bluuebunny/crossref_metadata_2025 huggingface dataset:
Table S6 from A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: September 2024

Detailed summary of therapeutic response at end-of-study time point, organized by study group—OncoTreat, OncoTarget, or Negative control—and then stratified by each individual drug arm. The study was underpowered for statistical analyses of therapeutic response in individual drug arms.
Table S4 from An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression
Authors: Indeglia Alexandra , Leung Jessica C. , Miller Sven A. , Leu Julia I-Ju , Dougherty James F. , Clarke Nicole L. , Kirven Nicole A. , Shao Chunlei , Ke Lei , Lovell Scott , Barnoud Thibaut , Lu David Y. , Lin Cindy , Kannan Toshitha , Battaile Kevin P. , Yang Tyler Hong Loong. , Batista Oliva Isabela , Claiborne Daniel T. , Vogel Peter , Liu Lijun , Liu Qin , Nefedova Yulia , Cassel Joel , Auslander Noam , Kossenkov Andrew V. , Karanicolas John , Murphy Maureen E.
Published: September 2024

Extra crystallographic data for p53Y107H.
Supplementary Figures S1-S8 from An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression
Authors: Indeglia Alexandra , Leung Jessica C. , Miller Sven A. , Leu Julia I-Ju , Dougherty James F. , Clarke Nicole L. , Kirven Nicole A. , Shao Chunlei , Ke Lei , Lovell Scott , Barnoud Thibaut , Lu David Y. , Lin Cindy , Kannan Toshitha , Battaile Kevin P. , Yang Tyler Hong Loong. , Batista Oliva Isabela , Claiborne Daniel T. , Vogel Peter , Liu Lijun , Liu Qin , Nefedova Yulia , Cassel Joel , Auslander Noam , Kossenkov Andrew V. , Karanicolas John , Murphy Maureen E.
Published: September 2024

Supplementary Figure S1. The Y107H variant of p53 is comparable to WT p53 for growth suppression and apoptosis.
Supplementary Figure S2. The Y107H variant is impaired for transactivation of a subset of p53 target genes, including PADI4, PLTP, and HHAT.
Supplementary Figure S3. The Y107H protein is impaired for binding to p53 response elements.
Supplementary Figure S4. Structural analysis of the Y107H variant shows similar structure but decreased thermal stability and increased propensity to misfold into mutant p53 conformation.
Supplementary Figure S5. Mice with the Y107H variant have increased cancer risk.
Supplementary Figure S6. Colorectal cancer cells harboring hypomorphic variants have increased sensitivity to the glutaminase inhibitor CB-839.
Supplementary Figure S7. PADI4 is a p53 target and has tumor suppressive activity.
Supplementary Figure S8. PADI4 correlates with increased immune signatures and wild-type p53 in human cancers.
Supplementary Table S1 from Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy GX. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Helena , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: September 2024

Data collection and refinement statistics for the IL-3R ternary complex crystal structure.
Figure S6 from Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy GX. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Helena , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: September 2024

Increasing IL3Rα/βc ratios lead to hexameric receptor assembly and augmented quiescence.
Supplementary Figures S1-S18 from FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer
Authors: Wilde Blake R. , Chakraborty Nishma , Matulionis Nedas , Hernandez Stephanie , Ueno Daiki , Gee Michayla E. , Esplin Edward D. , Ouyang Karen , Nykamp Keith , Shuch Brian , Christofk Heather R.
Published: September 2024

Supplementary Fig. S1: Analysis of FH variants and their associated interpretations of pathogenicity. Supplementary Fig. S2: Kinetic parameters for active/partially-active VUS/CI. Supplementary Fig. S3: Recombinant FH produced for 74 VUS/CI. Supplementary Fig. S4: Michaelis-Menten graphs for VUS/CI incubated with fumarate. Supplementary Fig. S5: Michaelis-Menten graphs for VUS/CI incubated with malate. Supplementary Fig. S6: Broad analysis of recombinant FH. Supplementary Fig. S7: Multimerization status of 74 VUS/CI. Supplementary Fig. S8: Tetramerization correlates with catalytic activity. Supplementary Fig. S9: Expression of FH variants in HLRCC cells. Supplementary Fig. S10: Fumarate accumulation decreases TCA intermediates. Supplementary Fig. S11: FH loss enhances de novo glutathione biosynthesis. Supplementary Fig. S12: Coessentiality of FH and nucleotide biosynthesis genes. Supplementary Fig. S13: Loss of FH activity disrupts de novo purine biosynthesis. Supplementary Fig. S14: Dysregulated purine metabolism is independent of HLRCC cell proliferation rate. Supplementary Fig. S15: FH-deficient cells use the purine salvage pathway to maintain purine nucleotide levels. Supplementary Fig. S16: Pyrimidine metabolism in FH-deficient and FH-expressing cells. Supplementary Fig. S17: Disrupting expression of purine salvage enzymes impairs tumor growth. Supplementary Fig. S18: Purine salvage inhibitor 6-mercaptopurine (6-MP) impairs tumor growth.
Supplementary Video S9 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Video S9 shows the clustering video of siALCAM1 transfected ST6KO cells presented in Fig.5E.
Supplementary Video S17 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Video S17 shows the clustering video of siCD97 transfected ST6WT cells presented in Supplementary Fig.S14B.
Supplementary Video S14 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Video S14 shows the clustering video of scrRNA transfected ST6WT cells presented in Fig.5E.
Supplementary Excel S5 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Excel S5 shows sialylopeptides of glycoproteins.
Supplementary Excel S2 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Excel S2 shows SNA binding on patient CTCs analyzed by flow cytometry.
Supplementary Figure S1-S6 from Mitochondrial-encoded complex I impairment induces a targetable dependency on aerobic fermentation in Hurthle cell carcinoma of the thyroid
Authors: Frank Anderson R. , Li Vicky , Shelton Spencer D. , Kim Jiwoong , Stott Gordon M. , Neckers Leonard M. , Xie Yang , Williams Noelle S. , Mishra Prashant , McFadden David G.
Published: September 2024

Supplementary Figure S1 shows validation of key genetic features in NCI-237 and metabolic characterization of thyroid cancer cell lines. Supplementary Figure S2 shows growth curves and depletion/enrichment plots for pooled CRISPR-Cas9 screens. Supplementary Figure S3 shows validation of complex I impairment conferring sensitivity to LDH inhibition. Supplementary Figure S4 shows metabolic profiling of LDH inhibition in NCI-237 cells. Supplementary Figure S5 shows the validation of NADH-oxidizing enzymes and that NAD+ regeneration rescues LDH inhibition. Supplementary Figure S6 shows that LDH inhibition impairs NCI-237-R PDX proliferation.
Supplementary Figure S2 from RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Toure B. Barry. , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schonherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: September 2024

Supplementary Figure 2. Treatment with RLY-4008 is well-tolerated and leads to dose-dependent inhibition of FGFR2 and tumor regression in multiple FGFR2-altered tumor models.
Supplementary Figure S1 from RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Toure B. Barry. , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schonherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: September 2024

Supplementary Figure 1. RLY-4008 is an irreversible inhibitor of FGFR2.
Table S8 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: September 2024

Comparisons in cell type proportions predicted by RCTD between LG and HGPDAC epilesional, jutxalesional, and perilesional spots.
Supplementary Video 3 from GABA regulates electrical activity and tumor initiation in melanoma
Authors: Tagore Mohita , Hergenreder Emiliano , Perlee Sarah C. , Cruz Nelly M. , Menocal Laura , Suresh Shruthy , Chan Eric , Baron Maayan , Melendez Stephanie , Dave Asim , Chatila Walid K. , Nsengimana Jeremie , Koche Richard P. , Hollmann Travis J. , Ideker Trey , Studer Lorenz , Schietinger Andrea , White Richard M.
Published: September 2024

3D rendering of gephyrin positive clusters in melanoma/keratinocyte co-cultures
Supplementary Video 2 from GABA regulates electrical activity and tumor initiation in melanoma
Authors: Tagore Mohita , Hergenreder Emiliano , Perlee Sarah C. , Cruz Nelly M. , Menocal Laura , Suresh Shruthy , Chan Eric , Baron Maayan , Melendez Stephanie , Dave Asim , Chatila Walid K. , Nsengimana Jeremie , Koche Richard P. , Hollmann Travis J. , Ideker Trey , Studer Lorenz , Schietinger Andrea , White Richard M.
Published: September 2024

3D rendering of melanoma/switched keratinocyte contacts and stained vesicles in human melanoma/keratinocyte co-cultures
Supplementary Table 2 from GABA regulates electrical activity and tumor initiation in melanoma
Authors: Tagore Mohita , Hergenreder Emiliano , Perlee Sarah C. , Cruz Nelly M. , Menocal Laura , Suresh Shruthy , Chan Eric , Baron Maayan , Melendez Stephanie , Dave Asim , Chatila Walid K. , Nsengimana Jeremie , Koche Richard P. , Hollmann Travis J. , Ideker Trey , Studer Lorenz , Schietinger Andrea , White Richard M.
Published: September 2024

RNA-seq and GSEA results in switched vs non-switched keratinocytes
Supplementary Table 1 from GABA regulates electrical activity and tumor initiation in melanoma
Authors: Tagore Mohita , Hergenreder Emiliano , Perlee Sarah C. , Cruz Nelly M. , Menocal Laura , Suresh Shruthy , Chan Eric , Baron Maayan , Melendez Stephanie , Dave Asim , Chatila Walid K. , Nsengimana Jeremie , Koche Richard P. , Hollmann Travis J. , Ideker Trey , Studer Lorenz , Schietinger Andrea , White Richard M.
Published: September 2024

LOPAC Screen results in melanoma keratinocyte co-cultures
Table S6 from Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment
Authors: van der Leun Anne M. , Traets Joleen J.H. , Vos Joris L. , Elbers Joris B.W. , Patiwael Sanne , Qiao Xiaohang , Machuca-Ostos Mercedes , Thommen Daniela S. , Haanen John B.A.G. , Schumacher Ton N.M. , Zuur Charlotte L.
Published: September 2024

Differentially expressed genes in the NK cell subpopulations of non-responding patients between post- versus pre-treatment.
Figure S2 from Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment
Authors: van der Leun Anne M. , Traets Joleen J.H. , Vos Joris L. , Elbers Joris B.W. , Patiwael Sanne , Qiao Xiaohang , Machuca-Ostos Mercedes , Thommen Daniela S. , Haanen John B.A.G. , Schumacher Ton N.M. , Zuur Charlotte L.
Published: September 2024

Cell state fractions and transcriptional differences at baseline.
Supplementary Table S4 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. , Janne Pasi A. , Haddox Candace L. , Papadopoulos Kyriakos P. , Henry Jason T. , Leventakos Konstantinos , Christensen James G. , Shazer Ronald , Olson Peter
Published: September 2024

Treatment-related treatment-emergent adverse events by preferred term and maximum grade safety population
Supplementary Table 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. , Janne Pasi A. , Haddox Candace L. , Papadopoulos Kyriakos P. , Henry Jason T. , Leventakos Konstantinos , Christensen James G. , Shazer Ronald , Olson Peter
Published: September 2024

Hematological parameters in CD-1 mice treated with MRTX11719
Supplementary Figures from Influence of adipose tissue distribution, sarcopenia, and nutritional status on clinical outcomes after CD19 CAR T-cell therapy
Authors: Rejeski Kai , Cordas dos Santos David M. , Parker Nathan H. , Bücklein Veit L. , Winkelmann Michael , Jhaveri Khushali S. , Liu Lian , Trinkner Paul , Günther Sophie , Karschnia Philipp , Blumenberg Viktoria , Schmidt Christian , Kunz Wolfgang G. , von Bergwelt-Baildon Michael , Jain Michael D. , Theurich Sebastian , Subklewe Marion
Published: September 2024

Supplementary Figures
Supplementary Figure 6 from Regional variation in the tumor microenvironment, immune escape and prognostic factors in breast cancer in sub-Saharan Africa
Authors: Bauer Marcus , Vetter Martina , Stückrath Kathrin , Yohannes Meron , Desalegn Zelalem , Yalew Tewodros , Bekuretsion Yonas , Kenea Tariku W. , Joffe Maureen , Van Den Berg Eunice J. , Nikulu Julien Ilunga. , Bakarou Kamaté , Manraj Shyam S. , Ogunbiyi Olufemi J. , Ekanem Ima-Obong , Igbinoba Festus , Diomande Mohenou , Adebamowo Clement , Dzamalala Charles P. , Anele Angelica A. , Zietsman Annelle , Galukande Moses , Foerster Milena , dos-Santos-Silva Isabel , Liu Biying , Santos Pablo , Jemal Ahmedin , Abebe Tamrat , Wickenhauser Claudia , Seliger Barbara , McCormack Valerie , Kantelhardt Eva J.
Published: September 2024

Figure S6: Multivariate Cox regression analysis of patient's survival.
Supplemental Table 2 from mWTX-330, an IL 12 INDUKINE Molecule, Activates and Reshapes Tumor-infiltrating CD8+ T and NK Cells to Generate Antitumor Immunity
Authors: Nirschl Christopher J. , Brodkin Heather R. , Domonkos Celesztina , Dwyer Connor J. , Hicklin Daniel J. , Ismail Nesreen , Seidel-Dugan Cynthia , Steiner Philipp , Steuert Zoe , Sullivan Jenna M. , Winston William M. , Salmeron Andres
Published: September 2024

Differential Gene Expression Analysis of Bulk RNA from MC38 Tumors After mWTX-330 Treatment
Table S3 from MYC induces immunotherapy and interferon-γ resistance through downregulation of JAK2
Authors: Markovits Ettai , Harush Ortal , Baruch Erez N. , Shulman Eldad D. , Debby Assaf , Itzhaki Orit , Anafi Liat , Danilevsky Artem , Shomron Noam , Ben-Betzalel Guy , Asher Nethanel , Shapira-Frommer Ronnie , Schachter Jacob , Barshack Iris , Geiger Tamar , Elkon Ran , Besser Michal J. , Markel Gal
Published: September 2024

Comparison between proteome and transcriptome profiling. Related to Figure 1.
Table S1 from MYC induces immunotherapy and interferon-γ resistance through downregulation of JAK2
Authors: Markovits Ettai , Harush Ortal , Baruch Erez N. , Shulman Eldad D. , Debby Assaf , Itzhaki Orit , Anafi Liat , Danilevsky Artem , Shomron Noam , Ben-Betzalel Guy , Asher Nethanel , Shapira-Frommer Ronnie , Schachter Jacob , Barshack Iris , Geiger Tamar , Elkon Ran , Besser Michal J. , Markel Gal
Published: September 2024

Primers and Antibodies used in this paper.
Supplementary Figure 8 from MYC induces immunotherapy and interferon-γ resistance through downregulation of JAK2
Authors: Markovits Ettai , Harush Ortal , Baruch Erez N. , Shulman Eldad D. , Debby Assaf , Itzhaki Orit , Anafi Liat , Danilevsky Artem , Shomron Noam , Ben-Betzalel Guy , Asher Nethanel , Shapira-Frommer Ronnie , Schachter Jacob , Barshack Iris , Geiger Tamar , Elkon Ran , Besser Michal J. , Markel Gal
Published: September 2024

Supplementary Figure 8
Supplementary Table 1 from CCRL2 expression by specialized lung capillary endothelial cells controls NK-cell homing in lung cancer
Authors: Sozio Francesca , Schioppa Tiziana , Laffranchi Mattia , Salvi Valentina , Tamassia Nicola , Bianchetto-Aguilera Francisco M. , Tiberio Laura , Bonecchi Raffaella , Bosisio Daniela , Parmentier Marc , Bottazzi Barbara , Leone Roberto , Russo Eleonora , Bernardini Giovanni , Garofalo Stefano , Limatola Cristina , Gismondi Angela , Sciumè Giuseppe , Mantovani Alberto , Del Prete Annalisa , Sozzani Silvano
Published: September 2024

Supplementary Table 1
Data from HER2∆16 Engages ENPP1 To Promote an Immune Cold Microenvironment in Breast Cancer
Authors: Attalla Sherif Samer. , Boucher Jonathan , Proud Hailey , Taifour Tarek , Zuo Dongmei , Sanguin-Gendreau Virginie , Ling Chen , Johnson Gabriella , Li Vincent , Luo Robin B. , Kuasne Hellen , Papavasiliou Vasilios , Walsh Logan A. , Barok Mark , Joensuu Heikki , Park Morag , Roux Philippe P. , Muller William J.
Published: September 2024

Abstract
The tumor immune microenvironment (TIME) is a critical determinant of therapeutic response. However, the mechanisms regulating its modulation are not fully understood. HER216, an oncogenic splice variant of the human epidermal growth factor receptor (HER2), has been implicated in breast cancer and other tumor types as a driver of tumorigenesis and metastasis. Nevertheless, the underlying mechanisms of HER2Δ16-mediated oncogenicity remain poorly understood. Here, we show that HER2∆16 expression is not exclusive to the clinically HER2+ subtype and associates with a poor clinical outcome in breast cancer. To understand how HER2 variants modulated the tumor microenvironment, we generated transgenic mouse models expressing either proto-oncogenic HER2 or HER2∆16 in the mammary epithelium. We found that HER2∆16 tumors were immune cold, characterized by low immune infiltrate and an altered cytokine profile. Using an epithelial cell surface proteomic approach, we identified ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) as a functional regulator of the immune cold microenvironment. We generated a knock-in model of HER2Δ16 under the endogenous promoter to understand the role of Enpp1 in aggressive HER2+ breast cancer. Knockdown of Enpp1 in HER2Δ16-derived tumor cells resulted in decreased tumor growth, which correlated with increased T-cell infiltration. These findings suggest that HER2Δ16-dependent Enpp1 activation associates with aggressive HER2+ breast cancer through its immune modulatory function. Our study provides a better understanding of the mechanisms underlying HER2Δ16-mediated oncogenicity and highlights ENPP1 as a potential therapeutic target in aggressive HER2+ breast cancer.
Supplementary Table S5 from In vivo screening unveils pervasive RNA-binding protein dependencies in leukemic stem cells and identifies ELAVL1 as a therapeutic target
Authors: Vujovic Ana , de Rooij Laura , Keyvani Chahi Ava , Chen He Tian , Yee Brian A. , Loganathan Sampath K. , Liu Lina , Chan Derek C. H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Balde Zaldy , Jahangiri Soheil , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J.
Published: September 2024

Table S5 shows the log2 fold change of differentially expressed transcripts from the ELAVL1 knockout RN2c RNA-sequencing data set.
Supplementary Figure S6 from In vivo screening unveils pervasive RNA-binding protein dependencies in leukemic stem cells and identifies ELAVL1 as a therapeutic target
Authors: Vujovic Ana , de Rooij Laura , Keyvani Chahi Ava , Chen He Tian , Yee Brian A. , Loganathan Sampath K. , Liu Lina , Chan Derek C. H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Balde Zaldy , Jahangiri Soheil , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J.
Published: September 2024

Supplemental Figure S6 shows the GSEA of ELAVL1 depletion in mouse RN2c and human primary AML cells, ELAVL1 subcellular localization in mouse and human AML, the qRT-PCR of ELAVL1 targets in MS-444-treated RN2c cells, and the integrative analysis of the mouse RNA-seq and eCLIP-seq.
Supplementary Tables S1, S2, S5-S13 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

Supplementary Tables S1, S2, S5-S13 includes Supplementary Tables S1, S2, S5-S13.
Supplementary Table S1 provides a summary of BL and DHL patient demographics for the immunohistochemistry study presented in Fig. 1, E and F.
Supplementary Table S2 lists the MYC-dysregulated genes whose expression is significantly altered following depletion of eIF5A or DHPS, related to Fig. 4F.
Supplementary Table S5 shows DHPS GISTIC count and survival of select TCGA PanCancer datasets, related to Fig. 7J.
Supplementary Table S6 shows the genetic mouse models used in this study, related to Methods.
Supplementary Table S7 shows the mouse and human cell lines used in this study, related to Methods.
Supplementary Table S8 lists the antibodies used in this study, related to Methods.
Supplementary Table S9 lists reagents used in this study, related to Methods.
Supplementary Table S10 summarizes the plasmids used in this study, related to Methods.
Supplementary Table S11 lists the sequences of the oligonucleotides used in this study, related to Methods.
Supplementary Table S12 lists accession numbers and publicly deposited data from this study, related to Methods.
Supplementary Table S13 lists software and algorithms used in this study, related to Methods.
Sotorasib in KRAS p.G12C-Mutated Pulmonary Sarcomatoid Carcinoma: Therapeutic Efficacy of a KRAS Inhibitor in Symptomatic Brain Metastases
Authors: Schmidt Jonas Frederik , Entz Dominik , Brasch Frank , Goerner Martin
Published: September 2024

Introduction: Pulmonary sarcomatoid carcinomas (PSCs) are a rare subgroup of non-small cell lung cancer (NSCLC). In contrast to other NSCLCs, PSCs have a poor prognosis due to limited efficacy of radiation and chemotherapy. Therefore, other therapeutic approaches are needed. KRAS mutations occur in PSC with a significant proportion of 30%, and most of them are G12C with the therapeutic option of sotorasib. Case Report: Here, we describe the case of a patient with PSC and pleural metastases. After first-line chemotherapy, the patient presented with new neurological symptoms such as a hemiparesis of the right arm and focal seizures. Following the detection of new brain metastases, we switched the therapy to sotorasib due to the presence of a KRAS G12C mutation. During treatment with sotorasib, the patient’s condition worsened progressively and his neurological symptoms got more severe. A CCT performed during the course of treatment showed progression of the brain metastases. After 48 days being on drug, decision to discontinuate therapy with sotorasib due to patient’s inability to take oral medication and change to a best supportive care concept was made. The patient died few weeks after termination of therapy with rapidly progressive disease. Discussion/Conclusion: This case emphasizes the poor prognosis of patients with PSC due to a lack of therapeutic response to chemotherapy, radiation, and, as seen in this case, current targeted therapy as well. Our case emphasizes the need to further evaluate therapeutic responses of targeted therapy in this rare subtype of NSCLC.
Desert–Oasis Convergence Line and Deep Convection Experiment (DECODE)
Authors: Meng Zhiyong , Meng Xuefeng , Wang Chenggang , Huang Yipeng , Zhang Shuhao , Liu Hongjun , Zhang Murong , Liu Yijing , Huang Hao , Su Lijuan , Cui Quxin , Lu Feng , Zhao Kun , Zhu Lei , Wang Li , Zhou Zhihua , Liu Linchun , Ma Xuefeng , Shan Jiutao , Xiao Yao , Zhu Daoru , Yang Zhengwei , Zheng Xucheng , Bo Fan , Bai Lanqiang , Yao Xiaojuan , Sun Yonggang , Lin Manyun , Zheng Zimeng , Zhou Liao , Wang Xuelei , Liu Ke , Chen Luyi , Yao Lebao , Guan Ming , Kong Weikang , Sun Shaoyang , Wang Jiaxin , Wu Yikai , Qin Yaqi , Jiang Xiaoying , Pan Xiang , Wang Mufei , Zhang Changan , Tuo Yanjun , Li Hanchao , Li Hui , Shi Lixia , Fang Xiaohong , Zhu Feng , Sun Xin , Yun Jingbo , Liu Shiyun , Wang Huiqing , Yang Yawen , Wen Jingyi , Wang Peiyu , Liu Lanbo , Ren Nan , Wu Xiufeng , Zhang Zhengyue , Pei Jianyu , Yang Zhi , Xia Cheng
Published: September 2024

The heterogeneous land surface spanning the Yellow River irrigated oasis and the adjacent Kubuqi and Ulan Buh Desert (Hetao area) in Inner Mongolia, China, has been noted to frequently generate planetary boundary layer convergence line (BLCL), providing an important source of low-level lifting for convection initiation (CI). As the first field experiment to collect comprehensive observations of vegetation-contrast-resulting thermal circulations that consistently generate BLCLs and lead to CI, the Desert–Oasis Convergence Line and Deep Convection Experiment (DECODE) was conducted from 5 July to 9 August 2022 in the Hetao area. Two oasis and four desert observation sites were set up in the region that exhibits the highest frequency of BLCL and CI occurrences, equipped with a suite of advanced instruments probing land–atmosphere interactions, planetary boundary layer processes, and evolution of BLCLs and their associated CI, including Doppler lidars, microwave radiometers, soil temperature and moisture sensors, eddy covariance systems, portable radiosondes, C-band polarimetric Doppler radar, aircraft, and Geostationary High-speed Imager onboard FY-4B satellite. DECODE captured 29 BLCLs (16 with CI), 66 gust fronts, 12 horizontal convective rolls, and one tornado. The observations unveiled full thermal circulations spanning the desert–oasis boundary characterized by a horizontal width of ∼25 km, a convergence height of ∼1 km above ground level (AGL), and divergence from 2 to ∼3.5 km AGL, with vertical wind speeds of up to 2 m s−1. Future publications stemming from DECODE will delve into a spectrum of scientific inquiries, including but not limited to land surface and boundary layer processes, BLCL dynamics, CI mechanisms, convective organization, predictability, and model evaluation.
Factors contributing to the development of health-promoting schools, applying Fullan’s triple change model – A qualitative study
Authors: Zak Yehuda Ayala , Baron-Epel Orna
Published: September 2024

Objective:

Schools and the education system are powerful tools for cultivating healthy lifestyles. This research focuses on characterising the factors contributing to the development of health-promoting schools in Israel, and understanding how schools can offer a framework for improving students’ health. Fullan’s triple change model with its focus on three phases in the change process in schools – the initiation phase, the implementation phase and the institutionalisation phase – served as a framework for analysis.

Design and setting:

This qualitative-constructivist study involved the analysis of data collected from 26 elementary school principals in Israel, 15 of whom belonged to the health promotion school network (HPSN) and 11 who did not. In addition, 10 health promotion leaders from within the schools were interviewed.

Methods:

Data collection took place by means of semi-structured interviews. in which the questions asked referred to the three phases identified in Fullan’s process of change model. We analysed the data using thematic content analysis.

Results:

Each identified theme was associated with one of the phases proposed in Fullan’s model of change. The initiation phase included collaboration with key stakeholders, principals’ personal commitment, and dissemination of ideas through personal connections. The implementation phase included gaining access to appropriate tools and materials, action to deal with barriers to change, and the creation of a holistic health promotion environment. The institutionalisation phase included the development of administrative strategies such as adherence to routines, the inclusion of regular events in the school calendar, and the allocation of time frames for the activities undertaken.

Conclusion:

Fullan’s model proved useful in analysing efforts to develop health-promoting schools. The model signalled the importance of using a structured approach throughout the institutionalisation phase in a manner attuned to the unique nature of the school. Alongside identifying key factors that support assimilation, it is crucial to assess their integration into the school culture. The school principal’s role is critical throughout all the phases of the development process.
Nine Critical Factors in Prosecution Decision-Making
Authors: Widdicombe Ben
Published: September 2024

Prosecutors are critical players in the criminal justice process. The decisions they make have huge implications for defendants, victims and the wider public. Yet, the factors that influence their decisions are little understood. This article presents new empirical findings drawn from interviews with Crown Prosecutors. It reveals nine important factors that influence Crown Prosecutor decision-making. Together, these nine factors paint a much wider and richer picture of how and why Crown Prosecutors make decisions than has hitherto been presented in research or that is described in the Code for Crown Prosecutors. The article concludes by considering the implications for prosecution policy and practice from this new, richer and wider perspective.
Open and Shut: Circulating People and Goods, Pollution, and History in the Canals of Suzhou
Authors: Carroll Peter J.
Published: September 2024

This article considers the twentieth- and twenty-first-century reinterpretation and reconfiguration of Suzhou’s canals in light of their use as a means of transport and flood control, and as a source of pollution. Throughout the Maoist period (1949-1976), the regime considered canals to be anachronistic impediments to urban renewal and filled in many urban waterways to create modern streets, industrial land, and fall-out shelters. Remaining canals were exploited for a variety of uses, including drains for pollutants as the city industrialized. In the Reform Era, from 1978 onwards, environmental protection mandates, fines for polluting paper mills and chemical plants, and the diversion of industrial and population growth to new sites restored Suzhou’s canals and public gardens as tourism and recreation assets. The archaic origin and historicity of the city’s canals, which previously inspired their destruction, now impels their refurbishment and validation as essential infrastructure of the modern city.
Numerical and experimental investigation of extrusion processes from coil
Authors: Leicht Miriam , Merklein Marion
Published: September 2024

The use of coil material as semi-finished product in sheet-bulk metal forming (SBMF), offers the possibility to use high-speed presses and thus to achieve high output quantities. However, compared to industrially established forming of pre-cut blanks, the reduced geometric accuracy of the parts due to the asymmetrical material flow represents a challenge. Against this background, the aim of this study is to gain an in-depth knowledge on the influence of the process setup on the material flow direction and on the forming of geared functional parts. A combined numerical-experimental approach of each a lateral and a backward extrusion process of a DC04 sheet metal ( t0 = 2 mm) is applied for a fundamental process analysis. For this purpose, process-dependent causes for the asymmetric part forming are analyzed by means of material flow simulations. Subsequently, the numerical results are verified experimentally in terms of the part geometry, the process force and grain structural changes. Based on the numerical and experimental results, cause-effect relations between material flow, part accuracy and tool load are derived. In addition, the transferability of the causes of the asymmetric material flow to processes with different primary material flow directions and part geometries is verified. The findings facilitate the future counteraction of asymmetrical material flow in SBMF from coil, which in turn leads to enhanced component quality.
Simultaneous effects of different nanoparticles integrations on fiberglass sandwich panels under low-velocity impact
Authors: Emamieh Hamid Reza , Tooski Mehdi Yar Mohammad
Published: September 2024

The incorporation of nanoparticles has been recognized as one of the methods of reinforcement of sandwich panels as an effective substitute for popular materials such as metals. This study has examined the low-velocity impact responses of two groups of nanocomposite sandwich panels at different energy levels. Clay-silica nanoparticles and nanoclay-carbon nanotube (CNT) were integrated as nanofillers into the face sheets of sandwich panels. The sandwich panel with glass fibers/epoxy face sheets and a PVC core was fabricated by the hand layup method. The Contact force-time and contact force-displacement curves were recorded at various energy levels of 15, 30, and 50 J. The simultaneous presence of nanoclay and CNT increased impact resistance by 43.2%, 19.8%, and 10.26% at energy levels of 15, 30, and 50 J, respectively, in comparison with the reference sample without nano-particle whereas the presence of nano-silica with nano-clay at some weight fractions weakened the impact resistance. The analysis of SEM images indicates the proper distribution of nanoparticles and the uniform distribution of CNT leading to the increase in impact properties, which are compatible with the mechanical results.
Toiling for oil: Daqing, real utopias and the production of livelihood in communist China
Authors: Collins Joe
Published: September 2024

This dialogical interrogation of Hou Li’s important history of Daqing examines the contradictions of structure and agency in the building of communist China’s first oil city. Three provocations are raised. Two relate to ecology: the first on the ecological dimension of extractivism, which requires careful consideration in light of the current status of CO2 emissions per capita, with China accounting for about half the emissions of fossil fuel exporters like Australia; the second on how extractivism and decarbonization can be considered in light of recent claims that the US military was the world’s largest consumer of hydrocarbons in 2019. The third relates to the ambiguity of the term “capital” in economic discourse, which invariably finds its way into cognate scholarly disciplines, such as historical inquiry and urban planning.
Revisiting Building for Oil: Daqing and the Formation of the Chinese Socialist State
Authors: Zhang Jing
Published: September 2024

This review provides a brief introduction and examination of Hou Li’s book Building for Oil: Daqing and the Formation of the Chinese Socialist State. It highlights the historical background of the book, identifies its research questions and summarizes its key themes. The review concludes with a discussion of the book’s distinctive contributions and critiques that may further enrich the analysis or inspire future book projects on the subject.
Assessment of Sodium Butyrate’s Pharmacological Effects on Gentamicin-induced Nephrotic Disorders in a Rat Model
Authors: Kumar Sunil , Sindhu Rakesh Kumar
Published: September 2024

Background

Sodium butyrate (SB) used to increase oxidative stress was reduced and the glutathione redox pathway was boosted. It inhibits proliferation, induction of differentiation, and induction or repression of gene expression and it has also anti-inflammatory action. This is endorsed for suppression of nephrotic symptoms.

Objectives

The present study was carried out to evaluate the nephroprotective activity of SB on gentamicin-induced nephrotoxicity in rats.

Materials and Methods

Present research work was designed to estimate pharmacological potential of SB in gentamicin-induced nephrotic disorder. The pharmacological prospective was estimated in gentamicin-induced rats through the oral administration of SB formulation 200 mg/kg and 300 mg/kg BW.

Results

The study observed that the SB significantly protects the kidneys from gentamicin-induced nephrotic disorders. Gentamicin 100 mg/kg for 7 days was used for induction of nephrotoxicity in Wistar rats by intraperitoneal administration. The administration of SB was observed to decrease the occurrence of glomerular congestion, vascular congestion, epithelial desquamation, inflammatory cell build-up, and kidney cell necrosis induced by gentamicin. The dose of SB maintained the gentamicin-induced increased creatinine (0.62±0.05), serum urea (18.10±0.79), uric acid (2.10±0.28), and blood urea nitrogen (BUN) (17.56±0.55) levels. This fact is further sustained by the histopathological examinations.

Conclusion

Sodium butyrate formulation with antinephrotic activity in maintaining uremic solutes such as urea, uric acid, creatinine, BUN, ketone, urobilinogen, glucose, specific gravity, and urine pH in Wistar rats with gentamicin-induced glomerulonephritis (GN). The SB was administered to the animals at doses of 200 and 300 mg/kg body weight. Pretreatment with the drug showed promising results in maintaining elevated parameters in nephritic rats within a short duration.
Risk Factors of Sepsis-Associated Thrombocytopenia among Patients with Sepsis Induced Coagulopathy
Authors: Cheng Jia-Jia , Liufu Rong , Zhuang Jian , Chen Miao-Yun
Published: September 2024

The study aims to evaluate the prognosis and risk factors of sepsis-associated thrombocytopenia (SAT) among patients with coagulopathy, and to provide evidence of the relationship between adverse outcomes and potential risks. Patients with sepsis-associated coagulopathy were included in the study from January 2014 to December 2022. The primary outcome was sepsis-associated thrombocytopenia (platelet count less than 100 *109/L), which was evaluated by logistic regression models adjusted for demographic characteristics and comorbidities. Among patients in the SAT group, 54% developed severe SAT, while 16% of these patients recovered from thrombocytopenia. The in-hospital mortality rate was significantly higher in the SAT group compared to the non-SAT group (31% in SAT group vs 23.9% in non-SAT group, p = 0.029). Even after adjusting for age, gender, Charlson comorbidity, white blood cell, and Sequential Organ Failure Assessment score, the differences in mortality rate persisted (Odds Ratio 0.72, [95% Confidence Interval 0.52–0.92]). Correlation analyses revealed that prothrombin time (r = 0.08, p = 0.50), international normalized ratio (r = 0.08, p = 0.42), prothrombin activity (r = −0.06, p > 0.999), D-dimer (r = −0.02, p > 0.999), and inflammatory parameters such as C-reactive protein (r = −0.11, p = 0.37) were not significantly correlated with platelet counts. According to subgroup analyses, patients with lung infection complicated by SAT had slightly higher mortality (OR 0.66, [95% CI, 0.46 to 0.94]). Sepsis-associated coagulopathy indicates a subset of critical ill patients, with those experiencing thrombocytopenia at greater risk for in-hospital death compared to those without it.
LMI-based state observer design for supercavitating vehicles with time delay
Authors: Han Yuntao , Sun Jie , Bai Tao , Li Yakun , Ma Xianjie
Published: September 2024

Due to the existence of the planing force, the control of the supercavitating vehicle is difficult, and the vertical velocity which has a great influence on the planing force cannot be directly measured. Therefore, considering the time-delay effect of the planing force and the external disturbance, the state observer and controller based on linear matrix inequality (LMI) have been designed. By decomposing the planing force into two parts of time delay and non-time delay, and a longitudinal plane Linear Parameter Varying (LPV) time-delay model for supercavitating vehicles is derived. In addition, the controller and state observer for the supercavitating vehicle system with time-delay characteristics and external disturbances are simultaneously designed. The gains of the controller and observer are obtained by combining the theory of linear matrix inequalities and convex polytopes, ensuring the convergence of estimation error. At the same time, taking into account the possibility of exceeding the physical limits of the actuator when the input value is too large, the compensator has been added. Finally, the simulation results demonstrate that the designed controller exhibits good stability and tracking performance.