which surface-layer stocks were depleted each afternoon and recharged the following night. Changes in nitrate concentrations were used to generate daily estimates of new primary production (182 ± 37 mg C m-2 d-1) and the f-ratio (0.25), i.e., the ratio of production based on nitrate to total production. These estimates, the first of their kind in Long Island Sound, were compared to values of community respiration, primary productivity, and net ecosystem metabolism, which were derived from in situ measurements of oxygen concentration. Daily averages of the three metabolic parameters were 1660 ± 431, 2080 ± 419, and 429 ± 203 mg C m-2 d-1, respectively. While the system remained weakly autotrophic over the duration of the study period, we observed very large day-to-day differences in the f-ratio and in the various metabolic parameters.This work was supported by the Yale Institute for Biospheric Studies, the Sounds Conservancy of the Quebec-Labrador Foundation, and the Yale School of Forestry and Environmental Studies Carpenter-Sperry Fund.2014-01-0

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins

Binding of calcium ions (Ca2+) to proteins can have profound effects on their structure and function. Common roles of calcium binding include structure stabilization and regulation of activity. It is known that diverse families – EF-hands being one of at least twelve – use a Dx[DN]xDG linear motif to bind calcium in near-identical fashion. Here, four novel structural contexts for the motif are described. Existing experimental data for one of them, a thermophilic archaeal subtilisin, demonstrate for the first time a role for Dx[DN]xDG-bound calcium in protein folding. An integrin-like embedding of the motif in the blade of a β-propeller fold – here named the calcium blade – is discovered in structures of bacterial and fungal proteins. Furthermore, sensitive database searches suggest a common origin for the calcium blade in β-propeller structures of different sizes and a pan-kingdom distribution of these proteins. Factors favouring the multiple convergent evolution of the motif appear to include its general Asp-richness, the regular spacing of the Asp residues and the fact that change of Asp into Gly and vice versa can occur though a single nucleotide change. Among the known structural contexts for the Dx[DN]xDG motif, only the calcium blade and the EF-hand are currently found intracellularly in large numbers, perhaps because the higher extracellular concentration of Ca2+ allows for easier fixing of newly evolved motifs that have acquired useful functions. The analysis presented here will inform ongoing efforts toward prediction of similar calcium-binding motifs from sequence information alone

Kryptoracemates

Racemic crystals normally crystallise in centrosymmetric spacegroups containing equal numbers of enantiomers. More rarely, racemates may crystallise in non-centrosymmetric space-groups having glide symmetry or, even more rarely, in space-groups devoid of a centre of inversion, having no rotary-inversion axes nor glide plane. The latter class of crystals form the subject of the present bibliographic review – a survey of kryptoracemic behaviour. The term kryptoracemic alludes to the presence of a hidden or non-crystallographic centre of inversion between two molecules that might otherwise be expected to crystallise in an achiral space-group, often about a centre of inversion. Herein, examples of molecules with stereogenic centres crystallising in one of the 65 Sohncke space-groups are described. Genuine kryptoracemates, i.e. crystals comprising only enantiomorphous pairs are described followed by an overview of non-genuine kryptoracemates whereby the crystal also contains other species such as solvent and/or counterions. A full range, i.e. one to six, stereogenic centres are noted in genuine kryptoracemates. Examples will also be described whereby there are more that one enantiomeric pair of molecules in the crystallographic asymmetric unit. A more diverse range of examples are available for non-genuine kryptoracemates. There are unbalanced species where in addition to the enantiomeric pair of molecules, there is another enantiomeric molecule present. There are examples of genuine co-crystals, solvated species and of salts. Finally, special examples will be highlighted where the counterions are chiral and where they are disparate, both circumstances promoting kryptoracemic behaviour