136 Works

Supplement: Multicenter validated detection of focal cortical dysplasia using deep learning

Ravnoor S Gill, Hyo M Lee, Benoit Caldairou, Seok-Jun Hong, Carmen Barba, Francesco Deleo, Ludovico D’Incerti, Vanessa C Mendes Coelho, Matteo Lenge, Mira Semmelroch, Dewi Schrader, Fabrice Bartolomei, Maxime Guye, Andreas Schulze-Bonhage, Horst Urbach, Kyoo Ho Cho, Fernando Cendes, Renzo Guerrini, Graeme Jackson, R Edward Hogan, Neda Bernasconi & Andrea Bernasconi
Objective. To test the hypothesis that a multicenter-validated computer deep learning algorithm detects MRI-negative focal cortical dysplasia (FCD). Methods. We used clinically acquired 3D T1-weighted and 3D FLAIR MRI of 148 patients (median age, 23 years [range, 2-55]; 47% female) with histologically verified FCD at nine centers to train a deep convolutional neural network (CNN) classifier. Images were initially deemed as MRI-negative in 51% of cases, in whom intracranial EEG determined the focus. For risk...

Sequential Learning of Regression Models by Penalized Estimation

Wessel N. van Wieringen & Harald Binder
When data arrive in a sequence of two or more datasets, modeling on the most recent dataset should take previous datasets into account. We specifically investigate a strategy for regression modeling when parameter estimates from previous data can be used as anchoring points, yet may not be available for all parameters, thus, covariance information cannot be reused. A procedure that updates through targeted penalized estimation, which shrinks the estimator toward a nonzero value, is presented....

sj-docx-1-tag-10.1177_17562848221100106 – Supplemental material for Impact of NAFLD on clinical outcomes in hepatocellular carcinoma treated with sorafenib: an international cohort study

Jessica Howell, Amit Samani, Binish Mannan, Saur Hajiev, Leila Motedayen Aval, Rebecca Abdelmalak, Vincent C. Tam, Dominik Bettinger, Robert Thimme, Tamar H. Taddei, David E. Kaplan, Max Seidensticker & Rohini Sharma
Supplemental material, sj-docx-1-tag-10.1177_17562848221100106 for Impact of NAFLD on clinical outcomes in hepatocellular carcinoma treated with sorafenib: an international cohort study by Jessica Howell, Amit Samani, Binish Mannan, Saur Hajiev, Leila Motedayen Aval, Rebecca Abdelmalak, Vincent C. Tam, Dominik Bettinger, Robert Thimme, Tamar H. Taddei, David E. Kaplan, Max Seidensticker and Rohini Sharma in Therapeutic Advances in Gastroenterology

Impact of NAFLD on clinical outcomes in hepatocellular carcinoma treated with sorafenib: an international cohort study

Jessica Howell, Amit Samani, Binish Mannan, Saur Hajiev, Leila Motedayen Aval, Rebecca Abdelmalak, Vincent C. Tam, Dominik Bettinger, Robert Thimme, Tamar H. Taddei, David E. Kaplan, Max Seidensticker & Rohini Sharma
Background:The impact of nonalcoholic fatty liver disease (NAFLD) on overall survival (OS), treatment response and toxicity in patients with hepatocellular carcinoma (HCC) treated with sorafenib is unknown. We examined the impact of NAFLD on survival and toxicity in an international cohort of patients receiving sorafenib.Methods:Clinical and demographic data were collected from patients consecutively treated at specialist centres in Europe and North America. The impact of NAFLD on OS, sorafenib-specific survival and toxicity compared with other...

Additional file 3 of Unraveling implementation context: the Basel Approach for coNtextual ANAlysis (BANANA) in implementation science and its application in the SMILe project

Juliane Mielke, Lynn Leppla, Sabine Valenta, Leah L. Zullig, Franziska Zúñiga, Sandra Staudacher, Alexandra Teynor & Sabina De Geest
Additional file 3. Overview of contextual factors most commonly reported in empirical evidence to influence implementation.

Unraveling implementation context: the Basel Approach for coNtextual ANAlysis (BANANA) in implementation science and its application in the SMILe project

Juliane Mielke, Lynn Leppla, Sabine Valenta, Leah L. Zullig, Franziska Zúñiga, Sandra Staudacher, Alexandra Teynor & Sabina De Geest
Abstract Background Designing intervention and implementation strategies with careful consideration of context is essential for successful implementation science projects. Although the importance of context has been emphasized and methodology for its analysis is emerging, researchers have little guidance on how to plan, perform, and report contextual analysis. Therefore, our aim was to describe the Basel Approach for coNtextual ANAlysis (BANANA) and to demonstrate its application on an ongoing multi-site, multiphase implementation science project to develop/adapt,...

Unraveling implementation context: the Basel Approach for coNtextual ANAlysis (BANANA) in implementation science and its application in the SMILe project

Juliane Mielke, Lynn Leppla, Sabine Valenta, Leah L. Zullig, Franziska Zúñiga, Sandra Staudacher, Alexandra Teynor & Sabina De Geest
Abstract Background Designing intervention and implementation strategies with careful consideration of context is essential for successful implementation science projects. Although the importance of context has been emphasized and methodology for its analysis is emerging, researchers have little guidance on how to plan, perform, and report contextual analysis. Therefore, our aim was to describe the Basel Approach for coNtextual ANAlysis (BANANA) and to demonstrate its application on an ongoing multi-site, multiphase implementation science project to develop/adapt,...

Krüppel-like factor 7 influences translation and pathways involved in ribosomal biogenesis in breast cancer

Anne-Marie Lüchtenborg, Patrick Metzger, Miguel Cosenza Contreras, Victor Oria, Martin L. Biniossek, Franziska Lindner, Klemens Fröhlich, Ambrus Malyi, Thalia Erbes, Nicole Gensch, Jochen Maurer, Andreas Thomsen, Melanie Boerries, Oliver Schilling, Martin Werner & Peter Bronsert
Abstract Background Ribosomal biogenesis and ribosomal proteins have attracted attention in the context of tumor biology in recent years. Instead of being mere translational machineries, ribosomes might play an active role in tumor initiation and progression. Despite its importance, regulation of ribosomal biogenesis is still not completely understood. Methods Using Gene Set Enrichment Analysis of RNA sequencing and proteomical mass spectrometry data in breast cancer cells expressing Krüppel-like factor 7 (KLF7), we identified processes altered...

Genetic and pathogenic variation of Botrytis cinerea, the causal agent of grey mould on Panax ginseng in China

Rong Wang, Kun Liu, Bingwei Chen, Wanlong Ding & Yong Li
Grey mould, caused by Botrytis cinerea, is an increasingly destructive disease of ginseng (Panax ginseng) in China. However, the extent of variation in the morphological characteristics of fungal colonies, genetic background and pathogenicity of different strains of this pathogen remains unknown. In this study, we isolated and identified 102 isolates of B. cinerea from ginseng. Among these, the sclerotial phenotype was dominant, followed by the mycelial and conidial phenotypes, with the proportion of each phenotype...

Diagnostic test accuracy of waist-to-height ratio as a screening tool for cardiovascular risk in children and adolescents: a meta-analysis

Fusheng Zhang, Yanbai Han, Hongli Wang, Yong Li & Zhiwei Yan
Waist-to-height ratio (WHtR) is a controversial evaluation index of cardiovascular risk factors (CVRFs) in children and adolescents. To assess the accuracy of WHtR as a measure to screen for clusters of at least one CVRF (CVRF1), two CVRFs (CVRF2), and three CVRFs (CVRF3) in different ages, sexes, regions and cut-offs. The PubMed, Web of Science, EBSCOhost, Springer, Taylor & Francis Online, Wiley Online Library, Wanfang, and CNKI databases were searched for eligible publications up to...

Additional file 5 of Circular RNA circPVT1 promotes nasopharyngeal carcinoma metastasis via the β-TrCP/c-Myc/SRSF1 positive feedback loop

Yongzhen Mo, Yumin Wang, Yian Wang, Xiangying Deng, Qijia Yan, Chunmei Fan, Shuai Zhang, Shanshan Zhang, Zhaojian Gong, Lei Shi, Qianjin Liao, Can Guo, Yong Li, Guiyuan Li, Zhaoyang Zeng, Weihong Jiang, Wei Xiong & Bo Xiang
Additional file 5: Supplemental Table 5. The potential circPVT1-interacting proteins in CNE2 cells identified by LC-MS/MS spectrometry after pull-down with the biontin-labeled circPVT1 probe.

Additional file 3 of Circular RNA circPVT1 promotes nasopharyngeal carcinoma metastasis via the β-TrCP/c-Myc/SRSF1 positive feedback loop

Yongzhen Mo, Yumin Wang, Yian Wang, Xiangying Deng, Qijia Yan, Chunmei Fan, Shuai Zhang, Shanshan Zhang, Zhaojian Gong, Lei Shi, Qianjin Liao, Can Guo, Yong Li, Guiyuan Li, Zhaoyang Zeng, Weihong Jiang, Wei Xiong & Bo Xiang
Additional file 3: Supplemental Table 3. Probes for fluorescence in situ hybridization and RNA pulldown, siRNAs, primers for qRT-PCR and vector construction.

Additional file 16 of Circular RNA circPVT1 promotes nasopharyngeal carcinoma metastasis via the β-TrCP/c-Myc/SRSF1 positive feedback loop

Yongzhen Mo, Yumin Wang, Yian Wang, Xiangying Deng, Qijia Yan, Chunmei Fan, Shuai Zhang, Shanshan Zhang, Zhaojian Gong, Lei Shi, Qianjin Liao, Can Guo, Yong Li, Guiyuan Li, Zhaoyang Zeng, Weihong Jiang, Wei Xiong & Bo Xiang
Additional file 16: Figure S7. c-Myc promotes circPVT1 generation by recruiting SRSF1 to couple transcription to splicing. A. The luciferase reporter gene activity of the PVT1 promoter was analyzed in NPC cells after overexpression of c-Myc. Data were represented as mean ± SD. ***, p < 0.001. B. The binding of transcription factor c-Myc to the PVT1 promoter detected by ChIP assay. Three sites on the PVT1 promoter were identified as potential c-Myc binding sites...

Additional file 7 of Circular RNA circPVT1 promotes nasopharyngeal carcinoma metastasis via the β-TrCP/c-Myc/SRSF1 positive feedback loop

Yongzhen Mo, Yumin Wang, Yian Wang, Xiangying Deng, Qijia Yan, Chunmei Fan, Shuai Zhang, Shanshan Zhang, Zhaojian Gong, Lei Shi, Qianjin Liao, Can Guo, Yong Li, Guiyuan Li, Zhaoyang Zeng, Weihong Jiang, Wei Xiong & Bo Xiang
Additional file 7: Supplemental Table 7. Proteomic analysis of circPVT1-regulated proteins in CNE2 cells after transfected with the circPVT1overexpression or empty vectors, followed by LC-MS/MS spectrometry.

Catering to the Patient

Miriam Urff, Antonio Krüger, Steffen Ruchholtz & Eva C. Stibane
Introduction: It has been shown that communication skills acquired during undergraduate medical education are of great importance. Hence, many countries require teaching communication as part of their medical curricula. To assess students’ learning progress, “Catering to the Patient”, as an aspect of showing empathy, should be evaluated. Since there was no description of a validated instrument fitting for this purpose, one had to be developed. To describe its process of development and its psychometric properties...

Additional file 1 of Planning preclinical confirmatory multicenter trials to strengthen translation from basic to clinical research – a multi-stakeholder workshop report

Natascha Ingrid Drude, Lorena Martinez-Gamboa, Meggie Danziger, Anja Collazo, Silke Kniffert, Janine Wiebach, Gustav Nilsonne, Frank Konietschke, Sophie K. Piper, Samuel Pawel, Charlotte Micheloud, Leonhard Held, Florian Frommlet, Daniel Segelcke, Esther M. Pogatzki-Zahn, Bernhard Voelkl, Tim Friede, Edgar Brunner, Astrid Dempfle, Bernhard Haller, Marie Juliane Jung, Lars Björn Riecken, Hans-Georg Kuhn, Matthias Tenbusch, Lina Maria Serna Higuita … & Ulf Toelch
Additional file 1: Figure S 1. Composition of workshop participants as per field of expertise. The organizing team mainly consists of meta-researchers with a clinical or preclinical background. Other refers to e.g., stakeholders from funding agencies that also attended the workshop. Methods S1. Multi-stakeholder workshop method-Workshop design. Glossary. Glossary of terms.

Additional file 1 of Planning preclinical confirmatory multicenter trials to strengthen translation from basic to clinical research – a multi-stakeholder workshop report

Natascha Ingrid Drude, Lorena Martinez-Gamboa, Meggie Danziger, Anja Collazo, Silke Kniffert, Janine Wiebach, Gustav Nilsonne, Frank Konietschke, Sophie K. Piper, Samuel Pawel, Charlotte Micheloud, Leonhard Held, Florian Frommlet, Daniel Segelcke, Esther M. Pogatzki-Zahn, Bernhard Voelkl, Tim Friede, Edgar Brunner, Astrid Dempfle, Bernhard Haller, Marie Juliane Jung, Lars Björn Riecken, Hans-Georg Kuhn, Matthias Tenbusch, Lina Maria Serna Higuita … & Ulf Toelch
Additional file 1: Figure S 1. Composition of workshop participants as per field of expertise. The organizing team mainly consists of meta-researchers with a clinical or preclinical background. Other refers to e.g., stakeholders from funding agencies that also attended the workshop. Methods S1. Multi-stakeholder workshop method-Workshop design. Glossary. Glossary of terms.

Planning preclinical confirmatory multicenter trials to strengthen translation from basic to clinical research – a multi-stakeholder workshop report

Natascha Ingrid Drude, Lorena Martinez-Gamboa, Meggie Danziger, Anja Collazo, Silke Kniffert, Janine Wiebach, Gustav Nilsonne, Frank Konietschke, Sophie K. Piper, Samuel Pawel, Charlotte Micheloud, Leonhard Held, Florian Frommlet, Daniel Segelcke, Esther M. Pogatzki-Zahn, Bernhard Voelkl, Tim Friede, Edgar Brunner, Astrid Dempfle, Bernhard Haller, Marie Juliane Jung, Lars Björn Riecken, Hans-Georg Kuhn, Matthias Tenbusch, Lina Maria Serna Higuita … & Ulf Toelch
Abstract Clinical translation from bench to bedside often remains challenging even despite promising preclinical evidence. Among many drivers like biological complexity or poorly understood disease pathology, preclinical evidence often lacks desired robustness. Reasons include low sample sizes, selective reporting, publication bias, and consequently inflated effect sizes. In this context, there is growing consensus that confirmatory multicenter studies -by weeding out false positives- represent an important step in strengthening and generating preclinical evidence before moving on...

Additional file 1 of Association of sex steroid hormones and new bone formation rate after iliac onlay grafting: a prospective clinical pilot study

Victoria Constanze Landwehr, Tobias Fretwurst, Julia Heinen, Kirstin Vach, Katja Nelson, Susanne Nahles & Gerhard Iglhaut
Additional file 1. Supplement 1. Body mass index (BMI), 17β-estradiol, testosterone, sex hormone binding globulin and meannew bone formation (NBF) in female and male patients. Supplement 2. Reference ranges (a) of the body mass index (BMI), according to the World HealthOrganization (WHO, 2000), regardless of gender and (b) of the sex steroid hormone serumconcentrations according to the criteria of the Labor Berlin - Charité Vivantes GmbH.

Association of sex steroid hormones and new bone formation rate after iliac onlay grafting: a prospective clinical pilot study

Victoria Constanze Landwehr, Tobias Fretwurst, Julia Heinen, Kirstin Vach, Katja Nelson, Susanne Nahles & Gerhard Iglhaut
Abstract Purpose The present prospective study evaluates the association between new bone formation rate in the iliac onlay graft and sex steroid hormone serum levels. Methods A total of 15 partially or completely edentulous postmenopausal females and 9 males with less than 5 mm height of the remaining alveolar bone underwent iliac onlay grafting followed by dental implant placement using a two-stage approach. Sex hormone binding globulin and 17β-estradiol serum levels were investigated by electrochemiluminescence...

Additional file 1 of Prognostic value of tumor-infiltrating immune cells and immune checkpoints in elderly head-and-neck squamous cell carcinoma patients undergoing definitive (chemo)radiotherapy

Alexander Rühle, Jovan Todorovic, Simon S. K. Spohn, Eleni Gkika, Christoph Becker, Andreas Knopf, Constantinos Zamboglou, Tanja Sprave, Martin Werner, Anca-Ligia Grosu, Gian Kayser & Nils H. Nicolay
Additional file 1: Table S1: Details about the antibodies used in the study.

Additional file 2 of Health and social care of home-dwelling frail older adults in Switzerland: a mixed methods study

Olivia Yip, Suzanne Dhaini, Jan Esser, Flaka Siqeca, Maria Jose Mendieta, Evelyn Huber, Andreas Zeller, Sabina De Geest, Mieke Deschodt, Franziska Zúñiga, Leah L. Zullig & Heather A. King
Additional file 2. INSPIRE population survey respondents and dichotomized responses by content domain.

Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100

Simona Capponi, Nadja Stöffler, Manuel Irimia, Frederik M.A. Van Schaik, Mercedes M. Ondik, Martin L. Biniossek, Lisa Lehmann, Julia Mitschke, Marit W. Vermunt, Menno P. Creyghton, Ann M. Graybiel, Thomas Reinheckel, Oliver Schilling, Benjamin J. Blencowe, Jill R. Crittenden & H. Th. Marc Timmers
Neuronal microexons represent the most highly conserved class of alternative splicing events and their timed expression shapes neuronal biology, including neuronal commitment and differentiation. The six-nt microexon 34ʹ is included in the neuronal form of TAF1 mRNA, which encodes the largest subunit of the basal transcription factor TFIID. In this study, we investigate the tissue distribution of TAF1-34ʹ mRNA and protein and the mechanism responsible for its neuronal-specific splicing. Using isoform-specific RNA probes and antibodies,...

Additional file 6 of PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma

Eyleen Corrales, Ella Levit-Zerdoun, Patrick Metzger, Ralf Mertes, Ariane Lehmann, Julia Münch, Steffen Lemke, Silke Kowar & Melanie Boerries
Additional file 5. Table S5A, B. Over-represented biological processes (GO-bp) among genes up- and down-regulated with increasing resistance in MaMel cell lines.

Additional file 7 of PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma

Eyleen Corrales, Ella Levit-Zerdoun, Patrick Metzger, Ralf Mertes, Ariane Lehmann, Julia Münch, Steffen Lemke, Silke Kowar & Melanie Boerries
Additional file 6. Table S6A, B. Over-represented hallmark gene sets among genes up- and down-regulated with increasing resistance in MaMel cell lines.

Registration Year

  • 2022
    129
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Affiliations

  • University Medical Center Freiburg
    136
  • University of Freiburg
    46
  • Jiangxi Agricultural University
    44
  • Huazhong University of Science and Technology
    44
  • Chengdu University of Traditional Chinese Medicine
    44
  • Capital Medical University
    44
  • Hubei University of Science and Technology
    44
  • Hubei University of Medicine
    44
  • Sun Yat-sen Memorial Hospital
    44
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    44