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Article ; Online: Perivascular space diffusivity and brain microstructural measures are associated with circadian time and sleep quality.

Brendstrup-Brix, Kristoffer / Ulv Larsen, Sara Marie / Lee, Hong-Hsi / Knudsen, Gitte Moos

2024 , Page(s) e14226

Abstract: The glymphatic system is centred around brain cerebrospinal fluid flow and is enhanced during sleep, and the synaptic homeostasis hypothesis proposes that sleep acts on brain microstructure by selective synaptic downscaling. While so far primarily ... ...

Abstract	The glymphatic system is centred around brain cerebrospinal fluid flow and is enhanced during sleep, and the synaptic homeostasis hypothesis proposes that sleep acts on brain microstructure by selective synaptic downscaling. While so far primarily studied in animals, we here examine in humans if brain diffusivity and microstructure is related to time of day, sleep quality and cognitive performance. We use diffusion weighted images from 916 young healthy individuals, aged between 22 and 37 years, collected as part of the Human Connectome Project to assess diffusion tensor image analysis along the perivascular space index, white matter fractional anisotropy, intra-neurite volume fraction and extra-neurite mean diffusivity. Next, we examine if these measures are associated with circadian time of acquisition, the Pittsburgh Sleep Quality Index (high scores correspond to low sleep quality) and age-adjusted cognitive function total composite score. Consistent with expectations, we find that diffusion tensor image analysis along the perivascular space index and orbitofrontal grey matter extra-neurite mean diffusivity are negatively and white matter fractional anisotropy positively correlated with circadian time. Further, we find that grey matter intra-neurite volume fraction correlates positively with Pittsburgh Sleep Quality Index, and that this correlation is driven by sleep duration. Finally, we find positive correlations between grey matter intra-neurite volume fraction and cognitive function total composite score, as well as negative interaction effects between cognitive function total composite score and Pittsburgh Sleep Quality Index on grey matter intra-neurite volume fraction. Our findings propose that perivascular flow is under circadian control and that sleep downregulates the intra-neurite volume in healthy adults with positive impact on cognitive function.
Language	English
Publishing date	2024-04-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1122722-9
ISSN	1365-2869 ; 0962-1105
ISSN (online)	1365-2869
ISSN	0962-1105
DOI	10.1111/jsr.14226
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Zs.A 3464: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Effects of COVID-19 Prevention Measures on Other Common Infections, Taiwan.

Lee, Hong-Hsi / Lin, Sheng-Hsuan

Emerging infectious diseases

2020 Volume 26, Issue 10, Page(s) 2509–2511

Abstract: To determine whether policies to limit transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hinder spread of other infectious diseases, we analyzed the National Health Insurance database in Taiwan. Rates of other infections were ... ...

Abstract	To determine whether policies to limit transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hinder spread of other infectious diseases, we analyzed the National Health Insurance database in Taiwan. Rates of other infections were significantly lower after SARS-CoV-2 prevention measures were announced. This finding can be applied to cost-effectiveness of SARS-CoV-2 prevention.
MeSH term(s)	Ambulatory Care/statistics & numerical data ; Betacoronavirus ; COVID-19 ; Coronavirus Infections/prevention & control ; Databases, Factual ; Enterovirus Infections/epidemiology ; Health Policy ; Humans ; Influenza, Human/epidemiology ; Pandemics/prevention & control ; Pneumonia, Viral/prevention & control ; SARS-CoV-2 ; Scarlet Fever/epidemiology ; Taiwan/epidemiology
Keywords	covid19
Language	English
Publishing date	2020-07-30
Publishing country	United States
Document type	Letter
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2610.203193
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Article ; Online: DIMOND: DIffusion Model OptimizatioN with Deep Learning.

Li, Zihan / Li, Ziyu / Bilgic, Berkin / Lee, Hong-Hsi / Ying, Kui / Huang, Susie Y / Liao, Hongen / Tian, Qiyuan

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2024 , Page(s) e2307965

Abstract: Diffusion magnetic resonance imaging is an important tool for mapping tissue microstructure and structural connectivity non-invasively in the in vivo human brain. Numerous diffusion signal models are proposed to quantify microstructural properties. ... ...

Abstract	Diffusion magnetic resonance imaging is an important tool for mapping tissue microstructure and structural connectivity non-invasively in the in vivo human brain. Numerous diffusion signal models are proposed to quantify microstructural properties. Nonetheless, accurate estimation of model parameters is computationally expensive and impeded by image noise. Supervised deep learning-based estimation approaches exhibit efficiency and superior performance but require additional training data and may be not generalizable. A new DIffusion Model OptimizatioN framework using physics-informed and self-supervised Deep learning entitled "DIMOND" is proposed to address this problem. DIMOND employs a neural network to map input image data to model parameters and optimizes the network by minimizing the difference between the input acquired data and synthetic data generated via the diffusion model parametrized by network outputs. DIMOND produces accurate diffusion tensor imaging results and is generalizable across subjects and datasets. Moreover, DIMOND outperforms conventional methods for fitting sophisticated microstructural models including the kurtosis and NODDI model. Importantly, DIMOND reduces NODDI model fitting time from hours to minutes, or seconds by leveraging transfer learning. In summary, the self-supervised manner, high efficacy, and efficiency of DIMOND increase the practical feasibility and adoption of microstructure and connectivity mapping in clinical and neuroscientific applications.
Language	English
Publishing date	2024-04-18
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202307965
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Article: Romer-EPTI: rotating-view motion-robust super-resolution EPTI for SNR-efficient distortion-free in-vivo mesoscale dMRI and microstructure imaging.

Dong, Zijing / Reese, Timothy G / Lee, Hong-Hsi / Huang, Susie Y / Polimeni, Jonathan R / Wald, Lawrence L / Wang, Fuyixue

bioRxiv : the preprint server for biology

2024

Abstract: Purpose: To overcome the major challenges in dMRI acquisition, including low SNR, distortion/blurring, and motion vulnerability.: Methods: A novel Romer-EPTI technique is developed to provide distortion-free dMRI with significant SNR gain, high ... ...

Abstract	Purpose: To overcome the major challenges in dMRI acquisition, including low SNR, distortion/blurring, and motion vulnerability. Methods: A novel Romer-EPTI technique is developed to provide distortion-free dMRI with significant SNR gain, high motion-robustness, sharp spatial resolution, and simultaneous multi-TE imaging. It introduces a ROtating-view Motion-robust supEr-Resolution technique (Romer) combined with a distortion/blurring-free EPTI encoding. Romer enhances SNR by a simultaneous multi-thick-slice acquisition with rotating-view encoding, while providing high motion-robustness through a motion-aware super-resolution reconstruction, which also incorporates slice-profile and real-value diffusion, to resolve high-isotropic-resolution volumes. The in-plane encoding is performed using distortion/blurring-free EPTI, which further improves effective spatial resolution and motion robustness by preventing not only T Results: Using Romer-EPTI, we demonstrate distortion-free whole-brain mesoscale in-vivo dMRI at both 3T (500-μm-iso) and 7T (485-μm-iso) for the first time, with high SNR efficiency (e.g., Conclusion: Romer-EPTI significantly improves SNR, motion-robustness, and image quality, providing a highly efficient acquisition for high-resolution dMRI and microstructure imaging.
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.26.577343
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Article ; Online: Optimization and Validation of the DESIGNER dMRI preprocessing pipeline in white matter aging.

Chen, Jenny / Ades-Aron, Benjamin / Lee, Hong-Hsi / Mehrin, Subah / Pang, Michelle / Novikov, Dmitry S / Veraart, Jelle / Fieremans, Els

ArXiv

2024

Abstract: Various diffusion MRI (dMRI) preprocessing pipelines are currently available to yield more accurate diffusion parameters. Here, we evaluated accuracy and robustness of the optimized Diffusion parameter EStImation with Gibbs and NoisE Removal (DESIGNER) ... ...

Abstract	Various diffusion MRI (dMRI) preprocessing pipelines are currently available to yield more accurate diffusion parameters. Here, we evaluated accuracy and robustness of the optimized Diffusion parameter EStImation with Gibbs and NoisE Removal (DESIGNER) pipeline in a large clinical dMRI dataset and using ground truth phantoms. DESIGNER has been modified to improve denoising and target Gibbs ringing for partial Fourier acquisitions. We compared the revisited DESIGNER (Dv2) (including denoising, Gibbs removal, correction for motion, EPI distortion, and eddy currents) against the original DESIGNER (Dv1) pipeline, minimal preprocessing (including correction for motion, EPI distortion, and eddy currents only), and no preprocessing on a large clinical dMRI dataset of 524 control subjects with ages between 25 and 75 years old. We evaluated the effect of specific processing steps on age correlations in white matter with DTI and DKI metrics. We also evaluated the added effect of minimal Gaussian smoothing to deal with noise and to reduce outliers in parameter maps compared to DESIGNER (Dv2)'s noise removal method. Moreover, DESIGNER (Dv2)'s updated noise and Gibbs removal methods were assessed using ground truth dMRI phantom to evaluate accuracy. Results show age correlation in white matter with DTI and DKI metrics were affected by the preprocessing pipeline, causing systematic differences in absolute parameter values and loss or gain of statistical significance. Both in clinical dMRI and ground truth phantoms, DESIGNER (Dv2) pipeline resulted in the smallest number of outlier voxels and improved accuracy in DTI and DKI metrics as noise was reduced and Gibbs removal was improved. Thus, DESIGNER (Dv2) provides more accurate and robust DTI and DKI parameter maps as compared to no preprocessing or minimal preprocessing.
Language	English
Publishing date	2024-03-15
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Universal Sampling Denoising (USD) for noise mapping and noise removal of non-Cartesian MRI.

Lee, Hong-Hsi / Keerthivasan, Mahesh Bharath / Lemberskiy, Gregory / Zhang, Jiangyang / Fieremans, Els / Novikov, Dmitry S

ArXiv

2023

Abstract: Random matrix theory (RMT) combined with principal component analysis has resulted in a widely used MPPCA noise mapping and denoising algorithm, that utilizes the redundancy in multiple acquisitions and in local image patches. RMT-based denoising relies ... ...

Abstract	Random matrix theory (RMT) combined with principal component analysis has resulted in a widely used MPPCA noise mapping and denoising algorithm, that utilizes the redundancy in multiple acquisitions and in local image patches. RMT-based denoising relies on the uncorrelated identically distributed noise. This assumption breaks down after regridding of non-Cartesian sampling. Here we propose a Universal Sampling Denoising (USD) pipeline to homogenize the noise level and decorrelate the noise in non-Cartesian sampled k-space data after resampling to a Cartesian grid. In this way, the RMT approaches become applicable to MRI of any non-Cartesian k-space sampling. We demonstrate the denoising pipeline on MRI data acquired using radial trajectories, including diffusion MRI of a numerical phantom and ex vivo mouse brains, as well as in vivo $T_2$ MRI of a healthy subject. The proposed pipeline robustly estimates noise level, performs noise removal, and corrects bias in parametric maps, such as diffusivity and kurtosis metrics, and $T_2$ relaxation time. USD stabilizes the variance, decorrelates the noise, and thereby enables the application of RMT-based denoising approaches to MR images reconstructed from any non-Cartesian data. In addition to MRI, USD may also apply to other medical imaging techniques involving non-Cartesian acquisition, such as PET, CT, and SPECT.
Language	English
Publishing date	2023-11-27
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
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Article ; Online: Removal of partial Fourier-induced Gibbs (RPG) ringing artifacts in MRI.

Lee, Hong-Hsi / Novikov, Dmitry S / Fieremans, Els

Magnetic resonance in medicine

2021 Volume 86, Issue 5, Page(s) 2733–2750

Abstract: Purpose: To investigate and remove Gibbs-ringing artifacts caused by partial Fourier (PF) acquisition and zero filling interpolation in MRI data.: Theory and methods: Gibbs ringing of fully sampled data, leading to oscillations around tissue ... ...

Abstract	Purpose: To investigate and remove Gibbs-ringing artifacts caused by partial Fourier (PF) acquisition and zero filling interpolation in MRI data. Theory and methods: Gibbs ringing of fully sampled data, leading to oscillations around tissue boundaries, is caused by the symmetric truncation of k-space. Such ringing can be removed by conventional methods, with the local subvoxel shifts method being the state-of-the-art. However, the asymmetric truncation of k-space in routinely used PF acquisitions leads to additional ringings of wider intervals in the PF sampling dimension that cannot be corrected solely based on magnitude images reconstructed via zero filling. Here, we develop a pipeline for the Removal of PF-induced Gibbs ringing (RPG) to remove ringing patterns of different periods by applying the conventional method twice. The proposed pipeline is validated on numerical phantoms, demonstrated on in vivo diffusion MRI measurements, and compared with the conventional method and neural network-based approach. Results: For PF = 7/8 and 6/8, Gibbs-ringings and subsequent bias in diffusion metrics induced by PF acquisition and zero filling are robustly removed by using the proposed RPG pipeline. For PF = 5/8, however, ringing removal via RPG leads to excessive image blurring due to the interplay of image phase and convolution kernel. Conclusions: RPG corrects Gibbs-ringing artifacts in magnitude images of PF acquired data and reduces the bias in quantitative MR metrics. Considering the benefit of PF acquisition and the feasibility of ringing removal, we suggest applying PF = 6/8 when PF acquisition is necessary.
MeSH term(s)	Algorithms ; Artifacts ; Diffusion Magnetic Resonance Imaging ; Image Processing, Computer-Assisted ; Magnetic Resonance Imaging ; Phantoms, Imaging
Language	English
Publishing date	2021-07-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	605774-3
ISSN	1522-2594 ; 0740-3194
ISSN (online)	1522-2594
ISSN	0740-3194
DOI	10.1002/mrm.28830
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Zs.A 1959: Show issues

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Article ; Online: Effects of COVID-19 Prevention Measures on Other Common Infections, Taiwan

Hong-Hsi Lee / Sheng-Hsuan Lin

Emerging Infectious Diseases, Vol 26, Iss 10, Pp 2509-

2020 Volume 2511

Abstract	To determine whether policies to limit transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hinder spread of other infectious diseases, we analyzed the National Health Insurance database in Taiwan. Rates of other infections were significantly lower after SARS-CoV-2 prevention measures were announced. This finding can be applied to cost-effectiveness of SARS-CoV-2 prevention.
Keywords	2019 novel coronavirus disease ; coronavirus disease ; COVID-19 ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; viruses ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216 ; covid19
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Effects of COVID-19 Prevention Measures on Other Common Infections, Taiwan

Lee, Hong-Hsi / Lin, Sheng-Hsuan

Emerg Infect Dis

Abstract	To determine whether policies to limit transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hinder spread of other infectious diseases, we analyzed the National Health Insurance database in Taiwan. Rates of other infections were significantly lower after SARS-CoV-2 prevention measures were announced. This finding can be applied to cost-effectiveness of SARS-CoV-2 prevention.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #690723
Database	COVID19

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Article ; Online: Physical and numerical phantoms for the validation of brain microstructural MRI: A cookbook.

Fieremans, Els / Lee, Hong-Hsi

NeuroImage

2018 Volume 182, Page(s) 39–61

Abstract: Phantoms, both numerical (software) and physical (hardware), can serve as a gold standard for the validation of MRI methods probing the brain microstructure. This review aims to provide guidelines on how to build, implement, or choose the right phantom ... ...

Abstract	Phantoms, both numerical (software) and physical (hardware), can serve as a gold standard for the validation of MRI methods probing the brain microstructure. This review aims to provide guidelines on how to build, implement, or choose the right phantom for a particular application, along with an overview of the current state-of-the-art of phantoms dedicated to study brain microstructure with MRI. For physical phantoms, we discuss the essential requirements and relevant characteristics of both the (NMR visible) liquid and (NMR invisible) phantom materials that induce relevant microstructural features detectable via MRI, based on diffusion, intra-voxel incoherent motion, magnetization transfer or magnetic susceptibility weighted contrast. In particular, for diffusion MRI, many useful phantoms have been proposed, ranging from simple liquids to advanced biomimetic phantoms consisting of hollow or plain microfibers and capillaries. For numerical phantoms, the focus is on Monte Carlo simulations of random walk, for which the basic principles, along with useful criteria to check and potential pitfalls are reviewed, in addition to a literature overview highlighting recent advances. While many phantoms exist already, the current review aims to stimulate further research in the field and to address remaining needs.
MeSH term(s)	Brain/anatomy & histology ; Brain/diagnostic imaging ; Humans ; Magnetic Resonance Imaging/methods ; Magnetic Resonance Imaging/standards ; Neuroimaging/methods ; Neuroimaging/standards ; Phantoms, Imaging/standards
Language	English
Publishing date	2018-06-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1147767-2
ISSN	1095-9572 ; 1053-8119
ISSN (online)	1095-9572
ISSN	1053-8119
DOI	10.1016/j.neuroimage.2018.06.046
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