Large-scale biometry with interpretable neural network regression on UK Biobank body MRI

Deep learning-based body composition analysis from whole-body magnetic resonance imaging to predict all-cause mortality in a large western population

BACKGROUND

Manually extracted imaging-based body composition measures from a single-slice area (A) have shown associations with clinical outcomes in patients with cardiometabolic disease and cancer. With advances in artificial intelligence, fully automated volumetric (V) segmentation approaches are now possible, but it is unknown whether these measures carry prognostic value to predict mortality in the general population. Here, we developed and tested a deep learning framework to automatically quantify volumetric body composition measures from whole-body magnetic resonance imaging (MRI) and investigated their prognostic value to predict mortality in a large Western population.

METHODS

The framework was developed using data from two large Western European population-based cohort studies, the UK Biobank (UKBB) and the German National Cohort (NAKO). Body composition was defined as (i) subcutaneous adipose tissue (SAT), (ii) visceral adipose tissue (VAT), (iii) skeletal muscle (SM), SM fat fraction (SMFF), and (iv) intramuscular adipose tissue (IMAT). The prognostic value of the body composition measures was assessed in the UKBB using Cox regression analysis. Additionally, we extracted body composition areas for every level of the thoracic and lumbar spine (i) to compare the proposed volumetric whole-body approach to the currently established single-slice area approach on the height of the L3 vertebra and (ii) to investigate the correlation between volumetric and single slice area body composition measures on the level of each vertebral body.

FINDINGS

In 36,317 UKBB participants (mean age 65.1 ± 7.8 years, age range 45-84 years; 51.7% female; 1.7% [634/36,471] all-cause deaths; median follow-up 4.8 years), Cox regression revealed an independent association between VSM (adjusted hazard ratio [aHR]: 0.88, 95% confidence interval [CI] [0.81-0.91], p = 0.00023), VSMFF (aHR: 1.06, 95% CI [1.02-1.10], p = 0.0043), and VIMAT (aHR: 1.19, 95% CI [1.05-1.35], p = 0.0056) and mortality after adjustment for demographics (age, sex, BMI, race) and cardiometabolic risk factors (alcohol consumption, smoking status, hypertension, diabetes, history of cancer, blood serum markers). This association was attenuated when using traditional single-slice area measures. Highest correlation coefficients (R) between volumetric and single-slice area body composition measures were located at vertebra L5 for SAT (R = 0.820) and SMFF (R = 0.947), at L3 for VAT (R = 0.892), SM (R = 0.944), and at L4 for IMAT (R = 0.546) (all p < 0.0001). A similar pattern was found in 23,725 NAKO participants (mean age 53.9 ± 8.3 years, age range 40-75; 44.9% female).

INTERPRETATION

Automated volumetric body composition assessment from whole-body MRI predicted mortality in a large Western population beyond traditional clinical risk factors. Single slice areas were highly correlated with volumetric body composition measures but their association with mortality attenuated after multivariable adjustment. As volumetric body composition measures are increasingly accessible using automated techniques, identifying high-risk individuals may help to improve personalised prevention and lifestyle interventions.

FUNDING

This project was conducted using data from the German National Cohort (NAKO) (www.nako.de). The NAKO is funded by the Federal Ministry of Education and Research (BMBF) [project funding reference numbers: 01ER1301A/B/C, 01ER1511D, and 01ER1801A/B/C/D], federal states of Germany and the Helmholtz Association, the participating universities and the institutes of the Leibniz Association. This research has been conducted using the UK Biobank Resource under Application Number 80337. MJ was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)-518480401. VKR was funded by American Heart Association Career Development Award 935176 and National Heart, Lung, and Blood Institute-K01HL168231.

Metabolic profiling of galectin-1 and galectin-3: a cross-sectional, multi-omics, association study

OBJECTIVES

Experimental studies indicate a role for galectin-1 and galectin-3 in metabolic disease, but clinical evidence from larger populations is limited.

METHODS

We measured circulating levels of galectin-1 and galectin-3 in the Prospective investigation of Obesity, Energy and Metabolism (POEM) study, participants (n = 502, all aged 50 years) and characterized the individual association profiles with metabolic markers, including clinical measures, metabolomics, adipose tissue distribution (Imiomics) and proteomics.

RESULTS

Galectin-1 and galectin-3 were associated with fatty acids, lipoproteins and triglycerides including lipid measurements in the metabolomics analysis adjusted for body mass index (BMI). Galectin-1 was associated with several measurements of adiposity, insulin secretion and insulin sensitivity, while galectin-3 was associated with triglyceride-glucose index (TyG) and fasting insulin levels. Both galectins were associated with inflammatory pathways and fatty acid binding protein (FABP)4 and -5-regulated triglyceride metabolic pathways. Galectin-1 was also associated with several proteins related to adipose tissue differentiation.

CONCLUSIONS

The association profiles for galectin-1 and galectin-3 indicate overlapping metabolic effects in humans, while the distinctly different associations seen with fat mass, fat distribution, and adipose tissue differentiation markers may suggest a functional role of galectin-1 in obesity.

Approximation of bone mineral density and subcutaneous adiposity using T1-weighted images of the human head

Bones and brain are intricately connected and scientific interest in their interaction is growing. This has become particularly evident in the framework of clinical applications for various medical conditions, such as obesity and osteoporosis. The adverse effects of obesity on brain health have long been recognised, but few brain imaging studies provide sophisticated body composition measures. Here we propose to extract the following bone- and adiposity-related measures from T1-weighted MR images of the head: an approximation of skull bone mineral density (BMD), skull bone thickness, and two approximations of subcutaneous fat (i.e., the intensity and thickness of soft non-brain head tissue). The measures pertaining to skull BMD, skull bone thickness, and intensi-ty-based adiposity proxy proved to be reliable ( r =.93/.83/.74, p <.001) and valid, with high correlations to DXA-de-rived head BMD values (rho=.70, p <.001) and MRI-derived abdominal subcutaneous adipose volume (rho=.62, p <.001). Thickness-based adiposity proxy had only a low retest reliability ( r =.58, p <.001).The outcomes of this study constitute an important step towards extracting relevant non-brain features from available brain scans.

IL32 downregulation lowers triglycerides and type I collagen in di-lineage human primary liver organoids

Steatotic liver disease (SLD) prevails as the most common chronic liver disease yet lack approved treatments due to incomplete understanding of pathogenesis. Recently, elevated hepatic and circulating interleukin 32 (IL-32) levels were found in individuals with severe SLD. However, the mechanistic link between IL-32 and intracellular triglyceride metabolism remains to be elucidated. We demonstrate in vitro that incubation with IL-32β protein leads to an increase in intracellular triglyceride synthesis, while downregulation of IL32 by small interfering RNA leads to lower triglyceride synthesis and secretion in organoids from human primary hepatocytes. This reduction requires the upregulation of Phospholipase A2 group IIA (PLA2G2A). Furthermore, downregulation of IL32 results in lower intracellular type I collagen levels in di-lineage human primary hepatic organoids. Finally, we identify a genetic variant of IL32 (rs76580947) associated with lower circulating IL-32 and protection against SLD measured by non-invasive tests. These data suggest that IL32 downregulation may be beneficial against SLD.

Determining body height and weight from thoracic and abdominal CT localizers in pediatric and young adult patients using deep learning

In this retrospective study, we aimed to predict the body height and weight of pediatric patients using CT localizers, which are overview scans performed before the acquisition of the CT. We trained three commonly used networks (EfficientNetV2-S, ResNet-18, and ResNet-34) on a cohort of 1009 and 1111 CT localizers of pediatric patients with recorded body height and weight (between January 2013 and December 2019) and validated them in an additional cohort of 116 and 127 localizers (acquired in 2020). The best-performing model was then tested in an independent cohort of 203 and 225 CT localizers (acquired between January 2021 and March 2023). In addition, a cohort of 1401 and 1590 localizers from younger adults (acquired between January 2013 and December 2013) was added to the training set to determine if it could improve the overall accuracy. The EfficientNetV2-S using the additional adult cohort performed best with a mean absolute error of 5.58 ± 4.26 cm for height and 4.25 ± 4.28 kg for weight. The relative error was 4.12 ± 4.05% for height and 11.28 ± 12.05% for weight. Our study demonstrated that automated estimation of height and weight in pediatric patients from CT localizers can be performed.

Artifact-free fat-water separation in Dixon MRI using deep learning

Chemical-shift encoded MRI (CSE-MRI) is a widely used technique for the study of body composition and metabolic disorders, where derived fat and water signals enable the quantification of adipose tissue and muscle. The UK Biobank is acquiring whole-body Dixon MRI (a specific implementation of CSE-MRI) for over 100,000 participants. Current processing methods associated with large whole-body volumes are time intensive and prone to artifacts during fat-water separation performed by the scanner, making quantitative analysis challenging. The most common artifacts are fat-water swaps, where the labels are inverted at the voxel level. It is common for researchers to discard swapped data (generally around 10%), which is wasteful and may lead to unintended biases. Given the large number of whole-body Dixon MRI acquisitions in the UK Biobank, thousands of swaps are expected to be present in the fat and water volumes from image reconstruction performed on the scanner. If they go undetected, errors will propagate into processes such as organ segmentation, and dilute the results in population-based analyses. There is a clear need for a robust method to accurately separate fat and water volumes in big data collections like the UK Biobank. We formulate fat-water separation as a style transfer problem, where swap-free fat and water volumes are predicted from the acquired Dixon MRI data using a conditional generative adversarial network, and introduce a new loss function for the generator model. Our method is able to predict highly accurate fat and water volumes free from artifacts in the UK Biobank. We show that our model separates fat and water volumes using either single input (in-phase only) or dual input (in-phase and opposed-phase) data, with the latter producing superior results. Our proposed method enables faster and more accurate downstream analysis of body composition from Dixon MRI in population studies by eliminating the need for visual inspection or discarding data due to fat-water swaps.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40537-022-00677-1.

The way forward for neuroethics in Japan: A review of five topics surrounding present challenges

Neuroethics is the study of how neuroscience impacts humans and society. About 15 years have passed since neuroethics was introduced to Japan, yet the field of neuroethics still seeks developed methodologies and an established academic identity. In light of progress in neuroscience and neurotechnology, the challenges for Japanese neuroethics in the 2020s can be categorized into five topics. (1) The need for further research into the importance of informed consent in psychiatric research and the promotion of public-patient engagement. (2) The need for a framework that constructs a global environment for neuroscience research that utilizes reliable samples and data. (3) The need for ethical support within a Japanese context regarding the construction of brain banks and the research surrounding their use. It is also important to reconsider the moral value of the human neural system and make comparisons with non-human primates. (4) An urgent need to study neuromodulation technologies that intervene in emotions. (5) The need to reconsider neuroscience and neurotechnology from social points of view. Rules for neuroenhancements and do-it-yourself neurotechnologies are urgently needed, while from a broader perspective, it is essential to study the points of contact between neuroscience and public health.

A Survey on the Role of Artificial Intelligence in Biobanking Studies: A Systematic Review

Introduction: In biobanks, participants' biological samples are stored for future research. The application of artificial intelligence (AI) involves the analysis of data and the prediction of any pathological outcomes. In AI, models are used to diagnose diseases as well as classify and predict disease risks. Our research analyzed AI's role in the development of biobanks in the healthcare industry, systematically. Methods: The literature search was conducted using three digital reference databases, namely PubMed, CINAHL, and WoS. Guidelines for preferred reporting elements for systematic reviews and meta-analyses (PRISMA)-2020 in conducting the systematic review were followed. The search terms included "biobanks", "AI", "machine learning", and "deep learning", as well as combinations such as "biobanks with AI", "deep learning in the biobanking field", and "recent advances in biobanking". Only English-language papers were included in the study, and to assess the quality of selected works, the Newcastle-Ottawa scale (NOS) was used. The good quality range (NOS ≥ 7) is only considered for further review. Results: A literature analysis of the above entries resulted in 239 studies. Based on their relevance to the study's goal, research characteristics, and NOS criteria, we included 18 articles for reviewing. In the last decade, biobanks and artificial intelligence have had a relatively large impact on the medical system. Interestingly, UK biobanks account for the highest percentage of high-quality works, followed by Qatar, South Korea, Singapore, Japan, and Denmark. Conclusions: Translational bioinformatics probably represent a future leader in precision medicine. AI and machine learning applications to biobanking research may contribute to the development of biobanks for the utility of health services and citizens.

MIMIR: Deep Regression for Automated Analysis of UK Biobank MRI Scans

UK Biobank (UKB) has recruited more than 500 000 volunteers from the United Kingdom, collecting health-related information on genetics, lifestyle, blood biochemistry, and more. Ongoing medical imaging of 100 000 participants with 70 000 follow-up sessions will yield up to 170 000 MRI scans, enabling image analysis of body composition, organs, and muscle. This study presents an experimental inference engine for automated analysis of UKB neck-to-knee body 1.5-T MRI scans. This retrospective cross-validation study includes data from 38 916 participants (52% female; mean age, 64 years) to capture baseline characteristics, such as age, height, weight, and sex, as well as measurements of body composition, organ volumes, and abstract properties, such as grip strength, pulse rate, and type 2 diabetes status. Prediction intervals for each end point were generated based on uncertainty quantification. On a subsequent release of UKB data, the proposed method predicted 12 body composition metrics with a 3% median error and yielded mostly well-calibrated individual prediction intervals. The processing of MRI scans from 1000 participants required 10 minutes. The underlying method used convolutional neural networks for image-based mean-variance regression on two-dimensional representations of the MRI data. An implementation was made publicly available for fast and fully automated estimation of 72 different measurements from future releases of UKB image data. Keywords: MRI, Adipose Tissue, Obesity, Metabolic Disorders, Volume Analysis, Whole-Body Imaging, Quantification, Supervised Learning, Convolutional Neural Network (CNN) © RSNA, 2022.

Uncertainty-aware body composition analysis with deep regression ensembles on UK Biobank MRI

Along with rich health-related metadata, medical images have been acquired for over 40,000 male and female UK Biobank participants, aged 44-82, since 2014. Phenotypes derived from these images, such as measurements of body composition from MRI, can reveal new links between genetics, cardiovascular disease, and metabolic conditions. In this work, six measurements of body composition and adipose tissues were automatically estimated by image-based, deep regression with ResNet50 neural networks from neck-to-knee body MRI. Despite the potential for high speed and accuracy, these networks produce no output segmentations that could indicate the reliability of individual measurements. The presented experiments therefore examine uncertainty quantification with mean-variance regression and ensembling to estimate individual measurement errors and thereby identify potential outliers, anomalies, and other failure cases automatically. In 10-fold cross-validation on data of about 8500 subjects, mean-variance regression and ensembling showed complementary benefits, reducing the mean absolute error across all predictions by 12%. Both improved the calibration of uncertainties and their ability to identify high prediction errors. With intra-class correlation coefficients (ICC) above 0.97, all targets except the liver fat content yielded relative measurement errors below 5%. Testing on another 1000 subjects showed consistent performance, and the method was finally deployed for inference to 30,000 subjects with missing reference values. The results indicate that deep regression ensembles could ultimately provide automated, uncertainty-aware measurements of body composition for more than 120,000 UK Biobank neck-to-knee body MRI that are to be acquired within the coming years.

Notable Papers and New Directions in Sensors, Signals, and Imaging Informatics

OBJECTIVE

To identify and highlight research papers representing noteworthy developments in signals, sensors, and imaging informatics in 2020.

METHOD

A broad literature search was conducted on PubMed and Scopus databases. We combined Medical Subject Heading (MeSH) terms and keywords to construct particular queries for sensors, signals, and image informatics. We only considered papers that have been published in journals providing at least three articles in the query response. Section editors then independently reviewed the titles and abstracts of preselected papers assessed on a three-point Likert scale. Papers were rated from 1 (do not include) to 3 (should be included) for each topical area (sensors, signals, and imaging informatics) and those with an average score of 2 or above were subsequently read and assessed again by two of the three co-editors. Finally, the top 14 papers with the highest combined scores were considered based on consensus.

RESULTS

The search for papers was executed in January 2021. After removing duplicates and conference proceedings, the query returned a set of 101, 193, and 529 papers for sensors, signals, and imaging informatics, respectively. We filtered out journals that had less than three papers in the query results, reducing the number of papers to 41, 117, and 333, respectively. From these, the co-editors identified 22 candidate papers with more than 2 Likert points on average, from which 14 candidate best papers were nominated after intensive discussion. At least five external reviewers then rated the remaining papers. The four finalist papers were found using the composite rating of all external reviewers. These best papers were approved by consensus of the International Medical Informatics Association (IMIA) Yearbook editorial board.

CONCLUSIONS

Sensors, signals, and imaging informatics is a dynamic field of intense research. The four best papers represent advanced approaches for combining, processing, modeling, and analyzing heterogeneous sensor and imaging data. The selected papers demonstrate the combination and fusion of multiple sensors and sensor networks using electrocardiogram (ECG), electroencephalogram (EEG), or photoplethysmogram (PPG) with advanced data processing, deep and machine learning techniques, and present image processing modalities beyond state-of-the-art that significantly support and further improve medical decision making.

Kidney segmentation in neck-to-knee body MRI of 40,000 UK Biobank participants

The UK Biobank is collecting extensive data on health-related characteristics of over half a million volunteers. The biological samples of blood and urine can provide valuable insight on kidney function, with important links to cardiovascular and metabolic health. Further information on kidney anatomy could be obtained by medical imaging. In contrast to the brain, heart, liver, and pancreas, no dedicated Magnetic Resonance Imaging (MRI) is planned for the kidneys. An image-based assessment is nonetheless feasible in the neck-to-knee body MRI intended for abdominal body composition analysis, which also covers the kidneys. In this work, a pipeline for automated segmentation of parenchymal kidney volume in UK Biobank neck-to-knee body MRI is proposed. The underlying neural network reaches a relative error of 3.8%, with Dice score 0.956 in validation on 64 subjects, close to the 2.6% and Dice score 0.962 for repeated segmentation by one human operator. The released MRI of about 40,000 subjects can be processed within one day, yielding volume measurements of left and right kidney. Algorithmic quality ratings enabled the exclusion of outliers and potential failure cases. The resulting measurements can be studied and shared for large-scale investigation of associations and longitudinal changes in parenchymal kidney volume.