bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures S1-S25 from Preexisting Skin-Resident CD8 and γδ T-cell Circuits Mediate Immune Response in Merkel Cell Carcinoma and Predict Immunotherapy Efficacy
Authors: Reinstein Zachary Z. , Zhang Yue , Ospina Oscar E. , Nichols Matt D. , Chu Victoria A. , Pulido Alvaro de Mingo , Prieto Karol , Nguyen Jonathan V. , Yin Rui , Moran Segura Carlos , Usman Ahmed , Sell Brittney , Ng Spencer , de la Iglesia Janis V. , Chandra Sunandana , Sosman Jeffrey A. , Cho Raymond J. , Cheng Jeffrey B. , Ivanova Ellie , Koralov Sergei B. , Slebos Robbert J.C. , Chung Christine H. , Khushalani Nikhil I. , Messina Jane L. , Sarnaik Amod A. , Zager Jonathan S. , Sondak Vernon K. , Vaske Charles , Kim Sungjune , Brohl Andrew S. , Mi Xinlei , Pierce Brian G. , Wang Xuefeng , Fridley Brooke L. , Tsai Kenneth Y. , Choi Jaehyuk
Published: September 2024

Supplementary Fig. S1: Patient level heatmaps by assay. Supplementary Fig. S2: Overview of modalities in database. Supplementary Fig. S3: Computational pipeline for single cell RNA-seq data processing. Supplementary Fig. S4: Quality control metrics of tissue single cell data set. Supplementary Fig. S5: Cell type clusters in single-cell PBMC dataset. Supplementary Fig. S6: Myeloid cells in Merkel cell carcinoma. Supplementary Fig. S7: Response to ICB is associated with tumor cell upregulation of an interferon-γ signature. Supplementary Fig. S8: GSEA on tumor cells controlling for proliferation. Supplementary Fig. S9: Dot plot of RNA markers in CD8 clusters (tissue). Supplementary Fig. S10: Clonotype distribution between CD8 T cell lineages. Supplementary Fig. S11: CD8 lineage characterization. Supplementary Fig. S12: Clonality and neoantigen metrics of metrics of CD8 T cells. Supplementary Fig. S13: Comparisons of cell type signatures and cell proportions separated by sample origin. Supplementary Fig. S14: Epitope screening results. Supplementary Fig. S15: Public epitopes. Supplementary Fig. S16: Expression of naïve-like markers on Vδ1 T cells. Supplementary Fig. S17: GeoMx quality control for regions of interest. Supplementary Fig. S18: GeoMx image and differential expression analysis. Supplementary Fig. S19: CosMx quality control for fields of view. Supplementary Fig. S20: CosMx degree of co-localization sensitivity test shows B cell, T cell, pDC, and DC interactions. Supplementary Fig. S21: Pre-post genes. Supplementary Fig. S22: MIXCR analysis of pre-post ICB clonal dynamics. Supplementary Fig. S23: Single cell analysis of pre-post ICB clonal dynamics. Supplementary Fig. S24: Functional convergence of CD8 and γT cells. Supplementary Fig. S25: Graphical model of immune checkpoint response in MCC.
Supplemental Figure S1 from D3S-001, a KRAS G12C Inhibitor with Rapid Target Engagement Kinetics, Overcomes Nucleotide Cycling, and Demonstrates Robust Preclinical and Clinical Activities
Authors: Zhang Jing , Lim Sun Min , Yu Mi Ra , Chen Cheng , Wang Jia , Wang Wenqian , Rui Haopeng , Lu Jingtao , Lu Shun , Mok Tony , Chen Zhi Jian , Cho Byoung Chul
Published: September 2024

Supplemental Figure S1 shows direct binging of D3S-001 to GDP-bound KRAS G12C but not GTP-bound KRAS G12C.
Table S3 from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Table S3. Demographic and clinical characteristics of the patients
Table S2 from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Table S2. X-ray crystallography data collection and refinement statistics
Table S1 from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Table S1. Cell lines used for cell-based pERK assays in Figure 1A
Supplementary Table 1 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

CRISPR Screen Scores
Supplementary Figure S5 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

CD79B immunohistochemistry is not predictive of Pola-V sensitivity
Supplementary Figure S2 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

Knockout of SLC35A1, SLC35A2, and ST6GAL1 decreases surface a2,6-linked sialic acid.
Supplementary Table S8 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Genes assayed with a mean target coverage of 500X.
Supplementary Table S7 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Representativeness of Study Participants.
Supplementary Table S6 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Adverse events, grade 3+ with attribution of possible, probable, or definite.
Supplementary Figure S5 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Pseudotime analysis of scRNASeq data.
Supplementary Table S5 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Table S5: SIDP results in MCF7 grown in white media (-E2). S5.1-5: the tables follow the same structure of S3.1-5.
Supplementary Figure S9 from Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis
Authors: Demajo Santiago , Ramis-Zaldivar Joan E. , Muiños Ferran , Grau Miguel L. , Andrianova Maria , López-Bigas Núria , González-Pérez Abel
Published: September 2024

Classification of blood mutations across UKB donors into four boostDM-CH tiers
Supplementary Figure S3 from Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis
Authors: Demajo Santiago , Ramis-Zaldivar Joan E. , Muiños Ferran , Grau Miguel L. , Andrianova Maria , López-Bigas Núria , González-Pérez Abel
Published: September 2024

Benchmark of boostDM-CH models
Supplementary Figure S9 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Figure 9. SIDP identifies regulatory regions with context-dependent activity in MCF7 cells.
Supplementary Figure S1 from Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis
Authors: Demajo Santiago , Ramis-Zaldivar Joan E. , Muiños Ferran , Grau Miguel L. , Andrianova Maria , López-Bigas Núria , González-Pérez Abel
Published: September 2024

Discovery index of the 12 high-quality boostDM-CH gene-models
Data from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

Abstract
Polatuzumab vedotin (Pola-V) is an antibody–drug conjugate directed to the CD79B subunit of the B-cell receptor (BCR). When combined with conventional immunochemotherapy, Pola-V improves outcomes in diffuse large B-cell lymphoma (DLBCL). To identify determinants of Pola-V sensitivity, we used CRISPR-Cas9 screening for genes that modulated Pola-V toxicity for lymphomas or the surface expression of its target, CD79B. Our results reveal the striking impact of CD79B glycosylation on Pola-V epitope availability on the lymphoma cell surface and on Pola-V toxicity. Genetic, pharmacological, and enzymatic approaches that remove sialic acid from N-linked glycans enhanced lymphoma killing by Pola-V. Pola-V toxicity was also modulated by KLHL6, an E3 ubiquitin ligase that is recurrently inactivated in germinal center derived lymphomas. We reveal how KLHL6 targets CD79B for degradation in normal and malignant germinal center B cells, thereby determining expression of the surface BCR complex. Our findings suggest precision medicine strategies to optimize Pola-V as a lymphoma therapeutic.

Significance: These findings unravel the molecular basis of response heterogeneity to Pola-V and identify approaches that might be deployed therapeutically to enhance the efficacy of CD79B-specific tumor killing. In addition, they reveal a novel post-translational mechanism used by normal and malignant germinal center B cells to regulate expression of the BCR.

See related commentary by Leveille, p. 1577

See related article by Meriranta et al.
Data from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Abstract
Juvenile myelomonocytic leukemia (JMML) is a hematologic malignancy of young children caused by mutations that increase Ras signaling output. Hematopoietic stem cell transplantation (HSCT) is a potentially curative treatment, but patients with relapsed or refractory (advanced) disease have dismal outcomes. This phase II trial evaluated the safety and efficacy of trametinib, an oral MEK1/2 inhibitor, in patients with advanced JMML. Ten infants and children were enrolled, and the objective response rate was 50%. Four patients with refractory disease proceeded to HSCT after receiving trametinib. Three additional patients completed all 12 cycles permitted on study and continue to receive off-protocol trametinib without HSCT. The remaining three patients had progressive disease with two demonstrating molecular evolution by the end of cycle 2. Transcriptomic and proteomic analyses provided novel insights into the mechanisms of response and resistance to trametinib in JMML. ClinicalTrials.gov Identifier: NCT03190915.

Significance: Trametinib was safe and effective in young children with relapsed or refractory JMML, a lethal disease with poor survival rates. Seven of 10 patients completed the maximum 12 cycles of therapy or used trametinib as a bridge to HSCT and are alive with a median follow-up of 24 months.

See related commentary by Ben-Crentsil and Padron, p. 1574
Supplementary Table S1 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Authors: Wijetunga N. Ari , Gessner Kathryn H. , Kanchi Krishna , Moore Jay A. , Fleischmann Zoe , Jin Dexter X. , Frampton Garrett M. , Sturdivant Michael , Repka Michael , Sud Shivani , Corcoran David L. , Galsky Matthew D. , Milowsky Matthew I. , Wobker Sara E. , Kim William Y. , Rose Tracy L. , Damrauer Jeffrey S.
Published: September 2024

Supplementary Table S1
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: September 2024

Kruskal-Walis test results comparing the deconvolved immune cell compositions between hypoxic and normoxic tumors.
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: September 2024

Cox proportional hazards model results for the interaction terms between hypoxia (binary, low or high) with microbe relative abundance in COADREAD tumors treated with radiotherapy.
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: September 2024

Differences in the tumor microbes in low and high hypoxia mouse tumors.
Challenges in the Management of Stage IV Clear Cell Sarcoma of Soft Tissue in Young Adults: Case Report and Review of the Literature
Authors: Iordache Diana , Kövendi Anita-Andrea , Fekete Zsolt , Popita Raluca , Cebotaru Iunia Patricia , Patka Annamaria , Năstase Ioana Cristina , Cebotaru Cristina Ligia
Published: September 2024

Introduction: Clear cell sarcoma (CCS) of soft tissue is a rare type of soft tissue sarcoma affecting usually lower extremities in young adults. The main challenges in the management of this disease include difficulties in diagnosis, aggressiveness of the cancer with rapid progression, and inadequate treatment, especially in small centers with few cases. Case Presentation: We present a case of a young woman diagnosed with CCS of soft tissue, stage IV. The patient benefited from a multidisciplinary approach including radiation therapy, surgery, chemotherapy, and targeted therapy with disease progression regardless of the therapeutic act. Despite all the efforts, the patient died from complications overlapping progression of the disease. Conclusion: The rarity of this sarcoma limits the amount of information available on the diagnosis and treatment process. The particularity of this case is the difficulty met in maintaining the disease under control using all the resources available due to lack of compliance of the patient in carrying out amputation at diagnosis, thus modifying the entire treatment algorithm. Targeted therapy showed promising results in the literature, however in our case resulted in an unexpected, rare adverse event aggravating the patient’s condition. In conclusion, patients with CCS should be referred to specialized centers for adequate multidisciplinary management and, if available, inclusion in clinical trials. New agents are needed to improve the survival of these patients.
Soft Tissue Tumor with PAK2::RAF1 Kinase Fusion: An Emerging Sarcoma Entity
Authors: Haglund Cecilia , Behrendtz Mikael , Hesla Asle , Haglund de Flon Felix
Published: September 2024

Introduction: Here, we report the first case of a soft tissue tumor with a PAK2::RAF1 fusion. Case Presentation: The patient was an 11-year-old female presenting with a 5 cm intramuscular mass in the lower leg. Microscopic examination revealed a mitotically active spindle cell lesion with monomorphic and moderately atypical cells growing in a patternless pattern with the presence of stromal and perivascular keloidal collagen with focal immunoreactivity for smooth muscle actin and S100; negative stains included cytokeratins, CD34, and caldesmon. Whole genome and RNA sequencing detected a chromosome 3 inversion and a resultant PAK2::RAF1 fusion as well as a CDKN2A homozygous deletion. The patient was treated with neoadjuvant chemoradiotherapy with only minimal response and the tumor was excised surgically. There was no evidence of disease progression at 4 months. Conclusion: This is the first case of a soft tissue tumor harboring a PAK2::RAF1 fusion with histological features in keeping with previous cases of RAF1 and other kinase fusion soft tissue tumors.
xcomet
: Transparent Machine Translation Evaluation through Fine-grained Error Detection
Authors: Guerreiro Nuno M. , Rei Ricardo , Stigt Daan van , Coheur Luisa , Colombo Pierre , Martins André F. T.
Published: September 2024

Widely used learned metrics for machine translation evaluation, such as Comet and Bleurt, estimate the quality of a translation hypothesis by providing a single sentence-level score. As such, they offer little insight into translation errors (e.g., what are the errors and what is their severity). On the other hand, generative large language models (LLMs) are amplifying the adoption of more granular strategies to evaluation, attempting to detail and categorize translation errors. In this work, we introduce xcomet, an open-source learned metric designed to bridge the gap between these approaches. xcomet integrates both sentence-level evaluation and error span detection capabilities, exhibiting state-of-the-art performance across all types of evaluation (sentence-level, system-level, and error span detection). Moreover, it does so while highlighting and categorizing error spans, thus enriching the quality assessment. We also provide a robustness analysis with stress tests, and show that xcomet is largely capable of identifying localized critical errors and hallucinations.
Taxonomic status of the genus Lunakia, including a redescription of the male and female genitalia of Lunakia alyssella (Klimesch, 1941) (Lepidoptera, Plutellidae)
Authors: BARANIAK EDWARD , HUEMER PETER
Published: September 2024

The genital morphology of the Lunakia alyssella (Klimesch, 1941) is redescribed. Additional details of both male and female genitalia are provided, supplemented with accompanying drawings. Anatomical evidence confirms that the genus Lunakia is distinct from the genus Eidophasia within the family Plutellidae. Males are characterized by long, curved appendages of the tegumen, and females by the antrum with a subgenital plate.
Describing the burden of disease amongst inpatients with treatment resistant major depressive disorder in Australia
Authors: Hurley Melanie , Komiti Angela , Hopwood Malcolm
Published: September 2024

Objective

To describe the quality of life and clinical characteristics of treatment-resistant depression (TRD) patients in an Australian patient cohort recruited cross-sectionally during admission.

Method

Inpatients admitted for TRD treatment completed a quality of life questionnaire (AQoL-8D) and a depression severity assessment (HAM-D). A chart review and patient interview occurred for demographic and patient characteristics. Comparisons between the mean AQoL-8D scores of the study population and Australian population norms occurred.

Results

79 TRD inpatients (70.9% female), mean age of 44.8 ± 14.9 years, were recruited, with 78.5% having an anxiety disorder, 48.1% post-traumatic stress disorder, and 30.4% a personality disorder. Adjunctive to antidepressants, 92.4% were taking antipsychotics and 55.7% were taking mood stabilisers. Approximately 42% of patients received transcranial magnetic stimulation, and 35.4% received electroconvulsive therapy. Mean HAM-D score was 20.3 ± 5.2, and AQoL-8D score (120.1 ± 16.5) was significantly higher than Australian population norms ( p < .001) indicating reduced quality of life.

Conclusions

Personal and clinical characteristics of patients hospitalised for TRD were similar to TRD globally with impaired quality of life relative to the general Australian population. TRD patients on average presented with moderate/severe depression, highlighting the need for greater support for these individuals.
Analytical solution for strongly nonlinear vibration of a stringer shell
Authors: Farea Nadia M. , Ismail Gamal M.
Published: September 2024

In this paper, a new approach called the global residue harmonic balance technique is applied to construct analytical solutions for nonlinear oscillators that appear in cylindrical shells. Periodic solution is analytically proved, and consequently, the relation between amplitude and frequency is obtained in an analytical form. Numerical and analytical comparisons with the Runge–Kutta method and previously existing homotopy perturbation method (HPM) are given, to show the stability, quality, and efficiency of the present approach. The GRHBM provides an outstanding agreement with the numerical results for different amplitude values, leading to sufficiently accurate solutions for nonlinear oscillators.
Pitfalls in the Evaluation of Respiratory Failure in Myasthenia Gravis Patients: A Case Series
Authors: Uysal Sanem Pinar , Li Yuebing
Published: September 2024

Objectives

To highlight the importance of recognizing different presentations of respiratory failure due to myasthenic and non-myasthenic etiologies in myasthenia gravis (MG) patients.

Methods

We describe 3 patients with different presentations of respiratory failure in MG.

Cases

Patient 1 is a 49-year-old female with longstanding MG who presented with lethargy and neck weakness without notable respiratory distress. She was found to be in hypercarbic respiratory failure, which improved with plasmapheresis treatment. Patient 2 is a 58-year-old female who presented with ptosis, dysphagia, and dyspnea requiring intubation. Her hypophonia and dyspnea persisted despite escalation in MG treatment, and further workup revealed glottal stenosis secondary to granulomatosis with polyangiitis. Patient 3 is an 85-year-old female with MG presenting with refractory hypoxia, which was secondary to a large patent foramen ovale resulting in right-to-left shunting.

Discussion

All 3 cases emphasize the role of clinical reasoning and careful analysis based on thorough history taking, detailed neurologic exam and comprehensive laboratory findings to determine the etiologies for respiratory dysfunction in MG and provide appropriate treatment.

Conclusion

A lack of overt signs of respiratory distress in MG does not rule out the presence of respiratory failure due to the sedating effect of hypercapnia. There is a need to consider alternative etiologies of hypoxia in MG patients if typical symptoms or signs of MG exacerbations are absent.
Sports Identification in Situational Problem-Solving: A Framework for Understanding Fans’ Communicative Behaviors in Sports Crises
Authors: He Mu
Published: September 2024

Sports have been enjoyed by people worldwide as an essential part of life. Inevitably, sports-related issues have also permeated into the industry. Specifically, scholars have called for more attention to fan-enacted crisis communication in sports. Based on the situational theory of problem-solving, this project incorporates sports identification, modified engagement in and disengagement from online communication, and self-mocking to examine fans’ online communicative behaviors regarding the National Football League (NFL) concussion issue and the Chinese men’s national soccer team crisis. The findings reveal that sports identification was a significant indicator that influenced fans’ perceptions of the issue. In addition, fans motivated to solve the problem were more likely to engage in online communication rather than disengage from it. Moreover, referent criterion and self-mocking were comparatively unique to the other factors in that they were sensitive to the case and the fans’ cultural background. Theoretical contributions, practical implications, and recommendations for future research are enclosed.
Detection and molecular characterization of major enteric pathogens in calves in central Ethiopia
Authors: Bergholm Julia , Tessema Tesfaye Sisay , Blomström Anne-Lie , Berg Mikael
Published: September 2024

Background

Calf diarrhea is a major cause of morbidity and mortality in the livestock sector worldwide and it can be caused by multiple infectious agents. In Ethiopia, cattle are the most economically important species within the livestock sector, but at the same time the young animals suffer from high rates of morbidity and mortality due to calf diarrhea. However, studies including both screening and molecular characterization of bovine enteric pathogens are lacking. Therefore, we aimed to both detect and molecularly characterize four of the major enteric pathogens in calf diarrhea, Enterotoxigenic Escherichia coli (E. coli K99 +), Cryptosporidium spp., rotavirus A (RVA), and bovine coronavirus (BCoV) in calves from central Ethiopia. Diarrheic and non-diarrheic calves were included in the study and fecal samples were analyzed with antigen-ELISA and quantitative real-time PCR (qPCR). Positive samples were further characterized by genotyping PCRs.

Results

All four pathogens were detected in both diarrheic and non-diarrheic calves using qPCR and further characterization showed the presence of three Cryptosporidium species, C. andersoni, C. bovis and C. ryanae. Furthermore, genotyping of RVA-positive samples found a common bovine genotype G10P[11], as well as a more unusual G-type, G24. To our knowledge this is the first detection of the G24 RVA genotype in Ethiopia as well as in Africa. Lastly, investigation of the spike gene revealed two distinct BCoV strains, one classical BCoV strain and one bovine-like CoV strain.

Conclusions

Our results show that Cryptosporidium spp., E. coli K99 + , RVA and BCoV circulate in calves from central Ethiopia. Furthermore, our findings of the rare RVA G-type G24 and a bovine-like CoV demonstrates the importance of genetic characterization.
Dynamic group fuzzy extractor
Authors: Chen Kaini , Shen Peisong , Lv Kewei , Tian Xue , Chen Chi
Published: September 2024

The group fuzzy extractor allows group users to extract and reproduce group cryptographic keys from their individual non-uniform random sources. It can be easily used in group-oriented cryptographic applications. However, current group fuzzy extractors are not dynamic, i.e. they spend a large cost when dealing with user revocation. In this work, we propose the formal definition and construction of dynamic group fuzzy extractor (DGFE) to address this issue. For the revocation, DGFE allows unrevoked group users to reproduce updated group keys from the existing group help data. Meanwhile, it prevents any revoked group user from generating new group keys using the previously authorized individual help data. We propose a DGFE construction based on the revocable group signature. Furthermore, we give formal proofs of reusability, anonymity and traceability of our construction.
Unveiling kinema: blending tradition and science in the Himalayan fermented soya delicacy
Authors: Tamang Jyoti Prakash
Published: September 2024

Kinema, a sticky-textured fermented soybean food with umami flavour, is originated in the historical Limbuwan region, now situated in the eastern districts of Nepal. It has since expanded to different areas in Darjeeling Hills and Sikkim in India and Bhutan. The Limboo community, one of the oldest indigenous groups in the Himalayas, has developed a method for fermenting soybeans to produce kinema. Bacillus is the main bacterial genus responsible for fermenting kinema, along with lactic acid bacteria, yeasts, and fungi. Kinema is full of nutrients like protein, fats, carbohydrates, amino acids, vitamins, and minerals and offers health benefits through its antioxidant, anti-inflammatory, antiobesity, and antidiabetic properties. A novel strain of Bacillus subtilis Tamang has been identified in kinema samples from Darjeeling Hills, India, exhibiting elevated levels of γ-PGA and various biomarker genes for health benefits and biological functionalities. Kinema contains secondary metabolites including several bioactive compounds, immunomodulators, vitamin B-complexes, and others that help promote good health. The transcriptome of the B. subtilis Tamang strain reveals genes associated with GABA production, Vitamin B12 synthesis, and fibrinolytic activity. Safety evaluations have demonstrated that the strain and the production of kinema do not pose any toxicity risks based on animal studies. Despite facing challenges in terms of its strong taste and slimy consistency for broader acceptance, the bioactive elements and safe starter cultures found in kinema hold promise for the development of functional food.
Validation of Non–Small Cell Lung Cancer Clinical Insights Using a Generalized Oncology Natural Language Processing Model
Authors: Kenney Rachel C. , Chen Xiaoren , Shintani Kazuki , Gagnon Clara , Liu John , DaCosta Byfield Stacey , Ochs Lorre , Currie Anne-Marie
Published: September 2024

PURPOSE

Limited studies have used natural language processing (NLP) in the context of non–small cell lung cancer (NSCLC). This study aimed to validate the application of an NLP model to an NSCLC cohort by extracting NSCLC concepts from free-text medical notes and converting them to structured, interpretable data.

METHODS

Patients with a lung neoplasm, NSCLC histology, and treatment information in their notes were selected from a repository of over 27 million patients. From these, 200 were randomly selected for this study with the longest and the most recent note included for each patient. An NLP model developed and validated on a large solid and blood cancer oncology cohort was applied to this NSCLC cohort. Two certified tumor registrars and a curator abstracted concepts from the notes: neoplasm, histology, stage, TNM values, and metastasis sites. This manually abstracted gold standard was compared with the NLP model output. Precision and recall scores were calculated.

RESULTS

The NLP model extracted the NSCLC concepts with excellent precision and recall with the following scores, respectively: Lung neoplasm 100% and 100%, NSCLC histology 99% and 88%, histology correctly linked to neoplasm 98% and 79%, stage value 98.8% and 92%, stage TNM value 93% and 98%, and metastasis site 97% and 89%. High precision is related to a low number of false positives, and therefore, extracted concepts are likely accurate. High recall indicates that the model captured most of the desired concepts.

CONCLUSION

This study validates that Optum's oncology NLP model has high precision and recall with clinical real-world data and is a reliable model to support research studies and clinical trials. This validation study shows that our nonspecific solid tumor and blood cancer oncology model is generalizable to successfully extract clinical information from specific cancer cohorts.
Genomic Landscape of Pancreatic Neuroendocrine Tumors and Implications for Clinical Practice
Authors: De Jesus-Acosta Ana , Mohindroo Chirayu
Published: September 2024

Pancreatic neuroendocrine tumors (pNETs) are the second most prevalent neoplasms of the pancreas with variable prognosis and clinical course. Our knowledge of the genetic alterations in patients with pNETs has expanded in the past decade with the availability of whole-genome sequencing and germline testing. This review will focus on potential clinical applications of the genetic testing in patients with pNETs. For somatic testing, we discuss the commonly prevalent somatic mutations and their impact on prognosis and treatment of patients with pNET. We also highlight the relevant genomic biomarkers that predict response to specific treatments. Previously, germline testing was only recommended for high-risk patients with syndromic features ( MEN1, VHL, TSC, and NF1), we review the evolving paradigm of germline testing in pNETs as recent studies have now shown that sporadic-appearing pNETs can also harbor germline variants.
Το φύλο και η σεξουαλικότητα ως άξονες δικαιωμάτων
Authors: Καλομοίρη Αγγελική
Published: September 2024

Ο σκοπός αυτής της μελέτης είναι η ανάδειξη του τρόπου και των μέσων κατασκευής «του καλύτερου εφικτού κόσμου» στο πλαίσιο των συγκαιρινών μας queer αναρχοφεμινιστικών ομάδων - για παράδειγμα, συνθέτουμε περιγραφές που αφορούν προεικονιστικές πρακτικές διαμόρφωσης μιας χειραφετητικής γλώσσας η οποία στηρίζει την αυτοέκφραση και τον αυτοπροσδιορισμό, ενώ αναλύουμε πώς αυτές καθαυτές οι σχέσεις αμοιβαιότητας, σεβασμού και αλληλεγγύης καθιστούν αχρείαστη την όποια τυπική και «απρόσωπη» μορφή οργάνωσης εντός των εν λόγω συλλογικοτήτων, και εμβαθύνουμε στην συγκαιρινής μας κινηματική και κουίρ φροντίδα αλλά και στην κουίρ αναρχοφεμινιστική ζωή, όπως αυτή κατασκευάζεται από τα μετέχοντα υποκείμενα στο πλαίσιο της ομάδας, της κοινότητας και του κουίρ αναρχοφεμινιστικού δικτύου. Στο πρόσφατο παρελθόν μια κουίρ αναρχοφεμινιστική ομάδα καλοδέχτηκε τη συμμετοχή μας σε εγχειρήματά της στο πλαίσιο αυτής της μελέτης, ενώ αυτή η συνύπαρξη διήρκησε περίπου οκτώ μήνες και μορφοποιήθηκε συγχρόνως με την αυθόρμητη (Watson, 2023) βούλησή μας να επιτελέσουμε μια ερευνητική προσέγγιση που να στηρίζει τον ερευνητικό μας σκοπό και συνάμα να αποτελεί εμπρόθετη αναγνώριση της κουλτούρας της κοινότητας, και αυτή η προσέγγιση δεν είναι άλλη από εκείνη την οποία μας διδάσκει ο Οικονομάκης ονομάζοντάς την άλλοτε «πολιτική εθνογραφία» (2020) και άλλοτε «εθνογραφία» (2021). Μέσα από επιτελέσεις των δικών του φροντιστικών ερμηνειών, λοιπόν, προσπαθήσαμε να αναλύουμε τη συγκαιρινή μας κουίρ αναρχοφεμινιστική κουλτούρα, καθώς και τον τρόπο ζωής και τα ήθη που αναπαράγουν οι ομάδες οι οποίες στηρίζουν αυτή την κοσμοθεωρία. Μελετήσαμε, δηλαδή, πρακτικές μορφοποίησης μιας κουίρ αναρχοφεμινιστικής κοινής ζωής η οποία κατασκευάζεται μέσα από την καθημερινή κατάργηση ιεραρχικών δομών και σχέσεων σε κάθε έκφανση της συλλογικής πραγματικότητας. Με άλλα λόγια, η παρούσα μελέτη -τόσο στο θεωρητικό όσο και στο εμπειρικό μέρος της- αναλύει κουίρ αναρχοφεμινιστικές προεικονιστικές πρακτικές και κουίρ αναρχοφεμινιστικά ήθη.
Multi-rotor real-time control based on visual servoing of evolving features
Authors: Ασπράγκαθος Σωτήριος
Published: September 2024

Τα Συστήματα μη Επανδρωμένων Αεροσκαφών (ΣμηΕΑ), έχουν εξελιχθεί σημαντικά καθοδηγούμενα από τα δυναμικά χαρακτηριστικά που τα δια-κατέχουν. Αυτή η διατριβή εξετάζει την ενσωμάτωσης κλασικών καμερών στον έλεγχο των ΣμηΕΑ, επαναπροσδιορίζοντας τον τρόπο συλλογής δεδομένων κα την αξιοποίησή τους. Καθώς οι δυνατότητες των ΣμηΕΑ με κάμερες επεκτείνονται, η οπτική εξυπηρέτηση, μια κεντρική τεχνική που συνδυάζει ρομποτική και όραση υπολογιστών, δίνει τη δυνατότητα για ακριβή έλεγχο και χειρισμό βασισμένο σε οπτικά στοιχεία. Επικεντρώνοντας στη χρήση καμερών στον τομέα της ρομποτικής, ιδίως στα ΣμηΕΑ, η μελέτη αντιμετωπίζει προκλήσεις στο πεδίο του αυτόνομου ελέγχου μέσω της διαχείρισης δυναμικών στόχων με μεταβαλλόμενα χαρακτηριστικά. Η παρούσα διατριβή παρουσιάζει καινοτόμες μεθόδους, ξεπερνώντας περιορισμούς σε υπάρχουσες προσεγγίσεις ελέγχου με χρήση οπτικής ανατροφοδότησης ενισχύοντας στρατηγικές ελέγχου με στόχο την εκτέλεση εφαρμογών επιτήρησης σε πραγματικές συνθήκες περιβάλλοντος. Η διατριβή εστιάζει στην ανάπτυξη προσαρμοστικών συστημάτων ελέγχου που αντιμετωπίζει άγνωστα χαρακτηριστικά δυναμικών στόχων. Εμβαθύνουμε στη βελτίωση στρατηγικών ελέγχου χρησιμοποιώντας τα στοιχεία του στόχου στην εικόνα που μεταβάλλονται και προηγμένες τεχνικές όρασης υπολογιστών, εξασφαλίζοντας σταθερότητα και ανθεκτικότητα στην παρακολούθηση απαιτητικών στόχων. Η έρευνα συμβάλλει στη συνεχή εξέλιξη των δυνατοτήτων των ΣμηΕΑ αντιμετωπίζοντας προκλήσεις που προκύπτουν από στόχους με εξελισσόμενα χαρακτηριστικά. Καθώς η τεχνολογία προχωρά και οι απαιτήσεις εφαρμογών εποπτείας εξελίσσονται, τα ευρήματα αυτής της διατριβής στοχεύουν στο να επεκτείνουν το εργαλείο των δυνατοτήτων των ΣμηΕΑ, παρέχοντας καινοτόμες λύσεις που ωθούν τα όρια των δυνατοτήτων της αεροπορικής εποπτείας και παρακολούθησης.
Axiological Aspects of Development of Communicative Strategies for Gender Balance in English
Authors: Shchedromirskaya Anna , Korenev A.
Published: September 2024

The article studies the issue of preserving and strengthening traditional values in English classes with the help of communicative strategies for gender balance. This issue seems relevant, since it seems necessary to consider how the implementation of state policy in moral education can influence the process of teaching a foreign language. The purpose of the study is to analyze educational literature used in English classes and assess the extent to which the characters and personalities mentioned in it contribute to the strengthening of traditional values and the formation of Russia’s positive contribution to world history and culture. The study is conducted using quantitative content analysis, which calculates the total number of male and female personalities and precedent names mentioned, as well as the number of male and female personalities related to the historical and cultural heritage of Russia. The analysis showed insufficient representation in textbooks on the subject “English language” of outstanding figures and famous personalities, both male and female, related to the culture and history of Russia, and therefore it seems possible to develop a requirement for balance as a unified approach to filling both textbooks, teaching aids, and pedagogical speech in foreign languages in general.
The Communicative Transformation of the Image of Russia in the Us Media after the Annexation of Crimea
Authors: Chebykina Ekaterina
Published: September 2024

The article is devoted to the analysis of the communicative transformation of the image of Russia in the American media after the annexation of Crimea to the Russian Federation in 2014. The relevance of the study is due to the increasing role of information warfare in the context of globalization and technology development, as well as the significance of the Crimean events as a turning point in Russian-American relations. The theoretical significance of the work lies in deepening the understanding of the role of communicative processes in international relations and their influence on the formation of the image of the state. The practical significance is related to the possibility of applying the results to analyze and predict the development of relations between Russia and the United States. The novelty of the research is due to a comprehensive approach to the analysis of the transformation of the image of Russia, taking into account not only political and sociological, but also linguistic aspects. The empirical base of the study was made up of a corpus of texts from leading American print publications and transcripts of TV channels for the period from the 2000s to December 2014 with a total volume of about 200 thousand word usage. The paper uses a method of qualitative text analysis aimed at identifying the dominant narratives, metaphors, stylistic techniques and communicative strategies of the representation of Russia.

The article shows that before the Ukrainian crisis, the coverage of Russia in the American media was characterized by a relative balance, including both critical and positive assessments. However, after the annexation of Crimea, there was a sharp negation of the image of Russia in the US media discourse, associated with the use of such discursive strategies as destructivization, demonization, archaization, personification of the "Russian threat" in the person of Vladimir Putin, securitization of the actions of the Russian Federation and embedding the Crimean events in the context of global ideological confrontation between Russia and the West. This transformation was carried out using a wide range of linguistic means, including negatively colored vocabulary, metaphors, allusions, and historical analogies. The result of the communicative transformation was the consolidation in the American media discourse of the stereotypical image of Russia as an authoritarian aggressor power, disregarding the norms of international law and posing a threat to the world order.
Various aspects of the doctor's quality of life
Authors: Leśkiewicz Michał , Składanek Justyna , Kopczyńska Barbara , Cieszkowska Joanna
Published: September 2024

Nowadays, more and more attention is paid to the quality of life. Both private and work-related. More and more actions are taken to improve the quality of life in order to reduce the phenomenon of professional burnout. This significantly improves work efficiency and allows employees to work longer.
It is no different in medical professions, including doctors. Fortunately, there is more and more scientific research on this topic.
This allowed us to write an illustrative article about various aspects of the doctor's quality of life. The article will provide information about what quality of life really is and how it is defined. We will present the impact of various factors influencing this, such as length of work, sleep time, age, shift work and work at irregular intervals.
We will also show how occupational factors influence health, which translates quite well into life expectancy. It is surprising that doctors have higher than expected risk factors for cardiovascular diseases such as hypertension, hypercholesterolemia, body mass. The cause is usually high stress and lack of time for physical activities after work. Specialization is also important when it comes to life expectancy. Charts with this information about expected age will be presented along with discussion in the text.
We hope that in the future there will be further research expanding knowledge on this very important topic. And employers will have developed appropriate standards to improve the quality of life among their employees.