tbuckley/cabot-search huggingface dataset:
A multi-country outbreak of Salmonella Mbandaka linked to pre-cooked, frozen chicken meat in ready-to-eat products, Finland, 2022 to 2023
Authors: Ana Cristina Gonzalez-Perez, Heidi Landgren, Anni Vainio, Wioleta Kitowska, Annika Pihlajasaari, Elina Leinonen, Henry Kuronen, Taru Lienemann, Heli Tapanainen, Niina E Kaartinen, Jelena Rjabinina, Jelena Sõgel, Ruska Rimhanen-Finne
Journal: Eurosurveillance (2025)

In May 2022, the Finnish Institute for Health and Welfare observed an increase in Salmonella Mbandaka cases. Whole genome sequencing (WGS) linked the outbreak strain to a previously reported strain in the United Kingdom. From April 2022 to January 2023, 97 cases were reported across 18 of Finland’s 21 hospital districts, with a median age of 27 years (range &lt;1–74 years) and 61% female cases. Based on trawling interviews and national food consumption data, cases were more likely to have eaten at a restaurant or takeaway (odds ratio (OR) = 115; 95% confidence interval (CI): 52–256; p &lt; 0.001) or consumed poultry products (OR = 28; 95% CI: 7–115; p &lt; 0.001). A case–case study linked cases with consumption of ready-to-eat products containing chicken from a specific company (OR = 28; 95% CI: 1.9–1,361; p = 0.004). Traceback investigations identified a pre-cooked, frozen chicken meat product from a country outside the European Union as the likely source. Salmonella Mbandaka was isolated from cases and linked by WGS to this chicken meat product. Our findings highlight the potential health risk of pre-cooked chicken meat containing Salmonella and the value of case–case studies and product images to assist recall during food-borne outbreak investigations.
Preliminary evidence for enhanced auditory cortex activation and mental development after gene therapy in children with autosomal recessive deafness 9
Authors: Jiajia Zhang, Zengzhi Guo, Changjie Pan, Chunchun Hu, Xinyang Weng, Yang-Wenyi Liu, Xiaoting Cheng, Jun Lv, Qi Cao, Hui Wang, Yuxin Chen, Daqi Wang, Shaowei Hu, Mengzhao Xun, Longlong Zhang, Zijing Wang, Honghai Tang, Biyun Zhu, Luo Guo, Sha Yu, Xiaoling Hu, Lin Chen, Bing Chen, Zheng-Yi Chen, Shan Sun, Xiu Xu, Huawei Li, Fei Chen, Yilai Shu
Journal: Nature Human Behaviour (2025)
CD56 expression modulates NAD+ metabolic landscape and predicts sensitivity to anti-CD38 therapies in multiple myeloma
Authors: Giulia Giorgetti, Elena Maroto-Martin, Debora Soncini, Daniela Fenoglio, Pamela Becherini, Andrea Benzi, Silvia Ravera, Isabella Traverso, Francesco Ladisa, Francesco Lai, Giulia Rivoli, Dario Truffelli, Aimable Nahimana, Antonia Cagnetta, Fabio Guolo, Chiara R M Uras, Anaïs Schavgoulidze, Jessica Fong Ng, Alessio Nencioni, Santina Bruzzone, Nikhil C Munshi, Roberto Massimo Lemoli, Mariateresa Fulciniti, Michele Cea
Journal: Blood Cancer Journal (2025)
SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data
Authors: Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman, Evan Murray, Robert Strasser, Jan Watter, Ofir Cohen, Orr Ashenberg, Daniel Abravanel, Judit Jané-Valbuena, Simon Mages, Ana Lako, Karla Helvie, Orit Rozenblatt-Rosen, Scott Rodig, Fei Chen, Nikhil Wagle, Aviv Regev, Johanna Klughammer
Journal: Genome biology (2025)

Abstract Solid tumors are spatially heterogeneous in their genetic, molecular, and cellular composition, but recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to identify copy number alterations (CNAs), we develop SlideCNA, a computational tool to extract CNA signals from sparse spatial transcriptomics data with near single cellular resolution. SlideCNA uses expression-aware spatial binning to overcome sparsity limitations while maintaining spatial signal to recover CNA patterns. We test SlideCNA on simulated and real Slide-seq data of (metastatic) breast cancer and demonstrate its potential for spatial subclone detection.
Enhanced nanoparticle delivery across vascular basement membranes of tumours using nitric oxide
Authors: Wei Jiang, Zixuan Guo, Qin Wang, Ziqi Chen, Wang Dong, Qirui Liang, Yinghong Hao, Huimin Pan, Cici Zeng, Hang Liu, Yucai Wang
Journal: Nature Biomedical Engineering (2025)
MANIFEST: Multiomic Platform for Cancer Immunotherapy
Authors: Kok Haw Jonathan Lim, Zayd Tippu, Pippa G. Corrie, Michael Hubank, James Larkin, Trevor D. Lawley, Mark Stares, Grant D. Stewart, Amy Strange, Stefan N. Symeonides, Bernadett Szabados, Nicholas C. Turner, Tom Waddell, Santiago Zelenay, Manuel Salto-Tellez, Caroline Dive, Samra Turajlic, Javier Alfaro, Raza Ali, Karen Ambrose, Anne Armstrong, Christopher Banerji, Bristi Basu, Veronique Birault, James-Baptiste Cazier, Benny Chain, Tapabrata Rohan Chakraborty, Jyoti Choudhary, Ananya Choudhury, Fiona Collinson, Natalie Cook, Johan de Bono, Corinne Faivre-Finn, James Fleming, Xiao Fu, Andrew J.S. Furness, Trevor Graham, Peter Hall, David J. Harrison, Jennifer Hay, Karibaan Hodivala-Dilke, Robert Huddart, Matthew Humphries, Will Ince, James O. Jones, George Kassiotis, Gavin Kelly, Dimitris Lagos, Alexander Laird, Rebecca Lee, Juanita Lopez, Paul C. Lorigan, Stuart McDonald, Alan Melcher, Christina Messiou, Florent Mouliere, Emma Nye, Brent O’Carrigan, Alicia Okines, Pedro Oliveira, Thomas Powles, Ajitha Rajan, Andy Riddell, Peter Schmid, Ines Sequeira, Kathryn Simpson, Fiona Thistlethwaite, Darren Treanor, Christopher Twelves, Naveen Vasudev, Brandon Witcher
Journal: Cancer Discovery (2025)

Summary: Immunotherapy has revolutionized survival outcomes for many patients diagnosed with cancer. However, biomarkers that can reliably distinguish treatment responders from nonresponders, predict potential life-threatening and life-changing drug-induced toxicities, or rationalize treatment choices are still lacking. In response to this unmet clinical need, we introduce Multiomic ANalysis of Immunotherapy Features Evidencing Success and Toxicity, a tumor type–agnostic platform to provide deep profiling of patients receiving immunotherapy that will enable integrative identification of biomarkers and discovery of novel targets using artificial intelligence and machine learning.
Correction: Alternative Lengthening of Telomeres in Cancer Confers a Vulnerability to Reactivation of p53 Function
Authors: Shawn J. Macha, Balakrishna Koneru, Trevor A. Burrow, Charles Zhu, Dzmitry Savitski, Rakshandra L. Rahman, Catherine A. Ronaghan, Jonas Nance, Kristyn McCoy, Cody Eslinger, C. Patrick Reynolds
Journal: Cancer Research (2025)
Launching SMART 3D Cancer Models
Authors: Sam Ernst, Olivier De Wever
Journal: Cancer Research (2025)

The tumor microenvironment plays a crucial role in shaping the tumor phenotype, yet replicating its complexity in vitro remains challenging. Traditional two-dimensional culture models lack physiologic relevance, and three-dimensional models often fail to fully capture native extracellular matrix (ECM) composition and cellular heterogeneity. In this issue of Cancer Research, Buckenmeyer and colleagues bridged this gap by integrating decellularized porcine-derived small intestinal submucosa ECM into monocellular spheroids, resulting in the formation of “MatriSpheres” with in vivo–like cancer cell heterogeneity. Although small intestinal submucosa ECM proved to be beneficial, several routes remain unexplored, such as incorporating other cell types (immune cells and cancer-associated fibroblasts) or species-, organ- or pathology-specific ECM or leveraging patient-derived tumor material. Pursuing these avenues of investigation to further develop Self-Matrix-Assembly to Recapitulate a Tumor (SMART) three-dimensional models could provide a powerful tool for cancer research, drug discovery, and personalized medicine. See related article by Buckenmeyer et al., p. 1577
Prenatal Chemotherapy and Its Impact on the Genome of Fetal Hematopoiesis
Authors: Ken Furudate, Koichi Takahashi
Journal: Cancer Discovery (2025)

Summary: The genotoxic impact of cancer chemotherapy administered during pregnancy on neonatal hematopoietic cells remains largely unknown. In this study, Struys and colleagues demonstrate that prenatal chemotherapy exposure leads to an increased somatic mutational burden in neonatal hematopoietic stem and progenitor cells, characterized by distinct mutational signatures, revealing a previously unrecognized consequence of in utero chemotherapy on fetal hematopoiesis and underscoring the need for further research to assess its long-term implications and potential risks. See related article by Struys et al., p. 903
Correction: SCFFBXW7/GSK3β-Mediated GFI1 Degradation Suppresses Proliferation of Gastric Cancer Cells
Authors: Xiaoling Kuai, Long Li, Ran Chen, Kangjunjie Wang, Min Chen, Binghau Cui, Yuxue Zhang, Junqiang Li, Hongwen Zhu, Hu Zhou, Jianfei Huang, Jun Qin, Zhiwei Wang, Wenyi Wei, Daming Gao
Journal: Cancer Research (2025)
TIER-LOC: Visual Query-based Video Clip Localization in fetal ultrasound videos with a multi-tier transformer
Authors: Divyanshu Mishra, Pramit Saha, He Zhao, Netzahualcoyotl Hernandez-Cruz, Olga Patey, Aris T Papageorghiou, J Alison Noble
Journal: Medical Image Analysis (2025)
Targeting pyroptosis for cancer immunotherapy: mechanistic insights and clinical perspectives
Authors: Chen Huang, Jiayi Li, Ruiyan Wu, Yangqian Li, Chenliang Zhang
Journal: Molecular Cancer (2025)

Pyroptosis is a distinct form of programmed cell death characterized by the rupture of the cell membrane and robust inflammatory responses. Increasing evidence suggests that pyroptosis significantly affects the tumor microenvironment and antitumor immunity by releasing damage-associated molecular patterns (DAMPs) and pro-inflammatory mediators, thereby establishing it as a pivotal target in cancer immunotherapy. This review thoroughly explores the molecular mechanisms underlying pyroptosis, with a particular focus on inflammasome activation and the gasdermin family of proteins (GSDMs). It examines the role of pyroptotic cell death in reshaping the tumor immune microenvironment (TIME) involving both tumor and immune cells, and discusses recent advancements in targeting pyroptotic pathways through therapeutic strategies such as small molecule modulators, engineered nanocarriers, and combinatory treatments with immune checkpoint inhibitors. We also review recent advances and future directions in targeting pyroptosis to enhance tumor immunotherapy with immune checkpoint inhibitors, adoptive cell therapy, and tumor vaccines. This study suggested that targeting pyroptosis offers a promising avenue to amplify antitumor immune responses and surmount resistance to existing immunotherapies, potentially leading to more efficacious cancer treatments.
Lymph node macrophage-targeted interferon alpha boosts anticancer immune responses by regulating CD169-positive phenotype of macrophages
Authors: Ryo Fukuda, Yukio Fujiwara, Hitoshi Maeda, Cheng Pan, Yuki Minayoshi, Hiromu Yano, Yuki Mizuta, Mei Takano, Rin Yamada, Yoichi Saito, Kenshiro Hirata, Shuhei Imoto, Keishi Yamasaki, Kentaro Oniki, Junji Saruwatari, Masaki Otagiri, Hiroshi Watanabe, Yoshihiro Komohara, Toru Maruyama
Journal: Molecular Cancer (2025)

Abstract Background CD169 + macrophages in lymph nodes (LNs) activate cytotoxic T lymphocytes (CTLs), which play a crucial role in anticancer immunity, through antigen presentation and co-stimulation by CD169. Interferon alpha (IFNα) is capable of inducing the CD169 + phenotype of macrophages; however, its clinical applications have been hindered by pharmacokinetic limitations—low LN distribution and an inability to target macrophages. To overcome these issues, this study genetically fused mouse IFNα (mIFNα) with mannosylated mouse serum albumin (Man-MSA), and investigated the antitumor effects of the hybrid protein (Man-MSA-mIFNα) or its add-on effects with programmed death-ligand 1 (PD-L1) blockade. Methods To confirm the possibility of CD169 + macrophage-mediated T cell priming, positional information about individual immune cells in LNs of cancer patients was obtained. Traits of Man-MSA-mIFNα, which was prepared using Pichia pastoris to form the high-mannose structure, were characterized by several physicochemical methods. To evaluate the lymphatic drainage of Man-MSA-mIFNα, radioiodine or Cy5-labeled Man-MSA-mIFNα was subcutaneously administered in mice, and then the radioactivity or fluorescence in LNs was analyzed. CD169-diphtheria toxin (DT) receptor (CD169-DTR) mice in which LN CD169 + macrophages can be depleted by DT injection were used to verify whether the antitumor effect of Man-MSA-mIFNα is dependent on LN CD169 + macrophages. Results Multiplex tissue imaging predicted close proximity of CD169 + macrophages and T cells and positive correlation between the number of CD169 + macrophages and T cells in neighborhoods in LNs of cancer patients. Physicochemical analyses showed that Man-MSA-mIFNα was formed from the fusion of the intact Man-MSA and mIFNα. Man-MSA-mIFNα efficiently induced the CD169 + phenotype of macrophages by its high LN distribution and macrophage-targeting capability, and significantly exerted antitumor activity through CD8 + T cell activation in the LNs, whereas its antitumor effects were canceled in CD169-DTR mice. Finally, combination therapy with PD-L1 blockade markedly suppressed tumor growth in MB49-bearing mice, which exhibit resistance to PD-L1 blockade monotherapy. Conclusions The present study successfully designed and developed Man-MSA-mIFNα, which efficiently induces the CD169 + phenotype in LN macrophages, contributing to the antitumor immunity. The findings suggest that our novel strategy targeting CD169⁺ macrophages could be a promising immunotherapy for cancer patients who are unresponsive to immune checkpoint inhibitors. Graphical Abstract
Post-diagnosis dietary and lifestyle factors and mortality outcomes among colorectal cancer patients: a meta-analysis
Authors: Qiao-Yi Chen, Nana Keum, Edward L Giovannucci
Journal: JNCI Journal of the National Cancer Institute (2025)

Abstract Background While dietary and lifestyle factors are well-studied for colorectal cancer (CRC) prevention, less evidence exists on their impact on CRC survival. Methods PubMed and Embase were searched from inception to September 2024. Summary relative risk (SRR) and 95% confidence interval (CI) were estimated using the DerSimonian-Laird random-effects model. Results Lower all-cause mortality was observed with unprocessed red meat (SRR 0.74, 95%CI 0.57-0.94), whole grains (SRR 0.77, 95%CI 0.66-0.90), coffee (SRR 0.65, 95%CI 0.55-0.77), milk (SRR 0.82, 95%CI 0.71-0.93), low-fat dairy (SRR 0.77, 95%CI 0.64-0.94), total calcium (SRR 0.76, 95%CI 0.61-0.94), alcohol intake under 45 g/day (J-shaped association), and physical activity (SRR 0.55, 95%CI 0.44-0.69). Higher all-cause mortality was observed with refined grains (SRR 1.55, 95%CI 1.03-2.33), high-fat dairy (SRR 1.34, 95%CI 1.05-1.71), smoking (current (SRR 1.49, 95%CI 1.24-1.78), former (SRR 1.18, 95%CI 1.04-1.34)), and television watching (SRR 1.28, 95%CI 1.06-1.55). Risk increased linearly with body mass index (BMI) greater than 27 kg/m2, but also increased towards lower BMI. For CRC-specific mortality, most of the results were largely consistent, with calcium supplement showing an inverse association (SRR 0.66, 95%CI 0.47-0.94). Conclusions Factors related to CRC survival share differences as well as similarities with established factors related to CRC prevention. To optimize CRC survival, CRC patients may be recommended to adopt a diet rich in whole grains, coffee, milk, and dietary calcium; but to avoid excessive alcohol, refined grains, high-fat dairy, sugar sweetened beverage, smoking, and sedentary lifestyle; and to engage in regular physical activity while maintaining a healthy weight.
Latent retinal structural patterns with aging
Authors: Kei Sano, Kota Fukai, Ryo Terauchi, Yuko Furuya, Shoko Nakazawa, Kosuke Sakai, Toru Honda, Yuya Watanabe, Takeshi Hayashi, Toru Nakagawa, Tadashi Nakano, Masayuki Tatemichi
Journal: npj Digital Medicine (2025)

Optical coherence tomography (OCT) is an efficient tool for non-invasively evaluating retinal structures. Retinal thinning changes assessed using OCT are recognized as potential biomarkers for systemic conditions such as Alzheimer's disease, Parkinson's disease, and chronic kidney disease. However, age-related retinal changes remain largely unexplored, complicating the differentiation between physiological and pathological alterations. Here, we introduced a highly granular approach to assess age-related spatial changes in the inner retina using latent retinal archetypes, identifying 36 retinal archetypes of macula and peripapillary sector images from 189,387 OCTs of 22,494 individuals. Subsequently, we evaluated the associations between these archetypes and age; age-related archetypes are characterized by total or superior thinning in the macula sector. Among individuals with myopia, the inferior thinning pattern in the macula ganglion cell-inner plexiform layer was associated with aging. The age-related effects in the peripapillary sector were primarily reflected in the shape of retinal artery trajectories. Overall, latent retinal archetypes would offer new avenues for the effective utilization of retinal biomarkers in age-related diseases.
Low Testosterone in Males and Its Impact on Cardiometabolic and Cardiovascular Disease Risk (A Review Article
Authors: William J Cobb
Journal: Clinical Cardiology and Cardiovascular Interventions (2025)

Testosterone, the primary male sex hormone, plays a crucial role in metabolic and cardiovascular health. Emerging evidence suggests that low testosterone levels in men are associated with increased risk of cardiometabolic diseases, including obesity, type 2 diabetes mellitus (T2DM), metabolic syndrome, and cardiovascular diseases (CVD) (Grossmann, 2011; Saad et al., 2011). This review explores the pathophysiological mechanisms linking low testosterone to these health risks and discusses potential clinical implications and therapeutic interventions.
QRS Dispersion Index During Tilt Test in Patients with Transient Loss of Consciousness
Authors: S. Mehran Hosseini
Journal: Clinical Cardiology and Cardiovascular Interventions (2025)

Objectives: The QRS dispersion index (QRSd) is the difference between the minimum and maximum duration of the QRS complex. QRSd is reported to have prognostic values and is associated with arrhythmias and mortality. There is a lack of information regarding QRSd changes during the tilt test (TT). This study was conducted to determine the QRSd changes during TT in patients with transient loss of consciousness. Methods: This descriptive-analytical study was conducted retrospectively. The QRSd was compared in the three stages of the TT: rest (baseline), tilt, and recovery. Repeated measure ANOVA was used for normally distributed variables; otherwise, Friedman's nonparametric test was used, and Bonferroni's adjusted test was used for pairwise comparisons in subgroups. Results: The mean and standard deviation of QRS complex duration in milliseconds (QRSt) in baseline, tilt, and recovery were 0.105±0.011, 0.099±0.015, and 0.103±0.013 in negative TT and 0.106±0.015, 0.099±0.017, and 0.170±0.103 in positive TT, respectively. There was a significant difference between baseline and tilt in the negative group and between baseline and tilt, and tilt and recovery in the positive group (P&lt;0.05). The mean and standard deviation of QRSd in both groups between baseline, tilt and recovery were 0.035±0.009, 0.033±0.01 and 0.027±0.01 in negative TT and 0.039±0.013, 0.039±0.013 and 0.025±0.009 in positive TT, respectively. A significant difference was found between baseline and recovery in the negative group (P=0.048) and between baseline and recovery, and tilt and recovery in the positive group. (P&lt;0.05). In women with positive TT, the QRSt was significantly different between baseline and tilt (P=0.005). This difference was not observed in men with positive TT. In the positive TT group, the comparison of QRSt and QRSd in sex and age subcategories had significant differences. This finding was not observed in the negative TT group. Conclusions: Patients with positive and negative TT have different QRSd changes. TT-induced QRSd changes may be sex and age- dependent. Hemodynamic-autonomic reflexes during TT are associated with increased inhomogeneity of conduction velocity during ventricular depolarization.
Are Hispanic Youth at Higher Risk for Cardiovascular Disease Due to Lower Levels of High-Density Lipoprotein Cholesterol?
Authors: Gary J. Luckasen
Journal: Clinical Cardiology and Cardiovascular Interventions (2025)

Background/Aim: Low levels of high-density lipoprotein (HDL) cholesterol in childhood are associated with an increased incidence of cardiovascular disease (CVD) in adulthood, making early detection of lipid abnormalities important in identifying CVD risk. Studies have shown differences in adult HDL levels between ethnic groups, suggesting that HDL is lower in Hispanic adults compared to Non-Hispanic White (NHW) adults. Since CVD and obesity are increasing in Hispanic adults disproportionately, studies on childhood risk factors affecting HDL are essential but limited. We hypothesize HDL levels differ between Hispanic and NHW children, with ethnicity and body mass index (BMI) as significant predictors of HDL levels. Materials and Methods: The UCHealth Healthy Hearts and Minds Program in Colorado conducted biometric screenings on elementary, middle, and high school students, with 14,532 voluntary HDL assessments from 8/2019 to 1/2024. ANOVA and multivariate linear regression models were used for statistical analysis. Results: HDL averages for Hispanic and NHW students were 46.2 mg/dL and 47.6 mg/dL, respectively (p-value &lt;0.001). Males students had a general trend of decreasing HDL levels with advancing age while females HDL levels remained relatively constant across grade levels. The effect of BMI resulted in ~0.8 mg/dL per BMI unit increase for both sexes while controlling for BMI showed no significant difference in HDL levels between ethnic groups. However, 41.35% of Hispanic students were overweight/obese compared to 22.53% of NHW students, accounting for the perceived mean differences in HDL. Conclusions: Observed differences in mean HDL levels between Hispanic and NHW students were due to the higher prevalence of overweight/obesity in the Hispanic sample.
Prophylactic Temporary Pacing During Percutaneous Coronary Intervention: Indications, Strategies, and Clinical Implications
Authors: Rohit Mody
Journal: Clinical Cardiology and Cardiovascular Interventions (2025)

Prophylactic temporary pacing is a critical consideration during percutaneous coronary intervention (PCI), particularly in scenarios where bradyarrhythmias or atrioventricular block are likely to complicate the procedure. This review examines the risk factors necessitating temporary pacing, evaluates different pacing techniques, and provides an overview of the associated clinical outcomes. We delve into specific interventions like rotational atherectomy and rheolytic thrombectomy, discussing their potential to induce transient cardiac rhythm disturbances and highlighting strategies to mitigate these risks. Evidence suggests diverse scenarios where prophylactic pacing may be beneficial, including coronary atherectomy and procedures involving severe coronary calcification. The efficacy of alternative pacing methods, such as transcoronary unipolar pacing and the use of specialized coronary guidewires, is also explored. This review underscores the importance of personalized pacing strategies tailored to patient-specific and procedural risk factors to optimize clinical outcomes during PCI.