bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S6 from Botensilimab, an Fc-Enhanced Anti–CTLA-4 Antibody, Is Effective against Tumors Poorly Responsive to Conventional Immunotherapy
Authors: Chand Dhan , Savitsky David A. , Krishnan Shanmugarajan , Mednick Gabriel , Delepine Chloe , Garcia-Broncano Pilar , Soh Kah Teong , Wu Wei , Wilkens Margaret K. , Udartseva Olga , Vincent Sylvia , Joshi Bishnu , Keith Justin G. , Manrique Mariana , Marques Marilyn , Tanne Antoine , Levey Daniel L. , Han Haiyong , Ng Serina , Ridpath Jackson , Huber Olivia , Morin Benjamin , Galand Claire , Bourdelais Sean , Gombos Randi B. , Ward Rebecca , Qin Yu , Waight Jeremy D. , Costa Matthew R. , Sebastian-Yague Alvaro , Rudqvist Nils-Petter , Pupecka-Swider Malgorzata , Venkatraman Vignesh , Slee Andrew , Patel Jaymin M. , Grossman Joseph E. , Wilson Nicholas S. , Von Hoff Daniel D. , Stebbing Justin , Curiel Tyler J. , Buell Jennifer S. , O’Day Steven J. , Stein Robert B.
Published: December 2024

This dataset presents results demonstrating the broad combination activity of Fc-enhanced anti-CTLA-4 in various poorly immunogenic tumor-bearing mouse models. It demonstrates the potential of Fc-enhanced anti-CTLA-4 antibodies to improve outcomes in various combination treatment strategies, supporting their broad applicability in cancer immunotherapy.
Figure S2 from RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis
Authors: Ben-Crentsil Nana Adjoa , Mohammed Ismail Wazim , Balasis Maria E. , Newman Hannah , Quintana Ariel , Binder Moritz , Kruer Traci , Neupane Surendra , Ferrall-Fairbanks Meghan C. , Fernandez Jenna , Lasho Terra L. , Finke Christy M. , Ibrahim Mohammed L. , McGraw Kathy L. , Wysota Michael , Aldrich Amy L. , Ryder Christopher B. , Letson Christopher T. , Traina Joshua , McLemore Amy F. , Droin Nathalie , Shastri Aditi , Yun Seongseok , Solary Eric , Sallman David A. , Beg Amer A. , Ma Li , Gaspar-Maia Alexandre , Patnaik Mrinal M. , Padron Eric
Published: December 2024

Contains data related to Figure 2 but which were not included in the main figure
Figure S1 from RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis
Authors: Ben-Crentsil Nana Adjoa , Mohammed Ismail Wazim , Balasis Maria E. , Newman Hannah , Quintana Ariel , Binder Moritz , Kruer Traci , Neupane Surendra , Ferrall-Fairbanks Meghan C. , Fernandez Jenna , Lasho Terra L. , Finke Christy M. , Ibrahim Mohammed L. , McGraw Kathy L. , Wysota Michael , Aldrich Amy L. , Ryder Christopher B. , Letson Christopher T. , Traina Joshua , McLemore Amy F. , Droin Nathalie , Shastri Aditi , Yun Seongseok , Solary Eric , Sallman David A. , Beg Amer A. , Ma Li , Gaspar-Maia Alexandre , Patnaik Mrinal M. , Padron Eric
Published: December 2024

Contains data related to Figure 1 but which were not included in the main figure
Supplementary Figure S14 from Botensilimab, an Fc-Enhanced Anti–CTLA-4 Antibody, Is Effective against Tumors Poorly Responsive to Conventional Immunotherapy
Authors: Chand Dhan , Savitsky David A. , Krishnan Shanmugarajan , Mednick Gabriel , Delepine Chloe , Garcia-Broncano Pilar , Soh Kah Teong , Wu Wei , Wilkens Margaret K. , Udartseva Olga , Vincent Sylvia , Joshi Bishnu , Keith Justin G. , Manrique Mariana , Marques Marilyn , Tanne Antoine , Levey Daniel L. , Han Haiyong , Ng Serina , Ridpath Jackson , Huber Olivia , Morin Benjamin , Galand Claire , Bourdelais Sean , Gombos Randi B. , Ward Rebecca , Qin Yu , Waight Jeremy D. , Costa Matthew R. , Sebastian-Yague Alvaro , Rudqvist Nils-Petter , Pupecka-Swider Malgorzata , Venkatraman Vignesh , Slee Andrew , Patel Jaymin M. , Grossman Joseph E. , Wilson Nicholas S. , Von Hoff Daniel D. , Stebbing Justin , Curiel Tyler J. , Buell Jennifer S. , O’Day Steven J. , Stein Robert B.
Published: December 2024

This dataset presents analysis of intratumoral regulatory T cells (Tregs) and CD8+ T cells in tumor biopsies from patients with advanced solid cancers before and after botensilimab treatment. Importantly, these data further support and confirm the changes previously reported by deconvolution analyses of RNA sequencing data. This corroboration between protein-level staining and transcriptomic analyses provides robust evidence of botensilimab's effects on the tumor immune microenvironment, offering valuable insights into its mechanism of action and potential to enhance anti-tumor immunity.
Supplementary Figure S12 from Botensilimab, an Fc-Enhanced Anti–CTLA-4 Antibody, Is Effective against Tumors Poorly Responsive to Conventional Immunotherapy
Authors: Chand Dhan , Savitsky David A. , Krishnan Shanmugarajan , Mednick Gabriel , Delepine Chloe , Garcia-Broncano Pilar , Soh Kah Teong , Wu Wei , Wilkens Margaret K. , Udartseva Olga , Vincent Sylvia , Joshi Bishnu , Keith Justin G. , Manrique Mariana , Marques Marilyn , Tanne Antoine , Levey Daniel L. , Han Haiyong , Ng Serina , Ridpath Jackson , Huber Olivia , Morin Benjamin , Galand Claire , Bourdelais Sean , Gombos Randi B. , Ward Rebecca , Qin Yu , Waight Jeremy D. , Costa Matthew R. , Sebastian-Yague Alvaro , Rudqvist Nils-Petter , Pupecka-Swider Malgorzata , Venkatraman Vignesh , Slee Andrew , Patel Jaymin M. , Grossman Joseph E. , Wilson Nicholas S. , Von Hoff Daniel D. , Stebbing Justin , Curiel Tyler J. , Buell Jennifer S. , O’Day Steven J. , Stein Robert B.
Published: December 2024

This figure describes the flow cytometry gating strategy used for T cell immune profiling in cryopreserved peripheral blood mononuclear cells (PBMCs) from patients with advanced solid cancers treated with botensilimab. The gating strategy allows for a comprehensive analysis of various CD4+ T cell subpopulations.
Supplementary Table S8 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

Phosphosite identification using mass spectrometry. Combined table of peptides identified using mass spectrometry.
Supplementary Table S4 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

Synergy score paralog combinations. Table of synergy scores calculated using GEMINI.
Supplementary table 1 from A Targetable Secreted Neural Protein Drives Pancreatic Cancer Metastatic Colonization and HIF1α Nuclear Retention
Authors: Yamaguchi Norihiro , Wu Y. Gloria , Ravetch Ethan , Takahashi Mai , Khan Abdul G. , Hayashi Akimasa , Mei Wenbin , Hsu Dennis , Umeda Shigeaki , de Stanchina Elisa , Lorenz Ivo C. , Iacobuzio-Donahue Christine A. , Tavazoie Sohail F.
Published: December 2024

table with primer sequence
Supplementary Figure S9 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

A, Sanger sequencing Chromatogram of NF2 locus in MDA-MB231 cells. B, C, Rescue experiment of MARK2+3dKO in Cas9+ YAPC cells following knockout of indicated genes. Data shown are the mean ± SD of %GFP+ (normalized to day 3 after infection). n=3. P values are calculated using a mixed effects model (considering the interaction of experimental groups over time) compared to Ctrl group and corrected with Bonferroni-Holm (BH). D, Western blot analysis of NF2 in A549 and MDA-MB231 cells. E, Rescue experiment of MARK2+3dKO in Cas9+ A549 following knockout of NF2 and expression of CRISPR resistant mutant NF2 cDNAs followed by knockout of indicated genes. Data shown are the mean ± SD of %GFP+ (normalized to day 3 after infection). n=3. P values are calculated using a mixed effects model (considering the interaction of experimental groups over time) compared to NFKO group and corrected with Bonferroni-Holm (BH).
Supplementary Figure S6 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

A-E, Western blot analysis of MARK2 specific substrates phosphorylation. Labeling as described in Fig 3D. Data are representative of two independent experiments. F, Lolli-pop illustration of MARK2-dependent phosphorylation sites on MST1/2 and MAP4K1-4,6,7 identified using mass spectrometry-based phosphoproteomics. SARAH= Sav/Rassf/Hpo domain, CNH= Citron homology domain. G, IP–western blot analysis evaluating the phosphorylation p-LATS2 (T1041) in the presence or absence of MARK2 or MARK3 following NF2 overexpression in HEK-293T cells. Data are representative of two independent experiments. H, IP–western blot analysis evaluating the phosphorylation p-LATS2 (T1041) after NF2 mutant overexpression in HEK-293T cells. Data are representative of two independent experiments. I, IP–western blot analysis evaluating p-LATS1 (T1079) in the presence of NF2 together with MARK2 overexpression in HEK-293T cells. Data are representative of two independent experiments. J, IP–western blot analysis evaluating the interaction of NF2 and MAP4K4,6,7 in the presence or absence of MARK2 overexpression in HEK-293T cells. Data are representative of two independent experiments. K, IP–western blot analysis evaluating the phosphorylation p-LATS1 (T1079) following indicated gene overexpression in HEK-293T cells. L, IP–western blot analysis evaluating the phosphorylation p-LATS1 (T1079) following indicated gene overexpression in HEK-293T cells. Data are representative of two independent experiments. M, IP–western blot analysis evaluating p-LATS1 (T1079) in the presence of MAP4K4 or MAP4K6 together with MARK2,3, kinase-dead MARK2K82H or empty vector control overexpression in HEK-293T cells. Data are representative of two independent experiments. N, O, IP–western blot analysis evaluating p-LATS1 (T1079) in the presence of MAP4K4 or MST1 mutants. Data are representative of two independent experiments. P, Coomassie stain of recombinant proteins used in in vitro kinase assays (Fig.4D, 3E), purified from bacteria (GST-YAP, GST-TAZ) and insect cells. Q, R, In vitro kinase assay using recombinant full-length GST-YAP (P) or synthetically synthesized S128-phosphorylated peptide (Q) together with recombinant LATS2 followed by Mass spectrometry analysis of double phosphorylated YAP peptides. F was created with BioRender.com.
Supplementary Figure S3 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

A, Mutational two-class comparison between 19 MARK2/3-dependent and 12 MARK2/3-independent human cancer cell lines (shown in B). Mutation data were obtained from the CCLE database. The effect size and P values were calculated for every mutated gene of the cell lines using a linear association model. B, C, Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of double guide RNAs (dgRNA) was linked to GFP). Heatmap color indicates the log2(fold-change) of normalized GFP (%GFP+ normalized to day 3 or 6 after infection). n=3. D, E, Western blot analysis in Cas9+ YAPC cells. F, Crystal violet stain of YAPC and CHL-1 (MARK2/3 independent) cells following dgRNA assisted lentiviral knockout of indicated genes. Data are representative of three independent experiments. G, CUT&RUN density profile of YAP/TAZ sensitive H3K27ac marked enhancer loci (n=7,896) following YAP+TAZdKO. Profiles shown are an average of 50bp bins around the summit of the enhancers. H, I, Occupancy profiles of public Chromatin immunoprecipitation sequencing (ChIP-seq) (TEAD4, YAP) (GSE66083) and CUT &RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci. (Three different dgRNAs for MARK2+3) (Data shown are an extension of Fig. 2I).
Supplementary Figure S10 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

A, Western blot analysis of YAP localization following doxycycline (Dox) induced empty vector control, MKIWT or MKIMUT expression for 24h in YAPC cells. Nuclear (Nuc) and cytosolic (Cyto) fractionation are indicated. (Data shown are an extension of Fig. 6E). B, Western blot analysis in YAPC cells. C, Gene set enrichment analysis (GSEA) of RNA-seq data from MKIWT compared to MKIMUT expressing MDA-MB231 cells. Normalized enrichment score (NES) and P value are shown. D, E, Western blot analysis of MARK2,3 specific substrates phosphorylation following MKI/MARK2,3 analog sensitive mutant co-overexpression in HEK-293T cells. F, Competition-based fitness assays in dCas9VPR-expressing YAPC cells after lentiviral expression of sgRNA targeting promoters of indicated genes and expression of MKI (expression of MKI was linked to GFP). Data are shown as mean ± SD of normalized %GFP+ (to day 3 after infection). n=3-9. G, qPCR of MARK2 mRNA following CRISPR activation in dCas9VPR expressing YAPC cells. Housekeeping gene and Ctrl normalized expression is shown. n=3. P value was calculated using a two-tailed parametric t-test with Welch’s correction. H, Tumor volume quantification using NIS-SPECT imaging at indicated time points. n=10 per group. P value was calculated using a two-tailed parametric t-test with Welch’s correction. I, Growth kinetics of subcutaneous YAPC xenografts implanted in immunodeficient mice. Expression of MKIWT from doxycycline (Dox)-inducible lentiviral construct was induced on day 10 post-injection of the cells. Data are shown as mean ± SD. n=5 per group. P values are calculated using a mixed effects model (considering the interaction of experimental groups over time) compared to Ctrl group (-Dox) and corrected with Bonferroni-Holm (BH). J, Tumor image at the end-point of the xenograft experiments shown in I.
Supplementary Figure S1 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

A,B, CRISPR screening results from 22 cancer cell lines. A, Abundance fold-change of positive controls (dgRNAs targeting essential genes n=28 paired with control) and negative controls (dgRNAs targeting non-coding regions n=54 and nontargeting dgRNAs n=97). Data are shown as mean ± SD B, Abundance fold-change of dgRNAs targeting MARK2+3. Each dot represents a single dgRNA. Data are shown as mean ± SD n=24 dgRNAs. C, Pearson correlation analysis of CRISPR screening data comparing log2 fold-changes of single and double gene knockout with published and replicate experiments. Functional domain class libraries are indicated. Data are shown as mean R2 ± SD n=2-8. D, CRISPR screening data from indicated Cas9-expressing cancer cell lines after lentiviral knockout of indicated genes (abundance was read out using next-generation sequencing). Heatmap color indicates the log2(fold-change) of normalized dgRNA abundance (normalized to doubling time 0). E, Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes with independent dgRNAs (expression of dgRNAs was linked with GFP) (Data shown are an extension of Fig. 1D). Data shown are the mean ± SD of %GFP+ (normalized to day 3 after infection). n=3. F, Western blot analysis of Cas9+ K-562 cells. G, Analysis of apoptosis assay using Annexin-V and DAPI in Cas9+ MDA-MB231 cells. Indicated genes were knocked out using lentiviral dgRNAs linked to GFP. Data are shown as mean ± SD. n=3-6. P value was calculated on change in viability compared to control with one-way ANOVA and Dunnett’s correction. H, EdU incorporation assays following indicated gene knock out using lentiviral dgRNAs linked to GFP in Cas9+ indicated cells. Data are shown as mean ± SD. n=3. P value was calculated on change in S-phase population to control with one-way ANOVA and Dunnett’s correction. I, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent experiments and an extension of Fig. 1G.
Supplementary Figure S5 from Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers
Authors: Loi Patrick , Schade Amy E. , Rodriguez Carrie L. , Krishnan Anjana , Perurena Naiara , Nguyen Van T.M. , Xu Yilin , Watanabe Marina , Davis Rachel A. , Gardner Alycia , Pilla Natalie F. , Mattioli Kaia , Popow Olesja , Gunduz Nuray , Lannagan Tamsin R.M. , Fitzgerald Samantha , Sicinska Ewa T. , Lin Jia-Ren , Tan William , Brais Lauren K. , Haigis Kevin M. , Giannakis Marios , Ng Kimmie , Santagata Sandro , Helin Kristian , Sansom Owen J. , Cichowski Karen
Published: December 2024

Extended data related to Figure 5.
Figure S6 from TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma
Authors: Gessain Grégoire , Anzali Ahmed-Amine , Lerousseau Marvin , Mulder Kevin , Bied Mathilde , Auperin Anne , Stockholm Daniel , Signolle Nicolas , Sassi Farah , Marques Da Costa Maria Eugenia , Marchais Antonin , Sayadi Alexandre , Weidner Daniela , Uderhardt Stefan , Blampey Quentin , Nakkireddy Sumanth Reddy , Broutin Sophie , Dutertre Charles-Antoine , Busson Pierre , Walter Thomas , Marhic Alix , Moya-Plana Antoine , Guerlain Johanne , Breuskin Ingrid , Casiraghi Odile , Gorphe Philippe , Classe Marion , Scoazec Jean-Yves , Blériot Camille , Ginhoux Florent
Published: December 2024

Immunohistochemistry for representative Visium markers
Figure S10 from TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma
Authors: Gessain Grégoire , Anzali Ahmed-Amine , Lerousseau Marvin , Mulder Kevin , Bied Mathilde , Auperin Anne , Stockholm Daniel , Signolle Nicolas , Sassi Farah , Marques Da Costa Maria Eugenia , Marchais Antonin , Sayadi Alexandre , Weidner Daniela , Uderhardt Stefan , Blampey Quentin , Nakkireddy Sumanth Reddy , Broutin Sophie , Dutertre Charles-Antoine , Busson Pierre , Walter Thomas , Marhic Alix , Moya-Plana Antoine , Guerlain Johanne , Breuskin Ingrid , Casiraghi Odile , Gorphe Philippe , Classe Marion , Scoazec Jean-Yves , Blériot Camille , Ginhoux Florent
Published: December 2024

Agreement between two pathologists
Figure S1 from TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma
Authors: Gessain Grégoire , Anzali Ahmed-Amine , Lerousseau Marvin , Mulder Kevin , Bied Mathilde , Auperin Anne , Stockholm Daniel , Signolle Nicolas , Sassi Farah , Marques Da Costa Maria Eugenia , Marchais Antonin , Sayadi Alexandre , Weidner Daniela , Uderhardt Stefan , Blampey Quentin , Nakkireddy Sumanth Reddy , Broutin Sophie , Dutertre Charles-Antoine , Busson Pierre , Walter Thomas , Marhic Alix , Moya-Plana Antoine , Guerlain Johanne , Breuskin Ingrid , Casiraghi Odile , Gorphe Philippe , Classe Marion , Scoazec Jean-Yves , Blériot Camille , Ginhoux Florent
Published: December 2024

Association between keratin, MGC and clinical outcome
Supplementary Table S3 from Identification and Characterization of Chemotherapy-Resistant High-Risk Neuroblastoma Persister Cells
Authors: Grossmann Liron D. , Chen Chia-Hui , Uzun Yasin , Thadi Anusha , Wolpaw Adam J. , Louault Kevin , Goldstein Yael , Surrey Lea F. , Martinez Daniel , Calafatti Matteo , Gerelus Mark , Gao Peng , Lee Lobin , Patel Khushbu , Kaufman Rebecca S. , Shani Guy , Farrel Alvin , Moshitch-Moshkovitz Sharon , Grimaldi Paris , Shapiro Matthew , Kendsersky Nathan M. , Lindsay Jarrett M. , Casey Colleen E. , Krytska Kateryna , Scolaro Laura , Tsang Matthew , Groff David , Matkar Smita , Kalna Josh R. , Mycek Emily , McDevitt Jayne , Runbeck Erin , Patel Tasleema , Bernt Kathrin M. , Asgharzadeh Shahab , DeClerck Yves A. , Mossé Yael P. , Tan Kai , Maris John M.
Published: December 2024

Supplementary Table S3 provides the genes of each persister subtype signature
Supplementary Figure 1 from TCR-Engineered T Cells Directed against Ropporin-1 Constitute a Safe and Effective Treatment for Triple-Negative Breast Cancer
Authors: Kortleve Dian , Hammerl Dora , van Brakel Mandy , Wijers Rebecca , Roelofs Daphne , Kroese Kim , Timmermans Mieke M. , Liao Chen-Yi , Huang Shaozhuo , Trapman-Jansen Anita , Foekens Renée , Michaux Justine , de Beijer Monique T.A. , Buschow Sonja I. , Demmers Jeroen A.A. , Kok Marleen , Danen Erik H.J. , Bassani-Sternberg Michal , Martens John W.M. , Abbott Rachel J.M. , Debets Reno
Published: December 2024

Expressions of ROPN1/B, NY-ESO1 and MAGE-A4 target antigens in healthy tissues, TNBC and other tumor types.
Supplementary Table S1 from Identification and Characterization of Chemotherapy-Resistant High-Risk Neuroblastoma Persister Cells
Authors: Grossmann Liron D. , Chen Chia-Hui , Uzun Yasin , Thadi Anusha , Wolpaw Adam J. , Louault Kevin , Goldstein Yael , Surrey Lea F. , Martinez Daniel , Calafatti Matteo , Gerelus Mark , Gao Peng , Lee Lobin , Patel Khushbu , Kaufman Rebecca S. , Shani Guy , Farrel Alvin , Moshitch-Moshkovitz Sharon , Grimaldi Paris , Shapiro Matthew , Kendsersky Nathan M. , Lindsay Jarrett M. , Casey Colleen E. , Krytska Kateryna , Scolaro Laura , Tsang Matthew , Groff David , Matkar Smita , Kalna Josh R. , Mycek Emily , McDevitt Jayne , Runbeck Erin , Patel Tasleema , Bernt Kathrin M. , Asgharzadeh Shahab , DeClerck Yves A. , Mossé Yael P. , Tan Kai , Maris John M.
Published: December 2024

Supplementary Table S1 shows the patient clinical characteristics and genetic alterations at diagnosis
Supplementary Figure 2 from Advancing Global Health Equity in Oncology Clinical Trial Access
Authors: Adewole Tolulope , Albrecht Bjorn , Beg Shaalan , Brawley Otis , Chang I-Fen , Daly Bobby , de Claro Angelo , Dent Jennifer , Dickler Maura , Ene-Obong Abasi , Fashoyin-Aje Lola , Finnegan Justin , Galbraith Susan , Gospodarowicz Mary , Gralow Julie , Haddad Tufia , Kalidas Chitkala , Katz Artur , Kaucic Karen , Keane Harriet , Lanasa Mark , Legos Jeff , Li Bob T. , Mills Jennifer , Oelrich Stefan , Olopade Stefan , Palma John , Pazdur Richard , Pilarski Piotr , Qian Jing , Rudd Kevin , Shokrpour Sepideh , Tendler Craig , Wilson Matt , Smart Victoria W. , Wu Yi-Long , Yan James , Zhang Lianshan , Li Diya , Shen Johanna , Silverstein Amy , Abou-Alfa Ghassan , Anderson Shelly , Beyrer Patrick , Carnival Danielle , Clarke Stephen , Conneran Terri , DeAngelis Lisa M. , Diakos Connie , Diaz Luis , dos Anjos Carlos Henrique , Drebin Jeffrey A. , Eisenmen Debra , Flannery Russell , Fredrickson David , Isbell James M. , Jones David R. , Joseph Adedayo , Kennedy Caroline , Kingham T. Peter , Lee Adrian , Lee Nancy Y. , Leigh Lillian , Li Zhi-Zhong , Liu An-Wen , Liu Dazhi , Liu Si-Yang , Maggie Liu Si-Yang , Makker Vicky , Mallafre-Larrosa Meritxell , McBride Sean , Mestres Isabel , Mondaca Sebastian , Nigro Paulo , Norton Larry , Oyler John V. , Pavlakis Nick , Powell Simon , Robinson Bruce , Qin Yi , Razavi Pedram , Reis-Filho Jorge , Rocco Gaetano , Rudin Charles M. , Schell Orville , Scher Howard I. , Schrag Deborah , Simon Greg , Smith Dorrance , Speece Morgan , Tu Hai-Yan , Umar-Sadiq Aminu , Wang Bu-Hai , Wheeler Helen , Xu Chong-Rui , Yan Li-Xu , Yang Fan , Yoon Byeong , Young Catharine , Zhang Jia-Tao , Zhou Qing
Published: December 2024

Supplementary Figure 2: Number of cancer cases and deaths across geography in 2020, Millions
Supplementary Figure 1 from Advancing Global Health Equity in Oncology Clinical Trial Access
Authors: Adewole Tolulope , Albrecht Bjorn , Beg Shaalan , Brawley Otis , Chang I-Fen , Daly Bobby , de Claro Angelo , Dent Jennifer , Dickler Maura , Ene-Obong Abasi , Fashoyin-Aje Lola , Finnegan Justin , Galbraith Susan , Gospodarowicz Mary , Gralow Julie , Haddad Tufia , Kalidas Chitkala , Katz Artur , Kaucic Karen , Keane Harriet , Lanasa Mark , Legos Jeff , Li Bob T. , Mills Jennifer , Oelrich Stefan , Olopade Stefan , Palma John , Pazdur Richard , Pilarski Piotr , Qian Jing , Rudd Kevin , Shokrpour Sepideh , Tendler Craig , Wilson Matt , Smart Victoria W. , Wu Yi-Long , Yan James , Zhang Lianshan , Li Diya , Shen Johanna , Silverstein Amy , Abou-Alfa Ghassan , Anderson Shelly , Beyrer Patrick , Carnival Danielle , Clarke Stephen , Conneran Terri , DeAngelis Lisa M. , Diakos Connie , Diaz Luis , dos Anjos Carlos Henrique , Drebin Jeffrey A. , Eisenmen Debra , Flannery Russell , Fredrickson David , Isbell James M. , Jones David R. , Joseph Adedayo , Kennedy Caroline , Kingham T. Peter , Lee Adrian , Lee Nancy Y. , Leigh Lillian , Li Zhi-Zhong , Liu An-Wen , Liu Dazhi , Liu Si-Yang , Maggie Liu Si-Yang , Makker Vicky , Mallafre-Larrosa Meritxell , McBride Sean , Mestres Isabel , Mondaca Sebastian , Nigro Paulo , Norton Larry , Oyler John V. , Pavlakis Nick , Powell Simon , Robinson Bruce , Qin Yi , Razavi Pedram , Reis-Filho Jorge , Rocco Gaetano , Rudin Charles M. , Schell Orville , Scher Howard I. , Schrag Deborah , Simon Greg , Smith Dorrance , Speece Morgan , Tu Hai-Yan , Umar-Sadiq Aminu , Wang Bu-Hai , Wheeler Helen , Xu Chong-Rui , Yan Li-Xu , Yang Fan , Yoon Byeong , Young Catharine , Zhang Jia-Tao , Zhou Qing
Published: December 2024

Supplementary Figure 1: Number of cancer cases and deaths across indications in 2020, Millions
Figure 6 from Dynamic Evolution of Fibroblasts Revealed by Single-Cell RNA Sequencing of Human Pancreatic Cancer
Authors: Dimitrieva Slavica , Harrison Jon M. , Chang Jonathan , Piquet Michelle , Mino-Kenudson Mari , Gabriel Millicent , Sagar Vivek , Horn Heiko , Lage Kasper , Kim Julie , Li Gang , Weng Shaobu , Harris Cynthia , Kulkarni Anupriya S. , Ting David T. , Qadan Motaz , Fagenholz Peter J. , Ferrone Cristina R. , Grauel Angelo L. , Laszewski Tyler , Raza Alina , Riester Markus , Somerville Tim , Wagner Joel P. , Dranoff Glenn , Engelman Jeffrey A. , Kauffmann Audrey , Leary Rebecca , Warshaw Andrew L. , Lillemoe Keith D. , Fernández-del Castillo Carlos , Ruddy David A. , Liss Andrew S. , Cremasco Viviana
Published: December 2024

Fibroblasts drive intercellular communication in the tumor microenvironment of PDAC. A, Aggregated cell–cell communication network in normal pancreas, pancreatitis, untreated PDAC, and NAT-PDAC samples showing the signaling (edges) sent from each cell population (nodes) inferred using CellChat. The edge weights between any two cell populations are scaled to reflect the total number of inferred interactions. All fibroblast cells are shown as one cell population, to depict the overall interactome driven by the fibroblast compartment as a totality. B, Comparison of incoming and outgoing signaling for different cell populations in each tissue type. C, Receptor–ligand interaction pairs regulating fibroblasts to epithelial cell communication. D, Visualization of inferred cellular communication between mesenchymal and ductal cell populations calculated based on the aggregated cell–cell communication network using CellChat. Each fibroblast subset is separated in this analysis to depict subset-specific interactions. E, Comparison of strengths of incoming and outgoing signaling in each fibroblast subset.
RESOLVE: Recurrence Posttransplant Observational Study in Focal Segmental Glomerulosclerosis and Minimal Change Disease
Authors: Salmon Eloise C. , Rahimi Ashley E. , Desmond Hailey E. , Putnam Nathaniel M. , Martinelli Elena , Hendren Elizabeth M. , Massengill Susan F. , Verghese Priya S. , Sanna-Cherchi Simone , Kretzler Matthias , Naik Abhijit S. , Trachtman Howard , Modi Zubin J.
Published: December 2024

Introduction: The morbidity of recurrent focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD) after transplant is well recognized. Additional collaborative research is necessary to advance understanding of recurrence epidemiology, mechanisms, interventions, and outcomes, particularly in children. Methods: RESOLVE is a multicenter, observational cohort study examining the posttransplant course of patients with FSGS and MCD across the lifespan. Multiple enrollment options will facilitate both retrospective and prospective collection of biospecimens, self-report items, and electronic health record data across pediatric and adult participants. The study offers a unique mobile health option for participants to enroll and engage with the study remotely. Logistic regression using a log link function will evaluate recurrence risk within 3 months of transplant based on clinical characteristics and assess the impact of social determinants of health on time to graft failure, following adjustment. Cox proportional hazards models with primary outcome of graft failure with competing risk of death will evaluate the impact of recurrence therapy and access to preventative versus reactive recurrence therapy. Independent logistic regression will evaluate the impact of recurrence therapy and endophenotypes on proteinuric outcomes. Conclusion: Multiple enrollment approaches and tailored site participation are needed while studying recurrent FSGS (rFSGS) due to its rarity and phenotypic variability. RESOLVE provides a framework for international collaboration to unravel the course of rFSGS through a biospecimen and data repository. It also explores the potential for mobile health tools to enhance recruitment of participants and to promote cooperation among researchers to advance understanding of recurrence mechanisms and treatments.
Green Synthesis of Silver Nanoparticles using the Algae
Authors: Ali Doaa Oday , Ali Liqaa Oday , Ali Samara Oday
Published: December 2024

Green methods of nanoparticle production have gained prominence due to their environmental and safety advantages. As reducing agents, these techniques employ biological substances, including bacteria, fungi, algae, and plants. In this study, the algae Chara vulgaris was used for the biosynthesis of silver nanoparticles as an environmentally friendly method. The synthesized nanoparticles were characterized using UV, FTIR, SEM, atomic absorption spectrometry, and zeta analysis. These nanoparticles have potential environmental applications in water treatment, especially in the removal of heavy metals such as cadmium, lead, and nickel at different concentrations (1, 3, 5, 7, and 9 ppm) over 12 and 24 hours. The results showed that lead had the highest removal rate of 99.5% for a concentration of 3 ppm at 24 hours. Cadmium showed the highest removal rate of 100% at 3 and 5 ppm concentrations at 24 h, and nickel recorded a removal rate of 83.2% for 1 ppm concentration at 24 h. This study highlights a low-cost, effective, and safer biological method with promising results in removing heavy metals from water.
Ecological Character of Water-Bioindicator Macroinvertebrates on Various Agricultural Management
Authors: Kurnianto Agung sih , Septiadi Luhur , Hamidah Wanda , Magvira Nur Laila , Sholikah Ummi
Published: December 2024

In Indonesia, horticulture is a crucial part of agriculture, heavily reliant on agrochemicals. This study in East Java's Jember and Bondowoso regencies compared conventional and organic farming methods, focusing on their effects on aquatic macroinvertebrates as bioindicators. Research included sites practicing conventional horticulture (cabbage, chili) and organic rice farming. Measurements of water current, pH, conductivity, dissolved oxygen, and temperature were taken, along with macroinvertebrate sampling. Significant differences were found in pH, conductivity, and water current, but not in dissolved oxygen and temperature. Organic farming showed higher macroinvertebrate diversity and lower dominance, especially the Baetidae family. While BMWP-ASPT and EPT scores were similar across methods, organic farming rated unpolluted in biotilik scores. Hierarchical cluster analysis, PCA, and CCA revealed factors influencing the ecological impacts of farming practices. The study underscores how different agricultural methods affect macroinvertebrate diversity, highlighting their role as environmental indicators. This reflects the diverse ecological impacts of agricultural management practices.
Role of MicroRNAs in Chronic Myeloid Leukemia (CML) Treatment, Biomarkers, and Resistance to Tyrosine Kinase Inhibitor: A Bioinformatics-Based Analysis
Authors: Mohamad Syarifah Faezah binti Syed , Ramlee Rabiatul Adawiyah , Elias Marjanu Hikmah
Published: December 2024

Chronic myeloid leukemia (CML) is a myeloproliferative disorder caused by the reciprocal translocation of the BCR-ABL1 oncogene, which activates tyrosine kinase resulting in uncontrolled cell proliferation and apoptosis suppression. Although Imatinib (IM) is an effective treatment, IM resistance remains a significant concern. Therefore, microRNAs (miRNAs) have emerged as potential alternative therapies. These short, non-coding RNAs (20-22 nucleotides) regulate gene expression by binding to the 3' untranslated region (3'UTR) of target genes. The study aims to identify miRNAs linked to CML, determine miRNA’s target genes, construct a protein-protein interaction (PPI) network, and analyze pathways and gene ontology. A literature search using the keywords “microRNA”, and “chronic myeloid leukemia” yielded relevant papers, which were screened and categorized into three groups: 1) miRNA associated with TKI resistance, 2) miRNA as biomarkers or leukemogenesis, and 3) miRNA as therapy. Target genes for the identified miRNAs were determined using DIANA tools and miRTarBase. Gene ontology and pathway analysis were conducted using DAVID, while PPI and network visualization were performed using STRING, Cytoscape, and ClueGO. Thirteen miRNAs were selected, targeting 782 genes and forming 16 clusters. ClueGO identified clusters associated with key biological processes, including G1/S cell cycle transition, miRNA-mediated gene silencing, hematopoietic stem cell differentiation, and apoptosis regulation. Target genes are also significant in the CML pathway and other cancer pathways, such as p53, ErbB, FoxO, autophagy, apoptosis, VEGF, TNF, and microRNA. Notably, hsa-miR-16 emerged as the most promising therapeutic and biomarker candidate for CML, highlighting its role in critical pathways.
Peli1 Deficiency in Macrophages Attenuates Pulmonary Hypertension by Enhancing Foxp1-Mediated Transcriptional Inhibition of IL-6
Authors: Lin Donghai , Hu Li , Wei Dong , Li Yan , Yu Yanfang , Wang Qiang , Sun Xiaoxuan , Shen Yueyao , Yu Youjia , Li Kai , Zhang Zhiwei , Cao Yue , Li Jiantao , Li Yuehua , Fulton David , Chen Jingyu , Wang Jie , Huang Huijie , Chen Feng
Published: December 2024

BACKGROUND:

The infiltration of macrophages into the lungs is a common characteristic of perivascular inflammation, contributing to vascular remodeling in pulmonary hypertension (PH). Peli1 (pellino E3 ubiquitin-protein ligase 1) plays a critical role in regulating the production of proinflammatory cytokines and the polarization of macrophages in various diseases. However, the role of Peli1 in PH remains to be investigated.

METHODS:

The expression and biological function of Peli1 were investigated in both human and experimental models of PH. Peli1-deficient mice and bone marrow transplant mice were utilized to explore the roles of Peli1 in macrophages in vivo. Proteomic analysis and molecular biology techniques were used to uncover the underlying mechanisms.

RESULTS:

The upregulation of Peli1 in the lungs and alveolar macrophages was observed in hypoxia-treated mice. Peli1 knockout mice and myeloid Peli1-deficient mice significantly ameliorated hypoxia-induced right ventricular systolic pressure, right ventricular hypertrophy, and pulmonary vascular remodeling. Mechanistically, Peli1 facilitated the ubiquitination and subsequent proteasomal degradation of Foxp1 (forkhead box p1), thereby alleviating its suppression of
IL
(
interleukin
)
-6
transcription and contributing to macrophage activation. Furthermore, myeloid Foxp1 deficiency partially eliminates the protective effect of myeloid Peli1 deficiency in hypoxia-induced PH mice.

CONCLUSIONS:

Our findings demonstrate that the Peli1-Foxp1-IL-6 pathway plays a crucial role in macrophage activation and recruitment during the development of PH, underscoring the potential of Peli1 as a therapeutic target for PH.
Analyzing the brain’s dynamic response to targeted stimulation using generative modeling
Authors: Maran Rishikesan , Müller Eli J. , Fulcher Ben D.
Published: December 2024

Generative models of brain activity have been instrumental in testing hypothesized mechanisms underlying brain dynamics against experimental datasets. Beyond capturing the key mechanisms underlying spontaneous brain dynamics, these models hold an exciting potential for understanding the mechanisms underlying the dynamics evoked by targeted brain stimulation techniques. This paper delves into this emerging application, using concepts from dynamical systems theory to argue that the stimulus-evoked dynamics in such experiments may be shaped by new types of mechanisms distinct from those that dominate spontaneous dynamics. We review and discuss (a) the targeted experimental techniques across spatial scales that can both perturb the brain to novel states and resolve its relaxation trajectory back to spontaneous dynamics and (b) how we can understand these dynamics in terms of mechanisms using physiological, phenomenological, and data-driven models. A tight integration of targeted stimulation experiments with generative quantitative modeling provides an important opportunity to uncover novel mechanisms of brain dynamics that are difficult to detect in spontaneous settings.
Rescue Conversations from Dead-ends: Efficient Exploration for Task-oriented Dialogue Policy Optimization
Authors: Zhao Yangyang , Dastani Mehdi , Long Jinchuan , Wang Zhenyu , Wang Shihan
Published: December 2024

Training a task-oriented dialogue policy using deep reinforcement learning is promising but requires extensive environment exploration. The amount of wasted invalid exploration makes policy learning inefficient. In this paper, we define and argue that dead-end states are important reasons for invalid exploration. When a conversation enters a dead-end state, regardless of the actions taken afterward, it will continue in a dead-end trajectory until the agent reaches a termination state or maximum turn. We propose a Dead-end Detection and Resurrection (DDR) method that detects dead-end states in an efficient manner and provides a rescue action to guide and correct the exploration direction. To prevent dialogue policies from repeating errors, DDR also performs dialogue data augmentation by adding relevant experiences that include dead-end states and penalties into the experience pool. We first validate the dead-end detection reliability and then demonstrate the effectiveness and generality of the method across various domains through experiments on four public dialogue datasets.
Filtered Corpus Training (FiCT) Shows that Language Models Can Generalize from Indirect Evidence
Authors: Patil Abhinav , Jumelet Jaap , Chiu Yu Ying , Lapastora Andy , Shen Peter , Wang Lexie , Willrich Clevis , Steinert-Threlkeld Shane
Published: December 2024

This paper introduces Filtered Corpus Training, a method that trains language models (LMs) on corpora with certain linguistic constructions filtered out from the training data, and uses it to measure the ability of LMs to perform linguistic generalization on the basis of indirect evidence. We apply the method to both LSTM and Transformer LMs (of roughly comparable size), developing filtered corpora that target a wide range of linguistic phenomena. Our results show that while transformers are better qua LMs (as measured by perplexity), both models perform equally and surprisingly well on linguistic generalization measures, suggesting that they are capable of generalizing from indirect evidence.
Roquea, a new genus of Lychnophorinae (Vernonieae, Asteraceae) from Brazil and its phylogenetic placement
Authors: LOEUILLE BENOÎT , ALMEIDA ROBERTO BAPTISTA PEREIRA , SINISCALCHI CAROLINA M. , LUSA MAKELI G. , ANTAR GUILHERME MEDEIROS
Published: December 2024

Lychnophorinae (Vernonieae, Asteraceae) consists of 21 genera and approximately 150 species, primarily distributed in the Brazilian Central Plateau, with several novelties recently described. With new botanical expeditions conducted in Serra da Formosa, state of Minas Gerais, a set of collections that belong to Lychnophorinae but were not easily assigned to a genus was discovered. After morphological and anatomical analyses and phylogenetic studies, we describe and illustrate Roquea, a new genus of Asteraceae from Brazil, to accommodate the new species Roquea multiserialis. Affinities of the new genus with other genera of Lychnophorinae are discussed along with a preliminary conservation status assessment, and notes on its distribution, ecology and affinities. This new finding contributes to the understanding of the taxonomy and evolution of Lychnophorinae and the campos rupestres and supports the urgent need to preserve Serra da Formosa, currently threatened by human activity.
Confusion about Pitcairnia aphelandriflora Lem. and a new well known related species
Authors: GOUDA ERIC J. , MANZANARES JOSÉ
Published: December 2024

Pitcairnia aphelandriflora Lem. has a long history known from Panama, Ecuador and Peru, but is actually an unresolved species from an island near the coast of Santa Catarina, Brazil and the species that is generally considered P. aphelandriflora is actually an unnamed species, described, illustrated and compared with its morphologically closest species below.
Three new species of Begonia (sect. Platycentrum) from South China
Authors: TIAN DAI-KE , ZHOU JIN-YE , XIAO YAN , WU YAN-NONG , HU REN-CHUAN , DONG XUN , GUAN SHI-KAI
Published: December 2024

Based on field surveys and a review of literature and herbarium specimens, three new Begonia in section Platycentrum from South China are confirmed and reported with morphological descriptions and illustrations, namely Begonia liangguangensis D.K.Tian & J.Y.Zhou, B. shaoqingii D.K.Tian & J.Y.Zhou, and B. qinzhouensis D.K.Tian & J.Y.Zhou. These three new species are morphologically compared with their allied species. Their conservation statuses are provisionally assessed as Endangered, Endangered, and Critically Endangered, respectively, according to Guidelines for Using IUCN Red List Categories and Criteria.
Math narratives and autobiographies
Authors: Jakopovic Paula M.
Published: December 2024

Elementary preservice teachers enter teacher preparation programs with preformed conceptions of their abilities as mathematics learners that directly influence their sense of self as mathematics teachers. Often, they have had experiences that leave them feeling anxious about their capability to be effective mathematics teachers, which negatively impacts student outcomes. Math autobiographies offer teacher educators a window into the historical factors that influence preservice teachers’ math identity development and help them reflect on how these experiences have shaped them. Providing counterpoint experiences in mathematics pedagogical coursework can help preservice teachers overcome past influences and foster positive identities as future mathematics teachers.
Everyone is a math person
Authors: Parker-Holliman Natalie , Marcel-Herbert Tenisha
Published: December 2024

Early intervention and identity-building can promote the idea among students that everyone is a math person. Natalie Parker-Holliman and Tenisha Marcel-Herbert share practical tools and strategies that schools and teachers can use to build students’ confidence and strengthen their mathematical foundation. They highlight the significance of culture and diversity in mathematics education and the impact of affirming messages on students’ mathematical identity, ultimately fostering a culture of belonging and success in mathematics.
POLICY SOLUTIONS: Should school board elections be partisan?
Authors: Collins Jonathan E.
Published: December 2024

Should school board elections be partisan? Jonathan E. Collins writes about the pros and cons of bringing political parties back into school board elections. While partisan elections can bring more voter participation and interest in school governance, they also run the risk of pushing aside real education issues for culture war distractions.
100 volumes of SIMULATION—20 years of DEVS research
Authors: Wainer Gabriel , Govind Sasisekhar
Published: December 2024

The growth of real-time embedded applications has surged in recent years, marked by both an increase in the number and complexity of tasks performed across various industries. Modeling and simulation (M&S) has been used for enhancing product quality while reducing lifecycle costs, primarily through improved testability and maintainability of real-time embedded systems applications, as M&S-based design approach allows for early hardware functionality testing, fosters collaboration between hardware and software teams, and shortens the product development cycle. The discrete-event system specification (DEVS) framework has been used for developing such discrete-event M&S systems. This article starts by highlighting the various DEVS publications in our journal over the past 20 years, reflecting the evolving landscape of simulation methodologies, which we organized into four categories: theory, methodology, tools, and applications. This curated selection reflects the diversity of topics and the evolution of scholarship within the field, encouraging further exploration and innovation. We conclude with recent research in the field, including our own research in real-time embedded systems development using DEVS software for modeling, simulation, and real-time execution of models. This paves the way for future discussions in this important field of research.