3,119 research outputs found
Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study.
Troponin C (TnC) is an important regulatory molecule in cardiomyocytes. Calcium binding to site II in TnC initiates a series of molecular events that result in muscle contraction. The most direct change upon Ca(2+) binding is an opening motion of the molecule that exposes a hydrophobic patch on the surface allowing for Troponin I to bind. Molecular dynamics simulations were used to elucidate the dynamics of this crucial protein in three different states: apo, Ca(2+)-bound, and Ca(2+)-TnI-bound. Dynamics between the states are compared, and the Ca(2+)-bound system is investigated for opening motions. On the basis of the simulations, NMR chemical shifts and order parameters are calculated and compared with experimental observables. Agreement indicates that the simulations sample the relevant dynamics of the system. Brownian dynamics simulations are used to investigate the calcium association of TnC. We find that calcium binding gives rise to correlative motions involving the EF hand and collective motions conducive of formation of the TnI-binding interface. We furthermore indicate the essential role of electrostatic steering in facilitating diffusion-limited binding of Ca(2+)
3D medical volume segmentation using hybrid multiresolution statistical approaches
This article is available through the Brunel Open Access Publishing Fund. Copyright © 2010 S AlZu’bi and A Amira.3D volume segmentation is the process of partitioning voxels into 3D regions (subvolumes) that represent meaningful physical entities which are more meaningful and easier to analyze and usable in future applications. Multiresolution Analysis (MRA) enables the preservation of an image according to certain levels of resolution or blurring. Because of multiresolution quality, wavelets have been deployed in image compression, denoising, and classification. This paper focuses on the implementation of efficient medical volume segmentation techniques. Multiresolution analysis including 3D wavelet and ridgelet has been used for feature extraction which can be modeled using Hidden Markov Models (HMMs) to segment the volume slices. A comparison study has been carried out to evaluate 2D and 3D techniques which reveals that 3D methodologies can accurately detect the Region Of Interest (ROI). Automatic segmentation has been achieved using HMMs where the ROI is detected accurately but suffers a long computation time for its calculations
Deep learning cardiac motion analysis for human survival prediction
Motion analysis is used in computer vision to understand the behaviour of
moving objects in sequences of images. Optimising the interpretation of dynamic
biological systems requires accurate and precise motion tracking as well as
efficient representations of high-dimensional motion trajectories so that these
can be used for prediction tasks. Here we use image sequences of the heart,
acquired using cardiac magnetic resonance imaging, to create time-resolved
three-dimensional segmentations using a fully convolutional network trained on
anatomical shape priors. This dense motion model formed the input to a
supervised denoising autoencoder (4Dsurvival), which is a hybrid network
consisting of an autoencoder that learns a task-specific latent code
representation trained on observed outcome data, yielding a latent
representation optimised for survival prediction. To handle right-censored
survival outcomes, our network used a Cox partial likelihood loss function. In
a study of 302 patients the predictive accuracy (quantified by Harrell's
C-index) was significantly higher (p < .0001) for our model C=0.73 (95 CI:
0.68 - 0.78) than the human benchmark of C=0.59 (95 CI: 0.53 - 0.65). This
work demonstrates how a complex computer vision task using high-dimensional
medical image data can efficiently predict human survival
Towards Data-Driven Large Scale Scientific Visualization and Exploration
Technological advances have enabled us to acquire extremely large
datasets but it remains a challenge to store, process, and extract
information from them. This dissertation builds upon recent advances
in machine learning, visualization, and user interactions to
facilitate exploration of large-scale scientific datasets. First, we
use data-driven approaches to computationally identify regions of
interest in the datasets. Second, we use visual presentation for
effective user comprehension. Third, we provide interactions for
human users to integrate domain knowledge and semantic information
into this exploration process.
Our research shows how to extract, visualize, and explore informative
regions on very large 2D landscape images, 3D volumetric datasets,
high-dimensional volumetric mouse brain datasets with thousands of
spatially-mapped gene expression profiles, and geospatial trajectories
that evolve over time. The contribution of this dissertation include:
(1) We introduce a sliding-window saliency model that discovers
regions of user interest in very large images; (2) We develop visual
segmentation of intensity-gradient histograms to identify meaningful
components from volumetric datasets; (3) We extract boundary surfaces
from a wealth of volumetric gene expression mouse brain profiles to
personalize the reference brain atlas; (4) We show how to efficiently
cluster geospatial trajectories by mapping each sequence of locations
to a high-dimensional point with the kernel distance framework.
We aim to discover patterns, relationships, and anomalies that would
lead to new scientific, engineering, and medical advances. This work
represents one of the first steps toward better visual understanding
of large-scale scientific data by combining machine learning and human
intelligence
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