77 Works

Additional file 1 of FoxP3 expression by retinal pigment epithelial cells: transcription factor with potential relevance for the pathology of age-related macular degeneration

Ahmad Samir Alfaar, Lucas Stürzbecher, Maria Diedrichs-Möhring, Marion Lam, Christophe Roubeix, Julia Ritter, Kathrin Schumann, Balasubramaniam Annamalai, Inga-Marie Pompös, Bärbel Rohrer, Florian Sennlaub, Nadine Reichhart, Gerhild Wildner & Olaf Strauß
Additional file 1. The additional file provides statistical comparison of gene expression between wildtype and Cx3cr1GFP/GFP mice at the different time points, control data for human FoxP3 staining, the growth rate of ARPE-19 to compare with Crisp/Cas treated ARPE-19 cells and uncropped dot plots.

Emergency medical care of patients with psychiatric disorders - challenges and opportunities: Results of a multicenter survey

Benedikt Schick, Benjamin Mayer, Markus Jäger, Bettina Jungwirth, Eberhard Barth, Martin Eble, Christoph Sponholz, Claus-Martin Muth & Carlos Schönfeldt-Lecuona
Abstract Background Pre-clinical psychiatric emergencies are generally treated by emergency medical staff. The subsequent clinical treatment is often conditioned by interaction problems between emergency medical staff and psychiatric clinical staff. Objectives To identify problems affecting interaction between emergency medical and psychiatric care of mentally ill patients and pinpoint aspects of optimized emergency care. Methods To shed light on the interaction problems an anonymous, questionnaire-based, nonrepresentative survey of 98 emergency physicians (EM) and 104 psychiatrists (PS)...

Subcutaneous fat necrosis in newborns: a systematic literature review of case reports and model of pathophysiology

Leonie Frank, Stephanie Brandt & Martin Wabitsch
Abstract Background Subcutaneous fat necrosis of the newborn (SCFN) is a rare disease occurring in the first days of life. Characteristically, the infants show hard nodules in subcutaneous tissue, purple or erythematous in color and appear on the upper back, cheeks, buttocks and limbs. In most cases, SCFN is a self-limiting disease, as the nodules disappear in up to 6 months. A severe complication associated with SCFN is hypercalcaemia. Pathophysiological mechanisms causing SCFN or associated...

Additional file 1 of Serum phosphorylated tau protein 181 and neurofilament light chain in cognitively impaired heart failure patients

Jan Traub, Markus Otto, Roxane Sell, Dennis Göpfert, György Homola, Petra Steinacker, Patrick Oeckl, Caroline Morbach, Stefan Frantz, Mirko Pham, Stefan Störk, Guido Stoll & Anna Frey
Additional file 1: Supplemental Methods. Table S1. Inclusion and exclusion criteria. Table S2. Outcome of the cognitive test battery. Table S3. Imaging protocol and sequence parameters. Table S4. Correlation of biomarkers to cognitive domains and brain morphology. Table S5. Extended clinical characteristics of NfL quartiles. Table S6. Extended clinical characteristics of pTau quartiles. Table S7. Mediation analysis of parameters affecting serum levels of Ln(NfL). Table S8. Mediation analysis of parameters affecting serum levels of Ln(pTau)....

Additional file 1 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 1: Table S1. T-LGL patient data. Table S2. Benign samples. Table S3. Sample overview. Table S4. Primer sequences and CpGs used in pyrosequencing. Table S5. CpGs validated by pyrosequencing. Table S6. Pearson correlation of results of bisulfite sequencing and methylation array data. Table S7. Chromatin states—description. Table S8. Taqman probes used in qPCR. Table S9. Differentially methylated probes and genomic features. Table S10. Differentially hypermethylated genes. Table S11. Differentially hypomethylated genes. Table S12....

Additional file 2 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 2: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 4 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 4: Fig. S3A. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. A Gene Ontology analysis of hypermethylated genes in T-LGL.

Additional file 5 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 5: Fig. S3B. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. B Gene Ontology analysis of hypomethylated genes in T-LGL.

Additional file 7 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 7: Fig. S5A. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). A Significant differentially methylated CpGs in BCL11B (T-LGLL compared to CD8+. memory T cells) were located in the gene body and assigned as enhancers by ENCODE, which match as enhancers in CD8-positive memory cells.

Additional file 8 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 8: Fig. S5B. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). B Significant differentially methylated CpGs in C14orf64 (LINC01550) (T-LGL compared to CD8 pos. memory T cells).

Genomic footprints of activated telomere maintenance mechanisms in cancer

Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe, Peter J Park, Roland Eils, Matthias Schlesner, Kadir C Akdemir, Eva G Alvarez, Adrian Baez-Ortega, Rameen Beroukhim, Paul C Boutros, David DL Bowtell, Benedikt Brors, Kathleen H Burns, Peter J Campbell, Kin Chan, Ken Chen, Ana Dueso-Barroso … & Christian von Mering
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the...

Cognition in the course of ALS—a meta-analysis

Julia Finsel, Ingo Uttner, Cynthia R. Vázquez Medrano, Albert C. Ludolph & Dorothée Lulé
Objective: The goal of this meta-analysis is to improve insight into the development of cognition over the course of ALS and to assess predictors of cognitive performance. Method: A literature search was conducted in Pubmed and Web of Science on 29 July 2019 and 16 March 2021. Data were screened in Endnote® Version X9 (London, UK). Meta-analyses and meta-regressions were calculated for cross-sectional data using Rstudio®. Studies were assigned to temporal and physical categories and...

Additional file 1 of Comparison of PSMA-TO-1 and PSMA-617 labeled with gallium-68, lutetium-177 and actinium-225

Catherine Meyer, Vikas Prasad, Andreea Stuparu, Peter Kletting, Gerhard Glatting, Jonathan Miksch, Christoph Solbach, Katharina Lueckerath, Lea Nyiranshuti, Shaojun Zhu, Johannes Czernin, Ambros J. Beer, Roger Slavik, Jeremie Calais & Magnus Dahlbom
Additional file 1: Supplementary preclinical and clinical information.

Comparison of PSMA-TO-1 and PSMA-617 labeled with gallium-68, lutetium-177 and actinium-225

Catherine Meyer, Vikas Prasad, Andreea Stuparu, Peter Kletting, Gerhard Glatting, Jonathan Miksch, Christoph Solbach, Katharina Lueckerath, Lea Nyiranshuti, Shaojun Zhu, Johannes Czernin, Ambros J. Beer, Roger Slavik, Jeremie Calais & Magnus Dahlbom
Abstract Background PSMA-TO-1 (“Tumor-Optimized-1”) is a novel PSMA ligand with longer circulation time than PSMA-617. We compared the biodistribution in subcutaneous tumor-bearing mice of PSMA-TO-1, PSMA-617 and PSMA-11 when labeled with 68Ga and 177Lu, and the survival after treatment with 225Ac-PSMA-TO-1/-617 in a murine model of disseminated prostate cancer. We also report dosimetry data of 177Lu-PSMA-TO1/-617 in prostate cancer patients. Methods First, PET images of 68Ga-PSMA-TO-1/-617/-11 were acquired on consecutive days in three mice bearing...

Subcutaneous fat necrosis in newborns: a systematic literature review of case reports and model of pathophysiology

Leonie Frank, Stephanie Brandt & Martin Wabitsch
Abstract Background Subcutaneous fat necrosis of the newborn (SCFN) is a rare disease occurring in the first days of life. Characteristically, the infants show hard nodules in subcutaneous tissue, purple or erythematous in color and appear on the upper back, cheeks, buttocks and limbs. In most cases, SCFN is a self-limiting disease, as the nodules disappear in up to 6 months. A severe complication associated with SCFN is hypercalcaemia. Pathophysiological mechanisms causing SCFN or associated...

Visinin-like protein 1 levels in blood and CSF as emerging markers for Alzheimer’s and other neurodegenerative diseases

Steffen Halbgebauer, Petra Steinacker, Daniel Riedel, Patrick Oeckl, Sarah Anderl-Straub, Jolina Lombardi, Christine A. F. von Arnim, Magdalena Nagl, Armin Giese, Albert C. Ludolph & Markus Otto
Abstract Background Visinin-like protein 1 (VILIP-1) belongs to the group of emerging biomarkers with the potential to support the early diagnosis of Alzheimer’s disease (AD). However, studies investigating the differential diagnostic potential in cerebrospinal fluid (CSF) are rare and are not available for blood. Methods We set up a novel, sensitive single molecule array (Simoa) assay for the detection of VILIP-1 in CSF and serum. In total, paired CSF and serum samples from 234 patients...

Serum phosphorylated tau protein 181 and neurofilament light chain in cognitively impaired heart failure patients

Jan Traub, Markus Otto, Roxane Sell, Dennis Göpfert, György Homola, Petra Steinacker, Patrick Oeckl, Caroline Morbach, Stefan Frantz, Mirko Pham, Stefan Störk, Guido Stoll & Anna Frey
Abstract Background Chronic heart failure (HF) is known to increase the risk of developing Alzheimer’s dementia significantly. Thus, detecting and preventing mild cognitive impairment, which is common in patients with HF, is of great importance. Serum biomarkers are increasingly used in neurological disorders for diagnostics, monitoring, and prognostication of disease course. It remains unclear if neuronal biomarkers may help detect cognitive impairment in this high-risk population. Also, the influence of chronic HF and concomitant renal...

Serum phosphorylated tau protein 181 and neurofilament light chain in cognitively impaired heart failure patients

Jan Traub, Markus Otto, Roxane Sell, Dennis Göpfert, György Homola, Petra Steinacker, Patrick Oeckl, Caroline Morbach, Stefan Frantz, Mirko Pham, Stefan Störk, Guido Stoll & Anna Frey
Abstract Background Chronic heart failure (HF) is known to increase the risk of developing Alzheimer’s dementia significantly. Thus, detecting and preventing mild cognitive impairment, which is common in patients with HF, is of great importance. Serum biomarkers are increasingly used in neurological disorders for diagnostics, monitoring, and prognostication of disease course. It remains unclear if neuronal biomarkers may help detect cognitive impairment in this high-risk population. Also, the influence of chronic HF and concomitant renal...

Additional file 1 of FoxP3 expression by retinal pigment epithelial cells: transcription factor with potential relevance for the pathology of age-related macular degeneration

Ahmad Samir Alfaar, Lucas Stürzbecher, Maria Diedrichs-Möhring, Marion Lam, Christophe Roubeix, Julia Ritter, Kathrin Schumann, Balasubramaniam Annamalai, Inga-Marie Pompös, Bärbel Rohrer, Florian Sennlaub, Nadine Reichhart, Gerhild Wildner & Olaf Strauß
Additional file 1. The additional file provides statistical comparison of gene expression between wildtype and Cx3cr1GFP/GFP mice at the different time points, control data for human FoxP3 staining, the growth rate of ARPE-19 to compare with Crisp/Cas treated ARPE-19 cells and uncropped dot plots.

Additional file 11 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 11: Material and Methods.

Additional file 11 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 11: Material and Methods.

Integrative pathway enrichment analysis of multivariate omics data

Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S Fox, Helen Zhu, Diala Abd-Rabbo, Miles W Mee, Paul C Boutros, Federico Abascal, Samirkumar B Amin, Gary D Bader, Rameen Beroukhim, Johanna Bertl, Keith A Boroevich, Søren Brunak, Peter J Campbell, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, Priyanka Dhingra, Klev Diamanti, Lars Feuerbach … & L van’t Veer
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated...

Emergency medical care of patients with psychiatric disorders - challenges and opportunities: Results of a multicenter survey

Benedikt Schick, Benjamin Mayer, Markus Jäger, Bettina Jungwirth, Eberhard Barth, Martin Eble, Christoph Sponholz, Claus-Martin Muth & Carlos Schönfeldt-Lecuona
Abstract Background Pre-clinical psychiatric emergencies are generally treated by emergency medical staff. The subsequent clinical treatment is often conditioned by interaction problems between emergency medical staff and psychiatric clinical staff. Objectives To identify problems affecting interaction between emergency medical and psychiatric care of mentally ill patients and pinpoint aspects of optimized emergency care. Methods To shed light on the interaction problems an anonymous, questionnaire-based, nonrepresentative survey of 98 emergency physicians (EM) and 104 psychiatrists (PS)...

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Shimin Shuai, Federico Abascal, Samirkumar B Amin, Gary D Bader, Pratiti Bandopadhayay, Jonathan Barenboim, Rameen Beroukhim, Johanna Bertl, Keith A Boroevich, Søren Brunak, Peter J Campbell, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, Priyanka Dhingra, Klev Diamanti, Lars Feuerbach, J Lynn Fink, Nuno A Fonseca, Joan Frigola, Carlo Gambacorti-Passerini, Dale W Garsed … & L van’t Veer
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features...

Pathway and network analysis of more than 2500 whole cancer genomes

Matthew A Reyna, David Haan, Marta Paczkowska, Lieven PC Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S Lawrence, Jakob Skou Pedersen, Mark A Rubin, David A Wheeler, Søren Brunak, Jose MG Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S Cenk Sahinalp, Alfonso Valencia, Federico Abascal, Samirkumar B Amin … & L van’t Veer
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding...

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Affiliations

  • University Hospital Ulm
    77
  • University of Ulm
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  • Essen University Hospital
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  • University Hospital Schleswig-Holstein
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  • Institució Catalana de Recerca i Estudis Avançats
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  • University of Duisburg-Essen
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  • Barcelona Supercomputing Center
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  • Cancer Research Center of Toulouse
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