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Article ; Online: Functional loops: Monitoring functional organization of deep neural networks using algebraic topology.

Zhang, Ben / Lin, Hongwei

Neural networks : the official journal of the International Neural Network Society

2024 Volume 174, Page(s) 106239

Abstract: Various topological methods have emerged in recent years to investigate the inner workings of deep neural networks (DNNs) based on the structural and weight information. However, their effectiveness is restricted due to the stratified structure and ... ...

Abstract	Various topological methods have emerged in recent years to investigate the inner workings of deep neural networks (DNNs) based on the structural and weight information. However, their effectiveness is restricted due to the stratified structure and volatile weight information. In this study, we explore the relationship between functional organizations and network performance using algebraic topology. Our results indicate that functional loops reveal functional interaction patterns of multiple neurons in DNNs. We also propose functional persistence as a measure of functional complexity and develop an early stopping criterion that achieves competitive results without requiring a validation set.
MeSH term(s)	Neural Networks, Computer ; Neurons
Language	English
Publishing date	2024-03-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	740542-x
ISSN	1879-2782 ; 0893-6080
ISSN (online)	1879-2782
ISSN	0893-6080
DOI	10.1016/j.neunet.2024.106239
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Article ; Online: Mitochondrial toxicants in Xian-Ling-Gu-Bao induce liver injury by regulating the PI3K/mTOR signaling pathway: an in vitro study.

Piao, Shujuan / Lin, Hongwei / Tao, Xia / Chen, Wansheng

BMC complementary medicine and therapies

2022 Volume 22, Issue 1, Page(s) 317

Abstract: Background: Drug-induced mitochondrial toxicity is thought to be a common mechanism of drug hepatotoxicity. Xian-Ling-Gu-Bao (XLGB) oral preparation is a commonly used drug for osteoporosis in China. Classical safety evaluation studies have shown that ... ...

Abstract	Background: Drug-induced mitochondrial toxicity is thought to be a common mechanism of drug hepatotoxicity. Xian-Ling-Gu-Bao (XLGB) oral preparation is a commonly used drug for osteoporosis in China. Classical safety evaluation studies have shown that the entire preparation and six Chinese herbal medicines have high safety, but the incidence of drug-induced liver damage due to XLGB remains high, the mechanism and toxic substances causing liver injury are still unclear. The purpose of this study is to identify compounds with potential mitochondrial liabilities in XLGB, and to clarify their underlying mechanisms and related pathways. Methods: The mitochondrial function analysis was performed using an extracellular flux assay, which simultaneously monitored both oxygen consumption rate (OCR) and extracellular acidification rate (ECAR). Through network pharmacology and in vitro experimental verification, the potential protein targets, signaling pathways and molecular mechanism of mitochondrial toxicity have been studied. Results: We observed a significant decrease in mitochondrial respiration of Psoraleae Fructus and its five compounds in fundamental bioenergetics parameters such as basal respiration, ATP-linked production and maximal respiration, indicating mitochondrial dysfunction. The network pharmacology results showed that the influence of XLGB on mitochondrial dysfunction was closely related to PI3K-Akt signaling pathway, mTOR signaling pathway and Apoptosis. Western blot showed that the levels of mTOR, p-mTOR (Ser2448), Raptor, PI3K (p110α), Beclin 1, ATG5 and Caspase-9 were up-regulated after treatment with psoralidin, psoralen and bavachin, and the expression of Bcl-2 was down-regulated after bavachinin treatment. Conclusions: The hepatotoxicity of XLGB is associated with mitochondrial dysfunction. Five compounds in Psoraleae Fructus showed mitochondrial damage, they are psoralidin, isobavachalcone, bavachinin, bavachin and psoralen, especially psoralidin showed significant reduction in reserve capacity and respiratory control ratios. The molecular mechanism is related to the activation of PI3K/mTOR signaling pathway to inhibit autophagy and induce mitochondrial apoptosis.
MeSH term(s)	Humans ; Phosphatidylinositol 3-Kinases ; TOR Serine-Threonine Kinases ; Mitochondria ; Signal Transduction ; Chemical and Drug Induced Liver Injury ; Furocoumarins
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; TOR Serine-Threonine Kinases (EC 2.7.11.1) ; Furocoumarins ; MTOR protein, human (EC 2.7.1.1)
Language	English
Publishing date	2022-12-01
Publishing country	England
Document type	Journal Article
ISSN	2662-7671
ISSN (online)	2662-7671
DOI	10.1186/s12906-022-03798-5
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Article ; Online: Mitochondrial toxicants in Xian-Ling-Gu-Bao induce liver injury by regulating the PI3K/mTOR signaling pathway: an in vitro study

Piao, Shujuan / Lin, Hongwei / Tao, Xia / Chen, Wansheng

BMC Complement Med Ther. 2022 Dec., v. 22, no. 1 p.317-317

2022

Abstract: BACKGROUND: Drug-induced mitochondrial toxicity is thought to be a common mechanism of drug hepatotoxicity. Xian-Ling-Gu-Bao (XLGB) oral preparation is a commonly used drug for osteoporosis in China. Classical safety evaluation studies have shown that ... ...

Abstract	BACKGROUND: Drug-induced mitochondrial toxicity is thought to be a common mechanism of drug hepatotoxicity. Xian-Ling-Gu-Bao (XLGB) oral preparation is a commonly used drug for osteoporosis in China. Classical safety evaluation studies have shown that the entire preparation and six Chinese herbal medicines have high safety, but the incidence of drug-induced liver damage due to XLGB remains high, the mechanism and toxic substances causing liver injury are still unclear. The purpose of this study is to identify compounds with potential mitochondrial liabilities in XLGB, and to clarify their underlying mechanisms and related pathways. METHODS: The mitochondrial function analysis was performed using an extracellular flux assay, which simultaneously monitored both oxygen consumption rate (OCR) and extracellular acidification rate (ECAR). Through network pharmacology and in vitro experimental verification, the potential protein targets, signaling pathways and molecular mechanism of mitochondrial toxicity have been studied. RESULTS: We observed a significant decrease in mitochondrial respiration of Psoraleae Fructus and its five compounds in fundamental bioenergetics parameters such as basal respiration, ATP-linked production and maximal respiration, indicating mitochondrial dysfunction. The network pharmacology results showed that the influence of XLGB on mitochondrial dysfunction was closely related to PI3K-Akt signaling pathway, mTOR signaling pathway and Apoptosis. Western blot showed that the levels of mTOR, p-mTOR (Ser2448), Raptor, PI3K (p110α), Beclin 1, ATG5 and Caspase-9 were up-regulated after treatment with psoralidin, psoralen and bavachin, and the expression of Bcl-2 was down-regulated after bavachinin treatment. CONCLUSIONS: The hepatotoxicity of XLGB is associated with mitochondrial dysfunction. Five compounds in Psoraleae Fructus showed mitochondrial damage, they are psoralidin, isobavachalcone, bavachinin, bavachin and psoralen, especially psoralidin showed significant reduction in reserve capacity and respiratory control ratios. The molecular mechanism is related to the activation of PI3K/mTOR signaling pathway to inhibit autophagy and induce mitochondrial apoptosis.
Keywords	Western blotting ; acidification ; apoptosis ; autophagy ; caspase-9 ; complement ; drugs ; energy metabolism ; hepatotoxicity ; liver ; mitochondria ; osteoporosis ; oxygen consumption ; pharmacology ; phosphatidylinositol 3-kinase ; psoralen ; toxic substances ; China
Language	English
Dates of publication	2022-12
Size	p. 317.
Publishing place	BioMed Central
Document type	Article ; Online
ISSN	2662-7671
DOI	10.1186/s12906-022-03798-5
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Improved Quantum Supersampling for Quantum Ray Tracing

Lu, Xi / Lin, Hongwei

2022

Abstract: Ray tracing algorithm is a category of rendering algorithms that calculate the color of pixels by simulating the physical movements of a huge amount of rays and calculating their energies, which can be implemented in parallel. Meanwhile, the ... ...

Abstract	Ray tracing algorithm is a category of rendering algorithms that calculate the color of pixels by simulating the physical movements of a huge amount of rays and calculating their energies, which can be implemented in parallel. Meanwhile, the superposition and entanglement property make quantum computing a natural fit for parallel tasks.Here comes an interesting question, is the inherently parallel quantum computing able to speed up the inherently parallel ray tracing algorithm? The ray tracing problem can be regarded as a high-dimensional numerical integration problem. Suppose $N$ queries are used, classical Monte Carlo approaches has an error convergence of $O(1/\sqrt{N})$, while the quantum supersampling algorithm can achieve an error convergence of approximately $O(1/N)$. However, the outputs of the origin form of quantum supersampling obeys a probability distribution that has a long tail, which shows up as many detached abnormal noisy dots on images. In this paper, we improve quantum supersampling by replacing the QFT-based phase estimation in quantum supersampling with a robust quantum counting scheme, the QFT-based adaptive Bayesian phase estimation. We quantitatively study and compare the performances of different quantum counting schemes. Finally, we do simulation experiments to show that the quantum ray tracing with improved quantum supersampling does perform better than classical path tracing algorithm as well as the original form of quantum supersampling. Comment: 12 pages, 15 figures
Keywords	Quantum Physics ; Computer Science - Graphics
Subject code	541
Publishing date	2022-08-10
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Reasonable thickness determination for implicit porous sheet structure using persistent homology

Yan, Jiacong / Lin, Hongwei

2022

Abstract: Porous structures are widely used in various industries because of their excellent properties. Porous surfaces have no thickness and should be thickened to sheet structures for further fabrication. However, conventional methods for generating sheet ... ...

Abstract	Porous structures are widely used in various industries because of their excellent properties. Porous surfaces have no thickness and should be thickened to sheet structures for further fabrication. However, conventional methods for generating sheet structures are inefficient for porous surfaces because of the complexity of the internal structures. In this study, we propose a novel method for generating porous sheet structures directly from point clouds sampled on a porous surface. The generated sheet structure is represented by an implicit B-spline function, which ensures smoothness and closure. Moreover, based on the persistent homology theory, the topology structure of the generated porous sheet structure can be controlled, and a reasonable range of the uniform thickness of the sheet structure can be calculated to ensure manufacturability and pore existence. Finally, the implicitly B-spline represented sheet structures are sliced directly with the marching squares algorithm, and the contours can be used for 3D printing. Experimental results show the superiority of the developed method in efficiency over the traditional methods. Comment: 13 pages, 13 figures
Keywords	Computer Science - Computational Geometry
Subject code	600
Publishing date	2022-12-20
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Forward looking statement, investor sentiment and stock liquidity

Li, Chenggang / Yan, Ying / Liu, Xiwei / Wan, Shengnan / Xu, Yunbao / Lin, Hongwei

Heliyon. 2023 Apr. 11, p.e15329-

2023

Abstract: Information is a critical element of capital markets, and liquidity is the lifeblood of capital markets. Relative to historical information, forward-looking information is of significant value to investors. Based on textual analysis calculations, we ... ...

Abstract	Information is a critical element of capital markets, and liquidity is the lifeblood of capital markets. Relative to historical information, forward-looking information is of significant value to investors. Based on textual analysis calculations, we selected Chinese A-share listed companies as a research sample to explore the impact of forward-looking information disclosure level on stock liquidity. It is found that the higher the level of forward-looking information disclosure, the better the stock liquidity. Investor sentiment is the transmission mechanism through which the forward looking statement disclosure level affects stock liquidity. The heterogeneity analysis shows that the level of forward-Looking statement disclosure has a more significant effect on stock liquidity improvement for state-owned enterprises and enterprises in low-market regions than those in regions with high marketization levels. The article expands and enriches the research on forward-looking information disclosure, and also has some reference value for regulators to formulate laws and regulations and regulate forward-looking information disclosure.
Keywords	business enterprises ; capital ; markets ; normal values ; public ownership ; sampling ; Forward-looking information ; Information disclosure ; Investor sentiment ; Stock liquidity ; Text information
Language	English
Dates of publication	2023-0411
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e15329
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Tussilagone protects acute lung injury from PM2.5 via alleviating Hif-1α/NF-κB-mediated inflammatory response.

Lin, Hongwei / Chen, Min / Gao, Yanjun / Wang, Zaiqiang / Jin, Faguang

Environmental toxicology

2022 Volume 37, Issue 5, Page(s) 1198–1210

Abstract: Environmental pollution, especially particulate matter in the air, is a serious threat to human health. Long-term inhalation of particulate matter with a diameter < 2.5 μm (PM2.5) induced irreversible respiratory and lung injury. However, it is not clear ...

Abstract	Environmental pollution, especially particulate matter in the air, is a serious threat to human health. Long-term inhalation of particulate matter with a diameter < 2.5 μm (PM2.5) induced irreversible respiratory and lung injury. However, it is not clear whether temporary exposure to massive PM2.5 would result in epithelial damage and lung injury. More importantly, it is urgent to clarify the mechanisms of PM2.5 cytotoxicity and develop a defensive and therapeutic approach. In this study, we demonstrated that temporary exposure with PM2.5 induced lung epithelial cell apoptosis via promoting cytokines expression and inflammatory factors secretion. The cytotoxicity of PM2.5 could be alleviated by tussilagone (TSL), which is a natural compound isolated from the flower buds of Tussilago farfara. The mechanism study indicated that PM2.5 promoted the protein level of Hif-1α by reducing its degradation mediated by PHD2 binding, which furtherly activated NF-κB signaling and inflammatory response. Meanwhile, TSL administration facilitated the interaction of the Hif-1α/PHD2 complex and restored the Hif-1α protein level increased by PM2.5. When PHD2 was inhibited in epithelial cells, the protective function of TSL on PM2.5 cytotoxicity was attenuated and the expression of cytokines was retrieved. Expectedly, the in vivo study also suggested that temporary PM2.5 exposure led to acute lung injury. TSL treatment could effectively relieve the damage and decrease the expression of inflammatory cytokines by repressing Hif-1α level and NF-κB activation. Our findings provide a new therapeutic strategy for air pollution-related respiratory diseases, and TSL would be a potential preventive medicine for PM2.5 cytotoxicity.
MeSH term(s)	Acute Lung Injury/chemically induced ; Acute Lung Injury/prevention & control ; Humans ; Lung Injury/chemically induced ; Lung Injury/prevention & control ; NF-kappa B/metabolism ; Particulate Matter/toxicity ; Sesquiterpenes
Chemical Substances	NF-kappa B ; Particulate Matter ; Sesquiterpenes ; tussilagone (95N0GBB2SX)
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1463449-1
ISSN	1522-7278 ; 1520-4081
ISSN (online)	1522-7278
ISSN	1520-4081
DOI	10.1002/tox.23476
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Article: Forward looking statement, investor sentiment and stock liquidity.

Li, Chenggang / Yan, Ying / Liu, Xiwei / Wan, Shengnan / Xu, Yunbao / Lin, Hongwei

Heliyon

2023 Volume 9, Issue 4, Page(s) e15329

Abstract	Information is a critical element of capital markets, and liquidity is the lifeblood of capital markets. Relative to historical information, forward-looking information is of significant value to investors. Based on textual analysis calculations, we selected Chinese A-share listed companies as a research sample to explore the impact of forward-looking information disclosure level on stock liquidity. It is found that the higher the level of forward-looking information disclosure, the better the stock liquidity. Investor sentiment is the transmission mechanism through which the forward looking statement disclosure level affects stock liquidity. The heterogeneity analysis shows that the level of forward-Looking statement disclosure has a more significant effect on stock liquidity improvement for state-owned enterprises and enterprises in low-market regions than those in regions with high marketization levels. The article expands and enriches the research on forward-looking information disclosure, and also has some reference value for regulators to formulate laws and regulations and regulate forward-looking information disclosure.
Language	English
Publishing date	2023-04-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e15329
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Article ; Online: The energy conservation and emission reduction co-benefits of China's emission trading system.

Li, Chenggang / Chen, Ziling / Hu, Yongxiang / Cai, Chengcheng / Zuo, Xintong / Shang, Guofei / Lin, Hongwei

Scientific reports

2023 Volume 13, Issue 1, Page(s) 13758

Abstract: Emission Trading System (ETS) is an innovative practice under the progress of green development in China. It is also an important method for China to achieve market-oriented environmental governance in ecological civilization construction. The ETS pilot ... ...

Abstract	Emission Trading System (ETS) is an innovative practice under the progress of green development in China. It is also an important method for China to achieve market-oriented environmental governance in ecological civilization construction. The ETS pilot policy has implemented for more than 10 years. However, the co-benefits of ETS pilot policy by the integration of energy consumption, carbon and sulfur dioxide emissions, and wastewater has not been evaluated. In order to fill this gap, we use the 2003-2017 annual data of 30 China's provinces (municipalities and autonomous regions), and utilize the Difference-in-Differences (DID) model and Propensity Score Matching (PSM-DID) methodology to evaluate the co-benefits of ETS pilot policy on energy conservation and emission reduction. We find that the ETS pilot policy significantly promote energy conservation and emission reduction. Eastern and central China have significantly benefited from the policy, while the western China has not due to the limited technology and innovation as well as an imbalance of the industrial structure. The results provide the policy reference for China's government and institutions as well as the governments and institutions around the world to fulfill their commitments to save energy and reduce emissions, and early achieve the carbon peaking and carbon neutralization.
Language	English
Publishing date	2023-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-40811-4
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Book ; Online: Functional Network

Zhang, Ben / Dong, Zhetong / Zhang, Junsong / Lin, Hongwei

A Novel Framework for Interpretability of Deep Neural Networks

2022

Abstract: The layered structure of deep neural networks hinders the use of numerous analysis tools and thus the development of its interpretability. Inspired by the success of functional brain networks, we propose a novel framework for interpretability of deep ... ...

Abstract	The layered structure of deep neural networks hinders the use of numerous analysis tools and thus the development of its interpretability. Inspired by the success of functional brain networks, we propose a novel framework for interpretability of deep neural networks, that is, the functional network. We construct the functional network of fully connected networks and explore its small-worldness. In our experiments, the mechanisms of regularization methods, namely, batch normalization and dropout, are revealed using graph theoretical analysis and topological data analysis. Our empirical analysis shows the following: (1) Batch normalization enhances model performance by increasing the global e ciency and the number of loops but reduces adversarial robustness by lowering the fault tolerance. (2) Dropout improves generalization and robustness of models by improving the functional specialization and fault tolerance. (3) The models with dierent regularizations can be clustered correctly according to their functional topological dierences, re ecting the great potential of the functional network and topological data analysis in interpretability.
Keywords	Computer Science - Machine Learning
Subject code	006
Publishing date	2022-05-23
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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