bluuebunny/crossref_metadata_2025 huggingface dataset:
Suppl. Table 2 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Mitochondrial and somatic nuclear DNA mutations identified in CLL using single cell DNA sequencing.
Suppl. Table 10 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Samples analyzed for this work using single cell sequencing platforms.
Suppl. Fig. 9 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Co-segregation of mitochondrial and somatic nuclear DNA mutations in AML bone marrow.
Suppl. Fig. 4 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Longitudinal changes of somatic nuclear and mitochondrial DNA mutations in evolving CLL.
Suppl. Fig. 17 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Identification of AML subclones using mitochondrial DNA (mtDNA) mutations.
Suppl. Fig. 16 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Deconvolution and identification of AML phenotypes in bone marrow using ASAP-seq.
Suppl. Fig. 15 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Differential phenotypes of physiologic (donor-) and malignant hematopoietic (recipient-derived) cells.
Suppl. Fig. 13 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Blood and bone marrow counts of immunosuppression tapering (IST) cohort from routine clinical measurements.
Suppl. Fig. 11 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Assessment of deconvolution performance of synthetic chimeric cell populations in in-silico mixing experiments.
Suppl. Fig. 10 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Applicability of expressed mitochondrial DNA (mtDNA) mutations to distinguish unrelated individuals.
Suppl. Fig. 1 from Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations
Authors: Penter Livius , Cieri Nicoletta , Maurer Katie , Kwok Marwan , Lyu Haoxiang , Lu Wesley S. , Oliveira Giacomo , Gohil Satyen H. , Leshchiner Ignaty , Lareau Caleb A. , Ludwig Leif S. , Neuberg Donna S. , Kim Haesook T. , Li Shuqiang , Bullinger Lars , Ritz Jerome , Getz Gad , Garcia Jacqueline S. , Soiffer Robert J. , Livak Kenneth J. , Wu Catherine J.
Published: November 2024

Extraction of mitochondrial DNA mutations from bulk RNA-seq data in CLL.
Supplementary Table 9 from Multiple Myeloma Risk and Outcomes Are Associated with Pathogenic Germline Variants in DNA Repair Genes
Authors: Thibaud Santiago , Subaran Ryan L. , Newman Scott , Lagana Alessandro , Melnekoff David T. , Bodnar Saoirse , Ram Meghana , Soens Zachry , Genthe William , Brander Tehilla , Mouhieddine Tarek H. , Van Oekelen Oliver , Houldsworth Jane , Cho Hearn Jay , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa , Chari Ajai , Moshier Erin , Jagannath Sundar , Parekh Samir , Onel Kenan
Published: November 2024

SUPPLEMENTARY TABLE 9: Matching Study Identifiers for MM patients included in the Discovery cohort to Publicly Available MMRF CoMMpass Ids
Supplementary Table 7 from Multiple Myeloma Risk and Outcomes Are Associated with Pathogenic Germline Variants in DNA Repair Genes
Authors: Thibaud Santiago , Subaran Ryan L. , Newman Scott , Lagana Alessandro , Melnekoff David T. , Bodnar Saoirse , Ram Meghana , Soens Zachry , Genthe William , Brander Tehilla , Mouhieddine Tarek H. , Van Oekelen Oliver , Houldsworth Jane , Cho Hearn Jay , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa , Chari Ajai , Moshier Erin , Jagannath Sundar , Parekh Samir , Onel Kenan
Published: November 2024

SUPPLEMENTARY TABLE 7: Comparative Per-variant PGV-C Burden Analysis in Multiple Myeloma Cohorts versus Non-Cancer gnomAD Control Populations
Supplementary Table 5 from Multiple Myeloma Risk and Outcomes Are Associated with Pathogenic Germline Variants in DNA Repair Genes
Authors: Thibaud Santiago , Subaran Ryan L. , Newman Scott , Lagana Alessandro , Melnekoff David T. , Bodnar Saoirse , Ram Meghana , Soens Zachry , Genthe William , Brander Tehilla , Mouhieddine Tarek H. , Van Oekelen Oliver , Houldsworth Jane , Cho Hearn Jay , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa , Chari Ajai , Moshier Erin , Jagannath Sundar , Parekh Samir , Onel Kenan
Published: November 2024

SUPPLEMENTARY TABLE 5: Comparative Per-gene PGV-A Burden Analysis in Multiple Myeloma Cohorts versus Non-Cancer gnomAD Control Populations
Supplementary Table 3 from Multiple Myeloma Risk and Outcomes Are Associated with Pathogenic Germline Variants in DNA Repair Genes
Authors: Thibaud Santiago , Subaran Ryan L. , Newman Scott , Lagana Alessandro , Melnekoff David T. , Bodnar Saoirse , Ram Meghana , Soens Zachry , Genthe William , Brander Tehilla , Mouhieddine Tarek H. , Van Oekelen Oliver , Houldsworth Jane , Cho Hearn Jay , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa , Chari Ajai , Moshier Erin , Jagannath Sundar , Parekh Samir , Onel Kenan
Published: November 2024

SUPPLEMENTARY TABLE 3: Per-Gene PGV Counts and Gene Pathway Enrichments
Supplementary Table 1 from Multiple Myeloma Risk and Outcomes Are Associated with Pathogenic Germline Variants in DNA Repair Genes
Authors: Thibaud Santiago , Subaran Ryan L. , Newman Scott , Lagana Alessandro , Melnekoff David T. , Bodnar Saoirse , Ram Meghana , Soens Zachry , Genthe William , Brander Tehilla , Mouhieddine Tarek H. , Van Oekelen Oliver , Houldsworth Jane , Cho Hearn Jay , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa , Chari Ajai , Moshier Erin , Jagannath Sundar , Parekh Samir , Onel Kenan
Published: November 2024

SUPPLEMENTARY TABLE 1: Clinical Characteristics by Cohort
Supplementary Figure 4 from Multiple Myeloma Risk and Outcomes Are Associated with Pathogenic Germline Variants in DNA Repair Genes
Authors: Thibaud Santiago , Subaran Ryan L. , Newman Scott , Lagana Alessandro , Melnekoff David T. , Bodnar Saoirse , Ram Meghana , Soens Zachry , Genthe William , Brander Tehilla , Mouhieddine Tarek H. , Van Oekelen Oliver , Houldsworth Jane , Cho Hearn Jay , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa , Chari Ajai , Moshier Erin , Jagannath Sundar , Parekh Samir , Onel Kenan
Published: November 2024

SUPPLEMENTARY FIGURE 4: Concordance of Genetically-Determined Ancestry and Self-Reported Race in a subset of patients from the Discovery Cohort (MMRF CoMMpass dataset)
Supplementary Figure 3 from Multiple Myeloma Risk and Outcomes Are Associated with Pathogenic Germline Variants in DNA Repair Genes
Authors: Thibaud Santiago , Subaran Ryan L. , Newman Scott , Lagana Alessandro , Melnekoff David T. , Bodnar Saoirse , Ram Meghana , Soens Zachry , Genthe William , Brander Tehilla , Mouhieddine Tarek H. , Van Oekelen Oliver , Houldsworth Jane , Cho Hearn Jay , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa , Chari Ajai , Moshier Erin , Jagannath Sundar , Parekh Samir , Onel Kenan
Published: November 2024

SUPPLEMENTARY FIGURE 3: PFS1 and OS in PGV-B/C carriers vs non-carriers (combined cohort)
Data from Therapy-Related Myeloid Neoplasms: Complex Interactions among Cytotoxic Therapies, Genetic Factors, and Aberrant Microenvironment
Authors: Singhal Deepak , Kutyna Monika M. , Hahn Christopher N. , Shah Mithun Vinod , Hiwase Devendra K.
Published: November 2024

Abstract
Therapy-related myeloid neoplasm (t-MN), characterized by its association with prior exposure to cytotoxic therapy, remains poorly understood and is a major impediment to long-term survival even in the era of novel targeted therapies due to its aggressive nature and treatment resistance. Previously, cytotoxic therapy–induced genomic changes in hematopoietic stem cells were considered sine qua non in pathogenesis; however, recent research demonstrates a complex interaction between acquired and hereditary genetic predispositions, along with a profoundly senescent bone marrow (BM) microenvironment. We review emerging data on t-MN risk factors and explore the intricate interplay among clonal hematopoiesis, genetic predisposition, and the abnormal BM microenvironment.

Significance: t-MN represents a poorly understood blood cancer with extremely poor survival and no effective therapies. We provide a comprehensive review of recent preclinical research highlighting complex interaction among emerging therapies, hereditary and acquired genetic factors, and BM microenvironment. Understanding the risk factors associated with t-MN is crucial for clinicians, molecular pathologists, and cancer biologists to anticipate and potentially reduce its incidence in the future. Moreover, better understanding of the molecular pathogenesis of t-MN may enable preemptive screening and even intervention in high-risk patients.
Table 2 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Association between ICI effectiveness predictors and irAEs in patients with NSCLC treated with atezolizumab
Table 1 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Frequency of irAEs of interest by grade in patients with NSCLC treated with atezolizumab
Supplementary Table S4 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Supplementary Table S4. Association between grade 1–2 irAEs and predictors of ICI effect a Mann–Whitney U Test. b Patients who had progression within 4 or 6 weeks after the initiation of treatment were excluded. Abbreviations: CRP, C-reactive protein; ICI, immune checkpoint inhibitor; IHC, immunohistochemical; irAE, immune-related adverse event; NLR, neutrophil-to-lymphocyte ratio; PD-L1, programmed death ligand-1; Q, quartile; SD, standard deviation.
Supplementary Table S2 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Supplementary Table S2. Univariable and multivariable analysis of OS Abbreviations: ECOG PS, Eastern Cooperative Oncology Group performance status; HR, hazard ratio; ICI, immune checkpoint inhibitor; IHC, immunohistochemistry; irAE, immune-related adverse event; OS, overall survival; PD-L1, programmed death ligand-1; TPS, tumor proportion score.
Supplementary Table S1 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Supplementary Table S1. Background demographic and clinical characteristics of patients with or without irAE Abbreviations: ECOG PS, Eastern Cooperative Oncology Group performance status; EGFR, epidermal growth factor receptor; ICIs, immune checkpoint inhibitors; IHC, immunohistochemical staining; irAE, immune-related adverse event; PD-L1, programmed death ligand-1; TPS, tumor proportion score. a Data were missing for one patient. b Other includes patients with pleural effusion. c Negative, all targSupplementary Table driver oncogene statuses (EGFR mutation status, ALK rearrangement status, ROS1 rearrangement status, and BRAF V600E mutation status) were negative; positive, one or more were positive; unknown, none of the positives, any were unknown or not tested
Supplementary Figure S4 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Supplementary Figure S4. OS according to number of whole irAEs Abbreviations: CI, confidence interval; HR, hazard ratio; irAE, immune-related adverse event; NE, not evaluable; NR, not reached; OS, overall survival
Supplementary Figure S2 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Supplementary Figure S2. PFS of irAE of skin or endocrine disorders (A) PFS of irAE of skin or endocrine disorders according to the onset (B) PFS of irAE of skin or endocrine disorders according to the grade One event with undetermined grade was excluded from the analysis according to grade. Abbreviations: CI, confidence interval; HR, hazard ratio; irAE, immune-related adverse event; PFS, progression-free survival 
Supplementary Figure S1 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Supplementary Figure S1. PFS according to the grade of irAE (A) 4 weeks landmark PFS of irAE according to the grade (B) 8 weeks landmark PFS of irAE according to the grade One event with undetermined grade was excluded from the analysis. Abbreviations: CI, confidence interval; HR, hazard ratio; irAE, immune-related adverse event; PFS, progression-free survival
Figure 3 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Association between the type of irAE and OS. A, OS according to the grade of irAE in skin or endocrine disorders and (B) OS according to the grade of irAEs affecting other systems (other than skin or endocrine disorders). One event with an undetermined grade was excluded from the analysis. NE, not evaluable; NR, not reached.
Figure 2 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Landmark analysis of OS according to the grade of irAE. A, Four-week landmark OS according to the grade of irAE, (B) 8-week landmark OS according to the grade of irAE, (C) 12-week landmark OS according to the grade of irAE, and (D) 24-week landmark OS according to the grade of irAE. One event with an undetermined grade was excluded from the analysis. NE, not evaluable.
Figure 1 from Association between Immune-Related Adverse Events and Atezolizumab in Previously Treated Patients with Unresectable Advanced or Recurrent Non–Small Cell Lung Cancer
Authors: Hayashi Hidetoshi , Nishio Makoto , Akamatsu Hiroaki , Goto Yasushi , Miura Satoru , Gemma Akihiko , Yoshino Ichiro , Misumi Toshihiro , Kijima Takashi , Takase Naoto , Fujita Masaki , Tasaka Sadatomo , Mouri Atsuto , Kondo Tetsuro , Takamura Kei , Kawashima Yosuke , Imaizumi Kazuyoshi , Iwasawa Shunichiro , Nakagawa Shintaro , Mitsudomi Tetsuya
Published: November 2024

Association between the occurrences of irAEs and OS or PFS. A, OS according to the onset of irAE, (B) OS according to the grade of irAE, (C) PFS according to the onset of irAE, and (D) PFS according to the grade of irAE. One event with undetermined grade was excluded from the analysis according to grade. NE, not evaluable; NR, not reached.
Pan-Cancer Analysis of Homologous Recombination Deficiency in Cell Lines
Authors: Dodson Anne E. , Shenker Sol , Sullivan Pamela , Nayak Sumeet U. , Middleton Chris , McGuire Michael , Chipumuro Edmond , Mishina Yuji , Tobin Erica R. , Cadzow Louise , Wylie Andrew A. , Sangurdekar Dipen
Published: November 2024

Homologous recombination deficiency (HRD) drives genomic instability in multiple cancer types and renders tumors vulnerable to certain DNA-damaging agents such as PARP inhibitors. Thus, HRD is emerging as an attractive biomarker in oncology. A variety of in silico methods are available for predicting HRD; however, few of these methods have been applied to cell lines in a comprehensive manner. Here, we utilized two of these methods, “Classifier of HOmologous Recombination Deficiency” and “HRDsum” scores, to predict HRD for 1,332 cancer cell lines and 84 noncancerous cell lines. Cell lines with biallelic mutations in BRCA1 or BRCA2, which encode key components of the homologous recombination pathway, showed the strongest HRD predictions, validating the two methods in cell lines. A small subset of BRCA1/2 wild-type cell lines was also classified as HRD, several of which showed evidence of epigenetic BRCA1 silencing. Similar to HRD in patient samples, HRD in cell lines was associated with p53 loss, was mutually exclusive with microsatellite instability, and occurred most frequently in breast and ovarian cancer types. In addition to validating previously identified associations with HRD, we leveraged cell line–specific datasets to gain new insights into HRD and its relation to various genetic dependency and drug sensitivity profiles. We found that in cell lines, HRD was associated with sensitivity to PARP inhibition in breast cancer but not at a pan-cancer level. By generating large-scale, pan-cancer datasets on HRD predictions in cell lines, we aim to facilitate efforts to improve our understanding of HRD and its utility as a biomarker.

Significance:

HRD is common in cancer and can be exploited therapeutically, as it sensitizes cells to DNA-damaging agents. Here, we scored more than 1,300 cancer cell lines for HRD using two different bioinformatic approaches, thereby enabling large-scale analyses that provide insights into the etiology and features of HRD.
Clinicopathological Characteristics and Perioperative Treatment of Epstein-Barr Virus-Associated Gastric Cancer: A Retrospective Study
Authors: Ji Zhi , Zhu Lila , Wang Xia , Li Hongli , Duan Jingjing , Zhang Le , Deng Ting , Liu Rui , Ba Yi
Published: November 2024

Introduction: The clinicopathological characteristics and efficacy of perioperative treatment of Epstein-Barr virus-associated gastric cancer (EBVaGC) were investigated. Methods: The clinicopathological characteristics and perioperative treatment outcomes of patients with EBVaGC who underwent radical gastrectomy in Tianjin Medical University Cancer Hospital from September 2016 to May 2022 were retrospectively reviewed. Disease-free survival (DFS) was analyzed, and Cox regression analysis was performed to identify risk factors. Results: The study cohort included 128 patients with EBVaGC. Histologically, 126 (98.4%) patients had adenocarcinoma and only 2 (1.6%) had adenosquamous carcinoma. In addition, 18 (14.1%) had nerve invasion and 29 (22.7%) had vascular invasion. Notably, 41 (32.0%) patients had tumors in the proximal stomach and 69 (53.9%) had no lymph node metastasis. Proficient mismatch repair was confirmed in all 104 patients with available results. Overall, 16 (12.5%) patients received neoadjuvant therapy, 81 (63.3%) received adjuvant therapy, and 10 (7.8%) received perioperative immunotherapy combined with chemotherapy. In total, 22 patients experienced disease progression or had died. The 3-year DFS rate was 75.0%. DFS was relatively poorer for patients with advanced tumor (T) stage, lymph node (N) stage, disease stage, and vascular invasion. Conclusion: EBVaGC had unique clinicopathological characteristics and prognosis. Advanced T, N, and disease stages, in addition to vascular invasion, were predictive of poorer DFS. However, the efficacy of perioperative treatment of EBVaGC remains uncertain.
Advances in Molecular Imaging of Kidney Diseases
Authors: Klinkhammer Barbara Mara , Ay Ilknur , Caravan Peter , Caroli Anna , Boor Peter
Published: November 2024

Background: Diagnosing and monitoring kidney diseases traditionally rely on blood and urine analyses and invasive procedures such as kidney biopsies, the latter offering limited possibilities for longitudinal monitoring and a comprehensive understanding of disease dynamics. Current noninvasive methods lack specificity in capturing intrarenal molecular processes, hindering patient stratification and patient monitoring in clinical practice and clinical trials. Summary: Molecular imaging enables noninvasive and quantitative assessment of physiological and pathological molecular processes. By using specific molecular probes and imaging technologies, e.g., magnetic resonance imaging, positron emission tomography, single-photon emission computed tomography, or ultrasound, molecular imaging allows the detection and longitudinal monitoring of disease activity with spatial and temporal resolution of different kidney diseases and disease-specific pathways. Several approaches have already shown promising results in kidneys and exploratory clinical studies, and validation is needed before implementation in clinical practice. Key Messages: Molecular imaging offers a noninvasive assessment of intrarenal molecular processes, overcoming the limitations of current diagnostic methods. It has the potential to serve as companion diagnostics, not only in clinical trials, aiding in patient stratification and treatment response assessment. By guiding therapeutic interventions, molecular imaging might contribute to the development of targeted therapies for kidney diseases.
Students’ competitiveness: motivation or fear?
Authors: Wu Lin , Purwaningrum Evi Kurniasari , Ho Yi Ming , Prihadi Kususanto Ditto , Cheng Chen , Qian Kuang
Published: November 2024

This study aimed to explore the factors that contribute to the high level of competitiveness among students in the People’s Republic of China (PRC). The expectancy value theory has suggested that the fear of failure (FOF) and a highly perceived value for achievement (expectancy value belief, EVB) are the key drivers of competitiveness. To examine this theory, the study analyzed data from 969 college students in the PRC using Bootstrap Analysis with 5,000 samples in a 95% confidence interval. The study found that while the value placed on academic achievement did motivate students to fear failure and become more competitive, perceived social support played a significant role in moderating this relationship. Specifically, the students’ perception of social support moderated the mediation of (FOF) on the link between EVB and competitiveness. These findings suggest that social support is a crucial factor in shaping the dynamics of competitiveness among PRC students. The study may have implications for educators and policymakers seeking to promote healthy competition and academic achievement in highly competitive education systems.
Grit among college students: social or personal?
Authors: Wong Bridgette Tsin Ee , Prihadi Kususanto Ditto , Ashok Arman Imran , Huan Tan Li , Jamaluddin Anne
Published: November 2024

Grit, the personal characteristic of perseverance and passion for long-term goals, plays a vital role in college students' success and well-being. This study aimed to investigate the contribution of optimism (a personal factor) and college mattering (a social factor), as well as their underlying mechanism on grit among college students. Data was collected from 186 participants from Selangor, Malaysia, who voluntarily responded to the college mattering scale (CMS), life orientation test-revised (LOT-R), and grit scale (Grit-S) Scale. The Bootstrap method with 5,000 resamples at a 95% confidence interval was employed for analysis. Our findings suggested that while college mattering and optimism did not significantly predict grit when controlling for each other, both social and personal factors are similarly important in predicting the development of grit, and that any intervention program or module to improve the students’ grit must encompass both social development and the improvement of social dynamics in the academic institutions.
Bibliometrics unleashed: navigating the landscape of classroom assessment
Authors: Wan Mat Wan Fazwani , Lian Lim Hooi
Published: November 2024

This bibliometric article examines the current state of publication in the field of classroom assessment, exploring the productivity and influence of countries, institutions, and authors. A search query of on the Scopus database using the term “classroom assessment” or “classroom-based assessment” or “assessment for learning” was performed retrieving 824 scholarly articles from 1985 to 2023. VOSviewer software was used to create maps based on network data of scientific publications displaying relationships among researchers, countries, and scientific journals. By analyzing citation patterns and keywords, it identifies popular themes among scholars and highlights areas requiring further research under keywords such as "assessment for learning", "feedback", and "validity". The study provides valuable insights into the evolving landscape of classroom assessment research, offering a comprehensive overview of the key contributors and trends shaping the field. Author keywords were used to explore the co-occurrence of different terms connected to classroom assessment. This study's findings provide a comprehensive comprehension of the current state of classroom assessment research, making a substantial contribution to the education and assessment literature and paving the way for future research directions.
Micro-credentials in higher education: a review and bibliometric
Authors: Johan Riche Cynthia , Rullyana Gema , Susilana Rudi , Emilzoli Mario
Published: November 2024

The objective of this study is to conduct a comprehensive review of research on “Micro-credentials in higher education” by doing a bibliometric analysis of 85 journal articles published between 2015 and 2023, obtained from the Scopus database. This study focuses on quantifying the number of publications and citations, as well as examining subject areas, connections, universities, countries, and identifying the most productive and prominent researchers. Apart from that, this research also identifies research topics that researchers have been working on in recent years. The findings show that publications and citations have increased in the last three years. The United States, Australia, and Canada are the most productive countries on this topic. T. J. Newby is the most productive researcher, while the most influential writer is D. -K. Mah. TechTrends and The International Journal of Information and Learning Technology are the journals that publish the most research. The university that made the top contribution was Purdue University (United States). The results of data analysis show that collaboration between authors researching “Micro-credentials in higher education” still needs improvement. This research contributes as a basis for further research in enriching and developing knowledge about micro-credentials, especially in higher education.
A recent study on islamic religious education teachers’ competencies in the digital age: a systematic literature review
Authors: Arif Muhamad , Aziz Mohd Kasturi Nor Abd , Ma'arif Muhammad Anas
Published: November 2024

Diverse research findings pertaining to the proficiency of Islamic religious education teachers may serve as a starting point, if not a benchmark, for the development of such instructors' proficiency, particularly with regard to the proficiencies that are imperative for educators in the digital age. Consequently, this study aims to investigate the competencies of Islamic religious education teachers that have been mentioned most frequently in research over the past decade, as well as strategies for developing those competencies and technological (digital) competencies. To achieve this aim, this study employed a systematic literature review method by utilizing publication data spanning a decade (2013–2023) to investigate a particular theme. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) was utilized to evaluate the findings. This research shows findings regarding teachers' obligations to develop technological (digital) competencies, in addition to the four teacher competencies (pedagogical, professional, personal, and social). The aforementioned conditions are predicated on the necessity for collaborative, creative, and creative learning, which makes it highly sought after by students. In contrast, forthcoming investigations should strive to gather empirical data regarding approaches to cultivating digital proficiency among Islamic religious education instructors, given the prevailing inclination towards learner-centered learning in the twenty-first century as opposed to teacher-centered learning.
Comparative learning holding on satisfaction, interest in learning, and academic performance of student
Authors: Fathonah Siti , Wahyuningsih Wahyuningsih , Rosidah Rosidah , Triatma Bambang , Astuti Romiyatun Mijiling , Fadilah Ahmad , Fatima Cikha Yulia , Ciskawati Dyah Ayu
Published: November 2024

The COVID-19 virus pandemic limits the movement of activities and learning is carried out online, followed by blended. After returning to normal offline. The research objectives are i) to analyze satisfaction, interest in learning and academic performance with online, blended and offline learning and ii) to differentiate between study programs in the Family Welfare Education. The research subjects were 5th semester students, cross-sectional study. Satisfaction, interest in learning and academic performance of students were measured using a questionnaire with a Likert scale of 1-5. Data analysis was descriptive percentages, difference tests with Kruskal-Wallis followed by Mann-Whitney, and correlation with the Gamma test. The level of student satisfaction with online, blended and offline learning is in the satisfied category. Interest in learning and academic performance in the good category. There are significant differences in the level of satisfaction, interest in learning and academic performance with online, blended and offline learning, as well as between study programs. There is a high relationship between the level of satisfaction and interest in learning with academic performance. The comparison of learning holding differs significantly in levels of satisfaction, interest, academic performance and between study programs, but in the same category (good). The best learning holding is offline.
Integrating creative thinking and cultural insights through the anthropological theory of didactics in university algebra
Authors: Ontiveros Yanko Ordóñez , González Julián Roa , Palencia José Luis Díaz
Published: November 2024

This discussion explored the integration of creative thinking pedagogy and the anthropological theory of didactics in university-level algebra education, emphasizing the importance of understanding the perspectives of both learners and teachers. The work began by highlighting the necessity of considering these viewpoints to create effective and responsive educational experiences. We then focused on designing classroom sessions for algebra, blending creative thinking with cultural and historical contexts. These sessions included applying creative approaches to group theory, exploring algebraic topology through innovative means, and understanding ring theory in practical scenarios like cryptography. Feedback from both learners and teachers was generally positive, with students appreciating the engaging and practical aspects and teachers recognizing the benefits of creative pedagogies. However, challenges in implementation, such as resource constraints and the need for professional development, were also identified. Suggestions for improvement included deeper content exploration, enhanced use of technology, and better alignment of creative teaching methods with assessment strategies.
Gendered pictorial in Indonesian EFL textbook “When English rings the bells”
Authors: Wiraningsih Putu , Suwastini Ni Komang Arie , Padmadewi Ni Nyoman
Published: November 2024

Sustainable development goal (SDG) 4 and 5 prioritize equal opportunities for all genders and socioeconomic backgrounds to get education. Textbook shapes students' perspectives on gender roles and possibilities for themselves and others thus playing a pivotal role in promoting equality and diversity in education. However, certain English as a foreign language (EFL) textbooks still uphold such biases in their content and images. Thus, this study aimed at describing the gender pictorial in the EFL textbook “When English rings the bells”. Applying textual along with multimodal analysis, this study analyzes the textbook following Pierce’s semiotics. Providing an in-depth analysis of how gender is represented, this study discovered that the textbook still perpetuates gender stereotypes in three areas: i) pictorial of the characters, ii) gender attributes, and iii) traditional roles. It also makes efforts to break these stereotypes by portraying diverse professions and activities. Hence, it may be inferred that the textbook made an effort to analyze and dismantle the notion of gender, yet ultimately reinforced existing preconceptions. It suggests that students can be encouraged to challenge traditional gender roles and aspire to a broader range of careers and life choices by promoting more diverse representations of males and females in textbooks.
A two-tier multiple-choice diagnostic test to find student misconceptions about the change of matter
Authors: Ningroom Rita Arfi Astuti , Yamtinah Sri , Riyadi Riyadi
Published: November 2024

There are a lot of very interesting scientific concepts to learn in natural and social science. The initial concepts that the student possesses may contradict the actual concepts, which is what causes misconceptions. Misconceptions are identified using misconception detection test tools. In fact, the development of the use of diagnostic test instruments in Indonesia is still very limited. The objective of the study is to create a diagnostic exam instrument that is two tiers and multiple-choice using certainty of response index (CRI) to identify misunderstandings that students have about changes in matters form in science learning. The research design was research and development (RnD). Development starts with literature studies, design and drafting product drafts, testing product validation with expert validation, and empirical testing. The result analysis showed that the two-tier multiple-choice diagnostic test has a high validity of 0.791. The difficulty level belongs to the moderate category, with a coefficient between 0.2 and 0.8 and a good differential and decaying power. Diagnostic tests are said to be suitable for the detection of misconceptions in science learning in elementary school. The outcome of this study contributes to increasing students' knowledge, understanding, critical thinking, and reducing the level of student misconceptions.
A literature review of flexibility in interactive mathematics classrooms: the role of teachers and students
Authors: Munaji Munaji , Rohaeti Titi , Mutadi Mutadi , Sumliyah Sumliyah , Kodirun Kodirun
Published: November 2024

The significance of flexibility in mathematics classrooms, particularly in interactive mathematics classrooms where students learn through hands-on experience, cannot be overstated. Teachers play a pivotal role in fostering students’ mathematical understanding by selecting appropriate tasks and providing expert guidance. Additionally, the patterns of interactions between teachers and students, such as elicitation and discussion patterns, and their relationship with teacher flexibility are examined. Developing adaptive expertise in mathematics involves the ability to think flexibly about mathematical concepts, which can be enhanced by teaching math in a way that promotes the development of expertise. Mathematical flexibility, a crucial aspect of mathematical competence, involves the creative and innovative use of mathematical concepts, numerical relations, and strategies. It requires a combination of procedural and conceptual knowledge, skills, and understanding, as well as motivational and affective dispositions. Pedagogical flexibility can significantly contribute to innovating classroom teaching and learning, and exploring the relationships between teachers’ pedagogical flexibility and students’ potential and actual mathematical flexibility development. The article also emphasizes the importance of developing adaptive competencies in mathematics education to prepare students for an uncertain future, with creativity being considered a key competency and flexibility being viewed as a vital element of creativity.
Entrepreneurial basic capital and its contribution to developing multicultural islamic education
Authors: Mariyono Dwi , Maskuri Maskuri , Ghony Muhammad Djunaidi
Published: November 2024

This research aims to explore the role of entrepreneurial spirit in the development of multicultural Islamic education at Bahrul Maghfiroh Islamic Boarding School in Malang. Using a qualitative approach with the ethnographic case study method. The research questions are: i) what entrepreneurial spirit is used as capital in developing multicultural Islamic education at Bahrul Maghfiroh Islamic Boarding School in Malang? and ii) how does the entrepreneurial spirit contribute to the development of multicultural Islamic education at Bahrul Maghfiroh Islamic Boarding School in Malang? data and data sources were obtained through interviews, observations, and documents. This study found that the spirit of entrepreneurship plays an important role in developing multicultural Islamic education in pesantren. Capital in entrepreneurship is not always synonymous with tangible things such as money and gold. The contribution of the entrepreneurial spirit is very real and significant because it helps create an inclusive and conducive learning environment and encourages the growth of creativity and innovation among students. In addition, social entrepreneurship in the pesantren environment can also grow and develop synergistically to improve people's lives.
Computational thinking skills profile in solving mathematical problems based on computational thinking attitude
Authors: Richardo Rino , Dwiningrum Siti Irene Astuti , Murti Rahayu Condro , Wijaya Ariyadi , Adawiya Robiatul , Ihwani Ivan Luthfi , Ardiyaningrum Martalia , Aryani Anggi Erna
Published: November 2024

The aim of this qualitative research is to describe the thinking process as a profile of students' mathematical computational thinking (CT) skills in terms of CT attitudes. The subjects in this study were 66 junior high school students in grade IX. There were three students taken by purposive sampling based on high, medium, and low CT attitude. The main research instrument was the researcher, while the auxiliary instruments were mathematical CT ability test and CT attitude scale questionnaire. Data analysis included 3 stages, namely data reduction, data presentation, and conclusion drawing. The data credibility test used triangulation techniques, namely tests and interviews. The results showed that subjects with high CT attitude were able to show all indicators of CT ability, namely abstraction, problem decomposition, algorithmic thinking and generalisation and pattern recognition. However, subjects with moderate and low CT attitudes were only able to show one of these indicators, namely abstraction. Based on the results of this study, researchers will create a mathematics learning model to develop CT skills, especially for number pattern material.