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Article: Machine learning reveals diverse cell death patterns in lung adenocarcinoma prognosis and therapy.

Wang, Shun / Wang, Ruohuang / Hu, Dingtao / Zhang, Caoxu / Cao, Peng / Huang, Jie

NPJ precision oncology

2024 Volume 8, Issue 1, Page(s) 49

Abstract: Cancer cell growth, metastasis, and drug resistance pose significant challenges in the management of lung adenocarcinoma (LUAD). However, there is a deficiency in optimal predictive models capable of accurately forecasting patient prognoses and guiding ... ...

Abstract	Cancer cell growth, metastasis, and drug resistance pose significant challenges in the management of lung adenocarcinoma (LUAD). However, there is a deficiency in optimal predictive models capable of accurately forecasting patient prognoses and guiding the selection of targeted treatments. Programmed cell death (PCD) pathways play a pivotal role in the development and progression of various cancers, offering potential as prognostic indicators and drug sensitivity markers for LUAD patients. The development and validation of predictive models were conducted by integrating 13 PCD patterns with comprehensive analysis of bulk RNA, single-cell RNA transcriptomics, and pertinent clinicopathological details derived from TCGA-LUAD and six GEO datasets. Utilizing the machine learning algorithms, we identified ten critical differentially expressed genes associated with PCD in LUAD, namely CHEK2, KRT18, RRM2, GAPDH, MMP1, CHRNA5, TMPRSS4, ITGB4, CD79A, and CTLA4. Subsequently, we conducted a programmed cell death index (PCDI) based on these genes across the aforementioned cohorts and integrated this index with relevant clinical features to develop several prognostic nomograms. Furthermore, we observed a significant correlation between the PCDI and immune features in LUAD, including immune cell infiltration and the expression of immune checkpoint molecules. Additionally, we found that patients with a high PCDI score may exhibit resistance to immunotherapy and standard adjuvant chemotherapy regimens; however, they may benefit from other FDA-supported drugs such as docetaxel and dasatinib. In conclusion, the PCDI holds potential as a prognostic signature and can facilitate personalized treatment for LUAD patients.
Language	English
Publishing date	2024-02-26
Publishing country	England
Document type	Journal Article
ISSN	2397-768X
ISSN	2397-768X
DOI	10.1038/s41698-024-00538-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Tartary Buckwheat Starch Modified with Octenyl Succinic Anhydride for Stabilization of Pickering Nanoemulsions.

Lin, Jie / Fan, Shasha / Ruan, Yuyue / Wu, Dingtao / Yang, Ting / Hu, Yichen / Li, Wei / Zou, Liang

Foods (Basel, Switzerland)

2023 Volume 12, Issue 6

Abstract: In this study, Tartary buckwheat starch was modified to different degrees of substitution (DS) with octenyl succinate anhydride (OS-TBS) in order to explore its potential for stabilizing Pickering nanoemulsions. OS-TBS was prepared by reacting Tartary ... ...

Abstract	In this study, Tartary buckwheat starch was modified to different degrees of substitution (DS) with octenyl succinate anhydride (OS-TBS) in order to explore its potential for stabilizing Pickering nanoemulsions. OS-TBS was prepared by reacting Tartary buckwheat starch with 3, 5 or 7% (
Language	English
Publishing date	2023-03-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods12061126
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Article ; Online: Genetic landscape and clinical significance of cuproptosis-related genes in liver hepatocellular carcinoma.

Hu, Dingtao / Wang, Yichuan / Shen, Xu / Mao, Tiantian / Liang, Xijun / Wang, Tengjiao / Shen, Weifeng / Zhuang, Yugang / Ding, Jin

Genes & diseases

2023 Volume 11, Issue 2, Page(s) 516–519

Language	English
Publishing date	2023-04-10
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.2023.03.010
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Article ; Online: Gefitinib metabolism-related lncRNAs for the prediction of prognosis, tumor microenvironment and drug sensitivity in lung adenocarcinoma.

Guo, Zishun / Zhang, Xin / Yang, Dingtao / Hu, Zhuozheng / Wu, Jiajun / Zhou, Weijun / Wu, Shuoming / Zhang, Wenxiong

Scientific reports

2024 Volume 14, Issue 1, Page(s) 10348

Abstract: The complete compound of gefitinib is effective in the treatment of lung adenocarcinoma. However, the effect on lung adenocarcinoma (LUAD) during its catabolism has not yet been elucidated. We carried out this study to examine the predictive value of ... ...

Abstract	The complete compound of gefitinib is effective in the treatment of lung adenocarcinoma. However, the effect on lung adenocarcinoma (LUAD) during its catabolism has not yet been elucidated. We carried out this study to examine the predictive value of gefitinib metabolism-related long noncoding RNAs (GMLncs) in LUAD patients. To filter GMLncs and create a prognostic model, we employed Pearson correlation, Lasso, univariate Cox, and multivariate Cox analysis. We combined risk scores and clinical features to create nomograms for better application in clinical settings. According to the constructed prognostic model, we performed GO/KEGG and GSEA enrichment analysis, tumor immune microenvironment analysis, immune evasion and immunotherapy analysis, somatic cell mutation analysis, drug sensitivity analysis, IMvigor210 immunotherapy validation, stem cell index analysis and real-time quantitative PCR (RT-qPCR) analysis. We built a predictive model with 9 GMLncs, which showed good predictive performance in validation and training sets. The calibration curve demonstrated excellent agreement between the expected and observed survival rates, for which the predictive performance was better than that of the nomogram without a risk score. The metabolism of gefitinib is related to the cytochrome P450 pathway and lipid metabolism pathway, and may be one of the causes of gefitinib resistance, according to analyses from the Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Immunological evasion and immunotherapy analysis revealed that the likelihood of immune evasion increased with risk score. Tumor microenvironment analysis found most immune cells at higher concentrations in the low-risk group. Drug sensitivity analysis found 23 sensitive drugs. Twenty-one of these drugs exhibited heightened sensitivity in the high-risk group. RT-qPCR analysis validated the characteristics of 9 GMlncs. The predictive model and nomogram that we constructed have good application value in evaluating the prognosis of patients and guiding clinical treatment.
MeSH term(s)	Humans ; Tumor Microenvironment/genetics ; Tumor Microenvironment/immunology ; Gefitinib/therapeutic use ; Gefitinib/pharmacology ; RNA, Long Noncoding/genetics ; Adenocarcinoma of Lung/genetics ; Adenocarcinoma of Lung/drug therapy ; Adenocarcinoma of Lung/pathology ; Adenocarcinoma of Lung/metabolism ; Prognosis ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Drug Resistance, Neoplasm/genetics ; Nomograms ; Female ; Male ; Gene Expression Regulation, Neoplastic ; Antineoplastic Agents/therapeutic use ; Antineoplastic Agents/pharmacology ; Middle Aged ; Aged
Chemical Substances	Gefitinib (S65743JHBS) ; RNA, Long Noncoding ; Antineoplastic Agents
Language	English
Publishing date	2024-05-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-61175-3
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Article ; Online: Polyphenol-enriched Penthorum chinense Pursh ameliorates alcohol-related liver injury through Ras/Raf/MEK/ERK pathway: Integrating network pharmacology and experiment validation.

Li, Rui / Wu, Dingtao / Hu, Jianping / Ma, Yuqi / Ba, Yabo / Zou, Liang / Hu, Yichen

Journal of ethnopharmacology

2023 Volume 321, Page(s) 117513

Abstract: Ethnopharmacological relevance: Penthorum chinense Pursh (PCP) has acknowledged as an edible herbal medicinal plant for the prevention and treatment of alcoholic liver injury (ALI). However, only few of researches focus on the chemical material basis ... ...

Abstract	Ethnopharmacological relevance: Penthorum chinense Pursh (PCP) has acknowledged as an edible herbal medicinal plant for the prevention and treatment of alcoholic liver injury (ALI). However, only few of researches focus on the chemical material basis and potential mechanisms of PCP against ALI. Aim of the study: Herein, we explored the therapeutic effects of PCP extract against ALI based on the integration of network pharmacology, molecular docking, and experiment validation. Methods: Based on the standard quality control of PCP herbs by UPLC fingerprint and quantitative determination, 80% ethanol extract fraction of PCP containing more polyphenols, compared to aqueous extract fraction of PCP, were chosen for further experiments. After oral administration of PCP ethanol extract, serum pharmacochemistry based on UPLC-Q-Exactive-MS analysis was implemented to evaluate the potential effective compounds. These absorbed prototypes in PCP were used to construct network pharmacology and predict the potential mechanisms of PCP extract against ALI. Then, the predicted targets and biological mechanisms of PCP extract were validated using animal experiments and molecular docking analysis. Results: Although totally 19 polyphenol compounds were identified in PCP ethanol extract by UPLC-MS analysis, only 18 absorbed prototypes were found in the serum collected from mice at 1 h post-administration with PCP extract. These candidate active compounds were further screened into 13 compounds to construct network pharmacology and 433 targets were identified as PCP targets. GO and KEGG pathway enrichment analyses indicated that the effects of PCP extract would involve in Ras signaling pathway. The animal experiments on chronic ALI model mice shown that the oral administration of PCP can alleviate ALI by attenuating hepatic oxidative stress, inflammation and down-regulating the target proteins in Ras/Raf/MEK/ERK pathway. Molecular docking analysis revealed the good binding ability between the three polyphenols (i.e. quercetin, apigenin, thonningianin B) in PCP with the top contribution in network pharmacology, and these target proteins (Ras, Raf, MEK1/2, and ERK1/2). Conclusion: Our results clarified that PCP ethanol extract could effectively alleviate ALI by down-regulating Ras/Raf/MEK/ERK signaling pathway promisingly. Quercetin, apigenin, and thonningianin B may be the active compounds of PCP, attributing to the intervention benefits of PCP against ALI.
MeSH term(s)	Mice ; Animals ; Polyphenols/pharmacology ; Polyphenols/therapeutic use ; Polyphenols/metabolism ; MAP Kinase Signaling System ; Quercetin/pharmacology ; Chromatography, Liquid ; Apigenin/pharmacology ; Molecular Docking Simulation ; Network Pharmacology ; Tandem Mass Spectrometry ; Ethanol/pharmacology ; Saxifragales/chemistry ; Liver ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Drugs, Chinese Herbal/pharmacology
Chemical Substances	Polyphenols ; thonningianin B ; Quercetin (9IKM0I5T1E) ; Apigenin (7V515PI7F6) ; Ethanol (3K9958V90M) ; Mitogen-Activated Protein Kinase Kinases (EC 2.7.12.2) ; Drugs, Chinese Herbal
Language	English
Publishing date	2023-11-29
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	134511-4
ISSN	1872-7573 ; 0378-8741
ISSN (online)	1872-7573
ISSN	0378-8741
DOI	10.1016/j.jep.2023.117513
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Article ; Online: Optimal Rain Gauge Network Design Aided by Multi-Source Satellite Precipitation Observation

Helong Wang / Wenlong Chen / Zukang Hu / Yueping Xu / Dingtao Shen

Remote Sensing, Vol 14, Iss 6142, p

2022 Volume 6142

Abstract: Optimized rain gauge networks minimize their input and maintenance costs. Satellite precipitation observations are particularly susceptible to the effects of terrain elevation, vegetation, and other topographical factors, resulting in large deviations ... ...

Abstract	Optimized rain gauge networks minimize their input and maintenance costs. Satellite precipitation observations are particularly susceptible to the effects of terrain elevation, vegetation, and other topographical factors, resulting in large deviations between satellite and ground-based precipitation data. Satellite precipitation observations are more inaccurate where the deviations change more drastically, indicating that rain gauge stations should be utilized at these locations. This study utilized satellite precipitation observation data to facilitate rain gauge network optimization. The deviations between ground-based precipitation data and three types of satellite precipitation observation data were used for entropy estimation. The rain gauge network in the Oujiang River Basin of China was optimally designed according to the principle of maximum joint entropy. Two optimization schemes of culling and supplementing 40 existing sites and 35 virtual sites were explored. First, the optimization and ranking of the rain gauge station network showed good stability and consistency. In addition, the joint entropy of deviation was larger than that of ground-based precipitation data alone, leading to a higher degree of discrimination between rain gauge stations and enabling the use of deviation data instead of ground-based precipitation data to assist network optimization, with more reasonable and interpretable results.
Keywords	rain gauge network ; optimization ; satellite precipitation observations ; information entropy ; Science ; Q
Subject code	550
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Predictive value of peripheral blood leukocytes-based methylation of Long non-coding RNA MALAT1 and H19 in the chemotherapy effect and prognosis of gastric cancer.

Wang, Fang / Hu, Dingtao / Lou, Xiaoqi / Wang, Linlin / Wang, Yuhua / Zhang, Tingyu / Yan, Ziye / Meng, Nana / Lei, Yu / Zou, Yanfeng

Translational oncology

2024 Volume 44, Page(s) 101929

Abstract: Background: The predictive value of the methylation of Long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and H19 promoters in peripheral blood leukocytes as a non-invasive biomarker for the chemotherapy effect ... ...

Abstract	Background: The predictive value of the methylation of Long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and H19 promoters in peripheral blood leukocytes as a non-invasive biomarker for the chemotherapy effect and prognosis gastric cancer (GC) is unclear. Methods: The DNA methylation of H19 and MALAT1 between chemotherapy-sensitive and non-sensitive groups and between groups with better and worse survival of GC was compared using regression analyses. Several predictive nomograms were constructed. The genetic alteration of MALAT1 and H19 and the association between gene expression and immune status in GC were also investigated using bioinformatics analysis. Results: Higher genetic methylations in peripheral blood were noticed in GC groups with poorer survival. The constructed nomograms presented strong predictive values for the chemotherapy effect and 3-year survival of disease-free survival, progression-free survival, and overall survival, with the area under the curve as 0.838, 0.838, 0.912, and 0.925, respectively. Significant correlations between MALAT1 or H19 expression and marker genes of immune checkpoints and immune pathways were noticed. The high infiltration of macrophages in H19-high and low infiltration of CD8+ T cells in MALAT1-high groups were associated with worse survival of GC. Conclusions: MALAT1 and H19 have the potential to predict the chemotherapy response and clinical outcomes of GC.
Language	English
Publishing date	2024-03-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2443840-6
ISSN	1936-5233
ISSN	1936-5233
DOI	10.1016/j.tranon.2024.101929
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Article: Integrated data-driven framework for anomaly detection and early warning in water distribution system

Hu, Zukang / Chen, Wenlong / Wang, Helong / Tian, Pei / Shen, Dingtao

Journal of cleaner production. 2022 Nov. 01, v. 373

2022

Abstract: Data-driven anomaly detection and early warning have been extensively used in water distribution systems (WDS). Events such as pipe bursts and sensor failure cause abnormal monitoring data. Anomaly detection during real-time data monitoring and ... ...

Abstract	Data-driven anomaly detection and early warning have been extensively used in water distribution systems (WDS). Events such as pipe bursts and sensor failure cause abnormal monitoring data. Anomaly detection during real-time data monitoring and identification of various events are crucial in WDS. This study proposes a framework for anomaly detection and early warning in WDS. This framework comprises four anomaly detection modules—single-point anomaly identification, sensor sequence, inter-sensor sequence, qualitative module. A case study is conducted using the Net3 pipe network model. The results indicate that the proposed method can accurately identify pipe bursts and detect situations causing abnormal sensor data.
Keywords	case studies ; models ; water distribution
Language	English
Dates of publication	2022-1101
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0959-6526
DOI	10.1016/j.jclepro.2022.133977
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Investigation of dynamic lake changes in Zhuonai Lake–Salt Lake Basin, Hoh Xil, using remote sensing images in response to climate change (1989–2018)

Zukang Hu / Debao Tan / Xiongfei Wen / Beiqing Chen / Dingtao Shen

Journal of Water and Climate Change, Vol 12, Iss 6, Pp 2199-

2021 Volume 2216

Abstract: The area covered by the four lakes in the Zhuonai Lake–Salt Lake Basin in Hoh Xil (Zhuonai Lake, Kusai Lake, Heidinor Lake, and Salt Lake) has changed significantly over the past 30 years. In this study, remote sensing image data gathered via the Landsat ...

Abstract	The area covered by the four lakes in the Zhuonai Lake–Salt Lake Basin in Hoh Xil (Zhuonai Lake, Kusai Lake, Heidinor Lake, and Salt Lake) has changed significantly over the past 30 years. In this study, remote sensing image data gathered via the Landsat thematic mapper, enhanced thematic mapper plus, and operational land imager from 1989 to 2018 were used to extract the areal parameters of four lakes. The total area of the four lakes had increased by 18% in the past 30 years due to climate change. Interpolated results based on the meteorological data from 28 meteorological stations in the basin were used for trend analysis. A single-layer lake evaporation model was utilized to study the changes in the annual lake evaporation in the basin. The annual lake evaporation slightly increased from 1989 to 1995, followed by a sharp decrease from 1995 to 2018. From 1989 to 2018, the annual evaporation in the basin ranged between 615.37 and 921.66 mm, with a mean of 769.73 mm. A mass balance model was developed to estimate the changes in the lake volumes due to precipitation and evaporation. The increase in precipitation and the decrease in the annual lake evaporation promote the expansion of the four lakes. Lake evaporation is the main factor inducing changes in the lake areas. HIGHLIGHTS A study of the evolution of ecological environment in the Tibetan Plateau was proposed.; Meteorological data from 28 meteorological stations were subjected to trend analysis.; A lake evaporation model was used to study the changes in annual lake evaporation.; Precipitation and evaporation were the main factors resulting in lake area changes.;
Keywords	climate change ; hoh xil ; lake area ; remote sensing ; Environmental technology. Sanitary engineering ; TD1-1066 ; Environmental sciences ; GE1-350
Subject code	550 ; 333
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	IWA Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Comparison of Soluble Dietary Fibers Extracted from Ten Traditional Legumes: Physicochemical Properties and Biological Functions.

Wu, Dingtao / Wan, Jiajia / Li, Wenxing / Li, Jie / Guo, Wang / Zheng, Xiaoqin / Gan, Ren-You / Hu, Yichen / Zou, Liang

Foods (Basel, Switzerland)

2023 Volume 12, Issue 12

Abstract: Soluble dietary fibers (SDFs) exist as the major bioactive components in legumes, which exhibit various biological functions. To improve the potential applications of legume SDFs as healthy value-added products in the functional food industry, the ... ...

Abstract	Soluble dietary fibers (SDFs) exist as the major bioactive components in legumes, which exhibit various biological functions. To improve the potential applications of legume SDFs as healthy value-added products in the functional food industry, the physicochemical properties and biological functions of SDFs from ten selected traditional legumes, including mung bean, adzuki bean, red bean, red sword bean, black bean, red kidney bean, speckled kidney bean, common bean, white hyacinth bean, and pea, were studied and compared. Results showed that the physicochemical properties of SDFs varied in different species of legumes. All legume SDFs almost consisted of complex polysaccharides, which were rich in pectic-polysaccharides, e.g., homogalacturonan (HG) and rhamnogalacturonan I (RG I) domains. In addition, hemicelluloses, such as arabinoxylan, xyloglucan, and galactomannan, existed in almost all legume SDFs, and a large number of galactomannans existed in SDFs from black beans. Furthermore, all legume SDFs exhibited potential antioxidant, antiglycation, immunostimulatory, and prebiotic effects, and their biological functions differed relative to their chemical structures. The findings can help reveal the physicochemical and biological properties of different legume SDFs, which can also provide some insights into the further development of legume SDFs as functional food ingredients.
Language	English
Publishing date	2023-06-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods12122352
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