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Article ; Online: Plug-in Models: A Promising Direction for Molecular Generation.

Liu, Ningfeng / Jin, Hongwei / Zhang, Liangren / Liu, Zhenming

Health data science

2023 Volume 3, Page(s) 92

Language	English
Publishing date	2023-10-09
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2765-8783
ISSN (online)	2765-8783
DOI	10.34133/hds.0092
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: New perspectives on the genetic structure of dotted gizzard shad (

Peng, Ying / Liu, Yifan / Li, Jiasheng / Zhang, Kun / Jin, Xun / Zheng, Sixu / Wang, Yunpeng / Lü, Zhenming / Liu, Liqin / Gong, Li / Liu, Bingjian

Marine life science & technology

2024 Volume 6, Issue 1, Page(s) 50–67

Abstract: To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary. : Supplementary information: The online version contains supplementary material available at 10.1007/ ... ...

Abstract	To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary. Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00216-2.
Language	English
Publishing date	2024-02-12
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	3006215-9
ISSN	2662-1746 ; 2096-6490
ISSN (online)	2662-1746
ISSN	2096-6490
DOI	10.1007/s42995-024-00216-2
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Article: High-efficiency depolymerization/degradation of polyethylene terephthalate plastic by a whole-cell biocatalyst.

Fang, Yaxuan / Chao, Kexin / He, Jin / Wang, Zhiguo / Chen, Zhenming

3 Biotech

2023 Volume 13, Issue 5, Page(s) 138

Abstract: Polyethylene terephthalate (PET) is the most abundantly produced plastic due to its excellent performance, but is also the primary source of poorly degradable plastic pollution. The development of environment-friendly PET biodegradation is attracting ... ...

Abstract	Polyethylene terephthalate (PET) is the most abundantly produced plastic due to its excellent performance, but is also the primary source of poorly degradable plastic pollution. The development of environment-friendly PET biodegradation is attracting increasing interest. The leaf-branch compost cutinase mutant ICCG (F243I/D238C/S283C/Y127G) exhibits the best hydrolytic activity and thermostability of all known PET hydrolases. However, its superior PET degradation is highly dependent on its preparation as a purified enzyme, which critically reduces its industrial utility. Herein, we report the use of rational design and combinatorial mutagenesis to develop a novel ICCG mutant RITK (D53R/R143I/D193T/E208K) that demonstrated excellent whole-cell biocatalytic activity. Whole cells expressing RITK showed an 8.33-fold increase in biocatalytic activity compared to those expressing ICCG. Thermostability was also improved. After reacting at 85 °C for 3 h, purified RITK exhibited a 12.75-fold increase in depolymerization compared to ICCG. These results will greatly enhance the industrial utility of PET hydrolytic enzymes and further the progress of PET recycling. Supplementary information: The online version contains supplementary material available at 10.1007/s13205-023-03557-4.
Language	English
Publishing date	2023-04-25
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-023-03557-4
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Article ; Online: Activation of peroxymonosulfate by catalysts derived from water treatment plant sludge for the simultaneous removal of Disperse Blue 56 and phosphates

Tang, Xing / Jin, Hongyi / Zou, Jing / Liu, Shupo / Li, Fei / Zhou, Zhenming

Environ Sci Pollut Res. 2023 Mar., v. 30, no. 13 p.35683-35697

2023

Abstract: In this study, calcined water treatment plant sludge (C-WTPS) was used as a catalyst for peroxymonosulfate (PMS) activation to simultaneously remove Disperse Blue 56 (DB56) and phosphates. Firstly, the performance of the C-WTPS/PMS system was examined ... ...

Abstract	In this study, calcined water treatment plant sludge (C-WTPS) was used as a catalyst for peroxymonosulfate (PMS) activation to simultaneously remove Disperse Blue 56 (DB56) and phosphates. Firstly, the performance of the C-WTPS/PMS system was examined for the degradation of DB56. The results showed that 96.7% of DB56 (400 mg L⁻¹) was removed within 60 min in the presence of 4.8 g L⁻¹ PMS and 0.8 g L⁻¹ C-WTPS at pH 3 and 50 °C. Hydroxyl radicals (·OH), sulfate radicals (SO₄·⁻), and singlet oxygen (¹O₂) were generated during the oxidation process, and ¹O₂ was the main active species. The relatively high surface area, proper Fe content, and abundant ketone groups on the catalyst surface were responsible for PMS activation. Furthermore, the possible degradation pathways of DB56 were proposed based on the gas chromatography–mass spectrometry (GC–MS) results. Secondly, the simultaneous removal of DB56 and phosphates by the C-WTPS/PMS system was investigated. Due to the different removal mechanisms, the effects of the initial phosphate concentration and water matrix species on the removal of DB56 and phosphates showed different trends. Reusability tests results showed that C-WTPS had relatively high stability. In addition, the C-WTPS/PMS system exhibited a high decolorization ratio and phosphate removal efficiency in real wastewater tests. This article offers a value-added approach for reusing WTPS as a catalyst for treating organic contaminants and phosphates.
Keywords	catalysts ; decolorization ; gas chromatography-mass spectrometry ; oxidation ; pH ; phosphates ; singlet oxygen ; sludge ; sulfates ; surface area ; value added ; wastewater ; water treatment
Language	English
Dates of publication	2023-03
Size	p. 35683-35697.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-24792-x
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Advanced nonlinearity equalizer with TC-NL-MLSE for transmitting beyond 200-Gb/s PAM-8 in IM/DD systems.

Zhou, Jiahao / Zhang, Jing / Zhao, Xue / Jin, Taowei / Hu, Shaohua / Lin, Hong / Zhenming, Yu / Zhang, Qianwu / Xu, Bo / Qiu, Kun

Optics express

2022 Volume 30, Issue 21, Page(s) 37416–37425

Abstract: The severe band-limited effect resulted from the low-cost optical transceiver increases the channel memory length and the number of taps of the equalizers. Besides, the interaction of fiber dispersion and square-law detection introduce nonlinear ... ...

Abstract	The severe band-limited effect resulted from the low-cost optical transceiver increases the channel memory length and the number of taps of the equalizers. Besides, the interaction of fiber dispersion and square-law detection introduce nonlinear distortions in intensity modulation and direct-detection (IM/DD) transmission systems. The serious band-limited effect and nonlinear distortions degrade the transmission performance and bring challenges to current equalizers for low-complexity implementation. In this paper, we propose a trellis-compression nonlinear maximum likelihood sequence estimation (TC-NL-MLSE) algorithm to compensate the linear and nonlinear distortions with lower complexity. In the TC-NL-MLSE, we introduce a polynomial nonlinear filter (PNLF) to partly compensate both the linear distortions and nonlinear distortions. Then, we establish a look-up-table (LUT) to calculate the nonlinear branch metric (BM). To simplify the calculation, two or three levels with the highest probabilities are selected according to decision thresholds for each symbol to compress the state-trellis graph (STG). This significantly reduces computational complexity on BM calculations especially for high-order modulations. We conduct experiments to transmit beyond the 200-Gb/s PAM-8 signal over 2-km standard single mode fiber (SSMF) at C-band. The TC-NL-MLSE outperforms the reduced-state MLSE with PNLF, and can reach the 7%-overhead hard-decision forward error correction threshold. Moreover, the TC-NL-MLSE reduces the complexity by 97% compared with standard LUT-MLSE, limiting the multipliers around 100 at the expense of only 0.2-dB receiver sensitivity penalty.
Language	English
Publishing date	2022-10-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.468519
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Article ; Online: Activation of peroxymonosulfate by catalysts derived from water treatment plant sludge for the simultaneous removal of Disperse Blue 56 and phosphates.

Tang, Xing / Jin, Hongyi / Zou, Jing / Liu, Shupo / Li, Fei / Zhou, Zhenming

Environmental science and pollution research international

2022 Volume 30, Issue 13, Page(s) 35683–35697

Abstract	In this study, calcined water treatment plant sludge (C-WTPS) was used as a catalyst for peroxymonosulfate (PMS) activation to simultaneously remove Disperse Blue 56 (DB56) and phosphates. Firstly, the performance of the C-WTPS/PMS system was examined for the degradation of DB56. The results showed that 96.7% of DB56 (400 mg L
MeSH term(s)	Sewage ; Phosphates ; Peroxides/chemistry ; Water Purification/methods
Chemical Substances	peroxymonosulfate (22047-43-4) ; Sewage ; 2-chloro-1,5-diamino-4,8-dihydroxyanthraquinone (K26YA0E1FU) ; Phosphates ; Peroxides
Language	English
Publishing date	2022-12-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-24792-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Phthalate metabolites in paired human serum and whole blood.

Li, Zhenming / Wu, Dexin / Guo, Yu / Mao, Weili / Zhao, Nan / Zhao, Meirong / Jin, Hangbiao

The Science of the total environment

2022 Volume 824, Page(s) 153792

Abstract: Presence of phthalate metabolites (PMs) in human serum has been well documented. However, the distribution pattern of PMs in different human blood matrixes remains not well known. To investigate this, paired serum and whole blood samples were collected ... ...

Abstract	Presence of phthalate metabolites (PMs) in human serum has been well documented. However, the distribution pattern of PMs in different human blood matrixes remains not well known. To investigate this, paired serum and whole blood samples were collected from 145 adults (76 males and 69 females) in Quzhou, China, and analyzed for nine PMs in this study. All PMs had high detection frequencies (> 70%) in human serum and whole blood, except mono benzyl phthalate. Total concentrations of detected PMs in serum and whole blood were 0.70-61 ng/mL (mean 12 ng/mL) and 1.6-33 ng/mL (7.5 ng/mL), respectively. Mono methyl phthalate (MMP), mono (2-ethylhexyl) phthalate, and mono butyl phthalate were consistently the predominant PMs in human serum and whole blood, with the mean concentrations of 3.4 and 2.0 ng/mL, 3.3 and 2.1 ng/mL, and 2.8 and 1.8 ng/mL, respectively. Females had higher mean serum concentrations of PMs, except MBP, than males. Youngest age group (20-30 years) consistently had the lowest mean whole blood levels of all PMs. For the first time, the distribution pattern of PMs in human blood was evaluated based on the calculated partitioning coefficient (K
MeSH term(s)	Adult ; Dibutyl Phthalate ; Environmental Exposure ; Environmental Pollutants/metabolism ; Female ; Humans ; Male ; Matrix Metalloproteinases ; Phthalic Acids/metabolism ; Young Adult
Chemical Substances	Environmental Pollutants ; Phthalic Acids ; Dibutyl Phthalate (2286E5R2KE) ; phthalic acid (6O7F7IX66E) ; Matrix Metalloproteinases (EC 3.4.24.-)
Language	English
Publishing date	2022-02-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.153792
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Article ; Online: Unraveling Intracellular Protein Corona Components of Nanoplastics via Photocatalytic Protein Proximity Labeling.

Zhang, Zhenduo / Dong, Xuepeng / Wan, Wang / Guo, Hengke / Sun, Rui / Feng, Huan / Wang, Mengdie / Wang, Zhiming / Jin, Hao / Sun, Jialu / Xia, Qiuxuan / Zhao, Qi / Shen, Di / Gao, Zhenming / Liu, Yu

Analytical chemistry

2024 Volume 96, Issue 12, Page(s) 4978–4986

Abstract: Bioaccumulation of nanoplastic particles has drawn increasing attention regarding environmental sustainability and biosafety. How nanoplastic particles interact with the cellular milieu still remains elusive. Herein, we exemplify a general approach to ... ...

Abstract	Bioaccumulation of nanoplastic particles has drawn increasing attention regarding environmental sustainability and biosafety. How nanoplastic particles interact with the cellular milieu still remains elusive. Herein, we exemplify a general approach to profile the composition of a "protein corona" interacting with nanoparticles via the photocatalytic protein proximity labeling method. To enable photocatalytic proximity labeling of the proteome interacting with particles, iodine-substituted BODIPY (I-BODIPY) is selected as the photosensitizer and covalently conjugated onto amino-polystyrene nanoparticles as a model system. Next, selective proximity labeling of interacting proteins is demonstrated using I-BODIPY-labeled nanoplastic particles in both
MeSH term(s)	Animals ; Mice ; Protein Corona ; Microplastics ; Proteome ; Proteomics ; Polystyrenes ; Nanoparticles ; Boron Compounds
Chemical Substances	4,4-difluoro-4-bora-3a,4a-diaza-s-indacene ; Protein Corona ; Microplastics ; Proteome ; Polystyrenes ; Boron Compounds
Language	English
Publishing date	2024-03-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.4c00050
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Article ; Online: The main protease and RNA-dependent RNA polymerase are two prime targets for SARS-CoV-2.

Jin, Zhenming / Wang, Haofeng / Duan, Yinkai / Yang, Haitao

Biochemical and biophysical research communications

2020 Volume 538, Page(s) 63–71

Abstract: The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses an unprecedented global health crisis. It is particularly urgent to develop clinically effective therapies to contain the ... ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses an unprecedented global health crisis. It is particularly urgent to develop clinically effective therapies to contain the pandemic. The main protease (M
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus Protease Inhibitors/chemistry ; Coronavirus Protease Inhibitors/pharmacology ; Coronavirus RNA-Dependent RNA Polymerase/antagonists & inhibitors ; Coronavirus RNA-Dependent RNA Polymerase/chemistry ; Drug Design ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Protein Conformation ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology
Chemical Substances	Antiviral Agents ; Coronavirus Protease Inhibitors ; Enzyme Inhibitors ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2020-11-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2020.10.091
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Article ; Online: Target Prediction Model for Natural Products Using Transfer Learning

Bo Qiang / Junyong Lai / Hongwei Jin / Liangren Zhang / Zhenming Liu

International Journal of Molecular Sciences, Vol 22, Iss 4632, p

2021 Volume 4632

Abstract: A large proportion of lead compounds are derived from natural products. However, most natural products have not been fully tested for their targets. To help resolve this problem, a model using transfer learning was built to predict targets for natural ... ...

Abstract	A large proportion of lead compounds are derived from natural products. However, most natural products have not been fully tested for their targets. To help resolve this problem, a model using transfer learning was built to predict targets for natural products. The model was pre-trained on a processed ChEMBL dataset and then fine-tuned on a natural product dataset. Benefitting from transfer learning and the data balancing technique, the model achieved a highly promising area under the receiver operating characteristic curve (AUROC) score of 0.910, with limited task-related training samples. Since the embedding distribution difference is reduced, embedding space analysis demonstrates that the model’s outputs of natural products are reliable. Case studies have proved our model’s performance in drug datasets. The fine-tuned model can successfully output all the targets of 62 drugs. Compared with a previous study, our model achieved better results in terms of both AUROC validation and its success rate for obtaining active targets among the top ones. The target prediction model using transfer learning can be applied in the field of natural product-based drug discovery and has the potential to find more lead compounds or to assist researchers in drug repurposing.
Keywords	target prediction ; deep learning ; transfer learning ; natural product ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	006
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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