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  1. Article: FET fusion oncoproteins disrupt physiologic DNA repair networks in cancer.

    Menon, Shruti / Breese, Marcus R / Lin, Yone Phar / Allegakoen, Hannah / Perati, Shruthi / Heslin, Ann / Horlbeck, Max A / Weissman, Jonathan / Sweet-Cordero, E Alejandro / Bivona, Trever G / Tulpule, Asmin

    bioRxiv : the preprint server for biology

    2023  

    Abstract: ... downstream effectors (e.g., ATM or p53 tumor suppressor mutations). Whether and how oncogenes can help "self ...

    Abstract While oncogenes promote cancer cell growth, unrestrained proliferation represents a significant stressor to cellular homeostasis networks such as the DNA damage response (DDR). To enable oncogene tolerance, many cancers disable tumor suppressive DDR signaling through genetic loss of DDR pathways and downstream effectors (e.g., ATM or p53 tumor suppressor mutations). Whether and how oncogenes can help "self-tolerize" by creating analogous functional deficiencies in physiologic DDR networks is not known. Here we focus on Ewing sarcoma, a FET fusion oncoprotein (EWS-FLI1) driven pediatric bone tumor, as a model for the class of FET rearranged cancers. Native FET protein family members are among the earliest factors recruited to DNA double-strand breaks (DSBs) during the DDR, though the function of both native FET proteins and FET fusion oncoproteins in DNA repair remains to be defined. Using preclinical mechanistic studies of the DDR and clinical genomic datasets from patient tumors, we discover that the EWS-FLI1 fusion oncoprotein is recruited to DNA DSBs and interferes with native FET (EWS) protein function in activating the DNA damage sensor ATM. As a consequence of FET fusion-mediated interference with the DDR, we establish functional ATM deficiency as the principal DNA repair defect in Ewing sarcoma and the compensatory ATR signaling axis as a collateral dependency and therapeutic target in multiple FET rearranged cancers. More generally, we find that aberrant recruitment of a fusion oncoprotein to sites of DNA damage can disrupt physiologic DSB repair, revealing a mechanism for how growth-promoting oncogenes can also create a functional deficiency within tumor suppressive DDR networks.
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.30.538578
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: FET fusion oncoproteins disrupt physiologic DNA repair networks and induce ATR synthetic lethality in cancer.

    Menon, Shruti / Breese, Marcus R / Lin, Yone Phar / Allegakoen, Hannah / Perati, Shruthi / Heslin, Ann / Horlbeck, Max A / Weissman, Jonathan / Sweet-Cordero, E Alejandro / Bivona, Trever G / Tulpule, Asmin

    Research square

    2023  

    Abstract: The genetic principle of synthetic lethality is clinically validated in cancers with loss of specific DNA damage response (DDR) pathway genes (i.e. BRCA1/2 tumor suppressor mutations). The broader question of whether and how oncogenes create tumor- ... ...

    Abstract The genetic principle of synthetic lethality is clinically validated in cancers with loss of specific DNA damage response (DDR) pathway genes (i.e. BRCA1/2 tumor suppressor mutations). The broader question of whether and how oncogenes create tumor-specific vulnerabilities within DDR networks remains unanswered. Native FET protein family members are among the earliest proteins recruited to DNA double-strand breaks (DSBs) during the DDR, though the function of both native FET proteins and FET fusion oncoproteins in DSB repair remains poorly defined. Here we focus on Ewing sarcoma (ES), an EWS-FLI1 fusion oncoprotein-driven pediatric bone tumor, as a model for FET rearranged cancers. We discover that the EWS-FLI1 fusion oncoprotein is recruited to DNA DSBs and interferes with native EWS function in activating the DNA damage sensor ATM. Using preclinical mechanistic approaches and clinical datasets, we establish functional ATM deficiency as a principal DNA repair defect in ES and the compensatory ATR signaling axis as a collateral dependency and therapeutic target in FET rearranged cancers. Thus, aberrant recruitment of a fusion oncoprotein to sites of DNA damage can disrupt normal DSB repair, revealing a mechanism for how oncogenes can create cancer-specific synthetic lethality within DDR networks.
    Language English
    Publishing date 2023-05-29
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2869150/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The Use of Perinatal 6-Hydroxydopamine to Produce a Rodent Model of Lesch-Nyhan Disease.

    Knapp, Darin J / Breese, George R

    Current topics in behavioral neurosciences

    2016  Volume 29, Page(s) 265–277

    Abstract: ... novel animal models (e.g., the HPRT-deficient mouse and the serendipitously discovered perinatal 6 ...

    Abstract Lesch-Nyhan disease is a neurologically, metabolically, and behaviorally devastating condition that has eluded complete characterization and adequate treatment. While it is known that the disease is intimately associated with dysfunction of the hypoxanthine phosphoribosyltransferase 1 (HPRT1) gene that codes for an enzyme of purine metabolism (hypoxanthine-guanine phosphoribosyltransferase) and is associated with neurological, behavioral, as well as metabolic dysfunction, the mechanisms of the neurobehavioral manifestations are as yet unclear. However, discoveries over the past few decades not only have created useful novel animal models (e.g., the HPRT-deficient mouse and the serendipitously discovered perinatal 6-hydroxydopamine (6-OHDA lesion model), but also have expanded into epigenetic, genomic, and proteomic approaches to better understand the mechanisms underlying this disease. The perinatal 6-OHDA model, in addition to modeling self-injury and dopamine depletion in the clinical condition, also underscores the profound importance of development in the differential course of maladaptive progression in the face of a common/single neurotoxic insult at different ages. Recent developments from clinical and basic science efforts attest to the fact that while the disease would seem to have a simple single gene defect at its core, the manifestations of this defect are profound and unexpectedly diverse. Future efforts employing the 6-OHDA model and others in the context of the novel technologies of genome editing, chemo- and opto-genetics, epigenetics, and further studies on the mechanisms of stress-induced maladaptations in brain all hold promise in taking our understanding of this disease to the next level.
    MeSH term(s) Adrenergic Agents/toxicity ; Animals ; Disease Models, Animal ; Lesch-Nyhan Syndrome/chemically induced ; Neurotoxins/toxicity ; Oxidopamine/toxicity ; Rats
    Chemical Substances Adrenergic Agents ; Neurotoxins ; Oxidopamine (8HW4YBZ748)
    Language English
    Publishing date 2016-03-24
    Publishing country Germany
    Document type Journal Article ; Review
    ISSN 1866-3370
    ISSN 1866-3370
    DOI 10.1007/7854_2016_444
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Ordered Mesoporous Boron Carbon Nitrides with Tunable Mesopore Nanoarchitectonics for Energy Storage and CO

    Sathish, C I / Kothandam, Gopalakrishnan / Selvarajan, Premkumar / Lei, Zhihao / Lee, Jangmee / Qu, Jiangtao / Al-Muhtaseb, Ala'a H / Yu, Xiaojiang / Breese, Mark B H / Zheng, Rongkun / Yi, Jiabao / Vinu, Ajayan

    Advanced science (Weinheim, Baden-Wurttemberg, Germany)

    2022  Volume 9, Issue 16, Page(s) e2105603

    Abstract: ... of the template. It is found that the optimized sample shows a high specific capacitance (296 F g ...

    Abstract Porous boron carbon nitride (BCN) is one of the exciting systems with unique electrochemical and adsorption properties. However, the synthesis of low-cost and porous BCN with tunable porosity is challenging, limiting its full potential in a variety of applications. Herein, the preparation of well-defined mesoporous boron carbon nitride (MBCN) with high specific surface area, tunable pores, and nitrogen contents is demonstrated through a simple integration of chemical polymerization of readily available sucrose and borane ammonia complex (BAC) through the nano-hard-templating approach. The bimodal pores are introduced in MBCN by controlling the self-organization of BAC and sucrose molecules within the nanochannels of the template. It is found that the optimized sample shows a high specific capacitance (296 F g
    Language English
    Publishing date 2022-04-05
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2808093-2
    ISSN 2198-3844 ; 2198-3844
    ISSN (online) 2198-3844
    ISSN 2198-3844
    DOI 10.1002/advs.202105603
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities.

    Schott, Courtney R / Koehne, Amanda L / Sayles, Leanne C / Young, Elizabeth P / Luck, Cuyler / Yu, Katharine / Lee, Alex G / Breese, Marcus R / Leung, Stanley G / Xu, Hang / Shah, Avanthi Tayi / Liu, Heng-Yi / Spillinger, Aviv / Behroozfard, Inge H / Marini, Kieren D / Dinh, Phuong T / Pons Ventura, Mar A V / Vanderboon, Emma N / Hazard, Florette K /
    Cho, Soo-Jin / Avedian, Raffi S / Mohler, David G / Zimel, Melissa / Wustrack, Rosanna / Curtis, Christina / Sirota, Marina / Sweet-Cordero, E Alejandro

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology, especially for highly aggressive cancers with a propensity for metastatic spread. Osteosarcoma is a rare cancer ... ...

    Abstract Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology, especially for highly aggressive cancers with a propensity for metastatic spread. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, a large panel of models is needed to fully elucidate key aspects of disease biology and to recapitulate clinically-relevant phenotypes. We describe the development and characterization of osteosarcoma patient-derived xenografts (PDXs) and a panel of PDX-derived cell lines. Matched patient samples, PDXs, and PDX-derived cell lines were comprehensively evaluated using whole genome sequencing and RNA sequencing. PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication (WGD) in a subset of cell lines. These cell line models were heterogeneous in their metastatic capacity and their tissue tropism as observed in both intravenous and orthotopic models. As proof-of-concept study, we used one of these models to test the preclinical effectiveness of a CDK inhibitor on the growth of metastatic tumors in an orthotopic amputation model. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden in this model.
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.19.524562
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach.

    Schott, Courtney R / Koehne, Amanda L / Sayles, Leanne C / Young, Elizabeth P / Luck, Cuyler / Yu, Katherine / Lee, Alex G / Breese, Marcus R / Leung, Stanley G / Xu, Hang / Shah, Avanthi Tayi / Liu, Heng-Yi / Spillinger, Aviv / Behroozfard, Inge H / Marini, Kieren D / Dinh, Phuong T / Pons Ventura, María V / Vanderboon, Emma N / Hazard, Florette K /
    Cho, Soo-Jin / Avedian, Raffi S / Mohler, David G / Zimel, Melissa / Wustrack, Rosanna / Curtis, Christina / Sirota, Marina / Sweet-Cordero, E Alejandro

    Clinical cancer research : an official journal of the American Association for Cancer Research

    2023  Volume 30, Issue 4, Page(s) 849–864

    Abstract: Purpose: Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with ... ...

    Abstract Purpose: Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, multiple models are needed to fully elucidate key aspects of disease biology and to recapitulate clinically relevant phenotypes.
    Experimental design: Matched patient samples, patient-derived xenografts (PDX), and PDX-derived cell lines were comprehensively evaluated using whole-genome sequencing and RNA sequencing. The in vivo metastatic phenotype of the PDX-derived cell lines was characterized in both an intravenous and an orthotopic murine model. As a proof-of-concept study, we tested the preclinical effectiveness of a cyclin-dependent kinase inhibitor on the growth of metastatic tumors in an orthotopic amputation model.
    Results: PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication in a subset of cell lines. The cell lines were heterogeneous in their metastatic capacity, and heterogeneous tissue tropism was observed in both intravenous and orthotopic models. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden.
    Conclusions: The variation in metastasis predilection sites between osteosarcoma PDX-derived cell lines demonstrates their ability to recapitulate the spectrum of the disease observed in patients. We describe here a panel of new osteosarcoma PDX-derived cell lines that we believe will be of wide use to the osteosarcoma research community.
    MeSH term(s) Humans ; Animals ; Mice ; Disease Models, Animal ; Drug Evaluation, Preclinical ; Xenograft Model Antitumor Assays ; Osteosarcoma/drug therapy ; Osteosarcoma/genetics ; Osteosarcoma/metabolism ; Cell Line, Tumor ; Bone Neoplasms/drug therapy ; Bone Neoplasms/genetics ; Bone Neoplasms/metabolism ; Cyclic N-Oxides ; Indolizines ; Pyridinium Compounds
    Chemical Substances dinaciclib (4V8ECV0NBQ) ; Cyclic N-Oxides ; Indolizines ; Pyridinium Compounds
    Language English
    Publishing date 2023-09-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1225457-5
    ISSN 1557-3265 ; 1078-0432
    ISSN (online) 1557-3265
    ISSN 1078-0432
    DOI 10.1158/1078-0432.CCR-23-0873
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: NUP98-NSD1 Driven MDS/MPN in Childhood Masquerading as JMML.

    Behnert, Astrid / Lee, Alex G / Young, Elizabeth P / Breese, Marcus R / Leung, Stanley G / Behroozfard, Inge / Maruffi, Maria / Sweet-Cordero, E Alejandro / Dvorak, Christopher C / Chu, Julia / Stieglitz, Elliot

    Journal of pediatric hematology/oncology

    2020  Volume 43, Issue 6, Page(s) e808–e811

    Abstract: Overlapping myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are clonal hematopoietic disorders with features of myelodysplasia and myeloproliferation. The only well-characterized MDS/MPN in children is juvenile myelomonocytic leukemia, an ... ...

    Abstract Overlapping myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are clonal hematopoietic disorders with features of myelodysplasia and myeloproliferation. The only well-characterized MDS/MPN in children is juvenile myelomonocytic leukemia, an aggressive disorder of infants and toddlers. The biochemical hallmark of this disease is hyperactivation of the Ras/MAPK signaling pathway caused by mutations in Ras pathway genes in more than 90% of patients. Translocations involving receptor tyrosine kinases have been identified in rare cases. Here, we report a 2-year-old patient who presented with MDS/MPN driven by a cytogenetically cryptic NUP98-NSD1 fusion, a translocation thought to exclusively occur in patients with acute myeloid leukemia.
    MeSH term(s) Child, Preschool ; Cytogenetics ; Female ; Humans ; Leukemia, Myelomonocytic, Juvenile/diagnosis ; Leukemia, Myelomonocytic, Juvenile/genetics ; Myelodysplastic-Myeloproliferative Diseases/diagnosis ; Myelodysplastic-Myeloproliferative Diseases/genetics ; Oncogene Proteins, Fusion/genetics ; Translocation, Genetic
    Chemical Substances NUP98-NSD1 protein, human ; Oncogene Proteins, Fusion
    Language English
    Publishing date 2020-08-12
    Publishing country United States
    Document type Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1231152-2
    ISSN 1536-3678 ; 1077-4114 ; 0192-8562
    ISSN (online) 1536-3678
    ISSN 1077-4114 ; 0192-8562
    DOI 10.1097/MPH.0000000000001913
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Host-dependent resistance of Group A Streptococcus to sulfamethoxazole mediated by a horizontally-acquired reduced folate transporter.

    Rodrigo, M Kalindu D / Saiganesh, Aarti / Hayes, Andrew J / Wilson, Alisha M / Anstey, Jack / Pickering, Janessa L / Iwasaki, Jua / Hillas, Jessica / Winslow, Scott / Woodman, Tabitha / Nitschke, Philipp / Lacey, Jake A / Breese, Karen J / van der Linden, Mark P G / Giffard, Philip M / Tong, Steven Y C / Gray, Nicola / Stubbs, Keith A / Carapetis, Jonathan R /
    Bowen, Asha C / Davies, Mark R / Barnett, Timothy C

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 6557

    Abstract: Described antimicrobial resistance mechanisms enable bacteria to avoid the direct effects of antibiotics and can be monitored by in vitro susceptibility testing and genetic methods. Here we describe a mechanism of sulfamethoxazole resistance that ... ...

    Abstract Described antimicrobial resistance mechanisms enable bacteria to avoid the direct effects of antibiotics and can be monitored by in vitro susceptibility testing and genetic methods. Here we describe a mechanism of sulfamethoxazole resistance that requires a host metabolite for activity. Using a combination of in vitro evolution and metabolic rescue experiments, we identify an energy-coupling factor (ECF) transporter S component gene (thfT) that enables Group A Streptococcus to acquire extracellular reduced folate compounds. ThfT likely expands the substrate specificity of an endogenous ECF transporter to acquire reduced folate compounds directly from the host, thereby bypassing the inhibition of folate biosynthesis by sulfamethoxazole. As such, ThfT is a functional equivalent of eukaryotic folate uptake pathways that confers very high levels of resistance to sulfamethoxazole, yet remains undetectable when Group A Streptococcus is grown in the absence of reduced folates. Our study highlights the need to understand how antibiotic susceptibility of pathogens might function during infections to identify additional mechanisms of resistance and reduce ineffective antibiotic use and treatment failures, which in turn further contribute to the spread of antimicrobial resistance genes amongst bacterial pathogens.
    MeSH term(s) Sulfamethoxazole/pharmacology ; Streptococcus pyogenes ; Anti-Bacterial Agents/pharmacology ; Substrate Specificity ; Folic Acid
    Chemical Substances Sulfamethoxazole (JE42381TNV) ; Anti-Bacterial Agents ; Folic Acid (935E97BOY8)
    Language English
    Publishing date 2022-11-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-34243-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Pretreatment brain CT perfusion thresholds for predicting final infarct volume in distal medium vessel occlusions.

    Yedavalli, Vivek / Hamam, Omar / Mohseni, Alireza / Chen, Kwan / Wang, Richard / Heo, Hye-Young / Heit, Jeremy / Marsh, Elisabeth Breese / Llinas, Raf / Urrutia, Victor / Xu, Risheng / Gonzalez, Fernando / Albers, Greg / Hillis, Argye / Nael, Kambiz

    Journal of neuroimaging : official journal of the American Society of Neuroimaging

    2023  Volume 33, Issue 6, Page(s) 968–975

    Abstract: Background and purpose: Quantitative CT perfusion (CTP) thresholds for assessing the extent of ischemia in patients with acute ischemic stroke (AIS) have been established; relative cerebral blood flow (rCBF) <30% is typically used for estimating ... ...

    Abstract Background and purpose: Quantitative CT perfusion (CTP) thresholds for assessing the extent of ischemia in patients with acute ischemic stroke (AIS) have been established; relative cerebral blood flow (rCBF) <30% is typically used for estimating estimated ischemic core volume and T
    Methods: In this retrospective study, consecutive AIS patients with anterior circulation DMVO who underwent pretreatment CTP and follow-up MRI/CT were included. The CTP data were processed by RAPID (iSchemaView, Menlo Park, CA) to generate estimated ischemic core volumes using rCBF <20%, <30%, <34%, and <38% and critical hypoperfused volumes using T
    Results: Fifty-five patients met our inclusion criteria (32 female [58.2%], 68.0 ± 12.1 years old [mean ± SD]). Recanalization was attempted with intravenous tissue-type plasminogen activator and mechanical thrombectomy in 27.7% and 38.1% of patients, respectively. Twenty-five patients (45.4%) were successfully recanalized. In the successfully recanalized patients, no CTP threshold significantly outperformed what is used in LVO setting (rCBF < 30%). All rCBF CTP thresholds demonstrated fair diagnostic performances for predicting FIV. In unsuccessfully recanalized patients, all T
    Conclusion: In AIS patients with DMVOs, longer T
    MeSH term(s) Humans ; Female ; Middle Aged ; Aged ; Aged, 80 and over ; Stroke/complications ; Retrospective Studies ; Ischemic Stroke/complications ; Tomography, X-Ray Computed/methods ; Brain ; Brain Ischemia/complications ; Perfusion ; Infarction/complications ; Perfusion Imaging/methods ; Cerebrovascular Circulation
    Language English
    Publishing date 2023-06-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1071724-9
    ISSN 1552-6569 ; 1051-2284
    ISSN (online) 1552-6569
    ISSN 1051-2284
    DOI 10.1111/jon.13142
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Complete Response to PD-1 Inhibition in an Adolescent With Relapsed Clear Cell Adenocarcinoma of the Cervix Predicted by Neoepitope Burden and APOBEC Signature.

    Levinson, Anya / Lee, Alex G / Martell, Henry J / Breese, Marcus R / Zaloudek, Charles / Van Ziffle, Jessica / Laguna, Benjamin / Leung, Stanley G / Chen, M Dwight / Chen, Lee-May / Pfeil, Jacob / Ladwig, Nicholas R / Shah, Avanthi Tayi / Behroozfard, Inge / Rao, Arjun Arkal / Salama, Sofie R / Sweet-Cordero, E Alejandro / Stieglitz, Elliot

    JCO precision oncology

    2020  Volume 4

    Language English
    Publishing date 2020-11-02
    Publishing country United States
    Document type Case Reports
    ISSN 2473-4284
    ISSN (online) 2473-4284
    DOI 10.1200/PO.20.00132
    Database MEDical Literature Analysis and Retrieval System OnLINE

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