bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S6 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Histology of baseline human tumors.
Supplementary Figure S5 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S5- ER-negative BT-20 cells do not exhibit increased DNA damage upon E2 treatment, while MCF-7/LTED show weak response.
Supplementary Figure S3 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S3- E2-induced DNA damage is dependent upon cell cycle progression.
Supplementary Figure S2 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S2- E2 induces DNA damage in LTED and ER-overexpressing cells.
Supplementary Figure S15 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S15- Individual growth curves of WHIM16 tumors from mice treated with a second cycle of E2 ± olaparib.
Supplementary Figure S12 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S12- ER overexpression promotes E2-induced R-loop formation.
Supplementary Figure S11 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S11- E2 stimulation induces DNA replication stress.
Supplementary Figure S10 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S10- Representative IHC images from WHIM16 and CTG-3346 tumors.
Supplementary Figure S1 from Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: July 2023

Supplementary Figure S1- E2 induces changes in overlapping sets of genes in HCC-1428 and HCC-1428/LTED cells.
Supplementary Table 3 from TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: July 2023

The raw data of 1C
Supplementary Table 2 from TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: July 2023

The raw data of 1B.
Supplementary Table 4 from Hierarchical Phosphorylation of HOXB13 by mTOR Dictates Its Activity and Oncogenic Function in Prostate Cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguère Vincent
Published: July 2023

Supplementary Table 4. Source data.
Supplementary Table 2 from Hierarchical Phosphorylation of HOXB13 by mTOR Dictates Its Activity and Oncogenic Function in Prostate Cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguère Vincent
Published: July 2023

Supplementary Table 2. RNA-seq analysis of LNCaP mTOR KD cells rescued with mTOR or empty vector (EV) control ± R1881 for 24h.
Figure S4 from TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: July 2023

Figure S4: The TRIM50 and JUP binding domain predicted by I-TASSER-MTD. Blue indicated TRIM50. Green indicated JUP. Purple highlighted the interaction sites in RING and PRY/SPRY domain.
Figure S3 from TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: July 2023

Figure S3A: Tumor photograph in the nude mouse subcutaneous xenograft model by implanting TRIM50 overexpressing (TRIM50) versus control empty vector (EV) MKN45 cells (n = 6 mice per group). Scale bar: 1 cm
Figure S3B: MKN74 cells were transfected with lentiviruses expressing TRIM50 shRNA. A universal nonsilencing shRNA was used as a negative control (sh-NC). Whole-cell lysates were subjected to immunoblot analysis with TRIM50 antibody.
Figure S3C: Tumor photograph in the nude mouse subcutaneous xenograft model by implanting TRIM50 knockdown (TRIM50 sh-1/TRIM50 sh-2) versus control (TRIM50 sh-NC) MKN74 cells (n = 6 mice per group). Scale bar: 1 cm
Figure S2 from TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: July 2023

Figure S2: Immunoblotting assay of TRIM50 expression in GC cells.
Figure S1 from TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: July 2023

Figure S1A: The expression of TRIM50 and UBE2QL1 in the Cancer Genome Atlas (TCGA) database.
Figure S1B: The IHC score of Figure 1F.
Supplementary Figure 5 from Hierarchical Phosphorylation of HOXB13 by mTOR Dictates Its Activity and Oncogenic Function in Prostate Cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguère Vincent
Published: July 2023

Supplementary Figure 5. HOXB13 transcriptional activity depends on its phosphorylation status.
Supplementary Figure 4 from Hierarchical Phosphorylation of HOXB13 by mTOR Dictates Its Activity and Oncogenic Function in Prostate Cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguère Vincent
Published: July 2023

Supplementary Figure 4. Androgen response dependency on HOXB13 phosphorylation.
Supplementary Figure 3 from Hierarchical Phosphorylation of HOXB13 by mTOR Dictates Its Activity and Oncogenic Function in Prostate Cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguère Vincent
Published: July 2023

Supplementary Figure 3. SKP2 is an E3 ligase for HOXB13.
Supplementary Figure 1 from Hierarchical Phosphorylation of HOXB13 by mTOR Dictates Its Activity and Oncogenic Function in Prostate Cancer
Authors: Chen Yonghong , Dufour Catherine R. , Han Lingwei , Li Ting , Xia Hui , Giguère Vincent
Published: July 2023

Supplementary Figure 1. mTOR negatively regulates HOXB13 protein stability
Data from TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP
Authors: Hu Jiajia , Huang Runjie , Liang Chengcai , Wang Yingnan , Wang Min , Chen Yanxing , Wu Chenyi , Zhang Jinling , Liu Zekun , Zhao Qi , Liu Zexian , Wang Feng , Yuan Shuqiang
Published: July 2023

Abstract
Gastric cancer is one of the most frequent cancers in the world. Emerging clinical data show that ubiquitination system disruptions are likely involved in carcinoma genesis and progression. However, the precise role of ubiquitin (Ub)-mediated control of oncogene products or tumor suppressors in gastric cancer is unknown. Tripartite motif-containing 50 (TRIM50), an E3 ligase, was discovered by high-output screening of ubiquitination-related genes in tissues from patients with gastric cancer to be among the ubiquitination-related enzymes whose expression was most downregulated in gastric cancer. With two different databases, we verified that TRIM50 expression was lower in tumor tissues relative to normal tissues. TRIM50 also suppressed gastric cancer cell growth and migration in vitro and in vivo. JUP, a transcription factor, was identified as a new TRIM50 ubiquitination target by MS and coimmunoprecipitation experiments. TRIM50 increases JUP K63-linked polyubiquitination mostly at the K57 site. We discovered that the K57 site is critical for JUP nuclear translocation by prediction with the iNuLoC website and further studies. Furthermore, ubiquitination of the K57 site limits JUP nuclear translocation, consequently inhibiting the MYC signaling pathway. These findings identify TRIM50 as a novel coordinator in gastric cancer cells, providing a potential target for the development of new gastric cancer treatment strategies.
Implications:
TRIM50 regulates gastric cancer tumor progression, and these study suggest TRIM50 as a new cancer target.
Supplementary Data from Activity and Safety of Mobocertinib (TAK-788) in Previously Treated Non–Small Cell Lung Cancer with EGFR Exon 20 Insertion Mutations from a Phase I/II Trial
Authors: Riely Gregory J. , Neal Joel W. , Camidge D. Ross , Spira Alexander I. , Piotrowska Zofia , Costa Daniel B. , Tsao Anne S. , Patel Jyoti D. , Gadgeel Shirish M. , Bazhenova Lyudmila , Zhu Viola W. , West Howard L. , Mekhail Tarek , Gentzler Ryan D. , Nguyen Danny , Vincent Sylvie , Zhang Steven , Lin Jianchang , Bunn Veronica , Jin Shu , Li Shuanglian , Jänne Pasi A.
Published: July 2023

Supplemental Information
Table S4 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Authors: Kim Beom-Jun , Zheng Ze-Yi , Lei Jonathan T. , Holt Matthew V. , Chen Anran , Peng Jianheng , Fandino Diana , Singh Purba , Kennedy Hilda , Dou Yongchao , Chica-Parrado María del Rosario , Bikorimana Emmanuel , Ye Dan , Wang Yunguan , Hanker Ariella B. , Mohamed Nada , Hilsenbeck Susan G. , Lim Bora , Asirvatham Jaya Ruth , Sreekumar Arun , Zhang Bing , Miles George , Anurag Meenakshi , Ellis Matthew J. , Chang Eric C.
Published: July 2023

Table S4. NF1 protein levels as measured by KIPA-SureQuant in the PDX models.
FIGURE 5 from Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness
Authors: Senosain Maria-Fernanda , Zou Yong , Patel Khushbu , Zhao Shilin , Coullomb Alexis , Rowe Dianna J. , Lehman Jonathan M. , Irish Jonathan M. , Maldonado Fabien , Kammer Michael N. , Pancaldi Vera , Lopez Carlos F.
Published: July 2023

Profiling of LUAD TME by single-cell RNA-seq analysis. A, Uniform Manifold Approximation and Projection (UMAP) representation colored by cell type using all cells (left) and by density grouped by risk group (right). B, UMAP representation colored by gene expression of top lineage gene markers for each main cell type. Reclustering analysis for T cells (C), myeloid cells (D), and B cells (E). UMAP representation colored by cluster, followed by UMAP representation colored by gene expression of some subset representative markers. On the far right, we have UMAP by density grouped by risk group (top) and differential abundance analysis (bottom). Y axis corresponds to the fraction of cells per patient sample. ns, P > 0.05; *, P < 0.05; **, P < 0.001.
Table S3 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Authors: Kim Beom-Jun , Zheng Ze-Yi , Lei Jonathan T. , Holt Matthew V. , Chen Anran , Peng Jianheng , Fandino Diana , Singh Purba , Kennedy Hilda , Dou Yongchao , Chica-Parrado María del Rosario , Bikorimana Emmanuel , Ye Dan , Wang Yunguan , Hanker Ariella B. , Mohamed Nada , Hilsenbeck Susan G. , Lim Bora , Asirvatham Jaya Ruth , Sreekumar Arun , Zhang Bing , Miles George , Anurag Meenakshi , Ellis Matthew J. , Chang Eric C.
Published: July 2023

Table S3. H-scores of NF1 protein levels in patient and PDX tumors as determined by IHC.
Table S1 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Authors: Kim Beom-Jun , Zheng Ze-Yi , Lei Jonathan T. , Holt Matthew V. , Chen Anran , Peng Jianheng , Fandino Diana , Singh Purba , Kennedy Hilda , Dou Yongchao , Chica-Parrado María del Rosario , Bikorimana Emmanuel , Ye Dan , Wang Yunguan , Hanker Ariella B. , Mohamed Nada , Hilsenbeck Susan G. , Lim Bora , Asirvatham Jaya Ruth , Sreekumar Arun , Zhang Bing , Miles George , Anurag Meenakshi , Ellis Matthew J. , Chang Eric C.
Published: July 2023

Table S1. Correlation between levels of NF1 and protein kinases in the PDXs.
FIGURE 2 from Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness
Authors: Senosain Maria-Fernanda , Zou Yong , Patel Khushbu , Zhao Shilin , Coullomb Alexis , Rowe Dianna J. , Lehman Jonathan M. , Irish Jonathan M. , Maldonado Fabien , Kammer Michael N. , Pancaldi Vera , Lopez Carlos F.
Published: July 2023

CyTOF analysis of LUAD samples reveal subsets associated with HLA-DR protein expression. A, Uniform Manifold Approximation and Projection (UMAP) representation colored by cell type [epithelial cancer cells (blue), endothelial cells (red), fibroblasts/mesenchymal cells (green), CD8+ T cells (orange), CD4+ T cells (pink), double-negative T cells (yellow), myeloid cells (purple), and other immune cells (gray)], by density, by patient ID, and by protein expression of lineage markers (bottom). B, Analysis workflow of the clustering by cell subset. C, Heat map of median protein expression per protein marker per cluster (left) and differential abundance analysis (right) for ECC (top) and fibroblast/mesenchymal cells (bottom). Y axis corresponds to the fraction of cells per patient sample. No star, P > 0.05; *, P < 0.05; **, P < 0.01; ***, P < 0.001. D, Spearman correlation analysis of the relative abundance of ECC3, 5 and Fmes 3 versus CD4+, CD8+ T cells, and myeloid cells, respectively.
Figure S4 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Authors: Kim Beom-Jun , Zheng Ze-Yi , Lei Jonathan T. , Holt Matthew V. , Chen Anran , Peng Jianheng , Fandino Diana , Singh Purba , Kennedy Hilda , Dou Yongchao , Chica-Parrado María del Rosario , Bikorimana Emmanuel , Ye Dan , Wang Yunguan , Hanker Ariella B. , Mohamed Nada , Hilsenbeck Susan G. , Lim Bora , Asirvatham Jaya Ruth , Sreekumar Arun , Zhang Bing , Miles George , Anurag Meenakshi , Ellis Matthew J. , Chang Eric C.
Published: July 2023

Figure S4. Tumor contents in the biopsy are comparable between the treatment sensitive and resistant groups.
FIGURE 6 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Authors: Kim Beom-Jun , Zheng Ze-Yi , Lei Jonathan T. , Holt Matthew V. , Chen Anran , Peng Jianheng , Fandino Diana , Singh Purba , Kennedy Hilda , Dou Yongchao , Chica-Parrado María del Rosario , Bikorimana Emmanuel , Ye Dan , Wang Yunguan , Hanker Ariella B. , Mohamed Nada , Hilsenbeck Susan G. , Lim Bora , Asirvatham Jaya Ruth , Sreekumar Arun , Zhang Bing , Miles George , Anurag Meenakshi , Ellis Matthew J. , Chang Eric C.
Published: July 2023

Assess the impact of NF1 protein levels on treatment responses in patient tumors. A, NF1 protein levels quantified by KIPA SureQuant (normalized by TIC) in each of the biopsy (orange circles) from a given POL patient were plotted and median is marked by a solid blue line. Blue and red dotted lines mark 75% and 25% quartile, respectively. The latter corresponds to 0.6 fmol/TIC. B, Tumors stratified by the 0.6 fmol/TIC cutoff were defined as NF1-high and NF1-low and their Ki67 levels pre-and post-letrozole treatment were plotted. P values were determined by paired t test.
FIGURE 1 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Authors: Kim Beom-Jun , Zheng Ze-Yi , Lei Jonathan T. , Holt Matthew V. , Chen Anran , Peng Jianheng , Fandino Diana , Singh Purba , Kennedy Hilda , Dou Yongchao , Chica-Parrado María del Rosario , Bikorimana Emmanuel , Ye Dan , Wang Yunguan , Hanker Ariella B. , Mohamed Nada , Hilsenbeck Susan G. , Lim Bora , Asirvatham Jaya Ruth , Sreekumar Arun , Zhang Bing , Miles George , Anurag Meenakshi , Ellis Matthew J. , Chang Eric C.
Published: July 2023

CNA complements mRNA for assessing NF1 status in ER+ PDX models. Sample map of 22 ER+ PDXs showing E2-dependent growth, patient disease state of sample used to generate the PDX, presence of recurring ESR1 mutations/fusions, mutation status of TP53, PIK3CA, and NF1. Also shown is NF1 CNAs where “0” represents no change in copy number, “–1” as shallow deletion, and “+1” and “+2” low- and high-level amplification, respectively. Full-length NF1 (NM_001042492) mRNA levels were determined by RNA-seq. The bottom panel shows NF1 exon expression by RNA-seq across NF1 CDS in PDX tumors.
Supplementary Table S1 from Natural killer cell activation by Ubiquitin-specific protease 6 (USP6) mediates tumor suppression in Ewing sarcoma
Authors: Jain Kanika , Henrich Ian C , Quick Laura , Young Robert , Mondal Shreya , Oliveira Andre M. , Blobel Gerd A. , Chou Margaret M
Published: July 2023

Flow antibodies used
Supplementary Figure S4 from Natural killer cell activation by Ubiquitin-specific protease 6 (USP6) mediates tumor suppression in Ewing sarcoma
Authors: Jain Kanika , Henrich Ian C , Quick Laura , Young Robert , Mondal Shreya , Oliveira Andre M. , Blobel Gerd A. , Chou Margaret M
Published: July 2023

RT-qPCR of surface markers induced by USP6
Supplementary Figure S3 from Natural killer cell activation by Ubiquitin-specific protease 6 (USP6) mediates tumor suppression in Ewing sarcoma
Authors: Jain Kanika , Henrich Ian C , Quick Laura , Young Robert , Mondal Shreya , Oliveira Andre M. , Blobel Gerd A. , Chou Margaret M
Published: July 2023

Primary mouse and human NK killing assays
Supplementary Figure S2 from Natural killer cell activation by Ubiquitin-specific protease 6 (USP6) mediates tumor suppression in Ewing sarcoma
Authors: Jain Kanika , Henrich Ian C , Quick Laura , Young Robert , Mondal Shreya , Oliveira Andre M. , Blobel Gerd A. , Chou Margaret M
Published: July 2023

Gating for NK populations and intratumoral quantification
Supplementary Figure S1 from Natural killer cell activation by Ubiquitin-specific protease 6 (USP6) mediates tumor suppression in Ewing sarcoma
Authors: Jain Kanika , Henrich Ian C , Quick Laura , Young Robert , Mondal Shreya , Oliveira Andre M. , Blobel Gerd A. , Chou Margaret M
Published: July 2023

NK depletion confirmation
Data from Integrated multi-omics analysis of early lung adenocarcinoma links tumor biological features with predicted indolence or aggressiveness
Authors: Senosain Maria-Fernanda , Zou Yong , Patel Khushbu , Zhao Shilin , Coullomb Alexis , Rowe Dianna J , Lehman Jonathan M , Irish Jonathan Michael , Maldonado Fabien , Kammer Michael N , Pancaldi Vera , Lopez Carlos F
Published: July 2023

Abstract
Lung adenocarcinoma (LUAD) is a heterogeneous group of tumors associated with different survival rates, even when detected at an early stage. Here, we aim to investigate the biological determinants of early LUAD indolence or aggressiveness using radiomics as a surrogate of behavior. We present a set of 92 LUAD patients with data collected across different methodologies. Patients were risk-stratified using the Computed Tomography–based Score Indicative of Lung cancer Aggression (SILA) tool (0=least aggressive, 1= most aggressive). We grouped the patients as indolent (x <= 0.4, n=14), intermediate (0.4 > x <= 0.6, n=27) and aggressive (0.6 > x <= 1, n=52). Using CyTOF, we identified subpopulations with high HLA-DR expression that were associated with indolent behavior. In the RNA-Seq dataset, pathways related to immune response were associated with indolent behavior, while pathways associated with cell cycle and proliferation were associated with aggressive behavior. We extracted quantitative radiomics features from the CT scans of the patients. Integrating these datasets we identified four feature signatures and four patient clusters that were associated with survival. Using single-cell RNA-Seq, we found that indolent tumors had significantly more T cells and less B cells than aggressive tumors, and that the latter had a higher abundance of regulatory T cells and T helpers. In conclusion, we were able to uncover a correspondence between radiomics and tumor biology, which could improve the discrimination between indolent and aggressive LUAD tumors, enhance our knowledge in the biology of these tumors and offer novel and personalized avenues for intervention.
Clinical and Prognostic Biomarker Value of Blood-Circulating Inflammatory Cytokines in Hepatocellular Carcinoma
Authors: Chamseddine Shadi , Mohamed Yehia I. , Lee Sunyoung S. , Yao James C. , Hu Zishuo Ian , Tran Cao Hop S. , Xiao Lianchun , Sun Ryan , Morris Jeffrey S. , Hatia Rikita I. , Hassan Manal , Duda Dan G. , Diab Maria , Mohamed Amr , Nassar Ahmed , Datar Saumil , Amin Hesham M. , Kaseb Ahmed Omar
Published: July 2023

Introduction: Circulating inflammatory cytokines play critical roles in tumor-associated inflammation and immune responses. Recent data have suggested that several interleukins (ILs) mediate carcinogenesis in hepatocellular carcinoma (HCC). However, the predictive and prognostic value of circulating ILs is yet to be validated. Our study aimed to evaluate the association of the serum ILs with overall survival (OS) and clinicopathologic features in a large cohort of HCC patients. Methods: We prospectively collected data and serum samples from 767 HCC patients treated at the University of Texas MD Anderson Cancer Center between 2001 and 2014, with a median follow-up of 67.4 months (95% confidence interval [CI]: 52.5, 83.3). Biomarker association with OS was evaluated by the log-rank method. Results: The median OS in this cohort was 14.2 months (95% CI: 12, 16.1 months). Clinicopathologic features were more advanced, and OS was significantly inferior in patients with high circulating levels of IL1-R1, IL-6, IL-8, IL-10, IL-15, IL-16, and IL-18. Conclusion: Our study shows that several serum IL levels are valid prognostic biomarker candidates and potential targets for therapy in HCC.
Developing a digital learning environment team-based project to support online learning in Indonesia
Authors: Fadhli Rahmat , Suharyadi Aris , Firdaus Fery Muhamad , Bustari Meilina
Published: July 2023

The purpose of this study is to describe the process of developing learning tools to support a team-based digital learning environment (DLE) project in library management courses. The analyze, design, develop, implement, and evaluate (ADDIE) development model is used in this study to investigate this type of research and development (R&D). The study included 162 students from four universities in Indonesia. Data is gathered through media and material validation questionnaires, learning management system (LMS) user satisfaction questionnaires, and lesson learning outcomes tests. Instruments include media and material validation sheets, LMS user satisfaction instruments, and lesson learning outcomes test instrument sheets. The media validation test and material results show that all media can be used with minor adjustments. Students have responded positively to the DLE application for online learning at universities. Learning tools are critical for raising motivation and accomplishing course learning outcomes. In the future, the evolution of learning media may be accompanied by the evolution of learning designs. As a result, the learning process and learning outcomes can be optimized. This study makes recommendations for revamping learning materials, media, and design to increase student motivation to learn.
Online learning in Indonesian higher education: New indicators during the COVID-19 pandemic
Authors: Haryani Fairusy Fitria , Sarwanto Sarwanto , Maryono Dwi
Published: July 2023

The COVID-19 pandemic has increasingly demanded the implementation of online learning in Indonesia. This study aimed to determine the indicators influencing the effectiveness of online learning in Indonesian higher education during the COVID-19 pandemic. The study employed a mixed-methods approach. We conducted an online survey of 201 lecturers teaching courses during the even semester of 2019/2020 and 1,983 students in 18 higher educations then followed up with an online interview with the lecturers, the head of the study program, and the institute of quality assurance of four chosen institutions. The results showed that besides the lecturer’s information technology capabilities, the new indicators of online learning effectiveness in higher education during the COVID-19 pandemic were the availability of assessment guidelines, semester learning plan guidelines, academic position, type of lecturer publication, lecturer certification, and workload.
Teacher-parent collaboration for developing student character in online learning
Authors: Aziz Rahmat , Susilowati Meinarni , Masturin Masturin , Prasojo Zaenuddin Hudi
Published: July 2023

Teachers, parents, and students have had difficulty with character development exercises in online learning programs. Students’ character quality has suffered as a result of these issues. This study described the essence of reading fondness, learning discipline, and social care in developing the students’ character development. In addition, this study also aimed to analyze the role of teachers and parents in character development during the online learning process. Students, teachers, and parents provided information via online questionnaires and interviews. Descriptive quantitative analysis, thematic analysis, and reflective thinking were used to analyze the data. The findings revealed that teachers and parents faced challenges that impacted student character quality. Teachers and parents have limited opportunities to shape a students’ character. Instead, they must collaborate to develop it. The limitation of this study lies in the online data collection process, thus suggesting the need to use a more in-depth method to gain a more comprehensive understanding of the case.
Chemistry private tutoring in Malaysia
Authors: Suan Ee Low , Ibrahim Nor Hasniza , Surif Johari
Published: July 2023

The unsatisfactory result obtained by Malaysian secondary students in international assessment has caused the Ministry of Education to put much effort into structuring the curriculum. Variety of teaching pedagogies has been suggested but not all the approaches are applicable due to many constraints. It leads students to enroll in extra private tutoring classes after their regular school hours. This research aimed to identify the reason students attend chemistry private tutoring, to explore the teaching pedagogies used in chemistry private tutoring, and to identify the perceptions of students on the pedagogies used in chemistry private tutoring. This is an exploratory qualitative study that is conducted among six tutors and five students in Malaysia. The result was analyzed through thematic analysis. Interestingly, the study has indicated that despite improving their academic result, students attend tuition to enhance their understanding and knowledge of chemistry as they were ably exposed to a variety of teaching methods. A new insight on pedagogies used in private tutoring lessons was determined, such as deductive learning, inquiry-based teaching and contextualization. It is found that student’s learning needs are highly emphasized in tuition classes. Students experience more meaningful learning and obtain interesting learning experiences in tuition.
Systematic review: Factors influencing creativity in the design discipline and assessment criteria
Authors: Zetian Dai , Tan Wee Hoe , Shumin Ren , Menglin Zhang , Amini Mansour , Shoushan Wang
Published: July 2023

Using psychological instrument to measure creativity is getting popular in design research. However, unlike quantifying general creativity using divergent thinking, the complexity and interdisciplinarity of the design discipline have made it difficult to explore research on design creativity. Therefore, to better quantify and measure design creativity, 31 relevant studies were retrieved by Google Scholar and the University of London Common Research in this article. This study summarizes the factors that influence design creativity in different design disciplines, the rules for setting the internal dimensions, and the valid instruments for measuring design creativity. The factors affecting design creativity can be divided into internal factors (aesthetic, spatial ability, and ambiguity tolerance) and external factors (environment and visual stimulation). Among these factors, different instruments and evaluation criteria considerably impact the result, while the measurement of design creativity is still not mature enough. A single scale evaluation or creative task evaluation cannot comprehensively evaluate the design creativity, which consists of aesthetic, functional, and technical aspects. In addition, the reference value of ordinary creativity remains to be further discussed in design. Under some professional design fields, the effect of widely recognized factors closely related to creativity, such as divergent thinking, imagination, and personality, is insignificant.
Exploration of factors affecting changes in student learning behavior: A systematic literature review
Authors: Mutiawati Mutiawati , Mailizar Mailizar , Johar Rahmah , Ramli Marwan
Published: July 2023

The general learning behavior has a major impact on the psychological and mental adjustment of students to learn. Therefore, this study reviews relevant studies on the factors causing changes in student learning behavior. The review used PRISMA, so several stages were carried out to filter and collect relevant information. The results of the synthesis revealed 19 broad factors influencing student learning behavior. Furthermore, these factors can be seen in more detail in four main groupings: i) Student learning behavior in the classroom; ii) Student learning behavior outside the classroom; iii) Student learning motivation; and iv) Student learning behavior results. Student learning behavior in the classroom is influenced by motivation, reflection, learning satisfaction, and learning activities. Meanwhile, student learning behavior outside the classroom is influenced by technology, independent learning abilities, learning resources, learning environment, and students’ internal conditions. The final result showed that students with a positive learning environment consistently acquire good knowledge in achieving learning objectives. There are many challenges in forming good student learning behavior. Therefore, this study benefits the education experts, counselors, teachers, parents, and the learning environment by increasing student motivation and satisfaction in learning to minimize the negative impact of changes in student learning behavior.
Exploring the pre-service basic science teachers’ misconceptions using the six-tier diagnostic test
Authors: Imaduddin Muhamad , Shofa Muhammad Mujahidus , Riza Muhammad Fatkhur , Fikri Achmad Ali
Published: July 2023

This study explored the pre-service basic science teachers’ misconceptions using a six-tier diagnostic (STD) test. This study used a cross-sectional survey research model with respondents, namely pre-service basic science teachers (PBSTs) who are first-year students. The six-tier diagnostic test consisted of three questions about change in matter (CIM), classification of matter (COM), and separation of mixtures (SOM). Each test package consists of six questions ranging from questions at the macroscopic level, microscopic communication, level of confidence, symbolic visualization to represent microscopic conditions, and self-confidence in representing concepts. The combination of answers and decisions in six-tier diagnostic includes scientific conception (SC), almost scientific conception (ASC), lack of confidence (LC), lack of knowledge (LK), misconception (MSC), have no conception (HNC). The study showed that the conceptual mastery condition is dominated by the misconceptions (MSC) category. The condition for pre-service basic science teachers’ mastery concepts having the most scientific conception category is related to changes in matter (CIM), while the condition that shows the least scientific conception category is related to material classification (COM). The results can map the conditions of mastery of the pre-service basic science teachers’ concept so that strategies can be designed to correct the emerging misconceptions.
Undergraduate students’ modular experiences in learning mathematics in the new normal education
Authors: Gaganao Rovinson Deladia , Discar Rey Naranja
Published: July 2023

The modular approach has been proven to be an effective tool in mathematics learning. However, this approach presents challenges regarding students’ learning. Hence, this study was conducted to determine and compare the modular experiences of 55 Bachelor of Secondary Education (BSED) Math students of Eastern Samar State University (ESSU) Salcedo based on gender, age, and year level. The study utilized a descriptive-comparative design and a survey questionnaire. Percentage, mean, t-test, and analysis of variance (ANOVA) were used to treat the data. The study revealed that respondents were satisfied with their modular experience in learning mathematics in the new normal education. Specifically, the respondents rated their experience satisfactory in good teaching, high in clear outcomes, manageable in appropriate workload, moderate in appropriate assessment, and average in generic skills. Furthermore, the study found a significant difference in good teaching, clear outcomes, appropriate workload, appropriate assessment, generic skills, and satisfaction with modular learning across the respondents’ year level, but insignificant across age and gender. Based on the findings, it is recommended that teachers should attend intensive seminars and training on current trends in math teaching and module development. Modules’ quality must be improved considering the workload, assessment, outcomes, and skills development.
Indonesian national assessment support: Can RE-STEM Android app improve students’ scientific literacy skills?
Authors: Subali Bambang , Ellianawati Ellianawati , Faizah Zulfatul , Sidiq Mohamad
Published: July 2023

The Indonesian National Assessment set by the government is in line with the Program for International Student Assessment (PISA) assessment which includes students’ scientific literacy skills for a 21st century education succeeds. This study determined the increase in students’ scientific literacy skills through ethnoscience, science, technology, engineering, mathematics or ethno-STEM learning assisted by RE-STEM App. A quasi-experimental design with the type of one-group pretest-posttest design was used to obtain data from the treatment. There were 102 students involved by purposive sampling technique from a 338 population of grade 8 students in a rural secondary school in Central Java, Indonesia. RE-STEM App involves four themes of Indonesian cultures as learning resources, namely tarutu, tin-telephone, calung, and bird whistle. This study revealed that students’ scientific literacy skills increased by 61.33% in the medium category in general, also in each aspect. Research data indicate that the RE-STEM App has supported teachers to improve students’ scientific literacy skills. By applying ethno-STEM through RE-STEM App, teachers can help students to investigate the science concepts in ethnoscience. This strategy proved that ethnoscience aspect can be an important factor in developing students’ scientific literacy skills.
Indonesian language teachers’ teaching performance and students’ learning outcomes
Authors: Werang Basilius Redan , Suarjana I Made , Dewi Kariyanti Kumala , Asaloei Sandra Ingried
Published: July 2023

Teachers are an important component in modern society because they have a very extraordinary role in the lives of children, especially in the early years of their development. This study aimed to describe the teaching performance of Indonesian language teachers and how it affects the Indonesian language learning outcomes of state junior high school students of Merauke, Indonesia. To achieve this goal, the researchers used a quantitative approach with a survey research design. Data on the teaching performance of Indonesian language teachers were obtained by distributing a survey questionnaire to students who had been designated as respondents, while data on students’ learning outcomes were obtained by getting their academic transcripts. Obtained data were statistically analyzed using the software statistical package for the social sciences (SPSS) version 21. The results showed that the teaching performance of Indonesian language teachers has a significant positive effect on the learning outcomes of the state junior high school students of Merauke, Indonesia. The result indicated the importance of the school principals to focus their efforts to improve the teaching performance of Indonesian language teachers in order that students’ learning outcomes are adequately addressed.
Blended learning in elementary school science learning: A systematic literature review
Authors: Purnama Herwulan Irine , Wilujeng Insih , Abdul Jabar Cepi Safruddin
Published: July 2023

This article presents a systematic literature review (SLR) on blended learning in elementary school science learning. The method used is SLR and PRISMA protocol with the stages of identification, screening, eligibility, inclusion, abstraction, and data analysis assisted by Publish or Perish 7, Mendeley, VOSviewer, and NVIVO 12 Plus applications. The findings in Scopus found 906 articles, and then filtered them according to compatible themes into 54 pieces. The topic findings were blended learning, science learning, elementary school, the concept of blended learning, type of blended learning, the impact of blended learning, flipped learning, flip classroom, distance learning, distance education, active learning, online learning, blended and face-to-face learning, STEM, which were directly and indirectly connected. The 54 articles were analyzed according to the defined topics through NVIVO 12 Plus, and the results were described according to the research questions. The research findings explain that blended learning in elementary school science learning is a mixed learning model with the integration of synchronous-asynchronous technology, information, and communication technology (ICT), technological pedagogical content knowledge (TPACK), multimedia, and Android from planning to evaluation. The most studied type of blended learning is the flipped classroom, with as many as 11 studies. The implementation of blended learning has more positive impacts on students and teachers. Future research needs to explore blended learning in elementary school science learning and what students, teachers, and technological developments need.
Mentoring relationships as an enhancer of mentees’ success
Authors: Ismail Azman , Mokhtar Aminudin , Tunca Mustafa Zihni , Genturk Mehmet , Ibrahim Zalina
Published: July 2023

A review of the recent studies about tertiary education student development reveals that when mentors do not practice effective relationships in mentoring programs regardless of how well designed the mentoring programs are, the goals will not be achieved. Even though many studies have been done, the role of mentoring relationships as a vital predicting variable is largely ignored in the tertiary education mentoring research literature. Hence, the current study is done to investigate the effect of mentoring relationships on mentees’ success. A cross-sectional method is used to collect survey questionnaires from undergraduate students in teaching-based universities in Sarawak. The SmartPLS is utilized to assess the quality of the study instrument and test the research hypotheses. The findings of the SmartPLS path model analysis reveal that implementation of comfortable communication and sufficient support by mentors in structured and unstructured mentoring activities has been an important antecedent of mentees’ career and leadership development. Thus, this finding may be used as significant guidelines by practitioners to understand diverse paradigms of mentoring relationship construct and planning collaborative and developmental mentoring programs to prepare mentees to become potential leaders in the 21st century of global market challenges and difficulties.
Environmental supplement book of flood disaster for university students
Authors: Ichsan Ilmi Zajuli , Purwanto Agung , Rahmayanti Henita
Published: July 2023

Solving natural disaster problems, especially floods, requires community participation. One of the efforts that can be done is by implementing the environmental supplement book of flood disasters based on innovation learning model for natural science and environmental learning (ILMIZI). The purpose of this research was to implement a supplementary book to improve university students’ higher order thinking skills (HOTS) and pro-environmental behavior (PEB). This was an experiment method consisting of experimental class and control class. The samples were 115 university students with 60 university students in experimental class and 55 university students in control class. The data analysis was a t-test that aims to test the significance of the difference in the mean HOTS and PEB scores for the experimental class and the control class. In addition to the t-test, descriptive analysis was also carried out by comparing the HOTS and PEB scores between the experimental class and the control class. The results of this study indicated that the t-test results were significant, which means that supplement books could increase HOTS and PEB of university students. The results of the descriptive analysis showed that university students were still weak in flood mitigation efforts related to the provision of disaster evacuation tools. In an effort to prevent disasters, it was necessary to innovate environmental learning to support sustainability. A conclusion can be drawn that the use of supplementary books can increase university students’ HOTS and PEB.
A systematic review on interventions for children with dyslexia
Authors: Wai Wai Lim , Kee Jiar Yeo , Handayani Lina
Published: July 2023

Dyslexia is often described as the most common learning disability among the students that affect their ability to read and write. Children with dyslexia persist to their reading difficulties into adolescence and adulthood if without effective intervention and instruction. Therefore, this paper aims to review on the current state of available interventions for children with dyslexia in Malaysia and compare the interventions conducted outside Malaysia instead of to identify the frequently used for assistive technology tools in improving literacy skills. A total of 30 articles published between 2009 and 2021 that met the inclusive criteria were downloaded from electronic databases such as Scopus, SpringerLink and ScienceDirect. The interventions were divided into two categories which are phonological-based and assistive technology-based. The findings indicated that most of the interventions are focused on assistive technology tools and mobile learning applications become the favorite choice in Malaysia to assist students with dyslexia in ameliorating their learning difficulties. However, the developed mobile learning applications are not focused on teaching phonics and combined all three language skills (reading, spelling, and writing) in an application. Hence, it is imperative that researchers in Malaysia take into account to develop more mobile learning applications that focus on English language phonics and encompass three language skills (reading, spelling and writing) in an application for students with dyslexia.