tbuckley/cabot-search huggingface dataset:
Deep learning in medical image analysis: introduction to underlying principles and reviewer guide using diagnostic case studies in paediatrics
Authors: Constance Dubois, David Eigen, Emmanuel Delmas, Margot Einfalt, Clara Lemaçon, Laureline Berteloot, Patrick M Bossuyt, David Drummond, Pauline Scherdel, François Simon, Héloïse Torchin, Yasaman Vali, Isabelle Bloch, Jérémie F Cohen
Journal: BMJ (2024)

Deep learning, a subset of artificial intelligence, has gained attention in recent years for its ability to achieve human level performance in medical image analysis. As deep learning is increasingly being studied in medical image analysis, it is essential that clinicians are familiar with its underlying principles, strengths, and possible pitfalls in their evaluation. This article aims to clarify deep learning techniques applied in medical image analysis and to help frontline clinicians understand how to read and appraise studies about this new and rapidly advancing technology. While image analysis using deep learning has the potential to enhance the diagnosis of various medical conditions, clinicians, policy makers, and patients should exercise caution when evaluating the available evidence.
Elucidating acquired PARP inhibitor resistance in advanced prostate cancer
Authors: George Seed, Nick Beije, Wei Yuan, Claudia Bertan, Jane Goodall, Arian Lundberg, Matthew Tyler, Ines Figueiredo, Rita Pereira, Chloe Baker, Denisa Bogdan, Lewis Gallagher, Jan-Phillipp Cieslik, Semini Greening, Maryou Lambros, Rui Neves, Lorena Magraner-Pardo, Gemma Fowler, Berni Ebbs, Susana Miranda, Penny Flohr, Diletta Bianchini, Pasquale Rescigno, Nuria Porta, Emma Hall, Bora Gurel, Nina Tunariu, Adam Sharp, Stephen Pettit, Nikolas H Stoecklein, Shahneen Sandhu, David Quigley, Christopher J Lord, Joaquin Mateo, Suzanne Carreira, Johann de Bono
Journal: Cancer Cell (2024)
Physical Activity and Reduced Mortality Regardless of Age—Considerations for Public Health
Authors: John M. Jakicic
Journal: JAMA Network Open (2024)

David Martinez-Gomez, PhD; Mengyun Luo, PhD; Yu Huang, PhD; Fernando Rodríguez-Artalejo, MD, PhD; Ulf Ekelund, PhD; Mercedes Sotos-Prieto, PhD; Ding Ding, PhD; Xiang-Quian Lao, MD, PhD; Verónica Cabanas-Sánchez, PhD
FOLFOX/FOLFIRI–Bevacizumab for Unresectable Colorectal Liver Metastases
Authors: Jan Franko, Viet H. Le
Journal: JAMA Oncology (2024)

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 Oncology HomeNew OnlineCurrent IssueFor Authors Podcast JAMA+ AI Journals 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 2024 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 Oncology journal
Mutation burden and anti-PD-1 outcomes are not universally associated with immune cell infiltration or lymphoid activation
Authors: David Hsiehchen, Andrew Elliott, Joanne Xiu, Andreas Seeber, Wafik El-Deiry, Emmanuel S Antonarakis, Stephanie L Graff, Michael J Hall, Hossein Borghaei, Dave S B Hoon, Stephen V Liu, Patrick C Ma, Rana R McKay, Trisha Wise-Draper, John Marshall, George W Sledge, David Spetzler, Hao Zhu
Journal: Cancer Cell (2024)
Dynamically monitoring minimal residual disease using circulating tumour cells to predict the recurrence of early-stage lung adenocarcinoma
Authors: Qi Zhang, Xiaoli Zhang, Zhuoheng Lv, Huandong Huo, Ligong Yuan, Duo Wan, Peipei Xie, Shujun Cheng, Kaitai Zhang, Wen Zhang, Yousheng Mao
Journal: Journal of Hematology & Oncology (2024)

Lung adenocarcinoma (LUAD) is one of the leading causes of cancer-related deaths worldwide, with a 5-year survival rate of approximately 19%. With the advent of screening and diagnostic techniques such as low-dose spiral CT and liquid biopsy, the detection rate of early stage LUAD is increasing. Even in stage I LUAD, the cumulative 5-year recurrence rate after radical surgical resection is 17.9%. This may be related to the presence of microscopic residual disease (MRD), a potential source of recurrence and metastasis. Circulating tumour cells (CTCs) are key biomarkers in liquid biopsies, but the ability of dynamic CTC detection to monitor MRD and warn of recurrence in patients with early LUAD has not been validated. Here, we conducted a prospective study using the telomerase reverse transcriptase-based CTC detection method (TBCD) to evaluate perioperative and follow-up CTC levels for dynamic monitoring to evaluate its clinical efficacy in predicting postoperative recurrence in early-stage LUAD. By longitudinal dynamic monitoring of CTC, we accurately predicted recurrence within 2 years after surgery, with an AUC of 0.9786, demonstrating the clinical values of CTC in predicting recurrence. The median lead time from positive detection of CTC to radiological recurrence was 183 days, with the earliest CT recurrence predicted 354 days in advance. Taken together, our study demonstrates that longitudinal monitoring of CTC is effective in early warning of LUAD recurrence and provides valuable information on early detection and intervention strategies for the management of LUAD.
Evidence of 18F-FDG Utility in Rare Case of Metastatic Anal Melanoma With Prolonged Survival
Authors: Jennifer Marie Catherine Ranes, Ana Jamelith Ormaza, Lesley Flynt
Journal: Clinical Nuclear Medicine (2024)

A 43-year-old woman presented with an anorectal mass at which time excision was performed, and biopsy revealed anorectal mucosal melanoma (AM), anal subtype. Postexcision, 18F-FDG PET/CT identified residual melanoma, confirmed on biopsy. Recurrence was monitored every 3 months using 18F-FDG, which identified a perirectal lymph node 2.5 years later positive for metastatic melanoma. Given the rarity of AM and often delayed diagnosis, patients often present with metastases, resulting in poor prognosis. This unique case of metastatic AM with prolonged survival of 7 years to date supports the implementation of 18F-FDG in the diagnostics and monitoring of AM.
Norepinephrine Transporter–Targeted Cancer Theranostics—New Horizons
Authors: Takahiro Higuchi, Konrad Klimek, Daniel Groener, Xinyu Chen, Rudolf A. Werner
Journal: Clinical Nuclear Medicine (2024)

In the evolving landscape of precision oncology, this review delineates the role of radiopharmaceuticals targeting the norepinephrine transporter (NET), with a particular focus on the current clinical application of 123I-MIBG diagnostic imaging and 131I-MIBG therapeutics, in particular for pheochromocytoma, neuroblastoma, or paraganglioma. We will also highlight recently introduced 18F-labeled NET targeting imaging radiotracers, which would offer unparalleled resolution, enhanced tumor localization, and staging properties. Complementing these novel second-generation PET agents in a theranostic approach, astatine-211 meta-astatobenzylguanidine (211At-MABG) would leverage the advantages of alpha-particles to selectively target and eradicate NET-expressing tumor cells with minimal off-target effects.
Myeloid activation clears ascites and reveals IL27-dependent regression of metastatic ovarian cancer
Authors: Brennah Murphy, Taito Miyamoto, Bryan S. Manning, Gauri Mirji, Alessio Ugolini, Toshitha Kannan, Kohei Hamada, Yanfang P. Zhu, Daniel T. Claiborne, Lu Huang, Rugang Zhang, Yulia Nefedova, Andrew Kossenkov, Filippo Veglia, Rahul Shinde, Nan Zhang
Journal: The Journal of Experimental Medicine (2024)

Patients with metastatic ovarian cancer (OvCa) have a 5-year survival rate of &amp;lt;30% due to the persisting dissemination of chemoresistant cells in the peritoneal fluid and the immunosuppressive microenvironment in the peritoneal cavity. Here, we report that intraperitoneal administration of β-glucan and IFNγ (BI) induced robust tumor regression in clinically relevant models of metastatic OvCa. BI induced tumor regression by controlling fluid tumor burden and activating localized antitumor immunity. β-glucan alone cleared ascites and eliminated fluid tumor cells by inducing intraperitoneal clotting in the fluid and Dectin-1-Syk–dependent NETosis in the omentum. In omentum tumors, BI expanded a novel subset of immunostimulatory IL27+ macrophages and neutralizing IL27 impaired BI efficacy in vivo. Moreover, BI directly induced IL27 secretion in macrophages where single agent treatment did not. Finally, BI extended mouse survival in a chemoresistant model and significantly improved chemotherapy response in a chemo-sensitive model. In summary, we propose a new therapeutic strategy for the treatment of metastatic OvCa.
scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes
Authors: Wenbo Guo, Xinqi Li, Dongfang Wang, Nan Yan, Qifan Hu, Fan Yang, Xuegong Zhang, Jianhua Yao, Jin Gu
Journal: Genome biology (2024)

Understanding tumor cell heterogeneity and plasticity is crucial for overcoming drug resistance. Single-cell technologies enable analyzing cell states at a given condition, but catenating static cell snapshots to characterize dynamic drug responses remains challenging. Here, we propose scStateDynamics, an algorithm to infer tumor cell state dynamics and identify common drug effects by modeling single-cell level gene expression changes. Its reliability is validated on both simulated and lineage tracing data. Application to real tumor drug treatment datasets identifies more subtle cell subclusters with different drug responses beyond static transcriptome similarity and disentangles drug action mechanisms from the cell-level expression changes.
<i>B. vulgatus</i> ameliorates high-fat diet-induced obesity through modulating intestinal serotonin synthesis and lipid absorption in mice
Authors: Xinxin Wen, Xiaoyan Feng, Fang Xin, Rui An, Huanwei Huang, Liyuan Mao, Ping Liu, Jin Zhang, Haixia Huang, Xicheng Liu, Wei Wang
Journal: Gut Microbes (2024)

The consumption of high-fat diets (HFD) and an imbalance in gut microbiome are linked to obesity. However, the intricate connection between them and the underlying mechanisms involved in lipid digestion and absorption remain largely unclear. This study shows that after 12 weeks of HFD feeding, C57BL/6J mice exhibit two distinct metabolic phenotypes with significant differences in gut microbiota composition. The LOW and LOW FMT group mice with increased Bacteroides are protected from obesity, insulin resistance, and lipid accumulation. Supplementation with B. vulgatus or cholic acid (CA) alleviates HFD-induced obesity and metabolic dysfunction. This is due to the accumulation of lipid droplets and the retention of chyle particles in jejunal epithelial cells, which reduces chyle intake in the jejunal mesentery after HFD. Decreased 5-HT synthesis in the jejunal enterochromaffin cells of these mice, along with reduced chyle intake in the jejunal mesentery after HFD in Tph1△IEC, suggests that intestinal 5-HT is required for host lipid absorption. TRPV1, a calcium-permeable ion channel, mediates the basolateral 5-HT-induced increase of Isc and ion channel open probability. This study uncovers a novel signaling axis of microbiota-metabolite-5-HT and intracellular calcium-dependent lipid absorption, which may serve as the potential therapeutic targets for treating HFD-induced obesity.
Author Correction: Subclassification of obesity for precision prediction of cardiometabolic diseases
Authors: Daniel E. Coral, Femke Smit, Ali Farzaneh, Alexander Gieswinkel, Juan Fernandez Tajes, Thomas Sparsø, Carl Delfin, Pierre Bauvin, Kan Wang, Marinella Temprosa, Diederik De Cock, Jordi Blanch, José Manuel Fernández-Real, Rafael Ramos, M. Kamran Ikram, Maria F. Gomez, Maryam Kavousi, Marina Panova-Noeva, Philipp S. Wild, Carla van der Kallen, Michiel Adriaens, Marleen van Greevenbroek, Ilja Arts, Carel Le Roux, Fariba Ahmadizar, Timothy M. Frayling, Giuseppe N. Giordano, Ewan R. Pearson, Paul W. Franks
Journal: Nature Medicine (2024)
The effect of pre-COVID and post-COVID vaccination on long COVID: a systematic review and meta-analysis
Authors: King Ngai Chow, Yuk Wah Tsang, Yan Hei Chan, Shalina Alisha Telaga, Lok Yan Andes Ng, Chit Ming Chung, Yan Ming Yip, Peter Pak Hang Cheung
Journal: Journal of Infection (2024)
Coverage with Influenza, Respiratory Syncytial Virus, and COVID-19 Vaccines Among Nursing Home Residents — National Healthcare Safety Network, United States, November 2024
Authors: Hannah E. Reses, George Segovia, Heather Dubendris, Kira Barbre, Sushmitha Ananth, Brynn Lape-Newman, Emily Wong, Molly Stillions, Theresa Rowe, Elizabeth Mothershed, Erika Wallender, Evelyn Twentyman, Ryan E. Wiegand, Pragna Patel, Andrea Benin, Jeneita M. Bell
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Nursing home residents are at elevated risk for severe complications from respiratory viruses, including SARS-CoV-2, influenza, and respiratory syncytial virus (RSV). Nursing homes are required to report COVID-19 vaccination coverage and can voluntarily report influenza and RSV vaccination coverage among residents to CDC's National Healthcare Safety Network. The purpose of this study was to assess COVID-19, influenza, and RSV vaccination coverage among nursing home residents early in the 2024-25 respiratory virus season. As of November 10, 2024, 29.7% of nursing home residents had received a 2024-2025 COVID-19 vaccine. Among residents at facilities that elected to report vaccination against influenza (59.4% of facilities) and RSV (51.8% of facilities), 58.4% had received influenza vaccination, and 17.9% had received RSV vaccination. Vaccination coverage varied by U.S. Department of Health and Human Services region, social vulnerability index level, and facility size. Addressing low coverage with COVID-19, influenza, and RSV vaccines is a priority to protect residents who are susceptible to severe outcomes associated with respiratory illnesses.
Detection of Real-Time Changes in Direction of COVID-19 Transmission Using National- and State-Level Epidemic Trends Based on <i>R</i> Estimates — United States Overall and New Mexico, April–October 2024
Authors: Danielle M. Richard, Zachary Susswein, Sarah Connolly, Adán Myers y Gutiérrez, Roselyn Thalathara, Kelly Carey, Emily H. Koumans, Diba Khan, Nina B. Masters, Nathan McIntosh, Patrick Corbett, Isaac Ghinai, Rebecca Kahn, Adrienne Keen, Juliet Pulliam, Daniel Sosin, Katelyn Gostic
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Public health practitioners rely on timely surveillance data for planning and decision-making; however, surveillance data are often subject to delays. Epidemic trend categories, based on time-varying effective reproductive number (R
<i>Notes from the Field:</i> Trends in Emergency Department Visits for Firearm Injuries — United States, January 2018–December 2023
Authors: Kristin M. Holland, Yushiuan Chen, Marissa L. Zwald, Steven A. Sumner, Katherine A. Fowler, Michael Sheppard, Thomas R. Simon
Journal: MMWR Morbidity and Mortality Weekly Report (2024)
Influenza, COVID-19, and Respiratory Syncytial Virus Vaccination Coverage Among Adults — United States, Fall 2024
Authors: Jennifer L. Kriss, Carla L. Black, Hilda Razzaghi, Mehreen Meghani, Ashley Tippins, Tammy A. Santibanez, Shannon Stokley, Kevin Chatham-Stephens, Nicole F. Dowling, Georgina Peacock, James A. Singleton
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

The Advisory Committee on Immunization Practices (ACIP) recommends annual influenza and COVID-19 vaccination for all persons aged ≥6 months, including adults aged ≥18 years. ACIP also recommends a single lifetime dose of respiratory syncytial virus (RSV) vaccine for adults aged ≥75 years and for those aged 60-74 years who are at increased risk for severe RSV disease. Data from the National Immunization Survey-Adult COVID Module, a random-digit-dialed cellular telephone survey of U.S. adults aged ≥18 years, are used to monitor influenza, COVID-19, and RSV vaccination coverage. By the week ending November 9, 2024, an estimated 34.7% of adults aged ≥18 years reported having received an influenza vaccine, and 17.9% reported having received a COVID-19 vaccine for the 2024-25 respiratory virus season; 39.7% of adults aged ≥75 years, and 31.6% of adults aged 60-74 years at increased risk for severe RSV, had ever received an RSV vaccine. Coverage varied by jurisdiction and demographic characteristics and was lowest among younger adults and those without health insurance. Although early season estimates indicate that many adults are unprotected from respiratory virus infections, many appeared open to vaccination: overall, approximately 35% and 41% of adults aged ≥18 years reported that they definitely or probably will receive or were unsure about receiving influenza and COVID-19 vaccines, respectively, and 40% of adults aged ≥75 years reported that they definitely or probably will receive or were unsure about receiving RSV vaccine. Health care providers and immunization programs still have time to expand outreach activities and promote vaccination to increase coverage in preparation for the height of the respiratory virus season. Using these data can help health care providers and immunization programs identify undervaccinated populations and understand vaccination patterns to guide planning, implementation, and evaluation of vaccination activities.
Genome-wide association study reveals mechanisms underlying dilated cardiomyopathy and myocardial resilience
Authors: Sean J. Jurgens, Joel T. Rämö, Daria R. Kramarenko, Leonoor F. J. M. Wijdeveld, Jan Haas, Mark D. Chaffin, Sophie Garnier, Liam Gaziano, Lu-Chen Weng, Alex Lipov, Sean L. Zheng, Albert Henry, Jennifer E. Huffman, Saketh Challa, Frank Rühle, Carmen Diaz Verdugo, Christian Krijger Juárez, Shinwan Kany, Constance A. van Orsouw, Kiran Biddinger, Edwin Poel, Amanda L. Elliott, Xin Wang, Catherine Francis, Richard Ruan, Satoshi Koyama, Leander Beekman, Dominic S. Zimmerman, Jean-François Deleuze, Eric Villard, David-Alexandre Trégouët, Richard Isnard, Dorret I. Boomsma, Eco J. C. de Geus, Rafik Tadros, Yigal M. Pinto, Arthur A. M. Wilde, Jouke-Jan Hottenga, Juha Sinisalo, Teemu Niiranen, Roddy Walsh, Amand F. Schmidt, Seung Hoan Choi, Kyong-Mi Chang, Philip S. Tsao, Paul M. Matthews, James S. Ware, R. Thomas Lumbers, Saskia van der Crabben, Jari Laukkanen, Aarno Palotie, Ahmad S. Amin, Philippe Charron, Benjamin Meder, Patrick T. Ellinor, Mark Daly, Krishna G. Aragam, Connie R. Bezzina
Journal: Nature Genetics (2024)

Abstract Dilated cardiomyopathy (DCM) is a heart muscle disease that represents an important cause of morbidity and mortality, yet causal mechanisms remain largely elusive. Here, we perform a large-scale genome-wide association study and multitrait analysis for DCM using 9,365 cases and 946,368 controls. We identify 70 genome-wide significant loci, which show broad replication in independent samples and map to 63 prioritized genes. Tissue, cell type and pathway enrichment analyses highlight the central role of the cardiomyocyte and contractile apparatus in DCM pathogenesis. Polygenic risk scores constructed from our genome-wide association study predict DCM across different ancestry groups, show differing contributions to DCM depending on rare pathogenic variant status and associate with systolic heart failure across various clinical settings. Mendelian randomization analyses reveal actionable potential causes of DCM, including higher bodyweight and higher systolic blood pressure. Our findings provide insights into the genetic architecture and mechanisms underlying DCM and myocardial function more broadly.
Cryptic phosphoribosylase activity of NAMPT restricts the virion incorporation of viral proteins
Authors: Shu Feng, Na Xie, Yongzhen Liu, Chao Qin, Ali Can Savas, Ting-Yu Wang, Shutong Li, Youliang Rao, Alexandra Shambayate, Tsui-Fen Chou, Charles Brenner, Canhua Huang, Pinghui Feng
Journal: Nature Metabolism (2024)
Web-browsing patterns reflect and shape mood and mental health
Authors: Christopher A. Kelly, Tali Sharot
Journal: Nature Human Behaviour (2024)

Abstract Humans spend on average 6.5 hours a day online. A large portion of that time is dedicated to information-seeking. How does this activity impact mental health? We assess this over four studies ( n = 1,145). We reveal that the valence of information sought affects mental health, which in turn influences the valence of information sought, forming a self-reinforcing loop. We quantified the valence of text on webpages participants chose to browse using natural language processing and found that browsing more negative information was associated with worse mental health and mood. By manipulating the webpages browsed and measuring mood and vice versa, we show that the relationship is causal and bidirectional. Finally, we developed an intervention that altered web-browsing patterns in a manner that improved mood. Together, the findings suggest that the information sought reflects mental state and shapes it, creating a loop that may perpetuate mental health problems. The results also provide a potential method for assessing and enhancing welfare in the digital age.