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  1. Article: A deep learning approach to predict collateral flow in stroke patients using radiomic features from perfusion images.

    Tetteh, Giles / Navarro, Fernando / Meier, Raphael / Kaesmacher, Johannes / Paetzold, Johannes C / Kirschke, Jan S / Zimmer, Claus / Wiest, Roland / Menze, Bjoern H

    Frontiers in neurology

    2023  Volume 14, Page(s) 1039693

    Abstract: Collateral circulation results from specialized anastomotic channels which are capable of providing oxygenated blood to regions with compromised blood flow caused by arterial obstruction. The quality of collateral circulation has been established as a ... ...

    Abstract Collateral circulation results from specialized anastomotic channels which are capable of providing oxygenated blood to regions with compromised blood flow caused by arterial obstruction. The quality of collateral circulation has been established as a key factor in determining the likelihood of a favorable clinical outcome and goes a long way to determining the choice of a stroke care model. Though many imaging and grading methods exist for quantifying collateral blood flow, the actual grading is mostly done through manual inspection. This approach is associated with a number of challenges. First, it is time-consuming. Second, there is a high tendency for bias and inconsistency in the final grade assigned to a patient depending on the experience level of the clinician. We present a multi-stage deep learning approach to predict collateral flow grading in stroke patients based on radiomic features extracted from MR perfusion data. First, we formulate a region of interest detection task as a reinforcement learning problem and train a deep learning network to automatically detect the occluded region within the 3D MR perfusion volumes. Second, we extract radiomic features from the obtained region of interest through local image descriptors and denoising auto-encoders. Finally, we apply a convolutional neural network and other machine learning classifiers to the extracted radiomic features to automatically predict the collateral flow grading of the given patient volume as one of three severity classes - no flow (0), moderate flow (1), and good flow (2). Results from our experiments show an overall accuracy of 72% in the three-class prediction task. With an inter-observer agreement of 16% and a maximum intra-observer agreement of 74% in a similar experiment, our automated deep learning approach demonstrates a performance comparable to expert grading, is faster than visual inspection, and eliminates the problem of grading bias.
    Language English
    Publishing date 2023-02-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564214-5
    ISSN 1664-2295
    ISSN 1664-2295
    DOI 10.3389/fneur.2023.1039693
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online ; Thesis: Analyzing Vascular Networks Extracted from Clinical Magnetic Resonance Angiography

    Tetteh, Giles Verfasser] / [Menze, Bjoern Holger [Akademischer Betreuer] / Menze, Bjoern Holger [Gutachter] / Wiestler, Benedikt [Gutachter]

    2023  

    Author's details Giles Tetteh ; Gutachter: Björn Menze, Benedikt Wiestler ; Betreuer: Björn Menze
    Keywords Naturwissenschaften ; Science
    Subject code sg500
    Language English
    Publisher Universitätsbibliothek der TU München
    Publishing place München
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  3. Book ; Online: A Deep Learning Approach to Predicting Collateral Flow in Stroke Patients Using Radiomic Features from Perfusion Images

    Tetteh, Giles / Navarro, Fernando / Paetzold, Johannes / Kirschke, Jan / Zimmer, Claus / Menze, Bjoern H.

    2021  

    Abstract: Collateral circulation results from specialized anastomotic channels which are capable of providing oxygenated blood to regions with compromised blood flow caused by ischemic injuries. The quality of collateral circulation has been established as a key ... ...

    Abstract Collateral circulation results from specialized anastomotic channels which are capable of providing oxygenated blood to regions with compromised blood flow caused by ischemic injuries. The quality of collateral circulation has been established as a key factor in determining the likelihood of a favorable clinical outcome and goes a long way to determine the choice of stroke care model - that is the decision to transport or treat eligible patients immediately. Though there exist several imaging methods and grading criteria for quantifying collateral blood flow, the actual grading is mostly done through manual inspection of the acquired images. This approach is associated with a number of challenges. First, it is time-consuming - the clinician needs to scan through several slices of images to ascertain the region of interest before deciding on what severity grade to assign to a patient. Second, there is a high tendency for bias and inconsistency in the final grade assigned to a patient depending on the experience level of the clinician. We present a deep learning approach to predicting collateral flow grading in stroke patients based on radiomic features extracted from MR perfusion data. First, we formulate a region of interest detection task as a reinforcement learning problem and train a deep learning network to automatically detect the occluded region within the 3D MR perfusion volumes. Second, we extract radiomic features from the obtained region of interest through local image descriptors and denoising auto-encoders. Finally, we apply a convolutional neural network and other machine learning classifiers to the extracted radiomic features to automatically predict the collateral flow grading of the given patient volume as one of three severity classes - no flow (0), moderate flow (1), and good flow (2).
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2021-10-24
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Application of machine learning to pretherapeutically estimate dosimetry in men with advanced prostate cancer treated with <sup>177</sup>Lu-PSMA I&T therapy.

    Xue, Song / Gafita, Andrei / Dong, Chao / Zhao, Yu / Tetteh, Giles / Menze, Bjoern H / Ziegler, Sibylle / Weber, Wolfgang / Afshar-Oromieh, Ali / Rominger, Axel / Eiber, Matthias / Shi, Kuangyu

    European journal of nuclear medicine and molecular imaging

    2022  Volume 49, Issue 12, Page(s) 4064–4072

    Abstract: Purpose: Although treatment planning and individualized dose application for emerging prostate-specific membrane antigen (PSMA)-targeted radioligand therapy (RLT) are generally recommended, it is still difficult to implement in practice at the moment. ... ...

    Abstract Purpose: Although treatment planning and individualized dose application for emerging prostate-specific membrane antigen (PSMA)-targeted radioligand therapy (RLT) are generally recommended, it is still difficult to implement in practice at the moment. In this study, we aimed to prove the concept of pretherapeutic prediction of dosimetry based on imaging and laboratory measurements before the RLT treatment.
    Methods: Twenty-three patients with metastatic castration-resistant prostate cancer (mCRPC) treated with <sup>177</sup>Lu-PSMA I&T RLT were included retrospectively. They had available pre-therapy <sup>68</sup> Ga-PSMA-HEBD-CC PET/CT and at least 3 planar and 1 SPECT/CT imaging for dosimetry. Overall, 43 cycles of <sup>177</sup>Lu-PSMA I&T RLT were applied. Organ-based standard uptake values (SUVs) were obtained from pre-therapy PET/CT scans. Patient dosimetry was calculated for the kidney, liver, spleen, and salivary glands using Hermes Hybrid Dosimetry 4.0 from the planar and SPECT/CT images. Machine learning methods were explored for dose prediction from organ SUVs and laboratory measurements. The uncertainty of these dose predictions was compared with the population-based dosimetry estimates. Mean absolute percentage error (MAPE) was used to assess the prediction uncertainty of estimated dosimetry.
    Results: An optimal machine learning method achieved a dosimetry prediction MAPE of 15.8 ± 13.2% for the kidney, 29.6% ± 13.7% for the liver, 23.8% ± 13.1% for the salivary glands, and 32.1 ± 31.4% for the spleen. In contrast, the prediction based on literature population mean has significantly larger MAPE (p < 0.01), 25.5 ± 17.3% for the kidney, 139.1% ± 111.5% for the liver, 67.0 ± 58.3% for the salivary glands, and 54.1 ± 215.3% for the spleen.
    Conclusion: The preliminary results confirmed the feasibility of pretherapeutic estimation of treatment dosimetry and its added value to empirical population-based estimation. The exploration of dose prediction may support the implementation of treatment planning for RLT.
    MeSH term(s) Dipeptides/therapeutic use ; Heterocyclic Compounds, 1-Ring/therapeutic use ; Humans ; Lutetium/therapeutic use ; Machine Learning ; Male ; Positron Emission Tomography Computed Tomography/methods ; Prostate-Specific Antigen ; Prostatic Neoplasms, Castration-Resistant/diagnostic imaging ; Prostatic Neoplasms, Castration-Resistant/drug therapy ; Prostatic Neoplasms, Castration-Resistant/radiotherapy ; Retrospective Studies ; Urea/analogs & derivatives
    Chemical Substances Dipeptides ; Heterocyclic Compounds, 1-Ring ; PSMA I&T ; Lutetium (5H0DOZ21UJ) ; Urea (8W8T17847W) ; Prostate-Specific Antigen (EC 3.4.21.77)
    Language English
    Publishing date 2022-06-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 8236-3
    ISSN 1619-7089 ; 0340-6997 ; 1619-7070
    ISSN (online) 1619-7089
    ISSN 0340-6997 ; 1619-7070
    DOI 10.1007/s00259-022-05883-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Deep Neural Network for Automatic Characterization of Lesions on 68Ga-PSMA PET/CT Images.

    Zhao, Yu / Gafita, Andrei / Tetteh, Giles / Haupt, Fabian / Afshar-Oromieh, Ali / Menze, Bjoern / Eiber, Matthias / Rominger, Axel / Shi, Kuangyu

    Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

    2020  Volume 2019, Page(s) 951–954

    Abstract: The emerging PSMA-targeted radionuclide therapy provides an effective method for the treatment of advanced metastatic prostate cancer. To optimize the therapeutic effect and maximize the theranostic benefit, there is a need to identify and quantify ... ...

    Abstract The emerging PSMA-targeted radionuclide therapy provides an effective method for the treatment of advanced metastatic prostate cancer. To optimize the therapeutic effect and maximize the theranostic benefit, there is a need to identify and quantify target lesions prior to treatment. However, this is extremely challenging considering that a high number of lesions of heterogeneous size and uptake may distribute in a variety of anatomical context with different backgrounds. This study proposes an end-to-end deep neural network to characterize the prostate cancer lesions on PSMA imaging automatically. A
    MeSH term(s) Automation, Laboratory ; Edetic Acid ; Humans ; Male ; Membrane Glycoproteins ; Neural Networks, Computer ; Organometallic Compounds ; Positron Emission Tomography Computed Tomography ; Prostatic Neoplasms
    Chemical Substances Membrane Glycoproteins ; Organometallic Compounds ; gallium 68 PSMA-11 ; Edetic Acid (9G34HU7RV0)
    Language English
    Publishing date 2020-01-26
    Publishing country United States
    Document type Journal Article
    ISSN 2694-0604
    ISSN (online) 2694-0604
    DOI 10.1109/EMBC.2019.8857955
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes.

    Tetteh, Giles / Efremov, Velizar / Forkert, Nils D / Schneider, Matthias / Kirschke, Jan / Weber, Bruno / Zimmer, Claus / Piraud, Marie / Menze, Björn H

    Frontiers in neuroscience

    2020  Volume 14, Page(s) 592352

    Abstract: We present DeepVesselNet, an architecture tailored to the challenges faced when extracting vessel trees and networks and corresponding features in 3-D angiographic volumes using deep learning. We discuss the problems of low execution speed and high ... ...

    Abstract We present DeepVesselNet, an architecture tailored to the challenges faced when extracting vessel trees and networks and corresponding features in 3-D angiographic volumes using deep learning. We discuss the problems of low execution speed and high memory requirements associated with full 3-D networks, high-class imbalance arising from the low percentage (<3%) of vessel voxels, and unavailability of accurately annotated 3-D training data-and offer solutions as the building blocks of DeepVesselNet. First, we formulate 2-D orthogonal cross-hair filters which make use of 3-D context information at a reduced computational burden. Second, we introduce a class balancing cross-entropy loss function with false-positive rate correction to handle the high-class imbalance and high false positive rate problems associated with existing loss functions. Finally, we generate a synthetic dataset using a computational angiogenesis model capable of simulating vascular tree growth under physiological constraints on local network structure and topology and use these data for transfer learning. We demonstrate the performance on a range of angiographic volumes at different spatial scales including clinical MRA data of the human brain, as well as CTA microscopy scans of the rat brain. Our results show that cross-hair filters achieve over 23% improvement in speed, lower memory footprint, lower network complexity which prevents overfitting and comparable accuracy that does not differ from full 3-D filters. Our class balancing metric is crucial for training the network, and transfer learning with synthetic data is an efficient, robust, and very generalizable approach leading to a network that excels in a variety of angiography segmentation tasks. We observe that sub-sampling and max pooling layers may lead to a drop in performance in tasks that involve voxel-sized structures. To this end, the DeepVesselNet architecture does not use any form of sub-sampling layer and works well for vessel segmentation, centerline prediction, and bifurcation detection. We make our synthetic training data publicly available, fostering future research, and serving as one of the first public datasets for brain vessel tree segmentation and analysis.
    Language English
    Publishing date 2020-12-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2020.592352
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Automatic opportunistic osteoporosis screening in routine CT: improved prediction of patients with prevalent vertebral fractures compared to DXA.

    Löffler, Maximilian T / Jacob, Alina / Scharr, Andreas / Sollmann, Nico / Burian, Egon / El Husseini, Malek / Sekuboyina, Anjany / Tetteh, Giles / Zimmer, Claus / Gempt, Jens / Baum, Thomas / Kirschke, Jan S

    European radiology

    2021  Volume 31, Issue 8, Page(s) 6069–6077

    Abstract: Objectives: To compare spinal bone measures derived from automatic and manual assessment in routine CT with dual energy X-ray absorptiometry (DXA) in their association with prevalent osteoporotic vertebral fractures using our fully automated framework ( ...

    Abstract Objectives: To compare spinal bone measures derived from automatic and manual assessment in routine CT with dual energy X-ray absorptiometry (DXA) in their association with prevalent osteoporotic vertebral fractures using our fully automated framework ( https://anduin.bonescreen.de ) to assess various bone measures in clinical CT.
    Methods: We included 192 patients (141 women, 51 men; age 70.2 ± 9.7 years) who had lumbar DXA and CT available (within 1 year). Automatic assessment of spinal bone measures in CT included segmentation of vertebrae using a convolutional neural network (CNN), reduction to the vertebral body, and extraction of bone mineral content (BMC), trabecular and integral volumetric bone mineral density (vBMD), and CT-based areal BMD (aBMD) using asynchronous calibration. Moreover, trabecular bone was manually sampled (manual vBMD).
    Results: A total of 148 patients (77%) had vertebral fractures and significantly lower values in all bone measures compared to patients without fractures (p ≤ 0.001). Except for BMC, all CT-based measures performed significantly better as predictors for vertebral fractures compared to DXA (e.g., AUC = 0.885 for trabecular vBMD and AUC = 0.86 for integral vBMD vs. AUC = 0.668 for DXA aBMD, respectively; both p < 0.001). Age- and sex-adjusted associations with fracture status were strongest for manual vBMD (OR = 7.3, [95%] CI 3.8-14.3) followed by automatically assessed trabecular vBMD (OR = 6.9, CI 3.5-13.4) and integral vBMD (OR = 4.3, CI 2.5-7.6). Diagnostic cutoffs of integral vBMD for osteoporosis (< 160 mg/cm
    Conclusions: Fully automatic osteoporosis screening in routine CT of the spine is feasible. CT-based measures can better identify individuals with reduced bone mass who suffered from vertebral fractures than DXA.
    Key points: • Opportunistic osteoporosis screening of spinal bone measures derived from clinical routine CT is feasible in a fully automatic fashion using a deep learning-driven framework ( https://anduin.bonescreen.de ). • Manually sampled volumetric BMD (vBMD) and automatically assessed trabecular and integral vBMD were the best predictors for prevalent vertebral fractures. • Except for bone mineral content, all CT-based bone measures performed significantly better than DXA-based measures. • We introduce diagnostic thresholds of integral vBMD for osteoporosis (< 160 mg/cm
    MeSH term(s) Absorptiometry, Photon ; Aged ; Bone Density ; Female ; Humans ; Lumbar Vertebrae/diagnostic imaging ; Lumbar Vertebrae/injuries ; Male ; Middle Aged ; Osteoporosis/complications ; Osteoporosis/diagnostic imaging ; Osteoporosis/epidemiology ; Spinal Fractures/diagnostic imaging ; Spinal Fractures/epidemiology ; Tomography, X-Ray Computed
    Language English
    Publishing date 2021-01-28
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1085366-2
    ISSN 1432-1084 ; 0938-7994 ; 1613-3749
    ISSN (online) 1432-1084
    ISSN 0938-7994 ; 1613-3749
    DOI 10.1007/s00330-020-07655-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Knowledge-Aided Convolutional Neural Network for Small Organ Segmentation.

    Zhao, Yu / Li, Hongwei / Wan, Shaohua / Sekuboyina, Anjany / Hu, Xiaobin / Tetteh, Giles / Piraud, Marie / Menze, Bjoern

    IEEE journal of biomedical and health informatics

    2019  Volume 23, Issue 4, Page(s) 1363–1373

    Abstract: Accurate and automatic organ segmentation is critical for computer-aided analysis towards clinical decision support and treatment planning. State-of-the-art approaches have achieved remarkable segmentation accuracy on large organs, such as the liver and ... ...

    Abstract Accurate and automatic organ segmentation is critical for computer-aided analysis towards clinical decision support and treatment planning. State-of-the-art approaches have achieved remarkable segmentation accuracy on large organs, such as the liver and kidneys. However, most of these methods do not perform well on small organs, such as the pancreas, gallbladder, and adrenal glands, especially when lacking sufficient training data. This paper presents an automatic approach for small organ segmentation with limited training data using two cascaded steps-localization and segmentation. The localization stage involves the extraction of the region of interest after the registration of images to a common template and during the segmentation stage, a voxel-wise label map of the extracted region of interest is obtained and then transformed back to the original space. In the localization step, we propose to utilize a graph-based groupwise image registration method to build the template for registration so as to minimize the potential bias and avoid getting a fuzzy template. More importantly, a novel knowledge-aided convolutional neural network is proposed to improve segmentation accuracy in the second stage. This proposed network is flexible and can combine the effort of both deep learning and traditional methods, consequently achieving better segmentation relative to either of individual methods. The ISBI 2015 VISCERAL challenge dataset is used to evaluate the presented approach. Experimental results demonstrate that the proposed method outperforms cutting-edge deep learning approaches, traditional forest-based approaches, and multi-atlas approaches in the segmentation of small organs.
    MeSH term(s) Adrenal Glands/diagnostic imaging ; Algorithms ; Fuzzy Logic ; Gallbladder/diagnostic imaging ; Humans ; Image Interpretation, Computer-Assisted/methods ; Neural Networks, Computer ; Pancreas/diagnostic imaging ; Tomography, X-Ray Computed
    Language English
    Publishing date 2019-01-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2695320-1
    ISSN 2168-2208 ; 2168-2194
    ISSN (online) 2168-2208
    ISSN 2168-2194
    DOI 10.1109/JBHI.2019.2891526
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: BraTS Toolkit: Translating BraTS Brain Tumor Segmentation Algorithms Into Clinical and Scientific Practice.

    Kofler, Florian / Berger, Christoph / Waldmannstetter, Diana / Lipkova, Jana / Ezhov, Ivan / Tetteh, Giles / Kirschke, Jan / Zimmer, Claus / Wiestler, Benedikt / Menze, Bjoern H

    Frontiers in neuroscience

    2020  Volume 14, Page(s) 125

    Abstract: Despite great advances in brain tumor segmentation and clear clinical need, translation of state-of-the-art computational methods into clinical routine and scientific practice remains a major challenge. Several factors impede successful implementations, ... ...

    Abstract Despite great advances in brain tumor segmentation and clear clinical need, translation of state-of-the-art computational methods into clinical routine and scientific practice remains a major challenge. Several factors impede successful implementations, including data standardization and preprocessing. However, these steps are pivotal for the deployment of state-of-the-art image segmentation algorithms. To overcome these issues, we present BraTS Toolkit. BraTS Toolkit is a holistic approach to brain tumor segmentation and consists of three components: First, the BraTS Preprocessor facilitates data standardization and preprocessing for researchers and clinicians alike. It covers the entire image analysis workflow prior to tumor segmentation, from image conversion and registration to brain extraction. Second, BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorithms for generation of fully-automated segmentations. Finally, Brats Fusionator can combine the resulting candidate segmentations into consensus segmentations using fusion methods such as majority voting and iterative SIMPLE fusion. The capabilities of our tools are illustrated with a practical example to enable easy translation to clinical and scientific practice.
    Language English
    Publishing date 2020-04-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2020.00125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Machine learning analysis of whole mouse brain vasculature.

    Todorov, Mihail Ivilinov / Paetzold, Johannes Christian / Schoppe, Oliver / Tetteh, Giles / Shit, Suprosanna / Efremov, Velizar / Todorov-Völgyi, Katalin / Düring, Marco / Dichgans, Martin / Piraud, Marie / Menze, Bjoern / Ertürk, Ali

    Nature methods

    2020  Volume 17, Issue 4, Page(s) 442–449

    Abstract: Tissue clearing methods enable the imaging of biological specimens without sectioning. However, reliable and scalable analysis of large imaging datasets in three dimensions remains a challenge. Here we developed a deep learning-based framework to ... ...

    Abstract Tissue clearing methods enable the imaging of biological specimens without sectioning. However, reliable and scalable analysis of large imaging datasets in three dimensions remains a challenge. Here we developed a deep learning-based framework to quantify and analyze brain vasculature, named Vessel Segmentation & Analysis Pipeline (VesSAP). Our pipeline uses a convolutional neural network (CNN) with a transfer learning approach for segmentation and achieves human-level accuracy. By using VesSAP, we analyzed the vascular features of whole C57BL/6J, CD1 and BALB/c mouse brains at the micrometer scale after registering them to the Allen mouse brain atlas. We report evidence of secondary intracranial collateral vascularization in CD1 mice and find reduced vascularization of the brainstem in comparison to the cerebrum. Thus, VesSAP enables unbiased and scalable quantifications of the angioarchitecture of cleared mouse brains and yields biological insights into the vascular function of the brain.
    MeSH term(s) Animals ; Brain/blood supply ; Imaging, Three-Dimensional ; Machine Learning ; Mice
    Language English
    Publishing date 2020-03-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-020-0792-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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