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Article ; Online: Contrastive Disentanglement for Quantitative Ultrasound Muscle Atrophy Evaluation.

Zhang, Yue / Zhan, Yonghua / Guo, Kaitai / Zheng, Yang / Tang, Liang / Guo, Jianzhong / Liang, Jimin

IEEE transactions on bio-medical engineering

2024 Volume PP

Abstract: Objective: Muscle atrophy reduces the quality of life and increases morbidity and mortality from other diseases. The development of non-invasive muscle atrophy evaluation method is of great practical value. The lack of gold standard for pathological ... ...

Abstract	Objective: Muscle atrophy reduces the quality of life and increases morbidity and mortality from other diseases. The development of non-invasive muscle atrophy evaluation method is of great practical value. The lack of gold standard for pathological grading usually allows only the duration of weightlessness as a criterion for the degree of atrophy. However, the adaptive reductive remodeling of muscle physiology and structure shows a trend of nonlinear changes in time. Consequently, using weightlessness time as a benchmark for the degree of atrophy is inaccurate. Methods: This paper proposes a new ultrasound imaging-based method for quantifying muscle atrophy that utilizes weakly supervised information between multiple data partitions with controlled variance components, overcoming the limitations of using the weightlessness time as a criterion. We introduce a group-supervised contrastive disentanglement network (GCDNet) to disentangle the individual variances, muscle growth and atrophy components of ultrasound images, and quantify the degree of atrophy using the disentangled atrophy component. Results: The feasibility of GCDNet is validated by the separability, independence, and representativeness of the disentangled components. To simplify the application of GCDNet, a muscle atrophy scoring network requiring no reference images is developed by distilling the GCDNet's knowledge of muscle atrophy quantization. The strength of the proposed methodology allows us, for the first time to our knowledge, to study the muscle growth attribute during hind-limb unloading and the spatial distribution of muscle atrophy.
Language	English
Publishing date	2024-02-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	160429-6
ISSN	1558-2531 ; 0018-9294
ISSN (online)	1558-2531
ISSN	0018-9294
DOI	10.1109/TBME.2024.3369072
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: High-Resolution Swin Transformer for Automatic Medical Image Segmentation.

Wei, Chen / Ren, Shenghan / Guo, Kaitai / Hu, Haihong / Liang, Jimin

Sensors (Basel, Switzerland)

2023 Volume 23, Issue 7

Abstract: The resolution of feature maps is a critical factor for accurate medical image segmentation. Most of the existing Transformer-based networks for medical image segmentation adopt a U-Net-like architecture, which contains an encoder that converts the high- ... ...

Abstract	The resolution of feature maps is a critical factor for accurate medical image segmentation. Most of the existing Transformer-based networks for medical image segmentation adopt a U-Net-like architecture, which contains an encoder that converts the high-resolution input image into low-resolution feature maps using a sequence of Transformer blocks and a decoder that gradually generates high-resolution representations from low-resolution feature maps. However, the procedure of recovering high-resolution representations from low-resolution representations may harm the spatial precision of the generated segmentation masks. Unlike previous studies, in this study, we utilized the high-resolution network (HRNet) design style by replacing the convolutional layers with Transformer blocks, continuously exchanging feature map information with different resolutions generated by the Transformer blocks. The proposed Transformer-based network is named the high-resolution Swin Transformer network (HRSTNet). Extensive experiments demonstrated that the HRSTNet can achieve performance comparable with that of the state-of-the-art Transformer-based U-Net-like architecture on the 2021 Brain Tumor Segmentation dataset, the Medical Segmentation Decathlon's liver dataset, and the BTCV multi-organ segmentation dataset.
MeSH term(s)	Humans ; Brain Neoplasms ; Electric Power Supplies ; Liver ; Masks ; Image Processing, Computer-Assisted
Language	English
Publishing date	2023-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s23073420
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Simulation study of inverse diffusion counterbalance method for super-resolution ion mobility spectrometry.

Guo, Kaitai / Zheng, Yang / Hu, Haihong / Liang, Jimin

Frontiers in chemistry

2022 Volume 10, Page(s) 1004615

Abstract: Ion mobility spectrometer (IMS) is a powerful chemical composition analysis tool working at atmospheric pressure that can be used to separate complex samples and study molecular structures. Resolution is a key parameter for evaluating the performance of ... ...

Abstract	Ion mobility spectrometer (IMS) is a powerful chemical composition analysis tool working at atmospheric pressure that can be used to separate complex samples and study molecular structures. Resolution is a key parameter for evaluating the performance of IMS. However, for the pulsed sampling technique used by drift tube IMS, there is an upper limit to the resolution due to the diffusion between ions and the drift gas. In this work, an inverse diffusion counterbalance method is proposed to break the resolution limit. The method is inspired by the stimulated emission depletion (STED). In optical microscopy systems, STED is used to break the optical diffraction limit by a ring of depleted light to counteract diffraction effects of the excited light. We modified this strategy and applied it to an IMS system for counteracting the diffusion effect of the pulsed ion packet. The method can increase the resolution up to 1.55 times through theoretical analysis, and the improvement is verified by simulations. The simulation results find that the initial width of the ion packet has an influence on the effectiveness of the method, and the narrower the initial width, the better the effect. The proposed inverse counterbalance strategy may also be applied to other spectral analysis instruments to break the resolution limit.
Language	English
Publishing date	2022-09-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711776-5
ISSN	2296-2646
ISSN	2296-2646
DOI	10.3389/fchem.2022.1004615
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Modeling the modulation characteristics of the Bradbury-Nielsen gate in ion mobility spectrometers.

Guo, Kaitai / Zhang, Chong / Ni, Kai / Wang, Xiaohao

The Review of scientific instruments

2022 Volume 93, Issue 8, Page(s) 84101

Abstract: The Bradbury-Nelson gate (BNG) is a common device used for ion control in time-of-flight mass spectrometry and ion mobility spectrometry (IMS). A dual-location control model was employed in order to better understand the behavior of ions around a ... ...

Abstract	The Bradbury-Nelson gate (BNG) is a common device used for ion control in time-of-flight mass spectrometry and ion mobility spectrometry (IMS). A dual-location control model was employed in order to better understand the behavior of ions around a modulated BNG. This model illustrated that the ions are released from the starting location and truncated at the cutoff location. The shapes of the starting and cutoff locations are both curved with similar curvature, and the cutoff location is situated further back. Therefore, the distance between the two locations is a key parameter leading to the ion loss during modulation and is influenced by the gating voltage difference. Through simulations and experiments, the ion loss is verified to increase with the increase in the gating voltage difference. Taking a Fourier transform IMS as an example, by reducing the gating voltage difference from 150 to 50 V, the signal-to-noise ratio of the time domain result was improved from 91.7 to 386.5 and the resolving power was improved from 40.9 to 63.6. In addition, the superposition effect of multicycle modulation is shown and explained by the model. When the modulated frequency is too rapid and the closing time is insufficient for all the ions to be consumed, some ions continue to exist between the two locations, and the residual ions then enter the drift region during the next few cycles. This phenomenon needs to be avoided because the total number of ions entering the drift region will then increase uncontrollably.
MeSH term(s)	Ions/chemistry ; Mass Spectrometry
Chemical Substances	Ions
Language	English
Publishing date	2022-08-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/5.0074709
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: High-Resolution Swin Transformer for Automatic Medical Image Segmentation

Wei, Chen / Ren, Shenghan / Guo, Kaitai / Hu, Haihong / Liang, Jimin

2022

Abstract: The Resolution of feature maps is critical for medical image segmentation. Most of the existing Transformer-based networks for medical image segmentation are U-Net-like architecture that contains an encoder that utilizes a sequence of Transformer blocks ... ...

Abstract	The Resolution of feature maps is critical for medical image segmentation. Most of the existing Transformer-based networks for medical image segmentation are U-Net-like architecture that contains an encoder that utilizes a sequence of Transformer blocks to convert the input medical image from high-resolution representation into low-resolution feature maps and a decoder that gradually recovers the high-resolution representation from low-resolution feature maps. Unlike previous studies, in this paper, we utilize the network design style from the High-Resolution Network (HRNet), replace the convolutional layers with Transformer blocks, and continuously exchange information from the different resolution feature maps that are generated by Transformer blocks. The newly Transformer-based network presented in this paper is denoted as High-Resolution Swin Transformer Network (HRSTNet). Extensive experiments illustrate that HRSTNet can achieve comparable performance with the state-of-the-art Transformer-based U-Net-like architecture on Brain Tumor Segmentation(BraTS) 2021 and the liver dataset from Medical Segmentation Decathlon. The code of HRSTNet will be publicly available at https://github.com/auroua/HRSTNet. Comment: 14 pages, 3 figures, 2 tables
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Artificial Intelligence
Subject code	004
Publishing date	2022-07-23
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Muscle Atrophy Evaluation via Radiomics Analysis Using Ultrasound Images: A Cohort Data Study.

Zhang, Yue / Du, Getao / Zhan, Yonghua / Guo, Kaitai / Zheng, Yang / Tang, Liang / Guo, Jianzhong / Liang, Jimin

IEEE transactions on bio-medical engineering

2022 Volume 69, Issue 10, Page(s) 3163–3174

Abstract: Objective: Existing methods for muscle atrophy evaluation based on muscle size measures from ultrasound images are inadequate in precision. Radiomics has been widely used in various medical studies, but its validity for the evaluation of muscle atrophy ... ...

Abstract	Objective: Existing methods for muscle atrophy evaluation based on muscle size measures from ultrasound images are inadequate in precision. Radiomics has been widely used in various medical studies, but its validity for the evaluation of muscle atrophy has not been fully explored. Methods: This study presents a radiomics analysis for muscle atrophy evaluation using ultrasound images. The hindlimb unloading rat model was developed to simulate weightlessness muscle atrophy and ultrasound images of the hind limbs were acquired for both the hindlimb unloaded (HU) and control groups during a 21-day HU period. A total of 368 radiomics features were extracted and the stable and informative features were selected through a two-stage feature selection procedure. The feature change trajectory of the stable features was analyzed using the hierarchical clustering method. Finally, an adaptive longitudinal feature selection and grading network, ALNet, was developed to evaluate muscle atrophy. Results: The clustering trajectories of ultrasound image features showed similar trends to the changes in muscle atrophy at the molecular level. The best grading accuracy achieved by the ALNet was 79.5% for the Soleus (Sol) muscle and 82.6% for the Gastrocnemius (Gas) muscle. Conclusion: The test-retest is essential in performing radiomics analysis on ultrasound images. The longitudinal feature selection is important for muscle atrophy grading. The ultrasound image features of the Gas muscle have better discrimination ability than that of the Sol muscle. This study proves for the first time the capability of ultrasound image features for muscle atrophy evaluation.
MeSH term(s)	Animals ; Cohort Studies ; Hindlimb Suspension/physiology ; Humans ; Muscle, Skeletal/diagnostic imaging ; Muscle, Skeletal/physiology ; Muscular Atrophy/diagnostic imaging ; Muscular Atrophy/pathology ; Rats ; Ultrasonography/methods
Language	English
Publishing date	2022-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	160429-6
ISSN	1558-2531 ; 0018-9294
ISSN (online)	1558-2531
ISSN	0018-9294
DOI	10.1109/TBME.2022.3162223
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Ion Distribution Profiling in an Ion Mobility Spectrometer by Laser-Induced Fluorescence

Guo, Kaitai / Binchao Tang / Kai Ni / Kunxiao Li / Quan Yu / Xiang Qian / Xiangxiang Song / Xiaohao Wang

Analytical chemistry. 2018 Feb. 28, v. 90, no. 7

2018

Abstract: Measuring the ion distribution pattern in a drift tube under atmospheric pressure is very useful for studies of ion motion and design of ion mobility spectrometers (IMS); however, no mature method is available for conducting such measurements at present. ...

Abstract	Measuring the ion distribution pattern in a drift tube under atmospheric pressure is very useful for studies of ion motion and design of ion mobility spectrometers (IMS); however, no mature method is available for conducting such measurements at present. We propose a simple and low-cost technique for profiling the two-dimensional ion distribution in any cross section of a drift tube. Similar to particle-image velocimetry, we first send sample ions with fluorescence properties into the drift tube and use a receiving plate to collect and accumulate them. Then, the receiving plate is illuminated by exciting light, and the ion distribution appears as a fluorescence image. In this study, Rhodamine 6G was selected as a typical fluorescence-tracer particle. Electrospray ionization (ESI) was chosen as an ionization source to keep the fluorophore undamaged. A plasma-cleaned coverslip was placed at the detection position as a receiving plate. When a layer of ions was collected, the slide was placed under the exciting light with a wavelength of 473 nm. A camera with a 490 nm high-pass light filter was used to capture the fluorescence image representing the ion distribution. The measured-ion detection efficiency of the method was 156 ion/dN, which is equivalent to the level of IonCCD. In addition, we studied the ion-passing characteristics of a Bradbury–Nielsen (BN) ion shutter and the ion-focusing effect in the drift tube using this method. The two-dimensional ion-distribution images behind the ion shutter and the images of the focused ion spot were first observed experimentally. Further theoretical analysis yielded the same conclusions as the experimental results, proving the feasibility of this method and producing a deeper understanding of ion motion in the IMS. This method has promising prospective application to the design, debugging, and optimization of IMS instruments and hyphenated systems.
Keywords	atmospheric pressure ; cameras ; fluorescence ; fluorescent dyes ; ionization ; ions ; rhodamines ; spectrometers ; velocimetry ; wavelengths
Language	English
Dates of publication	2018-0228
Size	p. 4514-4520.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.7b04912
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Ion Distribution Profiling in an Ion Mobility Spectrometer by Laser-Induced Fluorescence.

Guo, Kaitai / Ni, Kai / Song, Xiangxiang / Li, Kunxiao / Tang, Binchao / Yu, Quan / Qian, Xiang / Wang, Xiaohao

Analytical chemistry

2018 Volume 90, Issue 7, Page(s) 4514–4520

Abstract	Measuring the ion distribution pattern in a drift tube under atmospheric pressure is very useful for studies of ion motion and design of ion mobility spectrometers (IMS); however, no mature method is available for conducting such measurements at present. We propose a simple and low-cost technique for profiling the two-dimensional ion distribution in any cross section of a drift tube. Similar to particle-image velocimetry, we first send sample ions with fluorescence properties into the drift tube and use a receiving plate to collect and accumulate them. Then, the receiving plate is illuminated by exciting light, and the ion distribution appears as a fluorescence image. In this study, Rhodamine 6G was selected as a typical fluorescence-tracer particle. Electrospray ionization (ESI) was chosen as an ionization source to keep the fluorophore undamaged. A plasma-cleaned coverslip was placed at the detection position as a receiving plate. When a layer of ions was collected, the slide was placed under the exciting light with a wavelength of 473 nm. A camera with a 490 nm high-pass light filter was used to capture the fluorescence image representing the ion distribution. The measured-ion detection efficiency of the method was 156 ion/dN, which is equivalent to the level of IonCCD. In addition, we studied the ion-passing characteristics of a Bradbury-Nielsen (BN) ion shutter and the ion-focusing effect in the drift tube using this method. The two-dimensional ion-distribution images behind the ion shutter and the images of the focused ion spot were first observed experimentally. Further theoretical analysis yielded the same conclusions as the experimental results, proving the feasibility of this method and producing a deeper understanding of ion motion in the IMS. This method has promising prospective application to the design, debugging, and optimization of IMS instruments and hyphenated systems.
Language	English
Publishing date	2018-03-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.7b04912
Database	MEDical Literature Analysis and Retrieval System OnLINE

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