bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S6 from A Senescence-Mimicking (Senomimetic) VEGFR TKI Side Effect Primes Tumor Immune Responses via IFN/STING Signaling
Authors: Dolan Melissa , Shi Yuhao , Mastri Michalis , Long Mark D. , McKenery Amber , Hill James W. , Vaghi Cristina , Benzekry Sebastien , Barbi Joseph , Ebos John M.L.
Published: September 2024

Supplementary Figure S6: Extended Data from Fig 6 – SM+ tumor growth in vitro and in vivo. (A) Tumor size comparisons between Vehicle and Treated groups for Data shown in Fig 6B (T-tests shown). (B) Schematic for in vitro and in vivo assessment of growth differences between SM+ and SM− FACS-enriched tumor cells from EMT6CaR cells. (C) In vitro proliferation differences between sorted EMT6CaR SM+ and SM- tumor cells evaluated by MTS after 2 days (n=4). (D) In vivo primary tumor growth differences between EMT6CaR SM+ and SM- implanted tumors in Balb/c mice. Left, tumor volume curves (same as in Fig 6E; SM+ and SM- vehicle treated controls for PD-L1 treated groups) and difference in the Gompertz model parameter β (specific growth rate increase) from growth kinetics analysis of primary tumor growth (inset) (n=5). Cabozantinib-resistant (CaR); Senescence-marker (SM); Fluorescent-activated cell sorting (FACS); Fold Change (FC); Standard Deviation (SD); Primary tumor burden was assessed by caliper measurement. See Appendix 4 for details of reduced Gompertz and mixed-effects modeling to evaluate tumor growth kinetics. Quantitative data presented as mean ± SD. * p<0.05; ** p<0.01; Fig S6C represents vehicle control groups from Fig 6E.
Supplementary Figure S4 from A Senescence-Mimicking (Senomimetic) VEGFR TKI Side Effect Primes Tumor Immune Responses via IFN/STING Signaling
Authors: Dolan Melissa , Shi Yuhao , Mastri Michalis , Long Mark D. , McKenery Amber , Hill James W. , Vaghi Cristina , Benzekry Sebastien , Barbi Joseph , Ebos John M.L.
Published: September 2024

Figure S4: Senomimetic TKI effects induce opposing immune-regulatory molecule expression. (A-C) Gene Expression of antigen presentation molecules following treatment with Ca in (A) 4T1 cells (2µM), (B) EMT6M cells (2µM), and (C) LM2-4 cells (5µM) compared to vehicle treated controls by qRT-PCR (n=3). (D) Gene Expression of antigen presentation molecules in EMT6CaR cells compared to EMT6M by qRT-PCR (n=3). (E) PD-L1 expression in 4T1STING-KD cells after Ax treatment (0.5uM) by qRT-PCR (N=3) (F) Representative histogram and quantification of MHC-I or PD-L1 expression in SM+/SM- gated cell populations in 4T1AxR tumor cells by flow cytometry (n=3). (G) MHC-I and PD-L1 expression in SM+/SM- gated cell populations in EMT6CaR tumor cells by flow cytometry (n=3). Metastatic parental control for EMT6CaR (M); Axitinib-resistant (AxR); Cabozantinib-resistant (CaR); Standard deviation (SD); Median Fluorescent Intensity (MFI); Fold Change (FC). Quantitative data is shown as mean ± SD; * p<0.05; ** p<0.01; *** p<0.001; **** p < 0.0001
Supplementary Table S3 from Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation
Authors: Nguyen Lily L. , Watson Zachary L. , Ortega Raquel , Woodruff Elizabeth R. , Jordan Kimberly R. , Iwanaga Ritsuko , Yamamoto Tomomi M. , Bailey Courtney A. , To Francis , Jeong Abigail D. , Guntupalli Saketh R. , Behbakht Kian , Gibaja Veronica , Arnoult Nausica , Cocozaki Alexis , Chuong Edward B. , Bitler Benjamin G.
Published: September 2024

Supplementary Table S3 shows the antibody panels for the multispectral immunohistochemistry.
Supplementary Figure 6 from Enhancing Neutrophil Cytotoxicity of a Panel of Clinical EGFR Antibodies by Fc Engineering to IgA3.0
Authors: Chan Chilam , Jansen J.H. Marco , Hendriks Ilona S.T. , van der Peet Ida C. , Verdonschot Meggy E.L. , Passchier Elsemieke M. , Tsioumpekou Maria , Nederend Maaike , Klomp Sharon A. , Valerius Thomas , Peipp Matthias , Leusen Jeanette H.W. , Olofsen Patricia A.
Published: September 2024

Supplementary Figure 6: Efficacy of neutrophil depletion in the long i.p. A431-luc2 model.
Supplementary Table 3 from Hepatitis B Virus X Protein Represses Expression of Tumor Suppressor PTPN18 in Hepatocellular Carcinoma
Authors: Zhou Zhenyu , Yu Wei , Li Huoming , Shi Juanyi , Meng Shiyu , Yan Yongcong , Chen Ruibin , Liu Haohan , Wang Jie , Sun Jian , Xiao Zhiyu , Zhang Jianlong
Published: September 2024

Univariate and multivariate Cox regression analysis (DFS).
Supplementary Video 5 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Spontaneous Ca2+-activated Cl- flares.
Supplementary Video 2 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Synchronization of Ca2+ flares upon Yoda1 addition.
Supplementary Video 1 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Mitosis of a U87 cell visualized through the NucBlue dye.
Supplementary Figure S5 from USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming
Authors: Ekstrom Thomas L. , Hussain Sajjad , Bedekovics Tibor , Ali Asma , Paolini Lucia , Mahmood Hina , Rosok Raya M. , Koster Jan , Johnsen Steven A. , Galardy Paul J.
Published: September 2024

USP44 is expressed early in neural crest development.
Figure S1 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Spontaneous, asynchronous Ca2+ flares in U87 cells becomes synchronous upon addition of the Piezo1 activator Yoda1.
Supplementary Table S6 from miR-497 Target Gene Regulatory Network in Angiosarcoma
Authors: Benton Annaleigh , Moriarty Noah M. , Terwilliger Emma , Liu Bozhi , Murphy Ant , Maluvac Hannah , Shu Mae , Gartenhaus Lauren E. , Janson Nimod D. , Pfeffer Claire M. , Utturkar Sagar M. , Parkinson Elizabeth I. , Lanman Nadia A. , Hanna Jason A.
Published: September 2024

Gene Ontology analysis of miR-497 upregulated genes in ADC106 cells.
Supplementary Table S4 from miR-497 Target Gene Regulatory Network in Angiosarcoma
Authors: Benton Annaleigh , Moriarty Noah M. , Terwilliger Emma , Liu Bozhi , Murphy Ant , Maluvac Hannah , Shu Mae , Gartenhaus Lauren E. , Janson Nimod D. , Pfeffer Claire M. , Utturkar Sagar M. , Parkinson Elizabeth I. , Lanman Nadia A. , Hanna Jason A.
Published: September 2024

Antibodies used for immunoblots.
Supplementary Figure S2 from miR-497 Target Gene Regulatory Network in Angiosarcoma
Authors: Benton Annaleigh , Moriarty Noah M. , Terwilliger Emma , Liu Bozhi , Murphy Ant , Maluvac Hannah , Shu Mae , Gartenhaus Lauren E. , Janson Nimod D. , Pfeffer Claire M. , Utturkar Sagar M. , Parkinson Elizabeth I. , Lanman Nadia A. , Hanna Jason A.
Published: September 2024

MicroRNA target gene enrichment in miR-497 mimic transfected cells.
Figure 5 from Clinically Relevant Humanized Mouse Models of Metastatic Prostate Cancer Facilitate Therapeutic Evaluation
Authors: Kostlan Raymond J. , Phoenix John T. , Budreika Audris , Ferrari Marina G. , Khurana Neetika , Choi Jae E. , Juckette Kristin , Mahapatra Somnath , McCollum Brooke L. , Moskal Russell , Mannan Rahul , Qiao Yuanyuan , Vander Griend Donald J. , Chinnaiyan Arul M. , Kregel Steven
Published: September 2024

Myeloid-support exhibits immuno-dampened profile in huNOG-EXL 22Rv1 xenograft tumors. A, Gating strategy used to determine presence of human CD45+ cells in the NOG-EXL model. B, Representative data showing the abundance of various immune cell populations; human leukocytes, CD19+ cells, CD3+ cells, and double negative cells; MDSC and activated myeloid cells; and helper T cells (CD4+) and cytotoxic T cells (CD8+; top to bottom). C, Quantitated data comparing human CD45, CD3, CD4, and CD11b populations in tumors isolated from testosterone-implanted vehicle, intact vehicle, castrated vehicle, and castrated enzalutamide treated mice. D, Gating strategy for determining the activation state of MDSCs (CD3− CD19− CD11b+ CD14−). E, Representative data showing the activation state of the MDSC cells harvested from tumors under different treatment categories through the presence of the surface markers: CD25, CD44, CD69, and PD-1. F, Quantitated data showing the activation state of the MDSCs throughout the different treatments.
Data from Hepatitis B Virus X Protein Represses Expression of Tumor Suppressor PTPN18 in Hepatocellular Carcinoma
Authors: Zhou Zhenyu , Yu Wei , Li Huoming , Shi Juanyi , Meng Shiyu , Yan Yongcong , Chen Ruibin , Liu Haohan , Wang Jie , Sun Jian , Xiao Zhiyu , Zhang Jianlong
Published: September 2024

Abstract
HBV-associated hepatocellular carcinoma (HCC) represents the prevalent form of HCC, with HBx protein being a crucial oncoprotein. Numerous members of the protein tyrosine phosphatase nonreceptor (PTPN) family have been confirmed to be significantly associated with the occurrence and progression of malignant tumors. Our group previously identified the involvement of PTPN13 in HCC. However, the roles of other PTPNs in HCC require further investigation. In this study, we found that PTPN18 expression was significantly downregulated within HCC tissues compared with adjacent nontumor and reference liver tissues. Functionally, PTPN18 exerted inhibitory effects on the proliferation, migration, invasion, and sphere-forming capability of HCC cells while concurrently promoting apoptotic processes. Through phospho-protein microarray screening followed by subsequent validation experiments, we identified that PTPN18 could activate the p53 signaling pathway and suppress the AKT/FOXO1 signaling cascade in HCC cells. Moreover, the HBx protein mediated the repression of PTPN18 expression by upregulating miR-128-3p. Collectively, our study unveiled the role of PTPN18 as a tumor suppressor in HBV-related HCC.

Implications: Our findings revealed that PTPN18 might be a potential diagnostic and therapeutic target for HBV-related HCC.
Data from USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming
Authors: Ekstrom Thomas L. , Hussain Sajjad , Bedekovics Tibor , Ali Asma , Paolini Lucia , Mahmood Hina , Rosok Raya M. , Koster Jan , Johnsen Steven A. , Galardy Paul J.
Published: September 2024

Abstract
Neuroblastoma is an embryonic cancer that contributes disproportionately to death in young children. Sequencing data have uncovered few recurrently mutated genes in this cancer, although epigenetic pathways have been implicated in disease pathogenesis. We used an expression-based computational screen that examined the impact of deubiquitinating enzymes on patient survival to identify potential new targets. We identified the histone H2B deubiquitinating enzyme USP44 as the enzyme with the greatest impact on survival in patients with neuroblastoma. High levels of USP44 significantly correlate with metastatic disease, unfavorable histology, advanced patient age, and MYCN amplification. The subset of patients with tumors expressing high levels of USP44 had significantly worse survival, including those with tumors lacking MYCN amplification. We showed experimentally that USP44 regulates neuroblastoma cell proliferation, migration, invasion, and neuronal development. Depletion of the histone H2B ubiquitin ligase subunit RNF20 resulted in similar findings, strongly implicating this histone mark as the target of USP44 activity in this disease. Integration of transcriptome and epigenome in analyses demonstrates a distinct set of genes that are regulated by USP44, including those in Hallmark MYC target genes in both murine embryonic fibroblasts and the SH-SY5Y neuroblastoma cell line. We conclude that USP44 is a novel epigenetic regulator that promotes aggressive features and may be a novel target in neuroblastoma.

Implications: This study identifies a new genetic marker of aggressive neuroblastoma and identifies the mechanisms by which its overactivity contributes to the pathophysiology of this disease.
Supplementary Figure S5 from CHD2 Regulates Neuron–Glioma Interactions in Pediatric Glioma
Authors: Zhang Xu , Duan Shoufu , Apostolou Panagiota E. , Wu Xiaoping , Watanabe Jun , Gallitto Matthew , Barron Tara , Taylor Kathryn R. , Woo Pamelyn J. , Hua Xu , Zhou Hui , Wei Hong-Jian , McQuillan Nicholas , Kang Kyung-Don , Friedman Gregory K. , Canoll Peter D. , Chang Kenneth , Wu Cheng-Chia , Hashizume Rintaro , Vakoc Christopher R. , Monje Michelle , McKhann Guy M. , Gogos Joseph A. , Zhang Zhiguo
Published: September 2024

Calcium imaging in brain slices with SU-DIPG36 xenografts in hippocampal CA1.
Table S4 from MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer
Authors: Meena Jitendra K. , Wang Jarey H. , Neill Nicholas J. , Keough Dianne , Putluri Nagireddy , Katsonis Panagiotis , Koire Amanda M. , Lee Hyemin , Bowling Elizabeth A. , Tyagi Siddhartha , Orellana Mayra , Dominguez-Vidaña Rocio , Li Heyuan , Eagle Kenneth , Danan Charles , Chung Hsiang-Ching , Yang Andrew D. , Wu William , Kurley Sarah J. , Ho Brian M. , Zoeller Joseph R. , Olson Calla M. , Meerbrey Kristen L. , Lichtarge Olivier , Sreekumar Arun , Dacso Clifford C. , Guddat Luke W. , Rejman Dominik , Hocková Dana , Janeba Zlatko , Simon Lukas M. , Lin Charles Y. , Pillon Monica C. , Westbrook Thomas F.
Published: September 2024

Table S4 shows predictions of hypothetical purine nucleotide flux.
Supplemental Figure S7 from D3S-001, a KRAS G12C Inhibitor with Rapid Target Engagement Kinetics, Overcomes Nucleotide Cycling, and Demonstrates Robust Preclinical and Clinical Activities
Authors: Zhang Jing , Lim Sun Min , Yu Mi Ra , Chen Cheng , Wang Jia , Wang Wenqian , Rui Haopeng , Lu Jingtao , Lu Shun , Mok Tony , Chen Zhi Jian , Cho Byoung Chul
Published: September 2024

Supplemental Figure S7 shows data from translational exploration of CR6927 PDX model.
Supplemental Figure S5 from D3S-001, a KRAS G12C Inhibitor with Rapid Target Engagement Kinetics, Overcomes Nucleotide Cycling, and Demonstrates Robust Preclinical and Clinical Activities
Authors: Zhang Jing , Lim Sun Min , Yu Mi Ra , Chen Cheng , Wang Jia , Wang Wenqian , Rui Haopeng , Lu Jingtao , Lu Shun , Mok Tony , Chen Zhi Jian , Cho Byoung Chul
Published: September 2024

Supplemental Figure S5 shows D3S-001 additional in vivo efficacy and tolerability data.
Supplemental Figure S4 from D3S-001, a KRAS G12C Inhibitor with Rapid Target Engagement Kinetics, Overcomes Nucleotide Cycling, and Demonstrates Robust Preclinical and Clinical Activities
Authors: Zhang Jing , Lim Sun Min , Yu Mi Ra , Chen Cheng , Wang Jia , Wang Wenqian , Rui Haopeng , Lu Jingtao , Lu Shun , Mok Tony , Chen Zhi Jian , Cho Byoung Chul
Published: September 2024

Supplemental Figure S4 shows dose-dependent curves for each cell line.
Supplementary Methods from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Supplementary Methods, References
Supplementary Figure S6 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

Sialidase treatment reduces surface α2,6-linked sialic acid
Supplementary Figure S4 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

SLC35A2 targeted degradation by dTag modification synergizes with Pola-V.
Supplementary Figure S3 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

Small-molecule sialyltransferase inhibition synergizes with Pola-V in ABC and GCB DLBCL
Supplementary Table S5 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Genetic and methylation analysis across timepoints.
Supplementary Table S2 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Qualitative and Quantitative Summary of Abnormal Peripheral Blood and Bone Marrow Findings.
Supplementary Figure S6 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Gene Set Enrichment Analysis of single cell RNAseq data reveals downregulation of several inflammation-regulated pathways in monocytic populations.
Supplementary Table S18 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Table S18: Estimation of excess of mutations in the hormone-receptor positive breast cancer cohorts from the Hartwig Medical Foundation (HMF). The table lists, for each one of the regions showing an excess of functional alterations in the SIDV cohort (highlighted in table S13.1) the number of mutations in the region in both the SIDV and HMF cohort, along with the estimated background probability of seeing a mutation for the regions (using the HMF cohort) and the corresponding, empirical p-value of seeing the observed number of mutations, given the background probability (see Methods).
Supplementary Figure S8 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Figure 8. SIDP identifies regulatory regions with context-dependent activity in MCF7 cells.
Supplementary Figure S13 from Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis
Authors: Demajo Santiago , Ramis-Zaldivar Joan E. , Muiños Ferran , Grau Miguel L. , Andrianova Maria , López-Bigas Núria , González-Pérez Abel
Published: September 2024

Association between CH mutations and the development of hematologic cancers across UKB
Supplementary Figure S5 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Authors: Wijetunga N. Ari , Gessner Kathryn H. , Kanchi Krishna , Moore Jay A. , Fleischmann Zoe , Jin Dexter X. , Frampton Garrett M. , Sturdivant Michael , Repka Michael , Sud Shivani , Corcoran David L. , Galsky Matthew D. , Milowsky Matthew I. , Wobker Sara E. , Kim William Y. , Rose Tracy L. , Damrauer Jeffrey S.
Published: September 2024

Supplementary Figure S5
Supplementary Figure S3 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Authors: Wijetunga N. Ari , Gessner Kathryn H. , Kanchi Krishna , Moore Jay A. , Fleischmann Zoe , Jin Dexter X. , Frampton Garrett M. , Sturdivant Michael , Repka Michael , Sud Shivani , Corcoran David L. , Galsky Matthew D. , Milowsky Matthew I. , Wobker Sara E. , Kim William Y. , Rose Tracy L. , Damrauer Jeffrey S.
Published: September 2024

Supplementary Figure S3
Supplement Figure 3 from Anti-HDGF Antibody Targets EGFR Tyrosine Kinase Inhibitor–Tolerant Cells in NSCLC Patient-Derived Xenografts
Authors: Zhou Cindy Q. , Li Ariel , Ri Kaoru , Sultan Ahmed S. , Ren Hening
Published: September 2024

Supplement Figure 3 shows the Effect of anti-HDGF antibody H3 on post-progression tumor.
Rapid-Growing Phyllodes Tumor after an Accidental Bump on the Breast: A Case Report
Authors: Damaskos Christos , Garmpis Nikolaos , Kyriakopoulou Anna , Nikolettos Konstantinos , Garmpi Anna , Dimitroulis Dimitrios , Tsikouras Panagiotis , Nikolettos Nikolaos , Effraimidou Eleni I. , Vrettou Kleio , Psilopatis Iason
Published: September 2024

Introduction: Giant phyllodes tumors are fibroepithelial lesions whose diameters exceed 10 cm. Core biopsy represents the best diagnostic method in order to distinct fibroadenomas from phyllodes tumors. Wide surgical resection with clear margins is the standard of treatment. Case Presentation: In this report, we describe the case of a 41-year-old woman, who presented with a rapid growth of a phyllodes tumor after an accidental bump on the breast and had to undergo mastectomy followed by breast reconstruction. Conclusion: There is possibly an etiological correlation between accident and phyllodes tumor growth.
Development of a Diagnostic Model for Pancreatic Ductal Adenocarcinoma Using Machine Learning and Blood-Based miRNAs
Authors: Tang Jason Y. , Kouznetsova Valentina L. , Kesari Santosh , Tsigelny Igor F.
Published: September 2024

Introduction: Pancreatic ductal adenocarcinoma (PDAC) has the lowest survival rate among all major cancers due to a lack of symptoms in early stages, early detection tools, and optimal therapies for late-stage patients. Thus, effective and non-invasive diagnostic tests are greatly needed. Recently, circulating miRNAs have been reported to be altered in PDAC. They are promising biomarkers because of stability in the blood, ease of non-invasive detection, and convenient screening methods. This study aimed to use blood-based miRNA biomarkers and various analysis methods in the development of a machine-learning (ML) model for PDAC. Methods: Blood-based miRNAs associated with PDAC were collected from open sources. miRNA sequences, targeted genes, and involved pathways were used to construct a set of descriptors for an ML model. Results: Bioinformatics analysis revealed that most genes in pancreatic cancer and insulin signaling pathways were targeted by the PDAC-related miRNAs. The best-performing ML model with the Random Forest classifier was able to achieve an accuracy of 88.4%. Model evaluations of an independent PDAC-associated miRNAs test set had 100% accuracy while non-cancer miRNAs had 52.4% accuracy, indicating specificity to PDAC. Conclusions: Our results suggest an ML model developed using blood-based miRNA biomarkers’ target gene, pathway, and sequence features could be potentially implicated in PDAC diagnostics.
Comparison of Machine Learning Algorithms and Nomogram Construction for Diabetic Retinopathy Prediction in Type 2 Diabetes Mellitus Patients
Authors: Jiang Weiliang , Li Zijing
Published: September 2024

Introduction: The aim of this study was to compare various machine learning algorithms for constructing a diabetic retinopathy (DR) prediction model among type 2 diabetes mellitus (DM) patients and to develop a nomogram based on the best model. Methods: This cross-sectional study included DM patients receiving routine DR screening. Patients were randomly divided into training (244) and validation (105) sets. Least absolute shrinkage and selection operator regression was used for the selection of clinical characteristics. Six machine learning algorithms were compared: decision tree (DT), k-nearest neighbours (KNN), logistic regression model (LM), random forest (RF), support vector machine (SVM), and XGBoost (XGB). Model performance was assessed via receiver-operating characteristic (ROC), calibration, and decision curve analyses (DCAs). A nomogram was then developed on the basis of the best model. Results: Compared with the five other machine learning algorithms (DT, KNN, RF, SVM, and XGB), the LM demonstrated the highest area under the ROC curve (AUC, 0.894) and recall (0.92) in the validation set. Additionally, the calibration curves and DCA results were relatively favourable. Disease duration, DPN, insulin dosage, urinary protein, and ALB were included in the LM. The nomogram exhibited robust discrimination (AUC: 0.856 in the training set and 0.868 in the validation set), calibration, and clinical applicability across the two datasets after 1,000 bootstraps. Conclusion: Among the six different machine learning algorithms, the LM algorithm demonstrated the best performance. A logistic regression-based nomogram for predicting DR in type 2 DM patients was established. This nomogram may serve as a valuable tool for DR detection, facilitating timely treatment.
CreoleVal: Multilingual Multitask Benchmarks for Creoles
Authors: Lent Heather , Tatariya Kushal , Dabre Raj , Chen Yiyi , Fekete Marcell , Ploeger Esther , Zhou Li , Armstrong Ruth-Ann , Eijansantos Abee , Malau Catriona , Heje Hans Erik , Lavrinovics Ernests , Kanojia Diptesh , Belony Paul , Bollmann Marcel , Grobol Loïc , Lhoneux Miryam de , Hershcovich Daniel , DeGraff Michel , Søgaard Anders , Bjerva Johannes
Published: September 2024

Creoles represent an under-explored and marginalized group of languages, with few available resources for NLP research. While the genealogical ties between Creoles and a number of highly resourced languages imply a significant potential for transfer learning, this potential is hampered due to this lack of annotated data. In this work we present CreoleVal, a collection of benchmark datasets spanning 8 different NLP tasks, covering up to 28 Creole languages; it is an aggregate of novel development datasets for reading comprehension relation classification, and machine translation for Creoles, in addition to a practical gateway to a handful of preexisting benchmarks. For each benchmark, we conduct baseline experiments in a zero-shot setting in order to further ascertain the capabilities and limitations of transfer learning for Creoles. Ultimately, we see CreoleVal as an opportunity to empower research on Creoles in NLP and computational linguistics, and in general, a step towards more equitable language technology around the globe.
Amanita minqingensis, a novel taxon of Amanita section Vaginatae (Amanitaceae, Agaricales) from Southern China
Authors: GUAN XIAYU , ZHU MENGJIA , KEYHANI NEMAT O , DANG YUXIAO , LV HUAJUN , WU ZIYI , HENG ZHIANG , CHEN RUIYA , LIU SEN , LAI PENGYU , YANG CHENJIE , CHEN JINHUI , QIU JUNZHI
Published: September 2024

A new species of Amanita, A. minqingensis, is described from Fujian province, China, based on morphological and multi-phylogenetic sequencing including the nuclear ribosomal large subunit (nrLSU), nuclear ribosomal internal transcribed spacer (ITS), RNA polymerase large subunit-2 (rpb2), and translation elongation factor-α (tef1-α) loci. We identify the species as a member in Amanita section Vaginatae, subg. Amanita. The new species is characterized by its tan pileus with putty verrucose volval remnants, the absence of clamps and globose to sub-globose basidiospores ((9‒)9.2‒10.3‒11 × (8.5‒)9‒9.5‒10.5). Detailed descriptions, color photographs of fresh basidiomata, line drawing of microscopic characters and a phylogenetic tree based on ITS sequence data are are provided.
Swertia patnitopiansis, a new synonym of S. cordata (Gentianaceae)
Authors: ISLAM TAJAMUL , KHUROO ANZAR AHMAD , MAITY DEBABRATA , NAWCHOO IRSHAD A.
Published: September 2024

A critical evaluation of the diagnostic characters used in delimitation of Swertia patnitopiansis Singh from S. cordata Wall. ex C.B.Clarke revealed that the former is conspecific to the latter. Therefore, S. patnitopiansis is recognized as a new synonym of S. cordata. Comparison of taxonomic characters, photographic illustrations and distribution map are provided to ease the identification of the taxon.
A gender and size specific evaluation of Grammont-type inlay versus lateralizing onlay stem designs in achieving lateralization and distalization in reverse shoulder arthroplasty
Authors: Imiolczyk Jan-Phillip , Zeid Paula-Nevin Abu , Eckl Larissa , Imiolczyk Tankred , Gohlke Frank
Published: September 2024

Introduction

In reverse shoulder arthroplasty (RSA) new designs enable greater amounts of lateralization to prevent instability and scapular notching and increase range of motion, however, excessive lateralization leads to stress upon the acromion that can result in scapular spine fatigue fractures. Aim of this study was to gender- and size-specifically assess the influence of glenosphere size and different humeral designs on lateralization, distalization, and bony impingement-free range of motion (ROM) in patients undergoing RSA.

Methods

Computed tomography scans from 30 osteoarthritic patients (f:15, m:15) and 20 cuff tear arthropathy patients (f:10, m:10) were used to virtually simulate RSA implantation. The efficacy of an inlay Grammont-type system vs. an onlay lateralizing system combined with different glenosphere sizes (36 mm vs. 42 mm) in achieving ROM, lateralization, and distalization was evaluated. Moreover, gender and patient’s constitution were correlated to humeral size by radiologically measuring the best-fit circle of the humeral head.

Results

A different amount of relative lateralization was achieved in both genders using large glenospheres and onlay designs. Latter yielded a higher ROM in all planes for men and women with a 42 mm glenosphere; with the 36 mm glenosphere, an increased ROM was observed only in men. The 155° inlay design led to joint medialization only in men, whereas all designs led to lateralization in women. When adjusting the absolute amount of lateralization to humerus’ size (or patient’s height), regardless of implant type, women received greater relative lateralization using 36 mm glenosphere (inlay: 1%; onlay 12%) than men with 42 mm glenosphere (inlay: -3%; onlay: 8%).

Conclusion

The relative lateralization achieved using onlay design is much higher in women than men. Small glenospheres yield greater relative lateralization in women compared to large glenospheres in men. Humeral lateralization using onlay designs should be used cautiously in women, as they lead to great relative lateralization increasing stress onto the acromion.

Level of evidence

Basic Science Study, Computer Modeling.
Barriers of access to primary healthcare services by National Health Insurance Fund capitated members in Uasin Gishu county, Kenya
Authors: Were Barbara Nawire , Mwangi Eunice Muthoni , Muiruri Lillian Wambui
Published: September 2024

Purpose

The study identifies provision of primary healthcare services using the capitated health model as a prerequisite for promoting positive healthcare outcomes for a country’s population. However, capitated members have continued to face challenges in accessing primary healthcare services despite enrolment in the National Health Insurance Fund (NHIF). This study sought to determine if variables such as patient knowledge of the NHIF benefit package, NHIF Premium Payment processes, selecting NHIF capitated health facilities, and NHIF Communication to citizens’ influences access to primary healthcare services.

Method

A cross-sectional analytical research design was adopted. Data was collected from patients who were using NHIF cards, who were drawn from health facilities. Data was collected using a structured questionnaire where some of the questions were rated using the Likert scale to enable the generation of descriptive statistics. Data was analysed using descriptive and inferential statistics. Logistic regression was conducted to determine the relationship between the independent and the dependent variables.

Results

The study found that four independent variables (Patient knowledge of NHIF Benefit Package, NHIF Premium Payment processes, Selecting NHIF capitated Health Facility, and NHIF Communication to citizens) were significant predictors of access to capitated healthcare services with significance values of .001, .001, .001 and .001 respectively at 95% significance level.

Conclusions

The study found that familiarity with the NHIF benefit package significantly influenced NHIF capitated members' access to primary healthcare services in Uasin Gishu County. While most members were aware of their healthcare entitlements, there's a need for increased awareness regarding access to surgical services and dependents' inclusion. Facility selection also played a crucial role, influenced by factors like freedom of choice, NHIF facility selection rules, facility appearance, and proximity to members' homes. NHIF communication positively impacted access, with effective communication channels aiding service accessibility. Premium payment processes also significantly linked with service access, influenced by factors such as payment procedures, premium awareness, payment schedules, registration waiting periods, and penalties for defaults. Overall, patient knowledge, NHIF communication, premium payment processes, and facility selection all contributed positively to NHIF capitated members' access to primary healthcare services in Uasin Gishu County.
Greater exposure to PM2.5 and PM10 was associated with lower corneal nerve measures: the Maastricht study - a cross-sectional study
Authors: Mokhtar Sara B. A. , Viljoen Jessica , van der Kallen Carla J. H. , Berendschot Tos T. J. M. , Dagnelie Pieter C. , Albers Jeroen D. , Soeterboek Jens , Scarpa Fabio , Colonna Alessia , van der Heide Frank C. T. , van Greevenbroek Marleen M. J. , Bosm Hans , Kroon Abraham A. , Nuijts Rudy M. M. A. , Gijs Marlies , Lakerveld Jeroen , Malik Rayaz A. , Webers Carroll A. B. , Stehouwer Coen D. A. , Koster Annemarie
Published: September 2024

Background

Epidemiological and toxicological studies indicate that increased exposure to air pollutants can lead to neurodegenerative diseases. To further confirm this relationship, we evaluated the association between exposure to ambient air pollutants and corneal nerve measures as a surrogate for neurodegeneration, using corneal confocal microscopy.

Methods

We used population-based observational cross-sectional data from The Maastricht Study including N = 3635 participants (mean age 59.3 years, 51.6% were women, and 19.9% had type 2 diabetes) living in the Maastricht area. Using the Geoscience and hEalth Cohort COnsortium (GECCO) data we linked the yearly average exposure levels of ambient air pollutants at home address-level [particulate matter with diameters of ≤ 2.5 µm (PM2.5), and ≤ 10.0 µm (PM10), nitrogen dioxide (NO2), and elemental carbon (EC)]. We used linear regression analysis to study the associations between Z-score for ambient air pollutants concentrations (PM2.5, PM10, NO2, and EC) and Z-score for individual corneal nerve measures (corneal nerve bifurcation density, corneal nerve density, corneal nerve length, and fractal dimension).

Results

After adjustment for potential confounders (age, sex, level of education, glucose metabolism status, corneal confocal microscopy lag time, inclusion year of participants, smoking status, and alcohol consumption), higher Z-scores for PM2.5 and PM10 were associated with lower Z-scores for corneal nerve bifurcation density, nerve density, nerve length, and nerve fractal dimension [stβ (95% CI): PM2.5 -0.10 (-0.14; -0.05), -0.04 (-0.09; 0.01), -0.11 (-0.16; -0.06), -0.20 (-0.24; -0.15); and PM10 -0.08 (-0.13; -0.03), -0.04 (-0.09; 0.01), -0.08 (-0.13; -0.04), -0.17 (-0.21; -0.12)], respectively. No associations were found between NO2 and EC and corneal nerve measures.

Conclusions

Our population-based study demonstrated that exposure to higher levels of PM2.5 and PM10 are associated with higher levels of corneal neurodegeneration, estimated from lower corneal nerve measures. Our results suggest that air pollution may be a determinant for neurodegeneration assessed in the cornea and may impact the ocular surface health as well.
Is MIStreatment of women during facility-based childbirth an independent risk factor for POstpartum Depression in Ethiopia and Guinea? A mixed methods prospective study protocol—MISPOD study
Authors: Asefa Anteneh , Gebremedhin Samson , Delamou Alexandre , Marchal Bruno , Benová Lenka
Published: September 2024

Background

Worldwide, 10% of postpartum women experience postpartum depression, which can lead to diverse sequalae at individual, family, and societal levels. In sub-Saharan Africa, it is estimated that 17% of women experience depression in the postpartum period, which could be an underestimate as 48% of women in the region do not receive postnatal care (81% in Ethiopia and 51% in Guinea) and a large share of postpartum depression remains undiagnosed and untreated as a result. Globally, despite a critical evidence gap, there are growing reports of postpartum depression among women mistreated (disrespected and abused) during childbirth in health facilities, making a strong case to examine the association between mistreatment and postpartum depression. This study in Addis Ababa (Ethiopia) and Conakry (Guinea) uses a mixed methods design to 1) examine the link between mistreatment and postpartum depression, 2) explore the health system capacity to provide respectful maternity care and maternal mental health services, and 3) explore the experiences of women in accessing care and support for postpartum depression.

Methods

We will conduct a prospective longitudinal survey of women (434 in Addis Ababa and 408 in Conakry) from the third trimester of pregnancy to eight weeks postpartum and carry out in-depth interviews with key health system informants (20–25 in each city) and women who recovered from a clinically confirmed episode of postpartum depression (15–25 in each city). Quantitative data from the women’s survey will be analysed using a multilevel mixed-effects model; qualitative data from key-informants will be analysed by using a hybrid thematic analysis approach, whereas data from women’s in-depth interviews will be analysed using the phenomenological approach. The inclusion of two different settings in our study (Addis Ababa and Conakry) will enable us to apply a comparative health systems lens to explore the dynamics of respectful maternity care and maternal mental health services within the broader health systems of the two countries (Ethiopia and Guinea).

Discussion

The findings from this study will inform actions aimed at mitigating the mistreatment of women in maternity settings and improving promotive, preventive, and treatment interventions for postpartum depression in Ethiopia and Guinea. The findings can also be extrapolated to other low-resource settings.
Feasibility of a home-based home videogaming intervention with a family-centered approach for children with cerebral palsy: a randomized multiple baseline single-case experimental design
Authors: Chan-Víquez Daniela , Fernández-Huertas Heilyn , Montserrat-Gonzalez Carles , Khan Ajmal , Fehlings Darcy , Munce Sarah , Wright F. Virginia , Biddiss Elaine
Published: September 2024

Background

Worldwide, children with cerebral palsy (CP) living in underserved communities face barriers to accessing motor therapy services. This study assessed the implementation and effectiveness of an 8-week, upper limb (UL) home-based intervention with a movement-tracking videogame (Bootle Blast) in Costa Rican children with CP.

Methods

Children established a weekly playtime goal and two UL activities of daily living (ADLs) that they would like to improve on. A multiple-baseline, single-case experimental design, was used with the Performance Quality Rating Scale (PQRS) as the repeated measure to track changes in performance of the selected ADLs between the baseline (usual care) and intervention (Bootle Blast) phases. The Canadian Occupational Performance Measure (COPM), the Box and Blocks Test (BBT) and the Children’s Hand-Use Experience Questionnaire (CHEQ) were collected before and after the intervention. Technical barriers were documented during weekly video calls with a monitoring therapist. Treatment effect size, slope changes and percentage of non-overlapping data were identified for the PQRS. Descriptive statistics summarized results for the BBT, CHEQ, videogame logs (e.g., playtime) and technical barriers.

Results

Fifteen children participated and 13 completed the intervention. Both participants who dropped out did so after completing baseline assessments, but before experiencing Bootle Blast. Children’s mean active playtime (i.e., mini-games targeting the UL) across the 8-weeks was 377 min, while mean total time spent engaging with Bootle Blast (active + passive play time [e.g., time navigating menus, reviewing rewards]) was 728 min. In total, eight technical issues (from five children) were reported, and all but three were resolved within 48 h. Partial effectiveness was associated with the intervention. Specifically, 85% of participants improved on the PQRS and 69% achieved clinically important improvements ≥ 2 points in performance on the COPM. Children improved by 1.8 blocks on average on the BBT, while on the CHEQ, five children had a clinically important increase of 10% of the total number of UL activities performed with both hands.

Conclusion

Bootle Blast is a feasible and effective option to facilitate access and engage children with cerebral palsy in UL home rehabilitation.

Trial registration Trial registration number: NCT05403567.
Increased serum carboxylesterase-1 levels are associated with metabolic dysfunction associated steatotic liver disease and metabolic syndrome in children with obesity
Authors: Wang Huanyu , Wu Shimin , Weng Ying , Yang Xi , Hou Ling , Liang Yan , Wu Wei , Ying Yanqin , Ye Feng , Luo Xiaoping
Published: September 2024

Background

Carboxylesterase 1(CES1) is expressed mainly in the liver and adipose tissue and is highly hypothesized to play an essential role in metabolism. Our study aimed to investigate the association between CES1 and metabolic syndrome (MetS) and metabolic dysfunction associated steatotic liver disease (MASLD) in children with obesity in China.

Methods

This study included 72 children with obesity aged 6-13years (including 25(35%) diagnosed as MetS and 36(50%) diagnosed as MASLD). All subjects were measured in anthropometry, serum level of biochemical parameters related to obesity, circumstance levels of insulin-like growth factor1, adipokines (adiponectin, leptin and growth differentiation factor 15) and CES1.

Results

Higher serum CES1 level were found in the MetS group (P = 0.004) and the MASLD group (P < 0.001) of children with obesity. Serum CES1 levels were positively correlated with alanine aminotransferase, aspartate aminotransferase, triglyceride, cholesterol, low-density lipoprotein cholesterol, GDF15, Leptin and negatively correlated with high-density lipoprotein cholesterol, adiponectin and IGF1. We also found a multivariable logistic regression analysis of MASLD and MetS predicted by CES1 significantly (MASLD P < 0.01, MetS P < 0.05). The combination of CES1, sex, age and BMI Z-score showed a sensitivity and specificity of 92.7% for the identification of MASLD and 78.6% for the identification of MetS. The cutoff for CES1 of MASLD is 56.30 ng/mL and of MetS is 97.79 ng/mL.

Conclusions

CES1 is associated with an increasing risk of MetS and MASLD and can be established as a biomarker for metabolic syndrome and MASLD of children with obesity.