tbuckley/cabot-search huggingface dataset:
Clinical, Histopathologic, and Molecular Features and Treatment of Multiple Xanthogranuloma in Adults
Authors: Elissa Annabi, Thibault Mahévas, François Chasset, Julien Haroche, Didier Bessis, Nicolas Dupin, Camille Hua, Nicolas Kluger, Abdellatif Tazi, Marie Jachiet, Adèle de Masson, Jean-François Emile, Fanélie Jouenne, Baptiste Louveau, Pierre Sohier, Samia Mourah, Maxime Battistella, Jean-David Bouaziz
Journal: JAMA Dermatology (2025)

This case series describes the characteristics of cutaneous xanthogranuloma among a group of adult patients in France and explores the response profiles of several treatment options.
Meet the author: Hae Kyung Im
Authors: Hae Kyung Im
Journal: Cell Genomics (2025)

Hae Kyung Im's research group focuses on quantitative computational and statistical methods to tackle genomic data analysis and provides methods to translate the vast amount of genomic data for health research. In collaboration with Mengjie Chen's group, also based at the University of Chicago, Im et al. have published their article "scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework" in Cell Genomics. This is a powerful deep learning approach to improve transcriptome-wide association study analysis, and researchers can apply this method to better understand complex disease genomics.
Ethics choices during the Human Genome Project reflected their policy world, not ours
Authors: Jonathan E LoTempio, Christopher R Donohue, Jonathan D Moreno, Robert Cook-Deegan
Journal: Cell Genomics (2025)

Since human genomic data produced in the 1990s are still a significant part of the reference genome, decades-old decisions pertinent to the creation of these data persist. Here, we discuss how historical documents illustrate the 1990s policy and legal environment and how they affected ethical choices in the Human Genome Project (HGP). These documents inform current controversies about informed consent and how IRBs review similar protocols today. Finally, we discuss how this informs active work in large reference pangenome efforts.
Rarely Seen, Highly Significant: Aberrant Distal Esophageal Artery in TARE Treatments
Authors: Ismail Dilek, Alaaddin Nayman, Hasan Onner
Journal: Clinical Nuclear Medicine (2025)

Transarterial radioembolization (TARE) is a 2-stage procedure involving a simulation phase and a treatment phase. The initial phase aims to define hepatic arterial anatomy, tumor-feeding vessels, and variations, and to perform technical simulation for the treatment phase. The treatment phase involves the administration of Yttrium-90 (Y-90)-loaded microspheres. This report presents a 60-year-old man﻿ with cholangiocarcinoma, exhibiting a rare variation of a distal esophageal artery originating from the hepatic artery, detected using contrast-enhanced Cone-Beam CT during the simulation phase. SPECT after 99m Tc MAA injection confirmed extrahepatic accumulation in the distal esophagus and gastric cardia.
Total Metabolic Tumor Volume Is a Strong Independent Prognostic Factor in Follicular Lymphomas: Results From a Sub‐Study of the <scp>FOLL12</scp> Trial
Authors: Rexhep Durmo, Stephane Chauvie, Carla Minoia, Fabrizio Bergesio, Federico Fallanca, Simona Peano, Luigi Marcheselli, Antonella Anastasia, Carola Boccomini, Paolo Corradini, Jacopo Olivieri, Luca Arcaini, Federica Cavallo, Adalberto Ibatici, Luca Nassi, Vittoria Tarantino, Antonello Pinto, Caterina Stelitano, Alessandro Pulsoni, Francesca Ricci, Salvatrice Mancuso, Emanuele Cencini, Nicola Di Renzo, Clara Mannarella, Angelo Palmas, Pierluigi Zinzani, Caterina Bocci, Francesca Rossi, Angelo Michele Carella, Massimo Federico, Annibale Versari, Luca Guerra, Stefano Luminari
Journal: American Journal of Hematology (2025)

ABSTRACT Discordant results have been generated regarding the prognostic role of Total Metabolic Tumor Volume (TMTV) in Follicular Lymphoma (FL). The use of prospective data and the adoption of the newly defined standardized SUV4 method for calculating TMTV may generate stronger evidence. We conducted a pre‐planned post hoc analysis of the prospective multicenter randomized phase III FOLL12 trial for newly diagnosed high tumor burden FL (grade 1–3a), which mandated baseline staging with PET. Baseline PET/CT scans were reviewed centrally, and TMTV was calculated using the fixed threshold of SUV4. Kaplan–Meier and Cox regression were used for survival analysis. The primary study endpoint was Progression free Survival (PFS). A total of 689 FL patients were available for TMTV definition. Median TMTV was 161 mL (IQR 50 to 388 mL) and the best cutoff value was set at 180 mL. Patients with high TMTV had a significantly lower 5‐year PFS compared to those with low TMTV: 59% (95% CI, 53–65%) vs. 74% (95% CI, 69–78%) HR 1.61 (95% CI, 1.24–2.09). Prognostic role of TMTV was independent of study arm, chemotherapy regimen, and FLIPI2. Combined with FLIPI‐2, we identified three groups with different 5‐yr PFS rates, with the lowest rates (51%) for patients with high TMTV and high FLIPI2. Combined TMTV and FLIPI model was also prognostic to predict the risk of early progression and of death. Applying the SUV4 standard method pre‐treatment TMTV is confirmed as a strong and independent predictor of PFS in FL patients. Integrating TMTV with FLIPI‐2 improves risk assessment.
Intermuscular adipose tissue and lean muscle mass assessed with MRI in people with chronic back pain in Germany: a retrospective observational study
Authors: Sebastian Ziegelmayer, Hartmut Häntze, Christian Mertens, Felix Busch, Tristan Lemke, Jakob Nikolas Kather, Daniel Truhn, Su Hwan Kim, Benedikt Wiestler, Markus Graf, Avan Kader, Fabian Bamberg, Christopher L. Schlett, Jakob B. Weiss, Jeanette Schulz-Menger, Steffen Ringhof, Elif Can, Tobias Pischon, Thoralf Niendorf, Jacqueline Lammert, Matthias Schulze, Thomas Keil, Annette Peters, Martin Hadamitzky, Marcus R. Makowski, Lisa Adams, Keno Bressem
Journal: The Lancet Regional Health - Europe (2025)
Prognostic value of measurable residual disease (MRD) for venetoclax in combination with hypomethylating agents in patients diagnosed with acute myeloid leukemia: validation of the ELN-2021 MRD recommendations
Authors: Carlos Jimenez-Vicente, Aina Cardus, Sandra Castaño-Diez, Guillermo Ramil, Sara Garcia-Avila, Lucia Gomez-Perez, Daniel Esteban, Iago Arribas, Antonella Lucia Sturla, Monica Lopez-Guerra, Alexandra Martinez-Roca, Albert Cortes-Bullich, Amanda Isabel Perez-Valencia, Ines Zugasti, Ines Monge, Esther Carcelero, Ferran Vall-Llovera, Susana Vives, Jorge Sierra, Josep Nomdedeu, Guadalupe Oñate, Ana Garrido, Marta Pratcorona, Helena Pomares, Montserrat Arnan, Francesca Guijarro, Marina Diaz-Beya, Jordi Esteve
Journal: Blood Cancer Journal (2025)
A quantitative analysis of the use of anonymization in biomedical research
Authors: Thierry Meurers, Karen Otte, Hammam Abu Attieh, Farah Briki, Jérémie Despraz, Mehmed Halilovic, Bayrem Kaabachi, Vladimir Milicevic, Armin Müller, Grigorios Papapostolou, Felix Nikolaus Wirth, Jean Louis Raisaro, Fabian Prasser
Journal: npj Digital Medicine (2025)

Summary Anonymized biomedical data sharing faces several challenges. This systematic review analyzes 1084 PubMed-indexed studies (2018–2022) using anonymized biomedical data to quantify usage trends across geographic, regulatory, and cultural regions to identify effective approaches and inform implementation agendas. We identified a significant yearly increase in such studies with a slope of 2.16 articles per 100,000 when normalized against the total number of PubMed-indexed articles ( p = 0.021). Most studies used data from the US, UK, and Australia (78.2%). This trend remained when normalized by country-specific research output. Cross-border sharing was rare (10.5% of studies). We identified twelve common data sources, primarily in the US (seven) and UK (three), including commercial (seven) and public entities (five). The prevalence of anonymization in the US, UK, and Australia suggests their practices could guide broader adoption. Rare cross-border anonymized data sharing and differences between countries with comparable regulations underscore the need for global standards.
Activity-driven myelin sheath growth is mediated by mGluR5
Authors: Philipp N Braaker, Xuelong Mi, Daniel Soong, Jenea M Bin, Katy Marshall-Phelps, Stephen Bradley, Silvia Benito-Kwiecinski, Julia Meng, Donia Arafa, Claire Richmond, Marcus Keatinge, Guoqiang Yu, Rafael G Almeida, David A Lyons
Journal: Nature Neuroscience (2025)

Abstract Myelination by oligodendrocytes in the central nervous system is influenced by neuronal activity, but the molecular mechanisms by which this occurs have remained unclear. Here we employed pharmacological, genetic, functional imaging and optogenetic-stimulation approaches in zebrafish to assess activity-regulated myelination in vivo. Pharmacological inhibition and activation of metabotropic glutamate receptor 5 (mGluR5) impaired and promoted myelin sheath elongation, respectively, during development, without otherwise affecting the oligodendrocyte lineage. Correspondingly, mGluR5 loss-of-function mutants exhibit impaired myelin growth, while oligodendrocyte-specific mGluR5 gain of function promoted sheath elongation. Functional imaging and optogenetic-stimulation studies revealed that mGluR5 mediates activity-driven high-amplitude Ca 2+ transients in myelin. Furthermore, we found that long-term stimulation of neuronal activity drives myelin sheath elongation in an mGluR5-dependent manner. Together these data identify mGluR5 as a mediator of the influence of neuronal activity on myelination by oligodendrocytes in vivo, opening up opportunities to assess the functional relevance of activity-regulated myelination.
A compact, wireless system for continuous monitoring of breast milk expressed during breastfeeding
Authors: Jihye Kim, Seyong Oh, Raudel Avila, Hee-Sup Shin, Matthew Banet, Jennifer Wicks, Anthony R Banks, Yonggang Huang, Jae-Young Yoo, Daniel T Robinson, Craig F Garfield, John A Rogers
Journal: Nature Biomedical Engineering (2025)
Novel Aortic Dissection Model Links Endothelial Dysfunction and Immune Infiltration
Authors: Kenichi Kimura, Eri Motoyama, Sachiko Kanki, Keiichi Asano, Patrick Sips, Md Al Amin Sheikh, Maria Thea Rane Dela Cruz Clarin, Erna Raja, Mariko Takeda, Ryutaro Ishii, Kazuya Murata, Violette Deleeuw, Laura Muiño Mosquera, Julie De Backer, Seiya Mizuno, Lynn Y. Sakai, Tomoyuki Nakamura, Hiromi Yanagisawa
Journal: Circulation Research (2025)

BACKGROUND: Aortic dissection (AD) is the separation of medial layers of the aorta and is a major cause of death in patients with connective tissue disorders such as Marfan syndrome. However, molecular triggers instigating AD, its temporospatial progression, and how vascular cells in each vessel layer interact and participate in the pathological process remain incompletely understood. To unravel the underlying molecular mechanisms of AD, we generated a spontaneous AD mouse model. METHODS: We incorporated a novel missense variant (p.G234D) in FBN1 , the gene for fibrillin-1, identified in a patient with nonsyndromic familial AD into mice using the CRISPR/Cas9 system. We performed molecular pathological analyses of the aortic lesions by histology, immunofluorescence staining, electron microscopy, synchrotron-based imaging, and single-cell RNA sequencing. Biochemical analysis was performed to examine the binding capacity of mutant human FBN1G234D protein to LTBPs (latent TGFβ [transforming growth factor-beta] binding proteins), and signaling pathways in the mutant aortic wall were examined by the Western blot analysis. RESULTS: Fifty percent of the Fbn1 G234D/G234D mutant mice died within 5 weeks of age from multiple intimomedial tears that expanded longitudinally and progressed to aortic rupture accompanied by massive immune cell infiltration. Fbn1 G234D/G234D endothelial cells exhibited altered mechanosensing with loss of parallel alignment to blood flow and upregulation of VCAM-1 and ICAM-1 as early as 1 week of age. Single-cell RNA sequencing, validated by immunostaining, revealed a cluster of monocyte/macrophage predominantly in the intima at 3 weeks of age before the dissection, and the second cluster of macrophages increased during the progression of intimomedial tears, exhibiting strong CCR2+ and both M1- and M2-like features. Consistently, upregulation of MMP2/9 was observed. Biochemically, FBN1G234D lost the ability to bind to LTBP-1, -2, and -4, resulting in the downregulation of TGFβ signaling in the aortic wall. CONCLUSIONS: We show that interactions involving endothelial cells and macrophages/monocytes in the intima, where the ECM (extracellular matrix) microenvironment contains reduced TGFβ signaling, contribute to the initiation of AD. Our novel AD mouse model provides a unique opportunity to identify target molecules involved in the intimomedial tears that can be utilized for the development of therapeutic strategies.
New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis
Authors: Bingchao Wu, Dan Luo, Yuesen Yue, Haidong Yan, Min He, Xixi Ma, Bingyu Zhao, Bin Xu, Jie Zhu, Jing Wang, Jiyuan Jia, Min Sun, Zheni Xie, Xiaoshan Wang, Linkai Huang
Journal: Genome biology (2025)
Aging and injury drive neuronal senescence in the dorsal root ganglia
Authors: Lauren J Donovan, Chelsie L Brewer, Sabrina F Bond, Alexander M Laslavic, Aleishai Pena Lopez, Laura Colman, Claire E Jordan, Linus H Hansen, Oscar C González, Akshay Pujari, Luis de Lecea, Marco Quarta, Julie A Kauer, Vivianne L Tawfik
Journal: Nature Neuroscience (2025)
Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma
Authors: Melissa Barroux, Jacob Househam, Eszter Lakatos, Tahel Ronel, Ann-Marie Baker, Henrike Salié, Maximilian Mossner, Kane Smith, Chris Kimberley, Salpie Nowinski, Alison Berner, Vinaya Gunasri, Martin Borgmann, Sven Liffers, Marnix Jansen, Giulio Caravagna, Katja Steiger, Julia Slotta-Huspenina, Wilko Weichert, Luis Zapata, Eleftheria Giota, Sylvie Lorenzen, Markus Alberstmeier, Benny Chain, Helmut Friess, Bertram Bengsch, Roland M Schmid, Jens T Siveke, Michael Quante, Trevor A Graham
Journal: Nature Cancer (2025)
Ecological Affordances across Life Stages: An Affordance Management Framework
Authors: Ahra Ko, Steven L Neuberg
Journal: Behavioral and Brain Sciences (2025)

Abstract Although the interaction between humans and their environments is central to psychological science, its dynamics throughout the lifespan remain unexplored. We consider how ecological affordances —the opportunities and threats an environment poses for one’s goal achievement—can be differently perceived across developmental life stages. Integrating affordance-management and life-history perspectives, we propose that individuals perceive and respond to ecological affordances based on their prioritized goals, which shift systematically as they progress through life stages. The same environment can be perceived as posing an opportunity at one life stage, but as posing a threat or being irrelevant at other stages with different goal priorities. To illustrate the value of this framework, we focus on three environmental dimensions tied to recurring adaptive challenges in human history: genetic relatedness, physical violence, and sex-age ratio. We examine how individuals perceive and navigate ecological affordances across three key life stages—childhood, mating, and parenting—through multiple strategies: (a) recalibrating cognitive and affective attunement to relevant cues, (b) adjusting psychological and behavioral strategies, and (c) reconstructing their environments at various levels. By bridging social, developmental, and cognitive psychology with behavioral ecology and evolutionary biology, this framework advances our understanding of human-environment interactions by (a) challenging the assumption that environmental effects are static, (b) generating precise hypotheses about psychological and behavioral patterns, enabling systematic and holistic investigation, and (c) underscoring the potential for lifelong flexibility in ecological navigation.
Aligning AI principles and healthcare delivery organization best practices to navigate the shifting regulatory landscape
Authors: Alifia Hasan, Noah Prizant, Jee Young Kim, Shreya Rao, David Vidal, Keo Shaw, Danny Tobey, Alexandra Valladares, Shira Zilberstein, Manesh Patel, Suresh Balu, Mark Sendak, Mark Lifson
Journal: npj Digital Medicine (2025)
Development and validation of a deep learning model for diagnosing neuropathic corneal pain via in vivo confocal microscopy
Authors: Neslihan Dilruba Koseoglu, Eric Chen, Rudraksh Tuwani, Benjamin Kompa, Stephanie M Cox, M Cuneyt Ozmen, Mina Massaro-Giordano, Andrew L Beam, Pedram Hamrah
Journal: npj Digital Medicine (2025)

Neuropathic corneal pain (NCP) is an underdiagnosed ocular disorder caused by aberrant nociception and hypersensitivity of corneal nerves, often resulting in chronic pain and discomfort even in the absence of noxious stimuli. Recently, microneuromas (aberrant growth and swelling of the corneal nerve endings) detected using in vivo confocal microscopy (IVCM) have emerged as a promising biomarker for NCP. However, this process is time-intensive and error-prone, limiting its clinical use and availability. In this work, we present a new NCP screening system based on a deep learning model trained to detect microneuromas using a multisite dataset with a combined total of 103,168 IVCM images. Our model showed excellent discriminative ability detecting microneuromas (AuROC: 0.97) and the ability to generalize to data from a new institution (AuROC: 0.90). Additionally, our pipeline provides an uncertainty quantification mechanism that allows it to communicate when its predictions are reliable, further increasing its clinical relevance.
Engineered Chitosan‐Derived Nanocarrier for Efficient siRNA Delivery to Peripheral and Central Neurons
Authors: Ana P. Spencer, Adriana Vilaça, Miguel Xavier, Rafael Santos, Ariel Ionescu, María Lázaro, Victoria Leiro, Eran Perlson, Sofia C. Guimarães, Ben M. Maoz, Ana P. Pêgo
Journal: Advanced Healthcare Materials (2025)

Abstract Gene therapy using small interfering RNA (siRNA) holds promise for treating neurological disorders by silencing specific genes, like the phosphatase and tensin homolog ( PTEN ) gene, which restricts axonal growth. Effective siRNA delivery to neurons, however, poses challenges due to premature nucleic acid degradation and unspecific delivery. Chitosan‐based delivery systems, noted for their biocompatibility, face limitations such as low transfection efficiency and lack of neurotropism. Building on the previous successes with neuron‐targeted DNA delivery using chitosan, a novel approach for siRNA delivery aimed at PTEN downregulation is proposed. This involves using thiolated trimethyl chitosan (TMCSH)–based siRNA nanoparticles functionalized with the neurotropic C‐terminal fragment of the tetanus neurotoxin heavy chain (HC) for efficient delivery to peripheral and central neurons. These polyplexes demonstrate suitable physicochemical properties, biocompatibility, and no adverse effects on neuronal electrophysiology. Diverse neuronal models, including 3D ex vivo cultures and microfluidics, confirm the polyplexes’ efficiency and neurospecificity. HC‐functionalization significantly enhances neuronal binding, and live cell imaging reveals fivefold faster retrograde transport along axons. Furthermore, siRNA delivery targeting PTEN promoted axonal outgrowth in embryonic cortical neurons. In conclusion, the proposed polyplexes represent a promising platform for neuronal siRNA delivery, offering potential for clinical translation and therapeutic applications.
A Biocompatible, Magnetic‐Responsive Shape Memory Silicone Composite for Active Flow Controlling Valve
Authors: Yuchao Wu, Cheng Qiu, Congshan Mao, Wen Zhao, Alireza Mahjoubnia, Sonia Norouzi Esfahany, Aaron Webel, Shi‐You Chen, Yue Jin, Jian Lin
Journal: Advanced Healthcare Materials (2025)

Abstract A magnetically responsive shape memory silicone composite is developed for fabricating an active valve in biomedical fluidic systems. The composite consists of magnetic neodymium–iron–boron (NdFeB) microparticles (MPs) and poly(glycerol‐dodecanoate) (PGD) MPs in silicone. PGD has tunable transition temperatures ( T g ) of 42—50 °C, empowering shape programmability to the composite, while the NdFeB MPs make the composite responsive to a magnetic field gradient. The composite can be reprogrammed into a compact form for ease delivery and subsequently recovered to its original shape stimulated by external heat that is generated by an oscillation magnetic field ( B h ) applied to the NdFeB MPs. Because of the dramatically reduced stiffness above T g , the valve shape can be actuated to a different one by exerted torques induced by a simultaneously applied actuation magnetic field ( B a ). By tuning the magnetic density and direction of B a , the shape changing extent, e.g., bending angles, which determine the fluid flow resistance, can be modulated. This works provides a proof‐of‐concept for a programmable, remotely controlled valve for fluid regulation. The adaptability, biocompatibility, and capability for minimally invasive delivery highlight the potential of the valve for applications in drug delivery, embolization, and flow management in blood vessels and eyes.
Immunogenicity and efficacy of subcutaneous infliximab monotherapy versus combination therapy in IBD: a systematic review and meta-analysis
Authors: Suzanne I Anjie, Krisztina B Gecse, Chiara M Meloni, Andrés Vidal-Itriago, Mark Löwenberg, Geert R D'Haens
Journal: Clinical Gastroenterology and Hepatology (2025)
Piezoelectric Amplification of Cascade Enzymatic Catalysis and Nanomotor Propulsion for Synergistic Electrodynamic‐Starvation Tumor Therapy
Authors: Zhanlin Zhang, Kun Wei, Jie Meng, Junwu Wei, Yupeng Su, Huan Tan, Xiaohong Li
Journal: Advanced Healthcare Materials (2025)

Abstract Piezoelectrodynamic therapy (PEDT) is compromised by hypoxia dilemma of tumors, while starvation therapy is constrained by insufficient enzyme activities. To address these challenges, Janus piezoelectric nanoparticles (NPs) are proposed to spatially immobilize glucose oxidase (GOx) and catalase (CAT), enabling piezoelectric potential‐amplified enzyme activities and synergistic PEDT‐starvation tumor therapy. Here hollow barium titanate (hBT) NPs are synthesized using SiO 2 templates, followed by partial Au deposition via the Pickering emulsion‐masking method to create Janus hBT@Au NPs, which are then conjugated with GOx and CAT on opposing sides to yield C‐hBT@Au‐G NPs. The hollow structure of hBT enhances flexibility and deformation under ultrasonication, while Schottky heterojunctions with Au layers promote charge carrier transfer, amplifying piezoelectric effects and free electron transfer to boost GOx activities. Piezoelectric field‐enhances selective tumor cell internalization of NPs and PEDT generation of reactive oxygen species (ROS), coupled with self‐propagated GOx/CAT cascades, intensify tumor cytotoxicities and deplete intracellular adenosine triphosphate. The Janus architecture, ultrasonic cavitation, and O 2 generation collaboratively drive robust propulsion for efficient NP accumulation and deep ROS penetration into tumor tissues, thereby achieving full tumor suppression with negligible systemic toxicity. This design overcomes delivery barriers of tumor accumulation, intratumoral penetration, and cellular uptake and synergizes PEDT‐starvation tumor therapy.
Insulin-like Growth Factor-1 reflects liver disease stage and improves prediction of liver-related mortality
Authors: Carolin V Schneider, Stefan Gross, Sriram Balasubramani, Petra Tomanová, Christina Schrader, Malin Fromme, Mattias Mandorfer, Nurdan Guldiken, Kai Markus Schneider, Georg Lurje, Anastasia Raptis, Helen Ye Rim Huang, Sebastian Mueller, Thomas Reiberger, Pierre Nahon, Quentin M Anstee, Ann K Daly, Olivier Govaere, Pavel Strnad
Journal: Clinical Gastroenterology and Hepatology (2025)