A Study of the Dynamics of Cardiac Ischemia using Experimental and Modeling Approaches

The dynamics of cardiac ischemia was investigated using experimental studies and computer simulations. An experimental model consisting of an isolated and perfused canine heart with full control over blood flow rate to a targeted coronary artery was used in the experimental study and a realistically shaped computer model of a canine heart, incorporating anisotropic conductivity and realistic fiber orientation, was used in the simulation study. The phenomena investigated were: (1) the influence of fiber rotation on the epicardial potentials during ischemia and (2) the effect of conductivity changes during a period of sustained ischemia. Comparison of preliminary experimental and computer simulation results suggest that as the ischemic region grows from the endocardium towards the epicardium, the epicardial potential patterns follow the rotating fiber orientation in the myocardium. Secondly, in the experimental studies it was observed that prolonged ischemia caused a subsequent reduction in the magnitude of epicardial potentials. Similar results were obtained from the computer model when the conductivity of the tissue in the ischemic region was reduce

Mechanistic Inquiry into the Role of Tissue Remodeling in Fibrotic Lesions in Human Atrial Fibrillation

AbstractAtrial fibrillation (AF), the most common arrhythmia in humans, is initiated when triggered activity from the pulmonary veins propagates into atrial tissue and degrades into reentrant activity. Although experimental and clinical findings show a correlation between atrial fibrosis and AF, the causal relationship between the two remains elusive. This study used an array of 3D computational models with different representations of fibrosis based on a patient-specific atrial geometry with accurate fibrotic distribution to determine the mechanisms by which fibrosis underlies the degradation of a pulmonary vein ectopic beat into AF. Fibrotic lesions in models were represented with combinations of: gap junction remodeling; collagen deposition; and myofibroblast proliferation with electrotonic or paracrine effects on neighboring myocytes. The study found that the occurrence of gap junction remodeling and the subsequent conduction slowing in the fibrotic lesions was a necessary but not sufficient condition for AF development, whereas myofibroblast proliferation and the subsequent electrophysiological effect on neighboring myocytes within the fibrotic lesions was the sufficient condition necessary for reentry formation. Collagen did not alter the arrhythmogenic outcome resulting from the other fibrosis components. Reentrant circuits formed throughout the noncontiguous fibrotic lesions, without anchoring to a specific fibrotic lesion

Interpretable Modeling and Reduction of Unknown Errors in Mechanistic Operators

Prior knowledge about the imaging physics provides a mechanistic forward operator that plays an important role in image reconstruction, although myriad sources of possible errors in the operator could negatively impact the reconstruction solutions. In this work, we propose to embed the traditional mechanistic forward operator inside a neural function, and focus on modeling and correcting its unknown errors in an interpretable manner. This is achieved by a conditional generative model that transforms a given mechanistic operator with unknown errors, arising from a latent space of self-organizing clusters of potential sources of error generation. Once learned, the generative model can be used in place of a fixed forward operator in any traditional optimization-based reconstruction process where, together with the inverse solution, the error in prior mechanistic forward operator can be minimized and the potential source of error uncovered. We apply the presented method to the reconstruction of heart electrical potential from body surface potential. In controlled simulation experiments and in-vivo real data experiments, we demonstrate that the presented method allowed reduction of errors in the physics-based forward operator and thereby delivered inverse reconstruction of heart-surface potential with increased accuracy.Comment: 11 pages, Conference: Medical Image Computing and Computer Assisted Interventio

Influence of Material Parameter Variability on the Predicted Coronary Artery Biomechanical Environment via Uncertainty Quantification

Central to the clinical adoption of patient-specific modeling strategies is demonstrating that simulation results are reliable and safe. Simulation frameworks must be robust to uncertainty in model input(s), and levels of confidence should accompany results. In this study we applied a coupled uncertainty quantification-finite element (FE) framework to understand the impact of uncertainty in vascular material properties on variability in predicted stresses. Univariate probability distributions were fit to material parameters derived from layer-specific mechanical behavior testing of human coronary tissue. Parameters were assumed to be probabilistically independent, allowing for efficient parameter ensemble sampling. In an idealized coronary artery geometry, a forward FE model for each parameter ensemble was created to predict tissue stresses under physiologic loading. An emulator was constructed within the UncertainSCI software using polynomial chaos techniques, and statistics and sensitivities were directly computed. Results demonstrated that material parameter uncertainty propagates to variability in predicted stresses across the vessel wall, with the largest dispersions in stress within the adventitial layer. Variability in stress was most sensitive to uncertainties in the anisotropic component of the strain energy function. Unary and binary interactions within the adventitial layer were the main contributors to stress variance, and the leading factor in stress variability was uncertainty in the stress-like material parameter summarizing contribution of the embedded fibers to the overall artery stiffness. Results from a patient-specific coronary model confirmed many of these findings. Collectively, this highlights the impact of material property variation on predicted artery stresses and presents a pipeline to explore and characterize uncertainty in computational biomechanics.Comment: To appear: Biomechanics and Modeling in Mechanobiolog

Crop Updates 2009 - Cereals

This session covers twenty seven papers from different authors: PLENARY 1. Building soil carbon for productivity and implications for carbon accounting, Jeff Baldock, CSIRO Land and Water, Adelaide, SA 2. Fact or Fiction: Who is telling the truth and how to tell the difference, Doug Edmeades, agKnowledge Ltd, Hamilton 3. Four decades of crop sequence trials in Western Australia, Mark Seymour,Department of Agriculture and Food BREAK CROPS 4. 2008 Break Crops survey Report, Paul Carmody,Development Officer, Department of Agriculture and Food 5. Attitudes of Western Australian wheatbelt growers to ‘Break Crops’, Paul Carmody and Ian Pritchard, Development Officers, Department of Agriculture and Food 6. The value of organic nitrogen from lupins, Alan Meldrum, Pulse Australia 7.The area of break crops on farm: What farmers are doing compared to estimates based on maximising profit, Michael Robertson and Roger Lawes,CSIRO Floreat, Rob Sands,FARMANCO Farm Consultants, Peter White,Department of Agriculture and Food, Western Australia, Felicity Byrne and Andrew Bathgate,Farming Systems Analysis CROP SPECIFIC Breeding 8. Identification of WALAB2014 as a potential albus lupin variety for northern agricultural region of Western Australia, Kedar Adhikari, Department of Agriculture and Food 9. Enhancement of black spot resistance in field pea, Kedar Adhikari, Tanveer Khan, Stuart Morgan and Alan Harris, Department of Agriculture and Food 10. Desi chickpea breeding: Evaluation of advanced line, Khan, TN1, Harris, A1, Gaur, P2, Siddique, KHM3, Clarke, H4, Turner, NC4, MacLeod, W1, Morgan, S1 1Department of Agriculture and Food, Western Australia, 2International Crop Research Institute for the Semi Arid Tropics (ICRISAT), 3The University of Western Australia, 4Centre for Legumes in Mediterranean Agriculture 11. Pulse Breeding Australia-Australian Field Pea Improvement Program (AFPIP), Ian Pritchard1, Chris Veitch1, Stuart Morgan1, Alan Harris1 and Tony Leonforte 2 1 Department of Agriculture and Food, Western Australia, 2 Department off Primary Industries, Victoria Disease 12. Interaction between wheat varieties and fungicides to control stripe rust for grain and quality, Kith Jayasena, Geoff Thomas, Rob Loughman, Kazue Tanaka and Bill MacLeod, Department of Agriculture and Food 13. Findings of canola disease survey 2008 and its implications for better disease management in 2009, Ravjit Khangura, WJ MacLeod, P White, P Carmody and M Amjad, Department of Agriculture and Food 14. Combating wheat leaf diseases using genome sequencing and functional genomics, Richard Oliver, Australian Centre for Necrotrophic Fungal Pathogens, Murdoch University 15. Distribution and survival of wheat curl mite (Aceria tosichella), vector of Wheat Streak Mosaic Virus, in the WA grainbelt during 2008, Dusty Severtson, Peter Mangano, John Botha and Brenda Coutts, Department of Agriculture and Food 16. Partial resistance to Stagonspora (Septoria) Partial resistance to Stagonospora (Septoria) nodorum blotch and response to fungicide in a severe epidemic scenario, Manisha Shankar1, Richard Oliver2, Kasia Rybak2and Rob Loughman1 1Department of Agriculture and Food, Western Australia, 2Australian Centre for Necrotrophic Fungal Pathogens, Murdoch University, Western Australia 17. Black pod syndrome in lupins can be reduced by regular insecticide sprays, Peter White and Michael Baker,Department of Agriculture and Food Variety performance 18. Incorporating new herbicide tolerant juncea canola into low rainfall cropping systems in Western Australia, Mohammad Amjad, Department of Agriculture and Food 19. Varietal differences in germ end staining of barley, Andrea Hills,Department of Agriculture and Food 20. Wheat variety performance in the Central Agricultural Region in 2008, Shahajahan Miyan, Department of Agriculture and Food 21. Barley variety identification using DNA fingerprinting, Peter Portmann, Agriconnect, Perth WA Dr Nicole Rice, Southern Cross University, Lismore NSW Prof Robert Henry, Southern Cross University, Lismore NSW 22. Forecast disease resistance profile for the Western Australian barley crop over the next three years, Jeff J. Russell, Department of Agriculture and Food 23. Malting barley varieties differ in their flowering date and their response to changes in sowing date, BH Paynter and Jeff J. Russell,Department of Agriculture and Food 24. Market development for new barley varieties, Linda Price,Barley Australia 25. Response of wheat varieties to sowing time at Mt Barker, Katanning and Newdegate in 2008, Brenda Shackley and Vicki Scanlan,Department of Agriculture and Food 26. Flowering dates of wheat varieties in 2008 at three locations in Western Australia, Darshan Sharma, Brenda Shackley and Christine Zaicou-Kunesch, Department of Agriculture and Food 27. Agronomic responses of new wheat varieties in the norther agricultural region in 2008, Christine Zaicou-Kunesch, Department of Agriculture and Foo

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014–2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V

The 13th Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-IV Survey Mapping Nearby Galaxies at Apache Point Observatory

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) began observations in July 2014. It pursues three core programs: APOGEE-2,MaNGA, and eBOSS. In addition, eBOSS contains two major subprograms: TDSS and SPIDERS. This paper describes the first data release from SDSS-IV, Data Release 13 (DR13), which contains new data, reanalysis of existing data sets and, like all SDSS data releases, is inclusive of previously released data. DR13 makes publicly available 1390 spatially resolved integral field unit observations of nearby galaxies from MaNGA,the first data released from this survey. It includes new observations from eBOSS, completing SEQUELS. In addition to targeting galaxies and quasars, SEQUELS also targeted variability-selected objects from TDSS and X-ray selected objects from SPIDERS. DR13 includes new reductions ofthe SDSS-III BOSS data, improving the spectrophotometric calibration and redshift classification. DR13 releases new reductions of the APOGEE-1data from SDSS-III, with abundances of elements not previously included and improved stellar parameters for dwarf stars and cooler stars. For the SDSS imaging data, DR13 provides new, more robust and precise photometric calibrations. Several value-added catalogs are being released in tandem with DR13, in particular target catalogs relevant for eBOSS, TDSS, and SPIDERS, and an updated red-clump catalog for APOGEE.This paper describes the location and format of the data now publicly available, as well as providing references to the important technical papers that describe the targeting, observing, and data reduction. The SDSS website, http://www.sdss.org, provides links to the data, tutorials and examples of data access, and extensive documentation of the reduction and analysis procedures. DR13 is the first of a scheduled set that will contain new data and analyses from the planned ~6-year operations of SDSS-IV.PostprintPeer reviewe

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe