cMRI-BED: A novel informatics framework for cardiac MRI biomarker extraction and discovery applied to pediatric cardiomyopathy classification

Background\ud Pediatric cardiomyopathies are a rare, yet heterogeneous group of pathologies of the myocardium that are routinely examined clinically using Cardiovascular Magnetic Resonance Imaging (cMRI). This gold standard powerful non-invasive tool yields high resolution temporal images that characterize myocardial tissue. The complexities associated with the annotation of images and extraction of markers, necessitate the development of efficient workflows to acquire, manage and transform this data into actionable knowledge for patient care to reduce mortality and morbidity.\ud \ud Methods\ud We develop and test a novel informatics framework called cMRI-BED for biomarker extraction and discovery from such complex pediatric cMRI data that includes the use of a suite of tools for image processing, marker extraction and predictive modeling. We applied our workflow to obtain and analyze a dataset of 83 de-identified cases and controls containing cMRI-derived biomarkers for classifying positive versus negative findings of cardiomyopathy in children. Bayesian rule learning (BRL) methods were applied to derive understandable models in the form of propositional rules with posterior probabilities pertaining to their validity. Popular machine learning methods in the WEKA data mining toolkit were applied using default parameters to assess cross-validation performance of this dataset using accuracy and percentage area under ROC curve (AUC) measures.\ud \ud Results\ud The best 10-fold cross validation predictive performance obtained on this cMRI-derived biomarker dataset was 80.72% accuracy and 79.6% AUC by a BRL decision tree model, which is promising from this type of rare data. Moreover, we were able to verify that mycocardial delayed enhancement (MDE) status, which is known to be an important qualitative factor in the classification of cardiomyopathies, is picked up by our rule models as an important variable for prediction.\ud \ud Conclusions\ud Preliminary results show the feasibility of our framework for processing such data while also yielding actionable predictive classification rules that can augment knowledge conveyed in cardiac radiology outcome reports. Interactions between MDE status and other cMRI parameters that are depicted in our rules warrant further investigation and validation. Predictive rules learned from cMRI data to classify positive and negative findings of cardiomyopathy can enhance scientific understanding of the underlying interactions among imaging-derived parameters

Ultrastructure of egg membrane of rohu (Labeo rohita)

The fine structure of the egg envelope and micropyle of unfertilised spawned eggs of rohu (Labeo rohita) was observed using scanning electron microscope (SEM). The outer surface showed regularly arranged pores (dia. 0.20 - 0.25 μm) but was devoid of any filaments, fibrils or wrinkles. The micropyle was funnel shaped which exibited an outer pit (10 μm dia.) narrowing into a distinct canal (4.5 μm dia.). The larger diameter of the micropylar canal in comparison with the sperm head size of rohu and some other cyprinids make intergeneric and interspecific hybridisation easy in rohu

Fine structural changes of Rohu (Labeo rohita) sperm after dilution with cryoprotectants

Spermatozoa of rohu (Labeo rohita) were diluted in two cryodiluents and fine structural changes were investigated. Damages were observed in head, mid-piece and tail of about 51% spermatozoa immediately after dilution in one of the cryodiluents. After 10 minutes of equilibration period, the frequency of damaged sperms increased to 85%. The other diluent did not exhibit signif~cant structural changes unlike the former one and nearly 60% sperms remained visibly intact even after 10 minutes of equilibration time. The present investigation points out (1) diluents inhibiting sperm motility alone need not always be ideal for a species and (2) usefulness of ultrastructural images of fish sperms in determining the fertilizing ability of milt and in preliminary screening and selection of cryodiluents for deepfreezing programmes

Dynamics of a passive sliding particle on a randomly fluctuating surface

We study the motion of a particle sliding under the action of an external field on a stochastically fluctuating one-dimensional Edwards-Wilkinson surface. Numerical simulations using the single-step model shows that the mean-square displacement of the sliding particle shows distinct dynamic scaling behavior, depending on whether the surface fluctuates faster or slower than the motion of the particle. When the surface fluctuations occur on a time scale much smaller than the particle motion, we find that the characteristic length scale shows anomalous diffusion with $\xi(t)\sim t^{2\phi}$, where $\phi\approx 0.67$ from numerical data. On the other hand, when the particle moves faster than the surface, its dynamics is controlled by the surface fluctuations and $\xi(t)\sim t^{{1/2}}$. A self-consistent approximation predicts that the anomalous diffusion exponent is $\phi={2/3}$, in good agreement with simulation results. We also discuss the possibility of a slow cross-over towards asymptotic diffusive behavior. The probability distribution of the displacement has a Gaussian form in both the cases.Comment: 6 pages, 4 figures, error in reference corrected and new reference added, submitted to Phys. Rev.

Strong clustering of non-interacting, passive sliders driven by a Kardar-Parisi-Zhang surface

We study the clustering of passive, non-interacting particles moving under the influence of a fluctuating field and random noise, in one dimension. The fluctuating field in our case is provided by a surface governed by the Kardar-Parisi-Zhang (KPZ) equation and the sliding particles follow the local surface slope. As the KPZ equation can be mapped to the noisy Burgers equation, the problem translates to that of passive scalars in a Burgers fluid. We study the case of particles moving in the same direction as the surface, equivalent to advection in fluid language. Monte-Carlo simulations on a discrete lattice model reveal extreme clustering of the passive particles. The resulting Strong Clustering State is defined using the scaling properties of the two point density-density correlation function. Our simulations show that the state is robust against changing the ratio of update speeds of the surface and particles. In the equilibrium limit of a stationary surface and finite noise, one obtains the Sinai model for random walkers on a random landscape. In this limit, we obtain analytic results which allow closed form expressions to be found for the quantities of interest. Surprisingly, these results for the equilibrium problem show good agreement with the results in the non-equilibrium regime.Comment: 14 pages, 9 figure

Structure and evolution of the cold dome off northeastern Taiwan : a numerical study

Author Posting. © The Oceanography Society, 2013. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 26, no. 1 (2013): 66–79, doi:10.5670/oceanog.2013.06.Numerous observational and modeling studies of ocean circulation surrounding Taiwan have reported occurrences of cold water and doming of isotherms (called the cold dome) that result in the formation of coastal upwelling on the northeastern Taiwan shelf. We use a high-resolution (1/24°) ocean model based on the Massachusetts Institute of Technology general circulation model to study the evolution of this distinct shelf-slope circulation phenomenon. We performed a number of model simulations spanning a five-year period (2004–2008) using realistic atmospheric forcing and initial and open boundary conditions. The model solutions were compared with satellite measurements of sea surface height (SSH), sea surface temperature (SST), and historical temperature and salinity observations. The model showed a realistically shaped cold dome with a diameter of ~ 100 km and temperature of ~ 3°C below the ambient shelf waters at 50 m depth. The occurrences of simulated cold dome events appeared to be connected with the seasonal variability of the Kuroshio Current. The model simulations showed more upwelling events during spring and summer when the core of the Kuroshio tends to migrate away from the east coast of Taiwan, compared to fall and winter when the core of the Kuroshio is generally found closer to the east coast of Taiwan. The model also reproduced weak cyclonic circulation associated with the upwelling off northeastern Taiwan. We analyzed the spatio-temporal variability of the cold dome using the model solution as a proxy and designed a "cold dome index" based on the temperature at 50 m depth averaged over a 0.5° × 0.5° box centered at 25.5°N, 122°E. The cold dome index correlates with temperature at 50 m depth in a larger region, suggesting the spatial extent of the cold dome phenomenon. The index had correlation maxima of 0.78 and 0.40 for simulated SSH and SST, respectively, in and around the cold dome box region, and we hypothesize that it is a useful indicator of upwelling off northeastern Taiwan. In addition, both correlation and composite analysis between the temperature at 50 m depth and the East Taiwan Channel transport showed no cold dome events during low-transport events (often in winter) and more frequent cold dome events during high-transport events (often in summer). The simulated cold dome events had time scales of about two weeks, and their centers aligned roughly along a northeastward line starting from the northeastern tip of Taiwan.This work was supported by Office of Naval Research grant N00014-08- 1-0587

Prioritized Species for Mariculture in India

Mariculture holds tremendous potential for fulfilling the demand of fish, as a source of dietary protein in the country. Keeping this in hindsight, ICAR-Central Marine Fisheries Research Institute, for the past several years has been trying to transform the mariculture sector of the country. In India, the potential coastal water area available for mariculture includes about 8.9 million ha of inshore waters for open-sea farming and 1.7 million ha of estuaries, backwaters, brackishwater lakes and swamps. High valued finfishes, crustaceans, molluscs, seaweeds and other marine organisms, possessing high reproductive capacity, short larval development, fast rate of growth, and physiological features to adjust to wide changes in the environment are available in our coastal waters. A large number of unemployed and under-employed fishermen exists who could advantageously take up coastal aquaculture

Esterases in Indian major carps - 'Rohu' (Labeo rohita) and 'Mrigal' (Cirrhinus mrigala) (Teleostei, Cyprinidae)

Soluble esterases of rohu and mrigal were characterised by electrophoresis using different substrates and inhibitors. Four separable regions of esterolytic activity were observed in liver, brain and white muscle extracts of rohu and in three regions in mrigal, with liver of both species exhibiting maximum number of bands. Species-specific differences were observed in some of the regions. Striking substrate-specific reactions were not observed but based on sensitivity to inhibitors, the liver esterases of both species were classified into aryl, carboxyl, choline, ER and Esdp esterases