tbuckley/cabot-search huggingface dataset:
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database
Authors: Jake Lever, Martin R. Jones, Arpad M. Danos, Kilannin Krysiak, Melika Bonakdar, Jasleen K. Grewal, Luka Culibrk, Obi L. Griffith, Malachi Griffith, Steven J. M. Jones
Journal: Genome Medicine (2019)

Precision oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. To improve patient care, knowledge of diagnostic, prognostic, predisposing, and drug response markers is essential. Several knowledgebases have been created by different groups to collate evidence for these associations. These include the open-access Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. These databases rely on time-consuming manual curation from skilled experts who read and interpret the relevant biomedical literature. To aid in this curation and provide the greatest coverage for these databases, particularly CIViC, we propose the use of text mining approaches to extract these clinically relevant biomarkers from all available published literature. To this end, a group of cancer genomics experts annotated sentences that discussed biomarkers with their clinical associations and achieved good inter-annotator agreement. We then used a supervised learning approach to construct the CIViCmine knowledgebase. We extracted 121,589 relevant sentences from PubMed abstracts and PubMed Central Open Access full-text papers. CIViCmine contains over 87,412 biomarkers associated with 8035 genes, 337 drugs, and 572 cancer types, representing 25,818 abstracts and 39,795 full-text publications. Through integration with CIVIC, we provide a prioritized list of curatable clinically relevant cancer biomarkers as well as a resource that is valuable to other knowledgebases and precision cancer analysts in general. All data is publically available and distributed with a Creative Commons Zero license. The CIViCmine knowledgebase is available at http://bionlp.bcgsc.ca/civicmine/.
Perinatal Origins of Cardiovascular Health Disparities Across the Life Course
Authors: Casey Crump, Elizabeth A. Howell
Journal: JAMA Pediatrics (2019)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
Favorable Outcomes of Newly Diagnosed Intravascular Large B-Cell Lymphoma Patients Treated with R-CHOP Combined with High-Dose Methotrexate Plus Intrathecal Chemotherapy: Results from a Multicenter Phase 2 Trial (PRIMEUR-IVL)
Authors: Kazuyuki Shimada, Motoko Yamaguchi, Yoshiko Atsuta, Kosei Matsue, Keijiro Sato, Shigeru Kusumoto, Hirokazu Nagai, Jun Takizawa, Noriko Fukuhara, Koji Nagafuji, Kana Miyazaki, Eiichi Ohtsuka, Masataka Okamoto, Yasumasa Sugita, Toshiki Uchida, Satoshi Kayukawa, Atsushi Wake, Daisuke Ennishi, Yukio Kondo, Tohru Izumi, Yoshihiro Kin, Kunihiro Tsukasaki, Daigo Hashimoto, Masaaki Yuge, Atsumi Yanagisawa, Yachiyo Kuwatsuka, Satoko Shimada, Yasufumi Masaki, Nozomi Niitsu, Hitoshi Kiyoi, Ritsuro Suzuki, Takashi Tokunaga, Shigeo Nakamura, Tomohiro Kinoshita
Journal: Blood (2019)
Response to: ‘Overlap of systemic lupus erythematosus and myositis is rare in anti-Ku antibody-positive patients’ by Ogawa-Momohara <i>et al</i>
Authors: Lionel Spielmann, Benoit Nespola, Alain Meyer
Journal: Annals of the Rheumatic Diseases (2019)

Response to: 'Overlap of systemic lupus erythematosus and myositis is rare in anti-Ku antibody-positive patients' by Ogawa-Momohara et alWe thank Ogawa-Momohara et al for their comment 1 on our work in which we identified that anti-Ku patients with elevated serum creatine kinase (elevated CK) are at risk of interstitial lung disease (ILD), whereas anti-Ku patients with anti-double-strand DNA (dsDNA) antibodies frequently have systemic lupus erythematosus (SLE) and are at risk of glomerulonephritis. 2 The data reported by Ogawa-Momohara et al importantly complete our results since none of our anti-Ku patients had an Asian origin.Ogawa-Momohara et al retrospectively screened sera from 600 Japanese patients with connective tissue diseases and found 10 anti-Ku-positive patients.Their data confirm that anti-Ku patients with elevated CK are at risk of ILD and rarely overlap with anti-Ku patients with SLE who are at risk of glomerulonephritis.Among their five anti-Ku-positive patients with elevated CK, three had ILD and none had glomerulonephritis.By contrast, among the three patients diagnosed with SLE, none had increased CK; only one had ILD; and all had nephritis.Yet, in contrast with our cohort, when detected, anti-dsDNA antibodies were systematically found in patients with elevated CK (n=3/5), while none of their anti-Ku patients with SLE tested positive for anti-dsDNA.This finding is in contrast to several previous non-Asian series in which anti-dsDNA antibodies were more frequently [3][4][5] or even exclusively 6 detected in anti-Ku patients with SLE as compared with anti-Ku patients with other connective tissue diseases.As pointed by Ogawa-Momohara et al, this may indicate that genetic and/or environmental backgrounds may shape the anti-dsDNA profile of anti-Ku patients, although results may have also been influenced by detection methods used and/or delay between treatment onset and serum sampling.In conclusion, as pointed by Ogawa-Momohara et al, the patients' geographical origin must be taken into consideration when describing connective tissue diseases.In this regard, the data provided by Ogawa-Momohara et al represent an important addition to our own findings by shedding light on the spectrum of anti-Ku-related disease in Asian patients.
Long-Term Follow-Up of Serially Transplanted Mice Receiving Extended Reduced Intensity Selection of MGMT-P140K Expressing Murine Repopulating Stem Cells Demonstrates Stable Oligo- to Polyclonal Hematopoiesis without Clonal Exhaustion.
Authors: Claudia Ball, Manfred Schmidt, Ingo Pilz, Monika Schrempp, Christof von Kalle, Hanno Glimm
Journal: Blood (2005)
Core Competencies in Cardiac CT for Imaging Structural Heart Disease Interventions
Authors: Jonathon Leipsic, Bjarne L Nørgaard, Omar Khalique, João L Cavalcante, Dee Dee Wang, Hasan Jilaihawi, Victoria Delgado, Jeroen J Bax, Phlipp Blanke
Journal: JACC. Cardiovascular imaging (2019)
A supramolecular protein chaperone for vaccine delivery
Authors: Zhongyan Wang, Yuna Shang, Zhaoqi Tan, Xiaoyan Li, Guoliang Li, Chunhua Ren, Fuqiang Wang, Zhimou Yang, Jianfeng Liu
Journal: Theranostics (2019)

Rationale: Nanomaterials capable of specifically interacting with proteins are very important for protein storage and vaccine delivery. Supramolecular hydrogels based on peptides have emerged as promising vaccine adjuvants because of their good compatibility, ease of antigen incorporation and display, and efficiency in activating immune responses. Methods: We synthesized a self-assembling peptide (Fbp-GDFDFDYDK(γE)2-NH2, Comp. 1 ) serving as a supramolecular protein chaperone for protein antigen delivery. The gelation was triggered by simply mixing Comp. 1 and proteins. The vaccine adjuvant potential of Comp. 1 was demonstrated by using two protein antigens, ovalbumin (OVA) and hepatitis B surface antigen (HBsAg). Results: The peptide derivative Comp. 1 exhibited high protein binding capacity. Upon contacting proteins, Comp. 1 rapidly formed coassembled nanofibers/hydrogels with the proteins, which greatly delayed the release of protein antigens. Our supramolecular protein chaperone significantly stimulated specific antibody titers by assisting protein delivery to antigen-presenting cells, promoting dendritic cell (DC) maturation, prolonging antigen accumulation and retention in the lymph nodes, and eliciting the secretion of cytokines. Most importantly, our supramolecular protein chaperone strongly stimulated the cellular immune response and significantly retarded tumor growth. Conclusion: Our study demonstrated the great potential of the supramolecular protein chaperone in protein storage and delivery, vaccine production and tumor immunotherapy.
Extracellular UTP Affects In Vitro Migration and In Vivo Homing and Engraftment of CD34+ Hematopoietic Stem Cells.
Authors: Lara Rossi, Miriam Fogli, Davide Ferrari, Cinzia Pizzirani, Diletta Vaselli, Francesco Bertolini, Francesco Di Virgilio, Michele Baccarani, Roberto M. Lemoli
Journal: Blood (2004)
A multicentre observational study on the epidemiology, risk factors, management and outcomes of mucormycosis in India
Authors: A. Patel, H. Kaur, I. Xess, J.S. Michael, J. Savio, S. Rudramurthy, R. Singh, P. Shastri, P. Umabala, R. Sardana, A. Kindo, M.R. Capoor, S. Mohan, V. Muthu, R. Agarwal, A. Chakrabarti
Journal: Clinical Microbiology and Infection (2019)
Patients Who Respond to Donor Lymphocyte Infusion (DLI) Have an Antibody Response Against PDC-E2, the Immunodominant Autoantigens of Primary Biliary Cirrhosis (PBC), but with Different Specificity.
Authors: Roberto Bellucci, Meagan Gallagher, Sabine Oertelt, Emmanuel Zorn, Edwin P. Alyea, Robert J. Soiffer, Catherine J. Wu, Nikhil C. Munshi, Eric Gershwin, Jerome Ritz
Journal: Blood (2005)
Sonic Hedgehog, a Novel Endogenous Damage Signal, Activates Multiple Beneficial Functions of Human Endometrial Stem Cells
Authors: Se-Ra Park, Soo-Rim Kim, Chan Hum Park, Soyi Lim, Seung Yeon Ha, In-Sun Hong, Hwa-Yong Lee
Journal: Molecular Therapy (2019)

Local endometrial stem cells play an important role in regulating endometrial thickness, which is an essential factor for successful embryo implantation and pregnancy outcomes. Importantly, defects in endometrial stem cell function can be responsible for thin endometrium and subsequent recurrent pregnancy losses. Therefore, many researchers have directed their efforts toward finding a novel stimulatory factor that can enhance the regenerative capacity of endometrial stem cells. Sonic hedgehog (SHH) is a morphogen that plays a key role in regulating pattern formation throughout embryonic limb development. In addition to this canonical function, we identified for the first time that SHH is actively secreted as a stem cell-activating factor in response to tissue injury and subsequently stimulates tissue regeneration by promoting various beneficial functions of endometrial stem cells. Our results also showed that SHH exerts stimulatory effects on endometrial stem cells via the FAK/ERK1/2 and/or phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways. More importantly, we also observed that endometrial stem cells stimulated with SHH showed markedly enhanced differentiation and migratory capacities and subsequent in vivo therapeutic effects in an endometrial ablation animal model.
保乳手术至术后放疗的间隔时间对老年乳腺癌患者局部复发的影响：回顾性队列分析（摘要）
Authors: Rinaa, Ptmglia, Aldko, Saito, Bridget, Neville, Craig, Earle, Jane, 刘雨桃, 王燕
Journal: BMJ (2010)
Interleukin-10 Deficiency Alters Endothelial Progenitor Cell–Derived Exosome Reparative Effect on Myocardial Repair via Integrin-Linked Kinase Enrichment
Authors: Yujia Yue, Chunlin Wang, Cindy Benedict, Grace Huang, May Truongcao, Rajika Roy, Maria Cimini, Venkata Naga Srikanth Garikipati, Zhongjian Cheng, Walter J. Koch, Raj Kishore
Journal: Circulation Research (2019)

Rationale: Systemic inflammation compromises the reparative properties of endothelial progenitor cell (EPC) and their exosomes on myocardial repair, although the underlying mechanism of loss of function of exosomes from inflamed EPCs is still obscure. Objective: To determine the mechanisms of IL-10 (interleukin-10) deficient-EPC–derived exosome dysfunction in myocardial repair and to investigate if modification of specific exosome cargo can rescue reparative activity. Methods and Results: Using IL-10 knockout mice mimicking systemic inflammation condition, we compared therapeutic effect and protein cargo of exosomes isolated from wild-type EPC and IL-10 knockout EPC. In a mouse model of myocardial infarction (MI), wild-type EPC-derived exosome treatment significantly improved left ventricle cardiac function, inhibited cell apoptosis, reduced MI scar size, and promoted post-MI neovascularization, whereas IL-10 knockout EPC-derived exosome treatment showed diminished and opposite effects. Mass spectrometry analysis revealed wild-type EPC-derived exosome and IL-10 knockout EPC-derived exosome contain different protein expression pattern. Among differentially expressed proteins, ILK (integrin-linked kinase) was highly enriched in both IL-10 knockout EPC-derived exosome as well as TNFα (tumor necrosis factor-α)-treated mouse cardiac endothelial cell–derived exosomes (TNFα inflamed mouse cardiac endothelial cell–derived exosome). ILK-enriched exosomes activated NF-κB (nuclear factor κB) pathway and NF-κB–dependent gene transcription in recipient endothelial cells and this effect was partly attenuated through ILK knockdown in exosomes. Intriguingly, ILK knockdown in IL-10 knockout EPC-derived exosome significantly rescued their reparative dysfunction in myocardial repair, improved left ventricle cardiac function, reduced MI scar size, and enhanced post-MI neovascularization in MI mouse model. Conclusions: IL-10 deficiency/inflammation alters EPC-derived exosome function, content and therapeutic effect on myocardial repair by upregulating ILK enrichment in exosomes, and ILK-mediated activation of NF-κB pathway in recipient cells, whereas ILK knockdown in exosomes attenuates NF-κB activation and reduces inflammatory response. Our study provides new understanding of how inflammation may alter stem cell-exosome–mediated cardiac repair and identifies ILK as a target kinase for improving progenitor cell exosome-based cardiac therapies.
From Ex-Vivo T-Cell Depletion to Post-Transplant Cyclophosphamide: Improved GvHD-Free &amp; Relapse-Free Survival but Comparable Chronic GvHD Incidence in Haploidentical Transplantation. A 15 Years EBMT Registry Analysis on Behalf of the TCWP-EBMT
Authors: Maria Teresa Lupo-Stanghellini, Christophe Peczynski, Hildegard T. Greinix, Emmanuelle Polge, Mohamad Mohty, Ibrahim Yakoub-Agha, Silvia Montoto, Nicolaus Kröger, Zinaida Peric, Olaf Penack, Rafael F Duarte, Grzegorz W Basak
Journal: Blood (2019)
First-In-Human Study of Cemiplimab Alone or In Combination with Radiotherapy and/or Low-dose Cyclophosphamide in Patients with Advanced Malignancies
Authors: Kyriakos P. Papadopoulos, Melissa L. Johnson, Albert C. Lockhart, Kathleen Moore, Gerald S. Falchook, Silvia C. Formenti, Aung Naing, Richard D. Carvajal, Lee S. Rosen, Glen J. Weiss, Rom S. Leidner, Jingjin Li, Anne Paccaly, Minjie Feng, Elizabeth Stankevich, Israel Lowy, Matthew G. Fury, Marka R. Crittenden
Journal: Clinical Cancer Research (2019)

Abstract Purpose: This first-in-human study assessed the safety, tolerability, dose-limiting toxicities (DLT), antitumor activity, and pharmacokinetics of cemiplimab, a monoclonal anti-programmed cell death-1 (PD-1), as monotherapy and in combination with hypofractionated radiotherapy (hfRT) and/or cyclophosphamide (CPA) in patients with advanced solid tumors. Patients and Methods: Patients were enrolled in 1 of 10 dose escalation cohorts and received cemiplimab 1, 3, or 10 mg/kg every 2 weeks intravenously for up to 48 weeks. Depending on the cohort, patients received hfRT and/or low-dose (200 mg/m2) CPA. Safety was evaluated. Antitumor activity was assessed by Response Evaluation Criteria in Solid Tumors version 1.1. Results: Sixty patients were enrolled. The median duration of follow-up was 19.3 weeks (range, 2.3–84.3). There were no DLTs. The most common treatment-emergent adverse events (TEAEs) of any grade were fatigue (45.0%), nausea (36.7%), and vomiting (25.0%). The most common immune-related adverse events (irAEs) of any grade were arthralgia (10.0%), hypothyroidism (8.3%), and maculopapular rash (8.3%). Cemiplimab pharmacokinetic parameters increased in a close to dose-proportional manner and were similar regardless of combination therapy regimen. Two patients (one with cutaneous squamous cell carcinoma and one with cervical cancer) experienced a complete response; 7 had a partial response. Observed duration of response was ≥12 months in 6 patients. Conclusions: The safety profile of cemiplimab was comparable with other anti–PD-1 agents. Addition of hfRT and/or CPA did not appear to increase grade ≥3 irAEs, suggesting that cemiplimab can be safely administered with hfRT and/or CPA. Cemiplimab exhibited encouraging antitumor activity with 2 complete responses and 7 partial responses observed; responses were also durable.
Intravascular Lymphoma: Poor Outcomes May Be Improved with Aggressive Therapy.
Authors: Christopher A. Yasenchak, Ahmet Dogan, Joseph P. Colgan, Thomas M. Habermann, David J. Inwards, Patrick B. Johnston, Svetomir N. Markovic, Ivana N.M. Micallef, Luis F. Porrata, Thomas E. Witzig, Stephen M. Ansell
Journal: Blood (2005)
Parting the Clouds over Typhoid with a New Conjugate Vaccine
Authors: Florian Marks, Jerome H. Kim
Journal: New England Journal of Medicine (2019)

Typhoid fever is caused by fecal–oral transmission of Salmonella enterica serovar Typhi (S. Typhi). It has been a deadly companion to mankind for centuries, affecting 10.9 million persons and resulting in an estimated 116,800 deaths per year.1 Although vaccines against typhoid have been available for more than a century and have been shown to be protective,2,3 the approved vaccines (injectable Vi polysaccharide and oral, live-attenuated Ty21a typhoid vaccines) have not been useful in populations with a high typhoid burden, particularly in young children.4 To address this shortfall, the Bill and Melinda Gates Foundation, as well as other donors, has supported . . .
Differential Cytogenetic Pattern of Splenic Marginal Zone B-Cell Lymphoma CD5 Positive Versus CD5 Negative. Preliminary Results.
Authors: Eva Gimeno, Marta Salido, Isabel Granada, Blanca Espinet, Encarnacion Perez-Vila, Antonio Salar, Carles Besses, Mar Bellido, Alicia Domingo, Fuensanta Milla, Sergi Serrano, Soledad Woessner, Lourdes Florensa, Francesc Sole
Journal: Blood (2004)
DAPAGLIFLOZIN AND CARDIOVASCULAR OUTCOMES IN PATIENTS WITH TYPE 2 DIABETES AND PRIOR MYOCARDIAL INFARCTION: A SUB-ANALYSIS FROM DECLARE TIMI-58 TRIAL
Authors: Remo Holanda de Mendonca Furtado, Marc Bonaca, Itamar Raz, Thomas Zelniker, Ofri Mosenzon, Avivit Cahn, Julia Kuder, Sabina Murphy, Deepak L. Bhatt, Lawrence Leiter, Darren McGuire, John P.H. Wilding, Christian Ruff, Ingrid A.M. Gause-Nilsson, Martin Fredriksson, Anna Maria Langkilde, Marc Sabatine, Stephen Wiviott
Journal: Journal of the American College of Cardiology (2019)
Nurselike Cells in Chronic Lymphocytic Leukemia Have Gene Expression Profiles and Functional Characteristics That Are Distinct from Those of Monocytes or Dendritic Cells.
Authors: Davorka Messmer, Tomoyuki Endo, Bradley T. Messmer, Danelle James, Nathan J. Zvaifler, Ingo G.H. Schmidt-Wolf, Kipps J. Tom
Journal: Blood (2005)
Agonists and inhibitors of the STING pathway: Potential agents for immunotherapy
Authors: Jun‐Jun Wu, Lang Zhao, Hong‐Guo Hu, Wen‐Hao Li, Yan‐Mei Li
Journal: Medicinal Research Reviews (2019)

Since being discovered in 2008, the STING (stimulator of interferon genes) pathway has gradually been recognized as a central and promising target for immunotherapy. The STING pathway can be stimulated by cyclic dinucleotides (CDNs), leading to the type I interferons (IFN) production for immunotherapy for cancer or other diseases. However, the negative charges, hydrophilicity, and instability of CDNs have hindered their further applications. In addition, chronic activation of the STING pathway has been found to be involved in autoimmune diseases as IFN overproduction. Thus, research and development of STING agonists and inhibitors has been a hot field for the treatment of several diseases. The past several years, especially 2018, has seen increasingly rapid advances in this field. Here, this review summarizes the synthesis and modification of CDNs, the identification of nonnucleotide agonists, the recent progress in delivery systems and the medical applications, such as personalized vaccine adjuvants, in detail. In addition, in this review, we summarize the STING inhibitors' advances from two aspects, covalent, and noncovalent inhibitors.
Sequential Time-Point Mutational Analysis of TP53 in Follicular Lymphoma Undergoing Transformation to Large B-Cell Lymphoma.
Authors: Andrew J. Davies, Abigail M. Lee, Claire Taylor, Andrew J. Clear, Lindsey K. Goff, Sameena Iqbal, Darren Cuthbert-Heavens, Maria Calaminici, Andrew J. Norton, T. Andrew Lister, Jude Fitzgibbon
Journal: Blood (2004)
Dominant Role of Raf/MEK/ERK Signaling in Hematopoietic Cell Cycle Progression, Prevention of Apoptosis and Drug Resistance.
Authors: James A. McCubrey, Steven L. Abrams, Linda S. Steelman, Ellis W.T. Wong, William H. Chappell, Jorg Basecke, Franca Stivala, Massimo Libra, Michele Milella, Agostino Tafuri, Jacob Troppmair, Marina Konopleva, Michael Andreeff, Camilla Evangelisti, Alberto M. Martelli
Journal: Blood (2006)
An Artificial Neural Network Providing Highly Reliable Decision Support in a Routine Setting for Classification of B-Cell Neoplasms Based on Flow Cytometric Raw Data
Authors: Wolfgang Kern, Franz Elsner, Max Zhao, Nanditha Mallesh, Richard Schabath, Claudia Haferlach, Peter Krawitz, Hannes Lueling, Torsten Haferlach
Journal: Blood (2019)
Writing Poems About Patients
Authors: Michael Wynn
Journal: JAMA (2019)

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