11 results found
Bai W, Suzuki H, Huang J, et al., 2020, A population-based phenome-wide association study of cardiac and aortic structure and function, Nature Medicine, Vol: 26, Pages: 1654-1662, ISSN: 1078-8956
Differences in cardiac and aortic structure and function are associated with cardiovascular diseases and a wide range of other types of disease. Here we analyzed cardiovascular magnetic resonance images from a population-based study, the UK Biobank, using an automated machine-learning-based analysis pipeline. We report a comprehensive range of structural and functional phenotypes for the heart and aorta across 26,893 participants, and explore how these phenotypes vary according to sex, age and major cardiovascular risk factors. We extended this analysis with a phenome-wide association study, in which we tested for correlations of a wide range of non-imaging phenotypes of the participants with imaging phenotypes. We further explored the associations of imaging phenotypes with early-life factors, mental health and cognitive function using both observational analysis and Mendelian randomization. Our study illustrates how population-based cardiac and aortic imaging phenotypes can be used to better define cardiovascular disease risks as well as heart–brain health interactions, highlighting new opportunities for studying disease mechanisms and developing image-based biomarkers.
Arcucci R, Mottet L, Casas CAQ, et al., 2020, Adaptive Domain Decomposition for Effective Data Assimilation, Pages: 583-595, ISSN: 0302-9743
© 2020, Springer Nature Switzerland AG. We present a parallel Data Assimilation model based on an Adaptive Domain Decomposition (ADD-DA) coupled with the open-source, finite-element, fluid dynamics model Fluidity. The model we present is defined on a partition of the domain in sub-domains without overlapping regions. This choice allows to avoid communications among the processes during the Data Assimilation phase. However, during the balance phase, the model exploits the domain decomposition implemented in Fluidity which balances the results among the processes exploiting overlapping regions. Also, the model exploits the technology provided by the mesh adaptivity to generate an optimal mesh we name supermesh. The supermesh is the one used in ADD-DA process. We prove that the ADD-DA model provides the same numerical solution of the corresponding sequential DA model. We also show that the ADD approach reduces the execution time even when the implementation is not on a parallel computing environment. Experimental results are provided for pollutant dispersion within an urban environment.
Suzuki H, Venkataraman AV, Bai W, et al., 2019, Associations of regional brain structural differences with aging, modifiable risk factors for dementia, and cognitive performance, JAMA Network Open, Vol: 2, Pages: 1-19, ISSN: 2574-3805
Importance Identifying brain regions associated with risk factors for dementia could guide mechanistic understanding of risk factors associated with Alzheimer disease (AD).Objectives To characterize volume changes in brain regions associated with aging and modifiable risk factors for dementia (MRFD) and to test whether volume differences in these regions are associated with cognitive performance.Design, Setting, and Participants This cross-sectional study used data from UK Biobank participants who underwent T1-weighted structural brain imaging from August 5, 2014, to October 14, 2016. A voxelwise linear model was applied to test for regional gray matter volume differences associated with aging and MRFD (ie, hypertension, diabetes, obesity, and frequent alcohol use). The potential clinical relevance of these associations was explored by comparing their neuroanatomical distributions with the regional brain atrophy found with AD. Mediation models for risk factors, brain volume differences, and cognitive measures were tested. The primary hypothesis was that common, overlapping regions would be found. Primary analysis was conducted on April 1, 2018.Main Outcomes and Measures Gray matter regions that showed relative atrophy associated with AD, aging, and greater numbers of MRFD.Results Among 8312 participants (mean [SD] age, 62.4 [7.4] years; 3959 [47.1%] men), aging and 4 major MRFD (ie, hypertension, diabetes, obesity, and frequent alcohol use) had independent negative associations with specific gray matter volumes. These regions overlapped neuroanatomically with those showing lower volumes in participants with AD, including the posterior cingulate cortex, the thalamus, the hippocampus, and the orbitofrontal cortex. Associations between these MRFD and spatial memory were mediated by differences in posterior cingulate cortex volume (β = 0.0014; SE = 0.0006; P = .02).Conclusions and Relevance This cross-sectional study
Emam I, Elyasigomari V, Matthews A, et al., 2019, PlatformTM, a standards-based data custodianship platform for translational medicine research., Scientific Data, Vol: 6, Pages: 149-149, ISSN: 2052-4463
Biomedical informatics has traditionally adopted a linear view of the informatics process (collect, store and analyse) in translational medicine (TM) studies; focusing primarily on the challenges in data integration and analysis. However, a data management challenge presents itself with the new lifecycle view of data emphasized by the recent calls for data re-use, long term data preservation, and data sharing. There is currently a lack of dedicated infrastructure focused on the 'manageability' of the data lifecycle in TM research between data collection and analysis. Current community efforts towards establishing a culture for open science prompt the creation of a data custodianship environment for management of TM data assets to support data reuse and reproducibility of research results. Here we present the development of a lifecycle-based methodology to create a metadata management framework based on community driven standards for standardisation, consolidation and integration of TM research data. Based on this framework, we also present the development of a new platform (PlatformTM) focused on managing the lifecycle for translational research data assets.
Bai W, Chen C, Tarroni G, et al., 2019, Self-supervised learning for cardiac MR image segmentation by anatomicalposition prediction, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)
In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks. However, successfully learning these features requires a large amount of manuallyannotated data, which is expensive to acquire and limited by the availableresources of expert image analysts. Therefore, unsupervised, weakly-supervised and self-supervised feature learning techniques receive a lot of attention, which aim to utilise the vast amount of available data, while at the same time avoid or substantially reduce the effort of manual annotation. In this paper, we propose a novel way for training a cardiac MR image segmentation network, in which features are learnt in a self-supervised manner by predicting anatomical positions. The anatomical positions serve as a supervisory signal and do not require extra manual annotation. We demonstrate that this seemingly simple task provides a strong signal for feature learning and with self-supervised learning, we achieve a high segmentation accuracy that is better than or comparable to a U-net trained from scratch, especially at a small data setting. When only five annotated subjects are available, the proposed method improves the mean Dice metric from 0.811 to 0.852 for short-axis image segmentation, compared to the baseline U-net.
De Meulder B, Lefaudeux D, Bansal AT, et al., 2018, A computational framework for complex disease stratification from multiple large-scale datasets, BMC Systems Biology, Vol: 12, ISSN: 1752-0509
BACKGROUND: Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-'omics datasets on complex diseases are becoming more readily available and there is a need to set standards and good practices for integrated analysis of biological, clinical and environmental data. We present a framework to plan and generate single and multi-'omics signatures of disease states. METHODS: The framework is divided into four major steps: dataset subsetting, feature filtering, 'omics-based clustering and biomarker identification. RESULTS: We illustrate the usefulness of this framework by identifying potential patient clusters based on integrated multi-'omics signatures in a publicly available ovarian cystadenocarcinoma dataset. The analysis generated a higher number of stable and clinically relevant clusters than previously reported, and enabled the generation of predictive models of patient outcomes. CONCLUSIONS: This framework will help health researchers plan and perform multi-'omics big data analyses to generate hypotheses and make sense of their rich, diverse and ever growing datasets, to enable implementation of translational P4 medicine.
Oehmichen A, Guitton F, Agapow P, et al., 2018, A multi-tenant computational platform for translational medicine, 38th IEEE International Conference on Distributed Computing Systems (ICDCS), Publisher: IEEE, Pages: 1553-1556, ISSN: 1063-6927
Oehmichen A, Guitton F, Sun K, et al., 2017, eTRIKS analytical environment: A modular high performance framework for medical data analysis, 2017 IEEE International Conference on Big Data (BIGDATA), Pages: 353-360
Wang S, Pandis I, Johnson D, et al., 2014, Optimising Correlation Matrix Calculations on Gene Expression Data, BMC Bioinformatics, Vol: 15, ISSN: 1471-2105
Wang S, Pandis I, Wu C, et al., 2014, High Dimensional Biological Data Retrieval Optimization with NoSQL Technology, BMC Genomics, ISSN: 1471-2164
Wang S, Pandis I, Emam I, et al., 2014, DSIMBench: A benchmark for Microarray Data using R, the 40th International Conference on Very Large Databases (VLDB 2014)
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