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Article ; Online: Machine learning for percolation utilizing auxiliary Ising variables.

Zhang, Junyin / Zhang, Bo / Xu, Junyi / Zhang, Wanzhou / Deng, Youjin

2022 Volume 105, Issue 2-1, Page(s) 24144

Abstract: Machine learning for phase transition has received intensive research interest in recent years. However, its application in percolation still remains challenging. We propose an auxiliary Ising mapping method for the machine learning study of the standard ...

Abstract	Machine learning for phase transition has received intensive research interest in recent years. However, its application in percolation still remains challenging. We propose an auxiliary Ising mapping method for the machine learning study of the standard percolation as well as a variety of statistical mechanical systems in correlated percolation representation. We demonstrate that unsupervised machine learning is able to accurately locate the percolation threshold, independent of the spatial dimension of system or the type of phase transition, which can be first-order or continuous. Moreover, we show that, by neural network machine learning, auxiliary Ising configurations for different universalities can be classified with a high confidence level. Our results indicate that the auxiliary Ising mapping method, despite its simplicity, can advance the application of machine learning in statistical and condensed-matter physics.
Language	English
Publishing date	2022-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.105.024144
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Article ; Online: Huangyusang decoction for Type 2 diabetes: A protocol for systematic review and meta analysis.

He, Peiyu / Zhang, Junyin / Gao, Tianyu / Wang, Yingxiang / Peng, Teng

Medicine

2021 Volume 100, Issue 8, Page(s) e24576

Abstract: Background: Diabetes is a chronic metabolic disease characterized by elevated blood glucose levels due to insulin resistance and β-cell dysfunction. In China, Huangyusang decoction (HYS) has been widely used to treat Type 2 diabetes. However, there is ... ...

Abstract	Background: Diabetes is a chronic metabolic disease characterized by elevated blood glucose levels due to insulin resistance and β-cell dysfunction. In China, Huangyusang decoction (HYS) has been widely used to treat Type 2 diabetes. However, there is no systematic review found. In order to evaluate the efficacy and safety of HYS in the treatment of Type 2 diabetes, we need to conduct a meta-analysis and systematic evaluation. Methods: We will enroll the randomized controlled trials (RCTs) evaluating the effectiveness and safety of HYS in the treatment of Type 2 diabetes. Data come mainly from 4 Chinese databases (CNKI, Wanfang, CBM, and VIP Database) and 4 English databases (PubMed, Embase, Cochrane Library, and Web of science). The enrollment of RCTs is from the starting date of database establishment till January 30, 2021. Fasting blood glucose is considered as the main indicator of the dyslipidemia, while the body mass index, glycated hemoglobin, fasting insulin, triglycerides, and cholesterol are regarded as the secondary indicators. There are safety indicators including liver enzyme and kidney function. The work such as selection of literature, data collection, quality evaluation of included literature, and assessment of publication bias will be conducted by 2 independent researchers. Meta-analysis will be performed by RevMan 5.0 software. Results: This study will provide high-quality evidence for the effectiveness and safety of HYS in the treatment of type 2 diabetes. Conclusion: The results of the study will help us determine whether HYS can effectively treat type 2 diabetes. Ethics and dissemination: This study does not require ethical approval. We will disseminate our findings by publishing results in a peer-reviewed journal. Osf registration number: DOI 10.17605/OSF.IO/AXBRV.
MeSH term(s)	Blood Glucose ; Body Mass Index ; Diabetes Mellitus, Type 2/drug therapy ; Drugs, Chinese Herbal/administration & dosage ; Drugs, Chinese Herbal/adverse effects ; Drugs, Chinese Herbal/therapeutic use ; Glycated Hemoglobin ; Humans ; Kidney Function Tests ; Lipids/blood ; Liver Function Tests ; Randomized Controlled Trials as Topic ; Research Design ; Meta-Analysis as Topic ; Systematic Review as Topic
Chemical Substances	Blood Glucose ; Drugs, Chinese Herbal ; Glycated Hemoglobin A ; Lipids
Language	English
Publishing date	2021-02-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000024576
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Article ; Online: DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning.

Wang, Chen / Zhang, Junyin / Cheng, Li / Wu, Jiawei / Xiao, Minfeng / Xia, Junfeng / Bin, Yannan

IEEE journal of biomedical and health informatics

2022 Volume 26, Issue 10, Page(s) 5258–5266

Abstract: With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of data ... ...

Abstract	With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of data makes it possible to establish computational models for promoter identification with robustness. In this work, we introduce DPProm, a two-layer model composed of DPProm-1L and DPProm-2L, to predict promoters and their types for phages. On the first layer, as a dual-channel deep neural network ensemble method fusing multi-view features (sequence feature and handcrafted feature), the model DPProm-1L is proposed to identify whether a DNA sequence is a promoter or non-promoter. The sequence feature is extracted with convolutional neural network (CNN). And the handcrafted feature is the combination of free energy, GC content, cumulative skew, and Z curve features. On the second layer, DPProm-2L based on CNN is trained to predict the promoters' types (host or phage). For the realization of prediction on the whole genomes, the model DPProm, combines with a novel sequence data processing workflow, which contains sliding window and merging sequences modules. Experimental results show that DPProm outperforms the state-of-the-art methods, and decreases the false positive rate effectively on whole genome prediction. Furthermore, we provide a user-friendly web at http://bioinfo.ahu.edu.cn/DPProm. We expect that DPProm can serve as a useful tool for identification of promoters and their types.
MeSH term(s)	Bacteriophages/genetics ; DNA ; Deep Learning ; Genomics/methods ; Humans ; Promoter Regions, Genetic/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2695320-1
ISSN	2168-2208 ; 2168-2194
ISSN (online)	2168-2208
ISSN	2168-2194
DOI	10.1109/JBHI.2022.3193224
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Article ; Online: PhaGAA: an integrated web server platform for phage genome annotation and analysis.

Wu, Jiawei / Liu, Qingrui / Li, Min / Xu, Jiliang / Wang, Chen / Zhang, Junyin / Xiao, Minfeng / Bin, Yannan / Xia, Junfeng

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 3

Abstract: Motivation: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. ...

Abstract	Motivation: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed. Results: Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate the prophage genome at DNA and protein levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists and help advance the phage synthetic biology in basic and application research. Availability and implementation: PhaGAA is freely available at http://phage.xialab.info/.
MeSH term(s)	Bacteriophages/genetics ; Software ; Computers ; Metagenome ; Genome, Bacterial ; Molecular Sequence Annotation
Language	English
Publishing date	2023-03-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad120
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Article ; Online: The structures of two glucomannans from Bletilla formosana and their protective effect on inflammation via inhibiting NF-κB pathway.

Gu, Qinghui / Liu, Yaping / Zhen, Li / Zhao, Tianrui / Luo, Lan / Zhang, Junyin / Deng, Tuo / Wu, Mingyi / Cheng, Guiguang / Hu, Jiangmiao

Carbohydrate polymers

2022 Volume 292, Page(s) 119694

Abstract: Bletilla formosana is a traditional Chinese herbal medicine and is widely consumed as foods and medicines in China. However, the chemical structure and bioactivity of its polysaccharides remain unknown. Herein, two new polysaccharides, BFP60 and BFP80, ... ...

Abstract	Bletilla formosana is a traditional Chinese herbal medicine and is widely consumed as foods and medicines in China. However, the chemical structure and bioactivity of its polysaccharides remain unknown. Herein, two new polysaccharides, BFP60 and BFP80, with molecular weights of 3.99 kDa and 10.07 kDa, respectively, were isolated and purified from dried tuber of B. formosana. Structural analysis suggested that BFP60 and BFP80 may have backbone consisted of →4)-β-d-Man-(1→,→4)-β-d-Glc-(1→,→4)-2-O-acetyl-β-d-Man-(1→, and →4)-3-O-acetyl-β-d-Man-(1→. Inflammation assay in LPS-induced RAW264.7 cells showed that the productions of NO and pro-inflammatory cytokines including IL-6, IL-1β, TNF-α, and IFN-γ were significantly reduced, and the expression of iNOS, COX-2, and target proteins in the NF-κB pathway were suppressed after BFP60 and BFP80 pretreatment. These findings indicated that this novel polysaccharide had significant inflammatory protective effects in vitro.
MeSH term(s)	Animals ; Inflammation/chemically induced ; Inflammation/drug therapy ; Mannans/pharmacology ; Mice ; NF-kappa B/metabolism ; Orchidaceae/chemistry ; RAW 264.7 Cells ; Signal Transduction
Chemical Substances	Mannans ; NF-kappa B ; (1-6)-alpha-glucomannan (36W3E5TAMG)
Language	English
Publishing date	2022-06-06
Publishing country	England
Document type	Journal Article
ZDB-ID	1501516-6
ISSN	1879-1344 ; 0144-8617
ISSN (online)	1879-1344
ISSN	0144-8617
DOI	10.1016/j.carbpol.2022.119694
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Article ; Online: Structures of fructan and galactan from Polygonatum cyrtonema and their utilization by probiotic bacteria

Zhang, Junyin / Chen, Hulan / Luo, Lan / Zhou, Zhipeng / Wang, Yingxiang / Gao, Tianyu / Yang, Lian / Peng, Teng / Wu, Mingyi

Carbohydrate Polymers. 2021 Sept., v. 267 p.118219-

2021

Abstract: Polygonatum cyrtonema is a known tonic herb in Chinese Materia Medica, extensively consumed in China, but the structure and activity of its polysaccharide components remain to be clarified. Herein, two new polysaccharides (a fructan and a galactan) were ... ...

Abstract	Polygonatum cyrtonema is a known tonic herb in Chinese Materia Medica, extensively consumed in China, but the structure and activity of its polysaccharide components remain to be clarified. Herein, two new polysaccharides (a fructan and a galactan) were purified from the dried and the processed P. cyrtonema rhizome, respectively. Structural analysis suggested that the fructan consisted of a (2 → 6) linked β-d-Fruf residues backbone with an internal α-d-Glcp residue and two (2 → 1) linked β-d-Fruf residues branches, and that the galactan was a (1 → 4)-β-d-galactan branched with a single β-d-galactose at C-6 at about every nine residues in its main chain. The bioactive assay showed that the fructan and the galactan remarkably promoted growth of Bifidobacterium and Lactobacillus strains, indicating that they possess prebiotic activity. These findings may help expand the application of the polysaccharides from the tonic herb P. cyrtonema as functional ingredients in food products.
Keywords	Bifidobacterium ; Lactobacillus ; Polygonatum cyrtonema ; fructans ; homeopathic drugs ; prebiotics ; probiotics ; rhizomes ; China ; Polysaccharide ; Structural elucidation ; Bifidobacterium and Lactobacillus strains ; Prebiotic activity ; d-glucuronic acid (PubChem CID: 94715) ; d-glucose (PubChem CID: 5793) ; d-galactose (PubChem CID: 6036) ; d-galacturonic acid (PubChem CID: 439215) ; d-fructose (PubChem CID: 2723872) ; l-rhamnose (PubChem CID: 25310) ; d-mannose (PubChem CID: 18950) ; d-arabinose (PubChem CID: 66308) ; Trifluoroacetic acid (PubChem CID: 6422) ; Sodium borodeuteride (PubChem CID: 23673181)
Language	English
Dates of publication	2021-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1501516-6
ISSN	1879-1344 ; 0144-8617
ISSN (online)	1879-1344
ISSN	0144-8617
DOI	10.1016/j.carbpol.2021.118219
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The structures of two glucomannans from Bletilla formosana and their protective effect on inflammation via inhibiting NF-κB pathway

Gu, Qinghui / Liu, Yaping / Zhen, Li / Zhao, Tianrui / Luo, Lan / Zhang, Junyin / Deng, Tuo / Wu, Mingyi / Cheng, Guiguang / Hu, Jiangmiao

Carbohydrate Polymers. 2022 Sept., v. 292 p.119694-

2022

Abstract	Bletilla formosana is a traditional Chinese herbal medicine and is widely consumed as foods and medicines in China. However, the chemical structure and bioactivity of its polysaccharides remain unknown. Herein, two new polysaccharides, BFP60 and BFP80, with molecular weights of 3.99 kDa and 10.07 kDa, respectively, were isolated and purified from dried tuber of B. formosana. Structural analysis suggested that BFP60 and BFP80 may have backbone consisted of →4)-β-d-Man-(1→,→4)-β-d-Glc-(1→,→4)-2-O-acetyl-β-d-Man-(1→, and →4)-3-O-acetyl-β-d-Man-(1→. Inflammation assay in LPS-induced RAW264.7 cells showed that the productions of NO and pro-inflammatory cytokines including IL-6, IL-1β, TNF-α, and IFN-γ were significantly reduced, and the expression of iNOS, COX-2, and target proteins in the NF-κB pathway were suppressed after BFP60 and BFP80 pretreatment. These findings indicated that this novel polysaccharide had significant inflammatory protective effects in vitro.
Keywords	Bletilla ; Oriental traditional medicine ; chemical structure ; glucomannans ; inflammation ; interleukin-6 ; protective effect ; China ; d-Glucose (PubChem CID: 5793) ; d-Mannose (PubChem CID: 18950) ; Trifluoroacetic acid (PubChem CID: 6422) ; Sodium borodeuteride (PubChem CID: 23673181) ; 1-Phenyl-3-methyl-5-pyrazolone (PubChem CID: 4021) ; Acetic anhydride (PubChem CID: 7918) ; Bletilla formosana ; Polysaccharide ; Glucomannan
Language	English
Dates of publication	2022-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1501516-6
ISSN	1879-1344 ; 0144-8617
ISSN (online)	1879-1344
ISSN	0144-8617
DOI	10.1016/j.carbpol.2022.119694
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Article ; Online: High density lithium niobate photonic integrated circuits.

Li, Zihan / Wang, Rui Ning / Lihachev, Grigory / Zhang, Junyin / Tan, Zelin / Churaev, Mikhail / Kuznetsov, Nikolai / Siddharth, Anat / Bereyhi, Mohammad J / Riemensberger, Johann / Kippenberg, Tobias J

Nature communications

2023 Volume 14, Issue 1, Page(s) 4856

Abstract: Photonic integrated circuits have the potential to pervade into multiple applications traditionally limited to bulk optics. Of particular interest for new applications are ferroelectrics such as Lithium Niobate, which exhibit a large Pockels effect, but ... ...

Abstract	Photonic integrated circuits have the potential to pervade into multiple applications traditionally limited to bulk optics. Of particular interest for new applications are ferroelectrics such as Lithium Niobate, which exhibit a large Pockels effect, but are difficult to process via dry etching. Here we demonstrate that diamond-like carbon (DLC) is a superior material for the manufacturing of photonic integrated circuits based on ferroelectrics, specifically LiNbO
Language	English
Publishing date	2023-08-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40502-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structures of fructan and galactan from Polygonatum cyrtonema and their utilization by probiotic bacteria.

Zhang, Junyin / Chen, Hulan / Luo, Lan / Zhou, Zhipeng / Wang, Yingxiang / Gao, Tianyu / Yang, Lian / Peng, Teng / Wu, Mingyi

Carbohydrate polymers

2021 Volume 267, Page(s) 118219

Abstract	Polygonatum cyrtonema is a known tonic herb in Chinese Materia Medica, extensively consumed in China, but the structure and activity of its polysaccharide components remain to be clarified. Herein, two new polysaccharides (a fructan and a galactan) were purified from the dried and the processed P. cyrtonema rhizome, respectively. Structural analysis suggested that the fructan consisted of a (2 → 6) linked β-d-Fruf residues backbone with an internal α-d-Glcp residue and two (2 → 1) linked β-d-Fruf residues branches, and that the galactan was a (1 → 4)-β-d-galactan branched with a single β-d-galactose at C-6 at about every nine residues in its main chain. The bioactive assay showed that the fructan and the galactan remarkably promoted growth of Bifidobacterium and Lactobacillus strains, indicating that they possess prebiotic activity. These findings may help expand the application of the polysaccharides from the tonic herb P. cyrtonema as functional ingredients in food products.
MeSH term(s)	Bifidobacterium/metabolism ; Carbohydrate Sequence ; Fructans/chemistry ; Fructans/isolation & purification ; Fructans/metabolism ; Galactans/chemistry ; Galactans/isolation & purification ; Galactans/metabolism ; Lactobacillus/metabolism ; Molecular Weight ; Polygonatum/chemistry ; Prebiotics
Chemical Substances	Fructans ; Galactans ; Prebiotics
Language	English
Publishing date	2021-05-19
Publishing country	England
Document type	Journal Article
ZDB-ID	1501516-6
ISSN	1879-1344 ; 0144-8617
ISSN (online)	1879-1344
ISSN	0144-8617
DOI	10.1016/j.carbpol.2021.118219
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Article ; Online: Detailed Structural Analysis of the Immunoregulatory Polysaccharides from the Mycobacterium Bovis BCG.

Luo, Lan / Song, Xuemei / Chang, Xiao / Huang, Sheng / Zhou, Yunxi / Yang, Shengmei / Zhu, Yan / Zhang, Lanyan / Wu, Yongsheng / Zhang, Junyin / Zhou, Zhipeng / Wu, Mingyi

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 17

Abstract: Bacillus Calmette-Guérin polysaccharide and nucleic acid (BCG-PSN), extracted ... ...

Abstract	Bacillus Calmette-Guérin polysaccharide and nucleic acid (BCG-PSN), extracted from
MeSH term(s)	Adjuvants, Immunologic ; BCG Vaccine ; Mannans/pharmacology ; Mycobacterium bovis/chemistry ; Polysaccharides/pharmacology
Chemical Substances	Adjuvants, Immunologic ; BCG Vaccine ; Mannans ; Polysaccharides
Language	English
Publishing date	2022-09-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27175691
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