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  1. Article ; Online: Progressive myocardial lipomatous metaplasia following acute myocarditis.

    Moura-Ferreira, Sara / Van Cleemput, Johan / Verbeken, Eric / Jan, Bogaert

    European heart journal. Cardiovascular Imaging

    2019  Volume 21, Issue 6, Page(s) 705

    MeSH term(s) Acute Disease ; Humans ; Metaplasia/diagnostic imaging ; Myocardial Infarction ; Myocarditis/diagnostic imaging ; Myocardium
    Language English
    Publishing date 2019-12-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2638345-7
    ISSN 2047-2412 ; 2047-2404
    ISSN (online) 2047-2412
    ISSN 2047-2404
    DOI 10.1093/ehjci/jez314
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  2. Article ; Online: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.

    Cleemput, Sara / Dumon, Wim / Fonseca, Vagner / Abdool Karim, Wasim / Giovanetti, Marta / Alcantara, Luiz Carlos / Deforche, Koen / de Oliveira, Tulio

    Bioinformatics (Oxford, England)

    2020  Volume 36, Issue 11, Page(s) 3552–3555

    Abstract: ... that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2 ... all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also ...

    Abstract Summary: Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present the Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2000 sequences per submission and the analysis of a new whole-genome sequence will take approximately 1 min. The tool has been tested and validated with hundreds of whole genomes from 10 coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.
    Availability and implementation: https://www.genomedetective.com/app/typingtool/cov.
    Contact: koen@emweb.be or deoliveira@ukzn.ac.za.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Betacoronavirus/genetics ; COVID-19 ; China ; Coronavirus/genetics ; Coronavirus Infections/epidemiology ; Genome, Viral ; Humans ; Internet ; Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology ; SARS-CoV-2 ; Software ; Whole Genome Sequencing
    Keywords covid19
    Language English
    Publishing date 2020-02-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btaa145
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.

    Cleemput, Sara / Dumon, Wim / Fonseca, Vagner / Karim, Wasim Abdool / Giovanetti, Marta / Alcantara, Luiz Carlos / Deforche, Koen / de Oliveira, Tulio

    bioRxiv : the preprint server for biology

    2020  

    Abstract: ... coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and ...

    Abstract Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify novel coronavirus (2019-nCoV) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for 2019-nCoV. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines.
    Keywords covid19
    Language English
    Publishing date 2020-02-02
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.01.31.928796
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: On the whereabouts of SARS-CoV-2 in the human body: A systematic review.

    Trypsteen, Wim / Van Cleemput, Jolien / Snippenberg, Willem van / Gerlo, Sarah / Vandekerckhove, Linos

    PLoS pathogens

    2020  Volume 16, Issue 10, Page(s) e1009037

    Abstract: Since SARS-CoV-2 appeared in the human population, the scientific community has scrambled to gather ... virus. Here, we performed a systematic review of the current (pre)published SARS-CoV-2 literature ... with a focus on the evidence concerning SARS-CoV-2 distribution in human tissues and viral shedding ...

    Abstract Since SARS-CoV-2 appeared in the human population, the scientific community has scrambled to gather as much information as possible to find good strategies for the containment and treatment of this pandemic virus. Here, we performed a systematic review of the current (pre)published SARS-CoV-2 literature with a focus on the evidence concerning SARS-CoV-2 distribution in human tissues and viral shedding in body fluids. In addition, this evidence is aligned with published ACE2 entry-receptor (single cell) expression data across the human body to construct a viral distribution and ACE2 receptor body map. We highlight the broad organotropism of SARS-CoV-2, as many studies identified viral components (RNA, proteins) in multiple organs, including the pharynx, trachea, lungs, blood, heart, vessels, intestines, brain, male genitals and kidneys. This also implicates the presence of viral components in various body fluids such as mucus, saliva, urine, cerebrospinal fluid, semen and breast milk. The main SARS-CoV-2 entry receptor, ACE2, is expressed at different levels in multiple tissues throughout the human body, but its expression levels do not always correspond with SARS-CoV-2 detection, indicating that there is a complex interplay between virus and host. Together, these data shed new light on the current view of SARS-CoV-2 pathogenesis and lay the foundation for better diagnosis and treatment of COVID-19 patients.
    MeSH term(s) Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/pathogenicity ; COVID-19 ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Female ; Humans ; Lung/metabolism ; Lung/virology ; Male ; Pandemics ; Peptidyl-Dipeptidase A/drug effects ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; Receptors, Virus/drug effects ; Receptors, Virus/metabolism ; SARS-CoV-2
    Chemical Substances Antiviral Agents ; Receptors, Virus ; Peptidyl-Dipeptidase A (EC 3.4.15.1)
    Keywords covid19
    Language English
    Publishing date 2020-10-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1009037
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  5. Article ; Online: Personal characteristics and contextual factors that determine "helping," "joining in," and "doing nothing" when witnessing cyberbullying.

    Van Cleemput, Katrien / Vandebosch, Heidi / Pabian, Sara

    Aggressive behavior

    2014  Volume 40, Issue 5, Page(s) 383–396

    Abstract: In this article, we investigated several determinants of bystanders' reactive behaviors when confronted with cyberbullying using self-reported data from 2,333 Flemish 9-16 year olds. Structural equation modeling showed that adolescents that had joined in ...

    Abstract In this article, we investigated several determinants of bystanders' reactive behaviors when confronted with cyberbullying using self-reported data from 2,333 Flemish 9-16 year olds. Structural equation modeling showed that adolescents that had joined in on the cyberbullying were older, had lower levels of empathy and were more likely to have been involved in cyberbullying or traditional bullying as perpetrators. Adolescents who had helped the victim were younger, had higher levels of empathy and were more likely to have been a victim of cyberbullying or traditional bullying in the past months. Adolescents that did nothing when they witnessed cyberbullying, were also older, showed lower levels of empathy and were less likely to have been a victim of traditional bullying. Social anxiety was not related to joining in, helping and remaining passive. In the second part of the analysis, we found that bystanders' passive behavior could be explained in more detail by moral disengagement theory and other contextual factors. In the discussion, the implications of the findings for research on cyberbullying are addressed.
    MeSH term(s) Adolescent ; Anxiety/psychology ; Bullying/psychology ; Child ; Crime Victims ; Empathy ; Female ; Helping Behavior ; Humans ; Internet ; Male ; Models, Psychological ; Self Efficacy ; Self Report ; Social Behavior
    Language English
    Publishing date 2014-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 189812-7
    ISSN 1098-2337 ; 0096-140X
    ISSN (online) 1098-2337
    ISSN 0096-140X
    DOI 10.1002/ab.21534
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  6. Book ; Online: A Secure and Privacy-preserving Protocol for Smart Metering Operational Data Collection

    Mustafa, Mustafa A. / Cleemput, Sara / Aly, Abelrahaman / Abidin, Aysajan

    2018  

    Abstract: In this paper we propose a novel protocol that allows suppliers and grid operators to collect users' aggregate metering data in a secure and privacy-preserving manner. We use secure multiparty computation to ensure privacy protection. In addition, we ... ...

    Abstract In this paper we propose a novel protocol that allows suppliers and grid operators to collect users' aggregate metering data in a secure and privacy-preserving manner. We use secure multiparty computation to ensure privacy protection. In addition, we propose three different data aggregation algorithms that offer different balances between privacy-protection and performance. Our protocol is designed for a realistic scenario in which the data need to be sent to different parties, such as grid operators and suppliers. Furthermore, it facilitates an accurate calculation of transmission, distribution and grid balancing fees in a privacy-preserving manner. We also present a security analysis and a performance evaluation of our protocol based on well known multiparty computation algorithms implemented in C++.

    Comment: Accepted for publication at IEEE Transactions on Smart Grid
    Keywords Computer Science - Cryptography and Security
    Subject code 005 ; 303
    Publishing date 2018-01-25
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

    Cleemput, Sara / Dumon, Wim / Fonseca, Vagner / Abdool Karim, Wasim / Giovanetti, Marta / Alcantara, Luiz Carlos / Deforche, Koen / de Oliveira, Tulio

    bioRxiv

    Keywords covid19
    Language English
    Publishing date 2020-02-02
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.01.31.928796
    Database COVID19

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  8. Article: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

    Cleemput, Sara / Dumon, Wim / Fonseca, Vagner / Abdool Karim, Wasim / Giovanetti, Marta / Alcantara, Luiz Carlos / Deforche, Koen / de Oliveira, Tulio

    Bioinformatics

    Abstract: ... that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2 ... all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also ...

    Abstract SUMMARY: Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present the Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2000 sequences per submission and the analysis of a new whole-genome sequence will take approximately 1 min. The tool has been tested and validated with hundreds of whole genomes from 10 coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease. AVAILABILITY AND IMPLEMENTATION: https://www.genomedetective.com/app/typingtool/cov. CONTACT: koen@emweb.be or deoliveira@ukzn.ac.za. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #32108862
    Database COVID19

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  9. Article ; Online: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

    Cleemput, Sara / Dumon, Wim / Fonseca, Vagner / Abdool Karim, Wasim / Giovanetti, Marta / Alcantara, Luiz Carlos / Deforche, Koen / de Oliveira, Tulio

    Bioinformatics

    2020  Volume 36, Issue 11, Page(s) 3552–3555

    Abstract: ... that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2 ... all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also ...

    Abstract Abstract Summary Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present the Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2000 sequences per submission and the analysis of a new whole-genome sequence will take approximately 1 min. The tool has been tested and validated with hundreds of whole genomes from 10 coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease. Availability and implementation https://www.genomedetective.com/app/typingtool/cov Contact koen@emweb.be or deoliveira@ukzn.ac.za Supplementary information Supplementary data are available at Bioinformatics online.
    Keywords Statistics and Probability ; Computational Theory and Mathematics ; Biochemistry ; Molecular Biology ; Computational Mathematics ; Computer Science Applications ; covid19
    Language English
    Publisher Oxford University Press (OUP)
    Publishing country uk
    Document type Article ; Online
    ZDB-ID 1422668-6
    ISSN 1367-4803
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btaa145
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: SARS-CoV-2 vaccine antibody response and breakthrough infections in transplant recipients.

    Vanlerberghe, Benedict / Vrij, Casper / Bogaerts, Kris / Vermeersch, Pieter / Lagrou, Katrien / Molenberghs, Geert / Rega, Filip / Ceulemans, Laurens J / van Raemdonck, Dirk / Jochmans, Ina / Monbaliu, Diethard / Pirenne, Jacques / Vanuytsel, Tim / Gillard, Pieter / Schoemans, Hélène / Cleemput, Johan Van / Kuypers, Dirk / Vos, Robin / Nevens, Frederik /
    Verbeek, Jef

    Journal of medical virology

    2023  Volume 95, Issue 4, Page(s) e28736

    Abstract: Rates and modulators of SARS-CoV-2 vaccine nonresponse and breakthrough infections remain unclear ... solid organ and hematopoietic cell transplant recipients, with prior SARS-CoV-2 vaccination, were ... included between March 2021 and February 2022. SARS-CoV-2 anti-spike IgG antibodies were measured ...

    Abstract Rates and modulators of SARS-CoV-2 vaccine nonresponse and breakthrough infections remain unclear in serially vaccinated transplant recipients. In a prospective, mono-centric, observational study, 1878 adult solid organ and hematopoietic cell transplant recipients, with prior SARS-CoV-2 vaccination, were included between March 2021 and February 2022. SARS-CoV-2 anti-spike IgG antibodies were measured at inclusion and details on SARS-CoV-2 vaccine doses and infection were collected. No life-threatening adverse events were reported after a total of 4039 vaccine doses. In transplant recipients without prior SARS-CoV-2 infection (n = 1636), antibody response rates ranged widely, from 47% in lung transplant to 90% in liver transplant and 91% in hematopoietic cell transplant recipients after third vaccine dose. Antibody positivity rate and levels increased after each vaccine dose in all types of transplant recipients. In multivariable analysis, older age, chronic kidney disease and daily dose of mycophenolate and corticosteroids were negatively associated with antibody response rate. Overall rate of breakthrough infections was 25.2% and mainly (90.2%) occurred after third and fourth vaccine dose. Lung transplant recipients had the highest rates of severe breakthrough infection (10.5%) and death (2.5%). In multivariable analysis, older age, daily dose of mycophenolate and corticosteroids were associated with severe breakthrough infection. Transplant recipients with infection before first vaccine dose (n = 160) had higher antibody response rates and levels after each vaccine dose, and a significantly lower overall rate of breakthrough infections compared to those without prior infection. Antibody response after SARS-CoV-2 vaccination and rate of severe breakthrough infections vary largely between different transplant types and are modulated by specific risk factors. The observed heterogeneity supports a tailored approach against COVID-19 in transplant recipients.
    MeSH term(s) Adult ; Humans ; Antibodies, Viral ; Antibody Formation ; Breakthrough Infections ; COVID-19/prevention & control ; COVID-19 Vaccines/administration & dosage ; Hematopoietic Stem Cell Transplantation ; Immunoglobulin G ; Immunosuppressive Agents/adverse effects ; Prospective Studies ; SARS-CoV-2 ; Transplant Recipients
    Chemical Substances Antibodies, Viral ; COVID-19 Vaccines ; Immunoglobulin G ; Immunosuppressive Agents
    Language English
    Publishing date 2023-03-03
    Publishing country United States
    Document type Observational Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.28736
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