tbuckley/cabot-search huggingface dataset:
Characteristics of Patients Undergoing Endoscopic Retrograde Cholangiopancreatography for Sphincter of Oddi Disorders
Authors: Gregory A. Coté, Haley Nitchie, B. Joseph Elmunzer, Richard S. Kwon, Field F. Willingham, Sachin Wani, Daniel Mullady, Amitabh Chak, Vikesh Singh, Adam Slivka, Shyam Varadarajulu, Martin Freeman, Srinivas Gaddam, Priya Jamidar, Paul Tarnasky, Lydia Foster, Peter B. Cotton
Journal: Clinical Gastroenterology and Hepatology (2021)
P48.03 First-Line Durvalumab plus Platinum-Etoposide in ES-SCLC: Exploratory Analyses Based on Extent of Disease in CASPIAN
Authors: N. Reinmuth, M.C. Garassino, D. Trukhin, M.J. Hochmair, M. Özgüroğlu, L. Havel, J. Goldman, Y. Chen, G. Losonczy, F. Spinnato, N. Conev, J. Bar, H. Broadhurst, N. Byrne, H. Jiang, L. Paz-Ares
Journal: Journal of Thoracic Oncology (2021)
Myocardial T1 and T2 Mapping by Magnetic Resonance in Patients With Immune Checkpoint Inhibitor–Associated Myocarditis
Authors: Paaladinesh Thavendiranathan, Lili Zhang, Amna Zafar, Zsofia D. Drobni, Syed S. Mahmood, Marcella Cabral, Magid Awadalla, Anju Nohria, Daniel A. Zlotoff, Franck Thuny, Lucie M. Heinzerling, Ana Barac, Ryan J. Sullivan, Carol L. Chen, Dipti Gupta, Michael C. Kirchberger, Sarah E. Hartmann, Jonathan W. Weinsaft, Hannah K. Gilman, Muhammad A. Rizvi, Bojan Kovacina, Caroline Michel, Gagan Sahni, Ana González-Mansilla, Antonio Calles, Francisco Fernández-Avilés, Michael Mahmoudi, Kerry L. Reynolds, Sarju Ganatra, Juan José Gavira, Nahikari Salterain González, Manuel García de Yébenes Castro, Raymond Y. Kwong, Michael Jerosch-Herold, Otavio R. Coelho-Filho, Jonathan Afilalo, Eduardo Zataraín-Nicolás, A. John Baksi, Bernd J. Wintersperger, Oscar Calvillo-Arguelles, Stephane Ederhy, Eric H. Yang, Alexander R. Lyon, Michael G. Fradley, Tomas G. Neilan
Journal: Journal of the American College of Cardiology (2021)
P37.01 Detection of NTRK Rearrangements by Next-Generation Sequencing in Chinese Lung Carcinoma Patients
Authors: M. Wu, S. Pan, Q. Wang, Z. Wu, Q. Yan, C. Wu, Q. Pan, S. Gao, F. Wang, S. Zhang, M. Yao, K. Wang
Journal: Journal of Thoracic Oncology (2021)
Abstract P07: Inhibition of androgen-regulated TMPRSS2 and lipogenic enzymes in prostate and lung carcinoma cell lines by a cisplatin prodrug
Authors: Subham Guin, Bapurao Surnar, Uttara Basu, Shanta Dhar
Journal: Clinical Cancer Research (2021)

Abstract The main causative agent for the global pandemic of COVID-19 is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Developing therapeutic strategies to stop the virus is the hour of need. According to the recent clinical reports, it is seen that an androgen-regulated host cell serine protease TMPRSS2 acts on the spike protein of the SARS-CoV-2 virus which interacts with the host angiotensin-converting enzyme 2 (ACE2) and enters the host cell to cause the infection. Reports also suggest that TMPRSS2 is regulated by androgen present in prostate cells and it is highly expressed in PCa patients. Our lab has recently synthesized a new cisplatin prodrug which is a conjugate of lauric acid and cisplatin that potentially works very effectively in various androgen dependent and independent prostate cancer (PCa) cells. The cisplatin prodrug unlike other conventional platinum drugs is involved in inhibition of one of the major metabolic pathways of the PCa cells. Preliminary results show that, the prodrug in combination with the anti-androgen bicalutamide has an increased inhibition on the expression of TMPRSS2 in androgen dependent PCa and lung carcinoma cells along with down-regulation of some the lipogenic enzymes in-vitro. Here, we propose that the prodrug inhibits one of the mitochondrial metabolic pathways making the PCa cells sensitive towards cisplatin-based chemotherapy along with reducing the expression of TMPRSS2. Once completed, our work will provide an inside story of cisplatin prodrug mediated alteration of lipogenesis of cells in PCa tumor microenvironment resulting in a platform that has the potential to reduce the burden of cancer aggressiveness in both androgen dependent and independent PCa and also can be used as a potent chemotherapeutic agent against COVID-19. Citation Format: Subham Guin, Bapurao Surnar, Uttara Basu, Shanta Dhar. Inhibition of androgen-regulated TMPRSS2 and lipogenic enzymes in prostate and lung carcinoma cell lines by a cisplatin prodrug [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2021 Feb 3-5. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(6_Suppl):Abstract nr P07.
Impact of nitisinone treatment and discontinuation on the metabolome of wild type and hereditary tyrosinemia type 1 mice
Authors: Haaike Colemonts-Vroninks, Brendan P. Norman, Davison Andrew, Jessie Neuckermans, Marcelis Lionel, Mortier Anneleen, De Bundel Dimitri, Lakshminarayan Ranganath, Martens Geert, Tamara Vanhaecke, Gallagher James, Joery De Kock
Journal: Journal of Hepatology (2020)
Gut microbial metabolites facilitate anticancer therapy efficacy by modulating cytotoxic CD8+ T cell immunity
Authors: Yao He, Liuhui Fu, Yiping Li, Wenyan Wang, Mingli Gong, Jing Zhang, Xin Dong, Jiaoyan Huang, Quanbo Wang, Charles R. Mackay, Yang-Xin Fu, Yun Chen, Xiaohuan Guo
Journal: Cell Metabolism (2021)
Risk Factors for Severe Outcomes in Patients With Systemic Vasculitis and COVID‐19: A Binational, Registry‐Based Cohort Study
Authors: Matthew A. Rutherford, Jennifer Scott, Maira Karabayas, Marilina Antonelou, Seerapani Gopaluni, David Gray, Joe Barrett, Silke R. Brix, Neeraj Dhaun, Stephen P. McAdoo, Rona M. Smith, Colin C. Geddes, David Jayne, Raashid Luqmani, Alan D. Salama, Mark A. Little, Neil Basu
Journal: Arthritis & Rheumatology (2021)

COVID-19 is a novel infectious disease with a broad spectrum of clinical severity. Patients with systemic vasculitis have an increased risk of serious infections and may be at risk of severe outcomes following COVID-19. We undertook this study to establish the risk factors for severe COVID-19 outcomes in these patients, including the impact of immunosuppressive therapies.A multicenter cohort was developed through the participation of centers affiliated with national UK and Ireland vasculitis registries. Clinical characteristics and outcomes are described. Logistic regression was used to evaluate associations between potential risk factors and a severe COVID-19 outcome, defined as a requirement for advanced oxygen therapy, a requirement for invasive ventilation, or death.The cohort included 65 patients with systemic vasculitis who developed COVID-19 (median age 70 years, 49% women), of whom 25 patients (38%) experienced a severe outcome. Most patients (55 of 65 [85%]) had antineutrophil cytoplasmic antibody-associated vasculitis (AAV). Almost all patients required hospitalization (59 of 65 [91%]), 7 patients (11%) were admitted to intensive care, and 18 patients (28%) died. Background glucocorticoid therapy was associated with severe outcomes (adjusted odds ratio [OR] 3.7 [95% confidence interval 1.1-14.9]; P = 0.047), as was comorbid respiratory disease (adjusted OR 7.5 [95% confidence interval 1.9-38.2]; P = 0.006). Vasculitis disease activity and nonglucocorticoid immunosuppressive therapy were not associated with severe outcomes.In patients with systemic vasculitis, glucocorticoid use at presentation and comorbid respiratory disease were associated with severe outcomes in COVID-19. These data can inform clinical decision-making relating to the risk of severe COVID-19 in this vulnerable patient group.
Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses
Authors: Hong Zheng, Aditya M. Rao, Denis Dermadi, Jiaying Toh, Lara Murphy Jones, Michele Donato, Yiran Liu, Yapeng Su, Cheng L. Dai, Sergey A. Kornilov, Minas Karagiannis, Theodoros Marantos, Yehudit Hasin-Brumshtein, Yudong D. He, Evangelos J. Giamarellos-Bourboulis, James R. Heath, Purvesh Khatri
Journal: Immunity (2021)

Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.
OA01.04 Tumor Mutation Burden (TMB) by Next Generation Sequencing (NGS) Associates with Survival (OS) in Lung-MAP Immunotherapy Trials S1400I and S1400A
Authors: F. Hirsch, X. Hua, M. Wu, J. Neal, H. Cheng, S. Gettinger, L. Bazhenova, V. Papadimitrakopoulou, H. Borghaei, P. Mack, K. Kelly, R. Herbst, D. Gandara, M. Redman, D. Kozono
Journal: Journal of Thoracic Oncology (2021)
Associations between specific IgE sensitization to 26 respiratory allergen molecules and HLA class II alleles in the EGEA cohort
Authors: Hubert Gheerbrant, Alicia Guillien, Raphaël Vernet, Christian Lupinek, Christophe Pison, Isabelle Pin, Florence Demenais, Rachel Nadif, Jean Bousquet, Winfried F. Pickl, Rudolf Valenta, Emmanuelle Bouzigon, Valérie Siroux
Journal: Allergy (2021)

Allergy, the most frequent immune disorder affecting 30% of the world's population, is the consequence of immunoglobin E (IgE) sensitization to allergens. Among the genetic factors suspected to be involved in allergy, the HLA class-II genomic region is a strong candidate.To assess the association between HLA class-II alleles and specific IgE (sIgE) sensitization to a large number of respiratory allergen molecules.The analysis relied on 927 participants of the EGEA cohort, including 497 asthmatics. The study focuses on 26 aeroallergens recognized by sIgE in at least 5% of the study population (determined with the MEDALL chip with sIgE ≥ 0.3 ISU) and 23 imputed HLA class-II alleles. For each sIgE sensitization and HLA class-II allele, we fitted a logistic regression model accounting for familial dependence and adjusted for gender, age, and genetic principal components. p-values were corrected for multiple comparisons (False Discovery Rate).Most of the 19 statistically significant associations observed regard pollen allergens (mugwort Art v 1, olive tree Ole e 1, timothy grass Phl p 2, Phl p 5 and plantain Pla l 1), three were mold allergen (Alternaria Alt a 1), and a single one regards house dust mite allergen (Der p 7). No association was observed with pet allergens. The strongest associations were found with mugwort Art v 1 (OR = 5.42 (95%CI, 3.30; 8.88), 4.14 (2.65; 6.47), 3.16 (1.88; 5.31) with DQB1*05:01, DQA1*01:01 and DRB1*01:01, respectively).Our results support the important role of HLA class-II alleles as immune response genes predisposing their carriers for sensitization to various major pollen allergens.
MA12.08 Chemotherapy plus EGFR TKIs or Bevacizumab versus Chemotherapy Alone in SCLC-Transformed EGFR-Mutant Lung Adenocarcinoma
Authors: C. Zhang, S. Zhang, Y. Yao, Y. Gao, J. Huang, K. Peng, Q. Gao, H. Chen, C. Xu, X. Zhang, Y. Wu, J. Yang
Journal: Journal of Thoracic Oncology (2021)
Limitations and opportunities in the pharmacotherapy of ciliopathies
Authors: Max Duong Phu, Stefan Bross, Martin D. Burkhalter, Melanie Philipp
Journal: Pharmacology & Therapeutics (2021)

Ciliopathies are a family of rather diverse conditions, which have been grouped based on the finding of altered or dysfunctional cilia, potentially motile, small cellular antennae extending from the surface of postmitotic cells. Cilia-related disorders include embryonically arising conditions such as Joubert, Usher or Kartagener syndrome, but also afflictions with a postnatal or even adult onset phenotype, i.e. autosomal dominant polycystic kidney disease. The majority of ciliopathies are syndromic rather than affecting only a single organ due to cilia being found on almost any cell in the human body. Overall ciliopathies are considered rare diseases. Despite that, pharmacological research and the strive to help these patients has led to enormous therapeutic advances in the last decade. In this review we discuss new treatment options for certain ciliopathies, give an outlook on promising future therapeutic strategies, but also highlight the limitations in the development of therapeutic approaches of ciliopathies.
ヒト上皮成長因子受容体2(HER2)過剰発現原発性乳房腫瘍の転移部位におけるHER2発現の損失
Authors: Niikura Naoki, Liu Jun, Hayashi Naoki, A Mittendorf Elizabeth, Gong Yun, L Palla Shana, Tokuda Yutaka, M Gonzalez-Angula Ana, N Hortobagyi Gabriel, T Ueno Naoto
Journal: Journal of Clinical Oncology (2012)
Polymer-ritonavir derivate nanomedicine with pH-sensitive activation possesses potent anti-tumor activity in vivo via inhibition of proteasome and STAT3 signaling
Authors: Ladislav Sivák, Vladimír Šubr, Jiřina Kovářová, Barbora Dvořáková, Milada Šírová, Blanka Říhová, Eva Randárová, Michal Kraus, Jakub Tomala, Martin Studenovský, Michaela Vondráčková, Radislav Sedláček, Petr Makovický, Jitka Fučíková, Šárka Vošáhlíková, Radek Špíšek, Libor Kostka, Tomáš Etrych, Marek Kovář
Journal: Journal of Controlled Release (2021)
Author Correction: CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies
Authors: Rebecca Davies, Ling Liu, Sheng Taotao, Natasha Tuano, Richa Chaturvedi, Kie Kyon Huang, Catherine Itman, Amit Mandoli, Aditi Qamra, Changyuan Hu, David Powell, Roger J. Daly, Patrick Tan, Joseph Rosenbluh
Journal: Genome biology (2021)

An amendment to this paper has been published and can be accessed via the original article.
Occupational contact dermatitis: Retrospective analysis of North American Contact Dermatitis Group Data, 2001 to 2016
Authors: Joel G. DeKoven, Benjamin M. DeKoven, Erin M. Warshaw, C.G.T. Mathias, James S. Taylor, Denis Sasseville, Donald V. Belsito, Joseph F. Fowler, Melanie D. Pratt, Kathryn A. Zug, Howard I. Maibach, Vincent A. DeLeo, Jonathan I. Silverberg, Amber R. Atwater, Margo J. Reeder, D. Linn Holness
Journal: Journal of the American Academy of Dermatology (2021)
FP02.10 Predictors of Moderate-to-Severe Symptoms in Stage IV NSCLC: A Population-Based Study of Patient Reported Outcomes
Authors: M. Tjong, M. Doherty, L. Davis, W. Chan, H. Zhao, V. Delibasic, J. Hallet, A. Mahar, B. Kidane, F. Wright, G. Darling, N. Coburn, A. Louie
Journal: Journal of Thoracic Oncology (2021)
Abstract 11205: Sickle Cell Disease is a Prognostic Indicator of Increased In-hospital Mortality in Heart Failure Admissions: Results of a National Inpatient Sample Database Study
Authors: Maryam Gbadamosi-Akindele, Dinesh Reddy Apala, Janani Baskaran, Sara Albagoush, Aravdeep Jhand, Daniel Ermann, Sarah Aurit, Hussain Rangoonwala, Margaret Butler, Peter Silberstein
Journal: Circulation (2019)

Introduction: Cardiopulmonary disease is a leading cause of mortality in sickle cell disease (SCD). Although there are studies describing the various causes of mortality in SCD, none have specifica...
P09.53 Comparative Effectiveness of Crizotinib versus Entrectinib in ROS1+ Non-Small Cell Lung Cancer (NSCLC) using Clinical Trial and Real-World Data
Authors: M. Groff, G. Tremblay, L. Iadeluca, K. Wilner, R. Wiltshire, L. Bartolome, T. Usari, J. Cappelleri, R. Camidge
Journal: Journal of Thoracic Oncology (2021)
P22.02 Outcome of Heart Rupture Repair During Huge Mediastinal Mass Resection
Authors: R. Abdeljalil, M.K.A. Chaar, O. Al-Qudah, F. Alazzam, K.A. Zahra, M. Al-Hussaini, A. Gharaibeh
Journal: Journal of Thoracic Oncology (2021)
Genome-wide copy number analysis for genetic alterations involved in liver metastasis of the colon
Authors: Hideaki Tanami, Issei Imoto, Itaru Sonoda, Kenichi Sugihara, Johji Inazawa
Journal: Cancer Research (2004)

1724   It is controversial whether there is any genetic difference between primary colorectal carcinomas and liver metastases or not. In the previous reports comparative genomic hybridization (CGH) analyses were performed in both primary tumors and metastatic tumors respectively, and then CGH profiles were compared with each other. But there have been only a few studies with a limited number of cases analyzing paired samples. To determine the genetic aberrations involving metastasis-related genes, we carried out the subtractive CGH analysis using a series of paired samples. Material and methods; 20 paired samples from colorectal cancer patients with synchronous or metachronous liver metastasis were subjected to the subtractive CGH analysis. Relatively frequent DNA copy number gains detected by subtractive CGH were found in 6p. Further, to determine candidate genes within 6p amplification, three of 20 paired samples and COLO201 exhibiting 6p gains/amplification were analyzed by a CGH array, which was custom-made in our laboratory. In addition, we performed expression analysis of candidate target genes within the altered region by Quantitative Reverse Transcriptase-Polymerase Chain Reaction (Q-PCR). Results; The present study shows that 6p is detected as a predominantly amplified region in metastasis by subtractive CGH, indicating that 6p may harbor a metastasis-related gene(s), and our CGH array analyses could reveal one candidate gene, which is known implicated in the cell cycle regulation. Q-PCR showed that this gene was significantly up-regulated in liver metastatic lesion compared with in primary lesion (p
P76.92 TKI and Intrathoracic Perfusion in First-line Stage IV Lung Adenocarcinoma with EGFR Mutation and Malignant Pleural Effusion
Authors: W. Huang, P. Li, H. Xu, K. Xu, J. Weng, Y. Zhang, J. Liu
Journal: Journal of Thoracic Oncology (2021)
Interaction between the <i>STAT4</i> rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus
Authors: Sarah Reid, Niklas Hagberg, Johanna K Sandling, Andrei Alexsson, Pascal Pucholt, Christopher Sjöwall, Karoline Lerang, Andreas Jönsen, Iva Gunnarsson, Ann-Christine Syvänen, Anne Margrethe Troldborg, Anne Voss, Anders A Bengtsson, Øyvind Molberg, Søren Jacobsen, Elisabet Svenungsson, Lars Rönnblom, Dag Leonard
Journal: Annals of the Rheumatic Diseases (2021)

Objective To investigate how genetics influence the risk of smoking-related systemic lupus erythematosus (SLE) manifestations. Methods Patients with SLE (n discovery cohort =776, n replication cohort =836) were genotyped using the 200K Immunochip single nucleotide polymorphisms (SNP) Array (Illumina) and a custom array. Sixty SNPs with SLE association (p&lt;5.0×10 −8 ) were analysed. Signal transducer and activator of transcription 4 (STAT4) activation was assessed in in vitro stimulated peripheral blood mononuclear cells from healthy controls (n=45). Results In the discovery cohort, smoking was associated with myocardial infarction (MI) (OR 1.96 (95% CI 1.09 to 3.55)), with a greater effect in patients carrying any rs11889341 STAT4 risk allele (OR 2.72 (95% CI 1.24 to 6.00)) or two risk alleles (OR 8.27 (95% CI 1.48 to 46.27)). Smokers carrying the risk allele also displayed an increased risk of nephritis (OR 1.47 (95% CI 1.06 to 2.03)). In the replication cohort, the high risk of MI in smokers carrying the risk allele and the association between the STAT4 risk allele and nephritis in smokers were confirmed (OR 6.19 (95% CI 1.29 to 29.79) and 1.84 (95% CI 1.05 to 3.29), respectively). The interaction between smoking and the STAT4 risk allele resulted in further increase in the risk of MI (OR 2.14 (95% CI 1.01 to 4.62)) and nephritis (OR 1.53 (95% CI 1.08 to 2.17)), with 54% (MI) and 34% (nephritis) of the risk attributable to the interaction. Levels of interleukin-12-induced phosphorylation of STAT4 in CD8+ T cells were higher in smokers than in non-smokers (mean geometric fluorescence intensity 1063 vs 565, p=0.0063). Lastly, the IL12A rs564799 risk allele displayed association with MI in both cohorts (OR 1.53 (95% CI 1.01 to 2.31) and 2.15 (95% CI 1.08 to 4.26), respectively). Conclusions Smoking in the presence of the STAT4 risk gene variant appears to increase the risk of MI and nephritis in SLE. Our results also highlight the role of the IL12−STAT4 pathway in SLE-cardiovascular morbidity.
Predicting endoscopic remission in Crohn’s disease by the modified multiplier SES-CD (MM-SES-CD)
Authors: Neeraj Narula, Emily C L Wong, Jean-Frederic Colombel, William J Sandborn, John Kenneth Marshall, Marco Daperno, Walter Reinisch, Parambir S Dulai
Journal: Gut (2021)

The Simple Endoscopic Score for Crohn's disease (SES-CD) is the primary tool for measurement of mucosal inflammation in clinical trials but lacks prognostic potential. We set to develop and validate a modified multiplier of the SES-CD (MM-SES-CD), which takes into consideration each individual parameter's prognostic value for achieving endoscopic remission (ER) while on active therapy.In this posthoc analysis of three CD clinical trial programmes (n=350 patients, baseline SES-CD ≥ 3 with confirmed ulceration), data were pooled and randomly split into a 70% training and 30% testing cohort. The MM-SES-CD was designed using weights for individual parameters as determined by logistic regression modelling, with 1-year ER (SES-CD < 3) being the dependent variable. A cut point score for low and high probability of ER was determined by using the maximum Youden Index and validated in the testing cohort.Baseline ulcer size, extent of ulceration and presence of non-passable strictures had the strongest association with 1-year ER as compared with affected surface area, with differential weighting of individual parameters across disease segments being observed during logistic regression. The MM-SES-CD was generated using this weighted regression model and demonstrated strong discrimination for ER in the training dataset (area under the receiver operator curve (AUC) 0.83, 95% CI 0.78 to 0.94) and in the testing dataset (AUC 0.82, 95% CI 0.77 to 0.92). In comparison to the MM-SES-CD scoring model, the original SES-CD score lacks accuracy (AUC 0.60, 95% CI 0.55 to 0.65) for predicting the achievement of ER.We developed and internally validated the MM-SES-CD as an endoscopic severity assessment tool to predict one-year ER in patients with CD on active therapy.