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  • 11
    In: Acta Neuropathologica, Springer Science and Business Media LLC, Vol. 136, No. 2 ( 2018-8), p. 227-237
    Type of Medium: Online Resource
    ISSN: 0001-6322 , 1432-0533
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 1458410-4
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  • 12
    In: Critical Care, Springer Science and Business Media LLC, Vol. 26, No. 1 ( 2022-12)
    Abstract: It remains elusive how the characteristics, the course of disease, the clinical management and the outcomes of critically ill COVID-19 patients admitted to intensive care units (ICU) worldwide have changed over the course of the pandemic. Methods Prospective, observational registry constituted by 90 ICUs across 22 countries worldwide including patients with a laboratory-confirmed, critical presentation of COVID-19 requiring advanced organ support. Hierarchical, generalized linear mixed-effect models accounting for hospital and country variability were employed to analyse the continuous evolution of the studied variables over the pandemic. Results Four thousand forty-one patients were included from March 2020 to September 2021. Over this period, the age of the admitted patients (62 [95% CI 60–63] years vs 64 [62–66] years, p   〈  0.001) and the severity of organ dysfunction at ICU admission decreased (Sequential Organ Failure Assessment 8.2 [7.6–9.0] vs 5.8 [5.3–6.4] , p   〈  0.001) and increased, while more female patients (26 [23–29]% vs 41 [35–48] %, p   〈  0.001) were admitted. The time span between symptom onset and hospitalization as well as ICU admission became longer later in the pandemic (6.7 [6.2–7.2| days vs 9.7 [8.9–10.5] days, p   〈  0.001). The PaO 2 /FiO 2 at admission was lower (132 [123–141] mmHg vs 101 [91–113] mmHg, p   〈  0.001) but showed faster improvements over the initial 5 days of ICU stay in late 2021 compared to early 2020 (34 [20–48] mmHg vs 70 [41–100] mmHg, p  = 0.05). The number of patients treated with steroids and tocilizumab increased, while the use of therapeutic anticoagulation presented an inverse U-shaped behaviour over the course of the pandemic. The proportion of patients treated with high-flow oxygen (5 [4–7]% vs 20 [14–29] , p   〈  0.001) and non-invasive mechanical ventilation (14 [11–18]% vs 24 [17–33] %, p   〈  0.001) throughout the pandemic increased concomitant to a decrease in invasive mechanical ventilation (82 [76–86]% vs 74 [64–82] %, p   〈  0.001). The ICU mortality (23 [19–26]% vs 17 [12–25] %, p   〈  0.001) and length of stay (14 [13–16] days vs 11 [10–13] days, p   〈  0.001) decreased over 19 months of the pandemic. Conclusion Characteristics and disease course of critically ill COVID-19 patients have continuously evolved, concomitant to the clinical management, throughout the pandemic leading to a younger, less severely ill ICU population with distinctly different clinical, pulmonary and inflammatory presentations than at the onset of the pandemic.
    Type of Medium: Online Resource
    ISSN: 1364-8535
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2051256-9
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  • 13
    In: Infection, Springer Science and Business Media LLC, Vol. 49, No. 4 ( 2021-08), p. 703-714
    Abstract: Adequate patient allocation is pivotal for optimal resource management in strained healthcare systems, and requires detailed knowledge of clinical and virological disease trajectories. The purpose of this work was to identify risk factors associated with need for invasive mechanical ventilation (IMV), to analyse viral kinetics in patients with and without IMV and to provide a comprehensive description of clinical course. Methods A cohort of 168 hospitalised adult COVID-19 patients enrolled in a prospective observational study at a large European tertiary care centre was analysed. Results Forty-four per cent (71/161) of patients required invasive mechanical ventilation (IMV). Shorter duration of symptoms before admission (aOR 1.22 per day less, 95% CI 1.10–1.37, p   〈  0.01) and history of hypertension (aOR 5.55, 95% CI 2.00–16.82, p   〈  0.01) were associated with need for IMV. Patients on IMV had higher maximal concentrations, slower decline rates, and longer shedding of SARS-CoV-2 than non-IMV patients (33 days, IQR 26–46.75, vs 18 days, IQR 16–46.75, respectively, p   〈  0.01). Median duration of hospitalisation was 9 days (IQR 6–15.5) for non-IMV and 49.5 days (IQR 36.8–82.5) for IMV patients. Conclusions Our results indicate a short duration of symptoms before admission as a risk factor for severe disease that merits further investigation and different viral load kinetics in severely affected patients. Median duration of hospitalisation of IMV patients was longer than described for acute respiratory distress syndrome unrelated to COVID-19.
    Type of Medium: Online Resource
    ISSN: 0300-8126 , 1439-0973
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2006315-5
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  • 14
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 22, No. Supplement_3 ( 2020-12-04), p. iii308-iii308
    Abstract: By profiling enhancers in primary ependymoma tumors, we have recently identified putative oncogenes, molecular targets, and functional pathways. Inhibition of selected targets diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymoma. While enhancers frequently regulate the nearest gene, identification of enhancer target genes remains to be a challenge in the absence of chromosome conformation information. Consequently, we have now used HiC to map the 3-dimensional organization of tumor chromatin in the two most common and aggressive ependymoma subgroups: posterior fossa group A (PF-EPN-A) and supratentorial ependymomas with gene fusions involving the NF-κB subunit gene RELA (ST-EPN-RELA). By an integrative analysis of enhancer and gene expression in the context of the newly derived HiC data, we find that a large number of the predicted enhancer target genes are enriched for strong physical interactions. Importantly, we also identify many new putative tumor-dependency genes activated by long-range promoter-enhancer interactions and complex tumor-specific chromatin clusters of regulatory elements. Complementary to the analysis of gene-enhancer interactions, we have also leveraged the HiC data for resolving structural rearrangements underlying copy number alterations. Copy number gains of the 1q arm of chromosome 1 are especially associated with poor survival. Our preliminary results in PFA relapse samples show complex structural variants underlying 1q gain that lead to inter-chromosomal rearrangements and affect several genes that potentially contribute to poor survival. In ongoing work we are testing the relevance of the novel candidate genes for tumor cell growth and proliferation in-patient derived ependymoma models.
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2094060-9
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  • 15
    In: Nature Methods, Springer Science and Business Media LLC, Vol. 20, No. 4 ( 2023-04), p. 523-535
    Abstract: Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.
    Type of Medium: Online Resource
    ISSN: 1548-7091 , 1548-7105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2163081-1
    SSG: 12
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  • 16
    Online Resource
    Online Resource
    Elsevier BV ; 2010
    In:  Physica E: Low-dimensional Systems and Nanostructures Vol. 43, No. 2 ( 2010-12), p. 569-587
    In: Physica E: Low-dimensional Systems and Nanostructures, Elsevier BV, Vol. 43, No. 2 ( 2010-12), p. 569-587
    Type of Medium: Online Resource
    ISSN: 1386-9477
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2010
    detail.hit.zdb_id: 1466595-5
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  • 17
    In: TumorDiagnostik & Therapie, Georg Thieme Verlag KG, Vol. 42, No. 04 ( 2021-05), p. 277-283
    Abstract: Fragestellung Die COVID-19-Pandemie hat Auswirkungen auf die Versorgung von Tumorpatienten. Wie erleben Patienten mit Kopf-Hals-Tumoren (KHT) diese Situation und welche Coping-Strategien ergeben sich? Material und Methode Wir befragten in Studie 1 während des Lockdowns (15.04.–15.05.2020) 433 Tumorpatienten nach ihren Eindrücken/Belastungen (online, standardisiert, anonym). In Studie 2 wurden 292 Patienten nach dem Lockdown (06.05.–10.06.2020) zu ihren wahrgenommenen Veränderungen, Perspektivwechseln und Coping-Strategien mit standardisierten Tools (WHO-5, MLQ-10, GrAw-7) befragt. Für beide Studien analysierten wir die KHT. Ergebnisse An Studie 1 nahmen 91 Patienten mit KHT teil, in Studie 2 wurden 84 Patienten mit KHT aufgenommen. Studie 1 zeigte im Lockdown einen hohen Druck auf die Mehrheit der Patienten mit KHT (53,8 %). Es waren Ängste bezüglich der eigenen Krankheit (39,6 %), aber auch erwartete physische (24,7 %) und psychische Folgen (21,3 %) der Pandemie. Die soziale Isolation (Besuchsverbot) wurde als ein Hauptproblem (58,5 %) beschrieben. Studie 2 bestätigte diese Belastungen auch nach dem Lockdown. Intensivere Beziehungen in der Familie (60/100 Punkten) sowie eine Zuwendung zu Natur und Stille (58/100 Punkten) wurden als entlastend beschrieben. Eine hohe Inaktivität (MLQ-10) sowie ein vermindertes Wohlbefinden (WHO-5) und eine reduzierte Achtsamkeit (GrAw-7) waren Charakteristiken der KHT, die Ansatzpunkte für eine Stärkung der Resilienz sein können. Schlussfolgerung Patienten mit KHT haben einen hohen mentalen und psychischen Druck durch die Pandemie. Ihr Blickwinkel ergänzt unsere bisherige Sicht und kann zu einer verbesserten Gesamtversorgung dieser Patienten beitragen.
    Type of Medium: Online Resource
    ISSN: 0722-219X , 1439-1279
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    Language: German
    Publisher: Georg Thieme Verlag KG
    Publication Date: 2021
    detail.hit.zdb_id: 604664-2
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  • 18
    In: Acta Neuropathologica, Springer Science and Business Media LLC, Vol. 142, No. 2 ( 2021-08), p. 339-360
    Abstract: Ependymomas (EPN) are central nervous system tumors comprising both aggressive and more benign molecular subtypes. However, therapy of the high-risk subtypes posterior fossa group A (PF-A) and supratentorial RELA-fusion positive (ST-RELA) is limited to gross total resection and radiotherapy, as effective systemic treatment concepts are still lacking. We have recently described fibroblast growth factor receptors 1 and 3 ( FGFR1/FGFR3 ) as oncogenic drivers of EPN. However, the underlying molecular mechanisms and their potential as therapeutic targets have not yet been investigated in detail. Making use of transcriptomic data across 467 EPN tissues, we found that FGFR1 and FGFR3 were both widely expressed across all molecular groups. FGFR3 mRNA levels were enriched in ST-RELA showing the highest expression among EPN as well as other brain tumors. We further identified high expression levels of fibroblast growth factor 1 and 2 ( FGF1 , FGF2) across all EPN subtypes while FGF9 was elevated in ST-EPN. Interrogation of our EPN single-cell RNA-sequencing data revealed that FGFR3 was further enriched in cycling and progenitor-like cell populations. Corroboratively, we found FGFR3 to be predominantly expressed in radial glia cells in both mouse embryonal and human brain datasets. Moreover, we detected alternative splicing of the FGFR1/3-IIIc variant, which is known to enhance ligand affinity and FGFR signaling. Dominant-negative interruption of FGFR1/3 activation in PF-A and ST-RELA cell models demonstrated inhibition of key oncogenic pathways leading to reduced cell growth and stem cell characteristics. To explore the feasibility of therapeutically targeting FGFR, we tested a panel of FGFR inhibitors in 12 patient-derived EPN cell models revealing sensitivity in the low-micromolar to nano-molar range. Finally, we gain the first clinical evidence for the activity of the FGFR inhibitor nintedanib in the treatment of a patient with recurrent ST-RELA. Together, these preclinical and clinical data suggest FGFR inhibition as a novel and feasible approach to combat aggressive EPN.
    Type of Medium: Online Resource
    ISSN: 0001-6322 , 1432-0533
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 1458410-4
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  • 19
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 14_Supplement ( 2020-07-15), p. A25-A25
    Abstract: Introduction: The majority of pediatric supratentorial (ST) ependymomas (EPN) is driven by distinct gene fusions between C11orf95 and RELA. The resultant molecular group of ST-EPN-RELA tumors is characterized by constitutive activation of NF-κB signaling and deregulation of the p53 pathway. In contrast to surgery and radiotherapy, chemotherapy has failed to demonstrate significant benefit in the management of affected children. Alternative strategies including enhanced drug delivery, combination treatments, or application of new selective compounds are needed to tackle this disease. Material and Methods: RNAi and drug screening methods were applied to identify potential therapeutic approaches using ST-EPN-RELA cell lines. In order to identify optimal dosing strategies of selected drugs and to assess effects of combinatorial treatment approaches on blood-brain barrier (BBB) penetration, cerebral microdialysis combined with ultraperformance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS) was applied. This approach allowed for exact, continuous, and time-dependent drug quantification in tumors or healthy tissue in freely moving experimental mice. Patient-derived xenograft models of ST-EPN-RELA were treated to investigate toxicity and outcome parameters. Results: Regulation of p53 signaling and nuclear protein shuttling were identified as promising therapeutic approaches. While low-dose dactinomycin could successfully reestablish p53 function in ST-EPN-RELA cells in vitro, penetration of the drug across the BBB was found to be very poor and did not result in a survival benefit of tumor-bearing mice. Preliminary results of alternative strategies such as combination with efflux pump inhibitors, liposomal packaging, and inhibition of XPO1 being the sole nuclear exporter of p53 hold promise to overcome these constraints. Conclusion: Oncogenic dependencies of ST-EPN-RELA are currently difficult to target. Preclinical evaluation of effective drug disposition combined with long-term treatment studies may help to better select promising compounds and thereby increase success rates of early clinical trials in patients with ST-EPN-RELA in the future. Citation Format: Julia Benzel, Max Sauter, Norman Mack, Abigail Davis, Johanna Weiss, Philipp Uhl, Jürgen Burhenne, Kendra K. Maass, Jens-Martin Hübner, Hendrik Witt, Anang Shelat, Amar Gajjar, Santhosh A. Upadhyaya, Aylin Camgoz, Frank Buchholz, Sina Oppermann, Marcel Kool, Daisuke Kawauchi, Olaf Witt, Walter E. Haefeli, Stefan M. Pfister, Clinton Stewart, Kristian W. Pajtler. Evaluation of Drug Disposition in Supratentorial Ependymoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A25.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 20
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2023-04-21)
    Abstract: Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA -fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains (‘neo-TADs’) caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2553671-0
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