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  1. Article ; Online: Improved risk estimation of locoregional recurrence, secondary contralateral tumors and distant metastases in early breast cancer: the INFLUENCE 2.0 model.

    Völkel, Vinzenz / Hueting, Tom A / Draeger, Teresa / van Maaren, Marissa C / de Munck, Linda / Strobbe, Luc J A / Sonke, Gabe S / Schmidt, Marjanka K / van Hezewijk, Marjan / Groothuis-Oudshoorn, Catharina G M / Siesling, Sabine

    Breast cancer research and treatment

    2021  Volume 189, Issue 3, Page(s) 817–826

    Abstract: Purpose: To extend the functionality of the existing INFLUENCE nomogram for locoregional recurrence (LRR) of breast cancer toward the prediction of secondary primary tumors (SP) and distant metastases (DM) using updated follow-up data and the best ... ...

    Abstract Purpose: To extend the functionality of the existing INFLUENCE nomogram for locoregional recurrence (LRR) of breast cancer toward the prediction of secondary primary tumors (SP) and distant metastases (DM) using updated follow-up data and the best suitable statistical approaches.
    Methods: Data on women diagnosed with non-metastatic invasive breast cancer were derived from the Netherlands Cancer Registry (n = 13,494). To provide flexible time-dependent individual risk predictions for LRR, SP, and DM, three statistical approaches were assessed; a Cox proportional hazard approach (COX), a parametric spline approach (PAR), and a random survival forest (RSF). These approaches were evaluated on their discrimination using the Area Under the Curve (AUC) statistic and on calibration using the Integrated Calibration Index (ICI). To correct for optimism, the performance measures were assessed by drawing 200 bootstrap samples.
    Results: Age, tumor grade, pT, pN, multifocality, type of surgery, hormonal receptor status, HER2-status, and adjuvant therapy were included as predictors. While all three approaches showed adequate calibration, the RSF approach offers the best optimism-corrected 5-year AUC for LRR (0.75, 95%CI: 0.74-0.76) and SP (0.67, 95%CI: 0.65-0.68). For the prediction of DM, all three approaches showed equivalent discrimination (5-year AUC: 0.77-0.78), while COX seems to have an advantage concerning calibration (ICI < 0.01). Finally, an online calculator of INFLUENCE 2.0 was created.
    Conclusions: INFLUENCE 2.0 is a flexible model to predict time-dependent individual risks of LRR, SP and DM at a 5-year scale; it can support clinical decision-making regarding personalized follow-up strategies for curatively treated non-metastatic breast cancer patients.
    MeSH term(s) Breast Neoplasms/epidemiology ; Breast Neoplasms/therapy ; Combined Modality Therapy ; Female ; Humans ; Neoplasm Recurrence, Local/epidemiology ; Netherlands/epidemiology ; Nomograms
    Language English
    Publishing date 2021-08-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 604563-7
    ISSN 1573-7217 ; 0167-6806
    ISSN (online) 1573-7217
    ISSN 0167-6806
    DOI 10.1007/s10549-021-06335-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Fatal Carbapenem Resistance Development in Pseudomonas Aeruginosa Under Meropenem Monotherapy, Caused by Mutations in the OprD Outer Membrane Porin.

    Fluit, Ad C / Rentenaar, Rob J / Ekkelenkamp, Miquel B / Severs, Tim T / Mavinkurve-Groothuis, Annelies M C / Rogers, Malbert R C / Bruin, Marrie C A / Wolfs, Tom F W

    The Pediatric infectious disease journal

    2019  Volume 38, Issue 4, Page(s) 398–399

    Abstract: A 13-year old neutropenic boy succumbed to bacteremia and sepsis with a Pseudomonas aeruginosa strain that rapidly developed resistance to carbapenems during meropenem monotherapy. Whole genome sequencing of the susceptible and resistant blood culture ... ...

    Abstract A 13-year old neutropenic boy succumbed to bacteremia and sepsis with a Pseudomonas aeruginosa strain that rapidly developed resistance to carbapenems during meropenem monotherapy. Whole genome sequencing of the susceptible and resistant blood culture isolates revealed the meropenem-resistant phenotype to be caused by truncation of the OprD gene, which added to a preexisting inactivated mexR gene.
    MeSH term(s) Adolescent ; Anti-Bacterial Agents/administration & dosage ; Bacteremia/drug therapy ; Bacteremia/microbiology ; Blood Culture ; Fatal Outcome ; Humans ; Male ; Meropenem/administration & dosage ; Mutation ; Porins/genetics ; Pseudomonas Infections/drug therapy ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/drug effects ; Pseudomonas aeruginosa/genetics ; Sequence Deletion ; Whole Genome Sequencing ; beta-Lactam Resistance
    Chemical Substances Anti-Bacterial Agents ; Porins ; OprD protein, Pseudomonas aeruginosa (148412-32-2) ; Meropenem (FV9J3JU8B1)
    Language English
    Publishing date 2019-03-13
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 392481-6
    ISSN 1532-0987 ; 0891-3668
    ISSN (online) 1532-0987
    ISSN 0891-3668
    DOI 10.1097/INF.0000000000002244
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The many roads to cross-presentation.

    Groothuis, Tom A M / Neefjes, Jacques

    The Journal of experimental medicine

    2005  Volume 202, Issue 10, Page(s) 1313–1318

    Abstract: Cross-presentation of extracellular antigens by MHC class I molecules is required for priming cytotoxic T lymphocytes (CTLs) at locations remote from the site of infection. Various mechanisms have been proposed to explain cross-presentation. One such ... ...

    Abstract Cross-presentation of extracellular antigens by MHC class I molecules is required for priming cytotoxic T lymphocytes (CTLs) at locations remote from the site of infection. Various mechanisms have been proposed to explain cross-presentation. One such mechanism involves the fusion of the endoplasmic reticulum (ER) with the endosomal-phagosomal system, in which the machinery required for peptide loading of MHC class I molecules is introduced directly into the phagosome. Here, we discuss the evidence for and against the ER-phagosome concept as well as other possible mechanisms of cross-presentation.
    MeSH term(s) Animals ; Cross-Priming/immunology ; Endoplasmic Reticulum/immunology ; Humans ; Phagosomes/immunology ; T-Lymphocytes, Cytotoxic/immunology
    Language English
    Publishing date 2005-11-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 218343-2
    ISSN 1540-9538 ; 0022-1007
    ISSN (online) 1540-9538
    ISSN 0022-1007
    DOI 10.1084/jem.20051379
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Monitoring nutrient transport in tissue-engineered grafts.

    Liu, Jun / Hilderink, Janneke / Groothuis, Tom A M / Otto, Cees / van Blitterswijk, Clemens A / de Boer, Jan

    Journal of tissue engineering and regenerative medicine

    2015  Volume 9, Issue 8, Page(s) 952–960

    Abstract: Limited nutrient diffusion in three-dimensional (3D) constructs is a major concern in tissue engineering. Therefore, monitoring nutrient availability and diffusion within a scaffold is an important asset. Since nutrients come in various forms, we have ... ...

    Abstract Limited nutrient diffusion in three-dimensional (3D) constructs is a major concern in tissue engineering. Therefore, monitoring nutrient availability and diffusion within a scaffold is an important asset. Since nutrients come in various forms, we have investigated the diffusion of the oxygen, luciferin and dextran molecules within tissue-engineered constructs using optical imaging technologies. First, oxygen availability and diffusion were investigated, using transgenic cell lines in which a hypoxia-responsive element drives expression of the green fluorescent protein gene. Using confocal imaging, we observed oxygen limitation, starting at around 200 µm from the periphery in the context of agarose gel with 1 million CHO cells. Diffusion of luciferin was monitored real-time in agarose gels using a cell line in which the luciferase gene was driven by a constitutively active CMV promoter. Gel concentration affected the diffusion rate of luciferin. Furthermore, we assessed the diffusion rates of fluorescent dextran molecules of different molecular weights in biomaterials by fluorescence recovery after photobleaching (FRAP) and observed that diffusion depended on both molecular size and gel concentration. In conclusion, we have validated a set of efficient tools to investigate molecular diffusion of a range of molecules and to optimize biomaterials design in order to improve nutrient delivery.
    MeSH term(s) Animals ; Biocompatible Materials/chemistry ; CHO Cells ; Cell Survival ; Cricetinae ; Cricetulus ; Diffusion ; Firefly Luciferin/chemistry ; Fluorescence Recovery After Photobleaching ; Genes, Reporter ; Green Fluorescent Proteins/chemistry ; Green Fluorescent Proteins/metabolism ; Hypoxia ; Imaging, Three-Dimensional/methods ; Luciferases/metabolism ; Microscopy, Confocal ; Optics and Photonics ; Oxygen/chemistry ; Sepharose/chemistry ; Tissue Engineering/methods
    Chemical Substances Biocompatible Materials ; Green Fluorescent Proteins (147336-22-9) ; Firefly Luciferin (5TBB02N29K) ; Sepharose (9012-36-6) ; Luciferases (EC 1.13.12.-) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2015-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-7005
    ISSN (online) 1932-7005
    DOI 10.1002/term.1654
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Development and validation of the patient-reported "Facial Function Scale" for facioscapulohumeral muscular dystrophy.

    Mul, Karlien / Wijayanto, Feri / Loonen, Tom G J / Groot, Perry / Vincenten, Sanne C C / Knuijt, Simone / Groothuis, Jan T / Maal, Thomas J J / Heskes, Tom / Voermans, Nicol C / Engelen, Baziel G M van

    Disability and rehabilitation

    2022  Volume 45, Issue 9, Page(s) 1530–1535

    Abstract: Purpose: Facial weakness and its functional consequences are an often underappreciated clinical feature of facioscapulohumeral muscular dystrophy (FSHD) by healthcare professionals and researchers. This is at least in part due to the fact that there are ...

    Abstract Purpose: Facial weakness and its functional consequences are an often underappreciated clinical feature of facioscapulohumeral muscular dystrophy (FSHD) by healthcare professionals and researchers. This is at least in part due to the fact that there are few adequate clinical outcome measures available.
    Methods: We developed the Facial Function Scale, a Rasch-built questionnaire on the functional disabilities relating to facial weakness in FSHD. A preliminary 33-item questionnaire was created based on semi-structured interviews with 16 FSHD patients and completed by 119 patients. For reliability studies, 73 patients completed it again after a two-week interval. Data were subjected to semi-automated Rasch analysis to select the most appropriate item set to fit model expectations.
    Results: This resulted in a 25-item unidimensional, linear-weighted questionnaire with high internal consistency (person separation index = 0.92) and test-retest reliability (patients' locations ICC = 0.98 and items' locations ICC = 0.99). Good external construct validity scores were obtained through correlation with the Communicative Participation Item Bank questionnaire, examiner-reported Facial Weakness Score and facial weakness subscale of the FSHD evaluation score (respectively
    Conclusions: This study provides a linear-weighted, clinimetrically sound, patient-reported outcome measure on the functional disabilities relating to facial weakness in FSHD, to enable further research on this relevant topic.Implications for rehabilitationFacial weakness and its functional consequences are an often underappreciated clinical feature of facioscapulohumeral muscular dystrophy (FSHD), both in symptomatic treatment and in research.To enable the development and testing of therapeutic symptomatic interventions for facial weakness, clinical outcome measures are required.This study provides a linear-weighted, clinimetrically sound, patient-reported outcome measure on the functional disabilities relating to facial weakness in FSHD patients.
    MeSH term(s) Humans ; Muscular Dystrophy, Facioscapulohumeral/diagnosis ; Reproducibility of Results ; Face ; Communication ; Patient Reported Outcome Measures
    Language English
    Publishing date 2022-05-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1104775-6
    ISSN 1464-5165 ; 0963-8288
    ISSN (online) 1464-5165
    ISSN 0963-8288
    DOI 10.1080/09638288.2022.2066208
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Monitoring, documenting and reporting the quality of antibiotic use in the Netherlands: a pilot study to establish a national antimicrobial stewardship registry.

    Berrevoets, Marvin Ah / Ten Oever, Jaap / Sprong, Tom / van Hest, Reinier M / Groothuis, Ingeborg / van Heijl, Inger / Schouten, Jeroen A / Hulscher, Marlies E / Kullberg, Bart-Jan

    BMC infectious diseases

    2017  Volume 17, Issue 1, Page(s) 565

    Abstract: Background: The Dutch Working Party on Antibiotic Policy is developing a national antimicrobial stewardship registry. This registry will report both the quality of antibiotic use in hospitals in the Netherlands and the stewardship activities employed. ... ...

    Abstract Background: The Dutch Working Party on Antibiotic Policy is developing a national antimicrobial stewardship registry. This registry will report both the quality of antibiotic use in hospitals in the Netherlands and the stewardship activities employed. It is currently unclear which aspects of the quality of antibiotic use are monitored by antimicrobial stewardship teams (A-teams) and can be used as indicators for the stewardship registry. In this pilot study we aimed to determine which stewardship objectives are eligible for the envisioned registry.
    Methods: We performed an observational pilot study among five Dutch hospitals. We assessed which of the 14 validated stewardship objectives (11 process of care recommendations and 3 structure of care recommendations) the A-teams monitored and documented in individual patients. They provided, where possible, data to compute quality indicator (QI) performance scores in line with recently developed QIs to measure appropriate antibiotic use in hospitalized adults for the period of January 2015 through December 2015 RESULTS: All hospitals had a local antibiotic guideline describing recommended antimicrobial use. All A-teams monitored the performance of bedside consultations in Staphylococcus aureus bacteremia and the prescription of restricted antimicrobials. Documentation and reporting were the best for the use of restricted antimicrobials: 80% of the A-teams could report data. Lack of time and the absence of an electronic medical record system enabling documentation during the daily work flow were the main barriers hindering documentation and reporting.
    Conclusions: Five out of 11 stewardship objectives were actively monitored by A-teams. Without extra effort, 4 A-teams could report on the quality of use of restricted antibiotics. Therefore, this aspect of antibiotic use should be the starting point of the national antimicrobial stewardship registry. Our registry is expected to become a powerful tool to evaluate progress and impact of antimicrobial stewardship programs in hospitals.
    MeSH term(s) Adult ; Anti-Bacterial Agents/therapeutic use ; Anti-Infective Agents/therapeutic use ; Bacteremia/drug therapy ; Hospitals/statistics & numerical data ; Humans ; Netherlands ; Pilot Projects ; Registries/statistics & numerical data ; Staphylococcal Infections/drug therapy ; Staphylococcus aureus/pathogenicity
    Chemical Substances Anti-Bacterial Agents ; Anti-Infective Agents
    Language English
    Publishing date 2017-08-15
    Publishing country England
    Document type Journal Article
    ISSN 1471-2334
    ISSN (online) 1471-2334
    DOI 10.1186/s12879-017-2673-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Monitoring the distribution and dynamics of proteasomes in living cells.

    Groothuis, Tom A M / Reits, Eric A J

    Methods in enzymology

    2005  Volume 399, Page(s) 549–563

    Abstract: The proteasome is a large protease complex present in the cytoplasm and the nucleus of eukaryotic cells. This chapter describes how proteasomes in living cells can be visualized using fluorescently tagged subunits. The use of noninvasive fluorescent tags ...

    Abstract The proteasome is a large protease complex present in the cytoplasm and the nucleus of eukaryotic cells. This chapter describes how proteasomes in living cells can be visualized using fluorescently tagged subunits. The use of noninvasive fluorescent tags like the green fluorescent protein enables visualization of various subunits of the ubiquitin-proteasome system and prevents possible artefacts like disruption by microinjection or altered fluorescence distribution caused by fixation. Once quantitative incorporation of tagged subunits into proteasomes is ensured, the distribution of proteasome complexes can be visualized in vivo. In addition, different bleaching techniques can be applied to study the dynamics of proteasomes within the cell. Finally, we describe how proteasomes can be recruited to particular sites of degradation during various cellular conditions like aggregate formation and virus infection.
    MeSH term(s) Cell Line, Tumor ; Green Fluorescent Proteins/metabolism ; Humans ; Hydrolysis ; Proteasome Endopeptidase Complex/metabolism
    Chemical Substances Green Fluorescent Proteins (147336-22-9) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2005
    Publishing country United States
    Document type Journal Article
    ISSN 0076-6879
    ISSN 0076-6879
    DOI 10.1016/S0076-6879(05)99037-X
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Ubiquitin crosstalk connecting cellular processes.

    Groothuis, Tom A M / Dantuma, Nico P / Neefjes, Jacques / Salomons, Florian A

    Cell division

    2006  Volume 1, Page(s) 21

    Abstract: The polypeptide ubiquitin is used in many processes as different as endocytosis, multivesicular body formation, and regulation of gene transcription. Conjugation of a single ubiquitin moiety is typically used in these processes. A polymer of ubiquitin ... ...

    Abstract The polypeptide ubiquitin is used in many processes as different as endocytosis, multivesicular body formation, and regulation of gene transcription. Conjugation of a single ubiquitin moiety is typically used in these processes. A polymer of ubiquitin moieties is required for tagging proteins for proteasomal degradation. Besides its role in protein degradation, ubiquitin is also engaged as mono- or polymer in intracellular signalling and DNA repair. Since free ubiquitin is present in limiting amounts in cells, changes in the demands for ubiquitin in any of these processes is likely to indirectly affect other ubiquitin modifications. For example, proteotoxic stress strongly increases poly-ubiquitylated proteins at the cost of mono-ubiquitylated histones resulting in chromatin remodelling and altered transcription. Here we discuss the interconnection between ubiquitin-dependent processes and speculate on the functional significance of the ubiquitin equilibrium as a signalling route translating cellular stress into molecular responses.
    Language English
    Publishing date 2006-09-28
    Publishing country England
    Document type Journal Article
    ISSN 1747-1028
    ISSN (online) 1747-1028
    DOI 10.1186/1747-1028-1-21
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  9. Article: A dynamic ubiquitin equilibrium couples proteasomal activity to chromatin remodeling.

    Dantuma, Nico P / Groothuis, Tom A M / Salomons, Florian A / Neefjes, Jacques

    The Journal of cell biology

    2006  Volume 173, Issue 1, Page(s) 19–26

    Abstract: Protein degradation, chromatin remodeling, and membrane trafficking are critically regulated by ubiquitylation. The presence of several coexisting ubiquitin-dependent processes, each of crucial importance to the cell, is remarkable. This brings up ... ...

    Abstract Protein degradation, chromatin remodeling, and membrane trafficking are critically regulated by ubiquitylation. The presence of several coexisting ubiquitin-dependent processes, each of crucial importance to the cell, is remarkable. This brings up questions on how the usage of this versatile regulator is negotiated between the different cellular processes. During proteotoxic stress, the accumulation of ubiquitylated substrates coincides with the depletion of ubiquitylated histone H2A and chromatin remodeling. We show that this redistribution of ubiquitin during proteotoxic stress is a direct consequence of competition for the limited pool of free ubiquitin. Thus, the ubiquitin cycle couples various ubiquitin-dependent processes because of a rate-limiting pool of free ubiquitin. We propose that this ubiquitin equilibrium may allow cells to sense proteotoxic stress in a genome-wide fashion.
    MeSH term(s) Active Transport, Cell Nucleus/physiology ; Cell Compartmentation/physiology ; Cell Line, Tumor ; Chromatin Assembly and Disassembly/genetics ; Fungal Proteins/metabolism ; Gene Expression Regulation, Fungal/genetics ; Histones/genetics ; Histones/metabolism ; Humans ; Proteasome Endopeptidase Complex/genetics ; Proteasome Endopeptidase Complex/metabolism ; Protein Transport/physiology ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Stress, Physiological/genetics ; Stress, Physiological/metabolism ; Ubiquitin/metabolism
    Chemical Substances Fungal Proteins ; Histones ; Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2006-04-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.200510071
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: MHC class I alleles and their exploration of the antigen-processing machinery.

    Groothuis, Tom A M / Griekspoor, Alexander C / Neijssen, Joost J / Herberts, Carla A / Neefjes, Jacques J

    Immunological reviews

    2005  Volume 207, Page(s) 60–76

    Abstract: At the cell surface, major histocompatibility complex (MHC) class I molecules present fragments of intracellular antigens to the immune system. This is the end result of a cascade of events initiated by multiple steps of proteolysis. Only a small part of ...

    Abstract At the cell surface, major histocompatibility complex (MHC) class I molecules present fragments of intracellular antigens to the immune system. This is the end result of a cascade of events initiated by multiple steps of proteolysis. Only a small part of the fragments escapes degradation by interacting with the peptide transporter associated with antigen presentation and is translocated into the endoplasmic reticulum lumen for binding to MHC class I molecules. Subsequently, these newly formed complexes can be transported to the plasma membrane for presentation. Every step in this process confers specificity and determines the ultimate result: presentation of only few fragments from a given antigen. Here, we introduce the players in the antigen processing and presentation cascade and describe their specificity and allelic variation. We highlight MHC class I alleles, which are not only different in sequence but also use different aspects of the antigen presentation pathway to their advantage: peptide acquaintance.
    MeSH term(s) Animals ; Antigen Presentation/immunology ; Histocompatibility Antigens Class I/genetics ; Histocompatibility Antigens Class I/immunology ; Humans
    Chemical Substances Histocompatibility Antigens Class I
    Language English
    Publishing date 2005-10
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 391796-4
    ISSN 1600-065X ; 0105-2896
    ISSN (online) 1600-065X
    ISSN 0105-2896
    DOI 10.1111/j.0105-2896.2005.00305.x
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