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  1. Article: Roles of Non-coding RNAs in Respiratory Syncytial Virus (RSV) Infection.

    Tripp, Ralph A / Bakre, Abhijeet A

    Current topics in microbiology and immunology

    2017  Volume 419, Page(s) 215–241

    Abstract: Analysis of host gene expression profiles following viral infections of target cells/tissues can reveal crucial insights into the host: virus interaction and enables the development of novel therapeutics and prophylactics. Regions of the host genome that ...

    Abstract Analysis of host gene expression profiles following viral infections of target cells/tissues can reveal crucial insights into the host: virus interaction and enables the development of novel therapeutics and prophylactics. Regions of the host genome that do not code for protein, encode structural, and functional non-coding RNAs that are important not only in regulation of host gene expression but also may impact viral replication. This review summarizes the role of host non-coding RNAs during replication of multiple respiratory viruses with a focus on Respiratory Syncytial Virus (RSV), an important pediatric pathogen. This review highlights the current state of knowledge and understanding regarding the function(s) of ncRNAs for respiratory viral infection and host immunity in general.
    MeSH term(s) Host-Pathogen Interactions ; Humans ; RNA, Untranslated/genetics ; Respiratory Syncytial Virus Infections/genetics ; Respiratory Syncytial Virus Infections/immunology ; Respiratory Syncytial Virus Infections/virology ; Respiratory Syncytial Virus, Human/growth & development ; Respiratory Syncytial Virus, Human/immunology ; Respiratory Syncytial Virus, Human/pathogenicity ; Virus Replication
    Chemical Substances RNA, Untranslated
    Language English
    Publishing date 2017-08-04
    Publishing country Germany
    Document type Journal Article ; Review
    ISSN 0070-217X
    ISSN 0070-217X
    DOI 10.1007/82_2017_32
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: MicroRNA and Nonsense Transcripts as Putative Viral Evasion Mechanisms.

    Bakre, Abhijeet A / Maleki, Ali / Tripp, Ralph A

    Frontiers in cellular and infection microbiology

    2019  Volume 9, Page(s) 152

    Abstract: Viral proteins encode numerous antiviral activities to modify the host immunity. In this article, we hypothesize that viral genomes and gene transcripts interfere with host gene expression using passive mechanisms to deregulate host microRNA (miRNA) ... ...

    Abstract Viral proteins encode numerous antiviral activities to modify the host immunity. In this article, we hypothesize that viral genomes and gene transcripts interfere with host gene expression using passive mechanisms to deregulate host microRNA (miRNA) activity. We postulate that various RNA viruses mimic or block binding between a host miRNA and its target transcript, a phenomenon mediated by the miRNA seed site at the 5' end of miRNA. Virus-encoded miRNA seed sponges (vSSs) can potentially bind to host miRNA seed sites and prevent interaction with their native targets thereby relieving native miRNA suppression. In contrast, virus-encoded miRNA seed mimics (vSMs) may mediate considerable downregulation of host miRNA activity. We analyzed genomes from diverse RNA viruses for vSS and vSM signatures and found an abundance of these motifs indicating that this may be a mechanism of deceiving host immunity. Employing respiratory syncytial virus and measles virus as models, we reveal that regions surrounding vSS or vSM motifs have features characteristics of pre-miRNA templates and show that RSV viral transcripts are processed into small RNAs that may behave as vSS or vSM effectors. These data suggest that complex molecular interactions likely occur at the host-virus interface. Identifying the mechanisms in the network of interactions between the host and viral transcripts can help uncover ways to improve vaccine efficacy, therapeutics, and potentially mitigate the adverse events that may be associated with some vaccines.
    MeSH term(s) A549 Cells ; Animals ; Gene Expression ; Genome, Viral ; Host-Pathogen Interactions/genetics ; Humans ; Immune Evasion/genetics ; Immunity ; Mice ; MicroRNAs/genetics ; Porifera/virology ; RNA Viruses/genetics ; Sequence Alignment ; Viral Proteins
    Chemical Substances MicroRNAs ; Viral Proteins
    Language English
    Publishing date 2019-05-08
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2019.00152
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Small Non-coding RNA Expression Following Respiratory Syncytial Virus or Measles Virus Infection of Neuronal Cells.

    Bakre, Abhijeet A / Duffy, Catherine / Abdullah, Hani'ah / Cosby, S Louise / Tripp, Ralph A

    Frontiers in microbiology

    2021  Volume 12, Page(s) 671852

    Abstract: Respiratory syncytial virus (RSV) or measles virus (MeV) infection modifies host responses through small non-coding RNA (sncRNA) expression. We show that RSV or MeV infection of neuronal cells induces sncRNAs including various microRNAs and transfer RNA ... ...

    Abstract Respiratory syncytial virus (RSV) or measles virus (MeV) infection modifies host responses through small non-coding RNA (sncRNA) expression. We show that RSV or MeV infection of neuronal cells induces sncRNAs including various microRNAs and transfer RNA fragments (tRFs). We show that these tRFs originate from select tRNAs (GCC and CAC for glycine, CTT and AAC for Valine, and CCC and TTT for Lysine). Some of the tRNAs are rarely used by RSV or MeV as indicated by relative synonymous codon usage indices suggesting selective cleavage of the tRNAs occurs in infected neuronal cells. The data implies that differentially expressed sncRNAs may regulate host gene expression
    Language English
    Publishing date 2021-09-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.671852
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Detection of swine influenza virus in nasal specimens by reverse transcription-loop-mediated isothermal amplification (RT-LAMP)

    Bakre, Abhijeet A. / Jones, Les P. / Bennett, Hailey K. / Bobbitt, Davis E. / Tripp, Ralph A.

    Elsevier B.V. Journal of virological methods. 2021 Feb., v. 288

    2021  

    Abstract: Detection of swine influenza virus (SIV) in commercial swine herds is important for understanding the infection status of the herd and for controlling disease. Current molecular diagnostics require that specimens be submitted to a laboratory which ... ...

    Abstract Detection of swine influenza virus (SIV) in commercial swine herds is important for understanding the infection status of the herd and for controlling disease. Current molecular diagnostics require that specimens be submitted to a laboratory which provides results to the growers after some time which is generally too late to intercede in disease control. Moreover, current diagnostic assays are time-consuming, typically costly, and require skilled technical expertise. We have instituted a reverse transcription loop-mediated isothermal amplification (RT-LAMP) diagnostic assay based on conserved regions of the SIV matrix (M) gene and H1N1 hemagglutinin (HA) sequences. The RT-LAMP assay was optimized to use both colorimetric and fluorescent endpoints and was validated. The M and HA RT-LAMP assays have a limit-of-detection (LOD) sensitive to 11 and 8-log-fold dilutions of viral RNA, respectively, and are capable of discriminating between H1 and H3 strains of SIV. Additionally, the RT-LAMP assay was optimized for direct amplification of SIV from field samples without the need for viral RNA isolation. The direct RT-LAMP detected >86 % of qRT-PCR validated SIV samples, and >66 % of negative samples when spiked with viral RNA or SIV. The diagnostic RT-LAMP assay is a rapid, sensitive, specific, and cost-effective method for the detection of SIV in herds substantially aiding diagnosis and surveillance.
    Keywords Influenza A virus ; RNA ; colorimetry ; cost effectiveness ; diagnostic techniques ; disease control ; fluorescence ; genes ; hemagglutinins ; herds ; monitoring ; nose ; reverse transcription loop-mediated isothermal amplification ; swine
    Language English
    Dates of publication 2021-02
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 8013-5
    ISSN 1879-0984 ; 0166-0934
    ISSN (online) 1879-0984
    ISSN 0166-0934
    DOI 10.1016/j.jviromet.2020.114015
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Determining Immune and miRNA Biomarkers Related to Respiratory Syncytial Virus (RSV) Vaccine Types.

    Atherton, Lydia J / Jorquera, Patricia A / Bakre, Abhijeet A / Tripp, Ralph A

    Frontiers in immunology

    2019  Volume 10, Page(s) 2323

    Abstract: Respiratory Syncytial Virus (RSV) causes serious respiratory tract illness and substantial morbidity and some mortality in populations at the extremes of age, i.e., infants, young children, and the elderly. To date, RSV vaccine development has been ... ...

    Abstract Respiratory Syncytial Virus (RSV) causes serious respiratory tract illness and substantial morbidity and some mortality in populations at the extremes of age, i.e., infants, young children, and the elderly. To date, RSV vaccine development has been unsuccessful, a feature linked to the lack of biomarkers available to assess the safety and efficacy of RSV vaccine candidates. We examined microRNAs (miR) as potential biomarkers for different types of RSV vaccine candidates. In this study, mice were vaccinated with a live attenuated RSV candidate that lacks the small hydrophobic (SH) and attachment (G) proteins (CP52), an RSV G protein microparticle (GA2-MP) vaccine, a formalin-inactivated RSV (FI-RSV) vaccine or were mock-treated. Several immunological endpoints and miR expression profiles were determined in mouse serum and bronchoalveolar lavage (BAL) following vaccine priming, boost, and RSV challenge. We identified miRs that were linked with immunological parameters of disease and protection. We show that miRs are potential biomarkers providing valuable insights for vaccine development.
    MeSH term(s) Animals ; Biomarkers ; Female ; Immunization ; Lung/immunology ; Lung/pathology ; Mice ; Mice, Inbred BALB C ; MicroRNAs/immunology ; Respiratory Syncytial Virus Infections/immunology ; Respiratory Syncytial Virus Infections/prevention & control ; Respiratory Syncytial Virus Vaccines/immunology ; Respiratory Syncytial Virus, Human/immunology
    Chemical Substances Biomarkers ; MicroRNAs ; Respiratory Syncytial Virus Vaccines
    Language English
    Publishing date 2019-10-09
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2019.02323
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Detection of swine influenza virus in nasal specimens by reverse transcription-loop-mediated isothermal amplification (RT-LAMP).

    Bakre, Abhijeet A / Jones, Les P / Bennett, Hailey K / Bobbitt, Davis E / Tripp, Ralph A

    Journal of virological methods

    2020  Volume 288, Page(s) 114015

    Abstract: Detection of swine influenza virus (SIV) in commercial swine herds is important for understanding the infection status of the herd and for controlling disease. Current molecular diagnostics require that specimens be submitted to a laboratory which ... ...

    Abstract Detection of swine influenza virus (SIV) in commercial swine herds is important for understanding the infection status of the herd and for controlling disease. Current molecular diagnostics require that specimens be submitted to a laboratory which provides results to the growers after some time which is generally too late to intercede in disease control. Moreover, current diagnostic assays are time-consuming, typically costly, and require skilled technical expertise. We have instituted a reverse transcription loop-mediated isothermal amplification (RT-LAMP) diagnostic assay based on conserved regions of the SIV matrix (M) gene and H1N1 hemagglutinin (HA) sequences. The RT-LAMP assay was optimized to use both colorimetric and fluorescent endpoints and was validated. The M and HA RT-LAMP assays have a limit-of-detection (LOD) sensitive to 11 and 8-log-fold dilutions of viral RNA, respectively, and are capable of discriminating between H1 and H3 strains of SIV. Additionally, the RT-LAMP assay was optimized for direct amplification of SIV from field samples without the need for viral RNA isolation. The direct RT-LAMP detected >86 % of qRT-PCR validated SIV samples, and >66 % of negative samples when spiked with viral RNA or SIV. The diagnostic RT-LAMP assay is a rapid, sensitive, specific, and cost-effective method for the detection of SIV in herds substantially aiding diagnosis and surveillance.
    MeSH term(s) Animals ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A virus/genetics ; Molecular Diagnostic Techniques ; Nucleic Acid Amplification Techniques ; Reverse Transcription ; Sensitivity and Specificity ; Swine
    Language English
    Publishing date 2020-11-30
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 8013-5
    ISSN 1879-0984 ; 0166-0934
    ISSN (online) 1879-0984
    ISSN 0166-0934
    DOI 10.1016/j.jviromet.2020.114015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: MicroRNA-134 regulates poliovirus replication by IRES targeting.

    Bakre, Abhijeet A / Shim, Byoung-Shik / Tripp, Ralph A

    Scientific reports

    2017  Volume 7, Issue 1, Page(s) 12664

    Abstract: Global poliovirus eradication efforts include high vaccination coverage with live oral polio vaccine (OPV), surveillance for acute flaccid paralysis, and OPV "mop-up" campaigns. An important objective involves host-directed strategies to reduce PV ... ...

    Abstract Global poliovirus eradication efforts include high vaccination coverage with live oral polio vaccine (OPV), surveillance for acute flaccid paralysis, and OPV "mop-up" campaigns. An important objective involves host-directed strategies to reduce PV replication to diminish viral shedding in OPV recipients. In this study, we show that microRNA-134-5p (miR-134) can regulate Sabin-1 replication but not Sabin-2 or Sabin-3 via direct interaction with the PV 5'UTR. Hypochromicity data showed miR-134 binding to Sabin-1 and 3 but not Sabin-2 IRES. Transfection of a miR-134 mimic repressed translation of Sabin-1 5'UTR driven luciferase validating the mechanism of miR-134-mediated repression of Sabin-1. Further, site directed mutagenesis of the miR-134 binding site in Sabin-1 IRES relieved miR-134-mediated repression indicating that these regulatory molecules have an important role in regulating the host gene response to PV. Binding of miR-134 to Sabin-1 IRES caused degradation of the IRES transcript in a miR-134 and sequence specific manner. The miR-134 binding site was found to be highly conserved in wild type PV-1 as well as EV71 strains indicating that miR-134 may regulate function of these IRES sequences in circulation.
    MeSH term(s) 5' Untranslated Regions/genetics ; DNA Replication/genetics ; Humans ; Internal Ribosome Entry Sites/genetics ; MicroRNAs/genetics ; Poliomyelitis/genetics ; Poliomyelitis/prevention & control ; Poliomyelitis/virology ; Poliovirus/genetics ; Poliovirus/pathogenicity ; Poliovirus Vaccine, Oral/genetics ; Sewage/virology ; Virus Replication/genetics
    Chemical Substances 5' Untranslated Regions ; Internal Ribosome Entry Sites ; MIRN134 microRNA, human ; MicroRNAs ; Poliovirus Vaccine, Oral ; Sewage
    Language English
    Publishing date 2017-10-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-017-12860-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Innate Antiviral Cytokine Response to Swine Influenza Virus by Swine Respiratory Epithelial Cells.

    Bakre, Abhijeet A / Jones, Les P / Murray, Jackelyn / Reneer, Z Beau / Meliopoulos, Victoria A / Cherry, Sean / Schultz-Cherry, Stacey / Tripp, Ralph A

    Journal of virology

    2021  Volume 95, Issue 15, Page(s) e0069221

    Abstract: Swine influenza virus (SIV) can cause respiratory illness in swine. Swine contribute to influenza virus reassortment, as avian, human, and/or swine influenza viruses can infect swine and reassort, and new viruses can emerge. Thus, it is important to ... ...

    Abstract Swine influenza virus (SIV) can cause respiratory illness in swine. Swine contribute to influenza virus reassortment, as avian, human, and/or swine influenza viruses can infect swine and reassort, and new viruses can emerge. Thus, it is important to determine the host antiviral responses that affect SIV replication. In this study, we examined the innate antiviral cytokine response to SIV by swine respiratory epithelial cells, focusing on the expression of interferon (IFN) and interferon-stimulated genes (ISGs). Both primary and transformed swine nasal and tracheal respiratory epithelial cells were examined following infection with field isolates. The results show that IFN and ISG expression is maximal at 12 h postinfection (hpi) and is dependent on cell type and virus genotype.
    MeSH term(s) Animals ; Cell Line ; Cytokines/immunology ; Cytokines/metabolism ; Dogs ; Epithelial Cells/virology ; Host-Pathogen Interactions/immunology ; Influenza A Virus, H1N1 Subtype/growth & development ; Influenza A Virus, H1N1 Subtype/immunology ; Influenza A Virus, H1N2 Subtype/growth & development ; Influenza A Virus, H1N2 Subtype/immunology ; Influenza A Virus, H3N2 Subtype/growth & development ; Influenza A Virus, H3N2 Subtype/immunology ; Interferons/immunology ; Madin Darby Canine Kidney Cells ; Orthomyxoviridae Infections/immunology ; Respiratory Mucosa/cytology ; Respiratory Mucosa/immunology ; Swine ; Virus Replication/physiology
    Chemical Substances Cytokines ; Interferons (9008-11-1)
    Language English
    Publishing date 2021-07-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/JVI.00692-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: The Central Conserved Region (CCR) of Respiratory Syncytial Virus (RSV) G Protein Modulates Host miRNA Expression and Alters the Cellular Response to Infection.

    Bakre, Abhijeet A / Harcourt, Jennifer L / Haynes, Lia M / Anderson, Larry J / Tripp, Ralph A

    Vaccines

    2017  Volume 5, Issue 3

    Abstract: Respiratory Syncytial Virus (RSV) infects respiratory epithelial cells and deregulates host gene expression by many mechanisms including expression of RSV G protein (RSV G). RSV G protein encodes a central conserved region (CCR) containing a CX3C motif ... ...

    Abstract Respiratory Syncytial Virus (RSV) infects respiratory epithelial cells and deregulates host gene expression by many mechanisms including expression of RSV G protein (RSV G). RSV G protein encodes a central conserved region (CCR) containing a CX3C motif that functions as a fractalkine mimic. Disruption of the CX3C motif (a.a. 182-186) located in the CCR of the G protein has been shown to affect G protein function in vitro and the severity of RSV disease pathogenesis in vivo. We show that infection of polarized Calu3 respiratory cells with recombinant RSV having point mutations in Cys173 and 176 (C173/176S) (rA2-GC12), or Cys186 (C186S) (rA2-GC4) is associated with a decline in the integrity of polarized Calu-3 cultures and decreased virus production. This is accompanied with downregulation of miRNAs let-7f and miR-24 and upregulation of interferon lambda (IFNλ), a primary antiviral cytokine for RSV in rA2-GC12/rA2-GC4 infected cells. These results suggest that residues in the cysteine noose region of RSV G protein can modulate IFN λ expression accompanied by downregulation of miRNAs, and are important for RSV G protein function and targeting.
    Keywords covid19
    Language English
    Publishing date 2017-07-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines5030016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Zinc affects miR-548n, SMAD4, SMAD5 expression in HepG2 hepatocyte and HEp-2 lung cell lines.

    Grider, Arthur / Lewis, Richard D / Laing, Emma M / Bakre, Abhijeet A / Tripp, Ralph A

    Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine

    2015  Volume 28, Issue 6, Page(s) 959–966

    Abstract: MicroRNAs affect disease progression and nutrient status. miR-548n increased 57 % in Zn supplemented plasma from adolescent females (ages 9 to 13 years). The purpose of this study was to determine the effects of Zn concentration in cell culture on the ... ...

    Abstract MicroRNAs affect disease progression and nutrient status. miR-548n increased 57 % in Zn supplemented plasma from adolescent females (ages 9 to 13 years). The purpose of this study was to determine the effects of Zn concentration in cell culture on the expression of miR-548n, SMAD4 and SMAD5 in hepatocyte (HepG2) and lung epithelium (HEp-2) cell lines. Cells were incubated for 48 h in media containing 10 % Chelex 100-treated FBS (0 μM Zn), or with 15 or 50 μM Zn, before isolation of total RNA and cDNA. Expression of miR-548n, SMAD4 and SMAD5 was measured by qPCR. The ΔΔCT method was used to calculate the fold-change, and 15 µM expression levels were used as reference values. HepG2 miR-548n expression decreased 5-fold, and SMAD4 expression increased 4-fold in the absence of Zn, while HEp-2 miR-548n expression increased 10.5-fold, and SMAD5 expression increased 20-fold in the absence of Zn. HEp-2 miR-548n expression increased 23-fold, while SMAD4 expression decreased twofold, in 50 μM Zn-treated cells. However, SMAD4 and SMAD5 expression was not correlated. These data indicate that miR-548n expression is in part regulated by Zn in a cell-specific manner. SMAD4 and SMAD5 are genes in the TGF-β/BMP signaling pathway, and SMAD5 is a putative target for miR-548n; Zn participates in regulating this pathway through controlling SMAD4 and SMAD5 expression. However, SMAD5 expression may be more sensitive to Zn than to miR-548n since SMAD5 expression was not inversely correlated with miR-548n expression.
    MeSH term(s) Cell Line ; Child ; Dietary Supplements ; Epithelial Cells/cytology ; Epithelial Cells/drug effects ; Epithelial Cells/metabolism ; Female ; Gene Expression Regulation ; Hep G2 Cells ; Humans ; MicroRNAs/blood ; MicroRNAs/genetics ; Organ Specificity ; Respiratory Mucosa/cytology ; Respiratory Mucosa/drug effects ; Respiratory Mucosa/metabolism ; Signal Transduction ; Smad4 Protein/genetics ; Smad4 Protein/metabolism ; Smad5 Protein/genetics ; Smad5 Protein/metabolism ; Zinc Sulfate/blood ; Zinc Sulfate/pharmacology
    Chemical Substances MIRN548 microRNA, human ; MicroRNAs ; SMAD4 protein, human ; SMAD5 protein, human ; Smad4 Protein ; Smad5 Protein ; Zinc Sulfate (7733-02-0)
    Language English
    Publishing date 2015-12
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1112688-7
    ISSN 1572-8773 ; 0966-0844
    ISSN (online) 1572-8773
    ISSN 0966-0844
    DOI 10.1007/s10534-015-9880-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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