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  1. Article ; Online: Immune epitopes identification and designing of a multi-epitope vaccine against bovine leukemia virus: a molecular dynamics and immune simulation approaches.

    Samad, Abdus / Meghla, Nigar Sultana / Nain, Zulkar / Karpiński, Tomasz M / Rahman, Md Shahedur

    Cancer immunology, immunotherapy : CII

    2022  Volume 71, Issue 10, Page(s) 2535–2548

    Abstract: Background: Bovine leukemia virus (BLV) is an oncogenic delta-retrovirus causing bovine leucosis. Studies on BLV have shown the association with human breast cancer. However, the exact molecular mechanism is neither known nor their appropriate ... ...

    Abstract Background: Bovine leukemia virus (BLV) is an oncogenic delta-retrovirus causing bovine leucosis. Studies on BLV have shown the association with human breast cancer. However, the exact molecular mechanism is neither known nor their appropriate preventative measure to halt the disease initiation and progression. In this study, we designed a multi-epitope vaccine against BLV using a computational analyses.
    Methods: Following a rigorous assessment, the vaccine was constructed using the T-cell epitopes from each BLV-derived protein with suitable adjuvant and linkers. Both physicochemistry and immunogenic potency as well as the safeness of the vaccine candidate were assessed. Population coverage was done to evaluate the vaccine probable efficiency in eliciting the immune response worldwide. After homology modeling, the three-dimensional structure was refined and validated to determine the quality of the designed vaccine. The vaccine protein was then subjected to molecular docking with Toll-like receptor 3 (TLR3) to evaluate the binding efficiency followed by dynamic simulation for stable interaction.
    Results: Our vaccine construct has the potential immune response and good physicochemical properties. The vaccine is antigenic and immunogenic, and has no allergenic or toxic effect on the human body. This novel vaccine contains a significant interactions and binding affinity with the TLR3 receptor.
    Conclusions: The proposed vaccine candidate would be structurally stable and capable of generating an effective immune response to combat BLV infections. However, experimental evaluations are essential to validate the exact safety and immunogenic profiling of this vaccine.
    MeSH term(s) Computational Biology/methods ; Epitopes, B-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte ; Humans ; Leukemia Virus, Bovine ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Vaccines, Subunit
    Chemical Substances Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Vaccines, Subunit
    Language English
    Publishing date 2022-03-16
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 195342-4
    ISSN 1432-0851 ; 0340-7004
    ISSN (online) 1432-0851
    ISSN 0340-7004
    DOI 10.1007/s00262-022-03181-w
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    Zs.A 1237: Show issues Location:
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  2. Article ; Online: A Non-Linear Biostatistical Graphical Modeling of Preventive Actions and Healthcare Factors in Controlling COVID-19 Pandemic.

    Abdulla, Faruq / Nain, Zulkar / Karimuzzaman, Md / Hossain, Md Moyazzem / Rahman, Azizur

    International journal of environmental research and public health

    2021  Volume 18, Issue 9

    Abstract: Background: With the insurgence of the COVID-19 pandemic, many people died in the past several months, and the situation is ongoing with increasing health, social, and economic panic and vulnerability. As most of the countries relying on different ... ...

    Abstract Background: With the insurgence of the COVID-19 pandemic, many people died in the past several months, and the situation is ongoing with increasing health, social, and economic panic and vulnerability. As most of the countries relying on different preventive actions to control the outcomes of COVID-19, it is necessary to boost the knowledge about the effectiveness of such actions so that the policymakers take their country-based appropriate actions. This study generates evidence of taking the most impactful actions to combat COVID-19.
    Objective: In order to generate community-based scientific evidence, this study analyzed the outcome of COVID-19 in response to different control measures, healthcare facilities, life expectancy, and prevalent diseases.
    Methods: It used more than a hundred countries' data collected from different databases. We performed a comparative graphical analysis with non-linear correlation estimation using R.
    Results: The reduction of COVID-19 cases is strongly correlated with the earliness of preventive initiation. The apathy of taking nationwide immediate precaution measures has been identified as one of the critical reasons to make the circumstances worse. There is significant non-linear relationship between COVID-19 case fatality and number of physicians (NCC = 0.22;
    Conclusions: Enhancing healthcare facilities and early imposing the control measures could be valuable to prevent the COVID-19 pandemic. No association between COVID-19 and other comorbidities warranted further investigation at the pathobiological level.
    MeSH term(s) COVID-19 ; Delivery of Health Care ; Female ; Health Personnel ; Humans ; Male ; Pandemics ; SARS-CoV-2
    Language English
    Publishing date 2021-04-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2175195-X
    ISSN 1660-4601 ; 1661-7827
    ISSN (online) 1660-4601
    ISSN 1661-7827
    DOI 10.3390/ijerph18094491
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  3. Article ; Online: Structural basis and designing of peptide vaccine using PE-PGRS family protein of Mycobacterium ulcerans-An integrated vaccinomics approach.

    Nain, Zulkar / Karim, Mohammad Minnatul / Sen, Monokesh Kumer / Adhikari, Utpal Kumar

    Molecular immunology

    2020  Volume 120, Page(s) 146–163

    Abstract: Buruli ulcer is an emerging tissue-necrosis infectious disease, caused by the pathogen Mycobacterium ulcerans, leading to permanent deformity if untreated. Despite this debilitating condition, no specific disease-modifying therapeutics or vaccination is ... ...

    Abstract Buruli ulcer is an emerging tissue-necrosis infectious disease, caused by the pathogen Mycobacterium ulcerans, leading to permanent deformity if untreated. Despite this debilitating condition, no specific disease-modifying therapeutics or vaccination is available to date. Therefore, we aimed to design an effective multi-epitope vaccine against M. ulcerans using vaccinomics approach. Briefly, the highest antigenic PE-PGRS protein was selected from which the promiscuous T- and B-cell epitopes were predicted. After rigorous assessment, 15 promising T- and B-cell epitopes were selected. The identified T-cell epitopes showed marked interactions towards their HLA-binding alleles and provided 99.8 % world population coverage. Consequently, a vaccine chimera was designed by connecting these epitopes with suitable linkers and LprG adjuvant. The vaccine construct was highly antigenic, immunogenic and non-allergenic; hence, subjected to homology modelling. The molecular docking and dynamics simulation revealed a strong and stable interaction between vaccine and toll-like receptor 2. The binding energy and dissociation constant were -15.3 kcal/mol and 5.9 × 10
    MeSH term(s) Antigens, Bacterial/chemistry ; Antigens, Bacterial/genetics ; Antigens, Bacterial/immunology ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/immunology ; Bacterial Vaccines/chemistry ; Bacterial Vaccines/genetics ; Bacterial Vaccines/immunology ; Buruli Ulcer/immunology ; Buruli Ulcer/prevention & control ; Computer Simulation ; Drug Design ; Epitopes, B-Lymphocyte/chemistry ; Epitopes, B-Lymphocyte/genetics ; Epitopes, B-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte/genetics ; Epitopes, T-Lymphocyte/immunology ; HLA Antigens/chemistry ; HLA Antigens/immunology ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/immunology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mycobacterium ulcerans/chemistry ; Mycobacterium ulcerans/genetics ; Mycobacterium ulcerans/immunology ; Protein Engineering ; Vaccines, Subunit/chemistry ; Vaccines, Subunit/genetics ; Vaccines, Subunit/immunology ; Vaccines, Synthetic/chemistry ; Vaccines, Synthetic/genetics ; Vaccines, Synthetic/immunology
    Chemical Substances Antigens, Bacterial ; Bacterial Proteins ; Bacterial Vaccines ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; HLA Antigens ; Membrane Proteins ; PE-PGRS protein, Mycobacterium ; Vaccines, Subunit ; Vaccines, Synthetic
    Language English
    Publishing date 2020-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 424427-8
    ISSN 1872-9142 ; 0161-5890
    ISSN (online) 1872-9142
    ISSN 0161-5890
    DOI 10.1016/j.molimm.2020.02.009
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    Zs.A 166: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Identifying molecular insight of synergistic complexities for SARS-CoV-2 infection with pre-existing type 2 diabetes.

    Islam, M Babul / Chowdhury, Utpala Nanda / Nain, Zulkar / Uddin, Shahadat / Ahmed, Mohammad Boshir / Moni, Mohammad Ali

    Computers in biology and medicine

    2021  Volume 136, Page(s) 104668

    Abstract: The ongoing COVID-19 outbreak, caused by SARS-CoV-2, has posed a massive threat to global public health, especially to people with underlying health conditions. Type 2 diabetes (T2D) is lethal comorbidity of COVID-19. However, its pathogenetic link ... ...

    Abstract The ongoing COVID-19 outbreak, caused by SARS-CoV-2, has posed a massive threat to global public health, especially to people with underlying health conditions. Type 2 diabetes (T2D) is lethal comorbidity of COVID-19. However, its pathogenetic link remains unclear. This research aims to determine the genetic factors and processes contributing to the synergistic severity of SARS-CoV-2 infection among T2D patients through bioinformatics approaches. We analyzed two sets of transcriptomic data of SARS-CoV-2 infection obtained from lung epithelium cells and PBMCs, and two sets of T2D data from pancreatic islet cells and PBMCs to identify the associated differentially expressed genes (DEGs) followed by their functional enrichment analyses in terms of protein-protein interaction (PPI) to detect hub-proteins and associated comorbidities, transcription factors (TFs), microRNAs (miRNAs) as well as the potential drug candidates. In PPI analysis, four potential hub-proteins (i.e., BIRC3, C3, MME, and IL1B) were identified among 25 DEGs shared between the disease pair. Enrichment analyses using the mutually overlapped DEGs revealed the most prevalent GO and cell signalling pathways, including TNF signalling, cytokine-cytokine receptor interaction, and IL-17 signalling, which are related to cytokine activities. Furthermore, as significant TFs, we identified IRF1, KLF11, FOSL1, and CREB3L1 while miRNAs including miR-1-3p, 34a-5p, 16-5p, 155-5p, 20a-5p, and let-7b-5p were found to be noteworthy. The findings illustrated the significant association between COVID-19 and T2D at the molecular level. These genetic determinants can further be explored for their specific roles in disease progression and therapeutic intervention, while significant pathways can also be studied as molecular checkpoints. Finally, the identified drug candidates may be evaluated for their potency to minimize the severity of COVID-19 patients with pre-existing T2D.
    MeSH term(s) COVID-19 ; Computational Biology ; Diabetes Mellitus, Type 2/genetics ; Humans ; MicroRNAs/genetics ; SARS-CoV-2
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2021-07-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2021.104668
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    Zs.A 653: Show issues Location:
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  5. Article ; Online: A Non-Linear Biostatistical Graphical Modeling of Preventive Actions and Healthcare Factors in Controlling COVID-19 Pandemic

    Faruq Abdulla / Zulkar Nain / Md. Karimuzzaman / Md. Moyazzem Hossain / Azizur Rahman

    International Journal of Environmental Research and Public Health, Vol 18, Iss 4491, p

    2021  Volume 4491

    Abstract: Background: With the insurgence of the COVID-19 pandemic, many people died in the past several months, and the situation is ongoing with increasing health, social, and economic panic and vulnerability. As most of the countries relying on different ... ...

    Abstract Background: With the insurgence of the COVID-19 pandemic, many people died in the past several months, and the situation is ongoing with increasing health, social, and economic panic and vulnerability. As most of the countries relying on different preventive actions to control the outcomes of COVID-19, it is necessary to boost the knowledge about the effectiveness of such actions so that the policymakers take their country-based appropriate actions. This study generates evidence of taking the most impactful actions to combat COVID-19. Objective: In order to generate community-based scientific evidence, this study analyzed the outcome of COVID-19 in response to different control measures, healthcare facilities, life expectancy, and prevalent diseases. Methods: It used more than a hundred countries’ data collected from different databases. We performed a comparative graphical analysis with non-linear correlation estimation using R. Results: The reduction of COVID-19 cases is strongly correlated with the earliness of preventive initiation. The apathy of taking nationwide immediate precaution measures has been identified as one of the critical reasons to make the circumstances worse. There is significant non-linear relationship between COVID-19 case fatality and number of physicians (NCC = 0.22; p -value ≤ 0.001), nurses and midwives (NCC = 0.17; p -value ≤ 0.001), hospital beds (NCC = 0.20; p -value ≤ 0.001), life expectancy of both sexes (NCC = 0.22; p -value ≤ 0.001), life expectancy of female (NCC = 0.27; p -value ≤ 0.001), and life expectancy of male (NCC = 0.19; p -value ≤ 0.001). COVID-19 deaths were found to be reduced with increased medical personnel and hospital beds. Interestingly, no association between the comorbidities and severity of COVID-19 was found excluding asthma, cancer, Alzheimer’s, and smoking. Conclusions: Enhancing healthcare facilities and early imposing the control measures could be valuable to prevent the COVID-19 pandemic. No association between COVID-19 and other comorbidities ...
    Keywords COVID-19 pandemic ; social distance ; lockdown ; quarantine ; case fatality rate ; life expectancy ; Medicine ; R
    Subject code 360
    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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  6. Article: Exploring Lassa Virus Proteome to Design a Multi-epitope Vaccine Through Immunoinformatics and Immune Simulation Analyses.

    Sayed, Sifat Bin / Nain, Zulkar / Khan, Md Shakil Ahmed / Abdulla, Faruq / Tasmin, Rubaia / Adhikari, Utpal Kumar

    International journal of peptide research and therapeutics

    2020  Volume 26, Issue 4, Page(s) 2089–2107

    Abstract: Lassa virus (LASV) is responsible for a type of acute viral haemorrhagic fever referred to as Lassa fever. Lack of adequate treatment and preventive measures against LASV resulted in a high mortality rate in its endemic regions. In this study, a multi- ... ...

    Abstract Lassa virus (LASV) is responsible for a type of acute viral haemorrhagic fever referred to as Lassa fever. Lack of adequate treatment and preventive measures against LASV resulted in a high mortality rate in its endemic regions. In this study, a multi-epitope vaccine was designed using immunoinformatics as a prophylactic agent against the virus. Following a rigorous assessment, the vaccine was built using T-cell (N
    Keywords covid19
    Language English
    Publishing date 2020-01-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2192632-3
    ISSN 1573-3904 ; 1573-3149
    ISSN (online) 1573-3904
    ISSN 1573-3149
    DOI 10.1007/s10989-019-10003-8
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  7. Article ; Online: In silico formulation of a next-generation multiepitope vaccine for use as a prophylactic candidate against Crimean-Congo hemorrhagic fever.

    Alam, Rahat / Samad, Abdus / Ahammad, Foysal / Nur, Suza Mohammad / Alsaiari, Ahad Amer / Imon, Raihan Rahman / Talukder, Md Enamul Kabir / Nain, Zulkar / Rahman, Md Mashiar / Mohammad, Farhan / Karpiński, Tomasz M

    BMC medicine

    2023  Volume 21, Issue 1, Page(s) 36

    Abstract: Background: Crimean-Congo hemorrhagic fever (CCHF) is a widespread disease transmitted to humans and livestock animals through the bite of infected ticks or close contact with infected persons' blood, organs, or other bodily fluids. The virus is ... ...

    Abstract Background: Crimean-Congo hemorrhagic fever (CCHF) is a widespread disease transmitted to humans and livestock animals through the bite of infected ticks or close contact with infected persons' blood, organs, or other bodily fluids. The virus is responsible for severe viral hemorrhagic fever outbreaks, with a case fatality rate of up to 40%. Despite having the highest fatality rate of the virus, a suitable treatment option or vaccination has not been developed yet. Therefore, this study aimed to formulate a multiepitope vaccine against CCHF through computational vaccine design approaches.
    Methods: The glycoprotein, nucleoprotein, and RNA-dependent RNA polymerase of CCHF were utilized to determine immunodominant T- and B-cell epitopes. Subsequently, an integrative computational vaccinology approach was used to formulate a multi-epitopes vaccine candidate against the virus.
    Results: After rigorous assessment, a multiepitope vaccine was constructed, which was antigenic, immunogenic, and non-allergenic with desired physicochemical properties. Molecular dynamics (MD) simulations of the vaccine-receptor complex show strong stability of the vaccine candidates to the targeted immune receptor. Additionally, the immune simulation of the vaccine candidates found that the vaccine could trigger real-life-like immune responses upon administration to humans.
    Conclusions: Finally, we concluded that the formulated multiepitope vaccine candidates would provide excellent prophylactic properties against CCHF.
    MeSH term(s) Humans ; Animals ; Hemorrhagic Fever, Crimean/prevention & control ; Hemorrhagic Fever, Crimean/epidemiology ; Hemorrhagic Fever Virus, Crimean-Congo/genetics ; Viral Vaccines ; Disease Outbreaks/prevention & control ; Vaccination
    Chemical Substances Viral Vaccines
    Language English
    Publishing date 2023-02-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2131669-7
    ISSN 1741-7015 ; 1741-7015
    ISSN (online) 1741-7015
    ISSN 1741-7015
    DOI 10.1186/s12916-023-02750-9
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  8. Article ; Online: Inhibition of biofilm formation, quorum sensing and other virulence factors in

    Nain, Zulkar / Mansur, Fariha Jasin / Syed, Shifath Bin / Islam, Md Ariful / Azakami, Hiroyuki / Islam, Md Rezuanul / Karim, Mohammad Minnatul

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 12, Page(s) 5357–5371

    Abstract: Quorum sensing (QS) enables virulence factors in bacteria for biofilm formation and pathogenic invasion. Therefore, quorum quenching (QQ), disruption of QS circuit, becomes an alternative antimicrobial therapy. In this study, leaf extract ... ...

    Abstract Quorum sensing (QS) enables virulence factors in bacteria for biofilm formation and pathogenic invasion. Therefore, quorum quenching (QQ), disruption of QS circuit, becomes an alternative antimicrobial therapy. In this study, leaf extract of
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism ; Biofilms ; Plant Extracts/chemistry ; Plant Extracts/pharmacology ; Polyphenols/pharmacology ; Pseudomonas aeruginosa/metabolism ; Quercetin/pharmacology ; Quorum Sensing ; Virulence Factors/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Plant Extracts ; Polyphenols ; Virulence Factors ; Quercetin (9IKM0I5T1E)
    Language English
    Publishing date 2021-01-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1870563
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    Zs.A 2093: Show issues Location:
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  9. Article ; Online: In silico formulation of a next-generation multiepitope vaccine for use as a prophylactic candidate against Crimean-Congo hemorrhagic fever

    Rahat Alam / Abdus Samad / Foysal Ahammad / Suza Mohammad Nur / Ahad Amer Alsaiari / Raihan Rahman Imon / Md. Enamul Kabir Talukder / Zulkar Nain / Md. Mashiar Rahman / Farhan Mohammad / Tomasz M. Karpiński

    BMC Medicine, Vol 21, Iss 1, Pp 1-

    2023  Volume 19

    Abstract: Abstract Background Crimean-Congo hemorrhagic fever (CCHF) is a widespread disease transmitted to humans and livestock animals through the bite of infected ticks or close contact with infected persons’ blood, organs, or other bodily fluids. The virus is ... ...

    Abstract Abstract Background Crimean-Congo hemorrhagic fever (CCHF) is a widespread disease transmitted to humans and livestock animals through the bite of infected ticks or close contact with infected persons’ blood, organs, or other bodily fluids. The virus is responsible for severe viral hemorrhagic fever outbreaks, with a case fatality rate of up to 40%. Despite having the highest fatality rate of the virus, a suitable treatment option or vaccination has not been developed yet. Therefore, this study aimed to formulate a multiepitope vaccine against CCHF through computational vaccine design approaches. Methods The glycoprotein, nucleoprotein, and RNA-dependent RNA polymerase of CCHF were utilized to determine immunodominant T- and B-cell epitopes. Subsequently, an integrative computational vaccinology approach was used to formulate a multi-epitopes vaccine candidate against the virus. Results After rigorous assessment, a multiepitope vaccine was constructed, which was antigenic, immunogenic, and non-allergenic with desired physicochemical properties. Molecular dynamics (MD) simulations of the vaccine-receptor complex show strong stability of the vaccine candidates to the targeted immune receptor. Additionally, the immune simulation of the vaccine candidates found that the vaccine could trigger real-life-like immune responses upon administration to humans. Conclusions Finally, we concluded that the formulated multiepitope vaccine candidates would provide excellent prophylactic properties against CCHF.
    Keywords CCHF ; Multiepitope vaccine ; Immunoinformatics ; Immune simulation ; Molecular dynamics simulation ; Molecular docking ; Medicine ; R
    Subject code 616
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Energy-optimized pharmacophore coupled virtual screening in the discovery of quorum sensing inhibitors of LasR protein of

    Nain, Zulkar / Sayed, Sifat Bin / Karim, Mohammad Minnatul / Islam, Md Ariful / Adhikari, Utpal Kumar

    Journal of biomolecular structure & dynamics

    2019  Volume 38, Issue 18, Page(s) 5374–5388

    Abstract: Pseudomonas ... ...

    Abstract Pseudomonas aeruginosa
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/pharmacology ; Pseudomonas aeruginosa ; Quorum Sensing/drug effects ; Trans-Activators ; Virulence Factors
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Trans-Activators ; Virulence Factors
    Language English
    Publishing date 2019-12-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2019.1700168
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