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Concordance Analysis

Robert Kwiecien, Annette Kopp-Schneider, Maria Blettner
2011 Deutsches Ärzteblatt International  
►Cite this as: Kwiecien R, Kopp-Schneider A, Blettner M: Concordance analysis-part 16 of a series on evaluation of scientific publications. Dtsch Arztebl Int 2011; 108(30): 515-21.  ... 
doi:10.3238/arztebl.2011.0515 pmid:21904584 pmcid:PMC3165924 fatcat:t5vnamvosjh3thmhczhp3zgnnq

Origins of the mutational origin of cancer

Lutz Edler, Annette Kopp-Schneider
2005 International Journal of Epidemiology  
The mathematical and biological background for this model has been reviewed more recently by Tan 10 and Kopp-Schneider. 11 The two-stage model was generalized to incorporate more than one intermediate  ... 
doi:10.1093/ije/dyi134 pmid:16046521 fatcat:sjovrdk5srailfew5rggyg64s4

The Use of Cell Proliferation Data in Modeling of Skin Carcinogenesis

Annette Kopp-Schneider
1993 Environmental Health Perspectives  
The Use of Cell Proliferation Data in Modeling of Skin Carcinogenesis by Annette Kopp-Schneider A simple model for papilloma formation is used to analyze data from a mouse skin-painting experiment performed  ...  A more detailed analysis of the model parameters, a thorough discussion of the estimates, and a discussion of the reasons for the observed estimated parameters can be found in Kopp-Schneider and Portier  ... 
doi:10.2307/3431850 pmid:8013395 pmcid:PMC1519443 fatcat:cc4czbaqzbewziqhfya64upho4

Clustering of samples and variables with mixed-type data

Manuela Hummel, Dominic Edelmann, Annette Kopp-Schneider, Zhaohong Deng
2017 PLoS ONE  
OPEN ACCESS Citation: Hummel M, Edelmann D, Kopp-Schneider A (2017) Clustering of samples and variables with mixed-type data.  ... 
doi:10.1371/journal.pone.0188274 pmid:29182671 pmcid:PMC5705083 fatcat:3xukqqil6nhwzpttcypwiwhcgm

Optimal experimental designs for dose–response studies with continuous endpoints

Tim Holland-Letz, Annette Kopp-Schneider
2014 Archives of Toxicology  
Kopp-Schneider Biostatistics Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany e-mail: t.holland-letz@dkfz.de (NOAEL), when the study aim is to estimate  ... 
doi:10.1007/s00204-014-1335-2 pmid:25155192 pmcid:PMC4655015 fatcat:5mxbmt2h7nf3lehg7hoissjisu

Comparison of Mode of Action of Four Hepatocarcinogens: A Model-Based Approach

Jutta Groos, Peter Bannasch, Michael Schwarz, Annette Kopp-Schneider
2007 Toxicological Sciences  
The assumption of deterministic growth rate was found to be too restrictive and an approach with heterogeneous growth was developed Kopp-Schneider, 2004, 2006) .  ...  The CSM introduced by Kopp-Schneider et al. (1998) describes colonies of intermediate cells as entities of spherical shape which change their size by increase of radius.  ... 
doi:10.1093/toxsci/kfm183 pmid:17636249 fatcat:3tb4nso4nzezfd7rpcap32dtk4

A model for hepatocarcinogenesis with clonal expansion of three successive phenotypes of preneoplastic cells

Iris Geisler, Annette Kopp-Schneider
2000 Mathematical Biosciences  
A solution to this problem may be given by the so-called color-shift model presented by Kopp-Schneider et al. [23] .  ... 
doi:10.1016/s0025-5564(00)00044-4 pmid:11121564 fatcat:24kpka3rv5ej5fqjezhxrjkdfi

Stochastic time‐concentration activity models for cytotoxicity in 3D brain cell cultures

Maria Renner, Marie‐Gabrielle Zurich, Annette Kopp‐Schneider
2013 Theoretical Biology and Medical Modelling  
Kopp-Schneider [13] ).  ... 
doi:10.1186/1742-4682-10-19 pmid:23497233 pmcid:PMC3691759 fatcat:7d7xbdnionh6dadsnrwxwape4y

Robust biclustering by sparse singular value decomposition incorporating stability selection

Martin Sill, Sebastian Kaiser, Axel Benner, Annette Kopp-Schneider
2011 Computer applications in the biosciences : CABIOS  
Motivation: Over the past decade, several biclustering approaches have been published in the field of gene expression data analysis. Despite of huge diversity regarding the mathematical concepts of the different biclustering methods, many of them can be related to the singular value decomposition (SVD). Recently, a sparse SVD approach (SSVD) has been proposed to reveal biclusters in gene expression data. In this article, we propose to incorporate stability selection to improve this method.
more » ... lity selection is a subsampling-based variable selection that allows to control Type I error rates. The here proposed S4VD algorithm incorporates this subsampling approach to find stable biclusters, and to estimate the selection probabilities of genes and samples to belong to the biclusters. Results: So far, the S4VD method is the first biclustering approach that takes the cluster stability regarding perturbations of the data into account. Application of the S4VD algorithm to a lung cancer microarray dataset revealed biclusters that correspond to coregulated genes associated with cancer subtypes. Marker genes for different lung cancer subtypes showed high selection probabilities to belong to the corresponding biclusters. Moreover, the genes associated with the biclusters belong to significantly enriched cancer-related Gene Ontology categories. In a simulation study, the S4VD algorithm outperformed the SSVD algorithm and two other SVD-related biclustering methods in recovering artificial biclusters and in being robust to noisy data. Availability: R-Code of the S4VD algorithm as well as a documentation can be found at http://s4vd.r-forge.r-project.org/. Contact: m.sill@dkfz.de
doi:10.1093/bioinformatics/btr322 pmid:21636597 fatcat:6yo7f4hbubbg5mwju2ikaoniti

Biomedical Image Analysis Challenges (BIAS) Reporting Guideline [article]

Lena Maier-Hein, Annika Reinke, Michal Kozubek, Anne L. Martel, Tal Arbel, Matthias Eisenmann, Allan Hanbury, Pierre Jannin, Henning Müller, Sinan Onogur, Julio Saez-Rodriguez, Bram van Ginneken (+2 others)
2020 Zenodo  
The number of biomedical image analysis challenges organized per year is steadily increasing. These international competitions have the purpose of benchmarking algorithms on common data sets, typically to identify the best method for a given problem. Recent research, however, revealed that common practice related to challenge reporting does not allow for adequate interpretation and reproducibility of results. To address the discrepancy between the impact of challenges and the quality (control),
more » ... the Biomedical Image Analysis ChallengeS (BIAS) initiative developed a set of recommendations for the reporting of challenges. The BIAS statement aims to improve the transparency of the reporting of a biomedical image analysis challenge regardless of field of application, image modality or task category assessed. We present a checklist which authors of biomedical image analysis challenges are encouraged to include in their submission when giving a paper on a challenge into review. The purpose of the checklist is to standardize and facilitate the review process and raise interpretability and reproducibility of challenge results by making relevant information explicit.
doi:10.5281/zenodo.4008954 fatcat:5ub5eddlxvdxdawmab3jiikyuq

A decision-theoretic approach to Bayesian clinical trial design and evaluation of robustness to prior-data conflict

Silvia Calderazzo, Manuel Wiesenfarth, Annette Kopp-Schneider
2020 Biostatistics  
., it does not depend on whether the prior is fixed or adapts to the observed degree of conflict between historical and current information (see Kopp-Schneider and others, 2020) .  ... 
doi:10.1093/biostatistics/kxaa027 pmid:32735010 pmcid:PMC9118338 fatcat:pahg5bn5qjgfpccsu3npoddvfy

Dissecting and modeling the emergent murine TEC compartment during ontogeny

Fabian Brunk, Chloé Michel, Tim Holland-Letz, Alla Slynko, Annette Kopp-Schneider, Bruno Kyewski, Sheena Pinto
2017 European Journal of Immunology  
Supporting Information Figure 2 (A) Expression of Aire as a surrogate marker in MHCII hi CD80 hi , but not in MHCII hi CD80 -TECs during emrbyonic development. Results are representative of two to three independent experiments performed at the indicated time-points. Measurements for each experiment were based on 4-10 pooled embryonic or 2 adult thymi. (B) Representative dot plots of cell cycle analysis on E14.5 TEC subsets using Ki67 and DAPI. Cycling cells were defined as being Ki67 int/high
more » ... d DAPI + 2N, comprising G2/M-and S-cell cycle phases.
doi:10.1002/eji.201747006 pmid:28439878 fatcat:tkaaneg7ira6fduncfesr4u4va

Quantitative Dynamic 18F-FDG PET/CT in Survival Prediction of Metastatic Melanoma under PD-1 Inhibitors

Christos Sachpekidis, Jessica C Hassel, Annette Kopp-Schneider, Uwe Haberkorn, Antonia Dimitrakopoulou-Strauss
2021 Cancers  
The advent of novel immune checkpoint inhibitors has led to unprecedented survival rates in advanced melanoma. At the same time, it has raised relevant challenges in the interpretation of treatment response by conventional imaging approaches. In the present prospective study, we explored the predictive role of quantitative, dynamic 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) performed early during immunotherapy in metastatic melanoma patients
more » ... ing treatment with programmed cell death protein 1 (PD-1) inhibitors. Twenty-five patients under PD-1 blockade underwent dynamic and static 18F-FDG PET/CT before the start of treatment (baseline PET/CT) and after the initial two cycles of therapy (interim PET/CT). The impact of semiquantitatively (standardized uptake value, SUV) and quantitatively (based on compartment modeling and fractal analysis) derived PET/CT parameters, both from melanoma lesions and different reference tissues, on progression-free survival (PFS) was analyzed. At a median follow-up of 24.2 months, survival analysis revealed that the interim PET/CT parameters SUVmean, SUVmax and fractal dimension (FD) of the hottest melanoma lesions adversely affected PFS, while the parameters FD of the thyroid, as well as SUVmax and k3 of the bone marrow positively affected PFS. The herein presented findings highlight the potential predictive role of quantitative, dynamic, interim PET/CT in metastatic melanoma under PD-1 blockade. Therefore, dynamic PET/CT could be performed in selected oncological cases in combination with static, whole-body PET/CT in order to enhance the diagnostic certainty offered by conventional imaging and yield additional information regarding specific molecular and pathophysiological mechanisms involved in tumor biology and response to treatment.
doi:10.3390/cancers13051019 pmid:33804417 pmcid:PMC7957728 fatcat:gt4qfdwvfndvxc2q2jctszsf3a

Can 18F-NaF PET/CT before Autologous Stem Cell Transplantation Predict Survival in Multiple Myeloma?

Christos Sachpekidis, Annette Kopp-Schneider, Maximilian Merz, Anna Jauch, Marc-Steffen Raab, Hartmut Goldschmidt, Antonia Dimitrakopoulou-Strauss
2020 Cancers  
There is an unmet need for positron emission tomography (PET) radiotracers that can image bone disease in multiple myeloma (MM) in a more sensitive and specific way than the widely used 18F-fluorodeoxyglucose (18F-FDG). Sodium fluoride (18F-NaF) is a highly sensitive tracer of bone reconstruction, evolving as an important imaging agent for the assessment of malignant bone diseases. We attempted to investigate for the first time the prognostic significance of 18F-NaF PET/CT in newly diagnosed,
more » ... mptomatic MM patients planned for autologous stem cell transplantation (ASCT). Forty-seven patients underwent dynamic and static PET/CT with 18F-NaF before treatment. After correlation with the respective findings on CT and 18F-FDG PET/CT that served as reference, the 18F-NaF PET findings were compared with established factors of high-risk disease, like cytogenetic abnormalities as well as bone marrow plasma cell infiltration rate. Furthermore, the impact of 18F-NaF PET/CT on progression-free survival (PFS) was analyzed. Correlation analysis revealed a moderate, significant correlation of the 18F-NaF parameters SUVaverage and K1 in reference tissue with bone marrow plasma cell infiltration rate. However, no significant correlation was observed regarding all other 18F-NaF PET parameters. Survival analysis revealed that patients with a pathologic 18F-NaF PET/CT have a shorter PFS (median = 36.2 months) than those with a physiologic scan (median = 55.6 months) (p = 0.02). Nevertheless, no quantitative 18F-NaF parameter could be shown to adversely affect PFS. In contrast, the respective analysis for quantitative dynamic 18F-FDG PET/CT revealed that the parameters SUVmax, fractional blood volume (VB), k3 and influx from reference tissue as well as SUVaverage from MM lesions had a significant negative impact on patient survival. The herein presented findings highlight the rather limited role of 18F-NaF PET/CT as a single PET approach in MM.
doi:10.3390/cancers12051335 pmid:32456181 pmcid:PMC7281312 fatcat:zbrgzsyyp5drhkshcj3etzomoa

Corrigendum: Investigation of Nrf2, AhR and ATF4 Activation in Toxicogenomic Databases

Elias Zgheib, Alice Limonciel, Xiaoqi Jiang, Anja Wilmes, Steven Wink, Bob van de Water, Annette Kopp-Schneider, Frederic Y. Bois, Paul Jennings
2019 Frontiers in Genetics  
Copyright © 2019 Zgheib, Limonciel, Jiang, Wilmes, Wink, van de Water, Kopp-Schneider, Bois and Jennings.  ... 
doi:10.3389/fgene.2019.00517 pmid:31231426 pmcid:PMC6558953 fatcat:ylqts6zcyndbvfmzajmvm2gu54
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