141 Works

Sequential learning of regression models by penalized estimation

Wessel N. van Wieringen & Harald Binder
When data arrive in a sequence of two or more data sets, modeling on the most recent data set should take previous data sets 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 towards a nonzero...

Additional file 2 of Empirical evidence of study design biases in nutrition randomised controlled trials: a meta-epidemiological study

Julia Stadelmaier, Isabelle Roux, Maria Petropoulou & Lukas Schwingshackl
Additional file 2: Fig. S1. Example of calculating effect estimates. Fig. S2. Forest plot, random sequence (binary outcomes), main analysis. Fig. S3. Forest plot, random sequence (binary outcomes), sensitivity analysis: excluding highly correlated outcomes. Fig. S4. Forest plot, random sequence (binary outcomes), sensitivity analysis: including only one outcome per comparison. Fig. S5. Forest plot, random sequence (binary outcomes), subgroup analysis: clusters of interventions. Fig. S6. Forest plot, random sequence (binary outcomes), subgroup analysis: clusters of...

Additional file 1 of Hand hygiene improvement of individual healthcare workers: results of the multicentre PROHIBIT study

Tjallie van der Kooi, Hugo Sax, Hajo Grundmann, Didier Pittet, Sabine de Greeff, Jaap van Dissel, Lauren Clack, Albert W. Wu, Judith Davitt, Sofia Kostourou, Alison Maguinness, Anna Michalik, Viorica Nedelcu, Márta Patyi, Janja Perme Hajdinjak, Milena Prosen, David Tellez, Éva Varga, Fani Veini, Mirosław Ziętkiewicz & Walter Zingg
Additional file 1: Table S1. Association between hand hygiene and activity index during baseline and intervention; Table S2. Overall (i.e. for all HCWs) hand hygiene compliance per hospital, during baseline and the intervention period; Figure S1. Boxplot (median, quartiles and ranges) of individual HH compliance both during baseline and intervention period; Figure S2. Boxplot (median, quartiles and ranges) of hand hygiene increase (in percentage points) in the group of improving HCWs; Figure S3. Variability within...

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 4 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 4: Supplemental Table 4. List of antibodies for immunohistochemistry, western blotting, immunofluorescence, and RNA pull-down experiments.

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.

Additional file 8 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 8: Supplemental Table 8. Clinicopathological data of 3 NPC tissues measured by RNA pull-down.

Additional file 9 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 9: Supplemental Table 9. Clinicopathologicaldata of 30 paraffin-embedded NPC tissues for immunohistochemistry (IHC) and in situ hybridization (ISH).

Additional file 2 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 2. Key resources for each component of the Basel Approach for coNtextual ANAlysis (BANANA).

Additional file 4 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 4. Overview of variables assessed and themes explored in the SMILe project.

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

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...

Additional file 3 of 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
Additional file 3: Figure S3. Analysis of processes involved in ribosomal biogenesis in MCF7 cells. A) KLF7OE does not lead to significant changes in mRNA expression of the indicated genes in export, pseudouridylation, rRNA cleavage. B) No changes in POP1 and RMRP mRNA level by KLF7OE in MCF7 cells.

Additional file 3 of 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
Additional file 3: Figure S3. Analysis of processes involved in ribosomal biogenesis in MCF7 cells. A) KLF7OE does not lead to significant changes in mRNA expression of the indicated genes in export, pseudouridylation, rRNA cleavage. B) No changes in POP1 and RMRP mRNA level by KLF7OE in MCF7 cells.

Additional file 10 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 10: Figure S1. A. Thedifferentially expressed circRNAs between the high metastasis NPC cell line S18 and the low metastasis NPC cell line S26 (GSE137543, the RPM value ≥ 2and Fold changes ≥ 1.5). Circular RNA circPVT1 is highly expressed in NPC cell line S18. B. The Venn diagram of data sets GSE137543 and PRJNA391554. Circular RNA circPVT1 was identified for its high abundance in both sets of data.C. circPVT1 is mainly localized in...

Additional file 12 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 12: Figure S3. circPVT1 promotes the migration and invasion of NPC cells through binding to β-TrCP. A. The secondary ion flow diagram of β-TrCP identified by mass spectrometry according to the peptide sequence (DFITALPAR) of β -TrCP.B. Schematic diagram of binding sites betweent circPVT1 and β-TrCP using the catRAPID website.The 230-280 nt of circPVT1 was predicted to bind to β-TrCP protein with high interaction score.C. The secondary structure of circPVT1 changed when 230-280...

Additional file 13 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 13: Figure S4. The WD40 repeat domain of β-TrCP interacts with circPVT1. A. The functional domain of the of β-TrCP proteins are illustrated (top), including the F-box domain and the WD40 domain. The expressing plasmids for full-length β-TrCP or truncated fragments (F-box and WD40) were constructed and confirmed using anti-Flag antibody. B. Wound healing assay showed that overexpression of β-TrCP inhibited NPC cells migration. Data were represented as mean ± SD. ***, p...

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...

Supplementary document for Light as quantum back-action nullifying meter - 5830299.pdf

Sankar Davuluri & Yong Li
supplementary

Additional file 4 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 3. Table S3A–F. Over-represented biological processes (GO-bp) among over-expressed genes in MaMel cell lines.

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
Abstract Background Current therapeutic management of advanced melanoma patients largely depends on their BRAF mutation status. However, the vast heterogeneity of the tumors hampers the success of therapies targeting the MAPK/ERK pathway alone. Dissecting this heterogeneity will contribute to identifying key players in the oncogenic progression to tailor more effective therapies. Methods We performed a comprehensive molecular and phenotypic characterization of a panel of patient-derived BRAFV600E-positive melanoma cell lines. Transcriptional profiling was used to identify...

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 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.

Additional file 4 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 4. Joint display table integrating study findings from the INSPIRE population survey and interviews.

Additional file 10 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 9. Table S9A–D. Over-represented KEGG pathway among gene clusters in MaMe21, MaMel63a, HEM, and HDF.

Registration Year

  • 2022
    141

Resource Types

  • Text
    46
  • Dataset
    45
  • Collection
    30
  • Image
    20

Affiliations

  • University Medical Center Freiburg
    141
  • Jiangxi Agricultural University
    56
  • Huazhong University of Science and Technology
    56
  • Chengdu University of Traditional Chinese Medicine
    56
  • Capital Medical University
    56
  • Hubei University of Science and Technology
    56
  • Hubei University of Medicine
    56
  • Sun Yat-sen Memorial Hospital
    56
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    56
  • Alberta Health Services
    56