bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data Table 4 from A Potent, Selective, Small-Molecule Inhibitor of DHX9 Abrogates Proliferation of Microsatellite Instable Cancers with Deficient Mismatch Repair
Authors: Castro Jennifer , Daniels Matthew H. , Brennan David , Johnston Brian , Gotur Deepali , Lee Young-Tae , Knockenhauer Kevin E. , Lu Chuang , Wu Jie , Nayak Sunaina , Collins Cindy , Bansal Rishabh , Buker Shane M. , Case April , Liu Julie , Yao Shihua , Sparling Brian A. , Sickmier E. Allen , Silver Serena J. , Blakemore Stephen J. , Boriack-Sjodin P. Ann , Duncan Kenneth W. , Ribich Scott , Copeland Robert A.
Published: February 2025

Supplementary Data Table 4
Supplemental Table 5 from Imlunestrant Is an Oral, Brain-Penetrant Selective Estrogen Receptor Degrader with Potent Antitumor Activity in ESR1 Wild-Type and Mutant Breast Cancer
Authors: Bhagwat Shripad V. , Mur Cecilia , Vandekopple Matthew , Zhao Baohui , Shen Weihua , Marugán Carlos , Capen Andrew , Kindler Lisa , Stephens Jennifer R. , Huber Lysiane , Castanares Mark A. , Garcia-Tapia David , Cohen Jeff D. , Bastian Jolie , Mattioni Brian , Yuen Eunice , Baker Thomas K. , Rodriguez Cruz Vivian , Fei Dongling , Manro Jason R. , Pulliam Nicholas , Dowless Michele S. , Ortiz Ruiz Maria Jesus , Yu Chunping , Puca Loredana , Klippel Anke , Bacchion Francesca , Ismail-Khan Roohi , Rodrik-Outmezguine Vanessa , Peng Sheng-Bin , Lallena María Jose , Gong Xueqian , de Dios Alfonso
Published: February 2025

Statistical survival analysis and body weight change in MCF-7 intracranial model treated with imlunestrant or other SERDs.
Supplemental Figure 1 from Imlunestrant Is an Oral, Brain-Penetrant Selective Estrogen Receptor Degrader with Potent Antitumor Activity in ESR1 Wild-Type and Mutant Breast Cancer
Authors: Bhagwat Shripad V. , Mur Cecilia , Vandekopple Matthew , Zhao Baohui , Shen Weihua , Marugán Carlos , Capen Andrew , Kindler Lisa , Stephens Jennifer R. , Huber Lysiane , Castanares Mark A. , Garcia-Tapia David , Cohen Jeff D. , Bastian Jolie , Mattioni Brian , Yuen Eunice , Baker Thomas K. , Rodriguez Cruz Vivian , Fei Dongling , Manro Jason R. , Pulliam Nicholas , Dowless Michele S. , Ortiz Ruiz Maria Jesus , Yu Chunping , Puca Loredana , Klippel Anke , Bacchion Francesca , Ismail-Khan Roohi , Rodrik-Outmezguine Vanessa , Peng Sheng-Bin , Lallena María Jose , Gong Xueqian , de Dios Alfonso
Published: February 2025

Biochemical and in vitro characterization of imlunestrant.
Figure S3 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma
Authors: Turnham Rigney E. , Pitea Adriana , Jang Gwendolyn M. , Xu Zhong , Lim Huat Chye , Choi Alex L. , Von Dollen John , Levin Rebecca S. , Webber James T. , McCarthy Elizabeth , Hu Junjie , Li Xiaolei , Che Li , Singh Ananya , Yoon Alex , Chan Gary K.L. , Kelley Robin K. , Swaney Danielle L. , Zhang Wei , Bandyopadhyay Sourav , Theis Fabian J. , Eckhardt Manon , Chen Xin , Shokat Kevan M. , Ideker Trey , Krogan Nevan J. , Gordan John D.
Published: February 2025

Supplementary Figure 3
Table S4 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Table 4
Figure S3 from Breast Cancer Subtype–Specific Organotropism Is Dictated by FOXF2-Regulated Metastatic Dormancy and Recovery
Authors: Jiang Wen-Jing , Zhou Tian-Hao , Huang Huan-Jing , Li Lin-Sen , Tan Hao , Zhang Rui , Wang Qing-Shan , Feng Yu-Mei
Published: February 2025

Supplementary Figure 3
Supplementary Data Table 1 from A Potent, Selective, Small-Molecule Inhibitor of DHX9 Abrogates Proliferation of Microsatellite Instable Cancers with Deficient Mismatch Repair
Authors: Castro Jennifer , Daniels Matthew H. , Brennan David , Johnston Brian , Gotur Deepali , Lee Young-Tae , Knockenhauer Kevin E. , Lu Chuang , Wu Jie , Nayak Sunaina , Collins Cindy , Bansal Rishabh , Buker Shane M. , Case April , Liu Julie , Yao Shihua , Sparling Brian A. , Sickmier E. Allen , Silver Serena J. , Blakemore Stephen J. , Boriack-Sjodin P. Ann , Duncan Kenneth W. , Ribich Scott , Copeland Robert A.
Published: February 2025

Supplementary Data Table 1
Supplementary Data Figure 6 from A Potent, Selective, Small-Molecule Inhibitor of DHX9 Abrogates Proliferation of Microsatellite Instable Cancers with Deficient Mismatch Repair
Authors: Castro Jennifer , Daniels Matthew H. , Brennan David , Johnston Brian , Gotur Deepali , Lee Young-Tae , Knockenhauer Kevin E. , Lu Chuang , Wu Jie , Nayak Sunaina , Collins Cindy , Bansal Rishabh , Buker Shane M. , Case April , Liu Julie , Yao Shihua , Sparling Brian A. , Sickmier E. Allen , Silver Serena J. , Blakemore Stephen J. , Boriack-Sjodin P. Ann , Duncan Kenneth W. , Ribich Scott , Copeland Robert A.
Published: February 2025

Supplementary Data Figure 6
Supplementary Figures 1-12 from Plasma Cell–Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer
Authors: Sipola Joonatan , Munzur Aslı D. , Kwan Edmond M. , Seo Clara C.Y. , Hauk Benjamin J. , Parekh Karan , Liao Yi Jou (Ruby) , Bernales Cecily Q. , Donnellan Gráinne , Bloise Ingrid , Fung Emily , Ng Sarah W.S. , Wang Gang , Vandekerkhove Gillian , Nykter Matti , Annala Matti , Maurice-Dror Corinne , Chi Kim N. , Herberts Cameron , Wyatt Alexander W. , Takeda David Y.
Published: February 2025

Supplementary Figures 1-12 with embedded captions.
Table S3 from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

TLS signature genes.
Table S2. from Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity
Authors: Nie Jianhua , Zhang Shuyuan , Guo Ying , Liu Caiqi , Shi Jiaqi , Wu Haotian , Na Ruisi , Liang Yingjian , Yu Shan , Quan Fei , Liu Kun , Li Mingwei , Zhou Meng , Zhao Ying , Li Xuehan , Luo Shengnan , Zhang Qian , Wang Guangyu , Zhang Yanqiao , Yao Yuanfei , Xiao Yun , Tai Sheng , Zheng Tongsen
Published: February 2025

Single cell sequencing statistics.
Data from Adenosine Uptake through the Nucleoside Transporter ENT1 Suppresses Antitumor Immunity and T-cell Pyrimidine Synthesis
Authors: Allard David , Cormery Jeanne , Bricha Salma , Fuselier Camille , Abbas Aghababazadeh Farnoosh , Giraud Lucie , Skora Emma , Haibe-Kains Benjamin , Stagg John
Published: February 2025

Abstract
Immunosuppression by adenosine is an important cancer immune checkpoint. Extracellular adenosine signals through specific receptors and can be transported across the cell membrane through nucleoside transporters. Although adenosine receptors are well-known to regulate tumor immunity, the impact of adenosine transporters remains unexplored. In this study, we investigated the effect on tumor immunity of equilibrative nucleoside transporter-1 (ENT1), the major regulator of extracellular adenosine concentrations. Blocking or deleting host ENT1 significantly enhanced CD8+ T-cell–dependent antitumor responses. Tumors inoculated into ENT1-deficient mice showed increased infiltration of effector CD8+ T cells with an enhanced cytotoxic transcriptomic profile and significant upregulation of granzyme B, IFNγ, IL2, TNFα, and CXCL10. ENT1 deficiency was further associated with decreased tumor-infiltrating T regulatory cells and CD206high macrophages and suppressed CCL17 production. ENT1 deficiency notably potentiated the therapeutic activity of PD-1 blockade. T cells upregulated ENT1 upon activation, and blocking ENT1 enhanced their function when cocultured with cognate antigen/HLA-matched melanoma cells. Mechanistically, ENT1-mediated adenosine uptake inhibited the activity of phosphoribosyl pyrophosphate synthetase in activated T cells, thereby suppressing production of uridine 5′-monophosphate and its derivatives required for DNA and RNA synthesis. In summary, this study identified ENT1-mediated adenosine uptake as an important mechanism of adenosine-mediated immunosuppression and pyrimidine starvation that can be targeted to enhance antitumor T-cell responses.

Significance: ENT1 is a potential therapeutic target to overcome immunosuppression induced by extracellular adenosine and to increase the activity of PD-1 blockade.
Supplementary Table S5 from HMGA2 Expression Predicts Subtype, Survival, and Treatment Outcome in Pancreatic Ductal Adenocarcinoma
Authors: Yamamoto Naomi , Dobersch Stephanie , Loveless Ian , Samraj Annie N. , Jang Gun Ho , Haraguchi Miki , Kang Liang-I. , Ruzinova Marianna B. , Vij Kiran R. , Mudd Jacqueline L. , Walsh Thomas , Safyan Rachael A. , Chiorean Elena Gabriela , Hingorani Sunil R. , Bolton Nathan M. , Li Li , Fields Ryan C. , DeNardo David G. , Notta Faiyaz , Crawford Howard C. , Steele Nina G. , Kugel Sita
Published: February 2025

Supplementary Table S5. Representativeness of Study Participants.
Table 1 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Baseline characteristics of the study patients.
Supplementary Table S3 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Supplementary Table S3. Results of Student's t-tests comparing enrichment scores of CIBERSORTx-based immune cell populations in patients with PFS< or >4months.
Supplementary Table S1 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Supplementary Table S1. Representativeness of Study Participants.
Supplementary Methods S1 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Supplementary Methods S1. PBMC analysis, Gene expression profiling, and Cytokines Measurement.
Supplementary Figure S3 from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

Supplementary Figure S3. RNA-seq analysis of gene expression and pathways signatures.
Supplemental Table 5 from Duvelisib with Docetaxel for Patients with Anti–PD-1 Refractory, Recurrent, or Metastatic Head and Neck Squamous Cell Carcinoma
Authors: Hanna Glenn J. , Oakley L. B. , Shi R. , ONeill A. , Shin K. Y. , Scarfo N. , Sehgal K. , Dennis M. J. , Quinn N. , Jo V. Y. , Wong K. , Shvyrkova A. , Kushnarev V. , Shanthappa B. U. , Tkachuk A. , Kryukov K. , Sarachakov A. , Svekolkin V. , Lennerz J. , Waters S. , Haddad R. I.
Published: February 2025

Supplemental Table 5. Univariate Hazard ratio and 95% CI for Cox proportional hazard models on overall survival.
Supplementary Table S1 from Bladder Preservation with Durvalumab plus Tremelimumab and Concurrent Radiotherapy in Patients with Localized Muscle-Invasive Bladder Cancer (IMMUNOPRESERVE): A Phase II Spanish Oncology GenitoUrinary Group Trial
Authors: Garcia-del-Muro Xavier , P. Valderrama Begoña , Medina-Colmenero Ana , Etxaniz Olatz , Gironés Sarrió Regina , Juan-Fita María José , Costa-García Marcel , Moreno Rafael , Miras Rodríguez Isabel , Ortiz Irene , Cuéllar Andrés , Ferrer Ferran , Vigués Francesc , de Haro Piedra Roberto , Candal Gomez Arturo , Villà Salvador , Pontones José Luis , Murria Yasmina , Lendínez-Cano Guillermo , Alemany Ramon
Published: February 2025

Supplementary Table 1. Table of characteristics of the SOC cohort of patients.
Supplementary Figure 1 from A Phase I Study of FHD-609, a Heterobifunctional Degrader of Bromodomain-Containing Protein 9, in Patients with Advanced Synovial Sarcoma or SMARCB1-Deficient Tumors
Authors: Livingston J. Andrew , Blay Jean-Yves , Trent Jonathan , Valverde Claudia , Agulnik Mark , Gounder Mrinal , Le Cesne Axel , McKean Meredith , Wagner Michael J. , Stacchiotti Silvia , Agresta Samuel , Quintás-Cardama Alfonso , Reilly Sarah A. , Healy Kathleen , Hickman Denice , Zhao Tina , Ballesteros-Perez Alex , Khalil Alexis , Collins Michael P. , Piel Jessica , Horrigan Kim , Lefkovith Ariel , Innis Scott , Lazar Alexander J. , Cote Gregory M. , Wagner Andrew J.
Published: February 2025

Supplementary Figure 1
Supplementary Figure S4 from Bladder Preservation with Durvalumab plus Tremelimumab and Concurrent Radiotherapy in Patients with Localized Muscle-Invasive Bladder Cancer (IMMUNOPRESERVE): A Phase II Spanish Oncology GenitoUrinary Group Trial
Authors: Garcia-del-Muro Xavier , P. Valderrama Begoña , Medina-Colmenero Ana , Etxaniz Olatz , Gironés Sarrió Regina , Juan-Fita María José , Costa-García Marcel , Moreno Rafael , Miras Rodríguez Isabel , Ortiz Irene , Cuéllar Andrés , Ferrer Ferran , Vigués Francesc , de Haro Piedra Roberto , Candal Gomez Arturo , Villà Salvador , Pontones José Luis , Murria Yasmina , Lendínez-Cano Guillermo , Alemany Ramon
Published: February 2025

Supplementary Figure 4. Phenotype profiling of immune populations by flow cytometry in patients treated with standard of care (SOC), radiotherapy and chemotherapy plus cystectomy. A) Percentage of immune cellsRadar plots, showing the mean amount of cells/mL in blood, for each immune population grouped by treatment cohort at baseline (Basal), one week of treatment (1W), end of treatment (EOT) and 1-3 months after the EOT (ATm). B) Percentage of cells within CD8 or CD4 T populations (mean+SE). Statistics comparisons between each timepoint with the basal levels (U Mann-Whitney test, * < 0.05, ** < 0.01, *** < 0.001, **** < 0.0001).
Supplementary Figure S2 from Bladder Preservation with Durvalumab plus Tremelimumab and Concurrent Radiotherapy in Patients with Localized Muscle-Invasive Bladder Cancer (IMMUNOPRESERVE): A Phase II Spanish Oncology GenitoUrinary Group Trial
Authors: Garcia-del-Muro Xavier , P. Valderrama Begoña , Medina-Colmenero Ana , Etxaniz Olatz , Gironés Sarrió Regina , Juan-Fita María José , Costa-García Marcel , Moreno Rafael , Miras Rodríguez Isabel , Ortiz Irene , Cuéllar Andrés , Ferrer Ferran , Vigués Francesc , de Haro Piedra Roberto , Candal Gomez Arturo , Villà Salvador , Pontones José Luis , Murria Yasmina , Lendínez-Cano Guillermo , Alemany Ramon
Published: February 2025

Supplementary Figure 2. Analysis of potential prognostic factors. A) Forest plot for Bladder preserved free of tumor survival (BPFS), defined as the time from the start of immunotherapy to either the date of cystectomy, or the date of recurrence of muscle-invasive bladder carcinoma or distant recurrence, or death. B) Forest plot for Distant metastasis-free survival (DMFS), defined as the time from the start of therapy to distant recurrence, or death. C) Forest plot for Overall survival (OS). Hazard ratios obtained from a Cox univariate analysis are shown below of each Kaplan meier graph to depict correlation of molecular, and clinical characteristics.
Supplementary Figure S1 from Bladder Preservation with Durvalumab plus Tremelimumab and Concurrent Radiotherapy in Patients with Localized Muscle-Invasive Bladder Cancer (IMMUNOPRESERVE): A Phase II Spanish Oncology GenitoUrinary Group Trial
Authors: Garcia-del-Muro Xavier , P. Valderrama Begoña , Medina-Colmenero Ana , Etxaniz Olatz , Gironés Sarrió Regina , Juan-Fita María José , Costa-García Marcel , Moreno Rafael , Miras Rodríguez Isabel , Ortiz Irene , Cuéllar Andrés , Ferrer Ferran , Vigués Francesc , de Haro Piedra Roberto , Candal Gomez Arturo , Villà Salvador , Pontones José Luis , Murria Yasmina , Lendínez-Cano Guillermo , Alemany Ramon
Published: February 2025

Supplementary Figure 1. Competing risk analysis. A) Competing risk analysis showing the cumulative expected incidence of NMIBC in the presence of the following competing events: Death, Cystectomy and Muscle Invasive Bladder Cancer. B) Competing risk analysis showing the cumulative expected incidence of MIBC in the presence of Death and Cystectomy. C) Competing risk analysis showing the cumulative expected incidence of distant metastasis in the presence of Death.
Supplementary Table S6 from Next-Generation Sequencing–Based MSI Scoring Predicts Benefit in Mismatch Repair–Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D
Authors: Schoenfeld Jonathan D. , Azad Nilofer S. , Gross Jacob , Chen Li , Overman Michael J. , Kao Katrina , Jackson Latifa , Brunnquell Donna , Bu Xiangning , Coppola Christina , Guan Ping , Lee Jennifer , Sims David , Fuchs Rebecca , Weirather Jason L. , Pfaff Kathleen L. , Gunasti Lauren , Ranasinghe Srin , Hamilton Stanley R. , Wang Victoria , O’Dwyer Peter J. , Wu Catherine J. , Rodig Scott J. , Patton David R. , Harris Lyndsay
Published: February 2025

Collection of differentially expressed genes and resulting statistics from the DEseq2 segmented by clinical benefit
Supplemental Table 2 from Phase I/II Trial of Exportin 1 Inhibitor Selinexor plus Docetaxel in Previously Treated, Advanced KRAS-Mutant Non–Small Cell Lung Cancer
Authors: von Itzstein Mitchell S. , Burns Timothy F. , Dowell Jonathan E. , Horn Leora , Camidge D. Ross , York Sally J. , Eaton Keith D. , Kyle Kelly , Fattah Farjana , Liu Jialiang , Mu-Mosley Hong , Gupta Arjun , Nadeem Urooba , Gao Ang , Zhang Song , Gerber David E.
Published: February 2025

Supplemental Table 2. Treatment-emergent adverse events occurring in at least 10% of the overall cohort according to dose level of selinexor.
Table S7 from Multiomics Reveals the Immunologic Features and the Immune Checkpoint Blockade Potential of Colorectal Medullary Carcinoma
Authors: Liu Chao , Zou Haoyi , Ruan Yuli , Fang Lin , Wang Bojun , Cui Luying , Wu Tong , Chen Zhuo , Dang Tianjiao , Lan Ya , Zhao Wenyuan , Zhang Chunhui , Meng Hongxue , Zhang Yanqiao
Published: February 2025

Supplementary Table 7. Histologic types, group, TMB and MSI information about TCGA-COAD
Supplementary Table S7 from Smoking-Associated Carcinogen–Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation
Authors: Aggarwal Ritesh K. , Sidoli Simone , Wang Jingli , Sahu Srabani , Sanawar Rahul , Gupta Varun , Aluri Srinivas , Sukrithan Vineeth , Vegivinti Charan T.R. , Zavras Phaedon D. , Verma Divij , Gordon-Mitchell Shanisha , Agarwal Beamon , Verma Tanya , Starczynowski Daniel T. , Steidl Ulrich G. , Shastri Aditi , Halmos Balazs , LaFave Lindsay M. , Cheng Haiying , Verma Amit , Zou Yiyu
Published: February 2025

Supplementary Table S7. Phosphoproteomics results from purified microtubules in cells treated with vehicle vs CA4948 for 72 hours.
Table S15 from Multiomics Reveals the Immunologic Features and the Immune Checkpoint Blockade Potential of Colorectal Medullary Carcinoma
Authors: Liu Chao , Zou Haoyi , Ruan Yuli , Fang Lin , Wang Bojun , Cui Luying , Wu Tong , Chen Zhuo , Dang Tianjiao , Lan Ya , Zhao Wenyuan , Zhang Chunhui , Meng Hongxue , Zhang Yanqiao
Published: February 2025

Supplementary Table 15. KEGG results between MeC and nMeC
Data from The Prostaglandin EP4 Antagonist Vorbipiprant Combined with PD-1 Blockade for Refractory Microsatellite-Stable Metastatic Colorectal Cancer: A Phase Ib/IIa Trial
Authors: Pietrantonio Filippo , Morano Federica , Niger Monica , Ghelardi Filippo , Chiodoni Claudia , Palazzo Michele , Nichetti Federico , Manca Paolo , Cristarella Eleonora , Doldi Valentina , Zaffaroni Nadia , Sabella Giovanna , Brambilla Nadia , Benincasa Elena , Giacovelli Giampaolo , Vitalini Cristina , Girolami Federica , Rovati Lucio C.
Published: February 2025

AbstractPurpose:
Novel combinations are required to overcome resistance to immune checkpoint inhibitors in proficient mismatch repair (pMMR) or microsatellite-stable (MSS) metastatic colorectal cancer (mCRC). We aimed to determine whether vorbipiprant, a prostaglandin E2 receptor EP4 subtype antagonist, can convert immune-resistant mCRC into a tumor responsive to anti–PD-1 inhibition.
Patients and Methods:
This phase Ib/IIa prospective, open-label, single-arm trial followed a 3 + 3 dose-escalation and dose-optimization design. A total of 28 patients with chemorefractory pMMR/MSS mCRC were given dose-escalated oral vorbipiprant (30, 90, or 180 mg twice daily), along with biweekly intravenous balstilimab (3 mg/kg), an anti–PD-1 antibody. The primary endpoints included safety and the disease control rate (DCR). Secondary endpoints were the overall response rate, duration of response, progression-free survival, and overall survival.
Results:
No dose-limiting toxicities were observed. Of the 28 patients, seven (25%) experienced serious adverse events, but only one was attributed to vorbipiprant and one to balstilimab. The trial achieved a DCR of 50% observed across the entire cohort. In the subgroup of patients with liver metastases (n = 12), the DCR was 25%. The overall response rate was 11%, with three patients showing a partial response (median duration of response, 7.4 months). The median progression-free survival was 2.6 months, and the median overall survival was 14.2 months. Translational exploratory analyses suggested that vorbipiprant may boost response to anti–PD-1 in patients with immunogenic tumors.
Conclusions:
The combination of vorbipiprant and a PD-1 inhibitor (balstilimab) yielded sufficient activity in refractory pMMR/MSS mCRC, which is worthy of confirmation in future clinical trials in biomarker-enriched populations.
Data from Duvelisib with Docetaxel for Patients with Anti–PD-1 Refractory, Recurrent, or Metastatic Head and Neck Squamous Cell Carcinoma
Authors: Hanna Glenn J. , Oakley L. B. , Shi R. , ONeill A. , Shin K. Y. , Scarfo N. , Sehgal K. , Dennis M. J. , Quinn N. , Jo V. Y. , Wong K. , Shvyrkova A. , Kushnarev V. , Shanthappa B. U. , Tkachuk A. , Kryukov K. , Sarachakov A. , Svekolkin V. , Lennerz J. , Waters S. , Haddad R. I.
Published: February 2025

AbstractPurpose:
Treatments after anti–PD-1 therapy for patients with recurrent, metastatic head and neck squamous cell carcinoma (HNSCC) are limited. Blocking PI3K signaling may lead to tumor immunomodulation and enhanced taxane sensitivity. This phase 2 trial evaluated dual, selective PI3Kδ/γ inhibition with docetaxel in patients with anti–PD-1 refractory recurrent, metastatic HNSCC.
Patients and Methods:
Patients received duvelisib (25 mg orally twice daily) with docetaxel (75 mg/m2 IV) every 21 days. The primary endpoint was overall response rate (RECIST v1.1), using a Simon two-stage design. Secondary endpoints were safety, progression-free survival, and overall survival, and exploratory endpoints were correlating immunologic and genomic parameters with outcomes.
Results:
From 11/1/21 to 10/10/23, 26 patients were enrolled (median age: 64, 96% men, 54% with human papillomavirus+ disease; primary site: 12 oropharynx, 11 oral cavity, and 3 larynx/hypopharynx. The best overall response rate was 19% [5/26; 95% confidence interval (CI), 6.8%–40.7%]. All were partial responses [median duration: 5.1 months (0.7–15.5)]; 46% (12/26) exhibited stable disease, and 32% (8/26) exhibited progression (1 unevaluable). Two patients remain on-treatment at data cutoff; 25% (6/24) came off for toxicity. Grade 3+ treatment-related adverse events were observed in 50% (13/26), most often elevated liver function tests (6, 23%). No deaths were treatment-related. At median follow-up of 6.5 months (0.7–26), median progression-free survival was 2.8 months (95% CI, 1.9–7.0); 17/26 patients had died. Median overall survival was 10.2 months (95% CI, 6.7–15.9), favoring human papillomavirus–negative patients. Greater tumor CD3+/CD8+ T-cell infiltration trended with improved outcomes.
Conclusions:
We report a favorable response rate when combining a selective PI3K pathway inhibitor and taxane in patients with anti–PD-1 refractory HNSCC.
Data from Smoking-Associated Carcinogen–Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation
Authors: Aggarwal Ritesh K. , Sidoli Simone , Wang Jingli , Sahu Srabani , Sanawar Rahul , Gupta Varun , Aluri Srinivas , Sukrithan Vineeth , Vegivinti Charan T.R. , Zavras Phaedon D. , Verma Divij , Gordon-Mitchell Shanisha , Agarwal Beamon , Verma Tanya , Starczynowski Daniel T. , Steidl Ulrich G. , Shastri Aditi , Halmos Balazs , LaFave Lindsay M. , Cheng Haiying , Verma Amit , Zou Yiyu
Published: February 2025

AbstractPurpose:
Even though smoking is associated with lung cancer, the exact molecular pathways that link carcinogens with inflammation and oncogenic transformation are not well elucidated. Two major carcinogens in cigarette smoke, nicotine-derived nitrosamine ketone, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), and benzo(α)pyrene (BaP), have not been tested in models that mimic inhaled exposure for prolonged periods of time.
Experimental Design:
Mouse models were used for intratracheal delivery of NNK and BaP (NB) for 18 months. Tissue microarrays from human lung cancers were evaluated for IL-1 receptor–associated kinase-4 (IRAK4) expression. Functional effects of IRAK4 inhibition were evaluated in cell lines and xenografts.
Results:
Smoking-associated carcinogen–treated mice developed epithelial dysplasia followed by lung cancers at increased rates relative to controls. Histology revealed myeloid inflammation in murine lung tissues. Lung macrophages showed elevated levels of proinflammatory IL-1β when exposed to cigarette smoking condensate. A key downstream mediator of IL-1β signaling, IRAK4, was overexpressed in murine lung tissues exposed to carcinogens. The majority of human lung cancer samples also exhibited overactivated IRAK4 expression. IRAK4 localized in microtubules in lung cancer cell lines. Using mass spectrometry on isolated microtubules, we observed that IRAK4 inhibition was associated with decreased phosphorylation of tubular motility proteins, including myosin heavy-chain 9. Inhibition of IRAK4 resulted in decreased invasion in lung cancer cell lines and reduced growth of lung cancer xenografts.
Conclusions:
These data demonstrate that smoking-associated carcinogens can be linked to oncogenic transformation via inflammatory IRAK4 activation.
Data from Histologic and Immunologic Factors Associated with Response to Immune Checkpoint Inhibitors in Advanced Sarcoma
Authors: Lee Alex Q. , Hao Clara , Pan Minggui , Ganjoo Kristen N. , Bui Nam Q.
Published: February 2025

AbstractPurpose:
To characterize factors associated with response to immune checkpoint inhibitors (ICI) in advanced sarcoma.
Experimental Design:
This is a retrospective study with a cohort of 216 patients with advanced sarcoma treated with ICI between 2016 and 2023 at Stanford Health Care. Overall survival, progression-free survival (PFS), objective response rates (ORR) per RECIST criteria, and reason for ICI discontinuation were analyzed across histologic subtypes, ICI regimens, tumor mutational burden, and PD-L1 expression.
Results:
The overall ORR in the cohort was 16.7%. The histologic subtypes with the highest ORR were Kaposi sarcoma (KS, 66.7%), alveolar soft part sarcoma (ASPS, 50%), angiosarcoma (33.3%), myxofibrosarcoma (MFS, 28.6%), and undifferentiated pleomorphic sarcoma (UPS, 27.8%). The subtypes with the lowest ORR were osteosarcoma (0%), synovial sarcoma (0%), and liposarcoma (3.7%). The subtypes with the highest median PFS were KS (median not reached), ASPS (median not reached), MFS (27.4 months), and UPS (11.3 months). The ORR for sarcomas with PD-L1 ≥ 1% was 27.8% (P = 0.02), whereas the ORR for sarcomas with tumor mutational burden ≥10 mutations per megabase of DNA was 28.6% (P = 0.20).
Conclusions:
ORR and PFS were highly variable across sarcoma histologic subtypes. In this large analysis, KS, ASPS, angiosarcoma, MFS, and UPS demonstrated the highest ORR and longest PFS while osteosarcoma, synovial sarcoma, and liposarcoma had the lowest ORR and shortest PFS. PD-L1 expression was also associated with increased ORR. Our findings provide further insight into understanding the sarcoma histologic and immunologic factors that correspond with response to ICI.
Bladder Preservation with Durvalumab plus Tremelimumab and Concurrent Radiotherapy in Patients with Localized Muscle-Invasive Bladder Cancer (IMMUNOPRESERVE): A Phase II Spanish Oncology GenitoUrinary Group Trial
Authors: Garcia-del-Muro Xavier , P. Valderrama Begoña , Medina-Colmenero Ana , Etxaniz Olatz , Gironés Sarrió Regina , Juan-Fita María José , Costa-García Marcel , Moreno Rafael , Miras Rodríguez Isabel , Ortiz Irene , Cuéllar Andrés , Ferrer Ferran , Vigués Francesc , de Haro Piedra Roberto , Candal Gomez Arturo , Villà Salvador , Pontones José Luis , Murria Yasmina , Lendínez-Cano Guillermo , Alemany Ramon
Published: February 2025

Purpose:

The combination of radiation and immunotherapy potentiated antitumor activity in preclinical models. The purpose of this study is to explore the feasibility, safety, and efficacy of a bladder-preserving approach, including dual immune checkpoint blockade and radiotherapy, in patients with muscle-invasive bladder cancer (MIBC).

Patients and Methods:

Patients with localized MIBC underwent transurethral resection, followed by durvalumab (1,500 mg) plus tremelimumab (75 mg) every 4 weeks for three doses and concurrent radiotherapy (64–66 Gy to bladder). Patients with residual or relapsed MIBC underwent salvage cystectomy. The primary endpoint was complete response, defined as the absence of MIBC at posttreatment biopsy. Secondary endpoints were bladder-intact disease-free survival, distant metastasis–free survival, and overall survival.

Results:

Thirty-two patients were enrolled at six centers. Complete response was documented in 26 (81%) patients. Two patients had residual MIBC, and four patients were not evaluated. After a median follow-up of 27 months, 2 patients underwent salvage cystectomy. The 2-year rates for bladder-intact disease-free survival, distant metastasis–free survival, and overall survival were 65%, 83%, and 84%, respectively. The 2-year estimates of non–muscle-invasive bladder relapse, MIBC, and distant metastasis were 3%, 19%, and 16%, respectively. Grade 3 to 4 toxicities were reported in 31% of patients, with diarrhea (6%) and acute kidney failure (6%) being the most frequent.

Conclusions:

This multimodal approach including durvalumab plus tremelimumab with concurrent radiotherapy is feasible and safe, showing high efficacy in terms of response and eliciting bladder preservation in a large number of patients. Further research on this approach as an alternative to cystectomy is warranted.
Figure 1 from Dynamic Tracking of Tumor Microenvironment Modulation Using Kaede Photoconvertible Transgenic Mice Unveils New Biological Properties of Viral Immunotherapy
Authors: Diers Anne R. , Guo Qiuchen , Li Zhi , Richardson Erin , Idris Suaad , Willis Claire , Tak Paul P. , Withers David R. , Barone Francesca
Published: February 2025

CAN-2409 + prodrug inhibits tumor growth and increases lymphocyte infiltration in MC38 tumor–bearing C57BL/6 mice. A, MC38 tumor–bearing mice were treated with or without CAN-2409 i.t. (red arrow) followed by 4 days of i.p. administration of prodrug (blue arrows), and tumor growth was monitored. Left, tumor growth curves. Right, tumor growth inhibition rate after treatment. B, Endpoint analysis of tumor mass. C–G, Endpoint analysis tumor immune populations assessed by flow cytometry. N = 7–9 mice per group (some tumors are too small to be included in the immune cell analysis). Two-tailed t test, *, P < 0.05; **, P < 0.01; ****, P < 0.0001.
Transvalvular flow rates in patients with moderate-to-severe and severe aortic stenosis: clinical usefulness and risk-stratification
Authors: Kim Hyungseop , Kim In-Cheol , Lee Hee-Jeong
Published: February 2025

Objective: The definition of low-flow/low-gradient aortic stenosis (AS) using the stroke volume index (SVI) alone overlooks factors like vascular resistance and valve stiffness. Consequently, an SVI indicating a normal flow might indicate a low flow when used with the transvalvular flow rate (TFR), which incorporates ejection time. We compared the SVI (35 ml/m2) and TFR (250 ml/m2), and analyzed the outcomes for patients with and without aortic valve replacement (AVR).

Methods: From 2013 to 2016, we retrospectively evaluated the clinical data of patients with moderate-to-severe and severe AS, defined as a maximum aortic valve velocity ≥ 3.5 m/s or a valve area ≤ 1.3 cm². Patients were categorized into AVR and non-AVR groups. The non-AVR group was further classified by a TFR above or below 250 ml/m2. Moreover, we compared the SVIs with TFRs. We examined the rates of all-cause mortality and heart failure hospitalizations.

Results: Among 135 patients, 42 (31%) had mismatched SVIs and TFRs; 41 had a high SVI and a low TFR, whereas one had a low SVI and a high TFR. Among the 59 non-AVR patients, 25 (71.4%) of the 35 patients with a low TFR died, whereas 4 (16.7%) of the 24 patients with a high TFR died. The TFR in the 76 AVR patients was similar to that in the non-AVR patients, 3 of whom died (3.9%). The Kaplan-Meier analysis revealed that non-AVR patients with a low TFR had worse outcomes and the AVR patients fared best. The SVI was significantly less suitable than the TFR for risk stratification.

Conclusion: This study highlights that a high TFR, rather than a high SVI, is associated with a better prognosis, even among non-AVR patients, suggesting that the TFR is better for risk assessment and complements the SVI.
Hybrid methods to identify ovarian cancer from imbalanced high-dimensional microarray data
Authors: Sapitri Ni Kadek Emik , Sa'adah Umu , Shofianah Nur
Published: February 2025

Scientists have used microarray data to identify healthy people and patients with various types of cancer, including ovarian cancer. Ovarian cancer is the most dangerous of all types of cancer that attacks the female reproductive organ. The right combination of methods is needed to identify ovarian cancer from microarray data because that type of data is high-dimensional and imbalanced. This research aims to propose two hybrid methods which are a combination of infinite feature selection (IFS) as features selector with classification and regression tree (CART) as a classifier. IFS can work with two separate scenarios, namely supervised infinite feature selection (SIFS) and unsupervised infinite feature selection (UIFS). This research also compares the performance of the two hybrid methods proposed (SIFS-CART and UIFS-CART) with CART without IFS. The data used is OVA_ovary that has 10937 columns and 1545 rows. The results shows that SIFS-CART achieves maximum performance using 1000 features and UIFS-CART 5000 features. CART without IFS uses all 10935 features. The balanced accuracy results show SIFS-CART can outperform CART without IFS and UIFS-CART. Using less features to get highest balanced accuracy results, SIFS is more effective in performing feature selection on the OVA_ovary dataset compared to UIFS.
Advanced methodologies resolving dimensionality complications for autism neuroimaging dataset: a comprehensive guide for beginners
Authors: Malviya Meenakshi , Jayaraman Chandra
Published: February 2025

Autism spectrum disorder (ASD) is gender biased neurodevelopmental condition consisting of a triad of physiological symptoms. Neural images and neurobiology of cognitive disorders are complex but provide significant information and accurate visualization of developmental changes. The diagnosis is time-consuming and necessitates sufficient evidence to distinguish the disorder from other concomitant diseases. The most recent area of interest for cognitive research is neuroimaging, which is used to study the disorder's impact, affected region, and functional connectivity between the regions of interest. The challenges in the domain are the availability of data, the modalities of data, the selection of the correct processing strategies, and the result assessment complications. The study employed machine learning (ML) methods to process the autism data in both structural and functional data formats collected from the autism brain imaging data exchange (ABIDE) consortium. A comparative analysis among image processing methodologies with both data formats was successfully implemented. The variations in the processing pipeline and the outputs strongly suggest an emerging need for 3D/4D images to visualize better, accurate feature extraction and classification. The study aims to support the researchers in identifying the correct image format for specific objectives and the ML techniques, such as Gaussian median filters, segmentation methodologies for 2D data, or a well-defined preprocessing pipeline for 3D data, to achieve reliable and generalized results.
Heart disease approach using modified random forest and particle swarm optimization
Authors: Barry Khalidou Abdoulaye , Manzali Youness , Flouchi Rachid , Elfar Mohamed
Published: February 2025

For the past two decades, heart disease has been classified as one of the main causes of mortality globally. Fortunately, most researchers focused on data mining techniques, which play an important role in accurately predicting heart disease to develop their models. In this paper, by combining particle swarm optimization (PSO) and modified random forest (MRF), a new approach (PSO-MRF) is proposed to predict heart disease. The main purpose is to select the important features after the bootstrap method for each decision tree in the random forest, and then optimize the MRF by the PSO algorithm. The experiments are carried out using the publicly accessible UCI heart disease datasets. Thorough experimental analysis demonstrates that our approach has outperformed the random forest algorithm as well as many other classifiers. This model helps doctors and researchers improve the diagnosis and treatment of heart disease, resulting in more prompt, accurate patient care.
Crop classification using object-oriented method and Google Earth Engine
Authors: Desai Geeta T. , Gaikwad Abhay N.
Published: February 2025

Agriculture crop monitoring in real-time is crucial in formulating effective agricultural practices and management policies. The primary goal of the investigation is to explore how the utilization of Sentinel-1 data and its fusion with Sentinel-2 impact crop classification accuracy in a fragmented agricultural landscape in the Yavatmal District of Maharashtra, India. Pixel based classification and object-oriented classification approaches were implemented on Google Earth Engine (GEE), and obtained results were compared for different combinations of optical and microwave features. The research revealed that the object-based technique performed better than the pixel-based approach, with a 3.5% increase in overall accuracy. For 2022, crop-type mapping was generated with overall accuracies varying from 85.5% to 61% and a kappa coefficient between 0.77 and 0.37. These overall accuracies imply that joint use of optical and radar data has given a 24% improvement in overall accuracy compared to use of only optical data. In addition, the temporal change in the backscatter coefficients and different vegetation indices for different crops were examined over crop growth cycle. This work demonstrates the fusion of Sentinel-1 and Sentinel-2 data to classify wheat, chickpea, other crops, water and urban areas.
Hybrid model detection and classification of lung cancer
Authors: Yousuf Rami , Daraghmi Eman Yaser
Published: February 2025

Lung cancer ranks among the most prevalent malignancies worldwide. Early detection is pivotal to improving treatment outcomes for various cancer types. The integration of artificial intelligence (AI) into image processing, coupled with the availability of comprehensive historical lung cancer datasets, provides the chance to create a classification model based on deep learning, thus improving the precision and effectiveness of detecting lung cancer. This not only aids laboratory teams but also contributes to reducing the time to diagnosis and associated costs. Consequently, early detection serves to conserve resources and, more significantly, human lives. This study proposes convolutional neural network (CNN) models and transfer learning-based architectures, including ResNet50, VGG19, DenseNet169, and InceptionV3, for lung cancer classification. An ensemble approach is used to enhance overall cancer detection performance. The proposed ensemble model, composed of five effective models, achieves an F1-score of 97.77% and an accuracy rate of 97.5% on the IQ-OTH/NCCD test dataset. These findings highlight the effectiveness and dependability of our novel model in automating the classification of lung cancer, outperforming prior research efforts, streamlining diagnosis processes, and ultimately contributing to the preservation of patients' lives.
Hybrid object detection and distance measurement for precision agriculture: integrating YOLOv8 with rice field sidewalk detection algorithm
Authors: Tungkasthan Anucha , Jongsawat Nipat , Crisnapati Padma Nyoman , Thwe Yamin
Published: February 2025

This study aims to propose a new approach to semantic segmentation of sidewalk images in rice fields using the YOLOv8 algorithm, with the objective of enhancing agricultural monitoring and analysis. The experimental process involved preparing the development environment, extracting data from JSON, and training the model using YOLOv8. Evaluation reveals consistent and accurate sidewalk detection with a confidence score of 0.9-1.0 across various environmental conditions. Confusion matrix and precision-recall analysis confirmed the robustness and accuracy of the model. These findings validate the effectiveness of the approach in detecting and measuring sidewalks with high precision, potentially improving agricultural monitoring. The novelty of this study lies in the utilization of the RIFIS-D algorithm as an integral part of a hybrid approach with YOLOv8. This hybridization enriches the model with additional capability to detect the distance between the sidewalk and the tractor, addressing specific needs in agricultural applications. This contribution is significant in the advancement of automatic navigation and monitoring technology in agriculture, enabling the implementation of more sophisticated and efficient systems in field operations.
Deep learning-based techniques for video enhancement, compression and restoration
Authors: Lhiadi Redouane , Jaddar Abdessamad , Kaaouachi Abdelali
Published: February 2025

Video processing is essential in entertainment, surveillance, and communication. This research presents a strong framework that improves video clarity and decreases bitrate via advanced restoration and compression methods. The suggested framework merges various deep learning models such as super-resolution, deblurring, denoising, and frame interpolation, in addition to a competent compression model. Video frames are first compressed using the libx265 codec in order to reduce bitrate and storage needs. After compression, restoration techniques deal with issues like noise, blur, and loss of detail. The video restoration transformer (VRT) uses deep learning to greatly enhance video quality by reducing compression artifacts. The frame resolution is improved by the super-resolution model, motion blur is fixed by the deblurring model, and noise is reduced by the denoising model, resulting in clearer frames. Frame interpolation creates additional frames between existing frames to create a smoother video viewing experience. Experimental findings show that this system successfully improves video quality and decreases artifacts, providing better perceptual quality and fidelity. The real-time processing capabilities of the technology make it well-suited for use in video streaming, surveillance, and digital cinema.
Hindi spoken digit analysis for native and non-native speakers
Authors: Bhagath Parabattina , Shanmukha Malempati , Das Pradip K.
Published: February 2025

Automated speech recognition (ASR) is the process of using an algorithm or
automated system to recognize and translate spoken words of a specific language. ASR has various applications in fields such as mobile speech recognition, the internet of things and human-machine interaction. Researchers have been working on issues related to ASR for more than 60 years. One of the many use cases of ASR is designing applications such as digit recognition that aid differently-abled individuals, children and elderly people. However, there is a lack of spoken language data in under-developed and low-resourced languages, which presents difficulties. Although this is not a pivotal issue for highly established languages like English, it has a significant impact on less commonly spoken languages. In this paper, we discuss the development of a Hindi-spoken dataset and benchmark spoken digit models using convolutional neural networks (CNNs). The dataset includes both native and non-native Hindi speakers. The models built using CNN exhibit 88.44%, 95.15%, and 89.41% for non-native, native, and combined speakers respectively.