Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples

Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results—a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology

Sensitive Observations of Radio Recombination Lines in Orion and W51: The Data and Detection of Systematic Recombination Line Blueshifts Proportional to Impact Broadening

Sensitive spectral observations made in two frequency bands near 6.0 and 17.6 GHz are described for Orion and W51. Using frequency switching we were able to achieve a dynamic range in excess of 10,000 without fitting sinusoidal or polynomial baselines. This enabled us to detect lines as weak as T$_{A} ~1mK in these strong continuum sources. Hydrogen recombination lines with$\Delta n$ as high as 25 have been detected in Orion. In the Orion data, where the lines are stronger, we have also detected a systematic shift in the line center frequencies proportional to linewidth that cannot be explained by normal optical depth effects.Comment: 22 pages, 13 figures. Accepted for publication in Astrophysics and Space Scienc

Effects of magmatic volatile influx in mafic VMS hydrothermal systems: Evidence from the Troodos ophiolite, Cyprus

The Troodos ophiolite, Cyprus is the principal on- land analogue for mafic-hosted volcanogenic massive sulfide (VMS) deposits. This study, for the first time, presents sulfur isotope (δ34S) data on a regional scale from VMS deposits and other mineralised zones across the Troodos ophiolite. In combination δ34S, Se/S ratios and trace element chemistry (e.g., Se, Cu and Au) of different hydrothermal sulfides are used to assess variations in magmatic volatile influx and the source of metals and sulfur in ancient hydrothermal systems. Sulfur isotope analyses (n = 180) across 19 mineral deposits indicate a variable source of sulfur in the Troodos VMS hydrothermal system, this in turn allows a variable source of metals to be inferred. Pyrite δ34S range from −5.5‰ to +13.2‰ with an average of +4.6‰ (n = 160) for all deposits investigated. These δ34S variations cannot only be explained by variable proportions of thermochemical seawater sulfate reduction (δ34S +18 to +19‰) and leaching of primary magmatic sulfur from igneous rocks (δ34S 0-1‰). Consequently, two processes are proposed, explaining the trace metal and δ34S variation across the Troodos ore-forming systems including, i) a variable source of metals in the sheeted dyke complex and ii) the addition of a magmatic volatile-rich phase to the VMS hydrothermal systems. Two distinct lava units exist in the Troodos stratigraphy, namely the upper and lower pillow lavas (UPL and LPL). The more primitive UPL are enriched in Au, Se and Cu relative to As, Sb and Zn that are concentrated in the LPL. Some VMS deposits pre-date the formation of the UPL (e.g., Agrokipia A) suggesting Se, Cu and Au depleted source rocks. Hence, the stratigraphic position of VMS deposits and the ratio of UPL:LPL affinity elements (e.g., As + Zn + Sb vs. Cu + Se + Au) imply a systematic relationship between trace element distribution and stratigraphic depth; this relates to the relative proportion of UPL and LPL affinity lavas within the metal source region. δ34S values <0‰ recorded in some VMS deposits that are less than the Troodos magmatic mean of 0- 1‰ may be related to anhydrite buffering during fluid ascent, microbial sulfate reduction or the direct contribution of magmatically derived sulfur, to the hydrothermal system from an underlying magma chamber via volatile exsolution. We propose that negative δ34S values combined with Se/S 106 ratios >500 in pyrite suggest the contribution of a magmatic volatile component (e.g., Apliki and Skouriotissa). We demonstrate that the source of metals and sulfur in the Troodos VMS hydrothermal system is affected by regional scale processes related to i) variable source lithologies and, ii) the contribution of a magmatic volatile phase to some Troodos VMS hydrothermal systems

Height Systems and Vertical Datums: a Review in the Australian Context

This paper reviews (without equations) the various definitions of height systems and vertical geodetic datum surfaces, together with their practical realisation for users in Australia. Excluding geopotential numbers, a height system is a one-dimensional coordinate system used to express the metric distance (height) of a point from some reference surface. Its definition varies according to the reference surface chosen and the path along which the height is measured. A vertical geodetic datum is the practical realisation of a height system and its reference surface for users, nominally tied to mean sea level. In Australia, the normal-orthometric height system is used, which is embedded in the Australian Height Datum (AHD). The AHD was realised by the adjustment of ~195,000 km of spirit-levelling observations fixed to limited-term observations of mean sea level at multiple tide-gauges. The paper ends by giving some explanation of the problems with the AHD and of the differences between the AHD and the national geoid model, pointing out that it is preferable to recompute the AHD

Search for Tensor, Vector, and Scalar Polarizations in the Stochastic Gravitational-Wave Background

The detection of gravitational waves with Advanced LIGO and Advanced Virgo has enabled novel tests of general relativity, including direct study of the polarization of gravitational waves. While general relativity allows for only two tensor gravitational-wave polarizations, general metric theories can additionally predict two vector and two scalar polarizations. The polarization of gravitational waves is encoded in the spectral shape of the stochastic gravitational-wave background, formed by the superposition of cosmological and individually unresolved astrophysical sources. Using data recorded by Advanced LIGO during its first observing run, we search for a stochastic background of generically polarized gravitational waves. We find no evidence for a background of any polarization, and place the first direct bounds on the contributions of vector and scalar polarizations to the stochastic background. Under log-uniform priors for the energy in each polarization, we limit the energy densities of tensor, vector, and scalar modes at 95% credibility to Ω0T<5.58×10-8, Ω0V<6.35×10-8, and Ω0S<1.08×10-7 at a reference frequency f0=25 Hz. © 2018 American Physical Society

Tellurium and Selenium Systematics in Mafic VMS from Cyprus: Mineral, Mound and Regional Scale Controls

Tellurium (Te) and selenium (Se) are critical elements used in the production of photovoltaic solar cells. Their criticality is paralleled by a poor understanding of their distribution and enrichment in a range of ore forming environments. This study aims at understanding Te and Se systematics on a range of scales in mafic VMS systems. To investigate this, &gt;20 VMS of the Troodos ophiolite have been sampled. On a mineral scale, the distribution of Te and Se is not uniform between different sulfide phases; chalcopyrite is preferentially enriched in Se, averaging 1147 ppm (n=202), whilst pyrite averages 439 ppm (n=1570). In contrast, Te is preferentially incorporated in pyrite averaging 17 ppm compared to 6 ppm in chalcopyrite. Some VMS deposits exhibit evidence of Se remobilization leading to enrichment of Se in pyrite up to 4950 ppm. This demonstrates the significance of fluctuating fluid redox in VMS mineralisation and the enrichment of Se. Additionally, on an ophiolite scale, trace element distribution demonstrates a robust link between magmatic volatile influx and Te and Se enrichment in mafic VMS deposits

Tellurium and Selenium Systematics in Mafic VMS from Cyprus: Mineral, Mound and Regional Scale Controls

Tellurium (Te) and selenium (Se) are critical elements used in the production of photovoltaic solar cells. Their criticality is paralleled by a poor understanding of their distribution and enrichment in a range of ore forming environments. This study aims at understanding Te and Se systematics on a range of scales in mafic VMS systems. To investigate this, &gt;20 VMS of the Troodos ophiolite have been sampled. On a mineral scale, the distribution of Te and Se is not uniform between different sulfide phases; chalcopyrite is preferentially enriched in Se, averaging 1147 ppm (n=202), whilst pyrite averages 439 ppm (n=1570). In contrast, Te is preferentially incorporated in pyrite averaging 17 ppm compared to 6 ppm in chalcopyrite. Some VMS deposits exhibit evidence of Se remobilization leading to enrichment of Se in pyrite up to 4950 ppm. This demonstrates the significance of fluctuating fluid redox in VMS mineralisation and the enrichment of Se. Additionally, on an ophiolite scale, trace element distribution demonstrates a robust link between magmatic volatile influx and Te and Se enrichment in mafic VMS deposits