bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S7 from Immunogenetic metabolomics reveals key enzymes that modulate CAR T-cell metabolism and function
Authors: Renauer Paul , Park Jonathan J. , Bai Meizhu , Acosta Arianny , Lee Won-Ho , Lin Guang Han , Zhang Yueqi , Dai Xiaoyun , Wang Guangchuan , Errami Youssef , Wu Terence , Clark Paul , Ye Lupeng , Yang Quanjun , Chen Sidi
Published: September 2024

Supplementary Table S7
Supplementary Table S2 from Immunogenetic metabolomics reveals key enzymes that modulate CAR T-cell metabolism and function
Authors: Renauer Paul , Park Jonathan J. , Bai Meizhu , Acosta Arianny , Lee Won-Ho , Lin Guang Han , Zhang Yueqi , Dai Xiaoyun , Wang Guangchuan , Errami Youssef , Wu Terence , Clark Paul , Ye Lupeng , Yang Quanjun , Chen Sidi
Published: September 2024

Supplementary Table S2
Supplementary Table S1 from Immunogenetic metabolomics reveals key enzymes that modulate CAR T-cell metabolism and function
Authors: Renauer Paul , Park Jonathan J. , Bai Meizhu , Acosta Arianny , Lee Won-Ho , Lin Guang Han , Zhang Yueqi , Dai Xiaoyun , Wang Guangchuan , Errami Youssef , Wu Terence , Clark Paul , Ye Lupeng , Yang Quanjun , Chen Sidi
Published: September 2024

Supplementary Table S1
Supplementary Figure 6 from Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) Influence on Soluble and Membrane Bound ICOS in Combination with Immune Checkpoint Blockade
Authors: Li Xiaoyu , Li Jingjing , zheng Yue , Lee Sandra J. , Zhou Jun , Giobbie-Hurder Anita , Butterfield Lisa H. , Dranoff Glenn , Hodi F. Stephen.
Published: September 2024

Supplementary figure 6
Table S3 from Circulating and intratumoral immune determinants of response to atezolizumab plus bevacizumab in patients with variant histology or sarcomatoid renal cell carcinoma
Authors: Saliby Renee Maria , El Zarif Talal , Bakouny Ziad , Shah Valisha , Xie Wanling , Flippot Ronan , Denize Thomas , Kane M. Harry , Madsen Katrine N. , Ficial Miriam , Hirsch Laure , Wei Xiao X. , Steinarter John A. , Harshman Lauren C. , Vaishampayan Ulka N. , Severgnini Mariano , McDermott David F. , Lee Gwo-Shu Mary. , Xu Wenxin , Van Allen Eliezer M. , McGregor Bradley A. , Signoretti Sabina , Choueiri Toni K. , McKay Rana R. , Braun David A.
Published: September 2024

Supplementary table 3
Table S1 from Circulating and intratumoral immune determinants of response to atezolizumab plus bevacizumab in patients with variant histology or sarcomatoid renal cell carcinoma
Authors: Saliby Renee Maria , El Zarif Talal , Bakouny Ziad , Shah Valisha , Xie Wanling , Flippot Ronan , Denize Thomas , Kane M. Harry , Madsen Katrine N. , Ficial Miriam , Hirsch Laure , Wei Xiao X. , Steinarter John A. , Harshman Lauren C. , Vaishampayan Ulka N. , Severgnini Mariano , McDermott David F. , Lee Gwo-Shu Mary. , Xu Wenxin , Van Allen Eliezer M. , McGregor Bradley A. , Signoretti Sabina , Choueiri Toni K. , McKay Rana R. , Braun David A.
Published: September 2024

Supplementary table 1
Figure S3 from Circulating and intratumoral immune determinants of response to atezolizumab plus bevacizumab in patients with variant histology or sarcomatoid renal cell carcinoma
Authors: Saliby Renee Maria , El Zarif Talal , Bakouny Ziad , Shah Valisha , Xie Wanling , Flippot Ronan , Denize Thomas , Kane M. Harry , Madsen Katrine N. , Ficial Miriam , Hirsch Laure , Wei Xiao X. , Steinarter John A. , Harshman Lauren C. , Vaishampayan Ulka N. , Severgnini Mariano , McDermott David F. , Lee Gwo-Shu Mary. , Xu Wenxin , Van Allen Eliezer M. , McGregor Bradley A. , Signoretti Sabina , Choueiri Toni K. , McKay Rana R. , Braun David A.
Published: September 2024

Supplementary Figure 3
Figure S1 from Circulating and intratumoral immune determinants of response to atezolizumab plus bevacizumab in patients with variant histology or sarcomatoid renal cell carcinoma
Authors: Saliby Renee Maria , El Zarif Talal , Bakouny Ziad , Shah Valisha , Xie Wanling , Flippot Ronan , Denize Thomas , Kane M. Harry , Madsen Katrine N. , Ficial Miriam , Hirsch Laure , Wei Xiao X. , Steinarter John A. , Harshman Lauren C. , Vaishampayan Ulka N. , Severgnini Mariano , McDermott David F. , Lee Gwo-Shu Mary. , Xu Wenxin , Van Allen Eliezer M. , McGregor Bradley A. , Signoretti Sabina , Choueiri Toni K. , McKay Rana R. , Braun David A.
Published: September 2024

Supplementary Figure 1
Figure S7 from β-catenin drives butyrophilin-like molecule loss and γδ T-cell exclusion in colon cancer
Authors: Suzuki Toshiyasu , Kilbey Anna , Casa Rodriguez Nuria , Lawlor Amy , Georgakopoulou Anastasia , Hayman Hannah , Yin Swe Kyi Lai , Nordin Anna , Cantù Claudio , Vantourout Pierre , Ridgway Rachel A. , Byrne Ryan M. , Chen Lei , Verzi Michael P. , Gay David M. , Gil Vazquez Ester , Belnoue-Davis Hayley L. , Gilroy Kathryn , Kostner Anne Helene , Kersten Christian , Thuwajit Chanitra , Andersen Ditte K. , Wiesheu Robert , Jandke Anett , Blyth Karen , Roseweir Antonia K. , Leedham Simon J. , Dunne Philip D. , Edwards Joanne , Hayday Adrian , Sansom Owen J. , Coffelt Seth B.
Published: September 2024

Impact of Btnl1 and Btnl6 expression on Vgamma7+ cells and the tumor microenvironment
Figure S4 from β-catenin drives butyrophilin-like molecule loss and γδ T-cell exclusion in colon cancer
Authors: Suzuki Toshiyasu , Kilbey Anna , Casa Rodriguez Nuria , Lawlor Amy , Georgakopoulou Anastasia , Hayman Hannah , Yin Swe Kyi Lai , Nordin Anna , Cantù Claudio , Vantourout Pierre , Ridgway Rachel A. , Byrne Ryan M. , Chen Lei , Verzi Michael P. , Gay David M. , Gil Vazquez Ester , Belnoue-Davis Hayley L. , Gilroy Kathryn , Kostner Anne Helene , Kersten Christian , Thuwajit Chanitra , Andersen Ditte K. , Wiesheu Robert , Jandke Anett , Blyth Karen , Roseweir Antonia K. , Leedham Simon J. , Dunne Philip D. , Edwards Joanne , Hayday Adrian , Sansom Owen J. , Coffelt Seth B.
Published: September 2024

Correlation between gut-specific transcription factors, gamma delta T cell density and BTNL genes in human tumors
Supplementary Table 1 from Enhancing CAR T-cell therapy using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Mathew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Bai Yuchen V. , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: September 2024

Supplementary Table 1: Key Resources
Supplementary Tables from A bispecific γδ T-cell engager targeting EGFR activates a potent Vγ9Vδ2 T cell–mediated immune response against EGFR-expressing tumors
Authors: King Lisa A. , Toffoli Elisa C. , Veth Myrthe , Iglesias-Guimarais Victoria , Slot Manon C. , Amsen Derk , van de Ven Rieneke , Derks Sarah , Fransen Marieke F. , Tuynman Jurriaan B. , Riedl Thilo , Roovers Rob C. , Adang Anton E.P. , Ruben Jurjen M. , Parren Paul W.H.I. , de Gruijl Tanja D. , van der Vliet Hans J.
Published: September 2024

Supplementary tables 1-6
Supplementary Figure Legends from AXL inhibition improves the anti-tumor activity of chimeric antigen receptor T cells
Authors: Sakemura R. Leo , Hefazi Mehrdad , Cox Michelle J. , Siegler Elizabeth L. , Sinha Sutapa , Hansen Michael J. , Stewart Carli M. , Feigin Jennifer M. , Manriquez Roman Claudia , Schick Kendall J. , Can Ismail , Tapper Erin E. , Horvei Paulina , Adada Mohamad M. , Bezerra Evandro D. , Kankeu Fonkoua Lionel Aurelien. , Ruff Michael W. , Forsman Cynthia L. , Nevala Wendy K. , Boysen Justin C. , Tschumper Renee C. , Grand Cory L. , Kuchimanchi Kamesh R. , Mouritsen Lars , Foulks Jason M. , Warner Steven L. , Call Timothy G. , Parikh Sameer A. , Ding Wei , Kay Neil E. , Kenderian Saad S.
Published: September 2024

Supplementary Figure Legends
Supplementary Data from Cholesterol efflux drives the generation of immunosuppressive macrophages to promote the progression of human hepatocellular carcinoma
Authors: Li Zhixiong , Wang Yongchun , Xing Rui , Zeng Huilan , Yu Xing-Juan , Zhang Yao-jun , Xu Jing , Zheng Limin
Published: September 2024

Supplementary Figure S1-S5 and Table S1-S3
Supplementary Table S1 from Combinatorial immunotherapy with agonistic CD40 activates dendritic cells to express IL12 and overcomes PD-1 resistance
Authors: Krykbaeva Irina , Bridges Kate , Damsky William , Pizzurro Gabriela A. , Alexander Amanda F. , McGeary Meaghan K. , Park Koonam , Muthusamy Viswanathan , Eyles Jim , Luheshi Nadia , Turner Noel , Weiss Sarah A. , Olino Kelly , Kaech Susan M. , Kluger Harriet M. , Miller-Jensen Kathryn , Bosenberg Marcus
Published: September 2024

Supplementary Table S1
Supplementary Figures from Combinatorial immunotherapy with agonistic CD40 activates dendritic cells to express IL12 and overcomes PD-1 resistance
Authors: Krykbaeva Irina , Bridges Kate , Damsky William , Pizzurro Gabriela A. , Alexander Amanda F. , McGeary Meaghan K. , Park Koonam , Muthusamy Viswanathan , Eyles Jim , Luheshi Nadia , Turner Noel , Weiss Sarah A. , Olino Kelly , Kaech Susan M. , Kluger Harriet M. , Miller-Jensen Kathryn , Bosenberg Marcus
Published: September 2024

Figures S1-9
Supplementary Table S1 from Glioblastoma vascular plasticity limits effector T-cell infiltration and is blocked by cAMP activation
Authors: Qin Zixi , Huang Youwei , Li Zeying , Pan Guopeng , Zheng Liangying , Xiao Xiao , Wang Fang , Chen Jiahong , Chen Xueqin , Lin Xi , Li Kai , Yan Guangmei , Zhang Haipeng , Xing Fan
Published: September 2024

GdEC gene sets
Supplementary Figures from Glioblastoma vascular plasticity limits effector T-cell infiltration and is blocked by cAMP activation
Authors: Qin Zixi , Huang Youwei , Li Zeying , Pan Guopeng , Zheng Liangying , Xiao Xiao , Wang Fang , Chen Jiahong , Chen Xueqin , Lin Xi , Li Kai , Yan Guangmei , Zhang Haipeng , Xing Fan
Published: September 2024

Supplementary Figure 1-12
Data from CD69 Imposes Tumor-Specific CD8+ T-cell Fate in Tumor-Draining Lymph Nodes
Authors: Koyama-Nasu Ryo , Kimura Motoko Y. , Kiuchi Masahiro , Aoki Ami , Wang Yangsong , Mita Yukiyoshi , Hasegawa Ichita , Endo Yukihiro , Onodera Atsushi , Hirahara Kiyoshi , Motohashi Shinichiro , Nakayama Toshinori
Published: September 2024

Abstract
Tumor-specific CD8+ T cells play a pivotal role in antitumor immunity and are a key target of immunotherapeutic approaches. Intratumoral CD8+ T cells are heterogeneous; Tcf1+ stemlike CD8+ T cells give rise to their cytotoxic progeny—Tim-3+ terminally differentiated CD8+ T cells. However, where and how this differentiation process occurs has not been elucidated. We herein show that terminally differentiated CD8+ T cells can be generated within tumor-draining lymph nodes (TDLN) and that CD69 expression on tumor-specific CD8+ T cells controls its differentiation process through regulating the expression of the transcription factor TOX. In TDLNs, CD69 deficiency diminished TOX expression in tumor-specific CD8+ T cells, and consequently promoted generation of functional terminally differentiated CD8+ T cells. Anti-CD69 administration promoted the generation of terminally differentiated CD8+ T cells, and the combined use of anti-CD69 and anti–programmed cell death protein 1 (PD-1) showed an efficient antitumor effect. Thus, CD69 is an attractive target for cancer immunotherapy that synergizes with immune checkpoint blockade.
Data from Clec4A4 Acts as a Negative Immune Checkpoint Regulator to Suppress Antitumor Immunity
Authors: Uto Tomofumi , Fukaya Tomohiro , Mitoma Shuya , Nishikawa Yotaro , Tominaga Moe , Choijookhuu Narantsog , Hishikawa Yoshitaka , Sato Katsuaki
Published: September 2024

Abstract
Clec4A4 is a C-type lectin receptor (CLR) exclusively expressed on murine conventional dendritic cells (cDC) to regulate their activation status. However, the functional role of murine Clec4A4 (mClec4A4) in antitumor immunity remains unclear. Here, we show that mClec4A4 serves as a negative immune checkpoint regulator to impair antitumor immune responses. Deficiency of mClec4A4 lead to a reduction in tumor development, accompanied by enhanced antitumor immune responses and amelioration of the immunosuppressive tumor microenvironment (TME) mediated through the enforced activation of cDCs in tumor-bearing mice. Furthermore, antagonistic mAb to human CLEC4A (hCLEC4A), which is the functional orthologue of mClec4A4, exerted protection against established tumors without any apparent signs of immune-related adverse events in hCLEC4A-transgenic mice. Thus, our findings highlight the critical role of mClec4A4 expressed on cDCs as a negative immune checkpoint molecule in the control of tumor progression and provide support for hCLEC4A as a potential target for immune checkpoint blockade in tumor immunotherapy.
Table S4 from HTLV-1 bZIP factor-induced reprogramming of lactate metabolism and epigenetic status promote leukemic cell expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2024

Experimental reagents and resources with identifiers used in this study.
Figure S4 from HTLV-1 bZIP factor-induced reprogramming of lactate metabolism and epigenetic status promote leukemic cell expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2024

TAp73 significance in HBZ pathogenesis and its effect on cellular metabolism.
Figure S2 from HTLV-1 bZIP factor-induced reprogramming of lactate metabolism and epigenetic status promote leukemic cell expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: September 2024

HBZ protein alters epigenetic regulation of TAp73 by EZH2.
Table S6 from A SINGLE-CELL TAXONOMY PREDICTS INFLAMMATORY NICHE REMODELING TO DRIVE TISSUE FAILURE AND OUTCOME IN HUMAN AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , De Jong Madelon M E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc HGP.
Published: September 2024

Supplementary Table 6. Differentially expressed genes in BMSCs from AML vs. BMSCs from NBM (purified BMSC RNAseq)
Supplementary Figure 1-9 from A SINGLE-CELL TAXONOMY PREDICTS INFLAMMATORY NICHE REMODELING TO DRIVE TISSUE FAILURE AND OUTCOME IN HUMAN AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , De Jong Madelon M E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc HGP.
Published: September 2024

Fig S1-S9
Table S4 from Time-dependent prognostic value of serological and measurable residual disease assessments after idecabtagene vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesus G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesus F. , Munshi Nikhil C. , Kaiser Shari
Published: September 2024

HR and P values for landmark PFS within first year
Data from The Polyamine–Hypusine Circuit Controls an Oncogenic Translational Program Essential for Malignant Conversion in MYC-Driven Lymphoma
Authors: Nakanishi Shima , Li Jiannong , Berglund Anders E. , Kim Youngchul , Zhang Yonghong , Zhang Ling , Yang Chunying , Song Jinming , Mirmira Raghavendra G. , Cleveland John L.
Published: September 2024

Abstract
The MYC oncoprotein is activated in a broad spectrum of human malignancies and transcriptionally reprograms the genome to drive cancer cell growth. Given this, it is unclear if targeting a single effector of MYC will have therapeutic benefit. MYC activates the polyamine–hypusine circuit, which posttranslationally modifies the eukaryotic translation factor eIF5A. The roles of this circuit in cancer are unclear. Here we report essential intrinsic roles for hypusinated eIF5A in the development and maintenance of MYC-driven lymphoma, where the loss of eIF5A hypusination abolishes malignant transformation of MYC-overexpressing B cells. Mechanistically, integrating RNA sequencing, ribosome sequencing, and proteomic analyses revealed that efficient translation of select targets is dependent upon eIF5A hypusination, including regulators of G1–S phase cell-cycle progression and DNA replication. This circuit thus controls MYC's proliferative response, and it is also activated across multiple malignancies. These findings suggest the hypusine circuit as a therapeutic target for several human tumor types.
Significance:
Elevated EIF5A and the polyamine–hypusine circuit are manifest in many malignancies, including MYC-driven tumors, and eIF5A hypusination is necessary for MYC proliferative signaling. Not­ably, this circuit controls an oncogenic translational program essential for the development and maintenance of MYC-driven lymphoma, supporting this axis as a target for cancer prevention and treatment.

See related commentary by Wilson and Klein, p. 248.

This article is highlighted in the In This Issue feature, p. 247
Data from Time-Dependent Prognostic Value of Serological and Measurable Residual Disease Assessments after Idecabtagene Vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesús G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesús F. , Munshi Nikhil C. , Kaiser Shari M.
Published: September 2024

Abstract
The role of measurable residual disease (MRD) in multiple myeloma patients treated with chimeric antigen receptor (CAR) T cells is uncertain. We analyzed MRD kinetics during the first year after idecabtagene vicleucel (ide-cel) infusion in 125 relapsed/refractory multiple myeloma patients enrolled in KarMMa. At month 1 after ide-cel, there were no differences in progression-free survival (PFS) between patients in less than complete response (CR) versus those in CR; only MRD status was predictive of significantly different PFS at this landmark. In patients with undetectable MRD at 3 months and beyond, PFS was longer in those achieving CR versus −6 logarithmic range and reappearance of normal plasma cells in MRD-negative patients were associated with inferior PFS. This study unveils different prognostic implications of serological and MRD response dynamics after ide-cel and suggests the potential value of studying the reappearance of normal plasma cells as a surrogate of loss of CAR T-cell functionality.
Significance:
This is one of the first studies evaluating the impact of CR and MRD dynamics after CAR T therapy in relapsed/refractory multiple myeloma. These data help interpret the prognostic significance of serological and MRD responses at early and late time points after CAR T-cell infusion.

See related commentary by Landgren and Kazandjian, p. 346.

This article is featured in Selected Articles from This Issue, p. 337
Data from Time-dependent prognostic value of serological and measurable residual disease assessments after idecabtagene vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesus G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesus F. , Munshi Nikhil C. , Kaiser Shari
Published: September 2024

Abstract
The role of MRD in multiple myeloma patients treated with CAR T cells is uncertain. We analyzed MRD kinetics during the first year after idecabtagene vicleucel (ide-cel) infusion in 125 relapsed/refractory multiple myeloma patients enrolled in KarMMa. At month 1 after ide-cel, there were no differences in progression-free survival (PFS) between patients in less than complete response (CR) vs those in CR; only MRD status was predictive of significantly different PFS at this landmark. In patients with undetectable MRD at 3 months and beyond, PFS was longer in those achieving CR vs
Table S9 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Expression proteomic signature
Table S8 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Transcriptomic signature
Table S7 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Steroidomics
Table S6 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Photo affinity labelling (PAL)
Table S5 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Selectivity profile live cells (2D-TPP)
Table S3 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Kinobead assay (affinity enrichment chemoproteomics)
Table S1 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

panPARP matrix (affinity enrichment chemoproteomics)
Figure S5 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Co-inhibition of PARP and cholesterol biosynthesis pathway increase efficiency of tumor cell killing
Figure S4 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

Niraparib specific modulation of expression levels of proteins involved in cholesterol biosynthesis pathway in cancer cell lines (proteomics)
Figure 2 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation
Authors: Rutkowska Anna , Eberl H. Christian , Werner Thilo , Hennrich Marco L. , Sévin Daniel C. , Petretich Massimo , Reddington James P. , Pocha Shirin , Gade Stephan , Martinez-Segura Amalia , Dvornikov Dmytro , Karpiak Joel , Sweetman Gavain M.A. , Fufezan Christian , Duempelfeld Birgit , Braun Florian , Schofield Christopher , Keles Hakan , Alvarado David , Wang Zhuo , Jansson Keith H. , Faelth-Savitski Maria , Curry Edward , Remlinger Katja , Stronach Euan A. , Feng Bin , Sharma Geeta , Coleman Kevin , Grandi Paola , Bantscheff Marcus , Bergamini Giovanna
Published: September 2024

LSS is a novel niraparib-specific off-target. A, Chemical structure of the PARP photo affinity probe (TCO-PAL-PARP). B, Photoaffinity labeling with the TCO-PAL-PARP probe (1 μmol/L) and competition with olaparib and niraparib (5 μmol/L) in live T47D cells. Volcano plots display all identified proteins. Ratio is calculated as mean (n = 3), P value is calculated via paired T test; significance criteria: P < 0.01, |log2 fc| > log2(1.5), details in Supplementary Table S6. C, Bar plots display of mean (n = 3) competition for the indicated protein targets in photoaffinity labeling experiments described in B. D, Photoaffinity labeling experiments with TCO–PAL–PARP probe (1 μmol/L) and competition with niraparib (5 μmol/L) or LSS inhibitor Ro-48-8071 (2 μmol/L). Barplots display mean (n = 2) competition for the indicated protein targets. E, Docking poses of olaparib (magenta) and niraparib (orange) to human LSS (cyan) overlaid on the co-crystal pose of LSS inhibitor Ro 48-8071 (purple, PDB: 1W6J).
Role of Autologous Transplant in Newly Diagnosed Multiple Myeloma Patients Treated with Novel Triplets: A Systematic Review and Meta-Analysis
Authors: Amitai Irina , Gurion Ronit , Raanani Pia , Vaxman Iuliana , Yeshurun Moshe , Magen Hila , Gafter-Gvili Anat , Shargian Liat
Published: September 2024

Introduction: High-dose therapy with melphalan followed by autologous stem cell transplant in the upfront setting (upfront ASCT) has significantly improved clinical outcomes of myeloma patients and become the standard of care for the past 30 years. However, with the advent of modern induction therapy, the role of upfront ASCT approach has been called into question. Several prospective studies have examined whether continuing with triplet therapy as consolidation with optional ASCT at relapse (triplet-alone) could result in comparable outcomes. Methods: This was a systematic review and meta-analysis of randomized controlled trials comparing upfront ASCT versus triplet-alone approach among myeloma patients treated with triplet therapy, which included two novel agents and a corticosteroid, as induction. Cochrane Library, PubMed and conference proceedings were searched. Primary outcome was overall survival (OS). Secondary outcomes included progression-free survival (PFS), safety, and second primary malignancies (SPM). Subgroup analysis was conducted for high-risk cytogenetics. Results: Our search yielded three trials, conducted between 2010–2018, including 1,737 patients. Two trials evaluated bortezomib plus lenalidomide (VRd) induction and the third study tested carfilzomib plus lenalidomide (KRd) induction. Maintenance was given in all trials to both arms. There was no difference in OS between the arms; the pooled OS in all patients and those with high-risk cytogenetics was hazard ratio (HR) 1.03 (95% CI, 0.85–1.26; I2 = 0%; 1,737 patients, 3 trials) and 0.85 (95% CI, 0.59–1.23; I2 = 0%; 222 patients, 2 trials), respectively. The pooled PFS for upfront ASCT versus triplet-alone was significantly improved in all the patients and in the high-risk cytogenetics subgroup, HR 0.67 (95% CI 0.59–0.76; I2 = 0%; 1,737 patients, 3 trials) and HR 0.59 (95% CI: 0.44–0.7; I2 = 0%; 306 patients, 3 trials), respectively. The risk of any grade 3–4 adverse events was higher in the upfront ASCT arm versus triplet-alone approach (relative risk = 1.17 [95% CI, 1.12–1.23; 1,737 patients]). The risk of secondary malignancies was reported in all three trials and was comparable between both arms. Two trials reported on secondary myeloid neoplasms, which were significantly higher among upfront ASCT arm versus triplet-alone approach, OR 9.7 (1.8–52.25, I2 = 0%, 1,422 patients). Conclusion: Although upfront ASCT approach, in the era of triplet therapy, resulted in a significantly longer PFS among all patients, this did not translate into a survival benefit, regardless of cytogenetic risk. Upfront ASCT was associated with an increased rate of secondary myeloid neoplasms. In the current plethora of innovative therapies, the role of upfront ASCT is debatable.
Integration of Qualitative and Quantitative Approaches as a Methodological Issue in Social Psychology
Authors: Lipatov Sergei A. , Nesterova Ekaterina M.
Published: September 2024

Background. G.M. Andreeva set an issue in social psychology that still remains relevant today. It concerns the correlation of two series of patterns in the process of socio-psychological research. These patterns are social development and the development of the human psyche. In this regard, new tasks of intrascientific reflection arise, one of which is the analysis of the methodological problem of integrating qualitative and quantitative methods in socio-psychological research. The idea of integrating two classes of methods is reflected in the systemic approach of B.F. Lomov and remains relevant in the context of the trend towards mixed methods research in social sciences. The need to integrate qualitative and quantitative methods is due to the specifics of social psychology, which is located at the junction of sociology and psychology. Objective. The aim of the article is to identify the features of the integration of qualitative and quantitative approaches in social psychology through the prism of methodological levels. Methods. Theoretical analysis of Russian and foreign works and their systematization based on the levels of methodology. Results. At the level of general methodology, from the standpoint of post-non-classical rationality, the components of scientistic (quantitative) and qualitative methodological approaches are considered. The choice of pragmatism as the philosophical basis of “mixed methods” is justified. At the level of particular methodology, the principles of complementarity and expediency of integration specific to “mixed methods” are disclosed. The set of specific methodological research techniques is presented through options for combining qualitative and quantitative data in interpretation and report. Conclusions. The highlighted specificity of the integration of qualitative and quantitative methods at different levels of methodology outlines the direction for its further elaboration and refinement. It also allows to shift the focus from an intuitive combination of qualitative and quantitative methods to the reflective and conscious application of such a research strategy.
Tracing the Roots of Islamophobia in Recent Indian Films
Authors: Das Suchismita , Pal Satanik
Published: September 2024

This article analyses the recent rise of Islamophobic films in India. While it may seem that social media has led to a rise in Hindu nationalism and Islamophobia in the recent past, it is crucial to recognize that this narrative is incomplete. The rise of Islamophobia in the country can be traced back to the 20th century freedom struggle where a counter-narrative to Gandhian concepts of communal harmony can be found in the writings of various leaders, artists and activists. Social media has allowed for a re-proliferation of those strands of thought in recent times through the platforms such as Youtube, which has led to the success of movies like The Kashmir Files or The Kerala Story.
Introduction
Authors: Brym Robert
Published: September 2024

Pogroms are commonly defined as ethnic riots that last several days and involve a large number of assailants and victims. Some events that took place in Poland from 1935 to 1937 fit this definition, but conditions in Poland during this period more closely resemble what Leshchinsky calls a “permanent pogrom”—a single, sustained collective event stretching over nearly three years and involving many discrete bursts of property destruction and interpersonal violence varying widely in duration, intensity, and level of participation. The permanent pogrom normalized fear in Poland’s Jewish population. Organized groups of Jewish workers in particular managed to fight assailants and organize anti-pogrom protests, but on the whole Jewish resistance was piecemeal and largely ineffective. Leshchinsky recognized that the permanent pogrom stemmed from the incompatibility between Polish industrialization and the ethnic composition of the country’s class structure. However, the timing, scope, and severity of violence were largely the outcome of political circumstances.
2. Pogrom gunpowder
Authors: Leshchinsky Yankev
Published: September 2024

In this 1935 essay Leshchinsky is still reluctant to classify the episodic violence visited on Polish Jews as pogroms. He provides evidence that agitation in favour of pogroms and attacks on individual Jews are widespread, arguing that they are akin to gunpowder being amassed before a large explosion, with no group apart from organized workers standing in the way of pogrom agitation. He rails against the police and the government for doing little to quell the violence. Leshchinsky also calls on Jewish society to (1) explain to “the better parts of Polish society” that the violence is a danger to Polish society as a whole, (2) rally to compel the government to “stop the poison from spreading” and adopt severe measures against individuals attacks and small pogroms, and (3) organize itself to speak out against the pogroms and create a common front for self-defence. 13 November 1935.
5. Government antisemitism
Authors: Leshchinsky Yankev
Published: September 2024

Leshchinsky illustrates a “downward slide on the part of official circles toward the antisemitic program of the Endeks” (members of the Narodowa Demokracja party). He cites the Polish Prime Minister’s June 1936 statement in parliament legitimizing the “economic struggle” against Jews and noting that the Prime Minister was quoted by antisemitic lawyers and tens of Christian witnesses at the 1936 Pshitik pogrom trial. Leshchinsky shows that the “economic struggle” is widely interpreted to include not just boycotts but physical assaults with the aim of “eradicating and expelling Jews.” Meanwhile, “the government is keeping quiet about the pogroms against Jews.” Undated, 1936?
6. The first ghetto bench in the universities
Authors: Leshchinsky Yankev
Published: September 2024

Beginning at Lvov Polytechnic in 1935, Jews were assigned segregated seating in what were called “ghetto benches” and separate rooms for laboratory work. The practice soon spread to other institutions of higher education. Some Jewish students stand rather than move to segregated places. Some are dragged away and beaten. Others are expelled. Some classes are cancelled when Jewish students refuse to sit on ghetto benches. Most professors do nothing to stop such actions. 18 April 1936.
8. Jewish self-defence
Authors: Leshchinsky Yankev
Published: September 2024

Leshchinsky here addresses Polish Jewry’s position on the attacks against Jews and the government’s tolerance of those attacks. He notes that different classes respond differently to the attacks. Workers in Lodz and elsewhere were first to call for self-defence, including the acquisition of weapons. In Bialystok, the existence of a self-defence group led members of the National Radical party to stop wearing their uniforms for fear of being attacked by Jews. The regime reacted to the creation of self-defence groups by arresting Jews who were protecting women, children, seniors, and weak people. In Warsaw, after an initial period of disorientation, Jewish workers, porters, and youth also responded vigorously to attacks against Jews. Again, the authorities arrested more Jews than their assailants. Polish socialist workers joined their Jewish comrades in Warsaw in the fight against pogromists. In contrast, rabbis fasted in protest against attacks. Jewish politicians who had previously curried favour with the Jewish bourgeoisie, assuring them that the government would protect the Jewish community, felt duped and did not know what to do. Leshchinsky concludes that “demoralization and neglect have profoundly corroded Jewish bourgeois society.” Undated.
Texas Water Observatory: A Distributed Network for Monitoring Water, Energy, and Carbon Cycles under Variable Climate and Land Use on Gulf Coast Plains
Authors: Mohanty Binayak P. , Mbabazi Deanroy , Miller Gretchen , Moore Georgianne , Everett Mark , Rajan Nithya , Morgan Cristine L. S. , Gaur Nandita , Sehgal Vinit , Sedaghatdoost Amir , Hong Minki , Kathuria Dhruva , Deshpande Ajinkya , Singh Siddharth , Martin J. Michael , Calabrese Salvatore , Mishra Debasish , Singh Rishabh , Chun Beomseok , Souza Rodolfo , Knappett Peter S. K. , Smith Douglas R. , Jones Curtis
Published: September 2024

In the Gulf Coastal Plains of Texas, a state-of-the-art distributed network of field observatories, known as the Texas Water Observatory (TWO), is developed to better understand the water, energy, and carbon cycles across the critical zone (encompassing aquifers, soils, plants, and atmosphere) at different spatiotemporal scales. Using more than 300 advanced real-time/near-real-time sensors, this observatory monitors high-frequency water, energy, and carbon storage and fluxes in the Brazos River corridor, which are critical for coupled hydrologic, biogeochemical, and land–atmosphere process understanding in the region. TWO provides a regional resource for better understanding and/or managing agriculture, water resources, ecosystems, biodiversity, disasters, health, energy, and weather/climate. TWO infrastructure spans common land uses in this region, including traditional/aspirational cultivated agriculture, rangelands, native prairie, bottomland hardwood forest, and coastal wetlands. Sites represent landforms from low-relief erosional uplands to depositional lowlands across climatic and geologic gradients of central Texas. We present the overarching vision of TWO and describe site design, instrumentation specifications, data collection, and quality control protocols. We also provide a comparison of water, energy, and carbon budget across sites, including evapotranspiration, carbon fluxes, radiation budget, weather, profile soil moisture and soil temperature, soil hydraulic properties, hydrogeophysical surveys, groundwater levels, and groundwater quality reported at TWO primary sites for 2018–20 (with certain data gaps). In conjunction with various Earth-observing remote sensing and legacy databases, TWO provides a master testbed to evaluate process-driven or data-driven critical zone science, leading to improved natural resource management and decision support at different spatiotemporal scales.

Significance Statement

We provide the vision, design setup, and data acquisition of a state-of-the-art network of field observatories across the Gulf Coastal Plains of Texas. This observatory provides a wealth of measurements of the water, energy, and carbon fluxes, thereby providing a critical testbed for improving the understanding of terrestrial hydrological, biogeochemical, and atmospheric processes across diverse land-use and climate conditions.
Abyssal Slope Currents
Authors: Capó Esther , McWilliams James C. , Gula Jonathan , Molemaker M. Jeroen , Damien Pierre , Schubert René
Published: September 2024

Realistic computational simulations in different oceanic basins reveal prevalent prograde mean flows (in the direction of topographic Rossby wave propagation along isobaths; aka topostrophy) on topographic slopes in the deep ocean, consistent with the barotropic theory of eddy-driven mean flows. Attention is focused on the western Mediterranean Sea with strong currents and steep topography. These prograde mean currents induce an opposing bottom drag stress and thus a turbulent boundary layer mean flow in the downhill direction, evidenced by a near-bottom negative mean vertical velocity. The slope-normal profile of diapycnal buoyancy mixing results in downslope mean advection near the bottom (a tendency to locally increase the mean buoyancy) and upslope buoyancy mixing (a tendency to decrease buoyancy) with associated buoyancy fluxes across the mean isopycnal surfaces (diapycnal downwelling). In the upper part of the boundary layer and nearby interior, the diapycnal turbulent buoyancy flux divergence reverses sign (diapycnal upwelling), with upward Eulerian mean buoyancy advection across isopycnal surfaces. These near-slope tendencies abate with further distance from the boundary. An along-isobath mean momentum balance shows an advective acceleration and a bottom-drag retardation of the prograde flow. The eddy buoyancy advection is significant near the slope, and the associated eddy potential energy conversion is negative, consistent with mean vertical shear flow generation for the eddies. This cross-isobath flow structure differs from previous proposals, and a new one-dimensional model is constructed for a topostrophic, stratified, slope bottom boundary layer. The broader issue of the return pathways of the global thermohaline circulation remains open, but the abyssal slope region is likely to play a dominant role.
Modelling wound area in studies of wound healing interventions
Authors: Watson Samuel I. , Gkini Eleni , Bishop Jon , Scandrett Katie , Napit Indra , Lilford Richard J.
Published: September 2024

Background

Experimental studies of wound healing often use survival analysis and time to event outcomes or differences in wound area at a specific time point. However, these methods do not use a potentially large number of observations made over the course of a trial and may be inefficient. A model-based approach can leverage all trial data, but there is little guidance on appropriate models and functional forms to describe wound healing.

Methods

We derive a general statistical model and review a wide range of plausible mathematical models to describe wound healing. We identify a range of possible derived estimands and their derivation from the models. Using data from a trial of an intervention to promote ulcer healing in patients affected by leprosy that included three measurement methods repeated across the course of the study, we compare the goodness-of-fit of the models using a range of methods and estimate treatment effects and healing rate functions with the best-fitting models.

Results

Overall, we included 5,581 ulcer measurements of 1,578 unique images from 130 patients. We examined the performance of a range of models. The square root, log square root, and log quadratic models were the best fitting models across all outcome measurement methods. The estimated treatment effects magnitude and sign varied by time post-randomisation, model type, and outcome type, but across all models there was little evidence of effectiveness. The estimated effects were significantly more precise than non-parametric alternatives. For example, estimated differences from the three outcome measurements at 42-days post-randomisation were − 0.01 cm2 (-0.77, 0.74), -0.44 cm2 (-1.64, 0.76), and 0.11 cm2 (-0.87, 1.08) using a non-parametric method versus − 0.03 cm2 (-0.14, 0.06), 0.06 cm2 (-0.05, 0.17), and 0.03 cm2 (-0.07, 0.17) using a square-root model.

Conclusions

Model-based analyses can dramatically improve the precision of estimates but care must be taken to carefully compare and select the best fitting models. The (log) square-root model is strongly recommended reflecting advice from a century ago.