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Article ; Online: Epileptic Seizure Prediction Using Attention Augmented Convolutional Network.

Liu, Dongsheng / Dong, Xingchen / Bian, Dong / Zhou, Weidong

International journal of neural systems

2023 Volume 33, Issue 11, Page(s) 2350054

Abstract: Early seizure prediction is crucial for epilepsy patients to reduce accidental injuries and improve their quality of life. Identifying pre-ictal EEG from the inter-ictal state is particularly challenging due to their nonictal nature and remarkable ... ...

Abstract	Early seizure prediction is crucial for epilepsy patients to reduce accidental injuries and improve their quality of life. Identifying pre-ictal EEG from the inter-ictal state is particularly challenging due to their nonictal nature and remarkable similarities. In this study, a novel epileptic seizure prediction method is proposed based on multi-head attention (MHA) augmented convolutional neural network (CNN) to address the issue of CNN's limit of capturing global information of input signals. First, data enhancement is performed on original EEG recordings to balance the pre-ictal and inter-ictal EEG data, and the EEG recordings are sliced into 6-second-long EEG segments. Subsequently, EEG time-frequency distribution is obtained using Stockwell transform (ST), and the attention augmented convolutional network is employed for feature extraction and classification. Finally, post-processing is utilized to reduce the false prediction rate (FPR). The CHB-MIT EEG database was used to evaluate the system. The validation results showed a segment-based sensitivity of 98.24% and an event-based sensitivity of 94.78% with a FPR of 0.05/h were yielded, respectively. The satisfying results of the proposed method demonstrate its possible potential for clinical applications.
MeSH term(s)	Humans ; Quality of Life ; Electroencephalography/methods ; Seizures/diagnosis ; Epilepsy/diagnosis ; Neural Networks, Computer
Language	English
Publishing date	2023-09-07
Publishing country	Singapore
Document type	Journal Article
ISSN	1793-6462
ISSN (online)	1793-6462
DOI	10.1142/S0129065723500545
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Protocol for measuring NLRC4 inflammasome activation and pyroptosis in murine bone-marrow-derived macrophages.

Dong, Xingchen / Chen, Lin-Feng

STAR protocols

2021 Volume 2, Issue 4, Page(s) 100894

Abstract: NLR family CARD domain containing protein 4 (NLRC4) inflammasome activation and the associated pyroptosis are critical for protection against infection by bacterial pathogens. This protocol presents a detailed procedure to activate and measure NLRC4 ... ...

Abstract	NLR family CARD domain containing protein 4 (NLRC4) inflammasome activation and the associated pyroptosis are critical for protection against infection by bacterial pathogens. This protocol presents a detailed procedure to activate and measure NLRC4 inflammasome activation and pyroptosis upon
MeSH term(s)	Animals ; Apoptosis Regulatory Proteins/analysis ; Apoptosis Regulatory Proteins/metabolism ; Calcium-Binding Proteins/analysis ; Calcium-Binding Proteins/metabolism ; Inflammasomes/analysis ; Inflammasomes/metabolism ; Macrophages/cytology ; Macrophages/metabolism ; Mice ; Microscopy, Fluorescence ; Pyroptosis/physiology
Chemical Substances	Apoptosis Regulatory Proteins ; Calcium-Binding Proteins ; Inflammasomes ; Ipaf protein, mouse
Language	English
Publishing date	2021-10-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2021.100894
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Article ; Online: Epileptic Seizure Detection with an End-to-End Temporal Convolutional Network and Bidirectional Long Short-Term Memory Model.

Dong, Xingchen / Wen, Yiming / Ji, Dezan / Yuan, Shasha / Liu, Zhen / Shang, Wei / Zhou, Weidong

International journal of neural systems

2024 Volume 34, Issue 3, Page(s) 2450012

Abstract: Automatic seizure detection plays a key role in assisting clinicians for rapid diagnosis and treatment of epilepsy. In view of the parallelism of temporal convolutional network (TCN) and the capability of bidirectional long short-term memory (BiLSTM) in ... ...

Abstract	Automatic seizure detection plays a key role in assisting clinicians for rapid diagnosis and treatment of epilepsy. In view of the parallelism of temporal convolutional network (TCN) and the capability of bidirectional long short-term memory (BiLSTM) in mining the long-range dependency of multi-channel time-series, we propose an automatic seizure detection method with a novel end-to-end TCN-BiLSTM model in this work. First, raw EEG is filtered with a 0.5-45 Hz band-pass filter, and the filtered data are input into the proposed TCN-BiLSTM network for feature extraction and classification. Post-processing process including moving average filtering, thresholding and collar technique is then employed to further improve the detection performance. The method was evaluated on two EEG database. On the CHB-MIT scalp EEG database, our method achieved a segment-based sensitivity of 94.31%, specificity of 97.13%, and accuracy of 97.09%. Meanwhile, an event-based sensitivity of 96.48% and an average false detection rate (FDR) of 0.38/h were obtained. On the SH-SDU database we collected, the segment-based sensitivity of 94.99%, specificity of 93.25%, and accuracy of 93.27% were achieved. In addition, an event-based sensitivity of 99.35% and a false detection rate of 0.54/h were yielded. The total detection time consumed for 1[Formula: see text]h EEG data was 5.65[Formula: see text]s. These results demonstrate the superiority and promising potential of the proposed method in real-time monitoring of epileptic seizures.
MeSH term(s)	Humans ; Memory, Short-Term ; Seizures/diagnosis ; Epilepsy/diagnosis ; Electroencephalography/methods ; Databases, Factual ; Algorithms ; Signal Processing, Computer-Assisted
Language	English
Publishing date	2024-01-17
Publishing country	Singapore
Document type	Journal Article
ISSN	1793-6462
ISSN (online)	1793-6462
DOI	10.1142/S0129065724500126
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Article ; Online: Epileptic Seizure Prediction Using Spatiotemporal Feature Fusion on EEG.

Ji, Dezan / He, Landi / Dong, Xingchen / Li, Haotian / Zhong, Xiangwen / Liu, Guoyang / Zhou, Weidong

International journal of neural systems

2024 , Page(s) 2450041

Abstract: Electroencephalography (EEG) plays a crucial role in epilepsy analysis, and epileptic seizure prediction has significant value for clinical treatment of epilepsy. Currently, prediction methods using Convolutional Neural Network (CNN) primarily focus on ... ...

Abstract	Electroencephalography (EEG) plays a crucial role in epilepsy analysis, and epileptic seizure prediction has significant value for clinical treatment of epilepsy. Currently, prediction methods using Convolutional Neural Network (CNN) primarily focus on local features of EEG, making it challenging to simultaneously capture the spatial and temporal features from multi-channel EEGs to identify the preictal state effectively. In order to extract inherent spatial relationships among multi-channel EEGs while obtaining their temporal correlations, this study proposed an end-to-end model for the prediction of epileptic seizures by incorporating Graph Attention Network (GAT) and Temporal Convolutional Network (TCN). Low-pass filtered EEG signals were fed into the GAT module for EEG spatial feature extraction, and followed by TCN to capture temporal features, allowing the end-to-end model to acquire the spatiotemporal correlations of multi-channel EEGs. The system was evaluated on the publicly available CHB-MIT database, yielding segment-based accuracy of 98.71%, specificity of 98.35%, sensitivity of 99.07%, and
Language	English
Publishing date	2024-05-22
Publishing country	Singapore
Document type	Journal Article
ISSN	1793-6462
ISSN (online)	1793-6462
DOI	10.1142/S0129065724500412
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: FXR suppresses colorectal cancer by inhibiting the Wnt/β-catenin pathway via activation of TLE3.

Dong, Xingchen / Cai, Chunmiao / Fu, Ting

Genes & diseases

2022 Volume 10, Issue 3, Page(s) 719–722

Language	English
Publishing date	2022-10-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2821806-1
ISSN	2352-3042 ; 2352-3042
ISSN (online)	2352-3042
ISSN	2352-3042
DOI	10.1016/j.gendis.2022.09.006
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Article ; Online: Automatic Seizure Detection Based on Stockwell Transform and Transformer.

Zhong, Xiangwen / Liu, Guoyang / Dong, Xingchen / Li, Chuanyu / Li, Haotian / Cui, Haozhou / Zhou, Weidong

Sensors (Basel, Switzerland)

2023 Volume 24, Issue 1

Abstract: Epilepsy is a chronic neurological disease associated with abnormal neuronal activity in the brain. Seizure detection algorithms are essential in reducing the workload of medical staff reviewing electroencephalogram (EEG) records. In this work, we ... ...

Abstract	Epilepsy is a chronic neurological disease associated with abnormal neuronal activity in the brain. Seizure detection algorithms are essential in reducing the workload of medical staff reviewing electroencephalogram (EEG) records. In this work, we propose a novel automatic epileptic EEG detection method based on Stockwell transform and Transformer. First, the S-transform is applied to the original EEG segments, acquiring accurate time-frequency representations. Subsequently, the obtained time-frequency matrices are grouped into different EEG rhythm blocks and compressed as vectors in these EEG sub-bands. After that, these feature vectors are fed into the Transformer network for feature selection and classification. Moreover, a series of post-processing methods were introduced to enhance the efficiency of the system. When evaluating the public CHB-MIT database, the proposed algorithm achieved an accuracy of 96.15%, a sensitivity of 96.11%, a specificity of 96.38%, a precision of 96.33%, and an area under the curve (AUC) of 0.98 in segment-based experiments, along with a sensitivity of 96.57%, a false detection rate of 0.38/h, and a delay of 20.62 s in event-based experiments. These outstanding results demonstrate the feasibility of implementing this seizure detection method in future clinical applications.
MeSH term(s)	Humans ; Seizures/diagnosis ; Brain ; Algorithms ; Area Under Curve ; Databases, Factual
Language	English
Publishing date	2023-12-22
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/s24010077
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Article ; Online: Insight into the High-Efficiency Benzo(a)pyrene Degradation Ability of

Dong, Xingchen / Wu, Siyi / Rao, Zihuan / Xiao, Yaqian / Long, Yan / Xie, Zhixiong

International journal of molecular sciences

2023 Volume 24, Issue 20

Abstract: Polycyclic aromatic hydrocarbons (PAHs) are common carcinogens. Benzo(a)pyrene is one of the most difficult high-molecular-weight (HMW) PAHs to remove. Biodegradation has become an ideal method to eliminate PAH pollutants from the environment. The ... ...

Abstract	Polycyclic aromatic hydrocarbons (PAHs) are common carcinogens. Benzo(a)pyrene is one of the most difficult high-molecular-weight (HMW) PAHs to remove. Biodegradation has become an ideal method to eliminate PAH pollutants from the environment. The existing research is mostly limited to low-molecular-weight PAHs; there is little understanding of HMW PAHs, particularly benzo(a)pyrene. Research into the biodegradation of HMW PAHs contributes to the development of microbial metabolic mechanisms and also provides new systems for environmental treatments.
MeSH term(s)	Biodegradation, Environmental ; Benzo(a)pyrene/metabolism ; Pseudomonas/genetics ; Pseudomonas/metabolism ; Molecular Docking Simulation ; Polycyclic Aromatic Hydrocarbons/metabolism ; Soil Pollutants/metabolism
Chemical Substances	Benzo(a)pyrene (3417WMA06D) ; Polycyclic Aromatic Hydrocarbons ; Soil Pollutants
Language	English
Publishing date	2023-10-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms242015323
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Article ; Online: Pseudomonas benzopyrenica

Dong, Xingchen / Rao, Zihuan / Wu, Siyi / Peng, Fang / Xie, Zhixiong / Long, Yan

International journal of systematic and evolutionary microbiology

2023 Volume 73, Issue 9

Abstract: A Gram-negative, yellow-pigmented, aerobic and rod-shaped bacterium, designated as strain ... ...

Abstract	A Gram-negative, yellow-pigmented, aerobic and rod-shaped bacterium, designated as strain BaP3
MeSH term(s)	Benzo(a)pyrene ; Soil ; Base Composition ; Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Pseudomonas/genetics
Chemical Substances	Benzo(a)pyrene (3417WMA06D) ; Soil ; Fatty Acids ; RNA, Ribosomal, 16S ; DNA, Bacterial
Language	English
Publishing date	2023-09-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2002336-4
ISSN	1466-5034 ; 1466-5026
ISSN (online)	1466-5034
ISSN	1466-5026
DOI	10.1099/ijsem.0.006034
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Transgenic mice lacking FGF15/19-SHP phosphorylation display altered bile acids and gut bacteria, promoting nonalcoholic fatty liver disease.

Kim, Young-Chae / Qi, Ming / Dong, Xingchen / Seok, Sunmi / Sun, Hao / Kemper, Byron / Fu, Ting / Kemper, Jongsook Kim

The Journal of biological chemistry

2023 Volume 299, Issue 8, Page(s) 104946

Abstract: Dysregulated bile acid (BA)/lipid metabolism and gut bacteria dysbiosis are tightly associated with the development of obesity and non-alcoholic fatty liver disease (NAFLD). The orphan nuclear receptor, Small Heterodimer Partner (SHP/NR0B2), is a key ... ...

Abstract	Dysregulated bile acid (BA)/lipid metabolism and gut bacteria dysbiosis are tightly associated with the development of obesity and non-alcoholic fatty liver disease (NAFLD). The orphan nuclear receptor, Small Heterodimer Partner (SHP/NR0B2), is a key regulator of BA/lipid metabolism, and its gene-regulating function is markedly enhanced by phosphorylation at Thr-58 mediated by a gut hormone, fibroblast growth factor-15/19 (FGF15/19). To investigate the role of this phosphorylation in whole-body energy metabolism, we generated transgenic SHP-T58A knock-in mice. Compared with wild-type (WT) mice, the phosphorylation-defective SHP-T58A mice gained weight more rapidly with decreased energy expenditure and increased lipid/BA levels. This obesity-prone phenotype was associated with the upregulation of lipid/BA synthesis genes and downregulation of lipophagy/β-oxidation genes. Mechanistically, defective SHP phosphorylation selectively impaired its interaction with LRH-1, resulting in de-repression of SHP/LRH-1 target BA/lipid synthesis genes. Remarkably, BA composition and selective gut bacteria which are known to impact obesity, were also altered in these mice. Upon feeding a high-fat diet, fatty liver developed more severely in SHP-T58A mice compared to WT mice. Treatment with antibiotics substantially improved the fatty liver phenotypes in both groups but had greater effects in the T58A mice so that the difference between the groups was largely eliminated. These results demonstrate that defective phosphorylation at a single nuclear receptor residue can impact whole-body energy metabolism by altering BA/lipid metabolism and gut bacteria, promoting complex metabolic disorders like NAFLD. Since posttranslational modifications generally act in gene- and context-specific manners, the FGF15/19-SHP phosphorylation axis may allow more targeted therapy for NAFLD.
MeSH term(s)	Animals ; Mice ; Bile Acids and Salts/analysis ; Bile Acids and Salts/genetics ; Lipids/blood ; Mice, Inbred C57BL ; Mice, Transgenic ; Non-alcoholic Fatty Liver Disease/genetics ; Non-alcoholic Fatty Liver Disease/metabolism ; Non-alcoholic Fatty Liver Disease/microbiology ; Obesity/microbiology ; Phosphorylation ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Microbiome/physiology ; Male ; Anti-Bacterial Agents/pharmacology
Chemical Substances	Bile Acids and Salts ; Lipids ; Receptors, Cytoplasmic and Nuclear ; fibroblast growth factor 15, mouse ; Nr5a2 protein, mouse ; Anti-Bacterial Agents
Language	English
Publishing date	2023-06-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.104946
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Article ; Online: BRD4 Regulates Glycolysis-Dependent Nos2 Expression in Macrophages Upon H pylori Infection.

Modi, Nikita / Chen, Yanheng / Dong, Xingchen / Hu, Xiangming / Lau, Gee W / Wilson, Keith T / Peek, Richard M / Chen, Lin-Feng

Cellular and molecular gastroenterology and hepatology

2023 Volume 17, Issue 2, Page(s) 292–308.e1

Abstract: Background & aims: Metabolic reprogramming is essential for the activation and functions of macrophages, including bacterial killing and cytokine production. Bromodomain-containing protein 4 (BRD4) has emerged as a critical regulator of innate immune ... ...

Abstract	Background & aims: Metabolic reprogramming is essential for the activation and functions of macrophages, including bacterial killing and cytokine production. Bromodomain-containing protein 4 (BRD4) has emerged as a critical regulator of innate immune response. However, the potential role of BRD4 in the metabolic reprogramming of macrophage activation upon Helicobacter pylori infection remains unclear. Methods: Bone marrow-derived macrophages (BMDMs) from wild-type (WT) and Brd4-myeloid deletion conditional knockout (Brd4-CKO) mice were infected with H pylori. RNA sequencing was performed to evaluate the differential gene expression between WT and Brd4-deficient BMDMs upon infection. An in vivo model of H pylori infection using WT and Brd4-CKO mice was used to confirm the role of BRD4 in innate immune response to infection. Results: Depletion of Brd4 in BMDMs showed impaired H pylori-induced glycolysis. In addition, H pylori-induced expression of glycolytic genes, including Slc2a1 and Hk2, was decreased in Brd4-deficient BMDMs. BRD4 was recruited to the promoters of Slc2a1 and Hk2 via hypoxia-inducible factor-1α, facilitating their expression. BRD4-mediated glycolysis stabilized H pylori-induced nitric oxide synthase (Nos2) messenger RNA to produce nitric oxide. The NO-mediated killing of H pylori decreased in Brd4-deficient BMDMs, which was rescued by pyruvate. Furthermore, Brd4-CKO mice infected with H pylori showed reduced gastric inflammation and increased H pylori colonization with reduced inducible NO synthase expression in gastric macrophages. Conclusions: Our study identified BRD4 as a key regulator of hypoxia-inducible factor-1α-dependent glycolysis and macrophage activation. Furthermore, we show a novel regulatory role of BRD4 in innate immunity through glycolysis to stabilize Nos2 messenger RNA for NO production to eliminate H pylori infection.
MeSH term(s)	Animals ; Mice ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Helicobacter Infections/microbiology ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Helicobacter pylori/metabolism ; Macrophages/metabolism ; Nitric Oxide Synthase/metabolism ; RNA, Messenger/metabolism ; Glycolysis ; Nitric Oxide Synthase Type II/metabolism
Chemical Substances	Nuclear Proteins ; Hypoxia-Inducible Factor 1, alpha Subunit ; Nitric Oxide Synthase (EC 1.14.13.39) ; RNA, Messenger ; Nos2 protein, mouse (EC 1.14.13.39) ; Nitric Oxide Synthase Type II (EC 1.14.13.39)
Language	English
Publishing date	2023-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2819778-1
ISSN	2352-345X ; 2352-345X
ISSN (online)	2352-345X
ISSN	2352-345X
DOI	10.1016/j.jcmgh.2023.10.001
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