bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S5 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Figure S5 illustrates the estimated time-dependent ROC curves using the PCCox and PCCox BLUP models in the validation cohort for tamoxifen treatment. The area under the ROC curve (AUC) and its corresponding 95% confidence interval for the four sets of s and tau are embedded within the plots.
Supplementary Figure S1 from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Supplementary Figure S1 shows the estimated discontinuation curve in patients treated with anastrozole and tamoxifen, along with the p-value associated with the log-rank test.
Data from Dynamic Risk Prediction of Treatment Discontinuation Using Patient-Reported Outcomes Data in the Phase III NSABP B-35 Trial
Authors: Calsavara Vinicius F. , Henry Norah L. , Hays Ron D. , Kim Sungjin , Luu Michael , Diniz Márcio A. , Gresham Gillian , Cecchini Reena S. , Yothers Greg , Ganz Patricia A. , Rogatko André , Tighiouart Mourad
Published: November 2023

Abstract
Predicting an individual's risk of treatment discontinuation is critical for the implementation of precision chemoprevention. We developed partly conditional survival models to predict discontinuation of tamoxifen or anastrozole using patient-reported outcome (PRO) data from postmenopausal women with ductal carcinoma in situ enrolled in the NSABP B-35 clinical trial. In a secondary analysis of the NSABP B-35 clinical trial PRO data, we proposed two models for treatment discontinuation within each treatment arm (anastrozole or tamoxifen treated patients) using partly conditional Cox-type models with time-dependent covariates. A 70/30 split of the sample was used for the training and validation datasets. The predictive performance of the models was evaluated using calibration and discrimination measures based on the Brier score and AUC from time-dependent ROC curves. The predictive models stratified high-risk versus low-risk early discontinuation at a 6-month horizon. For anastrozole-treated patients, predictive factors included baseline body mass index (BMI) and longitudinal patient-reported symptoms such as insomnia, joint pain, hot flashes, headaches, gynecologic symptoms, and vaginal discharge, all collected up to 12 months [Brier score, 0.039; AUC, 0.76; 95% confidence interval (CI), 0.57–0.95]. As for tamoxifen-treated patients, predictive factors included baseline BMI, and time-dependent covariates: cognitive problems, feelings of happiness, calmness, weight problems, and pain (Brier score, 0.032; AUC, 0.78; 95% CI, 0.65–0.91). A real-time calculator based on these models was developed in Shiny to create a web-based application with a future goal to aid healthcare professionals in decision-making.
Prevention Relevance:
The dynamic prediction provided by partly conditional models offers valuable insights into the treatment discontinuation risks using PRO data collected over time from clinical trial participants. This tool may benefit healthcare professionals in identifying patients at high risk of premature treatment discontinuation and support interventions to prevent potential discontinuation.
Supplementary Table S9 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Top 5% transcription factor cistromes enriched at liver transposable elements
Supplementary Table S5 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Differentially enriched transposable element families between pluripotent stem cells and benign prostate tissue state
Supplementary Table S16 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

Onco-exaptated transposable elements in reprogrammed and constant PCa patients
Table S9 from Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways
Authors: Venneti Sriram , Kawakibi Abed Rahman , Ji Sunjong , Waszak Sebastian M. , Sweha Stefan R. , Mota Mateus , Pun Matthew , Deogharkar Akash , Chung Chan , Tarapore Rohinton S. , Ramage Samuel , Chi Andrew , Wen Patrick Y. , Arrillaga-Romany Isabel , Batchelor Tracy T. , Butowski Nicholas A. , Sumrall Ashley , Shonka Nicole , Harrison Rebecca A. , de Groot John , Mehta Minesh , Hall Matthew D. , Daghistani Doured , Cloughesy Timothy F. , Ellingson Benjamin M. , Beccaria Kevin , Varlet Pascale , Kim Michelle M. , Umemura Yoshie , Garton Hugh , Franson Andrea , Schwartz Jonathan , Jain Rajan , Kachman Maureen , Baum Heidi , Burant Charles F. , Mottl Sophie L. , Cartaxo Rodrigo T. , John Vishal , Messinger Dana , Qin Tingting , Peterson Erik , Sajjakulnukit Peter , Ravi Karthik , Waugh Alyssa , Walling Dustin , Ding Yujie , Xia Ziyun , Schwendeman Anna , Hawes Debra , Yang Fusheng , Judkins Alexander R. , Wahl Daniel , Lyssiotis Costas A. , de la Nava Daniel , Alonso Marta M. , Eze Augustine , Spitzer Jasper , Schmidt Susanne V. , Duchatel Ryan J. , Dun Matthew D. , Cain Jason E. , Jiang Li , Stopka Sylwia A. , Baquer Gerard , Regan Michael S. , Filbin Mariella G. , Agar Nathalie Y.R. , Zhao Lili , Kumar-Sinha Chandan , Mody Rajen , Chinnaiyan Arul , Kurokawa Ryo , Pratt Drew , Yadav Viveka N. , Grill Jacques , Kline Cassie , Mueller Sabine , Resnick Adam , Nazarian Javad , Allen Joshua E. , Odia Yazmin , Gardner Sharon L. , Koschmann Carl
Published: November 2023

Upregulated and downregulated genes in DIPG007 cells treated with ONC201 versus vehicle.
Supplementary Figure S7 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

This figure complements Figure 5 showcasing AR profiling and transcriptomic analysis results in CRISPRi 22Rv1 clones #1 and #3 nucleofected with control or Tigger3a gRNA combos (clone #2 is showcased in Figure 5)
Table S6 from Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways
Authors: Venneti Sriram , Kawakibi Abed Rahman , Ji Sunjong , Waszak Sebastian M. , Sweha Stefan R. , Mota Mateus , Pun Matthew , Deogharkar Akash , Chung Chan , Tarapore Rohinton S. , Ramage Samuel , Chi Andrew , Wen Patrick Y. , Arrillaga-Romany Isabel , Batchelor Tracy T. , Butowski Nicholas A. , Sumrall Ashley , Shonka Nicole , Harrison Rebecca A. , de Groot John , Mehta Minesh , Hall Matthew D. , Daghistani Doured , Cloughesy Timothy F. , Ellingson Benjamin M. , Beccaria Kevin , Varlet Pascale , Kim Michelle M. , Umemura Yoshie , Garton Hugh , Franson Andrea , Schwartz Jonathan , Jain Rajan , Kachman Maureen , Baum Heidi , Burant Charles F. , Mottl Sophie L. , Cartaxo Rodrigo T. , John Vishal , Messinger Dana , Qin Tingting , Peterson Erik , Sajjakulnukit Peter , Ravi Karthik , Waugh Alyssa , Walling Dustin , Ding Yujie , Xia Ziyun , Schwendeman Anna , Hawes Debra , Yang Fusheng , Judkins Alexander R. , Wahl Daniel , Lyssiotis Costas A. , de la Nava Daniel , Alonso Marta M. , Eze Augustine , Spitzer Jasper , Schmidt Susanne V. , Duchatel Ryan J. , Dun Matthew D. , Cain Jason E. , Jiang Li , Stopka Sylwia A. , Baquer Gerard , Regan Michael S. , Filbin Mariella G. , Agar Nathalie Y.R. , Zhao Lili , Kumar-Sinha Chandan , Mody Rajen , Chinnaiyan Arul , Kurokawa Ryo , Pratt Drew , Yadav Viveka N. , Grill Jacques , Kline Cassie , Mueller Sabine , Resnick Adam , Nazarian Javad , Allen Joshua E. , Odia Yazmin , Gardner Sharon L. , Koschmann Carl
Published: November 2023

Radiographic response versus gene expression Spearman's correlation coefficient for all protein-coding genes.
Supplementary Figure S4 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

This figure complements Figure 4, showcasing the enrichment of Porto AR cistromes and AR motif over reprogrammed transposable element families (with the exception of Tigger3a and L1MB4 that are showcased in Figure 4)
Supplementary Figure S1 from Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu
Published: November 2023

This figure contains the roadmap for all the different datasets used in this study. It also showcases transcription factor and motif enrichment over transposable element families enriched in different normal tissues states
Table S11 from Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways
Authors: Venneti Sriram , Kawakibi Abed Rahman , Ji Sunjong , Waszak Sebastian M. , Sweha Stefan R. , Mota Mateus , Pun Matthew , Deogharkar Akash , Chung Chan , Tarapore Rohinton S. , Ramage Samuel , Chi Andrew , Wen Patrick Y. , Arrillaga-Romany Isabel , Batchelor Tracy T. , Butowski Nicholas A. , Sumrall Ashley , Shonka Nicole , Harrison Rebecca A. , de Groot John , Mehta Minesh , Hall Matthew D. , Daghistani Doured , Cloughesy Timothy F. , Ellingson Benjamin M. , Beccaria Kevin , Varlet Pascale , Kim Michelle M. , Umemura Yoshie , Garton Hugh , Franson Andrea , Schwartz Jonathan , Jain Rajan , Kachman Maureen , Baum Heidi , Burant Charles F. , Mottl Sophie L. , Cartaxo Rodrigo T. , John Vishal , Messinger Dana , Qin Tingting , Peterson Erik , Sajjakulnukit Peter , Ravi Karthik , Waugh Alyssa , Walling Dustin , Ding Yujie , Xia Ziyun , Schwendeman Anna , Hawes Debra , Yang Fusheng , Judkins Alexander R. , Wahl Daniel , Lyssiotis Costas A. , de la Nava Daniel , Alonso Marta M. , Eze Augustine , Spitzer Jasper , Schmidt Susanne V. , Duchatel Ryan J. , Dun Matthew D. , Cain Jason E. , Jiang Li , Stopka Sylwia A. , Baquer Gerard , Regan Michael S. , Filbin Mariella G. , Agar Nathalie Y.R. , Zhao Lili , Kumar-Sinha Chandan , Mody Rajen , Chinnaiyan Arul , Kurokawa Ryo , Pratt Drew , Yadav Viveka N. , Grill Jacques , Kline Cassie , Mueller Sabine , Resnick Adam , Nazarian Javad , Allen Joshua E. , Odia Yazmin , Gardner Sharon L. , Koschmann Carl
Published: November 2023

Volcano plot of differentially expressed genes in DIPG007 cells treated with ONC201 versus vehicle.
Figure 3 from STX-478, a Mutant-Selective, Allosteric PI3Kα Inhibitor Spares Metabolic Dysfunction and Improves Therapeutic Response in PI3Kα-Mutant Xenografts
Authors: Buckbinder Leonard , St. Jean David J. , Tieu Trang , Ladd Brendon , Hilbert Brendan , Wang Weixue , Alltucker Jacob T. , Manimala Samantha , Kryukov Gregory V. , Brooijmans Natasja , Dowdell Gregory , Jonsson Philip , Huff Michael , Guzman-Perez Angel , Jackson Erica L. , Goncalves Marcus D. , Stuart Darrin D.
Published: November 2023

The effect of STX-478 and alpelisib on glucose homeostasis. A, Tumor-naive female BALB/c nude mice were dosed for 5 days as indicated (n = 5/group) and subjected to an ITT. On day 5, animals were fasted for 6 hours and dosed with drug by oral administration (p.o.) as indicated 1 hour prior to the end of the fast (−1 hour). At T = 0, animals were dosed with 0.75 U/kg by intraperitoneal (i.p.) insulin administration. Blood glucose levels were monitored over time, with group mean and standard error mean (SEM) indicated. B, AUCs were calculated from A; the AUC of each treatment group was compared with the vehicle group using ordinary one-way ANOVA and Dunnett multiple comparisons tests. C, An OGTT was performed similarly to the ITT (A), except at T = 0, when mice were dosed with 2 g/kg glucose and blood glucose was monitored over time, with group mean and SEM indicated. D, AUCs were calculated from C and analyzed by one-way ANOVA as described in B.
Supplementary Figure S6 from MRTX1719 Is an MTA-Cooperative PRMT5 Inhibitor That Exhibits Synthetic Lethality in Preclinical Models and Patients with MTAP-Deleted Cancer
Authors: Engstrom Lars D. , Aranda Ruth , Waters Laura , Moya Krystal , Bowcut Vickie , Vegar Laura , Trinh David , Hebbert Allan , Smith Christopher R. , Kulyk Svitlana , Lawson J. David , He Leo , Hover Laura D. , Fernandez-Banet Julio , Hallin Jill , Vanderpool Darin , Briere David M. , Blaj Alice , Marx Matthew A. , Rodon Jordi , Offin Michael , Arbour Kathryn C. , Johnson Melissa L. , Kwiatkowski David J. , Jänne Pasi A. , Haddox Candace L. , Papadopoulos Kyriakos P. , Henry Jason T. , Leventakos Konstantinos , Christensen James G. , Shazer Ronald , Olson Peter
Published: November 2023

Supplemental in vitro and in vivo efficacy of MRTX1719
Supplementary Figure S1 from MRTX1719 Is an MTA-Cooperative PRMT5 Inhibitor That Exhibits Synthetic Lethality in Preclinical Models and Patients with MTAP-Deleted Cancer
Authors: Engstrom Lars D. , Aranda Ruth , Waters Laura , Moya Krystal , Bowcut Vickie , Vegar Laura , Trinh David , Hebbert Allan , Smith Christopher R. , Kulyk Svitlana , Lawson J. David , He Leo , Hover Laura D. , Fernandez-Banet Julio , Hallin Jill , Vanderpool Darin , Briere David M. , Blaj Alice , Marx Matthew A. , Rodon Jordi , Offin Michael , Arbour Kathryn C. , Johnson Melissa L. , Kwiatkowski David J. , Jänne Pasi A. , Haddox Candace L. , Papadopoulos Kyriakos P. , Henry Jason T. , Leventakos Konstantinos , Christensen James G. , Shazer Ronald , Olson Peter
Published: November 2023

SDMA and MTAP IHC TMA data
Supplementary Table Legends from BCL2 Inhibition Reveals a Dendritic Cell–Specific Immune Checkpoint That Controls Tumor Immunosurveillance
Authors: Zhao Liwei , Liu Peng , Mao Misha , Zhang Shuai , Bigenwald Camille , Dutertre Charles-Antoine , Lehmann Christian H.K. , Pan Hui , Paulhan Nicolas , Amon Lukas , Buqué Aitziber , Yamazaki Takahiro , Galluzzi Lorenzo , Kloeckner Benoit , Silvin Aymeric , Pan Yuhong , Chen Hui , Tian Ai-Ling , Ly Pierre , Dudziak Diana , Zitvogel Laurence , Kepp Oliver , Kroemer Guido
Published: November 2023

This file contains full legends to all supplmentary tables.
Supplementary Figure S6 from BCL2 Inhibition Reveals a Dendritic Cell–Specific Immune Checkpoint That Controls Tumor Immunosurveillance
Authors: Zhao Liwei , Liu Peng , Mao Misha , Zhang Shuai , Bigenwald Camille , Dutertre Charles-Antoine , Lehmann Christian H.K. , Pan Hui , Paulhan Nicolas , Amon Lukas , Buqué Aitziber , Yamazaki Takahiro , Galluzzi Lorenzo , Kloeckner Benoit , Silvin Aymeric , Pan Yuhong , Chen Hui , Tian Ai-Ling , Ly Pierre , Dudziak Diana , Zitvogel Laurence , Kepp Oliver , Kroemer Guido
Published: November 2023

Supplementary Figure S6 demonstrates the specific activation of the Type I conventional DC (cDC1) subset by BCL2 inhibitors in different mouse orthotopic cancer models.
Data from SHP2: A Pleiotropic Target at the Interface of Cancer and Its Microenvironment
Authors: Sodir Nicole M. , Pathria Gaurav , Adamkewicz Joanne I. , Kelley Elizabeth H. , Sudhamsu Jawahar , Merchant Mark , Chiarle Roberto , Maddalo Danilo
Published: November 2023

Abstract
The protein phosphatase SHP2/PTPN11 has been reported to be a key modulator of proliferative pathways in a wide range of malignancies. Intriguingly, SHP2 has also been described as a critical regulator of the tumor microenvironment. Based on this evidence SHP2 is considered a multifaceted target in cancer, spurring the notion that the development of direct inhibitors of SHP2 would provide the twofold benefit of tumor intrinsic and extrinsic inhibition. In this review, we will discuss the role of SHP2 in cancer and the tumor microenvironment, and the clinical strategies in which SHP2 inhibitors are leveraged as combination agents to improve therapeutic response.
Significance:
The SHP2 phosphatase functions as a pleiotropic factor, and its inhibition not only hinders tumor growth but also reshapes the tumor microenvironment. Although their single-agent activity may be limited, SHP2 inhibitors hold the potential of being key combination agents to enhance the depth and the durability of tumor response to therapy.
Data from MRTX1719 Is an MTA-Cooperative PRMT5 Inhibitor That Exhibits Synthetic Lethality in Preclinical Models and Patients with MTAP-Deleted Cancer
Authors: Engstrom Lars D. , Aranda Ruth , Waters Laura , Moya Krystal , Bowcut Vickie , Vegar Laura , Trinh David , Hebbert Allan , Smith Christopher R. , Kulyk Svitlana , Lawson J. David , He Leo , Hover Laura D. , Fernandez-Banet Julio , Hallin Jill , Vanderpool Darin , Briere David M. , Blaj Alice , Marx Matthew A. , Rodon Jordi , Offin Michael , Arbour Kathryn C. , Johnson Melissa L. , Kwiatkowski David J. , Jänne Pasi A. , Haddox Candace L. , Papadopoulos Kyriakos P. , Henry Jason T. , Leventakos Konstantinos , Christensen James G. , Shazer Ronald , Olson Peter
Published: November 2023

Abstract
Previous studies implicated protein arginine methyltransferase 5 (PRMT5) as a synthetic lethal target for MTAP-deleted (MTAP del) cancers; however, the pharmacologic characterization of small-molecule inhibitors that recapitulate the synthetic lethal phenotype has not been described. MRTX1719 selectively inhibited PRMT5 in the presence of MTA, which is elevated in MTAP del cancers, and inhibited PRMT5-dependent activity and cell viability with >70-fold selecti­vity in HCT116 MTAP del compared with HCT116 MTAP wild-type (WT) cells. MRTX1719 demonstrated dose-dependent antitumor activity and inhibition of PRMT5-dependent SDMA modification in MTAP del tumors. In contrast, MRTX1719 demonstrated minimal effects on SDMA and viability in MTAP WT tumor xenografts or hematopoietic cells. MRTX1719 demonstrated marked antitumor activity across a panel of xenograft models at well-tolerated doses. Early signs of clinical activity were observed including objective responses in patients with MTAP del melanoma, gallbladder adenocarcinoma, mesothelioma, non–small cell lung cancer, and malignant peripheral nerve sheath tumors from the phase I/II study.
Significance:
PRMT5 was identified as a synthetic lethal target for MTAP del cancers; however, previous PRMT5 inhibitors do not selectively target this genotype. The differentiated binding mode of MRTX1719 leverages the elevated MTA in MTAP del cancers and represents a promising therapy for the ∼10% of patients with cancer with this biomarker.

See related commentary by Mulvaney, p. 2310.

This article is featured in Selected Articles from This Issue, p. 2293
Supplementary Figure legends from EDIL3 as an Angiogenic Target of Immune Exclusion Following Checkpoint Blockade
Authors: Tabasum Saba , Thapa Dinesh , Giobbie-Hurder Anita , Weirather Jason L. , Campisi Marco , Schol Pieter J. , Li Xiaoyu , Li Jingjing , Yoon Charles H. , Manos Michael P. , Barbie David A. , Hodi F. Stephen
Published: November 2023

Supplementary Figure legends
Supplementary Figure 3 from EDIL3 as an Angiogenic Target of Immune Exclusion Following Checkpoint Blockade
Authors: Tabasum Saba , Thapa Dinesh , Giobbie-Hurder Anita , Weirather Jason L. , Campisi Marco , Schol Pieter J. , Li Xiaoyu , Li Jingjing , Yoon Charles H. , Manos Michael P. , Barbie David A. , Hodi F. Stephen
Published: November 2023

Pre-treatment (Pre) and post-treatment (Post) MFGE8 antibody titers to Ipi-Bev therapy in melanoma patients
Supplementary Figure Legend from Targeted Inhibition of lncRNA Malat1 Alters the Tumor Immune Microenvironment in Preclinical Syngeneic Mouse Models of Triple-Negative Breast Cancer
Authors: Adewunmi Oluwatoyosi , Shen Yichao , Zhang Xiang H.-F. , Rosen Jeffrey M.
Published: November 2023

Figure legend for all supplementary data
Supplementary Figure 7 from Targeted Inhibition of lncRNA Malat1 Alters the Tumor Immune Microenvironment in Preclinical Syngeneic Mouse Models of Triple-Negative Breast Cancer
Authors: Adewunmi Oluwatoyosi , Shen Yichao , Zhang Xiang H.-F. , Rosen Jeffrey M.
Published: November 2023

Supplementary Figure 7
Supplementary Figure 4 from Targeted Inhibition of lncRNA Malat1 Alters the Tumor Immune Microenvironment in Preclinical Syngeneic Mouse Models of Triple-Negative Breast Cancer
Authors: Adewunmi Oluwatoyosi , Shen Yichao , Zhang Xiang H.-F. , Rosen Jeffrey M.
Published: November 2023

Supplementary Figure 4
Supplementary Figure 3 from Targeted Inhibition of lncRNA Malat1 Alters the Tumor Immune Microenvironment in Preclinical Syngeneic Mouse Models of Triple-Negative Breast Cancer
Authors: Adewunmi Oluwatoyosi , Shen Yichao , Zhang Xiang H.-F. , Rosen Jeffrey M.
Published: November 2023

Supplementary Figure 3
Supplementary Figure 1 from Targeted Inhibition of lncRNA Malat1 Alters the Tumor Immune Microenvironment in Preclinical Syngeneic Mouse Models of Triple-Negative Breast Cancer
Authors: Adewunmi Oluwatoyosi , Shen Yichao , Zhang Xiang H.-F. , Rosen Jeffrey M.
Published: November 2023

Supplementary Figure 1
Supplementary Table 1 from Sequential Exposure to IL21 and IL15 During Human Natural Killer Cell Expansion Optimizes Yield and Function
Authors: Zhang Caimei , Kadu Siddhant , Xiao Yansen , Johnson Omar , Kelly Andre , O'Connor Roddy S. , Lai Meizan , Kong Hong , Srivatsa Sriram , Tai Victoria , Greenblatt Eli , Holmes Matthew , Riley James L. , June Carl H. , Sheppard Neil C.
Published: November 2023

Antibody list for 28-color Symphony A5 NK pane
Supplementary Figure 5 from Sequential Exposure to IL21 and IL15 During Human Natural Killer Cell Expansion Optimizes Yield and Function
Authors: Zhang Caimei , Kadu Siddhant , Xiao Yansen , Johnson Omar , Kelly Andre , O'Connor Roddy S. , Lai Meizan , Kong Hong , Srivatsa Sriram , Tai Victoria , Greenblatt Eli , Holmes Matthew , Riley James L. , June Carl H. , Sheppard Neil C.
Published: November 2023

Figure S5. Statistical analysis of the cytotoxicity of expanded-NK cells against different tumor targets and their degranulation.
Supplementary Figure 4 from Sequential Exposure to IL21 and IL15 During Human Natural Killer Cell Expansion Optimizes Yield and Function
Authors: Zhang Caimei , Kadu Siddhant , Xiao Yansen , Johnson Omar , Kelly Andre , O'Connor Roddy S. , Lai Meizan , Kong Hong , Srivatsa Sriram , Tai Victoria , Greenblatt Eli , Holmes Matthew , Riley James L. , June Carl H. , Sheppard Neil C.
Published: November 2023

Figure S4. Expressions of the immune checkpoints on freshly isolated-NK cells and expanded-NK cells
Table S4 from Clinical Correlates of Venetoclax-Based Combination Sensitivities to Augment Acute Myeloid Leukemia Therapy
Authors: Eide Christopher A. , Kurtz Stephen E. , Kaempf Andy , Long Nicola , Joshi Sunil Kumar , Nechiporuk Tamilla , Huang Ariane , Dibb Charles A. , Taylor Akosha , Bottomly Daniel , McWeeney Shannon K. , Minnier Jessica , Lachowiez Curtis A. , Saultz Jennifer N. , Swords Ronan T. , Agarwal Anupriya , Chang Bill H. , Druker Brian J. , Tyner Jeffrey W.
Published: November 2023

Associations with mutations, immunophenotype, and cytogenetics
Table S1 from Clinical Correlates of Venetoclax-Based Combination Sensitivities to Augment Acute Myeloid Leukemia Therapy
Authors: Eide Christopher A. , Kurtz Stephen E. , Kaempf Andy , Long Nicola , Joshi Sunil Kumar , Nechiporuk Tamilla , Huang Ariane , Dibb Charles A. , Taylor Akosha , Bottomly Daniel , McWeeney Shannon K. , Minnier Jessica , Lachowiez Curtis A. , Saultz Jennifer N. , Swords Ronan T. , Agarwal Anupriya , Chang Bill H. , Druker Brian J. , Tyner Jeffrey W.
Published: November 2023

Novel VEN combo partner drugs, targets, and status
Figure S1 from IVIg Use Associated with Ten-Fold Reduction of Serious Infections in Multiple Myeloma Patients Treated with Anti-BCMA Bispecific Antibodies
Authors: Lancman Guido , Parsa Kian , Kotlarz Krzysztof , Avery Lisa , Lurie Alaina , Lieberman-Cribbin Alex , Cho Hearn Jay , Parekh Samir S. , Richard Shambavi , Richter Joshua , Rodriguez Cesar , Rossi Adriana , Sanchez Larysa J. , Thibaud Santiago , Jagannath Sundar , Chari Ajai
Published: November 2023

Absolute neutrophil counts over time in individual patients
Data from Clinical Correlates of Venetoclax-Based Combination Sensitivities to Augment Acute Myeloid Leukemia Therapy
Authors: Eide Christopher A. , Kurtz Stephen E. , Kaempf Andy , Long Nicola , Joshi Sunil Kumar , Nechiporuk Tamilla , Huang Ariane , Dibb Charles A. , Taylor Akosha , Bottomly Daniel , McWeeney Shannon K. , Minnier Jessica , Lachowiez Curtis A. , Saultz Jennifer N. , Swords Ronan T. , Agarwal Anupriya , Chang Bill H. , Druker Brian J. , Tyner Jeffrey W.
Published: November 2023

Abstract
The BCL2 inhibitor venetoclax combined with the hypomethylating agent azacytidine shows significant clinical benefit in a subset of patients with acute myeloid leukemia (AML); however, resistance limits response and durability. We prospectively profiled the ex vivo activity of 25 venetoclax-inclusive combinations on primary AML patient samples to identify those with improved potency and synergy compared with venetoclax + azacytidine (Ven + azacytidine). Combination sensitivities correlated with tumor cell state to discern three patterns: primitive selectivity resembling Ven + azacytidine, monocytic selectivity, and broad efficacy independent of cell state. Incorporation of immunophenotype, mutation, and cytogenetic features further stratified combination sensitivity for distinct patient subtypes. We dissect the biology underlying the broad, cell state–independent efficacy for the combination of venetoclax plus the JAK1/2 inhibitor ruxolitinib. Together, these findings support opportunities for expanding the impact of venetoclax-based drug combinations in AML by leveraging clinical and molecular biomarkers associated with ex vivo responses.
Significance:
By mapping drug sensitivity data to clinical features and tumor cell state, we identify novel venetoclax combinations targeting patient subtypes who lack sensitivity to Ven + azacytidine. This provides a framework for a taxonomy of AML informed by readily available sets of clinical and genetic features obtained as part of standard care.

See related commentary by Becker, p. 437.

This article is featured in Selected Articles from This Issue, p. 419
Pseudosperma quercinum sp. nov. (Inocybaceae) from the Himalayan forests of Pakistan
Authors: NASEER AROOJ , JABEEN SANA , ASHFAQ AMMARA , AKBAR MAHRUKH , HUSSAIN SYED IFTIKHAR , KHALID ABDUL NASIR
Published: November 2023

A new species, Pseudosperma quercinum, is described and illustrated from Pakistan. The species is characterized by a campanulate to conico-convex pileus, with dark brown umbo and yellow-brown fibrillose streaks on a creamy white context, creamy white to light silvery-brown lamellae, a cylindrical stipe with a fibrillose, furfuraceous, or almost flocculose stipe apex, ellipsoid to phaseoliform basidiospores, and clavate to cylindrical cheilocystidia. Molecular phylogenetic analysis inferred from the nuclear rDNA internal transcribed spacer region (ITS) and larger subunit region (LSU) confirms this species as new. In addition, we present a key and a table of comparisons to other species of this genus from Pakistan.
A new subtropical species of goby of the genus Luciogobius (Gobiidae) from southwestern Japan
Authors: KOREEDA REO , MAEDA KEN , MOTOMURA HIROYUKI
Published: November 2023

Luciogobius griseus n. sp., belonging to the Luciogobius platycephalus complex, is described on the basis of 40 specimens from the Nansei Islands, southwestern Japan (subtropical area). The new species is generally found in intertidal gravel sediments subjected to freshwater runoff from springs on coastal lines or river mouths and is characterized by the following combination of characters: total second dorsal-fin rays 9–12 (modally 11); total anal-fin rays usually 12–14 (modally 13); pectoral-fin rays 12–15 (modally 13); vertebrae 17 or 18 + 23 or 24 = 40–42 (18 + 23 = 41); uppermost 2–4 (2–3) rays on pectoral fin free; 8–12 pectoral-fin rays branched (uppermost free rays and sometimes lowermost ray unbranched); pectoral-fin membrane not strongly concave anteriorly (except for free rays); pelvic fins united, forming a disk; head relatively short, 13.9–20.8% of standard length (SL); relatively short pre-pelvic fin, length 14.4–22.1% of SL; relatively long pre-dorsal fin, length 68.9–72.9% of SL; relatively long pre-anal fin, length 63.5–67.7% of SL; relatively short pelvic fin, length 2.8–4.7% of SL; distance between posterior end of pelvic fin and anus relatively long, 32.0–36.4% of SL (aforementioned morphometrics each distinguishing L. griseus n. sp. from other species in the L. platycephalus complex); and fresh specimens with greenish dark brown or gray body. A key to the L. platycephalus complex is provided, together with limited descriptions and remarks on the other two members of the complex.
Determination and Method Optimization of Lianjie Liyan Compound Mixture
Authors: Jiang Min , Lin Yin , Li Jinghua , Yang Haoran , Fang Yingquan
Published: November 2023

Euchresta japonica, Platycodon grandiflorum, Belamcanda chinensis, and Adenophora tetraphylla are the four medicinal substances that make up the Lianjie Liyan compound mixture, a type of compound preparation for treating throat diseases such as pharyngitis
and laryngeal carcinoma. The preparation has been used clinically for a long time and has been proven that it has curative properties in terms of alleviating pain and other symptoms. However, no quality control research on this preparation has been done yet. The pharmacological components
in the main quality control standards, including Oxymatrine, matrine, N-methylcytisine, platycoside-D in Platycodon grandiflorum, and irisaxanthin in Shegan, were analyzed to further standardize the clinically rational use of this preparation and prevent the occurrence of adverse reactions
and side effects. In this study, the five active components in the mixture were determined concurrently for the first time with the help of Box-Behnken design and response surface approach. The properties of established model showed excellent resolution and sensitivity, good reproducibility
and speed, and accurate prediction thanks to the optimization of HPLC measurement conditions. The established approach was precise and trustworthy, and it offered helpful support and references for the construction of the Lianjie Liyan compound mixture as well as for the quality control.
Changes in Nitrogen and Humus During Aerobic Composting Under Antibiotic Composite Pollution
Authors: Zhang Lulu , Sun Yingying , Zeng Qiao , Wang Jing , Wei Yulu
Published: November 2023

Antibiotic residues have significantly effects on aerobic composting process. This study was targeted at antibiotic composite pollutants (e.g., sulfanilamides, tetracyclines, and quinolones) and probed into the effects of pollution levels on aerobic composting. With higher initial antibiotic
concentrations, the NH4+ –N and NO3− –N concentrations at the end of composting were higher, but TN content decreased, which may be due to the inhibition effects of antibiotics on nitrogen-fixing bacteria and thus were unfavorable
for nitrogen accumulation. Antibiotic pollution obviously delayed composting maturity, and the antibiotics at initial concentration above 306.12 mg/kg were significantly toxic to seeds. Analysis of structural changes in dissolved organic matter (DOM) showed the humification after treatments
CK and AT100 mainly occurred at the high-temperature stage (day 2–14) and later lower-temperature maturity stage (day 21–36). Humification after treatment AT300 mainly happened at the high-temperature stage (day 2–14), and that in AT600 mainly occurred at the early temperature
rise and high-temperature stage (day 2–7). This study comprehensively evaluated the effect of antibiotic composite pollution on the maturity of aerobic compost, and provided a theoretical basis for the treatment of antibiotic composite pollution materials in practical production.
Genome Survey Sequencing of the Medical Plant Dioscorea futschauensis: Genomic Characteristics Estimation and Genomic Resources Development
Authors: Luo Bizhen , Li Dong , Hu Ke , Chen Min , Sun Xiaoqin , Lu Ruisen , Wei Shujing
Published: November 2023

Dioscorea futschauensis Uline ex R. Knuth, a perennial climbing herb belonging to the Stenophora section of the genus Dioscorea L. (Dioscoreaceae), originates from Southeast China and is highly regarded for its medicinal properties. Despite its medicinal significance,
the absence of genomic information has impeded the effective utilization and conservation of this species. Here, we conducted genome survey sequencing of D. futschauensis to unveil its genomic characteristics and identify species-specific genomic markers, including whole plastome sequence,
plastome-divergent hotspots, single-copy nuclear genes and polymorphic nuclear SSRs. The genome of D. futschauensis was approximated to be 1392.76 Mb in length, accompanied by a substantial heterozygosity rate of 1.75% and a repeat content of 67.43%. Comparative plastome analysis illuminated
the conserved genome structure and gene content within D. futschauensis, and revealed four highly divergent hotspots (atpF intron, psbA-matK, matK -rps16, and rrn16-trnI) that could serve as molecular markers for D. futschauensis and its closely related species.
Furthermore, more than 200 single-copy nuclear genes and 78 polymorphic nuclear SSRs were identified within D. futschauensis. Overall, the comprehensive genomic information and abundant genetic resources provided herein will not only facilitate extended research in the realms of population
genetics, phylogenetics and conservation biology of D. futschauensis, but also hold considerable value for its cultivation and molecular breeding applications.
Comparing RMSEA-Based Indices for Assessing Measurement Invariance in Confirmatory Factor Models
Authors: Beribisky Nataly , Hancock Gregory R.
Published: November 2023

Fit indices are descriptive measures that can help evaluate how well a confirmatory factor analysis (CFA) model fits a researcher’s data. In multigroup models, before between-group comparisons are made, fit indices may be used to evaluate measurement invariance by assessing the degree to which multiple groups’ data are consistent with increasingly constrained nested models. One such fit index is an adaptation of the root mean square error of approximation (RMSEA) called RMSEAD. This index embeds the chi-square and degree-of-freedom differences into a modified RMSEA formula. The present study comprehensively compared RMSEAD to ΔRMSEA, the difference between two RMSEA values associated with a comparison of nested models. The comparison consisted of both derivations as well as a population analysis using one-factor CFA models with features common to those found in practical research. The findings demonstrated that for the same model, RMSEAD will always have increased sensitivity relative to ΔRMSEA with an increasing number of indicator variables. The study also indicated that RMSEAD had increased ability to detect noninvariance relative to ΔRMSEA in one-factor models. For these reasons, when evaluating measurement invariance, RMSEAD is recommended instead of ΔRMSEA.
‘Horn Please’: The evolution and regulation of traffic in twentieth-century India
Authors: Das Purbasha
Published: November 2023

The article explores the changes in behaviours and norms that followed the arrival of modern transport: trams, motor cars, buses and motor lorries. The article examines how new forms of behaviours such as the regulation of speed of motor cars, use of traffic lights, or newer methods of using streets such as walking on footpaths impacted the interaction between the authorities and people living within cities. The article shows that ideas of modern behaviour, centred on maintaining discipline and order on the streets were endorsed by the government but were contested and reluctantly adapted by the people. It also highlights the existence of social biases in administrative decisions connected to street use. This is evident in the analysis of accidents when the Indian driver and his lack of physical strength is equated with his incapability to drive a tram. This essentialisation takes place at both ends. Such debates occurred on the lines of race and class. For instance, the industrial workforce which migrated from rural areas had to learn new skills to navigate different spaces in the city. Apart from the factory, their activities on the streets were also scrutinised, such as when their inability to understand traffic rules was attributed to their rural background. Thus, in certain cases, transport mobility is incompatible with social mobility.
Unions and temporary workers’ wages in Spain: Testing solidarity in the good times and in the bad times
Authors: Canzio Leandro Iván
Published: November 2023

The labour market dualisation theory claims that labour unions bargain against the interests of temporary workers and that they foster inequalities between temporary and permanent employees. Conversely, the industrial relations literature argues that unions commonly follow solidaristic strategies towards outsiders. This study contributes to the literature by analysing unions’ associations with temporary workers’ hourly wages and the wage gap between permanent and temporary workers in Spain: one of the most prominent examples of labour market dualisation. By analysing cross-sectional surveys, unions’ influence through works councils, collective agreements and union density are studied during a period of economic growth (2006–2007) and a period of recession (2008–2010). Results show that there is generally no association between these three institutions and wage differences between permanent and temporary workers. The associations with temporary workers’ wages are insignificant or positive during both the period of economic growth and the period of recession.
Description of massage interventions in randomised clinical trials for neck pain; a review using the TIDieR checklist
Authors: Ishaq Iqra , Skinner Ian W , Mehta Poonam , Verhagen Arianne P
Published: November 2023

Objective

How interventions are reported can impact the ability to implement these intervention in clinical practice. Therefore, our aim is to assess the reporting of massage interventions in randomised controlled trials for patients with neck pain.

Data sources

This manuscript concerns a secondary analysis of trials evaluating massage for neck pain selected for a scoping review. An updated literature search was completed using four databases to 31 July 2023.

Review methods

Trials were selected that evaluate massage interventions. Two independent assessors extracted descriptive information, methodological quality (PEDro-scale) and assessed completeness of reporting of the intervention using the Template for Intervention Description and Replication (TIDier-checklist). We present frequencies of the extracted data.

Results

We included 35 trials (2840 patients) with neck pain. Most trials (n = 23) included patients with chronic non-specific neck pain. We found a wide variety of massage interventions from Chinese massage, Swedish massage to myofascial release. In addition, the dose, number of sessions and the duration of the intervention varied widely. The methodological quality overall was fair to good (varied between 4–8/10), and we found a moderate completeness of reporting. All trials provided the name of the intervention, 30 (86%) provided a rationale and 26 (74%) trials described details of the massage intervention.

Conclusion

The massage interventions were moderately described in trials in patients with neck pain, but provided enough information to guide the decision making for designing future Network Meta-analysis as to what trials need to be considered when grouping massage interventions in a clinically relevant way.
Vulvo-vaginal epithelial tumors in mares: A preliminary investigation on epithelial-mesenchymal transition and tumor-immune microenvironment
Authors: Armando Federico , Porcellato Ilaria , de Paolis Livia , Mecocci Samanta , Passeri Benedetta , Ciurkiewicz Małgorzata , Mechelli Luca , Grazia De Ciucis Chiara , Pezzolato Marzia , Fruscione Floriana , Brachelente Chiara , Montemurro Vittoria , Cappelli Katia , Puff Christina , Baumgärtner Wolfgang , Ghelardi Alessandro , Razzuoli Elisabetta
Published: November 2023

Vulvo-vaginal epithelial tumors are uncommon in mares, and data on the epithelial-to-mesenchymal transition (EMT) and the tumor-immune microenvironment (TIME) are still lacking. This is a study investigating the equus caballus papillomavirus type 2 (EcPV2) infection state as well as the EMT process and the tumor microenvironment in vulvo-vaginal preneoplastic/ benign (8/22) or malignant (14/22) epithelial lesions in mares. To do this, histopathological, immunohistochemical, transcriptomic, in situ hybridization, and correlation analyses were carried out. Immunohistochemistry quantification showed that cytoplasmic E-cadherin and β-catenin expression as well as nuclear β-catenin expression were features of malignant lesions, while benign/preneoplastic lesions were mainly characterized by membranous E-cadherin and β-catenin expression. Despite this, there were no differences between benign and malignant equine vulvo-vaginal lesions in the expression of downstream genes involved in the canonical and noncanonical wnt/β-catenin pathways. In addition, malignant lesions were characterized by a lower number of cells with cytoplasmic cytokeratin expression as well as a slightly higher cytoplasmic vimentin immunolabeling. The TIME of malignant lesions was characterized by more numerous CD204+ M2-polarized macrophages. Altogether, our results support the hypothesis that some actors in TIME such as CD204+ M2-polarized macrophages may favor the EMT process in equine vulvo-vaginal malignant lesions providing new insights for future investigations in the field of equine EcPV2-induced genital neoplastic lesions.
Defeating the ‘social danger’ of homosexuality while ‘forging the fatherland’: Sexual science and biotypology in Mexico’s national development, 1927–57
Authors: Jones Ryan M.
Published: November 2023

This article situates Mexican sexology, and how it engaged homosexuality and gender nonconformity, within more familiar nation-building projects in Mexico following the Revolution (1910–20). It argues that much like with understandings of race, Mexican sexologists, influenced by neo-Lamarckism and ‘Latin' eugenics, viewed sexuality as caused largely by social and environmental factors, rather than simply as a congenital characteristic. Such experts advocated for social solutions for what they saw as the ‘state of danger’ that homosexuality represented, targeting their interventions at youths, who were seen as pliable, future citizens, rather than adults, who were largely seen as irredeemable and best isolated from the national body. The article explores discursive, ideological, and methodological threads in Mexican sexology from the 19th to the mid-20th century, the field’s professionalization and transnational connections, case studies of youths in which the preferred solutions involved promoting family stability and coherence, and adult cases ranging from prison studies to the case of Marta Olmos, recipient of Mexico’s first widely known sex reassignment. Overall, it demonstrates important intersections between sexology and nation-building projects related to criminology, anthropology, and eugenics, and how the attempted management of homosexuality and gender nonconformity sheds light on Mexican development more broadly.
Associated factors of malnutrition status among children and adolescents living with HIV in Tanzania: Individual-level analysis and marginal effect estimation
Authors: Chacha Samuel , Hui Jing , Yuxin Teng , Ziping Wang , Yan Huang , Ali Saumu , Abeid Wahida , Dominick William , Malimu Emmanuel , Emanuel Florian , Saidi Saidi , Lyimo Deogratias , Mwanyika Veronica , Kumalija Elfrida , Dang Shaonong
Published: November 2023

Objectives

This study aimed to identify individual-level factors that affect malnutrition outcomes among children and adolescents living with HIV/AIDS in Tanzania.

Methods

We used data from the National AIDS Control Programme. 70,102 participants aged 5 to 19 years attending care and treatment clinics between January to December 2021 were included. Nutritional assessments were performed by anthropometric measurement. Logistic regression models were used to evaluate risk factors. We further estimated marginal prevalence and adjusted predictions by marginal effects. Supplementary analysis assessed the accuracy of the final fitted model.

Results

Prevalence of malnutrition for stunting, underweight, wasting, and anthropometric failure (CIAF) were 36.0%, 28.9%, 13.0%, and 48.0%, respectively. Several individual-level factors were significant determinants of malnutrition. Boys, participants aged 15-19 years, those switched to second- or third-line antiretroviral therapy (ART), initiated ART at ages of 5-14 years, ART duration less than 3 years, and were in advanced stages of WHO HIV clinical status had increased adjusted odds ratios and marginal prevalence. The larger AUC values for all models implied importance of identified factors accounted for malnutrition.

Conclusions

On long-term ART, nutritional interventions should be context-specific guidelines to improve growth, especially at ART initiation, ART regimen, and ART duration reckoning with age and sex.