tbuckley/cabot-search huggingface dataset:
A multimodal deep learning model for cardiac resynchronisation therapy response prediction
Authors: Esther Puyol-Antón, Baldeep S. Sidhu, Justin Gould, Bradley Porter, Mark K. Elliott, Vishal Mehta, Christopher A. Rinaldi, Andrew P. King
Journal: Medical Image Analysis (2022)

We present a novel multimodal deep learning framework for cardiac resynchronisation therapy (CRT) response prediction from 2D echocardiography and cardiac magnetic resonance (CMR) data. The proposed method first uses the 'nnU-Net' segmentation model to extract segmentations of the heart over the full cardiac cycle from the two modalities. Next, a multimodal deep learning classifier is used for CRT response prediction, which combines the latent spaces of the segmentation models of the two modalities. At test time, this framework can be used with 2D echocardiography data only, whilst taking advantage of the implicit relationship between CMR and echocardiography features learnt from the model. We evaluate our pipeline on a cohort of 50 CRT patients for whom paired echocardiography/CMR data were available, and results show that the proposed multimodal classifier results in a statistically significant improvement in accuracy compared to the baseline approach that uses only 2D echocardiography data. The combination of multimodal data enables CRT response to be predicted with 77.38% accuracy (83.33% sensitivity and 71.43% specificity), which is comparable with the current state-of-the-art in machine learning-based CRT response prediction. Our work represents the first multimodal deep learning approach for CRT response prediction.
The maternal gut microbiome during pregnancy and offspring allergy and asthma
Authors: Yuan Gao, Ralph Nanan, Laurence Macia, Jian Tan, Luba Sominsky, Thomas P. Quinn, Martin O’Hely, Anne-Louise Ponsonby, Mimi L.K. Tang, Fiona Collier, Deborah H. Strickland, Poshmaal Dhar, Susanne Brix, Simon Phipps, Peter D. Sly, Sarath Ranganathan, Jakob Stokholm, Karsten Kristiansen, Lawrence E.K. Gray, Peter Vuillermin
Journal: Journal of Allergy and Clinical Immunology (2021)
SO-10 An open-label, multi-centre, phase Ib/II study of PI3Kβ selective inhibitor GSK2636771 administered in combination with paclitaxel in patients with advanced gastric cancer having alterations in PI3K/Akt pathway
Authors: M. Jung, C. Kim, H. Kim, C. Lee, H. Lee, W. Bae, H. Jeung, D. Zang, S. Park, I. Hwang, H. Kim, S. Rha, H. Chung
Journal: Annals of Oncology (2021)
Single Agent and Synergistic Combinatorial Efficacy of First-in-Class Small Molecule Imipridone ONC201 in Hematological Malignancies In Vitro and In Vivo through Apoptosis Via the Integrated Stress Response Pathway
Authors: Varun Vijay Prabhu, Mala Kiran Talekar, Amriti R Lulla, C. Leah B Kline, Lanlan Zhou, Junior Hall, A. Pieter J Van den Heuvel, David T Dicker, Stephan A Grupp, Mathew Garnett, Ultan McDermott, Cyril H Benes, Jeffrey J Pu, David F Claxton, Wolfgang Oster, Joshua E. Allen, Wafik S. El-Deiry
Journal: Blood (2017)
Strategies to Overcome the Market Dominance of Hospitals—Reply
Authors: Soleil Shah, Amol S. Navathe, Robert P. Kocher
Journal: JAMA (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 HomeNew OnlineCurrent IssueFor Authors 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
P20-2 Comparison of triweekly cisplatin regimens in adjuvant chemoradiotherapy for locally advanced head and neck cancer
Authors: Yu Fujiwara, Yasuyoshi Sato, Naoki Fukuda, Naomi Hayashi, Xiaofei Wang, Kenji Nakano, Akihiro Ohmoto, Tetsuya Urasaki, Mayu Yunokawa, Makiko Ono, Junichi Tomomatsu, Takashi Toshiyasu, Hiroki Mitani, Shunji Takahashi
Journal: Annals of Oncology (2021)
Abstract 9989: Integration of Genetics with Metabolomics Identifies a Novel Gene Associated with Risk of Incident Cardiovascular Events: TRAF3IP2
Authors: Asad A Shah, Damian M Craig, Carol Haynes, James Bain, Robert Stevens, G C Hughes, L K Newby, Elizabeth R Hauser, William E Kraus, Christopher B Newgard, Simon G Gregory, Svati H Shah
Journal: Circulation (2011)

Background: Despite strong heritability, the genetic architecture of cardiovascular (CV) disease remains incompletely characterized. Plasma metabolite concentrations are heritable and have been ass...
Revisiting FDA Approval of Aducanumab
Authors: G. Caleb Alexander, David S. Knopman, Scott S. Emerson, Bruce Ovbiagele, Richard J. Kryscio, Joel S. Perlmutter, Aaron S. Kesselheim
Journal: New England Journal of Medicine (2021)

Interview with Dr. Gil Rabinovici on the FDA's controversial approval of a new treatment for Alzheimer's disease. (16:39)Download Given the scientific, regulatory, and clinical implications of the accelerated FDA approval of aducanumab for Alzheimer's disease, it's essential to consider beta-amyloid's suitability as a surrogate end point. Doing so casts doubt on the wisdom of the decision.
Evolution and domestication of watermelon inferred from population genomic analyses
Authors: Shaogui Guo, Shengie Zhao, Honghe Sun, Xin Wang, Shan Wu, Tao Lin, Yi Ren, Lei Gao, Yun Deng, Jie Zhang, Xuqiang Lu, Haiying Zhang, Jianli Shang, Guoyi Gong, Changlong Wen, Nan He, Shouwei Tian, Maoying Li, Junpu Liu, Yanping Wang, Yingchun Zhu, Robert J. Jarret, Ammon Levi, Xingping Zhang, Sanwen Huang, Zhangjun Fei, Yong Xu
Journal: Nature Genetics (2019)
The Added Value of Coronary Calcium Score in Predicting Cardiovascular Events in Familial Hypercholesterolemia
Authors: Antonio Gallo, Leopoldo Pérez de Isla, Sybil Charrière, Alexandre Vimont, Rodrigo Alonso, Ovidio Muñiz-Grijalvo, José L. Díaz-Díaz, Daniel Zambón, Philippe Moulin, Eric Bruckert, Pedro Mata, Sophie Béliard, Denis Angoulvant, Sophie Beliard, Franck Boccara, Eric Bruckert, Bertrand Cariou, Valérie Carreau, Alain Carrie, Sybil Charrieres, Yves Cottin, Mathilde Di Filippo, Pierre Henri Ducluzeau, Sonia Dulong, Vincent Durlach, Michel Farnier, Emile Ferrari, Dorota Ferrieres, Jean Ferrieres, Antonio Gallo, Philippe Giral, Sophie Gonbert, Regis Hankard, Jocelyn Inamo, Olga Kalmykova, Michel Krempf, Julie Lemale, Philippe Moulin, François Paillard, Noel Peretti, Agnes Perrin, Alain Pradignac, Jean Pierre Rabes, Vincent Rigalleau, François Schiele, Ariane Sultan, Patrick Tounian, René Valero, Bruno Verges, Cecile Yelnik, Olivier Ziegler, Rocío Aguado, Rodrigo Alonso, Ma Pilar Álvarez-Baños, Rosa Argüeso, Francisco Arrieta, Miguel Ángel Barba, Marta Casañas, José María Cepeda, Raimundo De Andrés, Gonzalo Díaz-Soto, Jose Luis Díaz-Diaz, Marta Dieguez, Ceferino Faedo, Francisco Fuentes, Juan A. Garrido, Aurora González, Pablo González-Bustos, Ma Dolores Mañas, Pedro Mata, Marta Mauri, Juan Diego Mediavilla, Alfredo Michán, Pablo Miramontes, Ovidio Muñiz, Leire Pérez, Leopoldo Perez De Isla, Xavier Pintó, Manuel J. Romero, Patricia Rubio, Juan F. Sánchez Muñoz-Torrero, Jose I. Vidal-Pardo, Daniel Zambón
Journal: JACC. Cardiovascular imaging (2021)
Changes in serological biomarkers (BM) of cell death during chemotherapy (CT) in patients with lymphoma
Authors: A. Greystoke, K. Linton, T. Illidge, R. Cowan, J. Cummings, T. Ward, C. Hamer, M. Ranson, A. Hughes, J. Radford, C. Dive
Journal: Annals of Oncology (2008)
Erratum. Associations Between Exposure to Gestational Diabetes Mellitus In Utero and Daily Energy Intake, Brain Responses to Food Cues, and Adiposity in Children. Diabetes Care 2021;44:1185–1193
Authors: Shan Luo, Brendan C. Angelo, Ting Chow, John R. Monterosso, Paul M. Thompson, Anny H. Xiang, Kathleen A. Page
Journal: Diabetes Care (2021)

In Table 1 of the above-cited article, data for GDM-exposed and unexposed children for characteristics daily energy intake (EI), moderate to vigorous physical activity (MVPA), and …
Discovery and 3D imaging of a novel ΔNp63-expressing basal cell type in human pancreatic ducts with implications in disease
Authors: Sandrina Martens, Katarina Coolens, Mathias Van Bulck, Tatjana Arsenijevic, Joan Casamitjana, Angel Fernandez Ruiz, Abdessamad El Kaoutari, Jaime Martinez de Villareal, Hediel Madhloum, Farzad Esni, Yves Heremans, Gunter Leuckx, Harry Heimberg, Luc Bouwens, Patrick Jacquemin, Diedert Luc De Paep, Peter in't Veld, Nicky D'Haene, Christelle Bouchart, Nelson Dusetti, Jean-Luc Van Laethem, Wim Waelput, Pierre Lefesvre, Francisco X Real, Meritxell Rovira, Ilse Rooman
Journal: Gut (2021)

Objective The aggressive basal-like molecular subtype of pancreatic ductal adenocarcinoma (PDAC) harbours a ΔNp63 (p40) gene expression signature reminiscent of a basal cell type. Distinct from other epithelia with basal tumours, ΔNp63 + basal cells reportedly do not exist in the normal pancreas. Design We evaluated ΔNp63 expression in human pancreas, chronic pancreatitis (CP) and PDAC. We further studied in depth the non-cancerous tissue and developed a three-dimensional (3D) imaging protocol (FLIP-IT, Fluorescence Light sheet microscopic Imaging of Paraffin-embedded or Intact Tissue) to study formalin-fixed paraffin-embedded samples at single cell resolution. Pertinent mouse models and HPDE cells were analysed. Results In normal human pancreas, rare ΔNp63 + cells exist in ducts while their prevalence increases in CP and in a subset of PDAC. In non-cancer tissue, ΔNp63 + cells are atypical KRT19 + duct cells that overall lack SOX9 expression while they do express canonical basal markers and pertain to a niche of cells expressing gastrointestinal stem cell markers. 3D views show that the basal cells anchor on the basal membrane of normal medium to large ducts while in CP they exist in multilayer dome-like structures. In mice, ΔNp63 is not found in adult pancreas nor in selected models of CP or PDAC, but it is induced in organoids from larger Sox9 low ducts. In HPDE, ΔNp63 supports a basal cell phenotype at the expense of a classical duct cell differentiation programme. Conclusion In larger human pancreatic ducts, basal cells exist. ΔNp63 suppresses duct cell identity. These cells may play an important role in pancreatic disease, including PDAC ontogeny, but are not present in mouse models.
Targeting c-Myc to Overcome Acquired Resistance of EGFR Mutant NSCLC Cells to the Third-Generation EGFR Tyrosine Kinase Inhibitor, Osimertinib
Authors: Lei Zhu, Zhen Chen, Hongjing Zang, Songqing Fan, Jiajia Gu, Guojing Zhang, Kevin D.-Y. Sun, Qiming Wang, Yong He, Taofeek K. Owonikoko, Suresh S. Ramalingam, Shi-Yong Sun
Journal: Cancer Research (2021)

Osimertinib (AZD9291 or TAGRISSO) is a promising and approved third-generation EGFR tyrosine kinase inhibitor (TKI) for treating patients with advanced non-small cell lung cancer (NSCLC) harboring EGFR-activating mutations or the resistant T790M mutation. However, the inevitable emergence of acquired resistance limits its long-term efficacy. A fuller understanding of the mechanism of action of osimertinib and its linkage to acquired resistance will enable the development of more efficacious therapeutic strategies. Consequently, we have identified a novel connection between osimertinib or other EGFR-TKIs and c-Myc. Osimertinib rapidly and sustainably decreased c-Myc levels primarily via enhancing protein degradation in EGFR-mutant (EGFRm) NSCLC cell lines and xenograft tumors. c-Myc levels were substantially elevated in different EGFRm NSCLC cell lines with acquired resistance to osimertinib in comparison with their corresponding parental cell lines and could not be reduced any further by osimertinib. Consistently, c-Myc levels were elevated in the majority of EGFRm NSCLC tissues relapsed from EGFR-TKI treatment compared with their corresponding untreated baseline c-Myc levels. Suppression of c-Myc through knockdown or pharmacologic targeting with BET inhibitors restored the response of resistant cell lines to osimertinib. These findings indicate that c-Myc modulation mediates the therapeutic efficacy of osimertinib and the development of osimertinib acquired resistance. Furthermore, they establish c-Myc as a potential therapeutic target and warrant clinical testing of BET inhibition as a potential strategy to overcome acquired resistance to osimertinib or other EGFR inhibitors. SIGNIFICANCE: This study demonstrates a critical role of c-Myc modulation in mediating therapeutic efficacy of osimertinib including osimertinib acquired resistance and suggests targeting c-Myc as a potential strategy to overcome osimertinib acquired resistance.
Localized Chemotherapy Based on Injectable Hydrogel Boosts the Antitumor Activity of Adoptively Transferred T Lymphocytes In Vivo
Authors: Yue Cao, Yuhao Zhou, Zhixiong Chen, Zhen Zhang, Xuesi Chen, Chaoliang He
Journal: Advanced Healthcare Materials (2021)

Abstract The adoptive transfer of antigen‐specific T cells has been successfully applied in the treatment of hematological malignancies. However, its application in the treatment of solid tumors has been overshadowed by the immunosuppressive tumor microenvironment. In this context, a preprocessing strategy is developed to reprogram the immunosuppressive tumor microenvironment using a thermoresponsive hydrogel loaded with doxorubicin (DOX@Gel). Compared with hydrogel‐based chemotherapy alone or adoptive T cell therapy alone, this combination exhibits enhanced anti‐tumor efficacy. In addition to the direct killing of tumor cells, the local chemotherapy releases tumor‐associated antigens which enhance the proliferation and effector function of endogenous and adoptively transferred T cells. Moreover, DOX@Gel significantly reduces the numbers of both myeloid derived suppressor cells and Tregs in tumor microenvironment. It is suggested that DOX@Gel promotes the efficacy of adoptively transferred T cells against solid tumors, overcoming the key limitations of adoptive T cell therapy.
P15-3 Practices of breast self-examination among female residents in Tangail city, Bangladesh: A cross sectional study
Authors: Mahmuda Khatun, Shariful Islam, Syeed Al- Habib, Majharul Islam, Jubayra Jafrin Shifa, Runa Akter, Farjana Yesmin, Mozibullah Md., Sohel Md., A.K.M. Mohiuddin
Journal: Annals of Oncology (2021)
MO26-5 HGCSG 1603: A phase 2 trial of ramucirumab plus irinotecan as second-line treatment for advanced gastric cancer
Authors: Kentaro Sawada, Yasuyuki Kawamoto, Satoshi Yuki, Michio Nakamura, Osamu Muto, Susumu Sogabe, Ysohiaki Shindo, Atsushi Ishiguro, Atsushi Sato, Yasushi Tsuji, Masayoshi Dazai, Hiroyuki Okuda, Takahide Sasaki, Kazuaki Harada, Shintaro Nakano, Hiroshi Nakatsumi, Mari Sekiguchi, Yuh Sakata, Naoya Sakamoto, Yoshito Komatsu
Journal: Annals of Oncology (2021)
Abstract 15222: 30-Day Readmission Following Non-ST Elevated Myocardial Infarction in Patients Who Did Not Have Percutaneous Coronary Intervention: Insight From Nationwide Readmission Database
Authors: Birendra Amgai, Adrija Hajra, Neel Patel, Dhrubajyoti Bandyopadhyay, Sandipan Chakraborty, Soniya Koirala, Tauseef Akhtar, Richa Sharma, Eyal Herzog
Journal: Circulation (2019)

Introduction: Patients with non-ST elevated myocardial infarction (NSTEMI) are managed with both medical as well as intervention. We have studied data from the national readmission database (NRD) t...
Two Reference-Quality Sea Snake Genomes Reveal Their Divergent Evolution of Adaptive Traits and Venom Systems
Authors: An Li, Junjie Wang, Kuo Sun, Shuocun Wang, Xin Zhao, Tingfang Wang, Liyan Xiong, Weiheng Xu, Lei Qiu, Yan Shang, Runhui Liu, Sheng Wang, Yiming Lu
Journal: Molecular Biology and Evolution (2021)

Abstract True sea snakes (Hydrophiini) are among the last and most successful clades of vertebrates that show secondary marine adaptation, exhibiting diverse phenotypic traits and lethal venom systems. To better understand their evolution, we generated the first chromosome-level genomes of two representative Hydrophiini snakes, Hydrophis cyanocinctus and H. curtus. Through comparative genomics we identified a great expansion of the underwater olfaction-related V2R gene family, consisting of more than 1,000 copies in both snakes. A series of chromosome rearrangements and genomic structural variations were recognized, including large inversions longer than 30 megabase (Mb) on sex chromosomes which potentially affect key functional genes associated with differentiated phenotypes between the two species. By integrating multiomics we found a significant loss of the major weapon for elapid predation, three-finger toxin genes, which displayed a dosage effect in H. curtus. These genetic changes may imply mechanisms that drove the divergent evolution of adaptive traits including prey preferences between the two closely related snakes. Our reference-quality sea snake genomes also enrich the repositories for addressing important issues on the evolution of marine tetrapods, and provide a resource for discovering marine-derived biological products.
MO29-6 Safety and tolerability of lazertinib and in combination with amivantamab in advanced EGFR-mutated Japanese NSCLC
Authors: Koichi Goto, Toyoaki Hida, Nobuyuki Funami, Ryota Iwasawa, Sachiko Mita, Aimi Yamashita, Keiichiro Imanaka, Sumiko Kitani, Yuichiro Ohe
Journal: Annals of Oncology (2021)
MO9-8 Development of a data management system for comprehensive genomic profiling tests
Authors: Keita Fukuyama, Masashi Kanai, Masahiro Yoshioka, Tomohiro Kondo, Quy Pham Nguyen, Junko Suga, Kumi Mukai, Kanami Ashida, Momoko Satou, Izumi Oogaki, Takahiro Yamada, Sachiko Minamiguchi, Manabu Muto
Journal: Annals of Oncology (2021)
Dose-dense brentuximab vedotin plus ifosfamide, carboplatin, and etoposide for second-line treatment of relapsed or refractory classical Hodgkin lymphoma: a single centre, phase 1/2 study
Authors: Ryan C Lynch, Ryan D Cassaday, Stephen D Smith, Jonathan R Fromm, Andrew J Cowan, Edus H Warren, Mazyar S Shadman, Andrei Shustov, Brian G Till, Chaitra S Ujjani, Edward N Libby, Mary Philip, Hilary Coye, Christen N Martino, Sandra L Bhark, Karolyn Morris, Heather Rasmussen, Sanaz Behnia, Jenna Voutsinas, Ajay K Gopal
Journal: The Lancet Haematology (2021)
<i>BrcaSeg</i>: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images
Authors: Zixiao Lu, Xiaohui Zhan, Yi Wu, Jun Cheng, Wei Shao, Dong Ni, Zhi Han, Jie Zhang, Qianjin Feng, Kun Huang
Journal: Genomics Proteomics & Bioinformatics (2021)

Abstract Epithelial and stromal tissues are components of the tumor microenvironment and play a major role in tumor initiation and progression. Distinguishing stroma from epithelial tissues is critically important for spatial characterization of the tumor microenvironment. Here, we propose BrcaSeg, an image analysis pipeline based on a convolutional neural network (CNN) model to classify epithelial and stromal regions in whole-slide hematoxylin and eosin (H&amp;E) stained histopathological images. The CNN model is trained using well-annotated breast cancer tissue microarrays and validated with images from The Cancer Genome Atlas (TCGA) Program. BrcaSeg achieves a classification accuracy of 91.02%, which outperforms other state-of-the-art methods. Using this model, we generate pixel-level epithelial/stromal tissue maps for 1000 TCGA breast cancer slide images that are paired with gene expression data. We subsequently estimate the epithelial and stromal ratios and perform correlation analysis to model the relationship between gene expression and tissue ratios. Gene Ontology (GO) enrichment analyses of genes that are highly correlated with tissue ratios suggest that the same tissue is associated with similar biological processes in different breast cancer subtypes, whereas each subtype also has its own idiosyncratic biological processes governing the development of these tissues. Taken all together, our approach can lead to new insights in exploring relationships between image-based phenotypes and their underlying genomic events and biological processes for all types of solid tumors. BrcaSeg can be accessed at https://github.com/Serian1992/ImgBio.
Tryptophan potentiates CD8<sup>+</sup>T cells against cancer cells by TRIP12 tryptophanylation and surface PD-1 downregulation
Authors: Rui Qin, Chen Zhao, Chen-Ji Wang, Wei Xu, Jian-Yuan Zhao, Yan Lin, Yi-Yuan Yuan, Peng-Cheng Lin, Yao Li, Shimin Zhao, Yan Huang
Journal: Journal for ImmunoTherapy of Cancer (2021)

Tryptophan catabolites suppress immunity. Therefore, blocking tryptophan catabolism with indoleamine 2,3-dioxygenase (IDO) inhibitors is pursued as an anticancer strategy.The intracellular level of tryptophan and kynurenine was detected by mass spectrum analysis. The effect of tryptophan and IDO inhibitors on cell surface programmed cell death protein 1 (PD-1) level were measured by flow cytometry. A set of biochemical analyses were used to figure out the underlying mechanism. In vitro co-culture system, syngeneic mouse models, immunofluorescent staining, and flow cytometry analysis were employed to investigate the role of tryptophan and IDO inhibitor in regulating the cytotoxicity of CD8+ T cells.Here, we reported that IDO inhibitors activated CD8+ T cells also by accumulating tryptophan that downregulated PD-1. Tryptophan and IDO inhibitors administration, both increased intracellular tryptophan, and tryptophanyl-tRNA synthetase (WARS) overexpression decreased Jurkat and mice CD8+ T cell surface PD-1. Mechanistically, WARS tryptophanylated lysine 1136 of and activated E3 ligase TRIP12 to degrade NFATc1, a PD-1 transcription activator. SIRT1 de-tryptophanylated TRIP12 and reversed the effects of tryptophan and WARS on PD-1. Tryptophan or IDO inhibitors potentiated CD8+ T cells to induce apoptosis of co-cultured cancer cells, increased cancer-infiltrating CD8+ T cells and slowed down tumor growth of lung cancer in mice.Our results revealed the immune-activating efficacy of tryptophan, and suggested tryptophan supplemental may benefit IDO inhibitors and PD-1 blockade during anticancer treatments.