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  1. Article ; Online: Privately vertically mining of sequential patterns based on differential privacy with high efficiency and utility.

    Liang, Wenjuan / Zhang, Wenke / Liang, Songtao / Yuan, Caihong

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 17866

    Abstract: Sequential pattern mining is one of the fundamental tools for many important data analysis tasks, such as web browsing behavior analysis. Based on frequent patterns, decision-makers can obtain both economic gains and social values. Sequential data, on ... ...

    Abstract Sequential pattern mining is one of the fundamental tools for many important data analysis tasks, such as web browsing behavior analysis. Based on frequent patterns, decision-makers can obtain both economic gains and social values. Sequential data, on the other hand, frequently contain sensitive information, and directly analyzing these data will raise user concerns from a privacy perspective. Differential privacy (DP), as the most popular privacy model, has been employed to address this privacy concern. Most existing DP-Solutions are designed to combine horizontal sequence pattern mining algorithms with differential privacy. Due to the inefficiency of horizontal algorithms, their DP-Solutions cannot ensure high efficiency and accuracy while offering a high privacy guarantee. Therefore, we proposed privVertical, a new private sequence pattern mining scheme combining the vertical mining algorithm with differential privacy to achieve the above objective. Unlike DP-solutions based on horizontal algorithms, privVertical can promote efficiency by avoiding performing costly database scans or costly projection database constructions. Moreover, to promote accuracy, a differentially private hash MapList (called privHashMap) is designed to record frequent concurrency items and their noisy support based on the Sparse Vector Technique. PrivHashMap is used to pre-pruning excessive infrequent candidate sequences in private mining, and Sparse Vector Technique is used to promote the accuracy of PrivHashMap. After pruning these invalid candidate sequences, less noise is required to achieve the same level of privacy, increasing the accuracy of private mining. Theoretical privacy analysis proves privVertical satisfies [Formula: see text]-differential privacy. Experiments show that privVertical achieves higher accuracy and efficiency while achieving the same privacy level.
    Language English
    Publishing date 2023-10-19
    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/s41598-023-43030-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Manipulation of a Single Polymer Chain: From the Nanomechanical Properties to Dynamic Structure Evolution

    Song, Yu / Ma, Ziwen / Zhang, Wenke

    Macromolecules. 2022 June 03, v. 55, no. 11

    2022  

    Abstract: Exploring the relationship between the polymer structure and property/function is a long-lasting topic in polymer science since relevant research is critical for the rational design of polymer materials or the control of biological functions. Due to the ... ...

    Abstract Exploring the relationship between the polymer structure and property/function is a long-lasting topic in polymer science since relevant research is critical for the rational design of polymer materials or the control of biological functions. Due to the complexity of the real material and biological systems, it is quite difficult to establish such a relationship using traditional ensemble measurements. Single-molecule force spectroscopy (SMFS), which can be used to manipulate individual polymer chains, is a powerful technology for investigating the inter- or intramolecular interactions, chain structures and their dynamic behaviors with piconewton force and subnanometer spatial precision at the single-molecule level. In this Perspective, focusing on atomic force microscopy (AFM)-based SMFS, we first highlight recent advances in the AFM-SMFS study of mechanical properties in polymer systems, including the structure–mechanics relationships in polymer single crystal, covalent mechanochemistry of polymer, and polymer–nanoparticle composites. Then we highlight the recent advancement in the exploration of higher-order structures and their dynamic conversion in DNA using SMFS. We emphasize the prominent role of the application expansion of SMFS, innovation of experimental methods and sample preparation. At the end, future challenges and opportunities on single-molecule manipulations of polymers are discussed. We hope that this Perspective will also attract further attention from the material, biological, and computational research community, which would speed up our understanding on the structure–property (function) relationship of polymers.
    Keywords DNA ; atomic force microscopy ; evolution ; mechanochemistry ; polymers ; spectroscopy
    Language English
    Dates of publication 2022-0603
    Size p. 4177-4199.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1491942-4
    ISSN 1520-5835 ; 0024-9297
    ISSN (online) 1520-5835
    ISSN 0024-9297
    DOI 10.1021/acs.macromol.2c00076
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Increasing carbon to nitrogen ratio promoted anaerobic ammonia-oxidizing bacterial enrichment and advanced nitrogen removal in mainstream anammox system.

    Zhang, Wenke / Zhang, Jianhua / Yu, Deshuang / Zhu, Ze / Miao, Yuanyuan

    Bioresource technology

    2023  Volume 393, Page(s) 130169

    Abstract: The effects of fluctuating organic carbon to nitrogen (C/N) ratios on mainstream simultaneous partial nitrification, anammox, and denitrification (SNAD) process were studied over 376-day period. The nitrogen removal efficiency decreased from 85.0 ± 6.6 % ...

    Abstract The effects of fluctuating organic carbon to nitrogen (C/N) ratios on mainstream simultaneous partial nitrification, anammox, and denitrification (SNAD) process were studied over 376-day period. The nitrogen removal efficiency decreased from 85.0 ± 6.6 % to 75.8 ± 2.8 % as C/N ratio decreased (3.4 → 1.7), but increased to 82.0 ± 1.9 % when C/N ratio raised to 2.9 and to 78.4 ± 3.0 % when C/N ratio decreased again (2.9 → 2.1), indicating that high C/N ratios promoted nitrogen removal. As C/N ratio raised (1.7 → 2.9), anaerobic ammonia-oxidizing bacteria (AnAOB) abundance increased from 1.3 × 10
    MeSH term(s) Denitrification ; Ammonia ; Sewage/microbiology ; Nitrogen/analysis ; Carbon ; Anaerobiosis ; Anaerobic Ammonia Oxidation ; Bioreactors/microbiology ; Oxidation-Reduction ; Nitrification
    Chemical Substances Ammonia (7664-41-7) ; Sewage ; Nitrogen (N762921K75) ; Carbon (7440-44-0)
    Language English
    Publishing date 2023-12-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 1065195-0
    ISSN 1873-2976 ; 0960-8524
    ISSN (online) 1873-2976
    ISSN 0960-8524
    DOI 10.1016/j.biortech.2023.130169
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Exploring the impact of PEGylation on the cell-nanomicelle interactions by AFM-based single-molecule force spectroscopy and force tracing.

    Hou, Jue / Li, Nan / Zhang, Wei / Zhang, Wenke

    Acta biomaterialia

    2022  Volume 157, Page(s) 310–320

    Abstract: PEGylation has been considered the gold standard method for the modification of various drug delivery systems since the last century. However, the impact of PEGylation on the dynamic interaction between drug carriers and cell membranes has not been ... ...

    Abstract PEGylation has been considered the gold standard method for the modification of various drug delivery systems since the last century. However, the impact of PEGylation on the dynamic interaction between drug carriers and cell membranes has not been quantitatively clarified. Herein, the cellular binding and receptor-mediated endocytosis of a model PEGylated polypeptide nanomicelle were systematically investigated at the single-particle level using AFM-based single-molecule force spectroscopy (SMFS) and force tracing. A self-assembled elastin-like polypeptide (ELP) nanomicelle, which is capable of cross-linking, gastrin-releasing peptide (GRP) modification, and PEGylation was prepared. The cross-linked ELP-based nanomicelles exhibited outstanding stability in a broad temperature range of 4-40 °C, which facilitate the drug loading, as well as our cell-nanomicelle study at the single particle level. The unbinding force between the cross-linked ELP-based nanomicelles and the GRP receptor (GRPR)-containing cell (PC-3) membranes was quantitatively measured by AFM-SMFS. It is found that the PEGylated GRP-displaying nanomicelles exhibit the highest unbinding force, indicating the enhanced specific binding effect of PEGylation. Furthermore, the receptor-mediated endocytosis of the cross-linked ELP-based nanomicelles was monitored with the help of force tracing based on AFM-SMFS. Our results show that PEGylation decreases the endocytic force, duration, and engulfment depth of the PEGylated GRP-displaying nanomicelles, but increases their endocytic velocity, which results from the elimination of non-specific interactions during endocytosis. These observations demonstrate the diverse and complex roles of PEGylation on the interaction of polypeptide nanomicelles to cell membranes and may shed light on the rational design of organic polymer-based drug delivery systems aiming for active and passive targeting strategies. STATEMENT OF SIGNIFICANCE: A self-assembled elastin-like polypeptide (ELP) nanomicelle, which can be easily cross-linked, gastrin-releasing peptide (GRP) modified, and PEGylated, is designed. The AFM-SMFS experiment shows that PEGylation can enhance specific binding of the nanomicelles to the receptors on cell membranes. The force tracing experiment indicates that PEGylation decreases the endocytic force as well as engulfment depth of the nanomicelles through the elimination of non-specific interactions. PEGylation can benefit the drug delivery systems aiming at active targeting, while might not be an ideal modification for drug carriers designed for passive targeting, whose cellular uptake mainly depends on non-specific interactions.
    MeSH term(s) Elastin/chemistry ; Gastrin-Releasing Peptide ; Micelles ; Drug Carriers/chemistry ; Peptides/chemistry ; Polyethylene Glycols/chemistry ; Spectrum Analysis
    Chemical Substances Elastin (9007-58-3) ; Gastrin-Releasing Peptide (80043-53-4) ; Micelles ; Drug Carriers ; Peptides ; Polyethylene Glycols (3WJQ0SDW1A)
    Language English
    Publishing date 2022-12-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2173841-5
    ISSN 1878-7568 ; 1742-7061
    ISSN (online) 1878-7568
    ISSN 1742-7061
    DOI 10.1016/j.actbio.2022.12.020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Increasing specific biomass nitrogen load facilitated nitrite accumulation in mainstream wastewater treatment

    Zhang, Jianhua / Zhang, Wenke / Bi, Xuejun / Gao, Zhongxiu / Li, Yitong / Miao, Yuanyuan

    Bioresource Technology. 2023 Oct., v. 385 p.129337-

    2023  

    Abstract: By regulating influent nitrogen loading rate (NLR) and solids retention time (SRT), the effect of specific biomass nitrogen load (BNL) on the start-up of mainstream partial nitrification (PN) was investigated in five parallel sequencing batch reactors ... ...

    Abstract By regulating influent nitrogen loading rate (NLR) and solids retention time (SRT), the effect of specific biomass nitrogen load (BNL) on the start-up of mainstream partial nitrification (PN) was investigated in five parallel sequencing batch reactors inoculated with ordinary nitrification sludge. The results showed that increasing BNL by both methods could achieve nitrite accumulation. Moreover, a high initial activity of ammonium oxidizing bacteria (AOB) accelerated nitrite accumulation. Increasing influent NLR (ammonium: 55–70 mg N/L) achieved only 30%–40% of nitrite accumulation ratio (NAR) and gradually decreased with reactor operation. By increasing BNL via controlling SRT (30 days), desirable PN with an average NAR of 81.7 ± 4.4% (effluent nitrite: ∼10 mg N/L) was obtained. Nitrite oxidizing bacteria (NOB) were effectively inhibited, and the AOB to NOB activity ratio increased from 1.5 to 7.8, promoting efficient nitrite accumulation. Overall, increasing BNL by regulating SRT was a potential method for start-up of mainstream PN.
    Keywords ammonium ; biomass ; nitrification ; nitrites ; nitrogen ; sludge ; wastewater treatment ; Mainstream partial nitrification ; Nitrification sludge ; Bacterial activity analysis ; Nitrogen loading rate ; Solids retention time
    Language English
    Dates of publication 2023-10
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ZDB-ID 1065195-0
    ISSN 1873-2976 ; 0960-8524
    ISSN (online) 1873-2976
    ISSN 0960-8524
    DOI 10.1016/j.biortech.2023.129337
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Treatment of Granulomatous Mastitis with Half-Yin and Half-Yang Syndrome

    Li, Zhikun / Cheng, Xufeng / Zhang, Wenke / Zhao, Huiduo

    Chinese medicine and natural products

    2023  Volume 03, Issue 03, Page(s) e102–e107

    Abstract: Granulomatous mastitis (GM) is a refractory chronic mastitis, which belongs to the category of “acne mammary abscess” and “ulcer” in Traditional Chinese External Medicine. According to yin-yang syndrome differentiation, the disease can be divided into ... ...

    Abstract Granulomatous mastitis (GM) is a refractory chronic mastitis, which belongs to the category of “acne mammary abscess” and “ulcer” in Traditional Chinese External Medicine. According to yin-yang syndrome differentiation, the disease can be divided into yin syndrome, yang syndrome, and half-yin and half-yang syndrome. Among them, the theories and treatment of yin syndrome and yang syndrome are relatively comprehensive in Traditional Chinese External Medicine. However, the half-yin and half-yang syndrome lacks a specific theoretical elaboration and treatment system, which is a special and complex syndrome of the disease, limiting the improvement of the clinical efficacy of the disease. The core pathogenesis of GM with half-yin and half-yang syndrome is “obstruction of nutritive and defensive phases, and yin-yang obstruction.” The clinical features are local yin syndrome complicated with yang syndrome, and the disease is lingering and difficult to cure. For syndrome differentiation, it is advisable to “attach more importance to the local while less importance to the whole body.” The treatment should be based on the general principle of “eliminating yin and transforming yang.” For the use of herbs, it is recommended to adopt the methods of “the combination of the herbs in cold and warm nature, mainly with herbs in warm nature, attaching more importance to use the herbs with the function of ascending and less to descending.” Finally, restore the normal circulation of qi and blood as well as the balance of yin and yang to achieve the purpose of treatment.
    Keywords granulomatous mastitis ; acne mammary abscess ; half-yin and half-yang syndrome ; eliminating yin to transform yang ; Chonghe Plaster ; Huoluo Xiaoling Bolus ; Neituo Shengji Powder
    Language English
    Publishing date 2023-09-01
    Publisher Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article
    ISSN 2749-568X ; 2096-918X
    ISSN (online) 2749-568X
    ISSN 2096-918X
    DOI 10.1055/s-0043-1773795
    Database Thieme publisher's database

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  7. Article ; Online: Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats.

    Zhang, Wenke / Fan, Xiaoqian / Shi, Haobo / Li, Jian / Zhang, Mingqian / Zhao, Jin / Su, Xiaoquan

    Microbiology spectrum

    2023  Volume 11, Issue 3, Page(s) e0056323

    Abstract: The 16S rRNA gene works as a rapid and effective marker for the identification of microorganisms in complex communities; hence, a huge number of microbiomes have been surveyed by 16S amplicon-based sequencing. The resolution of the 16S rRNA gene is ... ...

    Abstract The 16S rRNA gene works as a rapid and effective marker for the identification of microorganisms in complex communities; hence, a huge number of microbiomes have been surveyed by 16S amplicon-based sequencing. The resolution of the 16S rRNA gene is always considered only at the genus level; however, it has not been verified on a wide range of microbes yet. To fully explore the ability and potential of the 16S rRNA gene in microbial profiling, here, we propose Qscore, a comprehensive method to evaluate the performance of amplicons by integrating the amplification rate, multitier taxonomic annotation, sequence type, and length. Our
    MeSH term(s) RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; Microbiota/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.00563-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes.

    Zhang, Mingqian / Zhang, Wenke / Chen, Yuzhu / Zhao, Jin / Wu, Shunyao / Su, Xiaoquan

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 4

    Abstract: Motivation: Beta-diversity quantitatively measures the difference among microbial communities thus enlightening the association between microbiome composition and environment properties or host phenotypes. The beta-diversity analysis mainly relies on ... ...

    Abstract Motivation: Beta-diversity quantitatively measures the difference among microbial communities thus enlightening the association between microbiome composition and environment properties or host phenotypes. The beta-diversity analysis mainly relies on distances among microbiomes that are calculated by all microbial features. However, in some cases, only a small fraction of members in a community plays crucial roles. Such a tiny proportion is insufficient to alter the overall distance, which is always missed by end-to-end comparison. On the other hand, beta-diversity pattern can also be interfered due to the data sparsity when only focusing on nonabundant microbes.
    Results: Here, we develop Flex Meta-Storms (FMS) distance algorithm that implements the "local alignment" of microbiomes for the first time. Using a flexible extraction that considers the weighted phylogenetic and functional relations of microbes, FMS produces a normalized phylogenetic distance among members of interest for microbiome pairs. We demonstrated the advantage of FMS in detecting the subtle variations of microbiomes among different states using artificial and real datasets, which were neglected by regular distance metrics. Therefore, FMS effectively discriminates microbiomes with higher sensitivity and flexibility, thus contributing to in-depth comprehension of microbe-host interactions, as well as promoting the utilization of microbiome data such as disease screening and prediction.
    Availability and implementation: FMS is implemented in C++, and the source code is released at https://github.com/qdu-bioinfo/flex-meta-storms.
    MeSH term(s) Phylogeny ; Microbiota ; Software ; Algorithms
    Language English
    Publishing date 2023-03-22
    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/btad148
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: One-step, reagent-free construction of nano-enzyme as visual and reusable biosensor for oxidase substrates.

    Quan, Ke / Zeng, Yuqing / Zhang, Wenke / Li, Fengfeng / Li, Mengjiao / Qing, Zhihe / Wu, Linlin

    Analytica chimica acta

    2023  Volume 1285, Page(s) 342008

    Abstract: The substrates of oxidase are biologically essential substances that are closely associated with human physiological health. However, current biosensing methods suffer from tough recyclability and undesired denaturation of enzyme due to impurity ... ...

    Abstract The substrates of oxidase are biologically essential substances that are closely associated with human physiological health. However, current biosensing methods suffer from tough recyclability and undesired denaturation of enzyme due to impurity interference. Herein, we have developed a visual and reusable biosensor for detecting substrate using glucose oxidase (GOx) as a model oxidase. GOx was immobilized onto gold nanoparticles (AuNPs) at -20 °C in one step without additional reagents. The resulting nano-enzyme generated coloimetric signals by coupling with horseradish peroxidase (HRP) using TMB as the substrate. Our results demonstrated that the immobilized GOx exhibited satisfactory sensitivity (0.68 μM) for glucose detection and higher inherent stability than free GOx under harsh conditions, enabling reliable detection of glucose in complex fluids (colored beverages and saliva). Furthermore, the nano-enzyme retained 80 % activity even after four cycles of catalytic oxidation. This strategy constructs a universal biosensor for substrates with nano-enzyme which rely only on intrinsic cysteine within the oxidase while avoiding functional handle modification.
    MeSH term(s) Humans ; Oxidoreductases ; Enzymes, Immobilized/chemistry ; Gold ; Indicators and Reagents ; Metal Nanoparticles ; Glucose ; Glucose Oxidase/chemistry ; Biosensing Techniques/methods
    Chemical Substances Oxidoreductases (EC 1.-) ; Enzymes, Immobilized ; Gold (7440-57-5) ; Indicators and Reagents ; Glucose (IY9XDZ35W2) ; Glucose Oxidase (EC 1.1.3.4)
    Language English
    Publishing date 2023-11-09
    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.2023.342008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Polymer Research at the State Key Laboratory of Supramolecular Structure and Materials, Jilin University.

    An, Zesheng / Zhang, Wenke / Sun, Junqi

    Macromolecular rapid communications

    2021  Volume 41, Issue 24, Page(s) e2000630

    MeSH term(s) Humans ; Laboratories ; Macromolecular Substances ; Molecular Structure ; Polymers ; Universities
    Chemical Substances Macromolecular Substances ; Polymers
    Language English
    Publishing date 2021-01-25
    Publishing country Germany
    Document type Editorial
    ZDB-ID 1475027-2
    ISSN 1521-3927 ; 1022-1336
    ISSN (online) 1521-3927
    ISSN 1022-1336
    DOI 10.1002/marc.202000630
    Database MEDical Literature Analysis and Retrieval System OnLINE

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