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Article ; Online: Multi-stage adsorption of methyl orange on the nitrogen-rich biomass-derived carbon adsorbent: DFT and MD evaluation

Cheng, Xiaoxue / Jiang, Ding / Chen, Hao / Barati, Bahram / Yuan, Chuan / Li, Hongping / Wang, Shuang

Chemosphere. 2023 Oct., v. 338 p.139218-

2023

Abstract: Dyes that are released into the environment may have negative effects on living organisms. To address this issue, a biomass-derived carbon adsorbent made from Enteromorpha was tested for its ability to remove methyl orange (MO) from wastewater. The ... ...

Abstract	Dyes that are released into the environment may have negative effects on living organisms. To address this issue, a biomass-derived carbon adsorbent made from Enteromorpha was tested for its ability to remove methyl orange (MO) from wastewater. The adsorbent was found to be effective in removing MO, with a 1:4 impregnation ratio producing an adsorbent that could remove 96.34% of MO from a 200 mg/L solution using only 0.1 g of adsorbent. At higher concentrations, the adsorption capacity increased up to 269.58 mg/g. Through molecular dynamics simulations, it was discovered that after mono-layer adsorption reached saturation, the remaining MO molecules in solution formed hydrogen bonds with the adsorbed MO, which led to further aggregation on the adsorbent surface and increased adsorption capacity. Additionally, theoretical investigations revealed that the adsorption energy of anionic dyes increased with Nitrogen-doped carbon materials, with the pyrrolic-N site having the highest adsorption energy for MO. The carbon material derived from Enteromorpha showed promise in treating wastewater containing anionic dyes, thanks to its high adsorption capacity and strong electrostatic interaction with the sulfonic acid groups of MO.
Keywords	Ulva ; adsorbents ; adsorption ; carbon ; electrostatic interactions ; energy ; hydrogen ; methyl orange ; molecular dynamics ; sulfonic acids ; wastewater ; Pyrolytic carbon ; Multi-stage adsorption ; Sulfonic acid group ; Van der waals ; C–H … π interaction
Language	English
Dates of publication	2023-10
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2023.139218
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Article ; Online: Assessing the genetic relationship between gastroesophageal reflux disease and chronic respiratory diseases: a mendelian randomization study.

Cheng, Xiaoxue / Shi, Jiang / Zhang, Ding / Li, Caichen / Xu, Haoxiang / He, Jianxing / Liang, Wenhua

BMC pulmonary medicine

2023 Volume 23, Issue 1, Page(s) 243

Abstract: Background: Previous observational studies have found an association between gastroesophageal reflux disease (GERD) and chronic respiratory diseases, but it remains uncertain whether GERD causally influences these diseases. In this study, we aimed to ... ...

Abstract	Background: Previous observational studies have found an association between gastroesophageal reflux disease (GERD) and chronic respiratory diseases, but it remains uncertain whether GERD causally influences these diseases. In this study, we aimed to estimate the causal associations between GERD and 5 chronic respiratory diseases. Methods: 88 GERD-associated single nucleotide polymorphisms (SNPs) identified by the latest genome-wide association study were included as instrumental variables. Individual-level genetic summary data of participants were obtained from corresponding studies and the FinnGen consortium. We applied the inverse-variance weighted method to estimate the causality between genetically predicted GERD and 5 chronic respiratory diseases. Furthermore, the associations between GERD and common risk factors were investigated, and mediation analyses were conducted using multivariable MR. Various sensitivity analyses were also performed to verify the robustness of the findings. Results: Our study demonstrated that genetically predicted GERD was causally associated with an increased risk of asthma (OR 1.39, 95%CI 1.25-1.56, P < 0.001), idiopathic pulmonary fibrosis (IPF) (OR 1.43, 95%CI 1.05-1.95, P = 0.022), chronic obstructive disease (COPD) (OR 1.64, 95%CI 1.41-1.93, P < 0.001), chronic bronchitis (OR 1.77, 95%CI 1.15-2.74, P = 0.009), while no correlation was observed for bronchiectasis (OR 0.93, 95%CI 0.68-1.27, P = 0.645). Additionally, GERD was associated with 12 common risk factors for chronic respiratory diseases. Nevertheless, no significant mediators were discovered. Conclusions: Our study suggested that GERD was a causal factor in the development of asthma, IPF, COPD and chronic bronchitis, indicating that GERD-associated micro-aspiration of gastric contents process might play a role in the development of pulmonary fibrosis in these diseases.
MeSH term(s)	Humans ; Bronchitis, Chronic/complications ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Gastroesophageal Reflux/complications ; Gastroesophageal Reflux/genetics ; Asthma/epidemiology ; Asthma/genetics ; Asthma/complications ; Respiration Disorders/complications ; Idiopathic Pulmonary Fibrosis
Language	English
Publishing date	2023-07-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2059871-3
ISSN	1471-2466 ; 1471-2466
ISSN (online)	1471-2466
ISSN	1471-2466
DOI	10.1186/s12890-023-02502-8
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Article ; Online: Multi-stage adsorption of methyl orange on the nitrogen-rich biomass-derived carbon adsorbent: DFT and MD evaluation.

Cheng, Xiaoxue / Jiang, Ding / Chen, Hao / Barati, Bahram / Yuan, Chuan / Li, Hongping / Wang, Shuang

Chemosphere

2023 Volume 338, Page(s) 139218

Abstract	Dyes that are released into the environment may have negative effects on living organisms. To address this issue, a biomass-derived carbon adsorbent made from Enteromorpha was tested for its ability to remove methyl orange (MO) from wastewater. The adsorbent was found to be effective in removing MO, with a 1:4 impregnation ratio producing an adsorbent that could remove 96.34% of MO from a 200 mg/L solution using only 0.1 g of adsorbent. At higher concentrations, the adsorption capacity increased up to 269.58 mg/g. Through molecular dynamics simulations, it was discovered that after mono-layer adsorption reached saturation, the remaining MO molecules in solution formed hydrogen bonds with the adsorbed MO, which led to further aggregation on the adsorbent surface and increased adsorption capacity. Additionally, theoretical investigations revealed that the adsorption energy of anionic dyes increased with Nitrogen-doped carbon materials, with the pyrrolic-N site having the highest adsorption energy for MO. The carbon material derived from Enteromorpha showed promise in treating wastewater containing anionic dyes, thanks to its high adsorption capacity and strong electrostatic interaction with the sulfonic acid groups of MO.
MeSH term(s)	Wastewater ; Carbon ; Adsorption ; Water Pollutants, Chemical/analysis ; Nitrogen ; Biomass ; Coloring Agents/chemistry
Chemical Substances	Wastewater ; Carbon (7440-44-0) ; methyl orange (6B4TC34456) ; Water Pollutants, Chemical ; Nitrogen (N762921K75) ; Coloring Agents
Language	English
Publishing date	2023-07-04
Publishing country	England
Document type	Journal Article
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2023.139218
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Article: Activation of Nitrogen-Doped Carbon Materials on the C–N Bond and C–O Bond: Modeling Study Toward Enhanced Pyrolysis Products

Jiang, Ding / Li, Hongping / Cheng, Xiaoxue / Wang, Shuang / Abomohra, Abdelfatah / Cao, Bin

ACS sustainable chemistry & engineering. 2022 May 26, v. 10, no. 23

2022

Abstract: The present study investigated the effects of doped nitrogen atoms in carbon materials on the hydrodeoxygenation (HDO) and hydrodenitrogenation (HDN) processes. Density functional theory was used to evaluate the structural stability and catalytic ... ...

Abstract	The present study investigated the effects of doped nitrogen atoms in carbon materials on the hydrodeoxygenation (HDO) and hydrodenitrogenation (HDN) processes. Density functional theory was used to evaluate the structural stability and catalytic activity of different nitrogen-doped carbon cluster models for HDO and HDN reactions. The results showed that the carbon atom near the nitrogen in graphite is the active center of nitrogen-doped carbon catalytic activation of hydrogen. In the H₂-rich system, N@C catalysts can not only activate hydrogen molecules but also directly break the C–O/C–N bond. Results confirmed that the nitrogen assembly structure can affect the performance of C–O/C–N bond activation, and meta-doping nitrogen sites have the highest catalytic activity. This study provides theoretical guidance and views for the development of high-performance carbon catalysts that can replace conventional metal catalysts.
Keywords	catalytic activity ; density functional theory ; graphene ; green chemistry ; hydrogen ; nitrogen
Language	English
Dates of publication	2022-0526
Size	p. 7473-7484.
Publishing place	American Chemical Society
Document type	Article
ISSN	2168-0485
DOI	10.1021/acssuschemeng.1c08704
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Article: Adsorption properties of seaweed-based biochar with the greenhouse gases (CO2, CH4, N2O) through density functional theory (DFT)

Yang, Xuping / Jiang, Ding / Cheng, Xiaoxue / Yuan, Chuan / Wang, Shuang / He, Zhixia / Esakkimuthu, Sivakumar

Biomass and bioenergy. 2022 Aug., v. 163

2022

Abstract: Since the industrial revolution, greenhouse gas (GHG) emissions have increased dramatically, which has become a global concern. In this study, the interaction between biochar and GHG was calculated by building different models of seaweed-based biochar ... ...

Abstract	Since the industrial revolution, greenhouse gas (GHG) emissions have increased dramatically, which has become a global concern. In this study, the interaction between biochar and GHG was calculated by building different models of seaweed-based biochar through density functional theory (DFT). The adsorption mechanism of biochar was then analyzed by structural parameters, adsorption energy, charge transfer, and surface electronic properties. The results showed that the biochar with N and O heteroatom doping had better adsorption performance, and results also show that biochar is more sensitive to CO₂ and N₂O. In particular, the adsorption energies of CO₂ and N₂O on N-doped biochar were increased by 58.1% and 21.4%, respectively. Finally, quantitative conformational relationships (QSAR) with GHG adsorption energy were constructed using representative electronic properties of biochar model surfaces as descriptors. The results showed that the electrostatic potential on the surface of biochar, ELOMO and ΔEgₐₚ of α orbitals showed a good linear relationship with the adsorption energy, which can be used for the preliminary screening of GHG adsorbents. This contribution provides an insight into the mechanism of GHG adsorption at the molecular level and may help in the design of more efficient materials for environmental remediation.
Keywords	adsorbents ; adsorption ; biochar ; bioenergy ; biomass ; carbon dioxide ; density functional theory ; energy ; greenhouse gases ; greenhouses ; remediation
Language	English
Dates of publication	2022-08
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1090121-8
ISSN	0961-9534
ISSN	0961-9534
DOI	10.1016/j.biombioe.2022.106519
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Article ; Online: Single-Step and Highly Sensitive Imaging of Exosomal PD-L1 through Aptamer-Activated Cascade Primer Exchange Reaction-Generated Branched DNA Nanostructures.

Li, Xinyu / Li, Xinmin / Cheng, Xiaoxue / Bian, Xintong / Shen, Bo / Ding, Xiaojuan / Ding, Shijia

ACS sensors

2022 Volume 7, Issue 11, Page(s) 3571–3579

Abstract: Exosomal PD-L1 plays a critical role in tumor progress and immunotherapy. However, accurately analyzing exosomal PD-L1 is greatly limited by the small-sized and free-floating nature of exosomes and the few proteins each exosome carries. We described ... ...

Abstract	Exosomal PD-L1 plays a critical role in tumor progress and immunotherapy. However, accurately analyzing exosomal PD-L1 is greatly limited by the small-sized and free-floating nature of exosomes and the few proteins each exosome carries. We described herein a single-step and highly sensitive method, termed aptamer-triggered cascade primer exchange reaction (PER)-generated branched DNA nanostructures, for the quantification and imaging of exosomal PD-L1. The presence of exosomal PD-L1 converted the conformation of the recognition probe, accompanied by the exposure of primer 1. Then, primer 1 actuated the cascade PER, which generated branched DNA nanostructures containing numerous G-quadruplex for binding to thioflavin T (ThT) dye, leading to an amplified fluorescence signal. Profiting from directly growing branched DNA nanostructures on the surface of exosomes, the size of exosomes was enlarged and the movement of exosomes was limited, achieving the imaging of exosomal PD-L1 by conventional optical microscopy in a wash- and label-free fashion. Analyzing exosomal PD-L1 from serum samples of 15 cancer patients and 15 healthy volunteers demonstrated that this simple strategy could distinguish NSCLC patients from healthy donors with high clinical accuracy. Therefore, the developed assay has great potential as a transformative diagnostic toolkit for cancer detection and immunotherapy monitoring.
MeSH term(s)	Humans ; B7-H1 Antigen ; Carcinoma, Non-Small-Cell Lung ; Oligonucleotides ; Lung Neoplasms ; DNA ; Nanostructures
Chemical Substances	B7-H1 Antigen ; Oligonucleotides ; DNA (9007-49-2)
Language	English
Publishing date	2022-11-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2379-3694
ISSN (online)	2379-3694
DOI	10.1021/acssensors.2c01614
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Article ; Online: Mesoporous Nanozyme-Enhanced DNA Tetrahedron Electrochemiluminescent Biosensor with Three-Dimensional Walking Nanomotor-Mediated CRISPR/Cas12a for Ultrasensitive Detection of Exosomal microRNA.

Shen, Bo / Li, Li / Liu, Changjin / Li, Xinmin / Li, Xinyu / Cheng, Xiaoxue / Wu, Haiping / Yang, Tiantian / Cheng, Wei / Ding, Shijia

Analytical chemistry

2023 Volume 95, Issue 9, Page(s) 4486–4495

Abstract: Exosomal microRNAs (exomiRNAs) have emerged as ideal biomarkers for early clinical diagnostics. The accurate detection of exomiRNAs plays a crucial role in facilitating clinical applications. Herein, an ultrasensitive electrochemiluminescent (ECL) ... ...

Abstract	Exosomal microRNAs (exomiRNAs) have emerged as ideal biomarkers for early clinical diagnostics. The accurate detection of exomiRNAs plays a crucial role in facilitating clinical applications. Herein, an ultrasensitive electrochemiluminescent (ECL) biosensor was constructed using three-dimensional (3D) walking nanomotor-mediated CRISPR/Cas12a and tetrahedral DNA nanostructures (TDNs)-modified nanoemitters (TCPP-Fe@HMUiO@Au-ABEI) for exomiR-155 detection. Initially, the 3D walking nanomotor-mediated CRISPR/Cas12a strategy could effectively convert the target exomiR-155 into amplified biological signals for improving the sensitivity and specificity. Then, TCPP-Fe@HMUiO@Au nanozymes with excellent catalytic performance were used to amplify ECL signals because of the enhanced mass transfer and increased catalytic active sites, originating from its high surface areas (601.83 m
MeSH term(s)	Humans ; MicroRNAs/analysis ; CRISPR-Cas Systems ; DNA/chemistry ; Photometry ; Biosensing Techniques/methods
Chemical Substances	MicroRNAs ; DNA (9007-49-2)
Language	English
Publishing date	2023-02-20
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.2c05217
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Zs.A 4033: Show issues

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Article ; Online: A one-pot CRISPR-Cas12a-based toolbox enables determination of terminal deoxynucleotidyl transferase activity for acute leukemia screening.

Yi, Ming / Gong, Yao / Zhan, Qian / Dai, Yulian / Yang, Tiantian / Cheng, Xiaoxue / Ding, Shijia / Gu, Bing / Cheng, Wei / Zhang, Decai

Analytica chimica acta

2023 Volume 1254, Page(s) 341115

Abstract: An isothermal, one-pot toolbox (called OPT-Cas) based on CRISPR-Cas12a collateral cleavage capability is proposed for highly sensitive and selective determination of terminal deoxynucleotidyl transferase (TdT) activity. Oligonucleotide primers with 3'- ... ...

Abstract	An isothermal, one-pot toolbox (called OPT-Cas) based on CRISPR-Cas12a collateral cleavage capability is proposed for highly sensitive and selective determination of terminal deoxynucleotidyl transferase (TdT) activity. Oligonucleotide primers with 3'-hydroxyl (OH) terminal were randomly introduced for TdT-induced elongation. In the presence of TdT, dTTP nucleotides polymerized at the 3' terminals of the primers to generate abundant polyT-tails, which function as triggers for the synchronous activation of Cas12a proteins. Finally, the activated Cas12a trans-cleaved FAM and BHQ1 dual-labeled single-stranded DNA (ssDNA-FQ) reporters, producing significantly amplified fluorescence signals. This one-pot assay, that is primer, crRNA, Cas12a protein and ssDNA-FQ reporter are all in one tube, allows simple but high-sensitive quantification of TdT activity with a low detection limit of 6.16 × 10
MeSH term(s)	Humans ; CRISPR-Cas Systems ; DNA Nucleotidylexotransferase ; Biological Assay ; Biomedical Research ; DNA, Single-Stranded/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Biosensing Techniques
Chemical Substances	DNA Nucleotidylexotransferase (EC 2.7.7.31) ; DNA, Single-Stranded
Language	English
Publishing date	2023-03-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2023.341115
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Article ; Online: Multi-target Tracking Algorithm Based on Motion Information Optimized Correl-ation Filtering

MIAO Jiani, YANG Jinlong, CHENG Xiaoxue, GE Hongwei

Jisuanji kexue yu tansuo, Vol 15, Iss 7, Pp 1310-

2021 Volume 1321

Abstract: In multi-target tracking tasks combined with detector detection information, missing detections often lead to some targets missed, target identity tag conversion, etc., thereby reducing tracking accuracy. To solve this problem, a multi-target tracking ... ...

Abstract	In multi-target tracking tasks combined with detector detection information, missing detections often lead to some targets missed, target identity tag conversion, etc., thereby reducing tracking accuracy. To solve this problem, a multi-target tracking algorithm based on motion information optimization and correlation filter is proposed. After obtaining target detection information, kernelized correlation filter (KCF) is used to track target, and the target's motion information and image information are integrated to handle the problem of missing tracking due to inaccu-rate detection, reducing the fragmented trajectory. At the same time, the smoothing constraint of confidence map is introduced on the basis of KCF to evaluate occlusion degree of targets, which achieves the adaptive update of target template in KCF and deals with the problem of template pollution caused by occlusion. Finally, the experimental results on the MOT Challenge MOT17 data set show that compared with the traditional detection and tracking algor-ithm, high-speed tracking-by-detection without using image information (IOU17), multiple object tracking accuracy (MOTA) of proposed algorithm is improved by 2.43%, and it has better stability and accuracy.
Keywords	correlation filter ; detection and tracking ; smoothing filtering ; template update ; Electronic computers. Computer science ; QA75.5-76.95
Subject code	006
Language	Chinese
Publishing date	2021-07-01T00:00:00Z
Publisher	Journal of Computer Engineering and Applications Beijing Co., Ltd., Science Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: The Dawn After the Dark

Li, Junyi / Chen, Jie / Ren, Ruiyang / Cheng, Xiaoxue / Zhao, Wayne Xin / Nie, Jian-Yun / Wen, Ji-Rong

An Empirical Study on Factuality Hallucination in Large Language Models

2024

Abstract: In the era of large language models (LLMs), hallucination (i.e., the tendency to generate factually incorrect content) poses great challenge to trustworthy and reliable deployment of LLMs in real-world applications. To tackle the LLM hallucination, three ...

Abstract	In the era of large language models (LLMs), hallucination (i.e., the tendency to generate factually incorrect content) poses great challenge to trustworthy and reliable deployment of LLMs in real-world applications. To tackle the LLM hallucination, three key questions should be well studied: how to detect hallucinations (detection), why do LLMs hallucinate (source), and what can be done to mitigate them (mitigation). To address these challenges, this work presents a systematic empirical study on LLM hallucination, focused on the the three aspects of hallucination detection, source and mitigation. Specially, we construct a new hallucination benchmark HaluEval 2.0, and designs a simple yet effective detection method for LLM hallucination. Furthermore, we zoom into the different training or utilization stages of LLMs and extensively analyze the potential factors that lead to the LLM hallucination. Finally, we implement and examine a series of widely used techniques to mitigate the hallucinations in LLMs. Our work has led to several important findings to understand the hallucination origin and mitigate the hallucinations in LLMs. Our code and data can be accessed at https://github.com/RUCAIBox/HaluEval-2.0. Comment: 24 pages, 8 figures, 13 tables
Keywords	Computer Science - Computation and Language
Publishing date	2024-01-06
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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