bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from NUAK1-Mediated Phosphorylation of NADK Mitigates ROS Accumulation to Promote Osimertinib Resistance in Non–Small Cell Lung Carcinoma
Authors: Lin Wei , Wang Na , Wu Shihao , Diao Mingxin , Huang Quanfu , Li Kuo , Mei Peiyuan , Wang Xiaojun , Liao Yongde , Meng Yunchong
Published: December 2024

Abstract
Osimertinib, a third generation epidermal growth factor receptor tyrosine kinase inhibitor, is approved as a first-line therapy in patients with advanced non–small cell lung carcinoma (NSCLC) with EGFR-activating mutations or the T790M resistance mutation. However, the efficacy of osimertinib is limited due to acquired resistance, highlighting the need to elucidate resistance mechanisms to facilitate the development of improved treatment strategies. Here, we screened for significantly upregulated genes encoding protein kinases in osimertinib-resistant NSCLC cells and identified NUAK1 as a pivotal regulator of osimertinib resistance. NUAK1 was highly expressed in osimertinib-resistant NSCLC and promoted the emergence of osimertinib resistance. Genetic or pharmacological blockade of NUAK1 restored the sensitivity of resistant NSCLC cells to osimertinib in vitro and in vivo. Mechanistically, NUAK1 directly interacted with and phosphorylated nicotinamide adenine dinucleotide kinase (NADK) at serine 64 (S64), which mitigated osimertinib-induced accumulation of reactive oxygen species (ROS) and contributed to the acquisition of osimertinib resistance in NSCLC. Furthermore, virtual drug screening identified T21195 as an inhibitor of NADK-S64 phosphorylation, and T21195 synergized with osimertinib to reverse acquired resistance by inducing ROS accumulation. Collectively, these findings highlight the role of the NUAK1-NADK axis in governing osimertinib resistance in NSCLC and indicate the potential of targeting this axis as a strategy for circumventing resistance.

Significance: Phosphorylation of NADK by NUAK1 diminishes ROS accumulation and confers resistance to osimertinib, identifying NUAK1-NADK signaling as a potential therapeutic target for improving the response to EGFR inhibition in lung cancer.
Data from B7-H3–Targeted CAR-Vδ1T Cells Exhibit Potent Broad-Spectrum Activity against Solid Tumors
Authors: Jiang Licui , You Fengtao , Wu Hai , Qi Changsong , Xiang Shufen , Zhang Ping , Meng Huimin , Wang Min , Huang Jiequn , Li Yafen , Chen Dan , An Gangli , Yang Nan , Zhang Bozhen , Shen Lin , Yang Lin
Published: December 2024

Abstract
Vδ1T cells, a rare subset of γδT cells, hold promise for treating solid tumors. Unlike conventional T cells, they recognize tumor antigens independently of the MHC antigen presentation pathway, making them a potential “off-the-shelf” cell therapy product. However, isolation and activation of Vδ1T cells is challenging, which has limited their clinical investigation. Here, we developed a large-scale clinical-grade manufacturing process for Vδ1T cells and validated the therapeutic potential of B7-H3 chimeric antigen receptor (CAR)–modified Vδ1T cells in treating solid tumors. Coexpression of IL2 with the B7-H3-CAR led to durable antitumor activity of Vδ1T cells in vitro and in vivo. In multiple subcutaneous and orthotopic mouse xenograft tumor models, a single intravenous administration of the CAR-Vδ1T cells resulted in complete tumor regression. These modified cells demonstrated significant in vivo expansion and robust homing ability to tumors, akin to natural tissue-resident immune cells. Additionally, the B7-H3-CAR-Vδ1T cells exhibited a favorable safety profile. In conclusion, B7-H3-CAR–modified Vδ1T cells represent a promising strategy for treating solid tumors.

Significance: A clinical-grade expansion protocol enabled generation of B7-H3–targeted CAR-Vδ1T cells with robust anticancer activity and a favorable safety profile, supporting the potential of CAR-Vδ1T cells as an “off-the-shelf” therapy for solid tumors.
Data from MYC Drives mRNA Pseudouridylation to Mitigate Proliferation-Induced Cellular Stress during Cancer Development
Authors: Ding Jane , Bansal Mohit , Cao Yuxia , Ye Bingwei , Mao Rui , Gupta Anamika , Sudarshan Sunil , Ding Han-Fei
Published: December 2024

Abstract
Pseudouridylation is a common RNA modification that is catalyzed by the family of pseudouridine synthases (PUS). Pseudouridylation can increase RNA stability and rigidity, thereby impacting RNA splicing, processing, and translation. Given that RNA metabolism is frequently altered in cancer, pseudouridylation may be a functionally important process in tumor biology. Here, we show that the MYC family of oncoproteins transcriptionally upregulates PUS7 expression during cancer development. PUS7 is essential for the growth and survival of MYC-driven cancer cells and xenografts by promoting adaptive stress responses and amino acid biosynthesis and import. ATF4, a master regulator of stress responses and cellular metabolism, was identified as a key downstream mediator of PUS7 functional activity. Induction of ATF4 by MYC oncoproteins and cellular stress required PUS7, and ATF4 overexpression overcame the growth inhibition caused by PUS7 deficiency. Mechanistically, PUS7 induced pseudouridylation of MCTS1 mRNA, which enhanced its translation. MCTS1, a noncanonical translation initiation factor, drove stress-induced ATF4 protein expression. A PUS7 consensus pseudouridylation site in the 3′ untranslated region of ATF4 mRNA was crucial for the induction of ATF4 by cellular stress. These findings unveil an MYC-activated mRNA pseudouridylation program that mitigates cellular stress induced by MYC stimulation of proliferation and biomass production, suggesting that targeting PUS7 could be a therapeutic strategy selectively against MYC-driven cancers.

Significance: Oncogene activation of mRNA pseudouridylation is a mechanism that facilitates metabolic reprogramming and adaptive responses to overcome cellular stress during cancer development.
Supplementary Table S3 from Asymptomatic Incidence of Monoclonal Gammopathy of Undetermined Significance and Preclinical Duration to Myeloma Diagnosis: A Modeling Study
Authors: Ji Mengmeng , Shih Yi-Hsuan , Huber John H. , Wang Mei , Feuer Eric J. , Etzioni Ruth , Wang Shi-Yi , Chang Su-Hsin
Published: December 2024

Supplementary Table S3 presents estimates from the base case model and all sensitivity analyses. The 95% confidence intervals for all point estimates were also provided.
Supplementary Table S2 from Associations of Prostate Tumor Immune Landscape with Vigorous Physical Activity and Prostate Cancer Progression
Authors: Huang Lanshan , Winter Sarah J. , Olsson Linnea T. , Hamilton Alina M. , Halliday Sophia R. , Kirk Erin L. , Farnan Laura , Gerstel Adrian , Craig Stephanie G. , Finn Stephen P. , LaBonte Wilson Melissa , Jain Suneil , Troester Melissa A. , Butler Eboneé N. , Bensen Jeannette T. , Wobker Sara E. , Allott Emma H.
Published: December 2024

Supplementary Table S2. Associations between physical activity and odds of histological inflammation in prostate tumor core and tumor adjacent compartments.
Supplemental Table 3 from Adiposity throughout Adulthood and Risk of Young-Onset Breast Cancer Tumor Subtypes in the Young Women’s Health History Study
Authors: Marcus Post Lydia , Pathak Dorothy R. , Hamilton Ann S. , Hirko Kelly A. , Houang Richard T. , Guseman Emily H. , Sanfelippo Dan , Bohme Carnegie Nicole , Olson L. Karl , Rui Hallgeir , Schwartz Ann G. , Velie Ellen M.
Published: December 2024

Supplemental Table 3 shows associations between additional measures of adiposity throughout adulthood and odds of YOBC.
Supplementary Figure S1 from Reduced Platelet Activation in Triple-Negative Essential Thrombocythemia Compared with JAK2V617F-Mutated Essential Thrombocythemia
Authors: Dong Huan , Chen Jia , Zhang Jing , Xue Feng , Li Huiyuan , Zhang Donglei , Zhou Hu , Zhang Xian , Huang Yueting , Liu Xiaofan , Chen Yunfei , Liu Wei , Chi Ying , Wang Wentian , Sun Ting , Ju Mankai , Dai Xinyue , Gu Wenjing , Yang Renchi , Fu Rongfeng , Zhang Lei
Published: December 2024

Supplementary Figure S1. Platelet CD62P expression in JAK2V617F-positive ET patients and TN-ET patients of different age groups.
Supplementary Table S1 from Pilot Trial of Perampanel on Peritumoral Hyperexcitability in Newly Diagnosed High-grade Glioma
Authors: Tobochnik Steven , Regan Michael S. , Dorotan Maria K.C. , Reich Dustine , Lapinskas Emily , Hossain Md Amin , Stopka Sylwia , Meredith David M. , Santagata Sandro , Murphy Melissa M. , Arnaout Omar , Bi Wenya Linda , Chiocca E. Antonio , Golby Alexandra J. , Mooney Michael A. , Smith Timothy R. , Ligon Keith L. , Wen Patrick Y. , Agar Nathalie Y.R. , Lee Jong Woo
Published: December 2024

Supplementary Table 1. Mass Spectrometry Data. Cells with NA indicate exclusion due to treatment assignment or insufficient tissue for analysis. LLOQ, lower limit of quantitation; LOD, limit of detection.
Supplementary Table S2 from Association of Tumor Mutational Burden and PD-L1 with the Efficacy of Pembrolizumab with or without Chemotherapy versus Chemotherapy in Advanced Urothelial Carcinoma
Authors: Fléchon Aude , Morales-Barrera Rafael , Powles Thomas , Alva Ajjai , Özgüroğlu Mustafa , Csöszi Tibor , Loriot Yohann , Rodriguez-Vida Alejo , Géczi Lajos , Cheng Susanna Y. , Fradet Yves , Oudard Stéphane , Vulsteke Christof , Gunduz Seyda , Mamtani Ronac , Yu Evan Y. , Montesa Pino Alvaro , Anido Urbano , Sendur Mehmet A.N. , Gravis Gwenaelle , Révész János , Kostorov Vladimir , Huillard Olivier , Ma Junshui , Rajasagi Mohini , Vajdi Amir , Lunceford Jared , Cristescu Razvan , Imai Kentaro , Homet Moreno Blanca , Matsubara Nobuaki
Published: December 2024

Supplementary Table 2. Baseline characteristics for the evaluable TMB population
Supplementary Data Tables 1 from Characterization of FGFR Alterations and Activation in Patients with High-Risk Non–Muscle-Invasive Bladder Cancer
Authors: Eisner Joel R. , de Jong Florus C. , Shibata Yoichiro , Mayhew Gregory M. , Davison James M. , Carcione Jenna , Pappan Kirk L. , Thomas Shibu , Triantos Spyros , Santiago-Walker Ademi , Baig Mahadi , Milburn Michael V. , Beebe Kirk D. , Zuiverloon Tahlita C.M.
Published: December 2024

Supplementary Data Tables
Figure S6 from Characterization of FGFR Alterations and Activation in Patients with High-Risk Non–Muscle-Invasive Bladder Cancer
Authors: Eisner Joel R. , de Jong Florus C. , Shibata Yoichiro , Mayhew Gregory M. , Davison James M. , Carcione Jenna , Pappan Kirk L. , Thomas Shibu , Triantos Spyros , Santiago-Walker Ademi , Baig Mahadi , Milburn Michael V. , Beebe Kirk D. , Zuiverloon Tahlita C.M.
Published: December 2024

Figure S6
Figure S4 from Characterization of FGFR Alterations and Activation in Patients with High-Risk Non–Muscle-Invasive Bladder Cancer
Authors: Eisner Joel R. , de Jong Florus C. , Shibata Yoichiro , Mayhew Gregory M. , Davison James M. , Carcione Jenna , Pappan Kirk L. , Thomas Shibu , Triantos Spyros , Santiago-Walker Ademi , Baig Mahadi , Milburn Michael V. , Beebe Kirk D. , Zuiverloon Tahlita C.M.
Published: December 2024

Figure S4
Figure S2 from Characterization of FGFR Alterations and Activation in Patients with High-Risk Non–Muscle-Invasive Bladder Cancer
Authors: Eisner Joel R. , de Jong Florus C. , Shibata Yoichiro , Mayhew Gregory M. , Davison James M. , Carcione Jenna , Pappan Kirk L. , Thomas Shibu , Triantos Spyros , Santiago-Walker Ademi , Baig Mahadi , Milburn Michael V. , Beebe Kirk D. , Zuiverloon Tahlita C.M.
Published: December 2024

Figure S2
Figure S1 from Characterization of FGFR Alterations and Activation in Patients with High-Risk Non–Muscle-Invasive Bladder Cancer
Authors: Eisner Joel R. , de Jong Florus C. , Shibata Yoichiro , Mayhew Gregory M. , Davison James M. , Carcione Jenna , Pappan Kirk L. , Thomas Shibu , Triantos Spyros , Santiago-Walker Ademi , Baig Mahadi , Milburn Michael V. , Beebe Kirk D. , Zuiverloon Tahlita C.M.
Published: December 2024

Figure S1
Supplementary Data1 from Nivolumab in Patients with Metastatic Castration-Resistant Prostate Cancer with and without DNA Repair Defects
Authors: Isaacsson Velho Pedro , Bastos Diogo Assed , Saint’ana Pedro Tofani , Rigatti Brenda , da Costa Emily Tonin , Muniz David Q.B. , Andreis Felipe , Ferreira Rafael Dal Ponte , Giongo Pedrotti Luana , Maistro Simone , Katayama Maria Lucia Hirata , Folgueira Maria Aparecida Azevedo Koike , Morelle Alessandra , Leal Alessandro , de Castro Gilberto
Published: December 2024

WES raw data
Supplementary Data1 from Phase 2 Trial of Regorafenib in Recurrent/Metastatic Adenoid Cystic Carcinoma
Authors: Desilets Antoine , Vos Joris L. , Katabi Nora , Kuo Fengshen , Nadeem Zaineb , Linxweiler Maximilian , Ostrovnaya Irina , Baxi Shrujal , Dunn Lara A. , Sherman Eric J. , Pfister David G. , Morris Luc G.T. , Ho Alan L.
Published: December 2024

Supplementary Data
Supplementary Figure S8 from Combinations of HDAC Inhibitor and PPAR Agonist Induce Ferroptosis of Leukemic Stem Cell–like Cells in Acute Myeloid Leukemia
Authors: Zhou Hui , Qin Dongmei , Xie Chendi , Zhou Jie , Jia Shuman , Zhou Ziwei , Qiu Yi , Xu Bing , Zha Jie
Published: December 2024

Supplementary Figure S8. (A) The CD34+ and CD34- primary AML cells identified by flow cytometry using CD34, CD38, CD123, CD96, CD47, CD44, CD32, and CD25 antibodies. (B) The quantitative analysis for Western blotting analysis of HDAC3, SLC7A11, and GPX4 expression in primary CD34+ AML cells (n = 20) and CD34+ hematopoietic blood stem cells (HBSCs; n = 15). (C-D) HDAC3 protein levels were positively correlated with SLC7A11 protein levels (C) in primary CD34+ AML cells (n = 20), but not for GPX4 protein levels (D). The quantitative analysis of western blotting data was measured by image J software and the GAPDH serves as a loading control. (E) Representative image of colony formation in CD34+ HBSCs treated with CS055 and/or chiglitazar, with 3000 cells seeded per well. Scale bars, 500 μm. (F-H) Transmission electron microscopy revealed the morphology of primary CD34+ AML #1. Scale bars, 2 μm. The primary CD34+ AML cells treated with CS055 and/or chiglitazar for 24 h. The mitochondrial area was measured by the Image J Soft. (I) Cell viability was counted in primary CD34+ AML #1 cells after treatments with erastin (1.875 μM, 3.75 μM, 7.5 μM, 15 μM, 30 μM) for 24h. (J) primary CD34+ AML #1 cells treated with erastin (7.5 μM, 15 μM, 30 μM) for 24h and stained with C11-BODIPY and endogenous lipid peroxidation analysis by flow cytometry. (K-L) The glutamate release (K) and intracellular GSH (L) were detected in primary CD34+ AML #1 cells treated with erastin (15 μM, 30 μM) for 24h. (M) Cell viability was counted in primary CD34+ AML #1 cells after treatments with erastin (30 μM), Ferr-1 (2 μM), DFO (10 μM), Z-VAD (10 μM) and Nec-1 (10 μM) for 24 h. Clinical information of patients with AML is summarized in Supplementary Table S1. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.
Supplementary Figure S5 from Combinations of HDAC Inhibitor and PPAR Agonist Induce Ferroptosis of Leukemic Stem Cell–like Cells in Acute Myeloid Leukemia
Authors: Zhou Hui , Qin Dongmei , Xie Chendi , Zhou Jie , Jia Shuman , Zhou Ziwei , Qiu Yi , Xu Bing , Zha Jie
Published: December 2024

Supplementary Figure S5. The chiglitazar activates PPARα and transcriptionally represses HDAC3 expression. (A-B) Western blotting analysis of PPARα, HDAC1,2,3, and 10 expressions in KG-1α and Kasumi-1 cells treated with CS055 and/or chiglitazar for 24 h and removed dead cells by Dead Cell Removal kit. (C-E) Western blotting (C-D) and quantitative real-time PCR (E) analysis of PPARα and/or HDAC3 expressions in KG-1α and Kasumi-1 cells treated with chiglitazar (4 μM, 8 μM, 16 μM) for 24 h. (F) The chiglitazar significantly inhibit the transcriptional activity of the HDAC3 gene promoter in KG-1α and Kasumi-1 cells treated with chiglitazar (4 μM, 8 μM, 16 μM) for 24 h. (G) ChIP assay analyzed the recruitment of PPARα on the HADC3 gene promoter in KG-1α and Kasumi-1 cells treated with chiglitazar (16 μM) for 24 h. Western blotting data was quantified and analyzed by Image J Soft. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.
Supplementary Figure S10 from Combinations of HDAC Inhibitor and PPAR Agonist Induce Ferroptosis of Leukemic Stem Cell–like Cells in Acute Myeloid Leukemia
Authors: Zhou Hui , Qin Dongmei , Xie Chendi , Zhou Jie , Jia Shuman , Zhou Ziwei , Qiu Yi , Xu Bing , Zha Jie
Published: December 2024

Supplementary Figure S10. A proposed mechanism for the CS055/chiglitazar-induced ferroptosis-like cell death in LSC-like cells by blocking the HDAC3-SLC7A11-GSH-GPX4 pathway.
Supplemental Table 2 from A Novel Human SDHA-Knockout Cell Line Model for the Functional Analysis of Clinically Relevant SDHA Variants
Authors: Kent Jason D. , Klug Lillian R. , Heinrich Michael C.
Published: December 2024

Supplemental Table 2. Interpretations used for variant selection and control classification.
Supplementary Figure S6 from Determination of MYD88 and CXCR4 Mutations for Clinical Detection and Their Significance in Waldenström Macroglobulinemia
Authors: Yan Yuting , Yu Ying , Xiong Wenjie , Wang Jun , Yao Yao , Jia Yujiao , Huang Yanshan , Li Yuxi , Wang Tingyu , Lyu Rui , Sun Hao , Wang Haoxu , Wang Qi , Liu Wei , An Gang , Sui Weiwei , Xu Yan , Huang Wenyang , Yu Zhen , Zou Dehui , Hao Mu , Xiao Zhijian , Wang Jianxiang , Qiu Lugui , Yi Shuhua
Published: December 2024

Supplementary Figure 6. Survival outcomes for the entire cohort. (A) The progression free survival of the entire cohort; (B) The overall survival of the entire cohort.
Supplementary Figure S3 from Determination of MYD88 and CXCR4 Mutations for Clinical Detection and Their Significance in Waldenström Macroglobulinemia
Authors: Yan Yuting , Yu Ying , Xiong Wenjie , Wang Jun , Yao Yao , Jia Yujiao , Huang Yanshan , Li Yuxi , Wang Tingyu , Lyu Rui , Sun Hao , Wang Haoxu , Wang Qi , Liu Wei , An Gang , Sui Weiwei , Xu Yan , Huang Wenyang , Yu Zhen , Zou Dehui , Hao Mu , Xiao Zhijian , Wang Jianxiang , Qiu Lugui , Yi Shuhua
Published: December 2024

Supplementary Figure 3. The profiling of CXCR4 mutation. (A) Lollipop plot of CXCR4 mutations; (B) The proportion of different mutation types; (C) The number of CXCR4 mutations in different amino acid sites.
Figure S1. Accrual and follow-up1 from Safety, Efficacy, and Biomarker Analysis of Crizotinib in MET-Mutated Non–Small Cell Lung Cancer—Results from the Drug Rediscovery Protocol
Authors: Verkerk Karlijn , van der Wel Tijmen J.W.T. , Zeverijn Laurien J. , Geurts Birgit S. , Spiekman Ilse A.C. , de Wit Gijs F. , Roepman Paul , Jansen Anne M.L. , van der Noort Vincent , Smit Egbert F. , Hoeben Ann , Hendriks Lizza E.L. , van den Heuvel Michel M. , Piet Berber , Herder Gerarda J.M. , Hashemi Sayed M.S. , Gelderblom Hans , Verheul Henk M.W. , Voest Emile E. , de Langen Adrianus J.
Published: December 2024

Flowchart of the accrual and follow-up of the cohort. Abbreviations: NSCLC, non small cell lung cancer.
Table S5 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

primer sequences for EGR1 Chromatin Immunoprecipitation (ChIP) (related to Fig S2)
Table 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

gRNAs for generation of MALAT1 knockout THP-1 cells (related to Fig S7)
Supplementary Figure S15 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 shows that response to botensilimab, alone or with balstilimab, in patients with advanced cancers is independent of tumor neoantigen burden and FcγRIIIA allele status. This suggests that botensilimab's efficacy may be broad and not limited by these commonly used biomarkers typically associated with response to conventional immune checkpoint therapy. The data highlights a potential advantage of botensilimab over traditional immunotherapies, indicating it might be effective in a wider range of patients, including those who may not typically respond to standard checkpoint inhibitors.
Figure S6 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

suppl. Figure 6 showing AMIGO2 promotes HIF1a nuclear retention via specific HIF1a residues
Figure S3 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

suppl. Figure 3 showing NPTX1 is over-expressed in human primary and metastatic PDAC tumors
Figure S2 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

suppl. Figure 2 showing NPTX1 drives liver metastasis of PDAC
Supplementary Figure S3 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 3.
Supplementary Table 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

Top-ranked ROPN1/B peptides and their scores for immunogenicity, non-cross reactivity, HLA-A2 binding and immunogenicity.
Supplementary Table S4 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 S4 shows the most negatively enriched pathways in non-cycling persister cells by GSEA
Risk Factors for Severe Allergic Rhinitis and the Association with Serum sIgE Levels: A Study in Guangzhou, China
Authors: Shan Feng-Wen , Zhou Min , Zheng Xin-Yi , Wu Tong , Zhang Ya-Na , Wu Shuo , Shi Zhao-Hui , Luo Xin , Liang Gui-Xian , Zhang He , Jiang He-Xiao , Kang Ning , Chen Yu-Lian , Zhou Qi-Lin , Xiong Guo-Wei , Su Jing , Cheng Yun , Huang Xue-Kun , Dong Guang-Hui , Yang Qin-Tai
Published: December 2024

Background: The control of risk factors is crucial for the management of allergic rhinitis (AR), and it contributes to reduce both direct medical costs and indirect economic burdens. The research on risk factors for severe AR and the association between serum allergen-specific immunoglobulin E (sIgE) and the severity of AR is currently limited and inconsistent.
Methods: The study utilized data from a cross-sectional epidemiological survey conducted in Guangzhou, China, from April 2023 to March 2024, involved 638 AR patients. We used Visual Analogue Scale (VAS) scores to assess the severity of AR. Data of daily risk factors were collected through face-to-face questionnaires, and serum sIgE levels were measured using the AllergyScreen assay (Mediwiss-Analytic GmbH, Moers, Germany). A generalized linear model was used to investigate the associations.
Results: Our findings indicate that patients with severe AR exhibited more unhealthy lifestyle habits and lived in high-risk environments compared to non-severe patients. Physical activity more than three times per week was associated with a reduced risk of severe symptoms (OR: 0.55, 95% CI: 0.36, 0.82). Frequent indoor cleaning also lowered the risk of severe AR (OR: 0.70, 95% CI: 0.56, 0.87). Additionally, a one-level increase in serum sIgE was linked to higher odds of severe AR (OR: 1.26, 95% CI: 1.11, 1.43) after adjusting for risk factors.
Conclusion: Severe AR is associated with poor household cleaning and less exercise. Higher serum sIgE levels correspond to a higher risk of severe AR
Isolation, Screening, and Molecular Identification of Cellulolytic Bacteria From Supit Urang Municipal Landfill, Malang City
Authors: Maghfira Selia  , Irfan Mustafa  , Farida Rahayu
Published: December 2024

The municipal landfills contain substantial amounts of lignocellulosic waste that have not been adequately utilized. This waste can be processed using cellulolytic bacteria. Cellulolytic bacteria play an important role in the degradation of cellulose-based materials. This study aimed to isolate and identify cellulolytic bacteria based on 16S rDNA sequence obtained from the Supit Urang municipal landfill, Malang City. Bacteria were isolated from soil by cultivating on 1% carboxyl methyl cellulose (CMC) agar media. The cellulolytic activity was analyzed semi-quantitatively with flooded 1% Congo red and then washed with 1 M NaCl three times. Cellulase activity assay was measured using the 3.5-Dinitrosalicylic Acid (DNS) method. The most potential isolate in cellulose decomposition was identified. The most potential isolate in cellulose decomposition was identified. Twenty isolates of cellulolytic bacteria were obtained from the sample and sixteen isolates formed the clear zone. The cellulolytic index ranged between 0.26 and 1.52. Five isolates, SL1, SL2, SL10, SL16, and SL19 had the highest cellulolytic index. Isolate SL2 had the highest cellulase activity at 0.071 U/mL. Based on the 16S rDNA sequence, SL2 was identified as Bacillus amyloliquefaciens F98 with a similarity of 99.02%. This potential isolate has prospects for the biodegradation process from agricultural waste, which can be processed into valuable products.
Authentication of Barbonymus spp. From Lake Singkarak Using DNA Barcoding
Authors: Salis Viola Mutiara , Roesma Dewi Imelda , Tjong Djong Hon , Syaifullah  , Aadrean  , Dahelmi
Published: December 2024

The local community distinguishes between Barbonymus belinka (Balingka) and Barbonymus schwanefeldii (Kapiek) in Lake Singkarak based on size due to the morphological similarities between the two species. From previous reports, B. belinka (Balingka) is a fish endemic to Lake Singkarak, West Sumatra, while B. schwanefeldii has a wider distribution, including Sumatra, Kalimantan, and Java. Consequently, molecular identification is necessary to discern between the species and to understand the DNA barcode characteristics of fish belonging to the genus Barbonymus in Lake Singkarak. One molecular technique utilized for species identification is DNA barcoding, which focuses on the COI (Cytochrome Oxidase Subunit I) gene. Liver tissue samples from Balingka and Kapiek fish from Lake Singkarak were used in the study. Based on 585 bp of COI gene sequences and 30 comparison sequences from BOLD system and GenBank NCBI, seven samples from Lake Singkarak show a genetic distance of 0–1.2% from B. schwanefeldii populations elsewhere, with 15 differing nucleotide bases. Moreover, samples from Lake Singkarak show a genetic distance of 7.7–8.2% from B. belinka in the BOLD system from Aceh, with 42 differing nucleotide bases. Furthermore, two specific bases are present in B. schwanefeldii from Lake Singkarak. Based on the results of this research, it is known that all samples from Lake Singkarak, including Balingka and Kapiek, belong to the same species, namely B. schwanefeldii.
Effect of Agrodyke Foliar Application on Growth and Yield of Two Varieties of Capsicum annuum
Authors: Mazli Nurul Ain , Abd Manan Fazilah , Sarobo Zulaikha , Ridzuan Raihana
Published: December 2024

Capsicum annuum is one of the most popular chili species cultivated and has become an important commodity crop in Malaysia. To overcome the shortage of Capsicum supply, foliar application can be utilized to increase chili yields. Foliar application requires only a minimal amount for effective use, rectifies nutrient deficiencies, and stimulates a rapid growth response. This research studied the effect of Agrodyke foliar fertilizer on the growth and yield of two varieties of C. annuum. Three treatments were applied to each chili variety, T0: control (no foliar application); T1: once a week (3 g/L) and T2: twice a week (3 g/L). The foliar application was initiated four weeks after germination. The results showed that Agrodyke foliar application at T2 resulted in the highest plant height (84.3 ± 3.9 cm) and stem diameter (1.3 ± 0.0 cm) for the Solok variety. For chlorophyll content, Agrodyke foliar application at T2 showed the highest levels in both Solok and Kulai varieties (67.3 ± 0.8 SPAD value and 67.4 ± 2.8 SPAD value, respectively). For individual fruit weight, Agrodyke foliar application at T2 in the Solok variety showed the highest weight (22.9 ± 2.1 g). In terms of fruit yield, Agrodyke foliar application at T1 in the Kulai variety produced the highest yield (123.3 ± 16.9 g). Furthermore, certain growth and yield attributes were positively correlated. Therefore, it can be concluded that Agrodyke foliar application at T2 provided better growth performance in terms of plant height and stem diameter for the Solok variety compared to the Kulai variety.
Gringaidas: notes on the Etymology of ‘Gringo’
Authors: Blanchette Thaddeus Gregory
Published: December 2024

El presente artículo analiza la etimología del término gringo desde su origen en la Península Ibérica hasta su uso común en la actualidad. Utilizando investigaciones bibliográficas, etnográficas y lingüísticas, buscamos desentrañar algunos de los significados de los términos dentro del contexto brasileño, al tiempo que destacamos su potencial como categoría émica o analítica que describe acertadamente una clase cada vez más numerosa de personas en el mundo glocalizado de hoy. Argumentamos que, a pesar de sus interpretaciones y usos populares en otras partes de América Latina, el uso del término en Brasil recupera sus connotaciones originales de “extranjero de habla chistosa”, sin conexiones necesarias con el imperialismo angloamericano o la blancura. En este sentido, gringo, en Brasil, es un término que –tal cual “fremde” de Simmel- resalta “aquello que no es de nosotros pero está entre nosotros”. Sin embargo, los últimos 200 años de encuentros imperiales han hecho que el término se aplique cada vez más a ciertos tipos de extranjeros en Brasil: europeos blancos o estadounidenses.
Economía, una Ciencia Social: Maria da Conceição Tavares
Authors: Portella Onofre
Published: December 2024

Este texto es un homenaje póstumo a la profesora Maria da Conceição Tavares. El objetivo es presentar a la autora a través de algunos momentos de su larga trayectoria intelectual y, para ello, se ha elegido una obra de su etapa de desarrollista, vinculada a la CEPAL, y otra, involucrada a su etapa más próxima al tema geopolítico.
Hierarchical Indexing for Retrieval-Augmented Opinion
Summarization
Authors: Hosking Tom , Tang Hao , Lapata Mirella
Published: December 2024

We propose a method for unsupervised abstractive opinion summarization, that combines the attributability and scalability of extractive approaches with the coherence and fluency of Large Language Models (LLMs). Our method, HIRO, learns an index structure that maps sentences to a path through a semantically organized discrete hierarchy. At inference time, we populate the index and use it to identify and retrieve clusters of sentences containing popular opinions from input reviews. Then, we use a pretrained LLM to generate a readable summary that is grounded in these extracted evidential clusters. The modularity of our approach allows us to evaluate its efficacy at each stage. We show that HIRO learns an encoding space that is more semantically structured than prior work, and generates summaries that are more representative of the opinions in the input reviews. Human evaluation confirms that HIRO generates significantly more coherent, detailed, and accurate summaries.
Alibertia mahechae (Gardenieae, Rubiaceae), a new species from the Eastern Colombian Andes
Authors: CORTÉS-B. ROCIO , ZAPATA-CORREA DIEGO A. , PERSSON CLAES , DELPRETE PIERO G.
Published: December 2024

Alibertia mahechae (Gardenieae, Rubiaceae), a new tree species endemic to the forest of the Colombian Eastern Andes, is described and illustrated. The new species is distinguished by traits such as coriaceous, glabrous leaves, short stipules, pistillate flowers with 7–8-lobed corollas, and globose fruits with woody mesocarp. This new species is similar to A. occidentalis, from which it differs in the coriaceous leaf blades (vs. papyraceous in A. occidentalis), (5–)7–9 pairs of secondary veins [vs. 9–14(–16)], male flower with truncate calyx (vs. denticulate to slightly undulate), corolla tubes (15–)20–27 mm long (vs. 11–18 mm long), anthers 16–17.5 mm long (vs. 6.5–10 mm long), and female flower 7–8-merous (vs. 6-merous). A key to the Alibertia species occurring in Colombia is provided.
One new species and one new provincial record of Neoperla (Plecoptera: Perlidae) from Yunnan, China
Authors: MO RAORAO , LI WEIHAI , MURÁNYI DÁVID
Published: December 2024

A new species, Neoperla yiliangensis Mo, Li & Murányi, sp. nov., is proposed from Yunnan Province of southwestern China and compared with related congeners. An additional species, Neoperla forcipata Yang & Yang, 1992 is reported from Yunnan Province for the first time and the first descriptions of aedeagal sac and female are also presented.
First record of the leafhopper genus Pedionis (Hemiptera: Cicadellidae: Eurymelinae: Macropsini) from Malaysia with description of a new species
Authors: WANG DONGMING , ZHANG YALIN
Published: December 2024

The genus Pedionis with its species Pedionis (Pedionis) rufoscutellata Huang & Viraktamath, 1993 is recorded for the first time from Malaysia. A new species Pedionis (Pedionis) spiculata sp. nov. is described and illustrated. An updated species checklist with distribution of the genus Pedionis is also provided.
A new cryptic species of Galiblatta Hebard, 1926 (Blaberidae: Epilamprinae) from the Brazilian Amazon Basin and redescription of Galiblatta williamsi Roth, 1968
Authors: HELEODORO RAPHAEL AQUINO , FILHO WALTERLEY VILHENA PEREIRA , MENDES DIEGO MATHEUS DE MELLO
Published: December 2024

Galiblatta Hebard, 1926 is a genus of the Poroblattini (Blaberidae: Epilamprinae) comprising so far G. cribosa Hebard, 1926 (type species) and G. williamsi Roth, 1968, respectively from Guiana and Brazil. The latter species was described from the state of Amazonas, Manaus. We are describing the cryptic Galiblatta pipo sp. nov. that occurs in sympatry with G. williamsi, with a map with genus records. Furthermore, we provide images and redescribe G. williamsi.
FIRST PERSON: The person who taught me the most about teaching just graduated from high school
Authors: Goldman Steven
Published: December 2024

Author Steven Goldman reflects on the lessons he learned from his son Theo during their car rides to and from school. Theo, who has mild dyslexia, talked about what school was like from his point of view. His perspectives helped Goldman become a better teacher.
“We Love STEM Too”: Fostering STEM Engagement Among Gifted and Talented Black Students Using Contemporary Young STEM Black Models
Authors: Ford Donna Y. , Hines Erik M.
Published: December 2024

In our experiences as Black caregivers, we are very thoughtful and concerned about the STEM experiences of young Gifted and Talented (GATE) Black and other Students of Color in P-12 and higher education. In both academic settings, Black and Hispanic students are inequitably underrepresented in GATE, college, and Science, Technology, Engineering, and Math (STEM) (Hines et al., 2024a). Why does underrepresentation in such advanced programs exist? There is a myriad of factors, explained herein. In addition to presenting data, we share several barriers, recommendations, and resources. Also important, we highlight a sample of Black boys and girls who are trailblazers in STEM with the goal of explaining how educators can and must foster STEM engagement among all students, GATE Black and minoritized students.
Comparing the experiences of cancer survivors living with sleep disturbances between differing levels of psychological distress: a qualitative study
Authors: Chan Julia , Ng Danielle Wing Lam , Fielding Richard , Lam Wendy Wing Tak
Published: December 2024

Background

Psychological distress often co-occurs with sleep disturbances; but the specific mechanisms linking the two remain unclear. A qualitative study explored perceptions and factors associated with sleep disturbances in cancer survivors between patients with varying levels of psychological distress.

Methods

Thirty-three Cantonese speaking mixed type cancer survivors were recruited from a community cancer care program. Participants that scored > 5 on the Pittsburgh Sleep Quality Index and had non-clinical or borderline to clinical levels of psychological distress underwent semi-structured interviews. Interviews were analyzed using grounded theory.

Results

Common triggers of sleep disturbances included unresolved treatment side-effects, intrusive thoughts about cancer and fear of cancer recurrence or progression, poor sleep hygiene and a lack of routine. Those with higher levels of distress exhibited more worry about recovery after cancer. Further, they engaged in thought suppression and experienced meta-worry about negative emotions and worry of poor sleep impacting recovery and cancer progression. They commonly exhibited high sleep reactivity and were observed to have limited social support. In contrast, those with low distress adopted better adaptive mechanisms, including a changed commitment to prioritizing health and positive reappraisal of their recovery progress. Self-distraction was used to cope with sleep disturbances and they had fewer expectations of good sleep quality.

Conclusions

Findings provided insights into the suitability of interventions for patients with sleep disturbances. Interventions targeting maladaptive emotion-focused coping may be more effective in addressing sleep disturbances in cancer survivors with higher distress. Interventions adopting a stepped-care approach may be advantageous in managing sleep disturbances by catering for varying levels of distress.
The South African Competition Commission COVID-19 easing of competition rules for private healthcare to facilitate public-private interaction - a media content analysis
Authors: Abdullah Amina , Sefuthi Thatohatsi , Ramokgopa Mapato , Fonn Sharon , Nkonki Lungiswa
Published: December 2024

Background

Future emergencies from climate degradation or diseases are likely, prompting ongoing investment in emergency readiness and learning from country responses. South Africa’s healthcare system, divided into public and private sectors, required a coordinated, intersectoral response to the COVID-19 pandemic. A coordinated action that the South African government took was adapting competition regulations. The South African Department of Trade, Industry and Competition on 19 March 2020, published a block exemption (easing of competition rules) for healthcare to promote standardization of practices across the health sector and facilitate agreements between the National Department of Health and the private sector to ensure adequate service delivery to all South Africans.

Methods

We assessed how much coverage the block exemption for healthcare received in the media and if the scope included details of what the exemption meant, how stakeholders and the public could use it, and the resulting public sentiment. We conducted a media content analysis to select, screen and assess the media material. Online and social-media articles in the public domain from 19 March 2020 to 19 March 2021, in English were considered.

Results

We analysed 22 online media articles that matched our inclusion criteria. Twenty of these reflected a positive sentiment, and two were negative. Media reported on the COVID-19 block exemption in healthcare only in the first three months of our study period. The articles primarily communicated what the block exemption meant, focusing on allowing collaboration, the purpose of the exemption, the activities granted under the exemption and the actors to whom it applied. It’s estimated that these media articles could have been read by up to 432,003 people out of a total population of just under 43 million people over the age of 15 years.

Conclusion

In times of crisis, the media has a significant responsibility to provide accurate information to the public. However, the accuracy and reliability of such information depends on the quality of official sources on which the media relies. Our research shows that very few media reports were available about the block exemption for healthcare. While the government implemented the exemption, it did not communicate its purpose directly to the public. Our research highlights the need for better communication between policymakers and the media.
Inequalities in the prevalence recording of 205 chronic conditions recorded in primary and secondary care for 12 million patients in the English National Health Service
Authors: Wang Shaolin , Lau Yiu-Shing , Sutton Matt , Anderson Michael , Kypridemos Christodoulos , Head Anna , Barr Ben , Cookson Richard , Bentley Chris , Anselmi Laura
Published: December 2024

Background

Understanding the prevalence of diseases and where it is detected and recorded in healthcare settings is important for planning effective prevention and care provision. We examined inequalities in the prevalence of 205 chronic conditions and in the care setting where the related diagnoses were recorded in the English National Health Service.

Methods

We used data from the Clinical Practice Research Datalink Aurum linked with Hospital Episode Statistics for 12.8 million patients registered with 1406 general practices in 2018. We mapped diagnoses recorded in primary and secondary care in the previous 12 years. We used linear regressions to assess associations of ethnicity, deprivation, and general practice with a diagnosis being recorded in primary care only, secondary care only, or both settings.

Results

72.65% of patients had at least one diagnosis recorded in any care setting. Most diagnoses were reported only in primary care (62.56%) and a minority only in secondary care (15.24%) or in both settings (22.18%). Black (− 0.08 percentage points (pp)), Asian (− 0.08 pp), mixed (− 0.13 pp), and other ethnicity patients (− 0.31 pp) were less likely than White patients to have a condition recorded. Patients in most deprived areas were 0.27 pp more likely to have a condition recorded (+ 0.07 pp in secondary care only, + 0.10 pp in both primary and secondary care, and + 0.10 pp in primary care only). Differences in prevalence by ethnicity were driven by diagnostic recording in primary care. Higher recording of diagnoses in more deprived areas was consistent across care settings. There were large differences in prevalence and diagnostic recording between general practices after adjusting for patient characteristics.

Conclusions

Linked primary and secondary care records support the identification of disease prevalence more comprehensively. There are inequalities in the prevalence and setting of diagnostic recording by ethnicity, deprivation, and providers on average across conditions. Further research should examine inequalities for each specific condition and whether they reflect also differences in access or recording as well as disease burden. Improving recording where needed and making national linked records accessible for research are key to understanding and reducing inequalities in disease prevention and management.