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  1. Article ; Online: A meta-analysis of differentially expressed circulatory micro-RNAs in chronic traumatic encephalopathy and other tauopathies: A significant role of miR-181c-5p.

    Tak, Harshita / Chattopadhyay, Arpan / Banavath, Hemanth Naick

    Irish journal of medical science

    2023  Volume 193, Issue 2, Page(s) 999–1007

    Abstract: Background: Micro-RNA (miRs) targeting kinases and phosphatases regulate the hyper-phosphorylation of tau protein, which is a characteristic feature of Chronic Traumatic Encephalopathy (CTE).: Primary objective: Identification of lead dysregulated ... ...

    Abstract Background: Micro-RNA (miRs) targeting kinases and phosphatases regulate the hyper-phosphorylation of tau protein, which is a characteristic feature of Chronic Traumatic Encephalopathy (CTE).
    Primary objective: Identification of lead dysregulated miR expressed in CTE, and other similar tauopathies.
    Methods: A search strategy was devised using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to mine into multiple indexing databases such as Web of Science, Google Scholar, and PubMed spanning from 2005 to June 2022. Seven articles were screened out of 34,221 publications based on inclusion criteria and were categorized into two groups i.e., (1) CTE and its risk factors and (2) Age-related neurodegenerative disorders.
    Results: Statistical analysis [RevMan 5.4.1] results showed that the overall risk ratio (RR) of the first group is significant (RR = 0.62, 95% CI = [0.38, 1.00], z = 1.95, p = 0.05) whereas, the second group favours the control population (RR = 1.64, 95% CI = [0.85, 3.16], z = 1.14, p = 0.14).
    Conclusion: We observed that among all other dysregulated miRs, miR-181c-5p is significantly overexpressed in Alzhimers disease (AD) and CTE. Further, we found that miR-210-3p is also upregulated notably in all groups. In sum, we conclude that these miRs can be considered as potential target and biomarker in the diagnosis and treatment of various tauopathies.
    MeSH term(s) Humans ; Chronic Traumatic Encephalopathy/genetics ; MicroRNAs/genetics ; Tauopathies/genetics ; Tauopathies/metabolism
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2023-08-04
    Publishing country Ireland
    Document type Meta-Analysis ; Journal Article
    ZDB-ID 390895-1
    ISSN 1863-4362 ; 0021-1265
    ISSN (online) 1863-4362
    ISSN 0021-1265
    DOI 10.1007/s11845-023-03469-5
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  2. Article ; Online: Caffeic acid, a dietary polyphenol, pre-sensitizes pancreatic ductal adenocarcinoma to chemotherapeutic drug.

    Gupta, Shruti / Tak, Harshita / Rathore, Khushhal / Banavath, Hemanth Naick / Tejavath, Kiran Kumar

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–15

    Abstract: Resistance to chemotherapeutics is an eminent cause that leads to search for options that help in diminution of pancreatic ductal adenocarcinoma (PDAC) by overcoming resistance issues. Caffeic acid (CFA), a polyphenol occurring in many dietary foods, is ... ...

    Abstract Resistance to chemotherapeutics is an eminent cause that leads to search for options that help in diminution of pancreatic ductal adenocarcinoma (PDAC) by overcoming resistance issues. Caffeic acid (CFA), a polyphenol occurring in many dietary foods, is known to show antidiabetic and anticancer properties potential. To unveil the effect of CFA on PDAC, we carried out this research in PDAC cells, following which we checked the combination effect of CFA and chemotherapeutics and pre-sensitization effects of CFA. Multitudinous web-based approaches were applied for identifying CFA targets in PDAC and then getting their interconnections. Subsequently, we manifested CFA effects by
    Language English
    Publishing date 2024-02-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2318481
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  3. Article ; Online: Pharmacoinformatic screening of phytoconstituent and evaluation of its anti-PDAC effect using

    Gupta, Shruti / Banavath, Hemanth Naick / Tejavath, Kiran Kumar

    Journal of biomolecular structure & dynamics

    2022  Volume 41, Issue 20, Page(s) 10627–10641

    Abstract: With no prominent treatment for pancreatic ductal adenocarcinoma (PDAC) in conventional chemotherapy, recent studies have focused on uniting conventional and traditional medicines including plant phytoconstituents. Herein, we used pharmacoinformatic ... ...

    Abstract With no prominent treatment for pancreatic ductal adenocarcinoma (PDAC) in conventional chemotherapy, recent studies have focused on uniting conventional and traditional medicines including plant phytoconstituents. Herein, we used pharmacoinformatic studies to identify potent phytoconstituent as ligand having inhibition activities against canonical anticancer targets, and evaluated its effect on PDAC cell lines. SwissTargetPrediction and SuperPred tools were utilized to segregate protein targets of ligand in humans, following which FunRich was applied to garner its targets in PDAC. STRING analysis predicted protein-protein interactions and dynamic simulation studies confirmed stability of ligand-protein complex. For
    MeSH term(s) Humans ; Deoxycytidine/pharmacology ; Cyclooxygenase 2 ; Ligands ; Cell Line, Tumor ; Carcinoma, Pancreatic Ductal/genetics ; Gemcitabine ; Pancreatic Neoplasms/drug therapy ; Pancreatic Neoplasms/genetics ; Apoptosis ; Cell Proliferation ; Pancreatic Neoplasms
    Chemical Substances Deoxycytidine (0W860991D6) ; Cyclooxygenase 2 (EC 1.14.99.1) ; Ligands ; Gemcitabine
    Language English
    Publishing date 2022-12-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2022.2155701
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach

    Singh, Swati / Banavath, Hemanth Naick / Godara, Priya / Naik, Biswajit / Srivastava, Varshita / Prusty, Dhaneswar

    3 Biotech. 2022 Sept., v. 12, no. 9

    2022  

    Abstract: Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. ... ...

    Abstract Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; allergenicity ; computer simulation ; databases ; isoelectric point ; lead ; molecular dynamics ; pathogenicity ; peptides ; peptidyl-dipeptidase A ; therapeutics ; South Africa
    Language English
    Dates of publication 2022-09
    Size p. 198.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-022-03258-4
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  5. Article: Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach.

    Singh, Swati / Banavath, Hemanth Naick / Godara, Priya / Naik, Biswajit / Srivastava, Varshita / Prusty, Dhaneswar

    3 Biotech

    2022  Volume 12, Issue 9, Page(s) 198

    Abstract: Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. ... ...

    Abstract Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation.
    Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03258-4.
    Language English
    Publishing date 2022-08-01
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-022-03258-4
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  6. Article ; Online: Structure-based virtual screening against multiple Plasmodium falciparum kinases reveals antimalarial compounds.

    Godara, Priya / Reddy, K Sony / Sahu, Welka / Naik, Biswajit / Srivastava, Varshita / Das, Rusham / Mahor, Ajay / Kumar, Prateek / Giri, Rajanish / Anirudh, Jivanage / Tak, Harshita / Banavath, Hemanth Naick / Bhatt, Tarun Kumar / Goyal, Amit Kumar / Prusty, Dhaneswar

    Molecular diversity

    2023  

    Abstract: The continuous emergence of resistance against most frontline antimalarial drugs has led to countless deaths in malaria-endemic countries, counting 619,000 deaths in 2021, with mutation in drug targets being the sole cause. As mutation is correlated ... ...

    Abstract The continuous emergence of resistance against most frontline antimalarial drugs has led to countless deaths in malaria-endemic countries, counting 619,000 deaths in 2021, with mutation in drug targets being the sole cause. As mutation is correlated frequently with fitness cost, the likelihood of mutation emergence in multiple targets at a time is extremely low. Hence, multitargeting compounds may seem promising to address drug resistance issues with additional benefits like increased efficacy, improved safety profile, and the requirement of fewer pills compared to traditional single and combinational drugs. In this study, we attempted to use the High Throughput Virtual Screening approach to predict multitarget inhibitors against six chemically validated Plasmodium falciparum (Pf) kinases (PfPKG, PfMAP2, PfCDPK4, PfTMK, PfPK5, PfPI4K), resulting in 21 multitargeting hits. The molecular dynamic simulation of the top six complexes (Myricetin-MAP2, Quercetin-CDPK4, Myricetin-TMK, Quercetin-PKG, Salidroside-PK5, and Salidroside-PI4K) showed stable interactions. Moreover, hierarchical clustering reveals the structural divergence of the compounds from the existing antimalarials, indicating less chance of cross-resistance. Additionally, the top three hits were validated through parasite growth inhibition assays, with quercetin and myricetin exhibiting an IC
    Language English
    Publishing date 2023-12-21
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-023-10770-z
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  7. Article ; Online: Novel inhibitors of Rho-kinase mediated neuroinflammatory pathways and their potential application in recovery of injured spinal cord.

    Nimgampalle, Mallikarjuna / Banavath, Hemanth Naick / Chakravarthy, Harshini / Saxena, Ambrish / Devanathan, Vasudharani

    Journal of biomolecular structure & dynamics

    2019  Volume 38, Issue 16, Page(s) 4669–4686

    Abstract: Spinal cord injury (SCI) involves damage to any part of the spinal cord which results in temporary or permanent changes in its function. Spinal cord secondary injury activates Rho-associated protein kinase 2 (ROCK2), which is involved in ... ...

    Abstract Spinal cord injury (SCI) involves damage to any part of the spinal cord which results in temporary or permanent changes in its function. Spinal cord secondary injury activates Rho-associated protein kinase 2 (ROCK2), which is involved in neuroinflammation and cell death by mediating secretion of inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1 beta (IL-1β), interleukin-2 (IL-2), and CXC chemokines. Here we evaluated potential inhibitors of ROCK2, Caspase-1, and TNF-α from
    MeSH term(s) Humans ; Molecular Docking Simulation ; Spinal Cord Injuries/drug therapy ; Tumor Necrosis Factor-alpha ; rho-Associated Kinases
    Chemical Substances Tumor Necrosis Factor-alpha ; rho-Associated Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2019-11-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2019.1686066
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  8. Article: Femtosecond laser pulse assisted photoporation for drug delivery in Chronic myelogenous leukemia cells

    Banavath, Hemanth Naick / Alok Sharan / Baskaran Rajasekaran / Srinivasa Rao Allam / Stella Sravanthi Valathati

    Journal of photochemistry and photobiology. 2018,

    2018  

    Abstract: Chronic myelogenous leukemia (CML) is a myeloproliferative disorder occurs in the pluripotent hematopoietic stem cell. Currently, first-generation tyrosine kinase inhibitor (TKI) imatinib is the mainstay for the treatment of CML. Second generation TKI's ... ...

    Abstract Chronic myelogenous leukemia (CML) is a myeloproliferative disorder occurs in the pluripotent hematopoietic stem cell. Currently, first-generation tyrosine kinase inhibitor (TKI) imatinib is the mainstay for the treatment of CML. Second generation TKI's like ponatinib, dasatinib, nilotinib, and bafetinib were treated against resistant CML. However, several CML patients develop resistance towards all existing inhibitors. Curcumin (Curcuma longa) a plant-derived natural compound is an effective bioactive component against various cancers including CML. Many studies have shown that curcumin induces time- and dose-dependent apoptosis in CML cells by regulating various downstream molecular regulators. Despite curcumin's selective cytotoxicity towards cancer cells, it has very poor bioavailability both in in-vitro and in-vivo conditions. In this present study, we have used femtosecond laser (fs-laser) pulses to ablate the cell membrane and standardized the conditions required for creating a cell membrane pores with less lethality. Following, fs-laser pulse irradiated K562 cells were incubated along with curcumin 30 μM for 0 h, 6 h,12 h and 24 h interestingly irradiated cells have shown higher sensitivity towards curcumin than non-irradiated cells. Immunoblotting studies showed higher induction levels of cleaved caspase 3 and 9 in irradiated population than non-irradiated. In summary, the results prove that irradiation by fs-laser pulses enhanced the bioavailability of curcumin and shows caspase-mediated cell death in irradiated CML cells than other populations.
    Keywords apoptosis ; bioactive compounds ; bioavailability ; caspase-3 ; cell membranes ; Curcuma longa ; curcumin ; cytotoxicity ; dose response ; drugs ; enzyme inhibitors ; hematopoietic stem cells ; immunoblotting ; irradiation ; leukemia ; mortality ; neoplasm cells ; patients ; tyrosine
    Language English
    Size p. .
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 623022-2
    ISSN 1873-2682 ; 1011-1344
    ISSN (online) 1873-2682
    ISSN 1011-1344
    DOI 10.1016/j.jphotobiol.2018.07.031
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  9. Article ; Online: Femtosecond laser pulse assisted photoporation for drug delivery in Chronic myelogenous leukemia cells.

    Banavath, Hemanth Naick / Allam, Srinivasa Rao / Valathati, Stella Sravanthi / Sharan, Alok / Rajasekaran, Baskaran

    Journal of photochemistry and photobiology. B, Biology

    2018  Volume 187, Page(s) 35–40

    Abstract: Chronic myelogenous leukemia (CML) is a myeloproliferative disorder occurs in the pluripotent hematopoietic stem cell. Currently, first-generation tyrosine kinase inhibitor (TKI) imatinib is the mainstay for the treatment of CML. Second generation TKI's ... ...

    Abstract Chronic myelogenous leukemia (CML) is a myeloproliferative disorder occurs in the pluripotent hematopoietic stem cell. Currently, first-generation tyrosine kinase inhibitor (TKI) imatinib is the mainstay for the treatment of CML. Second generation TKI's like ponatinib, dasatinib, nilotinib, and bafetinib were treated against resistant CML. However, several CML patients develop resistance towards all existing inhibitors. Curcumin (Curcuma longa) a plant-derived natural compound is an effective bioactive component against various cancers including CML. Many studies have shown that curcumin induces time- and dose-dependent apoptosis in CML cells by regulating various downstream molecular regulators. Despite curcumin's selective cytotoxicity towards cancer cells, it has very poor bioavailability both in in-vitro and in-vivo conditions. In this present study, we have used femtosecond laser (fs-laser) pulses to ablate the cell membrane and standardized the conditions required for creating a cell membrane pores with less lethality. Following fs-laser pulse irradiation, K562 cells were incubated along with curcumin 30 μM for 0 h, 6 h,12 h and 24 h. Interestingly irradiated cells have shown higher sensitivity towards curcumin than non-irradiated cells. Immunoblotting studies showed higher induction levels of cleaved caspase 3 and 9 in irradiated population than non-irradiated. In summary, the results prove that irradiation by fs-laser pulses enhanced the bioavailability of curcumin and shows caspase-mediated cell death in irradiated CML cells than other populations.
    MeSH term(s) Apoptosis/drug effects ; Apoptosis/radiation effects ; Caspase 3/metabolism ; Caspase 9/metabolism ; Cell Survival/drug effects ; Cell Survival/radiation effects ; Curcumin/chemistry ; Curcumin/metabolism ; Curcumin/pharmacology ; Drug Carriers/chemistry ; Humans ; K562 Cells ; Lasers ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/metabolism ; Protein Kinase Inhibitors/pharmacology
    Chemical Substances Drug Carriers ; Protein Kinase Inhibitors ; Caspase 3 (EC 3.4.22.-) ; Caspase 9 (EC 3.4.22.-) ; Curcumin (IT942ZTH98)
    Language English
    Publishing date 2018-07-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 623022-2
    ISSN 1873-2682 ; 1011-1344
    ISSN (online) 1873-2682
    ISSN 1011-1344
    DOI 10.1016/j.jphotobiol.2018.07.031
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  10. Article ; Online: Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study.

    Banavath, Hemanth Naick / Sharma, Om Prakash / Kumar, Muthuvel Suresh / Baskaran, R

    Scientific reports

    2014  Volume 4, Page(s) 6948

    Abstract: BCR-ABL tyrosine kinase plays a major role in the pathogenesis of chronic myeloid leukemia (CML) and is a proven target for drug development. Currently available drugs in the market are effective against CML; however, side-effects and drug-resistant ... ...

    Abstract BCR-ABL tyrosine kinase plays a major role in the pathogenesis of chronic myeloid leukemia (CML) and is a proven target for drug development. Currently available drugs in the market are effective against CML; however, side-effects and drug-resistant mutations in BCR-ABL limit their full potential. Using high throughput virtual screening approach, we have screened several small molecule databases and docked against wild-type and drug resistant T315I mutant BCR-ABL. Drugs that are currently available, such as imatinib and ponatinib, were also docked against BCR-ABL protein to set a cutoff value for our screening. Selected lead compounds were further evaluated for chemical reactivity employing density functional theory approach, all selected ligands shows HLG value > 0.09900 and the binding free energy between protein-ligand complex interactions obtained was rescored using MM-GBSA. The selected compounds showed least ΔG score -71.53 KJ/mol to maximum -126.71 KJ/mol in both wild type and drug resistant T315I mutant BCR-ABL. Following which, the stability of the docking complexes were evaluated by molecular dynamics simulation (MD) using GROMACS4.5.5. Results uncovered seven lead molecules, designated with Drug-Bank and PubChem ids as DB07107, DB06977, ST013616, DB04200, ST007180 ST019342, and DB01172, which shows docking scores higher than imatinib and ponatinib.
    MeSH term(s) Drug Discovery ; Drug Resistance, Neoplasm/genetics ; Fusion Proteins, bcr-abl/chemistry ; Fusion Proteins, bcr-abl/genetics ; Fusion Proteins, bcr-abl/metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology ; Quantitative Structure-Activity Relationship
    Chemical Substances Ligands ; Protein Kinase Inhibitors ; Fusion Proteins, bcr-abl (EC 2.7.10.2)
    Language English
    Publishing date 2014-11-10
    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/srep06948
    Database MEDical Literature Analysis and Retrieval System OnLINE

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