bluuebunny/crossref_metadata_2025 huggingface dataset:
Table S3 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: June 2023

Detailed summary of drugs prioritized for testing in PDX models, based on rank of OncoTarget and OncoTreat predictions by –log10(Bonferroni p).
Table S1 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: June 2023

Summary of enrollment for the N of 1 trial to date, including numbers by cancer type, the attempt to develop a PDX, establishment of PDX, RNASeq/VIPER profiling of PDX when established, and completion of drug testing.
Supplementary Figures Part 1 from Analysis of Donor Pancreata Defines the Transcriptomic Signature and Microenvironment of Early Neoplastic Lesions
Authors: Carpenter Eileen S. , Elhossiny Ahmed M. , Kadiyala Padma , Li Jay , McGue Jake , Griffith Brian D. , Zhang Yaqing , Edwards Jacob , Nelson Sarah , Lima Fatima , Donahue Katelyn L. , Du Wenting , Bischoff Allison C. , Alomari Danyah , Watkoske Hannah R. , Mattea Michael , The Stephanie , Espinoza Carlos E. , Barrett Meredith , Sonnenday Christopher J. , Olden Nicholas , Chen Chin-Tung , Peterson Nicole , Gunchick Valerie , Sahai Vaibhav , Rao Arvind , Bednar Filip , Shi Jiaqi , Frankel Timothy L. , Pasca di Magliano Marina
Published: June 2023

Supplementary Figures 1-10 and associated legends
Supplementary Table S6 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Authors: Nowicki-Osuch Karol , Zhuang Lizhe , Cheung Tik Shing , Black Emily L. , Masqué-Soler Neus , Devonshire Ginny , Redmond Aisling M. , Freeman Adam , di Pietro Massimilliano , Pilonis Nastazja , Januszewicz Wladyslaw , O'Donovan Maria , Tavaré Simon , Shields Jacqueline D. , Fitzgerald Rebecca C.
Published: June 2023

This table contains marker genes identified in the pairwise comparison of clusters identified in fibroblast population
Supplementary Table S5 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Authors: Nowicki-Osuch Karol , Zhuang Lizhe , Cheung Tik Shing , Black Emily L. , Masqué-Soler Neus , Devonshire Ginny , Redmond Aisling M. , Freeman Adam , di Pietro Massimilliano , Pilonis Nastazja , Januszewicz Wladyslaw , O'Donovan Maria , Tavaré Simon , Shields Jacqueline D. , Fitzgerald Rebecca C.
Published: June 2023

This table contains details of mutations identified in WGS of E-GM samples.
Supplementary Table S3 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Authors: Nowicki-Osuch Karol , Zhuang Lizhe , Cheung Tik Shing , Black Emily L. , Masqué-Soler Neus , Devonshire Ginny , Redmond Aisling M. , Freeman Adam , di Pietro Massimilliano , Pilonis Nastazja , Januszewicz Wladyslaw , O'Donovan Maria , Tavaré Simon , Shields Jacqueline D. , Fitzgerald Rebecca C.
Published: June 2023

This table contains marker genes identified in the pairwise comparison of clusters defined as columnar cells.
Supplementary Table S1 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Authors: Nowicki-Osuch Karol , Zhuang Lizhe , Cheung Tik Shing , Black Emily L. , Masqué-Soler Neus , Devonshire Ginny , Redmond Aisling M. , Freeman Adam , di Pietro Massimilliano , Pilonis Nastazja , Januszewicz Wladyslaw , O'Donovan Maria , Tavaré Simon , Shields Jacqueline D. , Fitzgerald Rebecca C.
Published: June 2023

This file contains details of individual samples (including clinical data) used in the sutdy
Supplementary Tables S1-S8 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
Authors: Spain Lavinia , Coulton Alexander , Lobon Irene , Rowan Andrew , Schnidrig Desiree , Shepherd Scott T.C. , Shum Benjamin , Byrne Fiona , Goicoechea Maria , Piperni Elisa , Au Lewis , Edmonds Kim , Carlyle Eleanor , Hunter Nikki , Renn Alexandra , Messiou Christina , Hughes Peta , Nobbs Jaime , Foijer Floris , van den Bos Hilda , Wardenaar Rene , Spierings Diana C.J. , Spencer Charlotte , Schmitt Andreas M. , Tippu Zayd , Lingard Karla , Grostate Lauren , Peat Kema , Kelly Kayleigh , Sarker Sarah , Vaughan Sarah , Mangwende Mary , Terry Lauren , Kelly Denise , Biano Jennifer , Murra Aida , Korteweg Justine , Lewis Charlotte , O'Flaherty Molly , Cattin Anne-Laure , Emmerich Max , Gerard Camille L. , Pallikonda Husayn Ahmed , Lynch Joanna , Mason Robert , Rogiers Aljosja , Xu Hang , Huebner Ariana , McGranahan Nicholas , Al Bakir Maise , Murai Jun , Naceur-Lombardelli Cristina , Borg Elaine , Mitchison Miriam , Moore David A. , Falzon Mary , Proctor Ian , Stamp Gordon W.H. , Nye Emma L. , Young Kate , Furness Andrew J.S. , Pickering Lisa , Stewart Ruby , Mahadeva Ula , Green Anna , Larkin James , Litchfield Kevin , Swanton Charles , Jamal-Hanjani Mariam , Turajlic Samra
Published: June 2023

S. Table 1: List of PEACE Consortium members.
S. Table 2: Sample database used for the study for Panel, Exome and RNASeq samples.
S. Table 3: Overview of lines of treatment given to each patient.
S. Table 4: Lesions and patients included in the lesion-level response to ICI analysis.
S. Table 5: Hallmark genesets significantly upregulated in normal tissue vs tumor tissue. Table shows p-values for tissue type, purity; T value for tissue type, purity; q-value for tissue type, purity (FDR corrected).
S. Table 6: Hallmark genesets significantly upregulated in tumor tissue vs normal tissue. Table shows p-values for tissue type, purity; T value for tissue type, purity; q-value for tissue type, purity (FDR corrected).
S. Table 7: Genes included in the target panel.
S. Table 8: Tree topology comparisons between manually constructed trees and pairtree-constructed trees.
Figure 5 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
Authors: Spain Lavinia , Coulton Alexander , Lobon Irene , Rowan Andrew , Schnidrig Desiree , Shepherd Scott T.C. , Shum Benjamin , Byrne Fiona , Goicoechea Maria , Piperni Elisa , Au Lewis , Edmonds Kim , Carlyle Eleanor , Hunter Nikki , Renn Alexandra , Messiou Christina , Hughes Peta , Nobbs Jaime , Foijer Floris , van den Bos Hilda , Wardenaar Rene , Spierings Diana C.J. , Spencer Charlotte , Schmitt Andreas M. , Tippu Zayd , Lingard Karla , Grostate Lauren , Peat Kema , Kelly Kayleigh , Sarker Sarah , Vaughan Sarah , Mangwende Mary , Terry Lauren , Kelly Denise , Biano Jennifer , Murra Aida , Korteweg Justine , Lewis Charlotte , O'Flaherty Molly , Cattin Anne-Laure , Emmerich Max , Gerard Camille L. , Pallikonda Husayn Ahmed , Lynch Joanna , Mason Robert , Rogiers Aljosja , Xu Hang , Huebner Ariana , McGranahan Nicholas , Al Bakir Maise , Murai Jun , Naceur-Lombardelli Cristina , Borg Elaine , Mitchison Miriam , Moore David A. , Falzon Mary , Proctor Ian , Stamp Gordon W.H. , Nye Emma L. , Young Kate , Furness Andrew J.S. , Pickering Lisa , Stewart Ruby , Mahadeva Ula , Green Anna , Larkin James , Litchfield Kevin , Swanton Charles , Jamal-Hanjani Mariam , Turajlic Samra
Published: June 2023

Tissue-level amplifications and deletions associated with response to ICI. A large proportion of samples underwent WGD (A), with successive WGD events associated with increasing wGII (B). Letters in brackets indicate melanoma subtype: A = acral, C = cutaneous, M = mucosal, U = melanoma of unknown primary. ***, P < 0.001. GISTIC permutation analysis (C) associated MYC amplification (chromosome 8q) with a nonresponsive phenotype, as well as chromosome 1 amplification with a responsive phenotype. Horizontal black dashed lines in top two panels of C indicate significance (P < 0.05). NR, nonresponse; R, response. D, Significant amplifications on chromosomes 1 and 8 from C with COSMIC genes labeled.
Figure 2 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
Authors: Spain Lavinia , Coulton Alexander , Lobon Irene , Rowan Andrew , Schnidrig Desiree , Shepherd Scott T.C. , Shum Benjamin , Byrne Fiona , Goicoechea Maria , Piperni Elisa , Au Lewis , Edmonds Kim , Carlyle Eleanor , Hunter Nikki , Renn Alexandra , Messiou Christina , Hughes Peta , Nobbs Jaime , Foijer Floris , van den Bos Hilda , Wardenaar Rene , Spierings Diana C.J. , Spencer Charlotte , Schmitt Andreas M. , Tippu Zayd , Lingard Karla , Grostate Lauren , Peat Kema , Kelly Kayleigh , Sarker Sarah , Vaughan Sarah , Mangwende Mary , Terry Lauren , Kelly Denise , Biano Jennifer , Murra Aida , Korteweg Justine , Lewis Charlotte , O'Flaherty Molly , Cattin Anne-Laure , Emmerich Max , Gerard Camille L. , Pallikonda Husayn Ahmed , Lynch Joanna , Mason Robert , Rogiers Aljosja , Xu Hang , Huebner Ariana , McGranahan Nicholas , Al Bakir Maise , Murai Jun , Naceur-Lombardelli Cristina , Borg Elaine , Mitchison Miriam , Moore David A. , Falzon Mary , Proctor Ian , Stamp Gordon W.H. , Nye Emma L. , Young Kate , Furness Andrew J.S. , Pickering Lisa , Stewart Ruby , Mahadeva Ula , Green Anna , Larkin James , Litchfield Kevin , Swanton Charles , Jamal-Hanjani Mariam , Turajlic Samra
Published: June 2023

A, Phylogenies inferred for the 14 patients. Only WES samples are included. Letters in brackets indicate melanoma subtype: A = acral, C = cutaneous, M = mucosal, U = melanoma of unknown primary. Branch length is proportional to the number of mutations. Branch colors represent the mutational signatures of the mutations. For clarity, only the most common mutational signatures are shown; the remainder are categorized as “unknown.” Scale bars indicate the number of mutations. The legend includes etiologies for each signature (24). MMR, mismatch repair. B, Boxplots indicate the ratio of subclonal mutations (length of branches) to clonal mutations (length of the trunk) by subtype and chemotherapy status. Values smaller than zero indicate the dominance of truncal mutations. Mann–Whitney U test was used for statistical comparisons (**, P < 0.01; ***, P < 0.001). Cut., cutaneous; mut., mutation.
Supplementary Table S1 from Cell-Autonomous Cxcl1 Sustains Tolerogenic Circuitries and Stromal Inflammation via Neutrophil-Derived TNF in Pancreatic Cancer
Authors: Bianchi Anna , De Castro Silva Iago , Deshpande Nilesh U. , Singh Samara , Mehra Siddharth , Garrido Vanessa T. , Guo Xinyu , Nivelo Luis A. , Kolonias Despina S. , Saigh Shannon J. , Wieder Eric , Rafie Christine I. , Dosch Austin R. , Zhou Zhiqun , Umland Oliver , Amirian Haleh , Ogobuiro Ifeanyichukwu C. , Zhang Jian , Ban Yuguang , Shiau Carina , Nagathihalli Nagaraj S. , Montgomery Elizabeth A. , Hwang William L. , Brambilla Roberta , Komanduri Krishna , Villarino Alejandro V. , Toska Eneda , Stanger Ben Z. , Gabrilovich Dmitry I. , Merchant Nipun B. , Datta Jashodeep
Published: June 2023

Differentially expressed pathways comparing transcriptomes in KRAS-TP53 co-altered (n=23) and KRAS-altered/TP53WT (n=5) derived from Cancer Cell Line Encyclopedia
Supplementary Tables S1-S15 from Tracing Founder Mutations in Circulating and Tissue-Resident Follicular Lymphoma Precursors
Authors: Schroers-Martin Joseph G. , Soo Joanne , Brisou Gabriel , Scherer Florian , Kurtz David M. , Sworder Brian J. , Khodadoust Michael S. , Jin Michael C. , Bru Agnès , Liu Chih Long , Stehr Henning , Vineis Paolo , Natkunam Yasodha , Teras Lauren R. , Song Joo Y. , Nadel Bertrand , Diehn Maximilian , Roulland Sandrine , Alizadeh Ash A.
Published: June 2023

Supplementary Table S1. Patient and control clinical characteristics
Supplementary Table S2. Sequencing metrics for FL cases & controls
Supplementary Table S3. Identified mutations in EPIC FL pre-diagnostic samples
Supplementary Table S4. Identified mutations in control samples
Supplementary Table S5. Statistical significance for detection in prediagnostic samples with paired tumor biopsy
Supplementary Table S6. Identified mutations in FL tumors with detection in paired prediagnostic samples
Supplementary Table S7. Paired tumor cohort histology & sample characteristics
Supplementary Table S8. Identified mutations in paired biopsy samples
Supplementary Table S9. Clonal VDJ rearrangements in paired biopsies
Supplementary Table S10. Concordance analysis of paired biopsy samples
Supplementary Table S11. Patient characteristics, marrow and sorting studies
Supplementary Table S12. DNA and sequencing metrics for marrow and sorting studies
Supplementary Table S13. Monoclonal antibodies and manufacturers
Supplementary Table S14. Mutations detected in marrow and sorting studies
Supplementary Table S15. Genes fully or partially covered in lymphoma-focused CAPP-Seq selector
Supplementary Table S4 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: June 2023

Supplementary Table S4 shows the list of custom minipool sgRNA target genes.
Supplementary Table S3 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: June 2023

Supplementary Table S3 shows the rank order list of genes targeted by sgRNAs enriched in the genome-wide CRISPR/Cas9 knockout screens.
Supplementary Table S1 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: June 2023

Supplementary Table S1 shows the frequencies of TET2 and IDH mutations in clonal myeloid disorders.
Supplementary Figure S9: from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: June 2023

Genomic regions marked by increased trimethyl-H3K4 are enriched in IDH1-mutant glioma MCTS lines when compared to IDH1-wild-type MCTS lines.
Supplementary Figure S8 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: June 2023

Characterization of isogenic IHA cell lines.
Supplementary Figure S5 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: June 2023

Characterization of KDM5A mutants.
Supplementary Data: list of figures and tables from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: June 2023

List of supplementary figures and tables.
Supplementary Figure 7 from Combinatorial BCL2 Family Expression in Acute Myeloid Leukemia Stem Cells Predicts Clinical Response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppä Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Röllig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Müller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: June 2023

MAC-Score predict response within mutational subgroups
Supplementary Figure 6 from Combinatorial BCL2 Family Expression in Acute Myeloid Leukemia Stem Cells Predicts Clinical Response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppä Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Röllig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Müller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: June 2023

Comparison of MAC-Score and BH-3 profiling based response prediction
Supplementary Figure 5 from Combinatorial BCL2 Family Expression in Acute Myeloid Leukemia Stem Cells Predicts Clinical Response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppä Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Röllig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Müller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: June 2023

Subpopulation specific Bcl-2 family levels and time on HMA/Venetoclax
Supplementary Figure 3 from Combinatorial BCL2 Family Expression in Acute Myeloid Leukemia Stem Cells Predicts Clinical Response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppä Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Röllig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Müller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: June 2023

Bcl-2 family gene expression in LSCs predicts in vitro response to HMA/VEN
Supplementary Figure 2 from Combinatorial BCL2 Family Expression in Acute Myeloid Leukemia Stem Cells Predicts Clinical Response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppä Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Röllig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Müller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: June 2023

Transcriptomic and functional characterization of LSC-like cells
Supplementary Figure 1 from Combinatorial BCL2 Family Expression in Acute Myeloid Leukemia Stem Cells Predicts Clinical Response to Azacitidine/Venetoclax
Authors: Waclawiczek Alexander , Leppä Aino-Maija , Renders Simon , Stumpf Karolin , Reyneri Cecilia , Betz Barbara , Janssen Maike , Shahswar Rabia , Donato Elisa , Karpova Darja , Thiel Vera , Unglaub Julia M. , Grabowski Susanna , Gryzik Stefanie , Vierbaum Lisa , Schlenk Richard F. , Röllig Christoph , Hundemer Michael , Pabst Caroline , Heuser Michael , Raffel Simon , Müller-Tidow Carsten , Sauer Tim , Trumpp Andreas
Published: June 2023

Cell line sensitivity and additional patient data
Data from Analysis of Donor Pancreata Defines the Transcriptomic Signature and Microenvironment of Early Neoplastic Lesions
Authors: Carpenter Eileen S. , Elhossiny Ahmed M. , Kadiyala Padma , Li Jay , McGue Jake , Griffith Brian D. , Zhang Yaqing , Edwards Jacob , Nelson Sarah , Lima Fatima , Donahue Katelyn L. , Du Wenting , Bischoff Allison C. , Alomari Danyah , Watkoske Hannah R. , Mattea Michael , The Stephanie , Espinoza Carlos E. , Barrett Meredith , Sonnenday Christopher J. , Olden Nicholas , Chen Chin-Tung , Peterson Nicole , Gunchick Valerie , Sahai Vaibhav , Rao Arvind , Bednar Filip , Shi Jiaqi , Frankel Timothy L. , Pasca di Magliano Marina
Published: June 2023

Abstract
The adult healthy human pancreas has been poorly studied given the lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors, thus avoiding any warm ischemia time. The 30 donors were diverse in age and race and had no known pancreas disease. Histopathologic analysis of the samples revealed pancreatic intraepithelial neoplasia (PanIN) lesions in most individuals irrespective of age. Using a combination of multiplex IHC, single-cell RNA sequencing, and spatial transcriptomics, we provide the first-ever characterization of the unique microenvironment of the adult human pancreas and of sporadic PanIN lesions. We compared healthy pancreata to pancreatic cancer and peritumoral tissue and observed distinct transcriptomic signatures in fibroblasts and, to a lesser extent, macrophages. PanIN epithelial cells from healthy pancreata were remarkably transcriptionally similar to cancer cells, suggesting that neoplastic pathways are initiated early in tumorigenesis.
Significance:
Precursor lesions to pancreatic cancer are poorly characterized. We analyzed donor pancreata and discovered that precursor lesions are detected at a much higher rate than the incidence of pancreatic cancer, setting the stage for efforts to elucidate the microenvironmental and cell-intrinsic factors that restrain or, conversely, promote malignant progression.

See related commentary by Hoffman and Dougan, p. 1288.

This article is highlighted in the In This Issue feature, p. 1275
Supplementary Figures and Tables from Clonal Spreading of Tumor-Infiltrating T Cells Underlies the Robust Antitumor Immune Responses
Authors: Aoki Hiroyasu , Tsunoda Mikiya , Ogiwara Haru , Shimizu Haruka , Abe Haruka , Ogawa Tatsuro , Abe Takaya , Shichino Shigeyuki , Matsushima Kouji , Ueha Satoshi
Published: June 2023

Supplementary Figure S1-S5, Table S1-S12
Supplementary Table 3 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 I. , Bakarou Kamate , 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: June 2023

Supplementary Table 3
Supplementary Figure 4 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 I. , Bakarou Kamate , 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: June 2023

Figure S4:PD-L1 expression and cytotoxicity
Supplementary Methods File S1 from iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type–Specific Markers of Immune-Cell Infiltration
Authors: Turan Tolga , Kongpachith Sarah , Halliwill Kyle , McLaughlin Robert T. , Binnewies Mikhail , Reddy Dhemath , Zhao Xi , Mathew Rebecca , Ye Shiming , Jacob Howard J. , Samayoa Josue
Published: June 2023

Turan et. al Supplementary Methods File S1
Supplementary legends from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
Authors: Bedran Georges , Gasser Hans-Christof , Weke Kenneth , Wang Tongjie , Bedran Dominika , Laird Alexander , Battail Christophe , Zanzotto Fabio Massimo , Pesquita Catia , Axelson Håkan , Rajan Ajitha , Harrison David J. , Palkowski Aleksander , Pawlik Maciej , Parys Maciej , O'Neill J. Robert , Brennan Paul M. , Symeonides Stefan N. , Goodlett David R. , Litchfield Kevin , Fahraeus Robin , Hupp Ted R. , Kote Sachin , Alfaro Javier A.
Published: June 2023

Legends for Supplementary tables, supplementary figures, and supplementary notes.
Supplementary Table 4 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
Authors: Bedran Georges , Gasser Hans-Christof , Weke Kenneth , Wang Tongjie , Bedran Dominika , Laird Alexander , Battail Christophe , Zanzotto Fabio Massimo , Pesquita Catia , Axelson Håkan , Rajan Ajitha , Harrison David J. , Palkowski Aleksander , Pawlik Maciej , Parys Maciej , O'Neill J. Robert , Brennan Paul M. , Symeonides Stefan N. , Goodlett David R. , Litchfield Kevin , Fahraeus Robin , Hupp Ted R. , Kote Sachin , Alfaro Javier A.
Published: June 2023

Comparison data of COD-dipp ncMAPs with 4 other studies.
Figure 4 from Breast Cancer Stem Cell–Derived Tumors Escape from γδ T-cell Immunosurveillance In Vivo by Modulating γδ T-cell Ligands
Authors: Raute Katrin , Strietz Juliane , Parigiani Maria Alejandra , Andrieux Geoffroy , Thomas Oliver S. , Kistner Klaus M. , Zintchenko Marina , Aichele Peter , Hofmann Maike , Zhou Houjiang , Weber Wilfried , Boerries Melanie , Swamy Mahima , Maurer Jochen , Minguet Susana
Published: June 2023

γδ T cells fail to control BCSC5 xenografts in NOD SCID mice. A, Kaplan–Meier plot (left) of BCSC5 xenograft-bearing mice upon treatment with γδ T cells (blue), γδ T cells expressing MMP14 (red) or vehicle control (black; n = 6–7 mice per group). Differences were not statistically significant, log-rank test (Mantel-Cox). BCSC5 tumor growth curves (right) for individual mice after treatment start. B, γδ T cell-mediated degranulation (left) and cytotoxicity (right) of BCSC5 culture cells or xenograft-derived tumor cells (xeno). Xenograft-bearing mice were treated with γδ T cells, γδ T cells expressing MMP14 or vehicle. For the degranulation assay, γδ T cells were cocultured with the respective tumor cells for 3 hours. The percentage of CD107a+ cells of Vδ2+-gated cells is shown (means ± SEM). Four to six tumors were analyzed per group and each tumor was tested with 2 healthy donors of γδ T cells. For in vitro killing of 51Cr-labeled tumor cells, γδ T cells were cocultured with the target cells for 5 hours at an E:T ratio of 30:1. Results from three independent experiments with a total of 3 healthy donors of γδ T cells and three tumors per group were pooled (means ± SEM). One-way ANOVA followed by Dunnett post hoc test comparing xenograft with culture cells. C, Flow cytometry-based analysis of PD-L1 and PD-L2 expression levels in xenograft-derived EpCAM+ tumor cells (median, minimum to maximum). Mean fluorescence intensity (MFI) of 9–14 tumors per group is shown. Kruskal–Wallis test followed by Dunn post hoc test comparing xenograft with culture cells. D, Kaplan–Meier plots of NOD SCID mice upon treatment with vehicle control (black), γδ T cells (blue) or γδ T cells expressing MMP14 (red) in combination with an anti–PD-1 (nivolumab) or isotype control antibody (n = 5–6 per group). Treatment start was defined for each mouse individually when the first tumor reached a volume of at least 4 mm3. A total of 5 × 106 γδ T cells were injected intravenously three times per week. In addition, mice received 0.6 × 106 IU IL2 (Proleukin S) on the day of treatment start and every 21 days until the end of the experiment. The end of the experiment was defined by a tumor volume of 800 mm3. No significant differences were obtained, log-rank (Mantel-Cox) test. E, BCSC5 tumor growth curves for individual mice upon treatment with γδ T cells (blue), γδ T cells expressing MMP14 (red) or vehicle control (black) in combination with anti–PD-1 or isotype control antibody (n = 5–6 per group). *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001.
Data from Targeting the IL1β Pathway for Cancer Immunotherapy Remodels the Tumor Microenvironment and Enhances Antitumor Immune Responses
Authors: Diwanji Rohan , O'Brien Neil A. , Choi Jiyoung E. , Nguyen Beverly , Laszewski Tyler , Grauel Angelo L. , Yan Zheng , Xu Xin , Wu Jincheng , Ruddy David A. , Piquet Michelle , Pelletier Marc R. , Savchenko Alexander , Charette LaSalette , Rodrik-Outmezguine Vanessa , Baum Jason , Millholland John M. , Wong Connie C. , Martin Anne-Marie , Dranoff Glenn , Pruteanu-Malinici Iulian , Cremasco Viviana , Sabatos-Peyton Catherine , Jayaraman Pushpa
Published: June 2023

Abstract
High levels of IL1β can result in chronic inflammation, which in turn can promote tumor growth and metastasis. Inhibition of IL1β could therefore be a promising therapeutic option in the treatment of cancer. Here, the effects of IL1β blockade induced by the mAbs canakinumab and gevokizumab were evaluated alone or in combination with docetaxel, anti–programmed cell death protein 1 (anti–PD-1), anti-VEGFα, and anti-TGFβ treatment in syngeneic and humanized mouse models of cancers of different origin. Canakinumab and gevokizumab did not show notable efficacy as single-agent therapies; however, IL1β blockade enhanced the effectiveness of docetaxel and anti–PD-1. Accompanying these effects, blockade of IL1β alone or in combination induced significant remodeling of the tumor microenvironment (TME), with decreased numbers of immune suppressive cells and increased tumor infiltration by dendritic cells (DC) and effector T cells. Further investigation revealed that cancer-associated fibroblasts (CAF) were the cell type most affected by treatment with canakinumab or gevokizumab in terms of change in gene expression. IL1β inhibition drove phenotypic changes in CAF populations, particularly those with the ability to influence immune cell recruitment. These results suggest that the observed remodeling of the TME following IL1β blockade may stem from changes in CAF populations. Overall, the results presented here support the potential use of IL1β inhibition in cancer treatment. Further exploration in ongoing clinical studies will help identify the best combination partners for different cancer types, cancer stages, and lines of treatment.
Data 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 I. , Bakarou Kamate , 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: June 2023

Abstract
The low overall survival rates of patients with breast cancer in sub-Saharan Africa (SSA) are driven by regionally differing tumor biology, advanced tumor stages at diagnosis, and limited access to therapy. However, it is not known whether regional differences in the composition of the tumor microenvironment (TME) exist and affect patients’ prognosis. In this international, multicentre cohort study, 1,237 formalin-fixed, paraffin-embedded breast cancer samples, including samples of the “African Breast Cancer-Disparities in Outcomes (ABC-DO) Study,” were analyzed. The immune cell phenotypes, their spatial distribution in the TME, and immune escape mechanisms of breast cancer samples from SSA and Germany (n = 117) were investigated using histomorphology, conventional and multiplex IHC, and RNA expression analysis. The data revealed no regional differences in the number of tumor-infiltrating lymphocytes (TIL) in the 1,237 SSA breast cancer samples, while the distribution of TILs in different breast cancer IHC subtypes showed regional diversity, particularly when compared with German samples. Higher TIL densities were associated with better survival in the SSA cohort (n = 400), but regional differences concerning the predictive value of TILs existed. High numbers of CD163+ macrophages and CD3+CD8+ T cells accompanied by reduced cytotoxicity, altered IL10 and IFNγ levels and downregulation of MHC class I components were predominantly detected in breast cancer samples from Western SSA. Features of nonimmunogenic breast cancer phenotypes were associated with reduced patient survival (n = 131). We therefore conclude that regional diversity in the distribution of breast cancer subtypes, TME composition, and immune escape mechanisms should be considered for therapy decisions in SSA and the design of personalized therapies.

See related Spotlight by Bergin et al., p. 705
Percepción Moral y Conocimiento Práctico en el Estoicismo
Authors: Pineda Christian
Published: June 2023

In a paper published in 1998, Ricardo Salles argues that the Stoic theory of action cannot account for practical knowledge, i.e., knowledge about what action is appropriate to be carried out in certain circumstances. The aim of this paper is to propose a solution to this problem. For this aim, I argue that the Stoics developed a perceptual theory of moral knowledge. According to this theory, the moral properties instantiated in objects, people, and actions are known through perception. After explaining this theory, I argue that it allows us to show that the Stoics deemed perception as a source of practical knowledge.
A Note on Aristotle’s De Anima Α 1, 403a10-16
Authors: Karasmanis Orestis
Published: June 2023

In this paper I discuss passage 403a10-16 from Aristotle’s De Anima. In this passage Aristotle deals with whether the soul could be separate from the body and presents an analogy with geometrical entities. This passage is highly obscure and it presents many textual difficulties. The interpretation I offer resolves the textual problems without requiring emendations to the text as many commentators suggest.
How Does Aristotle Understand the Paradox of the Meno?
Authors: Elvidge Nathan
Published: June 2023

I focus on the distinction between universal and particular knowledge or knowledge simpliciter in APr 2.21 and APo 1.1 as Aristotle’s explicit response to the paradox of the Meno. I attempt to derive a picture of Aristotle’s understanding of the philosophical problem underlying that paradox by asking what that problem would have to be in order for this distinction to make sense as a response to it. I consider two ways of taking the distinction, and argue that both point towards a problem about deriving knowledge of particulars from knowledge of universals as the fundamental problem underlying Aristotle’s understanding of the Meno paradox.
The Problem of Modal Upgrading in Aristotle’s Apodictic Syllogistic
Authors: Botting David
Published: June 2023

This is another contribution to the unending controversy over the two Barbaras. My approach to the problem is hopefully quite new: I wish to view the issue through the prism of modal upgrading. Modal upgrading occurs when a subject term that has only been predicated of assertorically in the premises is predicated of apodictically either: i) in the conclusion of a given syllogism, or; ii) in some proposition that is derived from either the premises of the given syllogism alone or the premises in combination with other propositions that do not refer to the proposition’s subject term. I call the proposition after it has been upgraded the upgraded proposition.

When a conclusion is the upgraded proposition, it is obviously a different predicate being predicated than was predicated in the premises. Aristotle endorses this kind of upgrading; it is effectively what happens in any valid mixed modal syllogism when the minor premise is not apodictic (e.g., Barbara LXL).

In other cases the upgraded proposition is not a conclusion but still follows from the premises alone. In these cases it is the same predicate being predicated in the upgraded proposition as in the premises, although the quantity of the propositions are different (one is universal, another particular). Aristotle rejects this kind of upgrading and takes its occurrence as sufficient to deny the validity of the given syllogism (e.g., Barbara XLL).

I will describe a third type where both the predicate remains the same and the quantity of the proposition remains the same as in the premise, e.g., the upgrading of “All C are B” to “All C are necessarily B”. In these cases it will turn out that the upgraded proposition is not derived from the premises alone, or at least, not syllogistically from the premises alone. This kind of upgrading too is reason for denying the validity of any syllogism from which the upgraded proposition follows as a consequence. I will show that Barbara LXL entails this kind of modal upgrading and should be rejected for this reason.

Armed with this notion of modal upgrading I want to attack the problem of the two Barbaras in Aristotle’s apodictic syllogistic. Aristotle himself endorses mixed modal Barbara when the major is necessary and the minor is assertoric, thereby endorsing the first kind of modal upgrading, but rejects Barbara when the minor is necessary and the major is assertoric on the grounds that it leads to the second kind of modal upgrading. Theophrastus endorses the peioram rule which rejects both Barbaras on the grounds that the conclusion can only be as strong as the weakest premise. Łukasiewicz endorses both Barbaras. I will argue that both Barbaras lead to unacceptable modal upgrading and should be taken to be invalid for that reason. Hence, I agree with Theophrastus about the two Barbaras; however, I do not endorse the peioram rule because I think that the negative mixed modal syllogisms generally avoid this problem and is mostly correct.
Para uma semiótica do olfato
Authors: Rosa Débora dos Santos S.
Published: June 2023

Este artigo procura relacionar o olfato e seus impactos na subjetividade e na cultura a partir do conceito lotmaniano de fronteira. Para isso, a tópica da carnavalização bakhtiniana também será fundamental para pensar o corpo inserido nos conceitos citados. As reflexões semióticas, filosóficas e históricas aqui arroladas orbitam um objeto em comum: o olfato e seu caráter transgressivo no que tange às fronteiras, bem como suas representações – seja por odores corporais tidos como naturais, seja por perfumes elaborados por artistas da artesania própria deste objeto de luxo.
La Poétique de Vasyl Stus
Authors: Nivat Georges
Published: June 2023

L'article cherche à retracer la trajectoire de la vie et de l'œuvre du poète ukrainien Vasyl Stus, établissant des parallèles entre sa riche production poétique et les vicissitudes de sa vie en URSS, la dense érudition du poète, élevant la langue et la poésie ukrainiennes au niveau des grandes cultures et langues d'Europe.
Porphyry’s Life of Pythagoras and Athanasius’ Life of Antony
Authors: Cain Andrew
Published: June 2023

A little over a century ago, it was discovered that Athanasius’ Life of Antony echoes Porphyry’s Life of Pythagoras in two different passages, and scholars have since debated the implications of this clear intertextual linkage. Building on these initial findings, the present article adduces a previously undiscovered third echo of the Porphyrian Life and argues that Athanasius deploys this intertext in order simultaneously to subvert Porphyry’s idealized portraiture of Pythagoras and to elevate his own hagiographic protagonist Antony.
The relationship between temperature, growth rate and body condition of Bufo bufo toadlets prior to their first hibernation
Authors: Reading Christopher , Jofré Gabriela
Published: June 2023

The effect of environmental temperature on the growth and body condition of common toad (Bufo bufo) toadlets was studied during their first terrestrial growth season, following metamorphosis, at a pond in south Dorset, UK, between 2010 and 2021. Toadlet samples were collected annually on the first day of emergence and then approximately once a week until late September/early October. In total, 15-19 samples were collected annually depending on the duration of the toadlet activity season. Toadlet snout-vent length (mm) and body mass (mg) of each captured toadlet was measured and their body condition (Scaled Mass Index: SMI) estimated both annually and for each annual quarter season. Toadlet growth rate and SMI varied between years and were significantly correlated with the duration of their first growth season and its lowest recorded temperature. Growth rate declined as the duration of the growth season increased whilst the reverse was true for SMI. Growth rates also increased as temperatures increased and vice versa for SMI. SMI was inversely correlated to growth rate and suggest that toadlets may enter their first hibernation larger, but in poorer condition, following warm summers than cool summers, and that this may have the potential to reduce their survivorship during a following mild winter. Assuming that similar relationships, between growth rates, body condition and environmental temperatures are not restricted to toadlets during their first terrestrial growth season, then this scenario may also be applicable to subsequent juvenile stages, further increasing the potential consequences for individual survival and fitness.
New genotyping rescues old phenotypes: beneficial traits in Heterorhabditis bacteriophora wild type material and association to single nucleotide polymorphisms
Authors: Godina Giulia , Vandenbossche Bart , Centurión Alejandra , Dörfler Verena , Barg Mike , Ehlers Ralf-Udo , Molina Carlos
Published: June 2023

The entomopathogenic nematode (EPN), Heterorhabditis bacteriophora, is a biocontrol agent with almost world-wide distribution, thus providing a huge source of biodiversity available for exploitation in breeding programmes to improve beneficial traits. For management of economically important insect pests, the nematode is mass-produced in liquid culture, formulated with inert carriers, and transported under controlled temperature conditions to maintain its quality. The biocontrol potential of nematode materials is defined by their genetic background. Previous reports have assessed the phenotypic plasticity of H. bacteriophora. Major beneficial traits are field efficacy influenced by their virulence, longevity and field persistence and tolerance to abiotic stresses like oxidative stress, desiccation and extreme low and high temperatures. For several of these traits high heritability values (h2) have been reported, providing a platform for trait improvement by selection. Modern breeding uses molecular markers to track beneficial traits. Recent studies reported hundreds of single nucleotide polymorphisms (SNPs) in H. bacteriophora. This investigation revived a large set of cryopreserved wild types, hybrids and phenotyped materials of H. bacteriophora. Additional phenotypic data on the virulence (LC50) of H. bacteriophora strains against mealworm (Tenebrio molitor) were produced ranging from 1.4 ± 0.3 to 8.0 ± 3.6 nematodes per insect. Markers linked to beneficial traits were used for a comprehensive genotype analysis transferring reported SNP sequence information into the multiplex platform SeqSNP. Specific alleles associated to beneficial traits were identified and 65 materials were classified for the presence of relevant SNPs associated to beneficial traits. This information provides a valuable platform for exploitation of the nematode’s biodiversity for future breeding and selection approaches.
Erasmus among the Dialecticians: Copia and Its Discontents
Authors: Ettenhuber Katrin
Published: June 2023

Erasmus’ sceptical attitude towards the discipline of dialectic in his early writings is well known. In this article, I revisit Erasmus’ relationship with the arts of reasoning, tracing a trajectory from The Praise of Folly and De Copia to his final work, Ecclesiastes. Erasmus’ treatise on preaching, I suggest, develops a new approach to copious speech and writing by combining the resources of rhetoric and dialectic, in dialogue with the textbooks on the arts of discourse that had appeared in the 25 years since the composition of The Praise of Folly.