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  1. Article ; Online: Evaluating the D4Science virtual research environment platform for agro-climatic research

    Knapen, Rob / Lokers, Rob / Janssen, Sander

    Agricultural Systems. 2023 Aug., v. 210 p.103706-

    2023  

    Abstract: From its early beginnings the Internet has been used by scientists to collaborate and share information about their research. Increasing connectivity and networking capabilities have resulted in improved collaboration functionalities ultimately combined ... ...

    Abstract From its early beginnings the Internet has been used by scientists to collaborate and share information about their research. Increasing connectivity and networking capabilities have resulted in improved collaboration functionalities ultimately combined in complete virtual research environments (VRE) as a type of virtual laboratories. These aim at providing collaborative online workplaces with access to all needed tools, data, and computing resources, and supporting data sharing. Since each research domain has its own characteristics, requirements, and preferred tooling, VRE providers must make trade-offs between the specificity of components and the functionality provided. The D4Science VRE adopts a modular approach based on open standards for constructing VREs for interested communities. The agro-climatic science domain develops diverse analytical tools that it connects to heterogenous data sources (i.e. climate data, experimental fields, satellite data, soil samples) originating from other domains, which is often poorly standardised and sparsely interlinked at best. The aim of this paper is to test and evaluate the usefulness of the D4Science based VREs for this agro-climatic science domain, using crop growth simulation and crop phenology estimation as characteristic use cases, with specific attention to Open Science. Based on the needs of the use cases a VRE has been composed and further developed in an iterative approach and evaluated at the end of each implementation cycle. Both the development work and the evaluation results point at the foreseen potential benefits of adequate VREs and the current existence of sufficient opportunities and capabilities for constructing them. The focus when developing VREs should be on supporting research with proven and stable tools, instead of striving to include the latest and greatest. The agro-climatic research domain has ambitious requirements concerning the availability and integration of data and models, which proved to be particularly challenging for incorporating in a VRE. Yet, a clear but gradual adoption of digital techniques to further the science itself is happening and VREs represent an ultimate possible end-state of Open Science. To conclude, this paper provides a few recommendations that we think can help this ongoing transition.
    Keywords Internet ; meteorological data ; phenology ; remote sensing ; soil ; Open Science ; Big data ; Data engineering ; Crop growth simulation ; Crop phenology estimation
    Language English
    Dates of publication 2023-08
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ZDB-ID 413255-5
    ISSN 0308-521X
    ISSN 0308-521X
    DOI 10.1016/j.agsy.2023.103706
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Lysyl Oxidase Inhibition by Heparin in Idiopathic Pulmonary Fibrosis: Is There Still Hope?

    Janssen, Rob

    American journal of respiratory and critical care medicine

    2017  Volume 195, Issue 1, Page(s) 141–142

    Language English
    Publishing date 2017-01-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201604-0763LE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Can Bisphosphonates Prevent Vitamin K Antagonist Toxicity in Patients with Idiopathic Pulmonary Fibrosis?

    Janssen, Rob

    American journal of respiratory and critical care medicine

    2017  Volume 195, Issue 2, Page(s) 269–270

    Language English
    Publishing date 2017-01-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201605-1074LE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Evaluating the D4Science virtual research environment platform for agro-climatic research

    Knapen, Rob / Lokers, Rob / Janssen, Sander

    Agricultural Systems

    2023  Volume 210

    Abstract: CONTEXT: From its early beginnings the Internet has been used by scientists to collaborate and share information about their research. Increasing connectivity and networking capabilities have resulted in improved collaboration functionalities ultimately ... ...

    Abstract CONTEXT: From its early beginnings the Internet has been used by scientists to collaborate and share information about their research. Increasing connectivity and networking capabilities have resulted in improved collaboration functionalities ultimately combined in complete virtual research environments (VRE) as a type of virtual laboratories. These aim at providing collaborative online workplaces with access to all needed tools, data, and computing resources, and supporting data sharing. Since each research domain has its own characteristics, requirements, and preferred tooling, VRE providers must make trade-offs between the specificity of components and the functionality provided. The D4Science VRE adopts a modular approach based on open standards for constructing VREs for interested communities. The agro-climatic science domain develops diverse analytical tools that it connects to heterogenous data sources (i.e. climate data, experimental fields, satellite data, soil samples) originating from other domains, which is often poorly standardised and sparsely interlinked at best. OBJECTIVE: The aim of this paper is to test and evaluate the usefulness of the D4Science based VREs for this agro-climatic science domain, using crop growth simulation and crop phenology estimation as characteristic use cases, with specific attention to Open Science. METHODS: Based on the needs of the use cases a VRE has been composed and further developed in an iterative approach and evaluated at the end of each implementation cycle. RESULTS AND CONCLUSION: Both the development work and the evaluation results point at the foreseen potential benefits of adequate VREs and the current existence of sufficient opportunities and capabilities for constructing them. The focus when developing VREs should be on supporting research with proven and stable tools, instead of striving to include the latest and greatest. SIGNIFICANCE: The agro-climatic research domain has ambitious requirements concerning the availability and integration of data and ...
    Keywords Big data ; Crop growth simulation ; Crop phenology estimation ; Data engineering ; Open Science
    Subject code 020
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 413255-5
    ISSN 0308-521X
    ISSN 0308-521X
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Influence of female sex and double-quadruple semitendinosus-gracilis graft on the incidence of postoperative symptomatic cyclops lesions after ACL reconstruction.

    Arens, Tabea / van Melick, Nicky / van der Steen, Maria C / Janssen, Rob P A / Bogie, Rob

    Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA

    2024  

    Abstract: Purpose: Risk factors for the development of symptomatic cyclops lesion after anterior cruciate ligament reconstruction (ACLR) surgery are not entirely identified yet. This study aimed to investigate whether the choice of hamstring graft (semitendinosus- ...

    Abstract Purpose: Risk factors for the development of symptomatic cyclops lesion after anterior cruciate ligament reconstruction (ACLR) surgery are not entirely identified yet. This study aimed to investigate whether the choice of hamstring graft (semitendinosus-gracilis; STG vs. semitendinosus; ST) affects the risk of developing a symptomatic cyclops lesion after ACLR.
    Methods: This retrospective cohort study included 1416 patients receiving either an ST graft (n = 1209) or an STG graft (n = 207) ACLR with a follow-up of at least 2 years. A persisting extension limitation was clinically determined, and cyclops lesions were confirmed by magnetic resonance imaging (MRI) and second-look arthroscopy. Graft-specific incidence of cyclops lesions was examined with χ
    Results: In total, 46 patients developed symptomatic cyclops lesions (3.2%), with 36 having ACLR with an ST graft (3.0%) and 10 with an STG graft (4.8%) (n.s). The mean time from ACLR to the second-look arthroscopy for cyclops removal was 1.1 ± 0.6 years. Female patients were 2.5 times more likely to develop a cyclops lesion than male patients. Patients with an STG graft and larger graft diameters did not have a higher risk of developing cyclops lesions. Patients who received an STG graft with both tendons folded four times (double-quadruple) had significantly higher risk of developing a cyclops compared with all other numbers of graft bundles combined (8.3%, respectively 3.0%; p = 0.014).
    Conclusion: This study could not prove an increased risk of developing a symptomatic cyclops lesion for patients with an STG graft compared with an ST graft used for ACLR. However, patients with a double-quadruple ACLR had a higher percentage of cyclops lesions compared with all other numbers of graft bundles. Female sex was associated with an increased risk of developing cyclops lesions.
    Level of evidence: Level III.
    Language English
    Publishing date 2024-04-02
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1159064-6
    ISSN 1433-7347 ; 0942-2056
    ISSN (online) 1433-7347
    ISSN 0942-2056
    DOI 10.1002/ksa.12142
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Why Pregnant Women Should Avoid Any Form of Nicotine during Pregnancy: An Elastin-based Perspective.

    Janssen, Rob

    American journal of respiratory and critical care medicine

    2016  Volume 194, Issue 2, Page(s) 246–247

    Language English
    Publishing date 2016-07-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201603-0478LE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Magnesium to counteract elastin degradation and vascular calcification in chronic obstructive pulmonary disease.

    Janssen, Rob

    Medical hypotheses

    2017  Volume 107, Page(s) 74–77

    Abstract: Accelerated elastin degradation is an important pathogenic mechanism in chronic obstructive pulmonary disease (COPD) leading to irreversible lung function loss and cardiovascular comorbidities. The rate of elastin breakdown is a predictor of mortality in ...

    Abstract Accelerated elastin degradation is an important pathogenic mechanism in chronic obstructive pulmonary disease (COPD) leading to irreversible lung function loss and cardiovascular comorbidities. The rate of elastin breakdown is a predictor of mortality in patients with COPD. Decelerating elastinolysis might be an attractive therapeutic target in this debilitating condition. Vascular calcification starts in the elastin network of the arterial wall and is enhanced in patients with COPD. Elastin calcification is accompanied by an upregulation of matrix metalloproteinase gene expression and consequently a shift in the elastase/anti-elastase balance towards degradation. Magnesium can be regarded as a natural calcium antagonist and has the proven ability to ameliorate vascular calcification. Furthermore, an animal study has suggested that magnesium deficiency promotes elastin degradation. I hypothesize that inhibiting elastin calcification by means of magnesium supplementation might counteract both vascular calcification and elastin degradation in COPD. This could potentially have a favorable impact on cardiovascular and respiratory related morbidity/mortality in patients with COPD.
    Language English
    Publishing date 2017-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 193145-3
    ISSN 1532-2777 ; 0306-9877
    ISSN (online) 1532-2777
    ISSN 0306-9877
    DOI 10.1016/j.mehy.2017.08.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Comment on Kremer et al. Kidney Function-Dependence of Vitamin K-Status Parameters: Results from the TransplantLines Biobank and Cohort Studies.

    Janssen, Rob / Walk, Jona / Vermeer, Cees

    Nutrients

    2022  Volume 14, Issue 12

    Abstract: In the article "Kidney Function-Dependence of Vitamin K-Status Parameters: Results from the TransplantLines Biobank and Cohort Studies", Kremer et al. [ ... ]. ...

    Abstract In the article "Kidney Function-Dependence of Vitamin K-Status Parameters: Results from the TransplantLines Biobank and Cohort Studies", Kremer et al. [...].
    MeSH term(s) Biological Specimen Banks ; Cohort Studies ; Humans ; Kidney ; Nutrients ; Vitamin K
    Chemical Substances Vitamin K (12001-79-5)
    Language English
    Publishing date 2022-06-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2518386-2
    ISSN 2072-6643 ; 2072-6643
    ISSN (online) 2072-6643
    ISSN 2072-6643
    DOI 10.3390/nu14122439
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Anticoagulant Therapy in Idiopathic Pulmonary Fibrosis and Its Potential Effects on Pathogenesis.

    Janssen, Rob

    American journal of respiratory and critical care medicine

    2016  Volume 193, Issue 6, Page(s) 700–701

    MeSH term(s) Atrial Fibrillation/complications ; Atrial Fibrillation/drug therapy ; Humans ; Idiopathic Pulmonary Fibrosis/complications ; Male ; Thrombophlebitis/complications ; Thrombophlebitis/drug therapy ; Warfarin/adverse effects
    Chemical Substances Warfarin (5Q7ZVV76EI)
    Language English
    Publishing date 2016-03-15
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201510-2079LE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Comment on Sobczyk, M.K.; Gaunt, T.R. The Effect of Circulating Zinc, Selenium, Copper and Vitamin K

    Janssen, Rob / Vermeer, Cees / Walk, Jona / Linneberg, Allan

    Nutrients

    2022  Volume 14, Issue 5

    Abstract: Sobczyk and Gaunt genetically predicted circulating zinc, selenium, copper, and vitamin ... ...

    Abstract Sobczyk and Gaunt genetically predicted circulating zinc, selenium, copper, and vitamin K
    MeSH term(s) COVID-19 ; Copper ; Humans ; Mendelian Randomization Analysis ; Nutrients ; SARS-CoV-2 ; Selenium ; Vitamin K 1 ; Zinc
    Chemical Substances Copper (789U1901C5) ; Vitamin K 1 (84-80-0) ; Selenium (H6241UJ22B) ; Zinc (J41CSQ7QDS)
    Language English
    Publishing date 2022-03-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2518386-2
    ISSN 2072-6643 ; 2072-6643
    ISSN (online) 2072-6643
    ISSN 2072-6643
    DOI 10.3390/nu14051112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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