tbuckley/cabot-search huggingface dataset:
Ultraprocessed Food Consumption and Obesity Development in Canadian Children
Authors: Zheng Hao Chen, Sara Mousavi, Piushkumar J. Mandhane, Elinor Simons, Stuart E. Turvey, Theo J. Moraes, Padmaja Subbarao, Kozeta Miliku
Journal: JAMA Network Open (2025)

Importance Ultraprocessed foods (UPF), characterized as shelf-stable but nutritionally imbalanced foods, pose a public health crisis worldwide. In adults, UPF consumption is associated with increased obesity risk, but findings among children are inconsistent. Objectives To examine the associations among UPF intake, anthropometric adiposity indicators, and obesity status in Canadian children. Design, Setting, and Participants In the CHILD Cohort Study, one of the largest prospective, multicenter, population-based pregnancy cohorts in Canada, diet was assessed during the 3-year visit (September 2011 to June 2016), and anthropometric measurements were assessed at the 5-year visit (December 2013 to April 2018). Data analysis was performed between July 1, 2023, and June 30, 2024. Exposure Diet intake was assessed using a semiquantitative food frequency questionnaire at 3 years of age. UPFs were identified using the NOVA classification system. Main Outcomes and Measures Anthropometric adiposity indicators were measured at 5 years of age and used to calculate age- and sex-standardized z scores for body mass index (BMI), waist to height ratio, and subscapular and triceps skinfold thicknesses, and obesity, which was defined using BMI z score cutoffs. Multivariable-adjusted regression analyses were used to examine the associations of UPF with adiposity and obesity development, accounting for parental, birth, and early-childhood factors. Results Among 2217 participants included in this study, median age at the outcome assessment was 5.0 (IQR, 5.0-5.1) years, and 1175 (53.0%) were males. At 3 years of age, UPF contributed 45.0% of total daily energy intake. UPF energy contribution was higher in males vs females (46.0% vs 43.9%; P &amp;amp;lt; .001). Among all participants, higher UPF intake at 3 years of age was associated with higher anthropometric adiposity indicators at 5 years of age, primarily driven by males. In males, every 10% UPF energy increase was associated with higher adiposity indicator z scores for BMI (β, 0.08; 95% CI, 0.03-0.14), waist to height ratio (β, 0.07; 95% CI, 0.01-0.12), and subscapular (β, 0.12; 95% CI, 0.06-0.18) and triceps (β, 0.09; 95% CI, 0.03-0.15) skinfold thickness and higher odds of living with overweight or obesity (odds ratio, 1.19; 95% CI, 1.03-1.36). No significant associations were observed among females. Conclusions and Relevance In this cohort study of Canadian children, high UPF consumption during early childhood was associated with obesity development, primarily in males. These findings can inform targeted public health initiatives for early childhood centers and caregiver education programs to reduce UPF intake and prevent obesity.
Survival Among Patients With <i>ERBB2</i>-Positive Metastatic Breast Cancer and Central Nervous System Disease
Authors: Emanuela Ferraro, Anne S. Reiner, Rabih Bou Nassif, Umberto Tosi, Samantha Brown, Sabrina Zeller, Chau T. Dang, Andrew D. Seidman, Nelson S. Moss
Journal: JAMA Network Open (2025)

Importance Approximately one-third of patients with ERBB2 (formerly HER2 or HER2/neu )–positive ( ERBB2 + ) metastatic breast cancer (MBC) develop brain metastasis. It is unclear whether patients with disease limited to the central nervous system (CNS) have different outcomes and causes of death compared with those with concomitant extracranial metastasis. Objective To assess overall survival (OS) and CNS-related mortality among patients with ERBB2 + breast cancer and a diagnosis of CNS disease by disease distribution (CNS only vs CNS plus extracranial metastasis). Design, Setting, and Participants This single-center, retrospective cohort study included patients with ERBB2 + MBC and CNS disease, including parenchymal brain metastasis, leptomeningeal disease (LMD), or dural metastasis, who were treated between August 2010 and April 2022 at Memorial Sloan Kettering Cancer Center. Data were analyzed between December 2023 and August 2024. Main Outcomes and Measures Overall survival, estimated with the Kaplan-Meier method, and CNS-related mortality with cumulative incidence. Results The cohort included 274 patients (272 [99.3%] female). The median age was 53.7 years (range, 28.7-87.4 years); 125 patients (45.6%) presented with de novo MBC. At CNS metastasis diagnosis, 73 (26.6%) presented with CNS-only disease. There was a median follow-up of 3.7 years (range, 0.2-12.0 years) from CNS disease diagnosis among those alive at the end of follow-up. Both OS and CNS-related death were significantly correlated with the pattern of presentation: OS was shortest among patients with LMD (1.24 years; 95% CI, 0.89-2.08 years) followed by those with extracranial metastasis (2.16 years; 95% CI, 1.87-2.58 years) and was longest among patients with parenchymal or dural CNS disease only (3.57 years; 95% CI, 2.10-5.63 years) ( P = .001). Of 192 patients (70.1%) who died, 106 (55.2%) died of a CNS-related cause. The group with CNS-only disease remained at high risk of death from CNS causes, with a 3-year CNS-related death rate of 33.98% (95% CI, 22.84%-45.43%) and a 3-year death rate from other causes of 6.07% (95% CI, 1.93%-13.69%). On multivariable modeling for CNS-related death, LMD (hazard ratio, 1.87; 95% CI, 1.19-2.93; P = .007) and treatment with whole-brain radiotherapy (hazard ratio, 1.71; 95% CI, 1.13-2.58; P = .01) were associated with CNS-related death. Conclusions and Relevance In this cohort study, 55.2% of deaths among patients with ERBB2 + breast cancer and brain metastasis were due to CNS-related causes, with the greatest risk among patients with LMD. CNS-only presentation was associated with improved survival but a higher rate of CNS-related death, supporting an approach of aggressive local therapy for select patients.
CeO2 Nanozyme-Embedded Thermal-Deformative Polymer for Site-Specific Chemotherapy via HIF-1α-P-gp/Lipolysis Axis Reversal
Authors: Zhiyuan Tang, Yuening Sun, Quanhua Yi, Qian Ding, Yang Ding, Jianfei Huang
Journal: Asian Journal of Pharmaceutical Sciences (2025)
Eligibility criteria for lung cancer screening in France: a modelling study
Authors: Xiaoshuang Feng, Karine Alcala, Florence Guida, Marcel Goldberg, Marie Zins, Olivier Leleu, Pianpian Cao, Jihyoun Jeon, Sébastien Couraud, Mattias Johansson, Hilary A Robbins
Journal: The Lancet Regional Health - Europe (2025)
Defining hypoxia in cancer: A landmark evaluation of hypoxia gene expression signatures
Authors: Matteo Di Giovannantonio, Fiona Hartley, Badran Elshenawy, Alessandro Barberis, Dan Hudson, Hana S Shafique, Vincent E S Allott, David A Harris, Simon R Lord, Syed Haider, Adrian L Harris, Francesca M Buffa, Benjamin H L Harris
Journal: Cell Genomics (2025)

Tumor hypoxia drives metabolic shifts, cancer progression, and therapeutic resistance. Challenges in quantifying hypoxia have hindered the exploitation of this potential "Achilles' heel." While gene expression signatures have shown promise as surrogate measures of hypoxia, signature usage is heterogeneous and debated. Here, we present a systematic pan-cancer evaluation of 70 hypoxia signatures and 14 summary scores in 104 cell lines and 5,407 tumor samples using 472 million length-matched random gene signatures. Signature and score choice strongly influenced the prediction of hypoxia in vitro and in vivo. In cell lines, the Tardon signature was highly accurate in both bulk and single-cell data (94% accuracy, interquartile mean). In tumors, the Buffa and Ragnum signatures demonstrated superior performance, with Buffa/mean and Ragnum/interquartile mean emerging as the most promising for prospective clinical trials. This work delivers recommendations for experimental hypoxia detection and patient stratification for hypoxia-targeting therapies, alongside a generalizable framework for signature evaluation.
An integrative multiparametric approach stratifies putative distinct phenotypes of blast phase chronic myelomonocytic leukemia
Authors: Kristian Gurashi, Yu-Hung Wang, Fabio M R Amaral, Katherine Spence, Rachel Cant, Chi-Yuan Yao, Chien-Chin Lin, Christopher Wirth, David C Wedge, Guillermo Montalban-Bravo, Simona Colla, Hwei-Fang Tien, Tim C P Somervaille, Kiran Batta, Daniel H Wiseman
Journal: Cell Reports Medicine (2025)

Approximately 30% of patients with chronic myelomonocytic leukemia (CMML) undergo transformation to a chemo-refractory blastic phase (BP-CMML). Seeking novel therapeutic approaches, we profiled blast transcriptomes from 42 BP-CMMLs, observing extensive transcriptional heterogeneity and poor alignment to current acute myeloid leukemia (AML) classifications. BP-CMMLs display distinctive transcriptomic profiles, including enrichment for quiescence and variability in drug response signatures. Integrating clinical, immunophenotype, and transcriptome parameters, Random Forest unsupervised clustering distinguishes immature and mature subtypes characterized by differential expression of transcriptional modules, oncogenes, apoptotic regulators, and patterns of surface marker expression. Subtypes differ in predicted response to AML drugs, validated ex vivo in primary samples. Iteratively refined stratification resolves a classification structure comprising five subtypes along a maturation spectrum, predictive of response to novel agents including consistent patterns for receptor tyrosine kinase (RTK), cyclin-dependent kinase (CDK), mechanistic target of rapamycin (MTOR), and mitogen-activated protein kinase (MAPK) inhibitors. Finally, we generate a prototype decision tree to stratify BP-CMML with high specificity and sensitivity, requiring validation but with potential clinical applicability to guide personalized drug selection for improved outcomes.
2024 update of the AGIHO guideline on diagnosis and empirical treatment of fever of unknown origin (FUO) in adult neutropenic patients with solid tumours and hematological malignancies
Authors: Michael Sandherr, Jannik Stemler, Enrico Schalk, Tessa Hattenhauer, Marcus Hentrich, Bernd Hertenstein, Christian Hohmann, Sibylle C Mellinghoff, Rebekka Mispelbaum, Christina Rieger, Martin Schmidt-Hieber, Rosanne Sprute, Guenter Weiss, Oliver A Cornely, Larissa Henze, Cornelia Lass-Floerl, Gernot Beutel, Annika Y Classen, Noemi F Freise, Meinolf Karthaus, Philipp Koehler, Robert Krause, Julia Neuhann, Hans Martin Orth, Olaf Penack, Markus Schaich, Karsten Spiekermann, Sebastian Voigt, Florian Weissinger, Elena Busch
Journal: The Lancet Regional Health - Europe (2025)
Biased agonism in peptide-GPCRs: A structural perspective
Authors: Tharindunee Jayakody, Dinath Kavishka Budagoda, Krishan Mendis, Withanage Dhanuka Dilshan, Duvindu Bethmage, Rashmi Dissasekara, Gavin Stewart Dawe
Journal: Pharmacology & Therapeutics (2025)
Retraction Notice to: Hypoxia-induced lncHILAR promotes renal cancer metastasis via ceRNA for the miR-613/206/ 1-1-3p/Jagged-1/Notch/CXCR4 signaling pathway
Authors: Guanghui Hu, Junjie Ma, Jin Zhang, Yonghui Chen, Huan Liu, Yiran Huang, Junhua Zheng, Yunfei Xu, Wei Xue, Wei Zhai
Journal: Molecular Therapy (2025)
Author Correction: Single-dose suraxavir marboxil for acute uncomplicated influenza in adults and adolescents: a multicenter, randomized, double-blind, placebo-controlled phase 3 trial
Authors: Yeming Wang, Hong Wang, Yu Zhang, Anlin Ma, Dong Liu, Xiaoguang Li, Guoru Yang, Min Deng, Shaofang Wang, Yuanyuan Liu, Chuanmiao Liu, Fangqi Ge, Sikui Wang, Yunsong Yu, Ganzhu Feng, Zuke Xiao, Xing Li, Yilan Sun, Xuyan Chen, Zhaolong Cao, Yan Ding, Xiaoping Wu, Jun Wei, Bin Cao
Journal: Nature Medicine (2025)
Faecal microbiota transplantation in patients with systemic sclerosis and lower gastrointestinal tract symptoms in Norway (ReSScue): a phase 2, randomised, double-blind, placebo-controlled trial
Authors: Håvard Fretheim, Imon Barua, Gunnstein Bakland, Alvilde Dhainaut, Anne-Kristine Halse, Maylen N Carstens, Henriette Didriksen, Øyvind Midtvedt, Knut E A Lundin, Lars Aabakken, Vikas K Sarna, Hasse K Zaré, Dinesh Khanna, Oliver Distler, Tore Midtvedt, Espen S Bækkevold, Inge C Olsen, Diana Domanska, Maiju E Pesonen, Øyvind Molberg, Anna-Maria Hoffmann-Vold
Journal: The Lancet Rheumatology (2025)
Dupilumab for chronic obstructive pulmonary disease with type 2 inflammation: a pooled analysis of two phase 3, randomised, double-blind, placebo-controlled trials
Authors: Surya P Bhatt, Klaus F Rabe, Nicola A Hanania, Claus F Vogelmeier, Mona Bafadhel, Stephanie A Christenson, Alberto Papi, Dave Singh, Elizabeth Laws, Paula Dakin, Jennifer Maloney, Xin Lu, Deborah Bauer, Ashish Bansal, Raolat M Abdulai, Lacey B Robinson
Journal: The Lancet Respiratory Medicine (2025)
The KP.2-adapted COVID-19 vaccine improves neutralising activity against the XEC variant
Authors: Mehul S Suthar, Kelly E Manning, Madison L Ellis, Shilpi Jain, Kareem Bechnak, Jake Vander Velden, Farida Laboune, Amy R Henry, Sucheta Godbole, Sungjin Kim, Malaya K Sahoo, Isabel Paredes, Serena M Dib, Suha Kalash, Christelle Radi, Heather Hicks, Azaibi Tamin, Meredith Gardner, Nicole Bowen, Peter Cook, Clinton Paden, Jennifer Harcourt, Benjamin A Pinsky, Daniel C Douek, Nadine Rouphael, Alberto Moreno
Journal: The Lancet Infectious Diseases (2025)
Successful balloon fixation technique to prevent dislocation of a fully covered self-expanding metal stent for biliary stricture
Authors: Kosuke Takahashi, Eisuke Ozawa, Yasuhiko Nakao, Masanori Fukushima, Hisamitsu Miyaaki, Kazuhiko Nakao
Journal: Endoscopy (2025)

Fully covered self-expanding metal stents (FCSEMSs) are commonly used to manage benign biliary strictures [1]. However, stent migration and dislocation during and after endoscopic retrograde cholangiopancreatography (ERCP) remain a challenge [2] [3] [4] [5]. Stent dislocation rarely occurs when the delivery system catches on the stent during removal. This case report demonstrates the successful prevention of stent dislocation using a balloon catheter inserted through the percutaneous transhepatic biliary drainage (PTBD) route.
Over-the-scope clip on over-the-scope clip technique for closure of delayed perforation near a previously placed over-the-scope clip
Authors: Susumu Banjoya, Yohei Minato, Yuki Kano, Kohei Ono, Ryoju Negishi, Hideyuki Chiba, Ken Ohata
Journal: Endoscopy (2025)

The over-the-scope (OTS) clip is effective for defect closure during endoscopic treatment [1] [2]. OTS clip closure has been reported to be effective in preventing delayed perforation and bleeding, especially after duodenal endoscopic resection [3]. However, adverse events associated with the OTS clip itself have been reported, including bleeding, perforation, infection, and failure to attach [4] [5].
Flexible and stretchable bioelectronics for organoids
Authors: Jaeyong Lee, Jia Liu
Journal: Med-X (2025)

Abstract Organoids have gained significant interest due to their ability to recapitulate the structural, molecular, and functional complexity of corresponding organs. While methods have been developed to characterize and benchmark organoid structural and molecular properties, capturing the functional development and maturation of organoids remains challenging. To address this, the development of multifunctional bioelectronics for interfacing with organoids has been actively pursued. However, conventional electronics face limitations in achieving multifunctional recording and control across the entire three-dimensional (3D) volume of organoids in a long-term stable manner due to the large morphological and cellular composition changes during development. In this review, we first discuss the application of conventional electronics for organoid interfacing. We then focus on the development of flexible and stretchable electronics designed to create organoid/electronics hybrids for chronically stable interfaces. We also review recent advancements in flexible multifunctional electronics for charting multimodal cell activities throughout development. Furthermore, we explore the integration of flexible bioelectronics with other characterization modalities for comprehensive multimodal charting of cells within 3D tissues. Finally, we discuss the potential of integrating artificial intelligence into the organoid system through embedded electronics, harnessing organoid intelligence for biosymbiotic computational systems. These advancements could provide valuable tools for characterizing organoid functional development and maturation, establishing patient-specific models, developing therapeutic opportunities, and exploring novel computational strategies. Graphical abstract
Endoscopic transcecal appendectomy for a laterally spreading tumor of the appendiceal stump
Authors: Xin-Yue Li, Dan-Feng Zhang, Meng-Jiang He, Quan-Lin Li, Ping-Hong Zhou
Journal: Endoscopy (2025)

A 68-year-old woman, who was diagnosed with suppurative appendicitis 17 years previously and underwent appendectomy, was found during a recent colonoscopy, performed as part of a health-check, to have a 1.5-cm flat laterally spreading tumor (LST) at the appendiceal orifice ([Fig. 1] a). Biopsy indicated that the lesion was a tubular adenoma with low grade intraepithelial neoplasia (LGIN). Computed tomography revealed peristump exudation and pneumatosis. Endoscopic transcecal appendectomy (ETA) was recommended to remove the lesion at the appendiceal stump ([Video 1]).
Backward leap technique using a novel 0.018-inch guidewire
Authors: Kosuke Takahashi, Eisuke Ozawa, Yasuhiko Nakao, Masanori Fukushima, Hisamitsu Miyaaki, Kazuhiko Nakao
Journal: Endoscopy (2025)

Guidewire placement is the greatest challenge in endoscopic ultrasound (EUS)-guided hepaticogastrostomy (EUS-HGS) [1] [2] [3] [4] [5]. Following puncture, the guidewire often advances into the peripheral intrahepatic bile ducts, making it difficult to position the wire in the common bile duct. Here, we describe a new "backward leap technique" using a novel low-rigidity 0.018-inch guidewire ([Fig. 1], [Video 1]) to address these challenges.
A new innovative imaging modality: “extended reality” in endoscopic ultrasonography
Authors: Yuki Ishikawa-Kakiya, Hirotsugu Maruyama, Kojiro Tanoue, Akira Higashimori, Shusei Fukunaga, Yasuhiro Fujiwara
Journal: Endoscopy (2025)

Endoscopic ultrasonography (EUS) is essential for management of pancreaticobiliary diseases; it involves operating the endoscope, interpreting the EUS images, comparing them with other images, and considering needle biopsy or surgery. In addition, the anatomy of each patient must be considered; however, attaining an accurate understanding is a major challenge for trainees.
Round-robin comparison of RET rearrangement detection in ctDNA: A novel method for limited clinical samples
Authors: Cloud P. Paweletz, Alison Urvalek, Minh Ha, Kavita Garg, Aimee Bence Lin, Anna M. Szpurka, Anthony Sireci, Geoffrey R. Oxnard, Pasi A. Janne
Journal: Clinical Cancer Research (2025)

Abstract Purpose: Next-generation sequencing assays for circulating tumor DNA analysis are routinely used in the care of patients with advanced non-small cell lung cancer. However, variable assay sensitivities in detection of fusions have been reported. Here we report on the performance of detecting RET rearrangements in plasma across three commercial NGS laboratories. Methods: Banked plasma from the phase 3 LIBRETTO-431 trial was studied. For each patient (n=60) with a known RET fusion by local tumor tissue genotyping, pretreatment plasma was divided into two 3mL aliquots and tested on 2 of 3: Guardant Health’s Guardant360®, Foundation Medicine’s FoundationOne®Liquid CDx, and Resolution Bioscience’s ctDx-FirstTM. A round-robin comparison was performed across vendors using three pairwise comparisons of 20 patients each. On an exploratory basis, agreement of fusion breakpoint calling between plasma and tissue and determinants of false negatives in plasma were assessed. Results: Of 40 samples received by each laboratory, 100% (40/40), 92.5% (37/40), and 90% (36/40) were successfully sequenced by Guardant360, FoundationOne Liquid CDx, and ctDx-First, with a RET-fusion or rearrangement detected in 60% (24/40), 67.6% (25/37), and 63.9% (23/36) of cases, respectively. Discordant results included rare and common RET translocations but were usually below allelic frequency of 0.5%. Of samples with a RET fusion detected in plasma and a reported fusion partner by tumor assay, the same fusion partner was identified in tissue and liquid 81-89% of the time. Conclusion: Our results support the utility of ctDNA assays concurrently with tissue testing for detection of translocations, with opportunities to further optimize performance.
Mitochondrial transplantation as a novel therapeutic approach in idiopathic inflammatory myopathy
Authors: Jeong Yeon Kim, Young Cheol Kang, Min Jung Kim, Seon Uk Kim, Hae Rim Kang, Jeong Seon Yeo, Yujin Kim, Shin-Hye Yu, Byeongwook Song, Jung Wook Hwang, Yun-Sang Lee, Jung Woo Byun, Dae Hyun Yoo, Hyun Sook Kim, Kyuboem Han, Chun-Hyung Kim, Eun Young Lee
Journal: Annals of the Rheumatic Diseases (2025)

This study aimed to investigate the efficacy of mitochondrial transplantation as a therapeutic intervention for idiopathic inflammatory myopathy (IIM). This study used a comprehensive approach, incorporating both in vitro and in vivo IIM models, and conducted a first-in-human clinical trial to assess the effectiveness and safety of mitochondria isolated from human umbilical cord mesenchymal stem cells (PN-101). Mitochondria isolated from umbilical cord mesenchymal stem cells were designated as PN-101. The efficacy of PN-101 was assessed using myoblasts derived from patients with IIM and C2C12 mouse perforin/granzyme B-treated myoblasts as an in vitro IIM model. PN-101's effect on IIM was examined using C protein-induced myositis (CIM) mice as an in vivo model. The efficacy and safety of PN-101 were evaluated in a phase 1/2a clinical trial involving 9 adult patients with refractory polymyositis or dermatomyositis. The myoblasts derived from patients with IIM exhibited defects in mitochondrial function and myogenesis. PN-101 transplantation enhances muscle differentiation and mitochondrial function in IIM myoblasts. PN-101 also enhanced intracellular adenosine triphosphate content, cell viability, and myogenesis in C2C12 perforin/granzyme B-treated myoblasts. In an in vivo model, PN-101 reduced myositis severity by exhibiting anti-inflammatory effects and restoring the CIM-induced metabolic shift. In a phase 1/2a prospective clinical trial involving adult patients with refractory IIM, PN-101 demonstrated no severe adverse drug reactions and showed at least minimal improvement in the International Myositis Assessment and Clinical Studies Group (IMACS)-Total Improvement Scores (TISs) compared with baseline. PN-101 transplantation could serve as a novel treatment for IIM by enhancing mitochondrial repair and reducing inflammation in muscle tissues.