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  1. Article ; Online: Complete Genome Sequence of Vulcanisaeta souniana Strain IC-059, a Hyperthermophilic Archaeon Isolated from Hot Spring Water in Japan.

    Kato, Shingo / Itoh, Takashi / Wu, Linhuan / Ma, Juncai / Ohkuma, Moriya

    Microbiology resource announcements

    2023  Volume 12, Issue 1, Page(s) e0108022

    Abstract: Vulcanisaeta souniana strain IC- ... ...

    Abstract Vulcanisaeta souniana strain IC-059
    Language English
    Publishing date 2023-01-04
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01080-22
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  2. Article ; Online: Dynamic analysis of SARS-CoV-2 evolution based on different countries.

    Xiao, Binghan / Wu, Linhuan / Sun, Qinglan / Shu, Chang / Hu, Songnian

    Gene

    2024  Volume 916, Page(s) 148426

    Abstract: Since late 2019, COVID-19 has significantly impacted the world. Understanding the evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis of SARS-CoV-2 ... ...

    Abstract Since late 2019, COVID-19 has significantly impacted the world. Understanding the evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis of SARS-CoV-2 evolution by examining mutation prevalence from the source countries of VOCs: United Kingdom, India, Brazil, South Africa, plus two countries: United States, Russia, utilizing genomic sequences from GISAID. Our methodological approach involved large-scale genomic sequence alignment using MAFFT, Python-based data processing on a high-performance computing platform, and advanced statistical methods the Maximal Information Coefficient (MIC), and also Long Short-Term Memory (LSTM) models for correlation analysis. Our findings elucidate the dynamics of SARS-CoV-2 evolution, highlighting the virus's changing behaviour over various pandemic stages. Key results include the discovery of three temporal mutation patterns-lineage distinct, long-span, and competitive mutations-with varying levels of impact on the virus. Notably, we observed a convergence of advantageous mutations in the spike protein, especially in the later stages of the pandemic, indicating a substantial evolutionary pressure on the virus. One of the most significant revelations is the predominant role of natural immunity over vaccination-induced immunity in driving these evolutionary changes. This emphasizes the critical need for regular vaccine updates to maintain efficacy against evolving strains. In conclusion, our study not only sheds light on the evolutionary trajectory of SARS-CoV-2 but also underscores the urgency for robust, continuous global data collection and sharing. It highlights the necessity for rapid adaptations in medical countermeasures, including vaccine development, to stay ahead of pathogen evolution. This research provides valuable insights for future pandemic preparedness and response strategies.
    Language English
    Publishing date 2024-04-03
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2024.148426
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    Zs.A 1357: Show issues Location:
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  3. Article ; Online: Intelligent Reconfiguration-Promoted Cellular Internalization of Core-Shell DNA Nanoprobe Equipped with Successive Dual Stimuli-Responsive Protective Satellites for Amplification Fluorescence Imaging of Tumor Cells.

    Pan, Wenhao / Niu, Huimin / Luo, Shasha / Chen, Linhuan / Wu, Zai-Sheng

    Small (Weinheim an der Bergstrasse, Germany)

    2024  , Page(s) e2311388

    Abstract: Although DNA probes have attracted increasing interest for precise tumor cell identification by imaging intracellular biomarkers, the requirement of commercial transfection reagents, limited targeting ligands, and/or non-biocompatible inorganic ... ...

    Abstract Although DNA probes have attracted increasing interest for precise tumor cell identification by imaging intracellular biomarkers, the requirement of commercial transfection reagents, limited targeting ligands, and/or non-biocompatible inorganic nanostructures has hampered the clinic translation. To circumvent these shortcomings, a reconfigurable ES-NC (Na
    Language English
    Publishing date 2024-01-28
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2168935-0
    ISSN 1613-6829 ; 1613-6810
    ISSN (online) 1613-6829
    ISSN 1613-6810
    DOI 10.1002/smll.202311388
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  4. Article ; Online: Managing the Gate Assignment Problem in the Hub Airport with Satellite Halls

    Runfa Wu / Wenliang Zhou / Linhuan Zhong / Yihan Liu

    Computational Intelligence and Neuroscience, Vol

    A Transfer Demand-Oriented Approach

    2022  Volume 2022

    Abstract: This study focuses on managing the gate assignment in the hub airport with both main terminal and satellite halls. We first formulate the gate assignment problem (GAP) as a binary linear programming model with multi-objective functions, where the ... ...

    Abstract This study focuses on managing the gate assignment in the hub airport with both main terminal and satellite halls. We first formulate the gate assignment problem (GAP) as a binary linear programming model with multi-objective functions, where the practical constraints, e.g., gate time conflict and gate compatibility, are considered. Then, we incorporate the impact of gate assignment on transfer passengers and formulate the transfer demand-oriented gate assignment problem (TGAP) as a nonlinear model. A linearization approach and a heuristic approach are designed to solve the TGAP model. A case study is conducted based on the practical data of the Shanghai Pudong International Airport, where a comparison between the results of GAP and TGAP by the two proposed approaches is demonstrated. It shows that the proposed TGAP model and solution approaches can not only enhance the service for transfer passengers but also improve the gate utilization efficiency in the hub airport.
    Keywords Computer applications to medicine. Medical informatics ; R858-859.7 ; Neurosciences. Biological psychiatry. Neuropsychiatry ; RC321-571
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Persistent Targeting DNA Nanocarrier Made of 3D Structural Unit Assembled from Only One Basic Multi-Palindromic Oligonucleotide for Precise Gene Cancer Therapy.

    Wu, Jingting / Zheng, Xiaoqi / Lin, Wenqing / Chen, Linhuan / Wu, Zai-Sheng

    Advanced healthcare materials

    2024  Volume 13, Issue 11, Page(s) e2303865

    Abstract: Construction of a simple, reconfigurable, and stimuli-responsive DNA nanocarrier remains a technical challenge. In this contribution, by designing three palindromic fragments, a simplest four-sticky end-contained 3D structural unit (PS-unit) made of two ... ...

    Abstract Construction of a simple, reconfigurable, and stimuli-responsive DNA nanocarrier remains a technical challenge. In this contribution, by designing three palindromic fragments, a simplest four-sticky end-contained 3D structural unit (PS-unit) made of two same DNA components is proposed. Via regulating the rotation angle of central longitudinal axis of PS-unit, the oriented assembly of one-component spherical architecture is accomplished with high efficiency. Introduction of an aptamer and sticky tail warehouse into one component creates a size-change-reversible targeted siRNA delivery nanovehicle. Volume swelling of 20 nm allows one carrier to load 1987 siPLK1s. Once entering cancer cells and responding to glutathione (GSH) stimuli, siPLK1s are almost 100% released and original size of nanovehicle is restored, inhibiting the expression of PLK1 protein and substantially suppressing tumor growth (superior to commercial transfection agents) in tumor-bearing mice without systemic toxicity.
    MeSH term(s) Animals ; Humans ; Mice ; Polo-Like Kinase 1 ; RNA, Small Interfering/chemistry ; RNA, Small Interfering/genetics ; DNA/chemistry ; Genetic Therapy/methods ; Neoplasms/therapy ; Neoplasms/pathology ; Neoplasms/metabolism ; Protein Serine-Threonine Kinases/genetics ; Protein Serine-Threonine Kinases/metabolism ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; Cell Line, Tumor ; Nanoparticles/chemistry ; Mice, Nude ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Drug Carriers/chemistry ; Mice, Inbred BALB C ; Oligonucleotides/chemistry ; Oligonucleotides/pharmacology
    Chemical Substances Polo-Like Kinase 1 ; RNA, Small Interfering ; DNA (9007-49-2) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Proto-Oncogene Proteins ; Cell Cycle Proteins ; Drug Carriers ; Oligonucleotides
    Language English
    Publishing date 2024-02-11
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649576-4
    ISSN 2192-2659 ; 2192-2640
    ISSN (online) 2192-2659
    ISSN 2192-2640
    DOI 10.1002/adhm.202303865
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    Zs.A 6966: Show issues Location:
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  6. Article ; Online: Managing the Gate Assignment Problem in the Hub Airport with Satellite Halls: A Transfer Demand-Oriented Approach.

    Wu, Runfa / Zhou, Wenliang / Zhong, Linhuan / Liu, Yihan

    publication RETRACTED

    Computational intelligence and neuroscience

    2022  Volume 2022, Page(s) 5087941

    Abstract: This study focuses on managing the gate assignment in the hub airport with both main terminal and satellite halls. We first formulate the gate assignment problem (GAP) as a binary linear programming model with multi-objective functions, where the ... ...

    Abstract This study focuses on managing the gate assignment in the hub airport with both main terminal and satellite halls. We first formulate the gate assignment problem (GAP) as a binary linear programming model with multi-objective functions, where the practical constraints, e.g., gate time conflict and gate compatibility, are considered. Then, we incorporate the impact of gate assignment on transfer passengers and formulate the transfer demand-oriented gate assignment problem (TGAP) as a nonlinear model. A linearization approach and a heuristic approach are designed to solve the TGAP model. A case study is conducted based on the practical data of the Shanghai Pudong International Airport, where a comparison between the results of GAP and TGAP by the two proposed approaches is demonstrated. It shows that the proposed TGAP model and solution approaches can not only enhance the service for transfer passengers but also improve the gate utilization efficiency in the hub airport.
    MeSH term(s) Airports ; China ; Nonlinear Dynamics
    Language English
    Publishing date 2022-04-25
    Publishing country United States
    Document type Journal Article ; Retracted Publication
    ZDB-ID 2388208-6
    ISSN 1687-5273 ; 1687-5273
    ISSN (online) 1687-5273
    ISSN 1687-5273
    DOI 10.1155/2022/5087941
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  7. Article ; Online: Laboratory information management system for biosafety laboratory

    Dingzhong Sun / Linhuan Wu / Guomei Fan

    Journal of Biosafety and Biosecurity, Vol 3, Iss 1, Pp 28-

    Safety and efficiency

    2021  Volume 34

    Abstract: Laboratory information management system (LIMS) has been widely used to facilitate laboratory activities. However, the current LIMSs do not contain functions to improve the safety of laboratory work, which is the major concern of biosafety laboratories ( ... ...

    Abstract Laboratory information management system (LIMS) has been widely used to facilitate laboratory activities. However, the current LIMSs do not contain functions to improve the safety of laboratory work, which is the major concern of biosafety laboratories (BSLs). With tons of biosafety information that need to be managed and an increasing number of biosafety-related research projects under way, it is worthy of expanding the current framework of LIMS and building a system that is more suitable for BSL usage. Such a system should carefully trade off between the safety and efficiency of regular lab activities, allowing the laboratory staff to conduct their research as free as possible while ensuring their and the environment’s safety. In order to achieve this goal, the information on the research contents, laboratory personnel, experimental materials and experimental equipment need to be well collected and fully utilized by a centralized system and its databases.
    Keywords Laboratory information management system ; Biosafety ; Biological research laboratory ; Laboratory safety ; Workflow management ; Biology (General) ; QH301-705.5
    Subject code 020
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher KeAi Communications Co., Ltd.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Draft genome sequencing data of the moderately halophilic bacterium,

    Kingkaew, Engkarat / Yiamsombut, Supalurk / Poothong, Saranporn / Shi, Wenyu / Wu, Linhuan / Ma, Juncai / Tanasupawat, Somboon

    Data in brief

    2022  Volume 44, Page(s) 108549

    Abstract: A moderately halophilic, Gram-stain-positive, spore-forming rod-shaped bacterium, designated SKP2-8 was isolated from a traditional fermented shrimp paste ( ...

    Abstract A moderately halophilic, Gram-stain-positive, spore-forming rod-shaped bacterium, designated SKP2-8 was isolated from a traditional fermented shrimp paste (
    Language English
    Publishing date 2022-08-22
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2022.108549
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  9. Article ; Online: The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation.

    Wu, Linhuan / Ma, Juncai

    International journal of systematic and evolutionary microbiology

    2019  Volume 69, Issue 4, Page(s) 895–898

    Abstract: The World Federation of Culture Collections and the World Data Center for Microorganisms (wdcm) initiated an international community-led project to sequence and annotate newly described prokaryotic taxa. This sequencing project aims to cooperate with ... ...

    Abstract The World Federation of Culture Collections and the World Data Center for Microorganisms (wdcm) initiated an international community-led project to sequence and annotate newly described prokaryotic taxa. This sequencing project aims to cooperate with international culture collections and the International Journal of Systematic and Evolutionary Microbiology and contribute to the expansion of whole genome sequencing databases for type strains. It will provide global microbial taxonomists with free standard genome sequencing and annotation services. Taxonomists are encouraged to contact the wdcm and participant culture collections to submit a type strain sequencing proposal.
    MeSH term(s) Classification/methods ; Databases, Genetic ; Genomics/standards ; Prokaryotic Cells/classification ; Sequence Analysis, DNA/standards
    Language English
    Publishing date 2019-03-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2002336-4
    ISSN 1466-5034 ; 1466-5026
    ISSN (online) 1466-5034
    ISSN 1466-5026
    DOI 10.1099/ijsem.0.003276
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 409: Show issues Location:
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  10. Article: Laboratory information management system for biosafety laboratory: Safety and efficiency

    Sun, Dingzhong / Wu, Linhuan / Fan, Guomei

    Journal of biosafety and biosecurity. 2021 June, v. 3, no. 1

    2021  

    Abstract: Laboratory information management system (LIMS) has been widely used to facilitate laboratory activities. However, the current LIMSs do not contain functions to improve the safety of laboratory work, which is the major concern of biosafety laboratories ( ... ...

    Abstract Laboratory information management system (LIMS) has been widely used to facilitate laboratory activities. However, the current LIMSs do not contain functions to improve the safety of laboratory work, which is the major concern of biosafety laboratories (BSLs). With tons of biosafety information that need to be managed and an increasing number of biosafety-related research projects under way, it is worthy of expanding the current framework of LIMS and building a system that is more suitable for BSL usage. Such a system should carefully trade off between the safety and efficiency of regular lab activities, allowing the laboratory staff to conduct their research as free as possible while ensuring their and the environment’s safety. In order to achieve this goal, the information on the research contents, laboratory personnel, experimental materials and experimental equipment need to be well collected and fully utilized by a centralized system and its databases.
    Keywords biosafety ; biosecurity ; human resources ; information management ; management systems ; research equipment
    Language English
    Dates of publication 2021-06
    Size p. 28-34.
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ISSN 2588-9338
    DOI 10.1016/j.jobb.2021.03.001
    Database NAL-Catalogue (AGRICOLA)

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