tbuckley/cabot-search huggingface dataset:
Identification of three tumor antigens and immune subtypes for mRNA vaccine development in diffuse glioma
Authors: Quanwei Zhou, Xuejun Yan, Hecheng Zhu, Zhaoqi Xin, Jin Zhao, Wenyue Shen, Wen Yin, Youwei Guo, Hongjuan Xu, Ming Zhao, Weidong Liu, Xingjun Jiang, Caiping Ren
Journal: Theranostics (2021)

Rationale: Diffuse glioma patients have high mortality and recurrence despite multimodal therapies. This study aims to identify the potential tumor antigens for mRNA vaccines and subtypes suitable for the immunotherapy of patients with diffuse glioma. Methods: Gene expression profiles and corresponding clinical information were obtained from the Chinese Glioma Genome Atlas (CGGA) and the Cancer Genome Atlas (TCGA) databases. Genetic alterations were extracted from cBioPortal. Differential gene analysis, survival analysis, correlation analysis, consensus clustering analysis, and immune cell infiltration analysis were conducted based on the various databases. Finally, the hub genes, the modules related to tumor antigens, and the immune subtypes were identified using WGCNA method. Results: Three over-expressed, amplified, and mutated tumor antigens, including KDR, COL1A2, and SAMD9, were associated with clinical outcomes. The expression of the three genes had a positive correlation with the abundance of antigen-presenting cells (APCs) and APC marker expression. Subsequently, three immune subtypes (Ims1, Ims2, and Ims3) were distinguished in the TCGA cohort, which exhibited distinct molecular, cellular, and clinical characteristics consistent with the CGGA cohort. Diffuse gliomas with subtype Ims1 were more malignant with immunosuppressive phenotypes and more associated with poor prognosis than the other two subtypes. The three antigens and the immune checkpoints were differentially expressed among the three immune subtypes. Finally, functional enrichment analysis of the genes related to tumor antigens and immune subtypes suggested that they are enriched in many immune-associated processes. Conclusions: KDR, COL1A2, and SAMD9 are potential antigens for developing mRNA vaccines against diffuse glioma. The results suggest that immunotherapy targeting these three antigens is more suitable for patients with subtype Ims1. This study provides insights into immunotherapy for diffuse glioma.
Art in Endoscopy: Bridge over anastomotic stoma
Authors: Jingyu Zhu, Liang Liu, Xingjie Shen, Xiaoyan Zhu
Journal: Endoscopy (2021)

This image is from a patient who had undergone laparoscopic-assisted total gastrectomy 2 years previously for low-differentiation gastric adenocarcinoma. A large and thick mucosal bridge was found above the anastomotic stoma. Reality is this shore, the ideal is the other shore. The bridge at least means hope and success, no matter where it appears.
TCT-71 Characteristics and Outcomes of Men and Women Undergoing Chronic Total Occlusion Percutaneous Coronary Intervention: Individual Patient Data Pooled Analysis of 4 Multicenter Registries
Authors: Ilias Nikolakopoulos, Alexandre Quadros, Joseph Dens, Nidal Abi Rafeh, Pierfrancesco Agostoni, Khaldoon Alaswad, Alexandre Avran, Karlyse Belli, Carlos Campos, Mauro Carlino, James Choi, Felix Damas De Los Santos, Ahmed ElGuindy, Farouc Amin Jaffer, Dimitri Karmpaliotis, Jaikirshan Khatri, Dmitrii Khelimskii, Paul Knaapen, Oleg Krestyaninov, Alessio La Manna, Pablo Lamelas, Soledad Ojeda, Lucio Padilla, Pedro Piccaro de Oliveira, Stephane Rinfret, Ricardo Santiago, James Spratt, Simon Walsh, Spyridon Kostantinis, Bahadir Simsek, Judit Karacsonyi, Bavana Rangan, Evangelia Vemmou, Emmanouil Brilakis, Lorenzo Azzalini
Journal: Journal of the American College of Cardiology (2021)
Understanding Associations Between Attention-Deficit/Hyperactivity Disorder and Traumatic Brain Injury
Authors: Guido I. Guberman, Sheilagh Hodgins
Journal: JAMA Pediatrics (2021)

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
Eradication of Potential In-Transit Metastasis in Breast-Conserving Surgery
Authors: Xiaoti Lin, Weiyu Chen, Fengqin Wei
Journal: JAMA Surgery (2021)

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 Surgery 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 Surgery journal
Abstract 14118: Low Rate of Sudden Cardiac Death Following New Onset of a Wide Left Bundle Branch Block After Tavi Implantation Managed by an Electrophysiological Guided Strategy
Authors: lena Rivard, Anita Asgar, William Remillard, Rafik Tadros, Marc Dubuc, Peter G Guerra, Reda Ibrahim, Julia Cadrin-Tourigny, Blandine Mondesert, Laurent Macle, Denis Roy, Mario Talajic, Katia Dyrda, Bernard Thibault, Raoul Bonan, Jean-Francois Dorval, Raymond Cartier, Paul Khairy
Journal: Circulation (2018)

Introduction: New-onset persistent left bundle branch block (NOP-LBBB) is one of the most common conduction disturbances following transcatheter aortic valve implantation (TAVI). Patients with a wi...
Angiotensin receptor blocker, telmisartan, suppresses aldosterone and increases adiponectin production more effectively then ACE-inhibitor, perindopril in hypertension (A preliminary study)
Authors: T Nakamura, Yuichiro Saito, Kojyuro Morishita, Hoshino Jin, Tsutomu Hosoi, Tsutomu Iwasaki, Yoshio Ohyama, Masahiko Kurabayashi
Journal: Circulation (2007)
TCT-272 Influence of Activated Clotting Time on Early Myocardial Reperfusion in Patients With ST-Segment Elevation Myocardial Infarction: Results From the COMPARE CRUSH Trial
Authors: Rosanne Vogel, Jeroen Wilschut, Ronak Delewi, Miguel Lemmert, Roberto Diletti, Ria van Vliet, Nancy van der Waarden, Rutger Nuis, Valeria Paradies, Dimitrios Alexopoulos, Felix Zijlstra, Gilles Montalescot, Dominick Angiolillo, Nicolas Van Mieghem, Pieter Smits, Georgios Vlachojannis
Journal: Journal of the American College of Cardiology (2021)
Prevalence and impact of COVID-19 sequelae on treatment and survival of patients with cancer who recovered from SARS-CoV-2 infection: evidence from the OnCovid retrospective, multicentre registry study
Authors: David J Pinato, Josep Tabernero, Mark Bower, Lorenza Scotti, Meera Patel, Emeline Colomba, Saoirse Dolly, Angela Loizidou, John Chester, Uma Mukherjee, Alberto Zambelli, Alessia Dalla Pria, Juan Aguilar-Company, Diego Ottaviani, Amani Chowdhury, Eve Merry, Ramon Salazar, Alexia Bertuzzi, Joan Brunet, Matteo Lambertini, Marco Tagliamento, Anna Pous, Ailsa Sita-Lumsden, Krishnie Srikandarajah, Johann Colomba, Fanny Pommeret, Elia Seguí, Daniele Generali, Salvatore Grisanti, Paolo Pedrazzoli, Gianpiero Rizzo, Michela Libertini, Charlotte Moss, Joanne S Evans, Beth Russell, Nadia Harbeck, Bruno Vincenzi, Federica Biello, Rossella Bertulli, Raquel Liñan, Sabrina Rossi, Maria Carmen Carmona-García, Carlo Tondini, Laura Fox, Alice Baggi, Vittoria Fotia, Alessandro Parisi, Giampero Porzio, Maristella Saponara, Claudia Andrea Cruz, David García-Illescas, Eudald Felip, Ariadna Roqué Lloveras, Rachel Sharkey, Elisa Roldán, Roxana Reyes, Irina Earnshaw, Daniela Ferrante, Javier Marco-Hernández, Isabel Ruiz-Camps, Gianluca Gaidano, Andrea Patriarca, Riccardo Bruna, Anna Sureda, Clara Martinez-Vila, Ana Sanchez de Torre, Luca Cantini, Marco Filetti, Lorenza Rimassa, Lorenzo Chiudinelli, Michela Franchi, Marco Krengli, Armando Santoro, Aleix Prat, Mieke Van Hemelrijck, Nikolaos Diamantis, Thomas Newsom-Davis, Alessandra Gennari, Alessio Cortellini, Judith Swallow, Chris Chung, Gino Dettorre, Neha Chopra, Alvin JX Lee, Christopher CT Sng, Yien Ning Sophia Wong, Myria Galazi, Sarah Benafif, Palma Dileo, Grisma Patel, Anjui Wu, Alasdair Sinclair, Gehan Soosaipillai, Eleanor Jones, Nikolaos Diamantis, Uma Mukherjee, Amanda Jackson, Martine Piccart, Fanny Pommeret, Johann Colomba, Emeline Colomba-Blameble, Aleix Prat, Claudia A Cruz, Roxana Reyes, Elia Segui, Javier Marco-Hernández, Josep Tabernero, Juan Aguilar-Company, Isabel Ruiz-Camps, Laura Fox, David Garcia Illescas, Oriol Mirallas, Elisa Roldán, Anna Carbó, Isabel Garcia, Rachel Wuerstlein, Ricard Mesia, Clara Maluquer, Francesca D'Avanzo, Giuseppe Tonini, Salvatore Provenzano, Valeria Tovazzi, Corrado Ficorella, Paola Queirolo, Raffaele Giusti, Francesca Mazzoni, Federica Zoratto, Marco Tucci, Rossana Berardi, Annalisa Guida, Sergio Bracarda, Maria Iglesias
Journal: The Lancet Oncology (2021)
TCT-76 Cardiology Cathlab-Based Management of Thrombotic Carotid Stenoses in Acute Ischemic Stroke En Route to a Full Interventional Stroke Service – Tools, Techniques, Local Stroke-Unit Collaboration: Challenges and Patient Outcomes
Authors: Piotr Musialek, Adam Mazurek, Lukasz Tekieli, Tomasz Tomaszewski, Krzysztof Banaszkiewicz, R. Paweł Banyś, Artur Klecha, Mariusz Trystula, Iris Grunwald
Journal: Journal of the American College of Cardiology (2021)
Audio Interview: A New Monoclonal Antibody for Covid-19 and Potential Vaccination for Children
Authors: Eric J. Rubin, Lindsey R. Baden, Stephen Morrissey
Journal: New England Journal of Medicine (2021)

A New Monoclonal Antibody for Covid-19 and Potential Vaccination for Children In this audio interview conducted on October 26, 2021, the editors discuss the durability of vaccination against SARS-C...
Phase 1 TRANSCEND CLL 004 study of lisocabtagene maraleucel in patients with relapsed/refractory CLL or SLL
Authors: Tanya Siddiqi, Jacob D. Soumerai, Kathleen A. Dorritie, Deborah M. Stephens, Peter A. Riedell, Jon Arnason, Thomas J. Kipps, Heidi H. Gillenwater, Lucy Gong, Lin Yang, Ken Ogasawara, Jerill Thorpe, William G. Wierda
Journal: Blood (2021)

Bruton tyrosine kinase inhibitors (BTKi) and venetoclax are currently used to treat newly diagnosed and relapsed/refractory chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL). However, most patients eventually develop resistance to these therapies, underscoring the need for effective new therapies. We report results of the phase 1 dose-escalation portion of the multicenter, open-label, phase 1/2 TRANSCEND CLL 004 (NCT03331198) study of lisocabtagene maraleucel (liso-cel), an autologous CD19-directed chimeric antigen receptor (CAR) T-cell therapy, in patients with relapsed/refractory CLL/SLL. Patients with standard- or high-risk features treated with ≥3 or ≥2 prior therapies, respectively, including a BTKi, received liso-cel at 1 of 2 dose levels (50 × 106 or 100 × 106 CAR+ T cells). Primary objectives included safety and determining recommended dose; antitumor activity by 2018 International Workshop on CLL guidelines was exploratory. Minimal residual disease (MRD) was assessed in blood and marrow. Twenty-three of 25 enrolled patients received liso-cel and were evaluable for safety. Patients had a median of 4 (range, 2-11) prior therapies (100% had ibrutinib; 65% had venetoclax) and 83% had high-risk features including mutated TP53 and del(17p). Seventy-four percent of patients had cytokine release syndrome (9% grade 3) and 39% had neurological events (22% grade 3/4). Of 22 efficacy-evaluable patients, 82% and 45% achieved overall and complete responses, respectively. Of 20 MRD-evaluable patients, 75% and 65% achieved undetectable MRD in blood and marrow, respectively. Safety and efficacy were similar between dose levels. The phase 2 portion of the study is ongoing at 100 × 106 CAR+ T cells. This trial was registered at clinicaltrials.gov as NCT03331198.
Endoscopic abbreviations – Update 2021
Authors: Deborah E. Bowman, Peter D. Siersema, Michael B. Wallace, Teresa Brady
Journal: Endoscopy (2021)

Publication information This article is published simultaneously in the journals Endoscopy and Gastrointestinal Endoscopy. Copyright 2021 © by Georg Thieme Verlag KG and © by the American Society for Gastrointestinal Endoscopy
RO7062931 antisense oligonucleotide phase 1 study demonstrates target engagement in patients with chronic hepatitis B on established nucleos(t)ide therapy
Authors: Man-Fung Yuen, Edward Gane, Dong Joon Kim, Henry Chan, Bernadette Surujbally, Vedran Pavlovic, Miriam Triyatni, Joseph Grippo, Hyung Joon Kim, Apinya Leerapun, Tien Huey Lim, Young-Suk Lim, Tawesak Tanwandee, Won Kim, Wendy Cheng, Tsung-Hui Hu, Cynthia Wat
Journal: Journal of Hepatology (2020)
Tumor organoids: synergistic applications, current challenges, and future prospects in cancer therapy
Authors: Jingjing Qu, Farhin Shaheed Kalyani, Li Liu, Tianli Cheng, Lijun Chen
Journal: Cancer Communications (2021)

Abstract Patient‐derived cancer cells (PDCs) and patient‐derived xenografts (PDXs) are often used as tumor models, but have many shortcomings. PDCs not only lack diversity in terms of cell type, spatial organization, and microenvironment but also have adverse effects in stem cell cultures, whereas PDX are expensive with a low transplantation success rate and require a long culture time. In recent years, advances in three‐dimensional (3D) organoid culture technology have led to the development of novel physiological systems that model the tissues of origin more precisely than traditional culture methods. Patient‐derived cancer organoids bridge the conventional gaps in PDC and PDX models and closely reflect the pathophysiological features of natural tumorigenesis and metastasis, and have led to new patient‐specific drug screening techniques, development of individualized treatment regimens, and discovery of prognostic biomarkers and mechanisms of resistance. Synergistic combinations of cancer organoids with other technologies, for example, organ‐on‐a‐chip, 3D bio‐printing, and CRISPR‐Cas9‐mediated homology‐independent organoid transgenesis, and with treatments, such as immunotherapy, have been useful in overcoming their limitations and led to the development of more suitable model systems that recapitulate the complex stroma of cancer, inter‐organ and intra‐organ communications, and potentially multiorgan metastasis. In this review, we discuss various methods for the creation of organ‐specific cancer organoids and summarize organ‐specific advances and applications, synergistic technologies, and treatments as well as current limitations and future prospects for cancer organoids. Further advances will bring this novel 3D organoid culture technique closer to clinical practice in the future.
Hairy cell leukemia 2022: Update on diagnosis, risk‐stratification, and treatment
Authors: Xavier Troussard, Elsa Maître, Edouard Cornet
Journal: American Journal of Hematology (2021)

Hairy cell leukemia (HCL) and HCL-like disorders, including HCL variant (HCL-V) and splenic diffuse red pulp lymphoma (SDRPL), are a very heterogeneous group of mature lymphoid B-cell disorders characterized by the identification of hairy cells, a specific genetic profile, a different clinical course, and the need for appropriate treatment.Diagnosis of HCL is based on morphological evidence of hairy cells, an HCL immunologic score of 3 or 4 based on the CD11C, CD103, CD123, and CD25 expression, the trephine biopsy which makes it possible to specify the degree of tumoral medullary infiltration and the presence of BRAFV600E somatic mutation.Progression of patients with HCL is based on a large splenomegaly, leukocytosis, a high number of hairy cells in the peripheral blood, and the immunoglobulin heavy chain variable region gene mutational status. VH4-34-positive HCL cases are associated with a poor prognosis.Patients should be treated only if HCL is symptomatic. Chemotherapy with risk adapted therapy purine analogs (PNAs) are indicated in first-line HCL patients. The use of chemo-immunotherapy combining PNAs and rituximab (R) represents an increasingly used therapeutic approach. Management of relapsed/refractory disease is based on the use of BRAF inhibitors (BRAFi) plus rituximab or MEK inhibitors (MEKi), recombinant immunoconjugates targeting CD22 or Bruton Tyrosine Kinase inhibitors (BTKi). However, the optimal sequence of the different treatments remains to be determined. The Bcl2-inhibitors (Bcl-2i) can play a major role in the future.
Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission
Authors: Shu Horiuchi, Kohei Oishi, Lucia Carrau, Justin Frere, Rasmus Møller, Maryline Panis, Benjamin R. tenOever
Journal: Science Immunology (2021)

SARS-CoV-2 infection results in cellular memory that protects against variants of concern but fails to block transmission.
miR‐146a enhances regulatory T‐cell differentiation and function in allergic rhinitis by targeting STAT5b
Authors: Yu Zhang, Yujuan Yang, Jing Guo, Limei Cui, Liping Yang, Yumei Li, Yakui Mou, Chuanliang Jia, Luo Zhang, Xicheng Song
Journal: Allergy (2021)

MicroRNA (miR)-146a, as an important immune regulatory factor with an anti-inflammatory effect, plays a crucial role in regulatory T-cell (Tregs) differentiation and function in allergic rhinitis (AR). The present study aimed to investigate the regulatory mechanism employed by miR-146a to control Treg differentiation and function in AR.Expression of miR-146a and STAT5b in peripheral blood mononuclear cells (PBMCs) and nasal mucosa from patients with AR was detected by qPCR and Western blotting. Tregs were quantified by flow cytometry in miR-146a knockdown or STAT5b knockdown PBMCs. FOXP3, IL-10, and TGF-β levels were detected by Western blotting or ELISA in miR-146a knockdown or STAT5b overexpressing PBMCs, as well as in STAT5b knockdown PBMCs overexpressing miR-146a. The effect of miR-146a on STAT5b was observed by luciferase assay and knockdown experiments.Levels of miR146a and STAT5b in the nasal mucosa or PBMCs were significantly lower in the AR group than in the control group. There were significantly fewer Tregs in miR-146a knockdown or STAT5b knockdown PBMCs compared to control PBMCs. Expression of FOXP3, IL-10, and TGF-β was decreased in the miR-146a knockdown group but increased in the STAT5b overexpression group. In contrast, miR-146a overexpression increased the levels of these factors, but knockdown of STAT5b significantly inhibited this effect. Luciferase assay and knockdown experiments showed that miR-146a bound directly to STAT5b.miR-146a enhances Treg differentiation and function in AR by positively targeting STAT5b.
Biosimilar-to-Biosimilar Switching: What is the Rationale and Current Experience?
Authors: Eduardo Mysler, Valderilio Feijó Azevedo, Silvio Danese, Daniel Alvarez, Noriko Iikuni, Beverly Ingram, Markus Mueller, Laurent Peyrin-Biroulet
Journal: Drugs (2021)

Over time, clinicians have become increasingly comfortable embracing the prescription of biosimilars-highly similar versions of innovator or reference biological agents-for their patients with inflammatory diseases. Although a switch from a reference product to a licensed biosimilar version (or vice versa) is a medical decision robustly supported by the stepwise accumulation of clinical trial evidence concerning comparable safety, immunogenicity, and efficacy between these products, a switch from one biosimilar to another biosimilar of the same reference product, or a cross-switch, is not. Similarity among biosimilars of a reference product is not a regulatory agency concern and therefore is unlikely to be investigated in randomized controlled trials in the foreseeable future. Yet in clinical practice, across a diverse range of patients, the option to cross-switch from one biosimilar to another can and does arise for valid reasons such as convenience or tolerability issues, or driven by third parties (e.g., payers). In the absence of clinical trial data, clinicians must attempt to objectively evaluate the emerging real-world cross-switching evidence within the context of what is known about the science underpinning a designation of biosimilar. That knowledge then needs to be integrated with what clinicians know about their patients and their disease on a case-by-case basis. This review aims to consolidate relevant emerging real-world data and other key information about biosimilar-to-biosimilar cross-switching for prescribing clinicians. In the absence of clear clinical guidelines addressing this topic at present, this review may serve to facilitate discretionary and educated treatment decision making.
TCT-379 Transcatheter Mitral Valve Edge-to-Edge Repair for Patients With Surgical Mitral Valve Repair Failure and Severe Mitral Regurgitation
Authors: Homam Ibrahim, Cezar Staniloae, Ahmad Alkhalil, Illya Pushkar, Adil Sattar, Mathew Williams
Journal: Journal of the American College of Cardiology (2021)