tbuckley/cabot-search huggingface dataset:
Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays
Authors: Barbara Mühlemann, Samuel H. Wilks, Lauren Baracco, Meriem Bekliz, Juan Manuel Carreño, Victor M. Corman, Meredith E. Davis-Gardner, Wanwisa Dejnirattisai, Michael S. Diamond, Daniel C. Douek, Christian Drosten, Isabella Eckerle, Venkata-Viswanadh Edara, Madison Ellis, Ron A. M. Fouchier, Matthew Frieman, Sucheta Godbole, Bart Haagmans, Peter J. Halfmann, Amy R. Henry, Terry C. Jones, Leah C. Katzelnick, Yoshihiro Kawaoka, Janine Kimpel, Florian Krammer, Lilin Lai, Chang Liu, Sabrina Lusvarghi, Benjamin Meyer, Juthathip Mongkolsapaya, David C. Montefiori, Anna Mykytyn, Antonia Netzl, Simon Pollett, Annika Rössler, Gavin R. Screaton, Xiaoying Shen, Alex Sigal, Viviana Simon, Rahul Subramanian, Piyada Supasa, Mehul S. Suthar, Sina Türeli, Wei Wang, Carol D. Weiss, Derek J. Smith
Journal: Science Translational Medicine (2024)

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires ongoing monitoring to judge the ability of newly arising variants to escape the immune response. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal serum samples. We compared 18 datasets generated using human, hamster, and mouse serum and six different neutralization assays. Datasets using animal model serum samples showed higher titer magnitudes than datasets using human serum samples in this comparison. Fold change in neutralization of variants compared to ancestral SARS-CoV-2, immunodominance patterns, and antigenic maps were similar among serum samples and assays. Most assays yielded consistent results, except for differences in fold change in cytopathic effect assays. Hamster serum samples were a consistent surrogate for human first-infection serum samples. These results inform the transition of surveillance of SARS-CoV-2 antigenic variation from dependence on human first-infection serum samples to the utilization of serum samples from animal models.
Incidence and trends of first basal cell carcinomas in France between 1980 and 2019: a regional population-based registry study
Authors: Karima Hammas, Charlée Nardin, Séverine Boyer, Catherine Michel, François Aubin, Anne-Sophie Woronoff
Journal: British Journal of Dermatology (2024)

Abstract Background Basal cell carcinoma (BCC) is the most frequent malignancy reported in populations with fair skin. In most countries, BCCs are only partially or not at all recorded, and incidence data are lacking. Objectives This study assessed the current incidence rates and trends in the only two French départements where BCCs have been recorded for several decades. Methods This regional population-based study thus used data from two French cancer registries (Doubs and Haut-Rhin) where first-time BCC diagnoses were recorded. The European age-standardized incidence rates (EASR) were calculated per 100 000 person-years (PY). The trends and the annual percentages of change were assessed using joinpoint analysis. Results In all, 48 989 patients were diagnosed with a first BCC in the study period. The median age at diagnosis was 69 years and the BCCs were mainly located on the head and neck (68.8%). In the Doubs area between 1980 and 2016, the EASR of BCC increased from 59.9 to 183.1 per 100 000 PY. The annual increase for men was 5.73% before 1999 and 1.49% thereafter, and among women 4.56% before 2001 and 1.31% thereafter. In the Haut-Rhin area, the EASR increased from 139.2 in 1991 to 182.8 per 100 000 PY in 2019. Among men, the EASR increased annually by 2.31% before 2000, and by 0.29% after 2000; among women, it increased by 0.95% over the entire period (1991–2019). In the most recent period and for these two départements, the age-specific incidence rates of BCC for men and women were close before the age of 60 years, except for the 40–49-year age group, where the rates were significantly higher among women. For patients aged 60 years and over, men had much higher rates of BCC. Conclusions BCC incidence has increased since 1980 and is still rising, particularly among men and the elderly. A slowing was observed from 2000, which could be explained by a shift in the management of BCCs and by the possible efficacy of prevention actions. This study provides insight into the BCC burden in France and highlights the need to maintain effective prevention strategies, as incidence is still increasing.
SRC inhibition enables formation of a growth suppressive MAGI1-PP2A complex in isocitrate dehydrogenase-mutant cholangiocarcinoma
Authors: Iris S. Luk, Caroline M. Bridgwater, Angela Yu, Liberalis D. Boila, Mariana Yáñez-Bartolomé, Aaron E. Lampano, Taylor S. Hulahan, Myriam Boukhali, Meena Kathiresan, Teresa Macarulla, Heidi L. Kenerson, Naomi Yamamoto, David Sokolov, Ian A. Engstrom, Lucas B. Sullivan, Paul D. Lampe, Jonathan A. Cooper, Raymond S. Yeung, Tian V. Tian, Wilhelm Haas, Supriya K. Saha, Sita Kugel
Journal: Science Translational Medicine (2024)

Intrahepatic cholangiocarcinoma (ICC) is an aggressive bile duct malignancy that frequently exhibits isocitrate dehydrogenase (
HiChIP-based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 that Confers Genetic Susceptibility to Gastroesophageal Cancer.
Authors: Ansley Gnanapragasam, Eftyhios Kirbizakis, Anna Li, Kyle H. White, Katelyn L. Mortenson, Juliana Cavalcante de Moura, Wajih Jawhar, Yifei Yan, Reilly Falter, Colleen Russett, Betty Giannias, Sophie Camilleri-Broët, Nicholas Bertos, Jonathan Cools-Lartigue, Livia Garzia, Veena Sangwan, Lorenzo Ferri, Xiaoyang Zhang, Swneke D. Bailey
Journal: Cancer Research (2024)

Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNV) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and genes they modulate could help improve GEC prevention and treatment. Herein, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome-free regions (NFR) harboring potential causal SNVs in a single assay. The application of H3K27ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at 7 loci, a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene, seemed to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR-mediated inhibition of the UXS1 promoter reduced the viability of the GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease. Significance: Epigenomic footprinting using a histone posttranslational modification targeted 3D genomics methodology elucidates functional noncoding sequence variants and their target genes at cancer risk loci.
Volumetric microscopy of cerebral arteries with a miniaturized optical coherence tomography imaging probe
Authors: Vitor M. Pereira, Pedro Lylyk, Nicole Cancelliere, Pedro N. Lylyk, Ivan Lylyk, Vania Anagnostakou, Carlos Bleise, Hidehisa Nishi, Mark Epshtein, Robert M. King, Mohammed Salman Shazeeb, Ajit S. Puri, Conrad W. Liang, Ricardo A. Hanel, Julian Spears, Thomas R. Marotta, Demetrius K. Lopes, Matthew J. Gounis, Giovanni J. Ughi
Journal: Science Translational Medicine (2024)

Endovascular interventions are increasingly becoming the preferred approach for treating strokes and cerebral artery diseases. These procedures rely on sophisticated angiographical imaging guidance, which encounters challenges because of limited contrast and spatial resolution. Achieving a more precise visualization of the underlying arterial pathology and neurovascular implants is crucial for accurate procedural decision-making. In a human study involving 32 patients, we introduced the clinical application of a miniaturized endovascular neuro optical coherence tomography (
The DRAP1/DR1 Repressor Complex Increases mTOR Activity to Promote Progression and Confer Everolimus Sensitivity in Triple-Negative Breast Cancer
Authors: Min-Ying Huang, Shu-Yuan Hu, Jia Dong, Ling Deng, Lisa Andriani, Xiao-Yan Ma, Yin-Ling Zhang, Fang-Lin Zhang, Zhi-Ming Shao, Da-Qiang Li
Journal: Cancer Research (2024)

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Transcriptional dysregulation is a hallmark of cancer, and several transcriptional regulators have been demonstrated to contribute to cancer progression. In this study, we identified an upregulation of the transcriptional corepressor downregulator of transcription 1-associated protein 1 (DRAP1) in TNBC, which was closely associated with poor recurrence-free survival in patients with TNBC. DRAP1 promoted TNBC proliferation, migration, and invasion in vitro and tumor growth and metastasis in vivo. Mechanistically, the downregulator of transcription 1 (DR1)/DRAP1 heterodimer complex inhibited expression of the cytosolic arginine sensor for mTORC1 subunit 1 (CASTOR1) and thereby increased activation of mTOR, which sensitized TNBC to treatment with the mTOR inhibitor everolimus. DRAP1 and DR1 also formed a positive feedback loop. DRAP1 enhanced the stability of DR1 by recruiting the deubiquitinase USP7 to inhibit its proteasomal degradation; in turn, DR1 directly promoted DRAP1 transcription. Collectively, this study uncovered a DRAP1-DR1 bidirectional regulatory pathway that promotes TNBC progression, suggesting that targeting the DRAP1/DR1 complex might be a potential therapeutic strategy to treat TNBC. Significance: DR1 and DRAP1 form a positive feedback loop and a repressor complex to cooperatively inhibit cytosolic arginine sensor for mTORC1 subunit 1 transcription and stimulate mTOR signaling, leading to progression and increased everolimus sensitivity in triple-negative breast cancer.
Essential Mixed Cryoglobulinemic Vasculitis: Sole Onset with Acute Respiratory Distress Syndrome
Authors: Shigeto Horiuchi, Makoto Hibino, Shunichi Tobe, Kazunari Maeda, Riko Kamada, Shigehiro Watanabe, Tetsuri Kondo
Journal: American Journal of Respiratory and Critical Care Medicine (2024)
Targeting OXCT1-mediated ketone metabolism reprograms macrophages to promote antitumor immunity via CD8+ T cells in hepatocellular carcinoma
Authors: Chu-Xu Zhu, Kai Yan, Liang Chen, Rong-Rong Huang, Zhen-Hua Bian, Hao-Ran Wei, Xue-Mei Gu, Yang-Yang Zhao, Meng-Chu Liu, Cai-Xia Suo, Zhi-Kun Li, Zhi-Yi Yang, Min-Qiang Lu, Xue-Feng Hua, Liang Li, Zhi-Bin Zhao, Lin-Chong Sun, Hua-Feng Zhang, Ping Gao, Zhe-Xiong Lian
Journal: Journal of Hepatology (2024)
Developing Krüppel-Like Factor 15 Agonists for Kidney Disease
Authors: Andrew K. Chow, Yiqing Guo, Sandeep K. Mallipattu
Journal: Journal of the American Society of Nephrology (2024)

1Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, NY 2Renal Section, Northport VA Medical Center, Northport, NY aTo whom correspondence should be addressed: Sandeep K. Mallipattu, Department of Medicine/Nephrology, Stony Brook University, 100 Nicolls Road, HSCT17-090B, Stony Brook, NY, USA., Tel: 631-638-2164, Fax: 631-444-6174, Email: [email protected] #Both authors contributed equally to the work
SimCol3D - 3D reconstruction during colonoscopy challenge
Authors: Anita Rau, Sophia Bano, Yueming Jin, Pablo Azagra, Javier Morlana, Rawen Kader, Edward Sanderson, Bogdan J. Matuszewski, Jae Young Lee, Dong-Jae Lee, Erez Posner, Netanel Frank, Varshini Elangovan, Sista Raviteja, Zhengwen Li, Jiquan Liu, Seenivasan Lalithkumar, Mobarakol Islam, Hongliang Ren, Laurence B. Lovat, José M.M. Montiel, Danail Stoyanov
Journal: Medical Image Analysis (2024)
Glucagon-Like Peptide-1 Receptor Agonists Do Not Increase Aspiration During Upper Endoscopy in Patients With Diabetes
Authors: Trevor S Barlowe, Chelsea Anderson, Robert S Sandler, Disha Subramaniam, Alicia Muratore, John B Buse, Lindsey N Gouker, Rajiv T Majithia, Nicholas J Shaheen, Til Stürmer, Michael K Dougherty
Journal: Clinical Gastroenterology and Hepatology (2024)
Cardiovascular toxicity of immune therapies for cancer
Authors: Nicolas L Palaskas, Hyeon-Ju Ali, Efstratios Koutroumpakis, Sarju Ganatra, Anita Deswal
Journal: BMJ (2024)

In addition to conventional chemoradiation and targeted cancer therapy, the use of immune based therapies, specifically immune checkpoint inhibitors (ICIs) and chimeric antigen receptor T cell therapy (CAR-T), has increased exponentially across a wide spectrum of cancers. This has been paralleled by recognition of off-target immune related adverse events that can affect almost any organ system including the cardiovascular system. The use of ICIs has been associated with myocarditis, a less common but highly fatal adverse effect, pericarditis and pericardial effusions, vasculitis, thromboembolism, and potentially accelerated atherosclerosis. CAR-T resulting in a systemic cytokine release syndrome has been associated with myriad cardiovascular consequences including arrhythmias, myocardial infarction, and heart failure. This review summarizes the current state of knowledge regarding adverse cardiovascular effects associated with ICIs and CAR-T.
Enhancing Readability of Online Patient-Facing Content: The Role of AI Chatbots in Improving Cancer Information Accessibility
Authors: Andres A. Abreu, Gilbert Z. Murimwa, Emile Farah, James W. Stewart, Lucia Zhang, Jonathan Rodriguez, John Sweetenham, Herbert J. Zeh, Sam C. Wang, Patricio M. Polanco
Journal: Journal of the National Comprehensive Cancer Network (2024)

Background: Internet-based health education is increasingly vital in patient care. However, the readability of online information often exceeds the average reading level of the US population, limiting accessibility and comprehension. This study investigates the use of chatbot artificial intelligence to improve the readability of cancer-related patient-facing content. Methods: We used ChatGPT 4.0 to rewrite content about breast, colon, lung, prostate, and pancreas cancer across 34 websites associated with NCCN Member Institutions. Readability was analyzed using Fry Readability Score, Flesch-Kincaid Grade Level, Gunning Fog Index, and Simple Measure of Gobbledygook. The primary outcome was the mean readability score for the original and artificial intelligence (AI)–generated content. As secondary outcomes, we assessed the accuracy, similarity, and quality using F1 scores, cosine similarity scores, and section 2 of the DISCERN instrument, respectively. Results: The mean readability level across the 34 websites was equivalent to a university freshman level (grade 13±1.5). However, after ChatGPT’s intervention, the AI-generated outputs had a mean readability score equivalent to a high school freshman education level (grade 9±0.8). The overall F1 score for the rewritten content was 0.87, the precision score was 0.934, and the recall score was 0.814. Compared with their original counterparts, the AI-rewritten content had a cosine similarity score of 0.915 (95% CI, 0.908–0.922). The improved readability was attributed to simpler words and shorter sentences. The mean DISCERN score of the random sample of AI-generated content was equivalent to “good” (28.5±5), with no significant differences compared with their original counterparts. Conclusions: Our study demonstrates the potential of AI chatbots to improve the readability of patient-facing content while maintaining content quality. The decrease in requisite literacy after AI revision emphasizes the potential of this technology to reduce health care disparities caused by a mismatch between educational resources available to a patient and their health literacy.
Fair evaluation of federated learning algorithms for automated breast density classification: The results of the 2022 ACR-NCI-NVIDIA federated learning challenge
Authors: Kendall Schmidt, Benjamin Bearce, Ken Chang, Laura Coombs, Keyvan Farahani, Marawan Elbatel, Kaouther Mouheb, Robert Marti, Ruipeng Zhang, Yao Zhang, Yanfeng Wang, Yaojun Hu, Haochao Ying, Yuyang Xu, Conrad Testagrose, Mutlu Demirer, Vikash Gupta, Ünal Akünal, Markus Bujotzek, Klaus H. Maier-Hein, Yi Qin, Xiaomeng Li, Jayashree Kalpathy-Cramer, Holger R. Roth
Journal: Medical Image Analysis (2024)
MONAI Label: A framework for AI-assisted interactive labeling of 3D medical images
Authors: Andres Diaz-Pinto, Sachidanand Alle, Vishwesh Nath, Yucheng Tang, Alvin Ihsani, Muhammad Asad, Fernando Pérez-García, Pritesh Mehta, Wenqi Li, Mona Flores, Holger R. Roth, Tom Vercauteren, Daguang Xu, Prerna Dogra, Sebastien Ourselin, Andrew Feng, M. Jorge Cardoso
Journal: Medical Image Analysis (2024)
Gout risk in adults with pre-diabetes initiating metformin
Authors: Javier Marrugo, Leah M Santacroce, Misti L Paudel, Sho Fukui, Alexander Turchin, Sara K Tedeschi, Daniel H Solomon
Journal: Annals of the Rheumatic Diseases (2024)

Despite the strong association between gout and pre-diabetes, the role of metformin in gout among individuals with pre-diabetes remains uncertain. We compared the incidence rates of gout in adults with pre-diabetes starting metformin with those not using antidiabetic treatments.
Research progress in Alzheimer's disease and bone-brain axis
Authors: Fan Zhang, Wei Zhang
Journal: Ageing Research Reviews (2024)

Alzheimer's disease (AD) is the most common type of cognitive impairment. AD is closely related to orthopedic diseases, such as osteoporosis and osteoarthritis, in terms of epidemiology and pathogenesis. Brain and bone tissues can regulate each other in different manners through bone-brain axis. This article reviews the research progress of the relationship between AD and orthopedic diseases, bone-brain axis mechanisms of AD, and AD therapy by targeting bone-brain axis, in order to deepen the understanding of bone-brain communication, promote early diagnosis and explore new therapy for AD patients. Keywords
Alzheimer's disease pathophysiology in the Retina
Authors: Bhakta Prasad Gaire, Yosef Koronyo, Dieu-Trang Fuchs, Haoshen Shi, Altan Rentsendorj, Ron Danziger, Jean-Philippe Vit, Nazanin Mirzaei, Jonah Doustar, Julia Sheyn, Harald Hampel, Andrea Vergallo, Miyah R Davis, Ousman Jallow, Filippo Baldacci, Steven R Verdooner, Ernesto Barron, Mehdi Mirzaei, Vivek K Gupta, Stuart L Graham, Mourad Tayebi, Roxana O Carare, Alfredo A Sadun, Carol A Miller, Oana M Dumitrascu, Shouri Lahiri, Liang Gao, Keith L Black, Maya Koronyo-Hamaoui
Journal: Progress in Retinal and Eye Research (2024)

The retina is an emerging CNS target for potential noninvasive diagnosis and tracking of Alzheimer's disease (AD). Studies have identified the pathological hallmarks of AD, including amyloid β-protein (Aβ) deposits and abnormal tau protein isoforms, in the retinas of AD patients and animal models. Moreover, structural and functional vascular abnormalities such as reduced blood flow, vascular Aβ deposition, and blood-retinal barrier damage, along with inflammation and neurodegeneration, have been described in retinas of patients with mild cognitive impairment and AD dementia. Histological, biochemical, and clinical studies have demonstrated that the nature and severity of AD pathologies in the retina and brain correspond. Proteomics analysis revealed a similar pattern of dysregulated proteins and biological pathways in the retina and brain of AD patients, with enhanced inflammatory and neurodegenerative processes, impaired oxidative-phosphorylation, and mitochondrial dysfunction. Notably, investigational imaging technologies can now detect AD-specific amyloid deposits, as well as vasculopathy and neurodegeneration in the retina of living AD patients, suggesting alterations at different disease stages and links to brain pathology. Current and exploratory ophthalmic imaging modalities, such as optical coherence tomography (OCT), OCT-angiography, confocal scanning laser ophthalmoscopy, and hyperspectral imaging, may offer promise in the clinical assessment of AD. However, further research is needed to deepen our understanding of AD's impact on the retina and its progression. To advance this field, future studies require replication in larger and diverse cohorts with confirmed AD biomarkers and standardized retinal imaging techniques. This will validate potential retinal biomarkers for AD, aiding in early screening and monitoring.
Reply to: “Tailoring allocation policies and improving access to pediatric liver transplantation in Italy: outframing and concluding”
Authors: Marco Spada, Roberta Angelico, Silvia Trapani, Lucia Masiero, Francesca Puoti, Michele Colledan, Davide Cintorino, Renato Romagnoli, Umberto Cillo, Massimo Cardillo
Journal: Journal of Hepatology (2024)
Microbiota transplantation in restoring cesarean-related infant dysbiosis: a new frontier
Authors: Sina Liu, Xiaoxia Luo, Lepeng Zhou, Ri-hua Xie, Yan He
Journal: Gut Microbes (2024)

C-section is crucial in reducing maternal and neonatal mortality when medically indicated, but one of its side effects could be the disruption of vertical transmission of maternal-infant microbiota during delivery, potentially leading to gut dysbiosis and increased disease risks in C-section infants. To address such dysbiosis, it seems reasonable to supplement "what is missing" during C-section procedure. This idea has prompted several clinical trials, including proof-of-concept, investigating interventions like vaginal microbial seeding, oral administration of maternal vaginal microbes and even oral administration of maternal fecal materials. Hereby, we have summarized these trials to help understand the current state of these researches, highlighting the predominantly pilot nature of most of these studies and emphasizing the need for well-designed studies with larger sample to guide evidence-based medicine in the future.
Sociopolitical Factors and Mental Health Following the Turkey-Syria Earthquake
Authors: Wai Kai Hou, Tiffany Junchen Tao, Crystal Jingru Li, Evon Lam Wong, Aysuhan Tuba Saral, Huinan Liu, Sandro Galea
Journal: JAMA Network Open (2024)

This survey study evaluates the association between sociopolitical factors and mental health following the 2023 Turkey-Syria earthquake.
Drug Reaction With Eosinophilia and Systemic Symptoms With Pustulosis
Authors: Emma Hansen, Rachel M. Kirven, Matthew Gallardo, Catherine G. Chung, Kristopher Fisher, Benjamin H. Kaffenberger, Abraham M. Korman
Journal: JAMA Dermatology (2024)

This cohort study examines patients with drug reaction with eosinophilia and systemic symptoms who also have pustules.