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  1. Article ; Online: Clinical and prognostic significance analysis of glycolysis-related genes in HNSCC.

    Yuan, Qiuyun / Mao, Mengqian / Xia, Xiaoqiang / Yang, Wanchun

    The journal of gene medicine

    2024  Volume 26, Issue 2, Page(s) e3670

    Abstract: Background: Head and neck squamous cell carcinoma (HNSCC) represents one of the most malignant cancers worldwide, with poor survival. Experimental evidence implies that glycolysis/hypoxia is associated with HNSCC. In this study, we aimed to construct a ... ...

    Abstract Background: Head and neck squamous cell carcinoma (HNSCC) represents one of the most malignant cancers worldwide, with poor survival. Experimental evidence implies that glycolysis/hypoxia is associated with HNSCC. In this study, we aimed to construct a novel glycolysis-/hypoxia-related gene (GHRG) signature for survival prediction of HNSCC.
    Methods: A multistage screening strategy was used to establish the GHRG prognostic model by univariate/least absolute shrinkage and selection operator (LASSO)/step multivariate Cox regressions from The Cancer Genome Atlas cohort. A nomogram was constructed to quantify the survival probability. Correlations between risk score and immune infiltration and chemotherapy sensitivity were explored.
    Results: We established a 12-GHRG mRNA signature to predict the prognosis in HNSCC patients. Patients in the high-risk score group had a much worse prognosis. The predictive power of the model was validated by external HNSCC cohorts, and the model was identified as an independent factor for survival prediction. Immune infiltration analysis showed that the high-risk score group had an immunosuppressive microenvironment. Finally, the model was effective in predicting chemotherapeutic sensitivity.
    Conclusions: Our study demonstrated that the GHRG model is a robust prognostic tool for survival prediction of HNSCC. Findings of this work provide novel insights for immune infiltration and chemotherapy of HNSCC, and may be applied clinically to guide therapeutic strategies.
    MeSH term(s) Humans ; Prognosis ; Squamous Cell Carcinoma of Head and Neck/genetics ; Glycolysis/genetics ; Hypoxia ; Head and Neck Neoplasms/diagnosis ; Head and Neck Neoplasms/genetics ; Tumor Microenvironment/genetics
    Language English
    Publishing date 2024-02-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 1458024-x
    ISSN 1521-2254 ; 1099-498X
    ISSN (online) 1521-2254
    ISSN 1099-498X
    DOI 10.1002/jgm.3670
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5423: Show issues Location:
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  2. Article ; Online: The effects of land use types on microplastics in river water: A case study on the mainstream of the Wei River, China.

    Zhang, Le / Li, Xi / Li, Qi / Xia, Xiaoqiang / Zhang, Hang

    Environmental monitoring and assessment

    2024  Volume 196, Issue 4, Page(s) 349

    Abstract: Microplastics are widely found in rivers and their sediments, which will cause harm to the water ecological environment. The Wei River is a first-class tributary of the Yellow River, the fifth largest river in the world, and has vulnerable ecological ... ...

    Abstract Microplastics are widely found in rivers and their sediments, which will cause harm to the water ecological environment. The Wei River is a first-class tributary of the Yellow River, the fifth largest river in the world, and has vulnerable ecological environment and most sediment in the world. However, understanding how anthropogenic activities and environmental factors affect the microplastics distribution in this river is not clear. Based on this, the spatiotemporal distribution of microplastics in the Wei River were investigated. The abundance of microplastics ranged from 1033 to 8333 items/m
    MeSH term(s) Microplastics ; Plastics ; Rivers ; Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Water ; China
    Chemical Substances Microplastics ; Plastics ; Water Pollutants, Chemical ; Water (059QF0KO0R)
    Language English
    Publishing date 2024-03-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 782621-7
    ISSN 1573-2959 ; 0167-6369
    ISSN (online) 1573-2959
    ISSN 0167-6369
    DOI 10.1007/s10661-024-12430-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 5186: Show issues

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  3. Article ; Online: Shaoxia: a web-based interactive analysis platform for single cell RNA sequencing data.

    Wei, Weideng / Xia, Xiaoqiang / Li, Taiwen / Chen, Qianming / Feng, Xiaodong

    BMC genomics

    2024  Volume 25, Issue 1, Page(s) 402

    Abstract: Background: In recent years, Single-cell RNA sequencing (scRNA-seq) is increasingly accessible to researchers of many fields. However, interpreting its data demands proficiency in multiple programming languages and bioinformatic skills, which limited ... ...

    Abstract Background: In recent years, Single-cell RNA sequencing (scRNA-seq) is increasingly accessible to researchers of many fields. However, interpreting its data demands proficiency in multiple programming languages and bioinformatic skills, which limited researchers, without such expertise, exploring information from scRNA-seq data. Therefore, there is a tremendous need to develop easy-to-use software, covering all the aspects of scRNA-seq data analysis.
    Results: We proposed a clear analysis framework for scRNA-seq data, which emphasized the fundamental and crucial roles of cell identity annotation, abstracting the analysis process into three stages: upstream analysis, cell annotation and downstream analysis. The framework can equip researchers with a comprehensive understanding of the analysis procedure and facilitate effective data interpretation. Leveraging the developed framework, we engineered Shaoxia, an analysis platform designed to democratize scRNA-seq analysis by accelerating processing through high-performance computing capabilities and offering a user-friendly interface accessible even to wet-lab researchers without programming expertise.
    Conclusion: Shaoxia stands as a powerful and user-friendly open-source software for automated scRNA-seq analysis, offering comprehensive functionality for streamlined functional genomics studies. Shaoxia is freely accessible at http://www.shaoxia.cloud , and its source code is publicly available at https://github.com/WiedenWei/shaoxia .
    MeSH term(s) Single-Cell Analysis/methods ; Software ; Sequence Analysis, RNA/methods ; Internet ; Humans ; Computational Biology/methods ; RNA-Seq/methods ; User-Computer Interface
    Language English
    Publishing date 2024-04-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-024-10322-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Integrative analysis defines DDIT3 amplification as a correlative and essential factor for glioma malignancy.

    Mao, Mengqian / Yuan, Qiuyun / Xia, Xiaoqiang / Cui, Yiyuan / Chen, Mina / Yang, Wanchun

    American journal of cancer research

    2023  Volume 13, Issue 11, Page(s) 5418–5430

    Abstract: Glioma, particularly glioblastoma multiforme (GBM), is a highly aggressive and lethal primary brain tumor with poor prognosis. Metabolic reprogramming and endoplasmic reticulum (ER) stress are two crucial factors contributing to glioma pathogenesis. ... ...

    Abstract Glioma, particularly glioblastoma multiforme (GBM), is a highly aggressive and lethal primary brain tumor with poor prognosis. Metabolic reprogramming and endoplasmic reticulum (ER) stress are two crucial factors contributing to glioma pathogenesis. However, the intricate coordination between these processes remains incompletely understood. Here, we conducted an integrative analysis to elucidate the nodal role of DNA Damage Inducible Transcript 3 (DDIT3) to couple metabolisms and stress responses in glioma. We demonstrated a positive association between DDIT3 amplification/enhanced expression with glioma malignancy, indicating its potential as a novel biomarker for prognosis and treatment stratification. Genomic and transcriptomic analyses further revealed the involvement of DDIT3 enhancement in glioma progression. Moreover, immune infiltration analysis showed that distinct DDIT3 expression groups had different immune microenvironment. Finally,
    Language English
    Publishing date 2023-11-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2589522-9
    ISSN 2156-6976
    ISSN 2156-6976
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Clinical and molecular analysis of cilia-associated gene signature for prognostic prediction in glioma.

    Qi, Xin / Yuan, Qiuyun / Xia, Xiaoqiang / Li, Wenhao / Cao, Muqing / Yang, Wanchun

    Journal of cancer research and clinical oncology

    2023  Volume 149, Issue 13, Page(s) 11443–11455

    Abstract: Purpose: Glioma is a highly malignant and unfavorable cancer in the brain. Recent evidence highlights the vital role of cilia-related pathways as novel regulators of glioma development. However, the prognostic potential of ciliary pathways in glioma is ... ...

    Abstract Purpose: Glioma is a highly malignant and unfavorable cancer in the brain. Recent evidence highlights the vital role of cilia-related pathways as novel regulators of glioma development. However, the prognostic potential of ciliary pathways in glioma is still ambiguous. In this study, we aim to construct a gene signature using cilia-related genes to facilitate the prognostication of glioma.
    Methods: A multi-stage approach was employed to build the ciliary gene signature for prognostication of glioma. The strategy involved the implementation of univariate, LASSO, and stepwise multivariate Cox regression analyses based on TCGA cohort, followed by independent validation in CGGA and REMBRANDT cohort. The study further revealed molecular differences at the genomic, transcriptomic, and proteomic levels between distinct groups.
    Results: A prognostic tool utilizing a 9-gene signature based on ciliary pathways was developed to assess the clinical outcomes of glioma patients. The risk scores generated by the signature demonstrated a negative correlation with patient survival rates. The validation of the signature in an independent cohort reinforced its prognostic capabilities. In-depth analysis uncovered distinctive molecular characteristics at the genomic, transcriptomic, and protein-interactive levels in the high- and low-risk groups. Furthermore, the gene signature was able to predict the sensitivity of glioma patients to conventional chemotherapeutic drugs.
    Conclusion: This study has established the utility of a ciliary gene signature as a reliable prognostic predictor of glioma patient survival. Findings not only enhance our comprehension of the intricate molecular mechanisms of cilia pathways in glioma, but also hold significant clinical implications in directing chemotherapeutic strategies.
    MeSH term(s) Humans ; Cilia/genetics ; Prognosis ; Proteomics ; Glioma/genetics ; Brain
    Language English
    Publishing date 2023-06-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 134792-5
    ISSN 1432-1335 ; 0171-5216 ; 0084-5353 ; 0943-9382
    ISSN (online) 1432-1335
    ISSN 0171-5216 ; 0084-5353 ; 0943-9382
    DOI 10.1007/s00432-023-05022-4
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    In stock of ZB MED Cologne/Königswinter

    Uh III Zs.10: Show issues Location:
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  6. Article ; Online: Comparative analysis of two arecoline-induced oral submucous fibrosis models.

    Tang, Shijie / Jiang, Lanxin / Zhou, Ying / Zhou, Tong / Peng, Yang / Zhou, Shuting / Yue, Yuan / Xia, Xiaoqiang / Li, Jing / Chen, Qianming / Jiang, Yuchen / Feng, Xiaodong

    Oral diseases

    2023  

    Abstract: Objective: The limited understanding of the molecular mechanism for oral submucosal fibrosis (OSF) poses challenges to the development of effective prevention and treatment strategies. The lack of suitable animal models is a major hindrance. Therefore, ... ...

    Abstract Objective: The limited understanding of the molecular mechanism for oral submucosal fibrosis (OSF) poses challenges to the development of effective prevention and treatment strategies. The lack of suitable animal models is a major hindrance. Therefore, this study aimed to address this issue by comparing commonly used arecoline-induced water drinking and injection mouse models.
    Materials and methods: The mice were subjected to two protocols: receiving 2 mg/mL arecoline in drinking water and 4 mg/mL arecoline saline solution injections every other day. Tissues were collected at regular 4-week intervals, with a final time point of 20 weeks. Stereo microscopy and histomorphological analysis were performed on live and harvested tissues, respectively.
    Results: During arecoline treatment, collagen deposition and myofibroblast proliferation progressively increased in both models. Changes in the collagen I/III ratio indicated that both models exhibited characteristics of the early and intermediate stages of OSF after 20 weeks of arecoline induction. The water-drinking model also demonstrated multi-organ fibrosis involving the tongue, lungs, and small intestine.
    Conclusion: Both the water drinking and injection mouse models effectively induced OSF, but the water-drinking model better mirrored the observed pathogenesis in patients with OSF. These models provide valuable tools for investigating the mechanisms underlying OSF.
    Language English
    Publishing date 2023-12-14
    Publishing country Denmark
    Document type Journal Article
    ZDB-ID 1290529-x
    ISSN 1601-0825 ; 1354-523X
    ISSN (online) 1601-0825
    ISSN 1354-523X
    DOI 10.1111/odi.14825
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4427: Show issues Location:
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  7. Book ; Online: Writing Polishment with Simile

    Zhang, Jiayi / Cui, Zhi / Xia, Xiaoqiang / Guo, Yalong / Li, Yanran / Wei, Chen / Cui, Jianwei

    Task, Dataset and A Neural Approach

    2020  

    Abstract: A simile is a figure of speech that directly makes a comparison, showing similarities between two different things, e.g. "Reading papers can be dull sometimes,like watching grass grow". Human writers often interpolate appropriate similes into proper ... ...

    Abstract A simile is a figure of speech that directly makes a comparison, showing similarities between two different things, e.g. "Reading papers can be dull sometimes,like watching grass grow". Human writers often interpolate appropriate similes into proper locations of the plain text to vivify their writings. However, none of existing work has explored neural simile interpolation, including both locating and generation. In this paper, we propose a new task of Writing Polishment with Simile (WPS) to investigate whether machines are able to polish texts with similes as we human do. Accordingly, we design a two-staged Locate&Gen model based on transformer architecture. Our model firstly locates where the simile interpolation should happen, and then generates a location-specific simile. We also release a large-scale Chinese Simile (CS) dataset containing 5 million similes with context. The experimental results demonstrate the feasibility of WPS task and shed light on the future research directions towards better automatic text polishment.

    Comment: Accepted in AAAI2021
    Keywords Computer Science - Computation and Language
    Subject code 420
    Publishing date 2020-12-15
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Inhibition of mitochondrial carrier homolog 2 (MTCH2) suppresses tumor invasion and enhances sensitivity to temozolomide in malignant glioma.

    Yuan, Qiuyun / Yang, Wanchun / Zhang, Shuxin / Li, Tengfei / Zuo, Mingrong / Zhou, Xingwang / Li, Junhong / Li, Mao / Xia, Xiaoqiang / Chen, Mina / Liu, Yanhui

    Molecular medicine (Cambridge, Mass.)

    2021  Volume 27, Issue 1, Page(s) 7

    Abstract: Background: Malignant glioma exerts a metabolic shift from oxidative phosphorylation (OXPHOs) to aerobic glycolysis, with suppressed mitochondrial functions. This phenomenon offers a proliferation advantage to tumor cells and decrease mitochondria- ... ...

    Abstract Background: Malignant glioma exerts a metabolic shift from oxidative phosphorylation (OXPHOs) to aerobic glycolysis, with suppressed mitochondrial functions. This phenomenon offers a proliferation advantage to tumor cells and decrease mitochondria-dependent cell death. However, the underlying mechanism for mitochondrial dysfunction in glioma is not well elucidated. MTCH2 is a mitochondrial outer membrane protein that regulates mitochondrial metabolism and related cell death. This study aims to clarify the role of MTCH2 in glioma.
    Methods: Bioinformatic analysis from TCGA and CGGA databases were used to investigate the association of MTCH2 with glioma malignancy and clinical significance. The expression of MTCH2 was verified from clinical specimens using real-time PCR and western blots in our cohorts. siRNA-mediated MTCH2 knockdown were used to assess the biological functions of MTCH2 in glioma progression, including cell invasion and temozolomide-induced cell death. Biochemical investigations of mitochondrial and cellular signaling alternations were performed to detect the mechanism by which MTCH2 regulates glioma malignancy.
    Results: Bioinformatic data from public database and our cohort showed that MTCH2 expression was closely associated with glioma malignancy and poor patient survival. Silencing of MTCH2 expression impaired cell migration/invasion and enhanced temozolomide sensitivity of human glioma cells. Mechanistically, MTCH2 knockdown may increase mitochondrial OXPHOs and thus oxidative damage, decreased migration/invasion pathways, and repressed pro-survival AKT signaling.
    Conclusion: Our work establishes the relationship between MTCH2 expression and glioma malignancy, and provides a potential target for future interventions.
    MeSH term(s) Animals ; Apoptosis ; Brain Neoplasms/drug therapy ; Brain Neoplasms/genetics ; Brain Neoplasms/metabolism ; Cell Line, Tumor ; Cell Movement ; Drug Resistance, Neoplasm ; Gene Knockdown Techniques ; Glioma/drug therapy ; Glioma/genetics ; Glioma/metabolism ; Humans ; Mice ; Mitochondrial Membrane Transport Proteins/genetics ; Neoplasm Invasiveness ; Oxidative Phosphorylation ; Temozolomide/administration & dosage ; Temozolomide/pharmacology ; Xenograft Model Antitumor Assays
    Chemical Substances MTCH2 protein, human ; Mitochondrial Membrane Transport Proteins ; Temozolomide (YF1K15M17Y)
    Language English
    Publishing date 2021-01-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1283676-x
    ISSN 1528-3658 ; 1076-1551
    ISSN (online) 1528-3658
    ISSN 1076-1551
    DOI 10.1186/s10020-020-00261-4
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4456: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Rheb-regulated mitochondrial pyruvate metabolism of Schwann cells linked to axon stability.

    Jia, Lanlan / Liao, Maoxing / Mou, Aidi / Zheng, Quanzhen / Yang, Wanchun / Yu, Zongyan / Cui, Yiyuan / Xia, Xiaoqiang / Qin, Yue / Chen, Mina / Xiao, Bo

    Developmental cell

    2021  Volume 56, Issue 21, Page(s) 2980–2994.e6

    Abstract: The metabolic coupling of Schwann cells (SCs) and peripheral axons is poorly understood. Few molecules in SCs are known to regulate axon stability. Using SC-specific Rheb knockout mice, we demonstrate that Rheb-regulated mitochondrial pyruvate metabolism ...

    Abstract The metabolic coupling of Schwann cells (SCs) and peripheral axons is poorly understood. Few molecules in SCs are known to regulate axon stability. Using SC-specific Rheb knockout mice, we demonstrate that Rheb-regulated mitochondrial pyruvate metabolism is critical for SC-mediated non-cell-autonomous regulation of peripheral axon stability. Rheb knockout suppresses pyruvate dehydrogenase (PDH) activity (independently of mTORC1) and shifts pyruvate metabolism toward lactate production in SCs. The increased lactate causes age-dependent peripheral axon degeneration, affecting peripheral nerve function. Lactate, as an energy substrate and a potential signaling molecule, enhanced neuronal mitochondrial metabolism and energy production of peripheral nerves. Albeit beneficial to injured peripheral axons in the short term, we show that persistently increased lactate metabolism of neurons enhances ROS production, eventually damaging mitochondria, neuroenergetics, and axon stability. This study highlights the complex roles of lactate metabolism to peripheral axons and the importance of lactate homeostasis in preserving peripheral nerves.
    MeSH term(s) Animals ; Axons/metabolism ; Cells, Cultured ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Mice ; Mitochondria/metabolism ; Neurons/metabolism ; Pyruvates/metabolism ; Schwann Cells/metabolism ; Signal Transduction/physiology
    Chemical Substances Pyruvates ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1)
    Language English
    Publishing date 2021-10-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2021.09.013
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  10. Article ; Online: Elevated GIGYF2 expression suppresses tumor migration and enhances sensitivity to temozolomide in malignant glioma.

    Yang, Wanchun / Yuan, Qiuyun / Zhang, Shuxin / Zuo, Mingrong / Li, Tengfei / Li, Junhong / Zhou, Xingwang / Li, Mao / Feng, Wentao / Xia, Xiaoqiang / Chen, Mina / Liu, Yanhui

    Cancer gene therapy

    2021  Volume 29, Issue 6, Page(s) 750–757

    Abstract: Glioma is a common type of malignant and aggressive tumor in the brain. Despite progress on mechanistic studies, current understanding of the initiation and progression of glioma remains incomplete. GIGYF2 is a critical regulator in neural development ... ...

    Abstract Glioma is a common type of malignant and aggressive tumor in the brain. Despite progress on mechanistic studies, current understanding of the initiation and progression of glioma remains incomplete. GIGYF2 is a critical regulator in neural development and degeneration, however, its contribution in glioma is not yet elucidated. In this study, using an integrative approach spanning bioinformatic analysis and functional approaches, we explored the potential contribution of GIGYF2 in glioma. Bioinformatic data from public database and our cohort showed that GIGYF2 expression was closely associated with low glioma malignancy and better patient survival. Elevation of GIGYF2 expression impaired cell migration and enhanced temozolomide sensitivity of human glioma cells. We further establish its molecular mechanism by demonstrating that GIGYF2 inhibits MMP-9 mediated cell migration pathway and pro-survival AKT/Bax/Caspase-3 signaling. Our work identifies the suppressive role of GIGYF2 in gliomas, and clarifies the relationship between GIGYF2 expression and glioma malignancy, which may provide a potential target for future interventions.
    MeSH term(s) Brain Neoplasms/drug therapy ; Brain Neoplasms/genetics ; Brain Neoplasms/metabolism ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Cell Line, Tumor ; Cell Movement/genetics ; Cell Proliferation ; Glioma/drug therapy ; Glioma/genetics ; Glioma/metabolism ; Humans ; Signal Transduction ; Temozolomide/pharmacology
    Chemical Substances Carrier Proteins ; GIGYF2 protein, human ; Temozolomide (YF1K15M17Y)
    Language English
    Publishing date 2021-05-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1212513-1
    ISSN 1476-5500 ; 0929-1903
    ISSN (online) 1476-5500
    ISSN 0929-1903
    DOI 10.1038/s41417-021-00353-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4125: Show issues Location:
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