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  1. Article ; Online: The Transplant Bellwether: Endothelial Cells in Antibody-Mediated Rejection.

    Franco-Acevedo, Adriana / Pathoulas, Christopher L / Murphy, Patrick A / Valenzuela, Nicole M

    Journal of immunology (Baltimore, Md. : 1950)

    2023  Volume 211, Issue 9, Page(s) 1276–1285

    Abstract: Ab-mediated rejection of organ transplants remains a stubborn, frequent problem affecting patient quality of life, graft function, and grant survival, and for which few efficacious therapies currently exist. Although the field has gained considerable ... ...

    Abstract Ab-mediated rejection of organ transplants remains a stubborn, frequent problem affecting patient quality of life, graft function, and grant survival, and for which few efficacious therapies currently exist. Although the field has gained considerable knowledge over the last two decades on how anti-HLA Abs cause acute tissue injury and promote inflammation, there has been a gap in linking these effects with the chronic inflammation, vascular remodeling, and persistent alloimmunity that leads to deterioration of graft function over the long term. This review will discuss new data emerging over the last 5 y that provide clues into how ongoing Ab-endothelial cell interactions may shape vascular fate and propagate alloimmunity in organ transplants.
    MeSH term(s) Humans ; Endothelial Cells ; Quality of Life ; Graft Rejection ; Antibodies ; Inflammation ; HLA Antigens
    Chemical Substances Antibodies ; HLA Antigens
    Language English
    Publishing date 2023-10-16
    Publishing country United States
    Document type Review ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 3056-9
    ISSN 1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
    ISSN (online) 1550-6606
    ISSN 0022-1767 ; 1048-3233 ; 1047-7381
    DOI 10.4049/jimmunol.2300363
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Activated T-effector seeds: cultivating atherosclerotic plaque through alternative activation.

    Xu, Maria M / Murphy, Patrick A / Vella, Anthony T

    American journal of physiology. Heart and circulatory physiology

    2019  Volume 316, Issue 6, Page(s) H1354–H1365

    Abstract: Atherosclerosis is a chronic inflammatory pathology that precipitates substantial morbidity and mortality. Although initiated by physiological patterns of low and disturbed flow that differentially prime endothelial cells at sites of vessel branch points ...

    Abstract Atherosclerosis is a chronic inflammatory pathology that precipitates substantial morbidity and mortality. Although initiated by physiological patterns of low and disturbed flow that differentially prime endothelial cells at sites of vessel branch points and curvature, the chronic, smoldering inflammation of atherosclerosis is accelerated by comorbidities involving inappropriate activation of the adaptive immune system, such as autoimmunity. The innate contributions to atherosclerosis, especially in the transition of monocyte to lipid-laden macrophage, are well established, but the mechanisms underpinning the infiltration, persistence, and effector dynamics of CD8 T cells in particular are not well understood. Adaptive immunity is centered on a classical cascade of antigen recognition and activation, costimulation, and effector cytokine secretion upon recall of antigen. However, chronic inflammation can generate alternative cues that supplant this behavior pattern and promote the retention and activation of peripherally activated T cells. Furthermore, the atherogenic foci that activated immune cell infiltrate are unique lipid-laden environments that offer a diverse array of stimuli, including those of survival, antigen hyporesponsiveness, and inflammatory cytokine expression. This review will focus on how known cardiovascular comorbidities may be influencing CD8 T-cell activation and how, once infiltrated within atherogenic foci, these T cells face a multitude of cues that skew the classical cascade of T-cell behavior, highlighting alternative modes of activation that may help contextualize associations of autoimmunity, viral infection, and immunotherapy with cardiovascular morbidity.
    MeSH term(s) Adaptive Immunity ; Animals ; Arteries/immunology ; Arteries/metabolism ; Arteries/pathology ; Atherosclerosis/immunology ; Atherosclerosis/metabolism ; Atherosclerosis/pathology ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/metabolism ; Cellular Microenvironment ; Humans ; Inflammation/immunology ; Inflammation/metabolism ; Inflammation/pathology ; Lymphocyte Activation ; Plaque, Atherosclerotic ; Signal Transduction
    Language English
    Publishing date 2019-03-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 603838-4
    ISSN 1522-1539 ; 0363-6135
    ISSN (online) 1522-1539
    ISSN 0363-6135
    DOI 10.1152/ajpheart.00148.2019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Loss of Endothelial TDP-43 Leads to Blood Brain Barrier Defects in Mouse Models of Amyotrophic Lateral Sclerosis and Frontotemporal Dementia.

    Cheemala, Ashok / Kimble, Amy L / Tyburski, Jordan D / Leclair, Nathan K / Zuberi, Aamir R / Murphy, Melissa / Jellison, Evan R / Reese, Bo / Hu, Xiangyou / Lutz, Cathleen M / Yan, Riqiang / Murphy, Patrick A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Loss of nuclear TDP-43 occurs in a wide range of neurodegenerative diseases, and specific mutations in ... ...

    Abstract Loss of nuclear TDP-43 occurs in a wide range of neurodegenerative diseases, and specific mutations in the
    Language English
    Publishing date 2023-12-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.13.571184
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Targeted inCITE-Seq Analysis Identifies the Loss of Nuclear TDP-43 in Endothelium as a Mediator of Blood Brain Barrier Signaling Pathway Dysfunction in Neurodegeneration.

    Omar, Omar M F / Kimble, Amy L / Cheemala, Ashok / Tyburski, Jordan D / Pandey, Swati / Wu, Qian / Reese, Bo / Jellison, Evan R / Li, Yunfeng / Hao, Bing / Yan, Riqiang / Murphy, Patrick A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Despite the importance of the endothelium in the regulation of the blood brain barrier (BBB) in aging and neurodegenerative disease, difficulties in extracting endothelial cell (EC) nuclei have limited analysis of these cells. In addition, nearly all ... ...

    Abstract Despite the importance of the endothelium in the regulation of the blood brain barrier (BBB) in aging and neurodegenerative disease, difficulties in extracting endothelial cell (EC) nuclei have limited analysis of these cells. In addition, nearly all Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Degeneration (FTD), and a large portion of Alzheimer's Disease (AD) exhibit neuronal TDP-43 aggregation, leading to loss of nuclear function, but whether TDP-43 is similarly altered in human BBB ECs is unknown. Here we utilize a novel technique for the enrichment of endothelial and microglial nuclei from human cortical brain tissues, combined with inCITE-seq, to analyze nuclear proteins and RNA transcripts in a large cohort of healthy and diseased donors. Our findings reveal a unique transcriptional signature in nearly half of the capillary endothelial cells across neurodegenerative states, characterized by reduced levels of nuclear β-Catenin and canonical downstream genes, and an increase in TNF/NF-kB target genes. We demonstrate that this does not correlate with increased nuclear p65/NF-kB, but rather a specific loss of nuclear TDP-43 in these disease associated ECs. Comparative analysis in animal models with targeted disruption of TDP-43 shows that this is sufficient to drive these transcriptional alterations. This work reveals that TDP-43 is a critical governor of the transcriptional output from nuclear p65/NF-kB, which has paradoxical roles in barrier maintenance and also barrier compromising inflammatory responses, and suggests that disease specific loss in ECs contributes to BBB defects observed in the progression of AD, ALS and FTD.
    Language English
    Publishing date 2023-12-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.13.571178
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Alternative splicing of endothelial fibronectin is induced by disturbed hemodynamics and protects against hemorrhage of the vessel wall.

    Murphy, Patrick A / Hynes, Richard O

    Arteriosclerosis, thrombosis, and vascular biology

    2014  Volume 34, Issue 9, Page(s) 2042–2050

    Abstract: Objective: Abnormally low-flow conditions, sensed by the arterial endothelium, promote aneurysm rupture. Fibronectin (FN) is among the most abundant extracellular matrix proteins and is strongly upregulated in human aneurysms, suggesting a possible role ...

    Abstract Objective: Abnormally low-flow conditions, sensed by the arterial endothelium, promote aneurysm rupture. Fibronectin (FN) is among the most abundant extracellular matrix proteins and is strongly upregulated in human aneurysms, suggesting a possible role in disease progression. Altered FN splicing can result in the inclusion of EIIIA and EIIIB exons, generally not expressed in adult tissues. We sought to explore the regulation of FN and its splicing and their possible roles in the vascular response to disturbed flow.
    Approach and results: We induced low and reversing flow in mice by partial carotid ligation and assayed FN splicing in an endothelium-enriched intimal preparation. Inclusion of EIIIA and EIIIB was increased as early as 48 hours, with negligible increases in total FN expression. To test the function of EIIIA and EIIIB inclusion, we induced disturbed flow in EIIIAB(-/-) mice unable to include these exons and found that they developed focal lesions with hemorrhage and hypertrophy of the vessel wall. Acute deletion of floxed FN caused similar defects in response to disturbed flow, consistent with a requirement for the upregulation of the spliced isoforms, rather than a developmental defect. Recruited macrophages promote FN splicing because their depletion by clodronate liposomes blocked the increase in endothelial EIIIA and EIIIB inclusion in the carotid model.
    Conclusions: These results uncover a protective mechanism in the inflamed intima that develops under disturbed flow, by showing that splicing of FN mRNA in the endothelium, induced by macrophages, inhibits hemorrhage of the vessel wall.
    MeSH term(s) Adventitia/metabolism ; Alternative Splicing ; Animals ; Carotid Stenosis/genetics ; Carotid Stenosis/pathology ; Disease Models, Animal ; Disease Progression ; Endothelium, Vascular/metabolism ; Endothelium, Vascular/pathology ; Exons ; Extracellular Matrix/pathology ; Fibronectins/biosynthesis ; Fibronectins/deficiency ; Fibronectins/genetics ; Gene Deletion ; Hemorheology ; Hemorrhage/etiology ; Hemorrhage/physiopathology ; Hemorrhage/prevention & control ; Hypertrophy ; Ligation ; Macrophages/physiology ; Mice ; Mice, Inbred C57BL ; Tunica Intima/injuries ; Tunica Intima/metabolism ; Tunica Intima/pathology ; Tunica Media/metabolism
    Chemical Substances Fibronectins ; extra domain A fibronectin, mouse
    Language English
    Publishing date 2014-06-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 1221433-4
    ISSN 1524-4636 ; 1079-5642
    ISSN (online) 1524-4636
    ISSN 1079-5642
    DOI 10.1161/ATVBAHA.114.303879
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Identification of splice regulators of fibronectin-EIIIA and EIIIB by direct measurement of exon usage in a flow-cytometry based CRISPR screen.

    Hensel, Jessica A / Heineman, Brent D / Kimble, Amy L / Jellison, Evan R / Reese, Bo / Murphy, Patrick A

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 19835

    Abstract: The extracellular matrix protein fibronectin (FN) is alternatively spliced in a variety of inflammatory conditions, resulting in increased inclusion of alternative exons EIIIA and EIIIB. Inclusion of these exons affects fibril formation, fibrosis, and ... ...

    Abstract The extracellular matrix protein fibronectin (FN) is alternatively spliced in a variety of inflammatory conditions, resulting in increased inclusion of alternative exons EIIIA and EIIIB. Inclusion of these exons affects fibril formation, fibrosis, and inflammation. To define upstream regulators of alternative splicing in FN, we have developed an in vitro flow-cytometry based assay, using RNA-binding probes to determine alternative exon inclusion level in aortic endothelial cells. This approach allows us to detect exon inclusion in the primary transcripts themselves, rather than in surrogate splicing reporters. We validated this assay in cells with and without FN-EIIIA and -EIIIB expression. In a small-scale CRISPR KO screen of candidate regulatory splice factors, we successfully detected known regulators of EIIIA and EIIIB splicing, and detected several novel regulators. Finally, we show the potential in this approach to broadly interrogate upstream signaling pathways in aortic endothelial cells with a genome-wide CRISPR-KO screen, implicating the TNFalpha and RIG-I-like signaling pathways and genes involved in the regulation of fibrotic responses. Thus, we provide a novel means to screen the regulation of splicing of endogenous transcripts, and predict novel pathways in the regulation of FN-EIIIA inclusion.
    MeSH term(s) Alternative Splicing ; Animals ; Carrier Proteins ; Clustered Regularly Interspaced Short Palindromic Repeats ; Endothelial Cells/metabolism ; Exons ; Extracellular Matrix/metabolism ; Fibronectins/chemistry ; Fibronectins/metabolism ; Flow Cytometry ; Gene Expression Regulation ; Gene Knockout Techniques ; Genes, Reporter ; Mice ; Protein Binding ; Protein Interaction Domains and Motifs ; RNA, Messenger/genetics
    Chemical Substances Carrier Proteins ; Fibronectins ; RNA, Messenger
    Language English
    Publishing date 2021-10-06
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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/s41598-021-99079-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Quantification of

    Zhang, Jiangguo / Comstock, Jessica A / Cotter, Christopher R / Murphy, Patrick A / Nie, Weili / Welch, Roy D / Patel, Ankit B / Igoshin, Oleg A

    Microorganisms

    2021  Volume 9, Issue 9

    Abstract: Myxococcus ... ...

    Abstract Myxococcus xanthus
    Language English
    Publishing date 2021-09-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9091954
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images

    Zhang, Jiangguo / Comstock, Jessica A. / Cotter, Christopher R. / Murphy, Patrick A. / Nie, Weili / Welch, Roy D. / Patel, Ankit B. / Igoshin, Oleg A.

    Microorganisms. 2021 Sept. 14, v. 9, no. 9

    2021  

    Abstract: Myxococcus xanthus bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling ...

    Abstract Myxococcus xanthus bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling cell-density waves termed ripples. Both phase-contrast and fluorescence microscopy are used to observe these patterns but each has its limitations. Phase-contrast images have higher contrast, but the resulting image intensities lose their correlation with cell density. The intensities of fluorescence microscopy images, on the other hand, are well-correlated with cell density, enabling better segmentation of aggregates and better visualization of streaming patterns in between aggregates; however, fluorescence microscopy requires the engineering of cells to express fluorescent proteins and can be phototoxic to cells. To combine the advantages of both imaging methodologies, we develop a generative adversarial network that converts phase-contrast into synthesized fluorescent images. By including an additional histogram-equalized output to the state-of-the-art pix2pixHD algorithm, our model generates accurate images of aggregates and streams, enabling the estimation of aggregate positions and sizes, but with small shifts of their boundaries. Further training on ripple patterns enables accurate estimation of the rippling wavelength. Our methods are thus applicable for many other phenotypic behaviors and pattern formation studies.
    Keywords Myxococcus xanthus ; algorithms ; fluorescence ; fluorescence microscopy ; models ; phenotype ; phototoxicity ; predation ; wavelengths
    Language English
    Dates of publication 2021-0914
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9091954
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Tumor angiogenesis in the absence of fibronectin or its cognate integrin receptors.

    Murphy, Patrick A / Begum, Shahinoor / Hynes, Richard O

    PloS one

    2015  Volume 10, Issue 3, Page(s) e0120872

    Abstract: Binding of α5β1 and αvβ3/β5 integrin receptors on the endothelium to their fibronectin substrate in the extracellular matrix has been targeted as a possible means of blocking tumor angiogenesis and tumor growth. However, clinical trials of blocking ... ...

    Abstract Binding of α5β1 and αvβ3/β5 integrin receptors on the endothelium to their fibronectin substrate in the extracellular matrix has been targeted as a possible means of blocking tumor angiogenesis and tumor growth. However, clinical trials of blocking antibodies and peptides have been disappointing despite promising preclinical results, leading to questions about the mechanism of the inhibitors and the reasons for their failure. Here, using tissue-specific and inducible genetics to delete the α5 and αv receptors in the endothelium or their fibronectin substrate, either in the endothelium or globally, we show that both are dispensable for tumor growth, in transplanted tumors as well as spontaneous and angiogenesis-dependent RIP-Tag-driven pancreatic adenocarcinomas. In the nearly complete absence of fibronectin, no differences in vascular density or the deposition of basement membrane laminins, ColIV, Nid1, Nid2, or the TGFβ binding matrix proteins, fibrillin-1 and -2, could be observed. Our results reveal that fibronectin and the endothelial fibronectin receptor subunits, α5 and αv, are dispensable for tumor angiogenesis, suggesting that the inhibition of angiogenesis induced by antibodies or small molecules may occur through a dominant negative effect, rather than a simple functional block.
    MeSH term(s) Adenocarcinoma/metabolism ; Animals ; Basement Membrane/metabolism ; Calcium-Binding Proteins ; Cell Adhesion Molecules ; Endothelium/metabolism ; Extracellular Matrix/metabolism ; Fibrillin-1 ; Fibrillins ; Fibronectins/metabolism ; Integrin alpha5beta1/metabolism ; Integrins/metabolism ; Membrane Glycoproteins/metabolism ; Mice ; Microfilament Proteins/metabolism ; Neovascularization, Pathologic/metabolism ; Pancreatic Neoplasms/metabolism ; Transforming Growth Factor beta/metabolism
    Chemical Substances Calcium-Binding Proteins ; Cell Adhesion Molecules ; Fbn1 protein, mouse ; Fibrillin-1 ; Fibrillins ; Fibronectins ; Integrin alpha5beta1 ; Integrins ; Membrane Glycoproteins ; Microfilament Proteins ; Nid2 protein, mouse ; Transforming Growth Factor beta ; nidogen
    Language English
    Publishing date 2015-03-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0120872
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Splice factor polypyrimidine tract-binding protein 1 (Ptbp1) primes endothelial inflammation in atherogenic disturbed flow conditions.

    Hensel, Jessica A / Nicholas, Sarah-Anne E / Kimble, Amy L / Nagpal, Arjun S / Omar, Omar M F / Tyburski, Jordan D / Jellison, Evan R / Ménoret, Antoine / Ozawa, Manabu / Rodriguez-Oquendo, Annabelle / Vella, Anthony T / Murphy, Patrick A

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 30, Page(s) e2122227119

    Abstract: NF-κB-mediated endothelial activation drives leukocyte recruitment and atherosclerosis, in part through adhesion molecules Icam1 and Vcam1. The endothelium is primed for cytokine activation of NF-κB by exposure to low and disturbed blood flow (LDF)but ... ...

    Abstract NF-κB-mediated endothelial activation drives leukocyte recruitment and atherosclerosis, in part through adhesion molecules Icam1 and Vcam1. The endothelium is primed for cytokine activation of NF-κB by exposure to low and disturbed blood flow (LDF)but the molecular underpinnings are not fully understood. In an experimental in vivo model of LDF, platelets were required for the increased expression of several RNA-binding splice factors, including polypyrimidine tract binding protein (Ptbp1). This was coordinated with changes in RNA splicing in the NF-κB pathway in primed cells, leading us to examine splice factors as mediators of priming. Using Icam1 and Vcam1 induction by tumor necrosis factor (TNF)-α stimulation as a readout, we performed a CRISPR Cas9 knockout screen and identified a requirement for Ptbp1 in priming. Deletion of Ptbp1 had no effect on cell growth or response to apoptotic stimuli, but reversed LDF splicing patterns and inhibited NF-κB nuclear translocation and transcriptional activation of downstream targets, including Icam1 and Vcam1. In human coronary arteries, elevated PTBP1 correlates with expression of TNF pathway genes and plaque. In vivo, endothelial-specific deletion of Ptbp1 reduced Icam1 expression and myeloid cell infiltration at regions of LDF in atherosclerotic mice, limiting atherosclerosis. This may be mediated, in part, by allowing inclusion of a conserved alternative exon in Ripk1 leading to a reduction in Ripk1 protein. Our data show that Ptbp1, which is induced in a subset of the endothelium by platelet recruitment at regions of LDF, is required for priming of the endothelium for subsequent NF-κB activation, myeloid cell recruitment and atherosclerosis.
    MeSH term(s) Alternative Splicing ; Animals ; Atherosclerosis/genetics ; Atherosclerosis/metabolism ; Endothelium/metabolism ; Heterogeneous-Nuclear Ribonucleoproteins/genetics ; Humans ; Inflammation/genetics ; Inflammation/metabolism ; Mice ; NF-kappa B/genetics ; NF-kappa B/metabolism ; Polypyrimidine Tract-Binding Protein/genetics ; Polypyrimidine Tract-Binding Protein/metabolism
    Chemical Substances Heterogeneous-Nuclear Ribonucleoproteins ; NF-kappa B ; PTBP1 protein, human ; Ptbp1 protein, mouse ; Polypyrimidine Tract-Binding Protein (139076-35-0)
    Language English
    Publishing date 2022-07-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2122227119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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