Publications by authors named "Peter R Johnston"

52 Publications

Approaches for determining cardiac bidomain conductivity values: progress and challenges.

Med Biol Eng Comput 2020 Dec 22;58(12):2919-2935. Epub 2020 Oct 22.

School of Environment and Science, and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD, 4111, Australia.

Modelling the electrical activity of the heart is an important tool for understanding electrical function in various diseases and conduction disorders. Clearly, for model results to be useful, it is necessary to have accurate inputs for the models, in particular the commonly used bidomain model. However, there are only three sets of four experimentally determined conductivity values for cardiac ventricular tissue and these are inconsistent, were measured around 40 years ago, often produce different results in simulations and do not fully represent the three-dimensional anisotropic nature of cardiac tissue. Despite efforts in the intervening years, difficulties associated with making the measurements and also determining the conductivities from the experimental data have not yet been overcome. In this review, we summarise what is known about the conductivity values, as well as progress to date in meeting the challenges associated with both the mathematical modelling and the experimental techniques. Graphical abstract Epicardial potential distributions, arising from a subendocardial ischaemic region, modelled using conductivity data from the indicated studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11517-020-02272-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755382PMC
December 2020

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus 2020 10;11:14. Epub 2020 Jul 10.

International Commission on the Taxonomy of Fungi, Champaign, IL USA.

True fungi () and fungus-like organisms (e.g. , ) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-020-00033-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353689PMC
July 2020

A multigene phylogeny toward a new phylogenetic classification of .

IMA Fungus 2019 7;10. Epub 2019 Jun 7.

Department of Biostatistics, Yale University, 135 College St, New Haven, CT 06510 USA.

Fungi in the class are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented. To fill some of the taxonomic gaps in the 15-gene phylogeny, we further present an ITS gene tree, particularly targeting ex-type specimens of generic type species. A small number of novel taxa are proposed: ord. nov., and and fams. nov. The formal taxonomic changes are limited in part because of the ad hoc nature of taxon and specimen selection, based purely on the availability of data. The phylogeny constitutes a framework for enabling future taxonomically targeted studies using deliberate specimen selection. Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-019-0002-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325659PMC
June 2019

Three new species and a new combination of .

MycoKeys 2019 31;60:1-15. Epub 2019 Oct 31.

Manaaki Whenua Landcare Research, Private Bag 92170, Auckland 1142, New Zealand Manaaki Whenua Landcare Research Auckland New Zealand.

Triblidiaceae (Rhytismatales) currently consists of two genera: and . is the type genus and is characterised by melanized apothecia that occur scattered or in small clusters on the substratum, cleistohymenial (opening in the mesohymenial phase), inamyloid thin-walled asci and hyaline muriform ascospores. Before this study, only the type species, , had DNA sequences in the NCBI GenBank. In this study, six specimens of were collected from China and France and new ITS, mtSSU, LSU and RPB2 sequences were generated. Our molecular phylogenetic analysis and morphological study demonstrated three new species of , which are formally described here: , and . Additionally, our results indicated that that was considered to be distinct from because of its elongated, transversely-septate ascospores, is congeneric with . Therefore, we have placed in synonymy under , rendering Triblidiaceae a monotypic family.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3897/mycokeys.60.46645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838219PMC
October 2019

Differences between models of partial thickness and subendocardial ischaemia in terms of sensitivity analyses of ST-segment epicardial potential distributions.

Math Biosci 2019 12 21;318:108273. Epub 2019 Oct 21.

School of Environment and Science, and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.

Mathematical modelling is a useful technique to help elucidate the connection between non-transmural ischaemia and ST elevation and depression of the ECG. Generally, models represent non-transmural ischaemia using an ischaemic zone that extends from the endocardium partway to the epicardium. However, recent experimental work has suggested that ischaemia typically arises within the heart wall. This work examines the effect of modelling cardiac ischaemia in the left ventricle using two different models: subendocardial ischaemia and partial thickness ischaemia, representing the first and second scenarios, respectively. We found that it is possible, only in the model of subendocardial ischaemia, to see a single minimum on the epicardial surface above the ischaemic region, and this only occurs for low ischaemic thicknesses. This may help to explain the rarity of ST depression that is located over the ischaemic region. It was also found that, in both models, the epicardial potential distribution is most sensitive to the proximity of the ischaemic region to the epicardium, rather than to the thickness of the ischaemic region. Since proximity does not indicate the thickness of the ischaemic region, this suggests a reason why it may be difficult to determine the degree of ischaemia using the ST segment of the ECG.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mbs.2019.108273DOI Listing
December 2019

Overview of , including gen. nov. on .

IMA Fungus 2018 Jul 30;9:371-382. Epub 2018 Oct 30.

Department of Organismic and Evolutionary Biology, Harvard Herbarium, 22 Divinity Avenue, Cambridge MA 02138, United States of America.

The new genus is proposed to accommodate a single species that was repeatedly collected on fallen wood in forests of New Zealand and was previously misidentified as a species. This monotypic genus belongs to , a recently erected family in . is differentiated from other by phragmospores that do not form conidia either in or outside the asci, an exciple of with hyphae widely spaced and strongly gelatinized (plectenchyma), and apically flexuous, partly helicoid paraphyses. The asexual morph was studied in pure culture. Phylogenetic analyses of combined SSU, ITS and LSU sequences strongly support a sister relationship between the sexually typified and the asexually typified " characterized morphologically by forming endoconidia, a feature not found in the genetically distinct type species of . Based on our molecular results, we place the genus in the lineage within .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2018.09.02.08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317588PMC
July 2018

Accuracy of electrocardiographic imaging using the method of fundamental solutions.

Authors:
Peter R Johnston

Comput Biol Med 2018 11 29;102:433-448. Epub 2018 Sep 29.

School of Environment and Science and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia. Electronic address:

Solving the inverse problem of electrocardiology via the Method of Fundamental Solutions has been proposed previously. The advantage of this approach is that it is a meshless method, so it is far easier to implement numerically than many other approaches. However, determining the heart surface potential distribution is still an ill-posed problem and thus requires some form of Tikhonov regularisation to obtain the required distributions. In this study, several methods for determining an "optimal" regularisation parameter are compared in the context of solving the inverse problem of electrocardiology via the Method of Fundamental Solutions. It is found that the Robust Generalised Cross-Validation method most often yields epicardial potential distributions with the least relative error when compared to the input distribution. The study also compares the inverse solutions obtained with the Method of Fundamental Solutions with those obtained in a previous study using the boundary element method. It is found that choosing the best solution methodology and regularisation parameter determination method depends on the particular scenario being considered.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.compbiomed.2018.09.016DOI Listing
November 2018

Sensitivity analysis of ST-segment epicardial potentials arising from changes in ischaemic region conductivities in early and late stage ischaemia.

Comput Biol Med 2018 11 15;102:288-299. Epub 2018 Jun 15.

School of Environment and Science, and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia.

Although computational studies are increasingly used to gain insight into diseases such as myocardial ischaemia, there is still considerable uncertainty about the values for many of the parameters in these studies. This is particularly true for the bidomain conductivity values that are used in normal tissue and, even more so, in ischaemic tissue, when modelling ischaemia. In this work, we extended a previous study that used a half-ellipsoidal model and a realistic model to study subendocardial ischaemia during the ST segment, so that we could simulate both early and late stage ischaemia. We found that, for both stages of ischaemia, there was still the same connection between the degree of ischaemia and the development of features such as minima and maxima in the epicardial potential distribution (EPD), although the magnitudes of the potentials were very often less, which may be significant in terms of detecting them experimentally. Using uncertainty quantification associated with the ischaemic region conductivities, we also determined that the EPD features were sensitive to the ischaemic region extracellular normal and longitudinal conductivities during early stage ischaemia, whereas, during late stage ischaemia, the intracellular longitudinal conductivity was the most significant. However, since we again found that these effects were minor compared with the effects of fibre rotation angle and ischaemic depth, this might suggest that it is not necessary to use different conductivity values inside and outside the ischaemic region when modelling ST segment subendocardial ischaemia, unless the magnitudes of the potentials are an important part of the study.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.compbiomed.2018.06.005DOI Listing
November 2018

Import volumes and biosecurity interventions shape the arrival rate of fungal pathogens.

PLoS Biol 2018 05 31;16(5):e2006025. Epub 2018 May 31.

Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand.

Global trade and the movement of people accelerate biological invasions by spreading species worldwide. Biosecurity measures seek to allow trade and passenger movements while preventing incursions that could lead to the establishment of unwanted pests, pathogens, and weeds. However, few data exist to evaluate whether changes in trade volumes, passenger arrivals, and biosecurity measures have altered rates of establishment of nonnative species over time. This is particularly true for pathogens, which pose significant risks to animal and plant health and are consequently a major focus of biosecurity efforts but are difficult to detect. Here, we use a database of all known plant pathogen associations recorded in New Zealand to estimate the rate at which new fungal pathogens arrived and established on 131 economically important plant species over the last 133 years. We show that the annual arrival rate of new fungal pathogens increased from 1880 to about 1980 in parallel with increasing import trade volume but subsequently stabilised despite continued rapid growth in import trade and recent rapid increases in international passenger arrivals. Nevertheless, while pathogen arrival rates for crop and pasture species have declined in recent decades, arrival rates have increased for forestry and fruit tree species. These contrasting trends between production sectors reflect differences in biosecurity effort and suggest that targeted biosecurity can slow pathogen arrival and establishment despite increasing trade and international movement of people.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.2006025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5978781PMC
May 2018

Determining the most significant input parameters in models of subendocardial ischaemia and their effect on ST segment epicardial potential distributions.

Comput Biol Med 2018 04 10;95:75-89. Epub 2018 Feb 10.

School of Natural Sciences and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia.

There is considerable interest in simulating ischaemia in the ventricle and its effect on the electrocardiogram, because a better understanding of the connection between the two may lead to improvements in diagnosis of myocardial ischaemia. In this work we studied subendocardial ischaemia, in a simplified half-ellipsoidal bidomain model of a ventricle, and its effect on ST segment epicardial potential distributions (EPDs). We found that the EPD changed as the ischaemic depth increased, from a single minimum (min1) over the ischaemic region to a maximum (max) there, with min1 over the border of the region. Lastly, a second minimum (min2) developed on the opposite side of the ischaemic region, in addition to min1 and max. We replicated these results in a realistic ventricular model and showed that the min1 only case could be found for ischaemic depths of up to around 35% of the ventricular wall. In addition, we systematically examined the sensitivity of EPD parameters, such as the potentials and positions of min1, max and min2, to various inputs to the half-ellipsoidal model, such as fibre rotation angle, ischaemic depth and conductivities. We found that the EPD parameters were not sensitive to the blood or transverse bidomain conductivities and were most sensitive to either ischaemic depth and/or fibre rotation angle. This allowed us to conclude that the asynchronous development of the two minima might provide a way of distinguishing between low and high thickness subendocardial ischaemia, and that this method may well be valid despite variability in the population.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.compbiomed.2018.02.003DOI Listing
April 2018

Comparing diversity of fungi from living leaves using culturing and high-throughput environmental sequencing.

Mycologia 2017 Jul-Aug;109(4):643-654. Epub 2017 Nov 15.

a Landcare Research , Private Bag 92170 , Auckland 1142, New Zealand.

High-throughput sequencing technologies using amplicon approaches have changed the way that studies investigating fungal distribution are undertaken. These powerful and time-efficient technologies have the potential for the first time to accurately map fungal distributions across landscapes or changes in diversity across ecological or biological gradients of interest. There is no requirement for a fungus to form a fruiting body to be detected, and both culturable and nonculturable organisms can be detected. Here we use high-throughput amplicon sequencing from bulk DNA extracts to test the impact that biases associated with culture-based methods had on an earlier study that compared the influence of site and host on fungal diversity in Nothofagaceae forests in New Zealand. Both detection methods sampled tissue from the same set of symptomless, living leaves. We found that both the culturing and high-throughput approaches show that host is a stronger driver of fungal community structure than site, but that both methods have some taxonomic biases. We also found that the individual trees selected for high-throughput sampling can impact the alpha-diversity detected and through this could potentially affect subsequent analyses based on a comparison of this diversity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2017.1384712DOI Listing
November 2018

Quantifying the effect of uncertainty in input parameters in a simplified bidomain model of partial thickness ischaemia.

Med Biol Eng Comput 2018 May 20;56(5):761-780. Epub 2017 Sep 20.

Department of Computer Science and INSIGNEO Institute for in-silico Medicine, University of Sheffield, Sheffield, UK.

Reduced blood flow in the coronary arteries can lead to damaged heart tissue (myocardial ischaemia). Although one method for detecting myocardial ischaemia involves changes in the ST segment of the electrocardiogram, the relationship between these changes and subendocardial ischaemia is not fully understood. In this study, we modelled ST-segment epicardial potentials in a slab model of cardiac ventricular tissue, with a central ischaemic region, using the bidomain model, which considers conduction longitudinal, transverse and normal to the cardiac fibres. We systematically quantified the effect of uncertainty on the input parameters, fibre rotation angle, ischaemic depth, blood conductivity and six bidomain conductivities, on outputs that characterise the epicardial potential distribution. We found that three typical types of epicardial potential distributions (one minimum over the central ischaemic region, a tripole of minima, and two minima flanking a central maximum) could all occur for a wide range of ischaemic depths. In addition, the positions of the minima were affected by both the fibre rotation angle and the ischaemic depth, but not by changes in the conductivity values. We also showed that the magnitude of ST depression is affected only by changes in the longitudinal and normal conductivities, but not by the transverse conductivities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11517-017-1714-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906519PMC
May 2018

The effect of boundary conditions on epicardial potential distributions.

Comput Methods Biomech Biomed Engin 2017 Aug 19;20(10):1031-1037. Epub 2017 May 19.

a School of Natural Sciences and Queensland Micro- and Nanotechnology Centre , Griffith University , Nathan , Australia .

This study presents a comparison of semi-analytical and numerical solution techniques for solving the passive bidomain equation in simple tissue geometries containing a region of subendocardial ischaemia. When the semi-analytical solution is based on Fourier transforms, recovering the solution from the frequency domain via fast Fourier transforms imposes a periodic boundary condition on the solution of the partial differential equation. On the other hand, the numerical solution uses an insulation boundary condition. When these techniques are applied to calculate the epicardial surface potentials, both yield a three well potential distribution which is identical if fibre rotation within the tissue is ignored. However, when fibre rotation is included, the resulting three-well distribution rotates, but through different angles, depending on the solution method. A quantitative comparison between the semi-analytical and numerical solutiontechniques is presented in terms of the effect fibre rotation has on the rotation of the epicardial potential distribution. It turns out that the Fourier transform approach predicts a larger rotation of the epicardial potential distribution than the numerical solution. The conclusion from this study is that it is not always possible to use analytical or semi-analytical solutions to check the accuracy of numerical solution procedures. For the problem considered here, this checking is only possible when it is assumed that there is no fibre rotation through the tissue.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/10255842.2017.1327578DOI Listing
August 2017

Fusarium praegraminearum sp. nov., a novel nivalenol mycotoxin-producing pathogen from New Zealand can induce head blight on wheat.

Mycologia 2016 Nov/Dec;108(6):1229-1239

c Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, Illinois 61604.

We report on the molecular and morphological characterization of a novel type B trichothecene toxin-producing species (i.e. B clade) recovered from litter in a maize field near Wellington, New Zealand, which is described as Fusarium praegraminearum sp. nov. This species was initially identified as F. acuminatum based on morphological characters. However, it differs from this species by producing longer, slightly asymmetrically curved macroconidia in which the apical cell is not as pointed and by its much faster colony growth rate on agar. Molecular phylogenetic analyses of portions of 13 genes resolved F. praegraminearum as the most basal species within the B clade. Mycotoxin analyses demonstrated that it was able to produce 4-acetylnivalenol and 4,15-diacetylnivalenol trichothecenes, the nontrichothecene sesquiterpenes culmorin and hydroxy-culmorins, and the estrogen zearalenone in vitro. Results of a pathogenicity experiment revealed that F. praegraminearum induced moderate head blight on wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3852/16-110DOI Listing
January 2018

Taxonomic similarity, more than contact opportunity, explains novel plant-pathogen associations between native and alien taxa.

New Phytol 2016 Nov 21;212(3):657-667. Epub 2016 Jul 21.

Bio-Protection Research Centre, Lincoln University, PO Box 85084, Lincoln, 7647, New Zealand.

Novel associations between plants and pathogens can have serious impacts on managed and natural ecosystems world-wide. The introduction of alien plants increases the potential for biogeographically novel plant-pathogen associations to arise when pathogens are transmitted from native to alien plant species and vice versa. We quantified biogeographically novel associations recorded in New Zealand over the last 150 yr between plant pathogens (fungi, oomycetes and plasmodiophorids) and vascular plants. We examined the extent to which taxonomic similarity, pathogen traits, contact opportunity and sampling effort could explain the number of novel associates for host and pathogen species. Novel associations were common; approximately one-third of surveyed plants and pathogens were recorded with at least one biogeographically novel associate. Native plants had more alien pathogens than vice versa. Taxonomic similarity between the native and alien flora and the total number of recorded associations (a measure of sampling effort) best explained the number of novel associates among species. The frequency of novel associations and the importance of sampling effort as an explanatory variable emphasize the need for effective monitoring and risk assessment tools to mitigate the potential environmental and economic impact of novel pathogen associations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.14077DOI Listing
November 2016

Applying the stochastic Galerkin method to epidemic models with uncertainty in the parameters.

Math Biosci 2016 07 14;277:25-37. Epub 2016 Apr 14.

School of Natural Sciences, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia. Electronic address:

Parameters in modelling are not always known with absolute certainty. In epidemic modelling, this is true of many of the parameters. It is important for this uncertainty to be included in any model. This paper looks at using the stochastic Galerkin method to solve an SIR model with uncertainty in the parameters. The results obtained from the stochastic Galerkin method are then compared with results obtained through Monte Carlo sampling. The computational cost of each method is also compared. It is shown that the stochastic Galerkin method produces good results, even at low order expansions, that are much less computationally expensive than Monte Carlo sampling. It is also shown that the stochastic Galerkin method does not always converge and this non-convergence is explored.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mbs.2016.03.012DOI Listing
July 2016

Application of robust Generalised Cross-Validation to the inverse problem of electrocardiology.

Comput Biol Med 2016 Feb 29;69:213-25. Epub 2015 Dec 29.

School of Natural Sciences and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.

Robust Generalised Cross-Validation was proposed recently as a method for determining near optimal regularisation parameters in inverse problems. It was introduced to overcome a problem with the regular Generalised Cross-Validation method in which the function that is minimised to obtain the regularisation parameter often has a broad, flat minimum, resulting in a poor estimate for the parameter. The robust method defines a new function to be minimised which has a narrower minimum, but at the expense of introducing a new parameter called the robustness parameter. In this study, the Robust Generalised Cross-Validation method is applied to the inverse problem of electrocardiology. It is demonstrated that, for realistic situations, the robustness parameter can be set to zero. With this choice of robustness parameter, it is shown that the robust method is able to obtain estimates of the regularisation parameter in the inverse problem of electrocardiology that are comparable to, or better than, many of the standard methods that are applied to this inverse problem.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.compbiomed.2015.12.011DOI Listing
February 2016

Harorepupu aotearoa (Onygenales) gen. sp. nov.; a threatened fungus from shells of Powelliphanta and Paryphanta snails (Rhytididae).

IMA Fungus 2015 Jun 1;6(1):135-43. Epub 2015 Jun 1.

Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, Canada K1N 6N5 ; Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6.

A cleistothecial fungus, known only from the shells of giant land snails of the family Rhytidae, is described as a new genus and species within Onygenales, Harorepupu aotearoa gen. sp. nov. Known only from the sexual morph, this fungus is characterized morphologically by a membranous ascoma with no appendages and ascospores with a sparse network of ridges. Ribosomal DNA sequences place the new species within Onygenales, but comparison with the known genetic diversity within the order linked it to no existing genus or family. It is the first species of Onygenales reported from the shells of terrestrial snails. This fungus has been listed as Critically Endangered in New Zealand and has been previously referred to as 'Trichocomaceae gen. nov.' in those threat lists.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2015.06.01.08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500079PMC
June 2015

Determining six cardiac conductivities from realistically large datasets.

Math Biosci 2015 Aug 3;266:15-22. Epub 2015 Jun 3.

School of Natural Sciences and Queensland Micro and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.

Simulation studies of cardiac electrophysiological behaviour that use the bidomain model require accurate values for the bidomain extracellular and intracellular conductivities to produce useful results. This work considers an inversion algorithm, which has previously been shown, using simulated data, to be capable of retrieving six bidomain conductivities and the fibre rotation angle from measurements of electric potential made in the heart. The aim here is to see whether it is possible to improve the accuracy of the retrieved parameters. The scenario of retrieving only conductivities and not fibre rotation is examined but this does not lead to a worthwhile improvement in retrieval accuracy. It is also found that it is possible to retrieve the bidomain conductivities using not two but just one pass of the algorithm, made on a 'widely-spaced' electrode set. This appears to work because the algorithm is still very sensitive to the extracellular conductivities. However, the single-pass method is not recommended because the intracellular conductivities that are retrieved are not as accurate as those that are retrieved in the usual two-pass method, particularly for higher values of added noise. The second part of this work considers retrieving the six conductivities and fibre rotation from realistically large sets of potential measurements and identifies the best data analysis method. It is found that, even with added noise of up to 40%, the extracellular conductivities can still be retrieved extremely accurately (relative errors of around 2% on average) and so can the intracellular longitudinal conductivities and fibre rotation (errors less than 8% on average). The remaining intracellular conductivities have errors that are generally less than twice the added noise, particularly for the higher noise values.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mbs.2015.05.008DOI Listing
August 2015

Fusarium dactylidis sp. nov., a novel nivalenol toxin-producing species sister to F. pseudograminearum isolated from orchard grass (Dactylis glomerata) in Oregon and New Zealand.

Mycologia 2015 Mar-Apr;107(2):409-18. Epub 2014 Dec 30.

Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania 16802.

The B trichothecene toxin-producing clade (B clade) of Fusarium includes the etiological agents of Fusarium head blight, crown rot of wheat and barley and stem and ear rot of maize. B clade isolates also have been recovered from several wild and cultivated grasses, including Dactylis glomerata (orchard grass or cock's foot), one of the world's most important forage grasses. Two isolates from the latter host are formally described here as F. dactylidis. Phenotypically F. dactylidis most closely resembles F. ussurianum from the Russian Far East. Both species produce symmetrical sporodochial conidia that are similar in size and curved toward both ends. However, conidia of F. ussurianum typically end in a narrow apical beak while the apical cell of F. dactylidis is acute. Fusarium dactylidis produced nivalenol mycotoxin in planta as well as low but detectable amounts of the estrogenic mycotoxin zearalenone in vitro. Results of a pathogenicity test revealed that F. dactylidis induced mild head blight on wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3852/14-213DOI Listing
August 2015

Recommendations on generic names competing for use in Leotiomycetes (Ascomycota).

IMA Fungus 2014 Jun 18;5(1):91-120. Epub 2014 Jun 18.

Czech Collection of Microorganisms, Institute of Experimental Biology, Masaryk University, 625 00 Brno, Czech Republic.

In advancing to one scientific name for fungi, this paper treats genera competing for use in the phylogenetically defined class Leotiomycetes except for genera of Erysiphales. Two groups traditionally included in the so-called "inoperculate discomycetes" have been excluded from this class and are also not included here, specifically Geoglossomycetes and Orbiliomycetes. A recommendation is made about the generic name to use in cases in which two or more generic names are synonyms or taxonomically congruent along with the rationale for the recommendation. In some cases the recommended generic name does not have priority or is based on an asexual type species, thus needs to be protected and ultimately approved according to Art. 57.2 of the International Code of Nomenclature for algae, fungi and plants (ICN). A table is presented listing all competing generic names and their type species noting the recommended generic name. New combinations are introduced for the oldest epithet in the recommended genus including Ascocalyx berenice, Ascoconidium purpurascens, Ascocoryne albida, A. trichophora, Blumeriella filipendulae, B. ceanothi, Botrytis arachidis, B. fritillariae-pallidoflori, Calloria urticae, Calycellina aspera, Dematioscypha delicata, Dermea abietinum, D. boycei, D. stellata, Diplocarpon alpestre, D. fragariae, Godroniopsis peckii, Grovesinia moricola, Heterosphaera sublineolata, Hyphodiscus brachyconium, H. brevicollaris, H. luxurians, Leptotrochila campanulae, Monilinia polystroma, Neofabraea actinidae, N. citricarpa, N. vagabunda, Oculimacula aestiva, O. anguioides, Pezicula brunnea, P. californiae, P. cornina, P. diversispora, P. ericae, P. melanogena, P. querciphila, P. radicicola, P. rhizophila, Phialocephala piceae, Pilidium lythri, Rhabdocline laricis, Streptotinia streptothrix, Symphyosirinia parasitica, S. rosea, Unguiculariopsis caespitosa, and Vibrissea laxa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2014.05.01.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107902PMC
June 2014

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Authors:
Conrad L Schoch Barbara Robbertse Vincent Robert Duong Vu Gianluigi Cardinali Laszlo Irinyi Wieland Meyer R Henrik Nilsson Karen Hughes Andrew N Miller Paul M Kirk Kessy Abarenkov M Catherine Aime Hiran A Ariyawansa Martin Bidartondo Teun Boekhout Bart Buyck Qing Cai Jie Chen Ana Crespo Pedro W Crous Ulrike Damm Z Wilhelm De Beer Bryn T M Dentinger Pradeep K Divakar Margarita Dueñas Nicolas Feau Katerina Fliegerova Miguel A García Zai-Wei Ge Gareth W Griffith Johannes Z Groenewald Marizeth Groenewald Martin Grube Marieka Gryzenhout Cécile Gueidan Liangdong Guo Sarah Hambleton Richard Hamelin Karen Hansen Valérie Hofstetter Seung-Beom Hong Jos Houbraken Kevin D Hyde Patrik Inderbitzin Peter R Johnston Samantha C Karunarathna Urmas Kõljalg Gábor M Kovács Ekaphan Kraichak Krisztina Krizsan Cletus P Kurtzman Karl-Henrik Larsson Steven Leavitt Peter M Letcher Kare Liimatainen Jian-Kui Liu D Jean Lodge Janet Jennifer Luangsa-ard H Thorsten Lumbsch Sajeewa S N Maharachchikumbura Dimuthu Manamgoda María P Martín Andrew M Minnis Jean-Marc Moncalvo Giuseppina Mulè Karen K Nakasone Tuula Niskanen Ibai Olariaga Tamás Papp Tamás Petkovits Raquel Pino-Bodas Martha J Powell Huzefa A Raja Dirk Redecker J M Sarmiento-Ramirez Keith A Seifert Bhushan Shrestha Soili Stenroos Benjamin Stielow Sung-Oui Suh Kazuaki Tanaka Leho Tedersoo M Teresa Telleria Dhanushka Udayanga Wendy A Untereiner Javier Diéguez Uribeondo Krishna V Subbarao Csaba Vágvölgyi Cobus Visagie Kerstin Voigt Donald M Walker Bevan S Weir Michael Weiß Nalin N Wijayawardene Michael J Wingfield J P Xu Zhu L Yang Ning Zhang Wen-Ying Zhuang Scott Federhen

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

A multi-electrode array and inversion technique for retrieving six conductivities from heart potential measurements.

Med Biol Eng Comput 2013 Dec 28;51(12):1295-303. Epub 2013 Jul 28.

School of Biomolecular and Physical Science, Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD, 4111, Australia,

A method for accurately finding cardiac bidomain conductivity parameters is a crucial part of efforts to study and understand the electrical functioning of the heart. The bidomain model considers current flowing along (longitudinal) and across (transverse) sheets of cardiac fibres, as well as between these sheets (normal), in both the extracellular and intracellular domains, which leads to six conductivity values. To match experimental studies, such a method must be able to determine these six conductivity values, not just the four where it is assumed that the transverse and normal conductivities are equal. This study presents a mathematical model, solution technique, multi-electrode array and two-pass inversion method, which can be used to retrieve all six conductivities from measurements of electrical potential made on the array. Simulated measurements of potential, to which noise is added, are used to demonstrate the ability of the method to retrieve the conductivity values. It is found that not only is it possible to accurately retrieve all six conductivity values, as well as a value for fibre rotation angle, but that the accuracy of such retrievals is comparable to the accuracy found in a previous study when only four conductivities (and fibre rotation) were retrieved.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11517-013-1101-2DOI Listing
December 2013

A new species of the lenticel fungal genus Claviradulomyces (Ostropales) from the Brazilian Atlantic forest tree Xylopia sericea (Annonaceae).

IMA Fungus 2012 Dec 15;3(2):135-41. Epub 2012 Nov 15.

Departamento de Fitopatologia, Universidade Federal de Viçosa, 36750 Viçosa, Minas Gerais, Brazil;

Claviradulomyces xylopiae sp. nov. is introduced for a fungus occurring in association with abnormal (enlarged, spongy) lenticels of Xylopia sericea (Annonaceae), a common tree of the Atlantic forest and Cerrado ecosystems in Brazil. This is the second species described in the genus and, although it is morphologically distinct from the type species, C. dabeicola from West Africa, it possesses the same characteristics. Apothecial ascomata have periphysoids and paraphyses that are inflated apically (clavate), and ornamented with denticles (raduliform). Furthermore, similar to the type species, it also has long-cylindric or acerose, aseptate ascospores and conidia. An additional asexual morph was produced in culture and is described. Molecular studies of C. dabeicola and the new species confirmed a placement in Ostropales, although a relationship to Odontotremataceae was not supported. Both species were consistently in association with abnormal lenticular development on their woody hosts. It remains to be ascertained, however, if these are the causal agents of the bark disorders, or, simply, opportunistic colonisers. The finding of the second species in the genus Claviradulomyces on a plant from a distantly related family to that of the host of C. dabeicola (Erythroxylaceae) for the genus on a different continent suggests that fungi in this genus may be common on lenticels of other woody plants, and could even have a pantropical distribution. It is possible that fungi in the genus have remained unreported until now because lenticels have remained neglected as a habitat surveyed by mycologists.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2012.03.02.05DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539316PMC
December 2012

The amsterdam declaration on fungal nomenclature.

IMA Fungus 2011 Jun 7;2(1):105-12. Epub 2011 Jun 7.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, E-28040 Madrid, Spain; and Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK;

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2011.02.01.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317370PMC
June 2011

Patterns of fungal diversity in New Zealand Nothofagus forests.

Fungal Biol 2012 Mar 17;116(3):401-12. Epub 2012 Jan 17.

Landcare Research, Private Bag 92170, Auckland 1142, New Zealand.

The development of protocols for the conservation of fungi requires knowledge of the factors controlling their distribution, diversity, and community composition. Here we compare patterns of variation in fungal communities across New Zealand's Nothofagus forests, reportedly the most myco-diverse in New Zealand and hence potentially key to effective conservation of fungi in New Zealand. Diversity of leaf endophytic fungi, as assessed by culturing on agar plates, is assessed for three Nothofagus sp. growing in mixed stands from four sites. Host species was found to have a greater influence on fungal community assemblage than site. The leaf endophyte communities associated with Nothofagus solandri and Nothofagus fusca (both Nothofagus subgenus Fuscopora), were more similar to each other than either were to the community associated with Nothofagus menziesii (Nothofagus subgenus Lophozonia). The broad taxonomic groups isolated, identified on the basis of internal transcribed spacer (ITS) sequences, were similar to those found in similar studies from other parts of the world, and from an earlier study on the endophyte diversity in four podocarp species from New Zealand, but there were few matches at species level. Average levels of endophyte species diversity associated with single Nothofagus species and single podocarp species were similar, despite historical literature and collection data recording more than twice as many fungal species on average from the Nothofagus species. The significance of these findings to fungal conservation is discussed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.funbio.2011.12.010DOI Listing
March 2012

Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST.

Mycologia 2012 Mar-Apr;104(2):427-45. Epub 2011 Nov 15.

National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Peoria, IL 61604-3999, USA.

We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed at the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to aid molecular identifications of unknowns via the FUSARIUM-ID and Fusarium MLST online databases and analysis packages. Analyses of a 190-taxon, two-locus dataset, which included 159 isolates from insects, indicated that: (i) insect-associated fusaria were nested within 10 species complexes spanning the phylogenetic breadth of Fusarium, (ii) novel, putatively unnamed insecticolous species were nested within 8/10 species complexes and (iii) Latin binomials could be applied with confidence to only 18/58 phylogenetically distinct fusaria associated with pest insects. Phylogenetic analyses of an 82-taxon, three-locus dataset nearly fully resolved evolutionary relationships among the 10 clades containing insecticolous fusaria. Multilocus typing of isolates within four species complexes identified surprisingly high genetic diversity in that 63/65 of the fusaria typed represented newly discovered haplotypes. The DNA sequence data, together with corrected ABI sequence chromatograms and alignments, have been uploaded to the following websites dedicated to identifying fusaria: FUSARIUM-ID (http://isolate.fusariumdb.org) at Pennsylvania State University's Department of Plant Pathology and Fusarium MLST (http://www.cbs.knaw.nl/fusarium) at the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3852/11-179DOI Listing
July 2013

A sensitivity study of conductivity values in the passive bidomain equation.

Authors:
Peter R Johnston

Math Biosci 2011 Aug 23;232(2):142-50. Epub 2011 May 23.

School of Biomolecular and Physical Sciences, Griffith University, Nathan, QLD, Australia.

There is a complex interplay between the four conductivity values used in the bidomain equation and the resulting electric potential distribution in cardiac tissue arising from subendocardial ischaemia. Based on the three commonly used experimentally derived conductivity data sets, a non-dimensional formulation of the passive bidomain equation is derived, which gives rise naturally to several dimensionless conductivity ratios. The data sets are then used to define a parameter space of these ratios, which is studied by considering the correlation coefficients between different epicardial potential distributions. From this study, it is shown that the ratio of the intracellular longitudinal conductivity to the intracellular transverse conductivity is the key parameter in explaining the differences between the epicardial potential distributions observed with these three data sets.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mbs.2011.05.004DOI Listing
August 2011

Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.

PLoS One 2011 Apr 21;6(4):e19039. Epub 2011 Apr 21.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019039PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080880PMC
April 2011

A nondimensional formulation of the passive bidomain equation.

Authors:
Peter R Johnston

J Electrocardiol 2011 Mar-Apr;44(2):184-8. Epub 2011 Jan 20.

School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Rd, Nathan, QLD 4111, Australia.

Simulation studies of ST depression arising from subendocardial ischemia show a marked difference in the resulting epicardial potential distributions depending on which of the 3 common experimentally determined bidomain conductivity data sets is chosen. Here, the governing equation is rendered nondimensional by dividing by the difference in normal and ischemic transmembrane potentials during the ST segment and by the sum of the intracellular and extracellular conductivities in the transverse direction, yielding the ratio of the sum of the intracellular and extracellular longitudinal conductivities divided by the sum of the intracellular and extracellular transverse conductivities as a dimensionless group. Averaging this ratio over the 3 sets of experimentally determined data gives the value of 3.21 ± 0.08. The effect of this narrow range means that the left-hand side of the governing equation can be considered, as a good approximation, to be the same for all these sets of conductivity data. Hence, the right hand of the nondimensional differential equation contains all the necessary information to compare the effect different conductivity data sets have on the epicardial potential distribution. As an example, an explanation is given as to why values from one data set give rise to epicardial distributions that are markedly different from those obtained from the other 2 data sets.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jelectrocard.2010.11.015DOI Listing
July 2011