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  1. Article ; Online: Establishment of a high-content imaging assay for tau aggregation in hiPSC-derived neurons differentiated from two protocols to routinely evaluate compounds and genetic perturbations.

    Bahnassawy, Lamiaa / Nicolaisen, Nathalie / Untucht, Christopher / Mielich-Süss, Benjamin / Reinhardt, Lydia / Ried, Janina S / Morawe, Martina P / Geist, Daniela / Finck, Anja / Käfer, Elke / Korffmann, Jürgen / Townsend, Matthew / Ravikumar, Brinda / Lakics, Viktor / Cik, Miroslav / Reinhardt, Peter

    SLAS discovery : advancing life sciences R & D

    2023  Volume 29, Issue 2, Page(s) 100137

    Abstract: Aberrant protein aggregation is a pathological cellular hallmark of many neurodegenerative diseases, such as Alzheimer's disease (AD) and frontotemporal dementia (FTD), where the tau protein is aggregating, forming neurofibrillary tangles (NFTs), and ... ...

    Abstract Aberrant protein aggregation is a pathological cellular hallmark of many neurodegenerative diseases, such as Alzheimer's disease (AD) and frontotemporal dementia (FTD), where the tau protein is aggregating, forming neurofibrillary tangles (NFTs), and propagating from neuron to neuron. These processes have been linked to disease progression and a decline in cognitive function. Various therapeutic approaches aim at the prevention or reduction of tau aggregates in neurons. Human induced pluripotent stem cells (hiPSCs) are a very valuable tool in neuroscience discovery, as they offer access to potentially unlimited amounts of cell types that are affected in disease, including cortical neurons, for in vitro studies. We have generated an in vitro model for tau aggregation that uses hiPSC - derived neurons expressing an aggregation prone, fluorescently tagged version of the human tau protein after lentiviral transduction. Upon addition of tau seeds in the form of recombinant sonicated paired helical filaments (sPHFs), the neurons show robust, disease-like aggregation of the tau protein. The model was developed as a plate-based high content screening assay coupled with an image analysis algorithm to evaluate the impact of small molecules or genetic perturbations on tau. We show that the assay can be used to evaluate small molecules or screen targeted compound libraries. Using siRNA-based gene knockdown, genes of interest can be evaluated, and we could show that a targeted gene library can be screened, by screening nearly 100 deubiquitinating enzymes (DUBs) in that assay. The assay uses an imaging-based readout, a relatively short timeline, quantifies the extent of tau aggregation, and also allows the assessment of cell viability. Furthermore, it can be easily adapted to different hiPSC lines or neuronal subtypes. Taken together, this complex and highly relevant approach can be routinely applied on a weekly basis in the screening funnels of several projects and generates data with a turnaround time of approximately five weeks.
    MeSH term(s) Humans ; tau Proteins/genetics ; tau Proteins/metabolism ; Induced Pluripotent Stem Cells/metabolism ; Alzheimer Disease/metabolism ; Neurons/metabolism
    Chemical Substances tau Proteins
    Language English
    Publishing date 2023-12-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2885123-7
    ISSN 2472-5560 ; 2472-5552
    ISSN (online) 2472-5560
    ISSN 2472-5552
    DOI 10.1016/j.slasd.2023.12.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Arrayed CRISPR reveals genetic regulators of tau aggregation, autophagy and mitochondria in Alzheimer's disease model.

    Duan, Lishu / Hu, Mufeng / Tamm, Joseph A / Grinberg, Yelena Y / Shen, Fang / Chai, Yating / Xi, Hualin / Gibilisco, Lauren / Ravikumar, Brinda / Gautam, Vivek / Karran, Eric / Townsend, Matthew / Talanian, Robert V

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 2879

    Abstract: Alzheimer's disease (AD) is a common neurodegenerative disease with poor prognosis. New options for drug discovery targets are needed. We developed an imaging based arrayed CRISPR method to interrogate the human genome for modulation of in vitro ... ...

    Abstract Alzheimer's disease (AD) is a common neurodegenerative disease with poor prognosis. New options for drug discovery targets are needed. We developed an imaging based arrayed CRISPR method to interrogate the human genome for modulation of in vitro correlates of AD features, and used this to assess 1525 human genes related to tau aggregation, autophagy and mitochondria. This work revealed (I) a network of tau aggregation modulators including the NF-κB pathway and inflammatory signaling, (II) a correlation between mitochondrial morphology, respiratory function and transcriptomics, (III) machine learning predicted novel roles of genes and pathways in autophagic processes and (IV) individual gene function inferences and interactions among biological processes via multi-feature clustering. These studies provide a platform to interrogate underexplored aspects of AD biology and offer several specific hypotheses for future drug discovery efforts.
    MeSH term(s) Alzheimer Disease/genetics ; Alzheimer Disease/pathology ; Autophagy/genetics ; Brain/pathology ; CRISPR-Cas Systems/genetics ; Cell Line, Tumor ; Gene Expression Regulation ; Genetic Engineering ; Humans ; Machine Learning ; Mitochondria/genetics ; Mitochondria/pathology ; Models, Genetic ; Neurons ; Protein Aggregation, Pathological/genetics ; Protein Aggregation, Pathological/pathology ; Signal Transduction/genetics ; tau Proteins/metabolism
    Chemical Substances tau Proteins
    Language English
    Publishing date 2021-02-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-82658-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Arrayed CRISPR reveals genetic regulators of tau aggregation, autophagy and mitochondria in Alzheimer’s disease model

    Lishu Duan / Mufeng Hu / Joseph A. Tamm / Yelena Y. Grinberg / Fang Shen / Yating Chai / Hualin Xi / Lauren Gibilisco / Brinda Ravikumar / Vivek Gautam / Eric Karran / Matthew Townsend / Robert V. Talanian

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 17

    Abstract: Abstract Alzheimer’s disease (AD) is a common neurodegenerative disease with poor prognosis. New options for drug discovery targets are needed. We developed an imaging based arrayed CRISPR method to interrogate the human genome for modulation of in vitro ...

    Abstract Abstract Alzheimer’s disease (AD) is a common neurodegenerative disease with poor prognosis. New options for drug discovery targets are needed. We developed an imaging based arrayed CRISPR method to interrogate the human genome for modulation of in vitro correlates of AD features, and used this to assess 1525 human genes related to tau aggregation, autophagy and mitochondria. This work revealed (I) a network of tau aggregation modulators including the NF-κB pathway and inflammatory signaling, (II) a correlation between mitochondrial morphology, respiratory function and transcriptomics, (III) machine learning predicted novel roles of genes and pathways in autophagic processes and (IV) individual gene function inferences and interactions among biological processes via multi-feature clustering. These studies provide a platform to interrogate underexplored aspects of AD biology and offer several specific hypotheses for future drug discovery efforts.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Pharmacological mTOR-inhibition facilitates clearance of AD-related tau aggregates in the mouse brain.

    Morawe, Martina P / Liao, Fan / Amberg, Willi / van Bergeijk, Jeroen / Chang, Rui / Gulino, Mary / Hamilton, Caitlin / Hoft, Carolin / Lumpkin, Casey / Mastis, Bryan / McGlame, Emily / Nuber, Judith / Plaas, Christian / Ravikumar, Brinda / Roy, Kaushambi / Schanzenbächer, Marion / Tierno, Joseph / Lakics, Viktor / Dellovade, Tammy /
    Townsend, Matthew

    European journal of pharmacology

    2022  Volume 934, Page(s) 175301

    Abstract: In this study we aimed to reduce tau pathology, a hallmark of Alzheimer's Disease (AD), by activating mTOR-dependent autophagy in a transgenic mouse model of tauopathy by long-term dosing of animals with mTOR-inhibitors. Rapamycin treatment reduced the ... ...

    Abstract In this study we aimed to reduce tau pathology, a hallmark of Alzheimer's Disease (AD), by activating mTOR-dependent autophagy in a transgenic mouse model of tauopathy by long-term dosing of animals with mTOR-inhibitors. Rapamycin treatment reduced the burden of hyperphosphorylated and aggregated pathological tau in the cerebral cortex only when applied to young mice, prior to the emergence of pathology. Conversely, PQR530 which exhibits better brain exposure and superior pharmacokinetic properties, reduced tau pathology even when the treatment started after the onset of pathology. Our results show that dosing animals twice per week with PQR530 resulted in intermittent, rather than sustained target engagement. Nevertheless, this pulse-like mTOR inhibition followed by longer intervals of re-activation was sufficient to reduce tau pathology in the cerebral cortex in P301S tau transgenic mice. This suggests that balanced therapeutic dosing of blood-brain-barrier permeable mTOR-inhibitors can result in a disease-modifying effect in AD and at the same time prevents toxic side effects due to prolonged over activation of autophagy.
    MeSH term(s) Animals ; Mice ; Alzheimer Disease/drug therapy ; Alzheimer Disease/pathology ; tau Proteins/metabolism ; TOR Serine-Threonine Kinases/metabolism ; Mice, Transgenic ; Brain ; Sirolimus/pharmacology ; Disease Models, Animal
    Chemical Substances tau Proteins ; TOR Serine-Threonine Kinases (EC 2.7.11.1) ; Sirolimus (W36ZG6FT64)
    Language English
    Publishing date 2022-09-30
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 80121-5
    ISSN 1879-0712 ; 0014-2999
    ISSN (online) 1879-0712
    ISSN 0014-2999
    DOI 10.1016/j.ejphar.2022.175301
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Plasma membrane helps autophagosomes grow.

    Ravikumar, Brinda / Moreau, Kevin / Rubinsztein, David C

    Autophagy

    2010  Volume 6, Issue 8, Page(s) 1184–1186

    Abstract: The membrane origin of autophagosomes has long been a mystery and it may involve multiple sources. In this punctum, we discuss our recent finding that the plasma membrane contributes to the formation of pre-autophagic structures via clathrin-mediated ... ...

    Abstract The membrane origin of autophagosomes has long been a mystery and it may involve multiple sources. In this punctum, we discuss our recent finding that the plasma membrane contributes to the formation of pre-autophagic structures via clathrin-mediated endocytosis. Our study suggests that Atg16L1 interacts with clathrin heavy-chain/AP2 and is also localized on vesicles (positive for clathrin or cholera toxin B) close to the plasma membrane. Live-cell imaging studies revealed that the plasma membrane contributes to Atg16L1-positive structures and that this process and autophagosome formation are impaired by knockdowns of genes regulating clathrin-mediated endocytosis.
    MeSH term(s) Animals ; Autophagy ; Cell Membrane/metabolism ; Endocytosis ; Endosomes/metabolism ; Humans ; Microtubule-Associated Proteins/metabolism ; Models, Biological ; Phagosomes/metabolism
    Chemical Substances Microtubule-Associated Proteins
    Language English
    Publishing date 2010-11-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2454135-7
    ISSN 1554-8635 ; 1554-8627
    ISSN (online) 1554-8635
    ISSN 1554-8627
    DOI 10.4161/auto.6.8.13428
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Role of autophagy in the clearance of mutant huntingtin: a step towards therapy?

    Ravikumar, Brinda / Rubinsztein, David C

    Molecular aspects of medicine

    2006  Volume 27, Issue 5-6, Page(s) 520–527

    Abstract: Macroautophagy (henceforth referred to simply as autophagy) is a bulk degradation process involved in the clearance of long-lived proteins, protein complexes and organelles. A portion of the cytosol, with its contents to be degraded, is enclosed by ... ...

    Abstract Macroautophagy (henceforth referred to simply as autophagy) is a bulk degradation process involved in the clearance of long-lived proteins, protein complexes and organelles. A portion of the cytosol, with its contents to be degraded, is enclosed by double-membrane structures called autophagosomes/autophagic vacuoles, which ultimately fuse with lysosomes where their contents are degraded. In this review, we will describe how induction of autophagy is protective against toxic intracytosolic aggregate-prone proteins that cause a range of neurodegenerative diseases. Autophagy is a key clearance pathway involved in the removal of such proteins, including mutant huntingtin (that causes Huntington's disease), mutant ataxin-3 (that causes spinocerebellar ataxia type 3), forms of tau that cause tauopathies, and forms of alpha-synuclein that cause familial Parkinson's disease. Induction of autophagy enhances the clearance of both soluble and aggregated forms of such proteins, and protects against toxicity of a range of these mutations in cell and animal models. Interestingly, the aggregates formed by mutant huntingtin sequester and inactivate the mammalian target of rapamycin (mTOR), a key negative regulator of autophagy. This results in induction of autophagy in cells with these aggregates.
    MeSH term(s) Animals ; Autophagy ; Humans ; Huntington Disease/genetics ; Huntington Disease/metabolism ; Huntington Disease/therapy ; Mutation/genetics ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism
    Chemical Substances Nerve Tissue Proteins ; Nuclear Proteins
    Language English
    Publishing date 2006-09-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 197640-0
    ISSN 1872-9452 ; 0098-2997
    ISSN (online) 1872-9452
    ISSN 0098-2997
    DOI 10.1016/j.mam.2006.08.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Dual role of select plant based nutraceuticals as antimicrobial agents to mitigate food borne pathogens and as food preservatives

    Subramaniam, Shankar / Muralidharan, Sai brinda / Rajendran, Narendran / Raju, Ravikumar / Sivasubramanian, Aravind / Subramaniam, Gayathri

    RSC advances. 2015 Sept. 11, v. 5, no. 94

    2015  

    Abstract: The present work presents the unique dual role of commercially important nutraceuticals from plants that potentiate the therapeutic effect of commercial antibiotics to combat food pathogens. They also effectively enhance the food preservative value of ... ...

    Abstract The present work presents the unique dual role of commercially important nutraceuticals from plants that potentiate the therapeutic effect of commercial antibiotics to combat food pathogens. They also effectively enhance the food preservative value of nisin by doubling the shelf life of fruit juices.
    Keywords dietary supplements ; food pathogens ; food preservatives ; fruit juices ; nisin ; shelf life ; therapeutics
    Language English
    Dates of publication 2015-0911
    Size p. 77168-77174.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ISSN 2046-2069
    DOI 10.1039/c5ra15039f
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Arf6 promotes autophagosome formation via effects on phosphatidylinositol 4,5-bisphosphate and phospholipase D.

    Moreau, Kevin / Ravikumar, Brinda / Puri, Claudia / Rubinsztein, David C

    The Journal of cell biology

    2012  Volume 196, Issue 4, Page(s) 483–496

    Abstract: Macroautophagy (in this paper referred to as autophagy) and the ubiquitin-proteasome system are the two major catabolic systems in cells. Autophagy involves sequestration of cytosolic contents in double membrane-bounded vesicles called autophagosomes. ... ...

    Abstract Macroautophagy (in this paper referred to as autophagy) and the ubiquitin-proteasome system are the two major catabolic systems in cells. Autophagy involves sequestration of cytosolic contents in double membrane-bounded vesicles called autophagosomes. The membrane source for autophagosomes has received much attention, and diverse sources, such as the plasma membrane, Golgi, endoplasmic reticulum, and mitochondria, have been implicated. These may not be mutually exclusive, but the exact sources and mechanism involved in the formation of autophagosomes are still unclear. In this paper, we identify a positive role for the small G protein Arf6 in autophagosome formation. The effect of Arf6 on autophagy is mediated by its role in the generation of phosphatidylinositol 4,5-bisphosphate (PIP(2)) and in inducing phospholipase D (PLD) activity. PIP(2) and PLD may themselves promote autophagosome biogenesis by influencing endocytic uptake of plasma membrane into autophagosome precursors. However, Arf6 may also influence autophagy by indirect effects, such as either by regulating membrane flow from other compartments or by modulating PLD activity independently of the mammalian target of rapamycin.
    MeSH term(s) ADP-Ribosylation Factors/genetics ; ADP-Ribosylation Factors/metabolism ; Animals ; Autophagy ; Autophagy-Related Proteins ; Blotting, Western ; CHO Cells ; Carrier Proteins/metabolism ; Cell Membrane/drug effects ; Cell Membrane/metabolism ; Cricetinae ; Endocytosis/drug effects ; Endocytosis/physiology ; Endoplasmic Reticulum/drug effects ; Endoplasmic Reticulum/metabolism ; Fluorescent Antibody Technique ; GTPase-Activating Proteins/metabolism ; Golgi Apparatus/drug effects ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins/metabolism ; HeLa Cells ; Humans ; Immunosuppressive Agents/pharmacology ; Phagosomes/drug effects ; Phagosomes/physiology ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Phospholipase D/metabolism ; Sirolimus/pharmacology ; TOR Serine-Threonine Kinases/metabolism
    Chemical Substances ARHGAP26 protein, human ; ATG16L1 protein, human ; Autophagy-Related Proteins ; Carrier Proteins ; GTPase-Activating Proteins ; Immunosuppressive Agents ; Phosphatidylinositol 4,5-Diphosphate ; Green Fluorescent Proteins (147336-22-9) ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; Phospholipase D (EC 3.1.4.4) ; ADP-Ribosylation Factors (EC 3.6.5.2) ; ADP-ribosylation factor 6 (EC 3.6.5.2) ; Sirolimus (W36ZG6FT64)
    Language English
    Publishing date 2012-02-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.201110114
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Can autophagy protect against neurodegeneration caused by aggregate-prone proteins?

    Ravikumar, Brinda / Rubinsztein, David C

    Neuroreport

    2004  Volume 15, Issue 16, Page(s) 2443–2445

    Abstract: Protein conformation disorders or proteinopathies are a growing family of human diseases that are characterized by the accumulation of proteins in intracellular aggregates (also known as inclusions) in specific tissues/organs. The role of aggregates in ... ...

    Abstract Protein conformation disorders or proteinopathies are a growing family of human diseases that are characterized by the accumulation of proteins in intracellular aggregates (also known as inclusions) in specific tissues/organs. The role of aggregates in these diseases has been a subject of vigorous debate. However, irrespective of the nature(s) of the toxic species, it is desirable for cells to be able to control the levels of these toxic proteins and restrict their accumulation. Here we discuss how the autophagy-lysosome pathway may regulate protein clearance in some of the protein conformation disorders and why this pathway may represent a possible therapeutic target in such conditions.
    MeSH term(s) Animals ; Autophagy/physiology ; Humans ; Lysosomes/physiology ; Neurodegenerative Diseases/chemically induced ; Neurodegenerative Diseases/prevention & control ; Protein Conformation ; Protein Folding ; Proteins/toxicity
    Chemical Substances Proteins
    Language English
    Publishing date 2004-10-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1049746-8
    ISSN 1473-558X ; 0959-4965
    ISSN (online) 1473-558X
    ISSN 0959-4965
    DOI 10.1097/00001756-200411150-00001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Differential efficacy of the TSPO ligands etifoxine and XBD-173 in two rodent models of Multiple Sclerosis.

    Ravikumar, Brinda / Crawford, Dan / Dellovade, Tammy / Savinainen, Anneli / Graham, Danielle / Liere, Philippe / Oudinet, Jean-Paul / Webb, Mike / Hering, Heike

    Neuropharmacology

    2016  Volume 108, Page(s) 229–237

    Abstract: Neurosteroids such as progesterone and allopregnanolone have been shown to exert neuroprotective effects under a variety of pathological or insult conditions, and there is evidence that the neurosteroid system is perturbed in Multiple Sclerosis (MS) ... ...

    Abstract Neurosteroids such as progesterone and allopregnanolone have been shown to exert neuroprotective effects under a variety of pathological or insult conditions, and there is evidence that the neurosteroid system is perturbed in Multiple Sclerosis (MS) patients. Neurosteroids are synthesized in the central nervous system (CNS) through a series of metabolic transformations, beginning with a rate-limiting step of cholesterol transport through the outer mitochondrial membrane via the transporter translocator protein (TSPO). We examined the effects of etifoxine and XBD-173, two different brain penetrant TSPO agonists, for their ability to ameliorate clinical signs in two different experimental autoimmune encephalitis (EAE) models. Etifoxine, as previously reported, was efficacious in EAE, while XBD-173 was not. Surprisingly, XBD-173, but not etifoxine elevated relevant neurosteroids in brain of female rats and differed in its ability to exert anti-inflammatory and direct neuroprotective effects in vitro as compared to etifoxine. We conclude that the neurosteroid elevations produced in brain by XBD-173 are not sufficient to ameliorate EAE and suggest that etifoxine may have additional mechanisms of action that provide therapeutic benefit in this model system.
    MeSH term(s) Animals ; Cell Line, Tumor ; Cells, Cultured ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Encephalomyelitis, Autoimmune, Experimental/drug therapy ; Encephalomyelitis, Autoimmune, Experimental/metabolism ; Female ; Ligands ; Mice ; Mice, Inbred C57BL ; Multiple Sclerosis/drug therapy ; Multiple Sclerosis/metabolism ; Oxazines/metabolism ; Oxazines/therapeutic use ; Purines/metabolism ; Purines/therapeutic use ; Rats ; Receptors, GABA/metabolism ; Treatment Outcome
    Chemical Substances Bzrp protein, mouse ; Ligands ; N-benzyl-N-ethyl-2-(7,8-dihydro-7-methyl-8-oxo-2-phenyl-9H-purin-9-yl)acetamide ; Oxazines ; Purines ; Receptors, GABA ; etifoxine (X24X82MX4X)
    Language English
    Publishing date 2016-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 218272-5
    ISSN 1873-7064 ; 0028-3908
    ISSN (online) 1873-7064
    ISSN 0028-3908
    DOI 10.1016/j.neuropharm.2016.03.053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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