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  1. Article: Single amino acid and trinucleotide repeats: function and evolution.

    Faux, Noel

    Advances in experimental medicine and biology

    2013  Volume 769, Page(s) 26–40

    Abstract: The most well known effect of single amino acid repeat expansion, beyond a certain threshold, is the development of a specific disease, depending on the protein in which the expansion has occurred. For example, the expansion of the glutamine repeat in ... ...

    Abstract The most well known effect of single amino acid repeat expansion, beyond a certain threshold, is the development of a specific disease, depending on the protein in which the expansion has occurred. For example, the expansion of the glutamine repeat in huntingtin leads to the debilitating neurodegenerative disease, Huntington's disease. Similarly, there are a range of other disorders caused by trinucleotide repeat expansions encoding polyglutamine or polyalanine tracts. The age of onset of the polyglutamine-induced neurodegenerative diseases is usually negatively correlated with the length of expanded CAG/glutamine repeat. However, recent studies have given evidence that single amino acid repeats may also play critical roles in normal protein function and that changes in the length of single amino acid repeats is likely to play a beneficial role in evolution. This chapter will look at the prevalence, function and possible role single amino acid repeats have in evolution and other biological processes.
    MeSH term(s) Amino Acids/genetics ; Animals ; Base Composition ; Biological Evolution ; Codon ; Genome, Human ; Humans ; Neurodegenerative Diseases/genetics ; Peptides/genetics ; Selection, Genetic ; Trinucleotide Repeat Expansion
    Chemical Substances Amino Acids ; Codon ; Peptides ; polyalanine (25191-17-7) ; polyglutamine (26700-71-0)
    Language English
    Publishing date 2013-03-22
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-1-4614-5434-2_3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Process mining-driven analysis of COVID-19's impact on vaccination patterns.

    Augusto, Adriano / Deitz, Timothy / Faux, Noel / Manski-Nankervis, Jo-Anne / Capurro, Daniel

    Journal of biomedical informatics

    2022  Volume 130, Page(s) 104081

    Abstract: Process mining is a discipline sitting between data mining and process science, whose goal is to provide theoretical methods and software tools to analyse process execution data, known as event logs. Although process mining was originally conceived to ... ...

    Abstract Process mining is a discipline sitting between data mining and process science, whose goal is to provide theoretical methods and software tools to analyse process execution data, known as event logs. Although process mining was originally conceived to facilitate business process management activities, research studies have shown the benefit of leveraging process mining in healthcare contexts. However, applying process mining tools to analyse healthcare process execution data is not straightforward. In this paper, we show a methodology to: i) prepare general practice healthcare process data for conducting a process mining analysis; ii) select and apply suitable process mining solutions for successfully executing the analysis; and iii) extract valuable insights from the obtained results, alongside leads for traditional data mining analysis. By doing so, we identified two major challenges when using process mining solutions for analysing healthcare process data, and highlighted benefits and limitations of the state-of-the-art process mining techniques when dealing with highly variable processes and large data-sets. While we provide solutions to the identified challenges, the overarching goal of this study was to detect differences between the patients' health services utilization pattern observed in 2020-during the COVID-19 pandemic and mandatory lock-downs -and the one observed in the prior four years, 2016 to 2019. By using a combination of process mining techniques and traditional data mining, we were able to demonstrate that vaccinations in Victoria did not drop drastically-as other interactions did. On the contrary, we observed a surge of influenza and pneumococcus vaccinations in 2020, as opposed to other research findings of similar studies conducted in different geographical areas.
    MeSH term(s) COVID-19/epidemiology ; COVID-19/prevention & control ; Communicable Disease Control ; Data Mining/methods ; Humans ; Pandemics/prevention & control ; Vaccination
    Language English
    Publishing date 2022-05-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2057141-0
    ISSN 1532-0480 ; 1532-0464
    ISSN (online) 1532-0480
    ISSN 1532-0464
    DOI 10.1016/j.jbi.2022.104081
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Disease progression modelling of Alzheimer's disease using probabilistic principal components analysis.

    Saint-Jalmes, Martin / Fedyashov, Victor / Beck, Daniel / Baldwin, Timothy / Faux, Noel G / Bourgeat, Pierrick / Fripp, Jurgen / Masters, Colin L / Goudey, Benjamin

    NeuroImage

    2023  Volume 278, Page(s) 120279

    Abstract: The recent biological redefinition of Alzheimer's Disease (AD) has spurred the development of statistical models that relate changes in biomarkers with neurodegeneration and worsening condition linked to AD. The ability to measure such changes may ... ...

    Abstract The recent biological redefinition of Alzheimer's Disease (AD) has spurred the development of statistical models that relate changes in biomarkers with neurodegeneration and worsening condition linked to AD. The ability to measure such changes may facilitate earlier diagnoses for affected individuals and help in monitoring the evolution of their condition. Amongst such statistical tools, disease progression models (DPMs) are quantitative, data-driven methods that specifically attempt to describe the temporal dynamics of biomarkers relevant to AD. Due to the heterogeneous nature of this disease, with patients of similar age experiencing different AD-related changes, a challenge facing longitudinal mixed-effects-based DPMs is the estimation of patient-realigning time-shifts. These time-shifts are indispensable for meaningful biomarker modelling, but may impact fitting time or vary with missing data in jointly estimated models. In this work, we estimate an individual's progression through Alzheimer's disease by combining multiple biomarkers into a single value using a probabilistic formulation of principal components analysis. Our results show that this variable, which summarises AD through observable biomarkers, is remarkably similar to jointly estimated time-shifts when we compute our scores for the baseline visit, on cross-sectional data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Reproducing the expected properties of clinical datasets, we confirm that estimated scores are robust to missing data or unavailable biomarkers. In addition to cross-sectional insights, we can model the latent variable as an individual progression score by repeating estimations at follow-up examinations and refining long-term estimates as more data is gathered, which would be ideal in a clinical setting. Finally, we verify that our score can be used as a pseudo-temporal scale instead of age to ignore some patient heterogeneity in cohort data and highlight the general trend in expected biomarker evolution in affected individuals.
    MeSH term(s) Humans ; Alzheimer Disease/diagnostic imaging ; Cross-Sectional Studies ; Neuroimaging/methods ; Biomarkers ; Disease Progression ; Cognitive Dysfunction ; Magnetic Resonance Imaging
    Chemical Substances 3-(3,5-dichlorophenyl)-1-methyl-2,5-pyrrolidinedione (93553-55-0) ; Biomarkers
    Language English
    Publishing date 2023-07-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1147767-2
    ISSN 1095-9572 ; 1053-8119
    ISSN (online) 1095-9572
    ISSN 1053-8119
    DOI 10.1016/j.neuroimage.2023.120279
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: “Escalibur”—A practical pipeline for the de novo analysis of nucleotide variation in nonmodel eukaryotes

    Korhonen, Pasi K. / Shaban, Babak / Faux, Noel G. / Kinkar, Liina / Chang, Bill C. H. / Wang, Daxi / Yang, Bicheng / Young, Neil D. / Gasser, Robin B.

    Molecular ecology resources. 2022 July, v. 22, no. 5

    2022  

    Abstract: The revolution in genomics has enabled large‐scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated ... ...

    Abstract The revolution in genomics has enabled large‐scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated and automated software pipelines, which are easy to use, efficient, reliable, reproducible and run in multiple computational environments, are required. A number of software workflows have been developed to handle and process such data sets for population genetic analyses, but effective, specialized pipelines for genetic and statistical analyses of nonmodel organisms are lacking. For most species, resources for variomes (sets of genetic variations found in populations of species) are not available, and/or genome assemblies are often incomplete and fragmented, complicating the selection of the most suitable reference genome when multiple assemblies are available. Additionally, the biological samples used often contain extraneous DNA from sources other than the species under investigation (e.g., microbial contamination), which needs to be removed prior to genetic analyses. For these reasons, we established a new pipeline, called Escalibur, which includes: functionalities, such as data trimming and mapping; selection of a suitable reference genome; removal of contaminating read data; recalibration of base calls; and variant‐calling. Escalibur uses a proven gatk variant caller and workflow description language (WDL), and is, therefore, a highly efficient and scalable pipeline for the genome‐wide identification of nucleotide variation in eukaryotes. This pipeline is available at https://gitlab.unimelb.edu.au/bioscience/escalibur (version 0.3‐beta) and is essentially applicable to any prokaryote or eukaryote.
    Keywords DNA ; automation ; computer software ; ecology ; eukaryotic cells ; genetic variation ; genome ; genomics ; microbial contamination ; population genetics
    Language English
    Dates of publication 2022-07
    Size p. 2120-2126.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2406816-0
    ISSN 1471-8286 ; 1755-098X
    ISSN (online) 1471-8286
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13600
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: A blood-based signature of cerebrospinal fluid Aβ

    Goudey, Benjamin / Fung, Bowen J / Schieber, Christine / Faux, Noel G

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 4163

    Abstract: It is increasingly recognized that Alzheimer's disease (AD) exists before dementia is present and that shifts in amyloid beta occur long before clinical symptoms can be detected. Early detection of these molecular changes is a key aspect for the success ... ...

    Abstract It is increasingly recognized that Alzheimer's disease (AD) exists before dementia is present and that shifts in amyloid beta occur long before clinical symptoms can be detected. Early detection of these molecular changes is a key aspect for the success of interventions aimed at slowing down rates of cognitive decline. Recent evidence indicates that of the two established methods for measuring amyloid, a decrease in cerebrospinal fluid (CSF) amyloid β
    MeSH term(s) Aged ; Aged, 80 and over ; Alzheimer Disease/blood ; Alzheimer Disease/cerebrospinal fluid ; Amyloid beta-Peptides/blood ; Amyloid beta-Peptides/cerebrospinal fluid ; Apolipoproteins E/blood ; Biomarkers/blood ; Chemokine CCL26/blood ; Chromogranin A/blood ; Female ; Humans ; Male ; Peptide Fragments/blood ; Peptide Fragments/cerebrospinal fluid ; Predictive Value of Tests
    Chemical Substances Amyloid beta-Peptides ; Apolipoproteins E ; Biomarkers ; Chemokine CCL26 ; Chromogranin A ; Peptide Fragments ; amyloid beta-protein (1-42)
    Language English
    Publishing date 2019-03-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-018-37149-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: An evaluation of existing text de-identification tools for use with patient progress notes from Australian general practice.

    El-Hayek, Carol / Barzegar, Siamak / Faux, Noel / Doyle, Kim / Pillai, Priyanka / Mutch, Simon J / Vaisey, Alaina / Ward, Roger / Sanci, Lena / Dunn, Adam G / Hellard, Margaret E / Hocking, Jane S / Verspoor, Karin / Boyle, Douglas Ir

    International journal of medical informatics

    2023  Volume 173, Page(s) 105021

    Abstract: Introduction: Digitized patient progress notes from general practice represent a significant resource for clinical and public health research but cannot feasibly and ethically be used for these purposes without automated de-identification. ... ...

    Abstract Introduction: Digitized patient progress notes from general practice represent a significant resource for clinical and public health research but cannot feasibly and ethically be used for these purposes without automated de-identification. Internationally, several open-source natural language processing tools have been developed, however, given wide variations in clinical documentation practices, these cannot be utilized without appropriate review. We evaluated the performance of four de-identification tools and assessed their suitability for customization to Australian general practice progress notes.
    Methods: Four tools were selected: three rule-based (HMS Scrubber, MIT De-id, Philter) and one machine learning (MIST). 300 patient progress notes from three general practice clinics were manually annotated with personally identifying information. We conducted a pairwise comparison between the manual annotations and patient identifiers automatically detected by each tool, measuring recall (sensitivity), precision (positive predictive value), f1-score (harmonic mean of precision and recall), and f2-score (weighs recall 2x higher than precision). Error analysis was also conducted to better understand each tool's structure and performance.
    Results: Manual annotation detected 701 identifiers in seven categories. The rule-based tools detected identifiers in six categories and MIST in three. Philter achieved the highest aggregate recall (67%) and the highest recall for NAME (87%). HMS Scrubber achieved the highest recall for DATE (94%) and all tools performed poorly on LOCATION. MIST achieved the highest precision for NAME and DATE while also achieving similar recall to the rule-based tools for DATE and highest recall for LOCATION. Philter had the lowest aggregate precision (37%), however preliminary adjustments of its rules and dictionaries showed a substantial reduction in false positives.
    Conclusion: Existing off-the-shelf solutions for automated de-identification of clinical text are not immediately suitable for our context without modification. Philter is the most promising candidate due to its high recall and flexibility however will require extensive revising of its pattern matching rules and dictionaries.
    MeSH term(s) Humans ; Electronic Health Records ; Confidentiality ; Data Anonymization ; Australia ; Natural Language Processing ; General Practice
    Language English
    Publishing date 2023-02-11
    Publishing country Ireland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1466296-6
    ISSN 1872-8243 ; 1386-5056
    ISSN (online) 1872-8243
    ISSN 1386-5056
    DOI 10.1016/j.ijmedinf.2023.105021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Association of Cerebrospinal Fluid Ferritin Level With Preclinical Cognitive Decline in APOE-ε4 Carriers.

    Ayton, Scott / Faux, Noel G / Bush, Ashley I

    JAMA neurology

    2016  Volume 74, Issue 1, Page(s) 122–125

    MeSH term(s) Aged ; Aged, 80 and over ; Amyloid beta-Peptides/cerebrospinal fluid ; Apolipoprotein E4/cerebrospinal fluid ; Apolipoprotein E4/genetics ; Cognitive Dysfunction/cerebrospinal fluid ; Cognitive Dysfunction/genetics ; Female ; Ferritins/cerebrospinal fluid ; Humans ; Male ; Neuropsychological Tests ; Peptide Fragments/cerebrospinal fluid
    Chemical Substances Amyloid beta-Peptides ; Apolipoprotein E4 ; Peptide Fragments ; amyloid beta-protein (1-42) ; Ferritins (9007-73-2)
    Language English
    Publishing date 2016-11-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2702023-X
    ISSN 2168-6157 ; 2168-6149
    ISSN (online) 2168-6157
    ISSN 2168-6149
    DOI 10.1001/jamaneurol.2016.4406
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Ferritin levels in the cerebrospinal fluid predict Alzheimer's disease outcomes and are regulated by APOE.

    Ayton, Scott / Faux, Noel G / Bush, Ashley I

    Nature communications

    2015  Volume 6, Page(s) 6760

    Abstract: Brain iron elevation is implicated in Alzheimer's disease (AD) pathogenesis, but the impact of iron on disease outcomes has not been previously explored in a longitudinal study. Ferritin is the major iron storage protein of the body; by using ... ...

    Abstract Brain iron elevation is implicated in Alzheimer's disease (AD) pathogenesis, but the impact of iron on disease outcomes has not been previously explored in a longitudinal study. Ferritin is the major iron storage protein of the body; by using cerebrospinal fluid (CSF) levels of ferritin as an index, we explored whether brain iron status impacts longitudinal outcomes in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. We show that baseline CSF ferritin levels were negatively associated with cognitive performance over 7 years in 91 cognitively normal, 144 mild cognitive impairment (MCI) and 67 AD subjects, and predicted MCI conversion to AD. Ferritin was strongly associated with CSF apolipoprotein E levels and was elevated by the Alzheimer's risk allele, APOE-ɛ4. These findings reveal that elevated brain iron adversely impacts on AD progression, and introduce brain iron elevation as a possible mechanism for APOE-ɛ4 being the major genetic risk factor for AD.
    MeSH term(s) Aged ; Aged, 80 and over ; Alzheimer Disease/cerebrospinal fluid ; Apolipoproteins E/genetics ; Atrophy ; Brain/metabolism ; Cognition ; Cognition Disorders/cerebrospinal fluid ; Cohort Studies ; Databases, Factual ; Female ; Ferritins/cerebrospinal fluid ; Gene Expression Regulation ; Genotype ; Humans ; Iron/cerebrospinal fluid ; Longitudinal Studies ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Risk Factors ; Treatment Outcome
    Chemical Substances Apolipoproteins E ; Ferritins (9007-73-2) ; Iron (E1UOL152H7)
    Language English
    Publishing date 2015-05-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/ncomms7760
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: "Escalibur"-A practical pipeline for the de novo analysis of nucleotide variation in nonmodel eukaryotes.

    Korhonen, Pasi K / Shaban, Babak / Faux, Noel G / Kinkar, Liina / Chang, Bill C H / Wang, Daxi / Yang, Bicheng / Young, Neil D / Gasser, Robin B

    Molecular ecology resources

    2022  Volume 22, Issue 5, Page(s) 2120–2126

    Abstract: The revolution in genomics has enabled large-scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated ... ...

    Abstract The revolution in genomics has enabled large-scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated and automated software pipelines, which are easy to use, efficient, reliable, reproducible and run in multiple computational environments, are required. A number of software workflows have been developed to handle and process such data sets for population genetic analyses, but effective, specialized pipelines for genetic and statistical analyses of nonmodel organisms are lacking. For most species, resources for variomes (sets of genetic variations found in populations of species) are not available, and/or genome assemblies are often incomplete and fragmented, complicating the selection of the most suitable reference genome when multiple assemblies are available. Additionally, the biological samples used often contain extraneous DNA from sources other than the species under investigation (e.g., microbial contamination), which needs to be removed prior to genetic analyses. For these reasons, we established a new pipeline, called Escalibur, which includes: functionalities, such as data trimming and mapping; selection of a suitable reference genome; removal of contaminating read data; recalibration of base calls; and variant-calling. Escalibur uses a proven gatk variant caller and workflow description language (WDL), and is, therefore, a highly efficient and scalable pipeline for the genome-wide identification of nucleotide variation in eukaryotes. This pipeline is available at https://gitlab.unimelb.edu.au/bioscience/escalibur (version 0.3-beta) and is essentially applicable to any prokaryote or eukaryote.
    MeSH term(s) Computational Biology ; Eukaryota/genetics ; Genome ; High-Throughput Nucleotide Sequencing ; Nucleotides ; Polymorphism, Single Nucleotide ; Software
    Chemical Substances Nucleotides
    Language English
    Publishing date 2022-03-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13600
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Identification of Leukocyte Surface P2X7 as a Biomarker Associated with Alzheimer's Disease.

    Li, Yihan / Huang, Xin / Fowler, Christopher / Lim, Yen Y / Laws, Simon M / Faux, Noel / Doecke, James D / Trounson, Brett / Pertile, Kelly / Rumble, Rebecca / Doré, Vincent / Villemagne, Victor L / Rowe, Christopher C / Wiley, James S / Maruff, Paul / Masters, Colin L / Gu, Ben J

    International journal of molecular sciences

    2022  Volume 23, Issue 14

    Abstract: Alzheimer's disease (AD) has shown altered immune responses in the periphery. We studied P2X7 (a proinflammatory receptor and a scavenger receptor) and two integrins, CD11b and CD11c, on the surface of circulating leukocytes and analysed their ... ...

    Abstract Alzheimer's disease (AD) has shown altered immune responses in the periphery. We studied P2X7 (a proinflammatory receptor and a scavenger receptor) and two integrins, CD11b and CD11c, on the surface of circulating leukocytes and analysed their associations with Aβ-PET, brain atrophy, neuropsychological assessments, and cerebrospinal fluid (CSF) biomarkers. Total 287 age-matched, sex-balanced participants were recruited in a discovery cohort and two validation cohorts through the AIBL study and studied using tri-colour flow cytometry. Our results demonstrated reduced expressions of P2X7, CD11b, and CD11c on leukocytes, particularly monocytes, in Aβ +ve cases compared with Aβ -ve controls. P2X7 and integrin downregulation was observed at pre-clinical stage of AD and stayed low throughout disease course. We further constructed a polygenic risk score (PRS) model based on 12
    MeSH term(s) Alzheimer Disease/pathology ; Amyloid beta-Peptides/cerebrospinal fluid ; Biomarkers/cerebrospinal fluid ; Humans ; Integrins ; Leukocytes/pathology ; Peptide Fragments/cerebrospinal fluid ; tau Proteins/cerebrospinal fluid
    Chemical Substances Amyloid beta-Peptides ; Biomarkers ; Integrins ; Peptide Fragments ; tau Proteins
    Language English
    Publishing date 2022-07-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23147867
    Database MEDical Literature Analysis and Retrieval System OnLINE

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