tbuckley/cabot-search huggingface dataset:
Clinical-genomic profiling of MDS to inform allo-HSCT:Recommendations from an international panel on behalf of the EBMT
Authors: Carmelo Gurnari, Marie Robin, Lionel Adès, Mahmoud Aljurf, Antonio M Almeida, Fernando Barroso Duarte, Elsa Bernard, Corey S. Cutler, Matteo Giovanni Della Porta, Theo M de Witte, Amy E. DeZern, Joanna Drozd-Sokolowska, Eric J Duncavage, Pierre Fenaux, Nico Gagelmann, Guillermo Garcia-Manero, Claudia Haferlach, Torsten Haferlach, Robert P. Hasserjian, Eva S Hellstrom-Lindberg, Meagan A Jacoby, Austin G Kulasekararaj, R. Coleman Lindsley, Jaroslaw P. Maciejewski, Hideki Makishima, Luca Malcovati, Moshe Mittelman, Anders Eivind Myhre, Seishi Ogawa, Francesco Onida, Elli Papaemmanuil, Jakob R Passweg, Uwe Platzbecker, Lisa Pleyer, Kavita Raj, Valeria Santini, Anna Sureda, Magnus Tobiasson, Maria Teresa Voso, Ibrahim Yakoub-Agha, Amer M. Zeidan, Matthew J Walter, Nicolaus Kröger, Donal P McLornan, Mario Cazzola
Journal: Blood (2025)
Immunoactinopathies revisited: Understanding clinical manifestations and biological pathways
Authors: Fleur Hiensch, Loic Dupre, Elisabeth Salzer
Journal: Blood (2025)

Immune cell functionality is highly dependent on the actin cytoskeleton. The actin cytoskeleton is regulated by a complex molecular machinery, involving multiple genes. Mutations in these genes can cause inborn errors of immunity, also termed immunoactinopathies, of which Wiskott Aldrich Syndrome is the best-characterized entity. At present, mutations in 23 genes can be considered causative of immunoactinopathies. Immunoactinopathies are rare disease entities with complex combinations of clinical manifestations, including immunodeficiency, immune dysregulation, malignancies, atopy, thrombocytopenia and bleeding, skin involvement or congenital defects. Prompt diagnosis is of crucial importance, as HSCT in an early phase can offer cure and prevent further complications. This review provides a detailed summary of the clinical experience with immunoactinopathies so far, elaborates on the most distinguishing features among immunoactinopathies by providing a clinical categorization, and links this information to the biological pathways that are involved. This information may be of help for clinicians to diagnose patients and eventually improve patient care.
Reply to: Enfortumab Vedotin: A Promising Therapy for Head and Neck Cancer With Potential Links to Human Papillomavirus
Authors: Paul L. Swiecicki, Emrullah Yilmaz, Ari Joseph Rosenberg, Takao Fujisawa, Justine Yang Bruce, Changting Meng, Michele Wozniak, Yongyun Zhao, Michael Mihm, Jason Kaplan, Seema Gorla, Jessica L. Geiger
Journal: Journal of Clinical Oncology (2025)
Intravital imaging of pulmonary lymphatics in inflammation and metastatic cancer
Authors: Simon J. Cleary, Longhui Qiu, Yurim Seo, Peter Baluk, Dan Liu, Nina K. Serwas, Catherine A. Taylor, Dongliang Zhang, Jason G. Cyster, Donald M. McDonald, Matthew F. Krummel, Mark R. Looney
Journal: The Journal of Experimental Medicine (2025)

Intravital microscopy has enabled the study of immune dynamics in the pulmonary microvasculature, but many key events remain unseen because they occur in deeper lung regions. We therefore developed a technique for stabilized intravital imaging of bronchovascular cuffs and collecting lymphatics surrounding pulmonary veins in mice. Intravital imaging of pulmonary lymphatics revealed ventilation dependence of steady-state lung lymph flow and ventilation-independent lymph flow during inflammation. We imaged the rapid exodus of migratory dendritic cells through lung lymphatics following inflammation and measured effects of pharmacologic and genetic interventions targeting chemokine signaling. Intravital imaging also captured lymphatic immune surveillance of lung-metastatic cancers and lymphatic metastasis of cancer cells. To our knowledge, this is the first imaging of lymph flow and leukocyte migration through intact pulmonary lymphatics. This approach will enable studies of protective and maladaptive processes unfolding within the lungs and in other previously inaccessible locations.
Cold snare endoscopic mucosal resection versus standard hot technique for large flat non-pedunculated colonic lesions: Results of the CS-EMR 2019 randomized controlled trial
Authors: Oscar Nogales, Carlos Carbonell-Blanco, Sheyla Montori Pina, Maria Pellisé, Juan Martínez-Sempere, Fausto Riu Pons, Carolina Mangas-Sanjuan, Maria Daca-Alvarez, Hugo Uchima, Javier Aranda Hernández, Alberto Alvarez Delgado, Enrique Rodriguez de Santiago, Jose Santiago Garcia, Angel Cañete Ruiz, Pablo Miranda Garcia, Henar Nuñez Rodriguez, Alberto Herreros de Tejada, Eduardo Valdivielso Cortázar, Pedro De María, David Busquets, Alfonso Elosua, Liseth Rivero-Sánchez, Maria Lopez-Ibanez, Marco Antonio Alvarez-Gonzalez, Eduardo Albéniz
Journal: Endoscopy (2025)

Backgrounds and Aims: Cold snare EMR (CS-EMR) in large flat non-pedunculated colonic lesions (LFNPCLs) is an alternative to the standard EMR procedure with a better safety profile, but scientific evidence on its efficacy is unavailable. Primary objective: To compare the recurrence rate between the two techniques at six months. Secondary objectives: comparison of the safety profile and several procedure-related outcomes. Patients and methods: This was a noninferiority, multicentric, open-label, randomized controlled trial of consecutive large (&gt;20 mm) LFNPCLs without suspicious features of submucosal invasion. Results: A total of 229 patients were randomized to receive CS-EMR (n=115) or EMR (n=114), with adenomas (76.4%) and a median size of 25 mm. The trial was stopped early by clinical consensus according to a safety monitoring board. At first surveillance colonoscopy (n=220) the recurrence rate (RR) was significantly greater in the CS-EMR group than in the EMR group: 33.0% vs. 16.2% (p=0.004) and 34.7% vs. 14.8% (p=0.001) in the ITT and PP analyses, respectively. According to the subgroup analysis, the RR was significantly greater for LFNPCLs &gt;30 mm (18.2% EMR vs. 43.1% CS-EMR). There was no difference in the rate of adverse events. The use of clips was more common in the EMR group (2.21 vs. 1.30). Conclusions: Compared with the conventional hot technique, the RR of LFNPCL after CS-EMR was significantly greater. A similar safety profile was found between groups.
Has racism in medicine improved since 2020?
Authors: Mala Rao, Victor Adebowale
Journal: BMJ (2025)

Five years on from The BMJ's special issue on racism in medicine—and after a global pandemic—has anything improved in the NHS and UK medicine? <b>Mala Rao</b> sees shoots of hope, but <b>Victor Adebowale</b> argues that any progress still has a long way to go
Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential
Authors: Cynthia O. Akagbosu, Kathryn E. McCauley, Sivaranjani Namasivayam, Hector N. Romero-Soto, Wade O’Brien, Mickayla Bacorn, Eric Bohrnsen, Benjamin Schwarz, Shreni Mistry, Andrew S. Burns, P. Juliana Perez-Chaparro, Qing Chen, Phoebe LaPoint, Anal Patel, Lauren E. Krausfeldt, Poorani Subramanian, Brian A. Sellers, Foo Cheung, Richard Apps, Iyadh Douagi, Shira Levy, Evan P. Nadler, Suchitra K. Hourigan
Journal: Gut Microbes (2025)

Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown. Here, we show that adolescents exhibit significant gut microbiome and metabolome shifts several months after laparoscopic vertical sleeve gastrectomy (VSG), with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited a potentially inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG. We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.
A Theoretical Approach in Applying High-Frequency Acoustic and Elasticity Microscopy to Assess Cells and Tissues
Authors: Frank Winterroth, Jing Wang, Onno Wink, Bart Carelsen, Jeremy Dahl, Avnesh S. Thakor
Journal: Annual Review of Biomedical Engineering (2025)

Medical ultrasound is a diagnostic imaging modality used for visualizing internal organs; the frequencies typically used are 2–10 MHz. Scanning acoustic microscopy (SAM) is a form of ultrasound where frequencies typically exceed 50 MHz. Increasing the acoustic frequency increases the specimen's spatial resolution but reduces the imaging depth. The advantages of using SAM over conventional light and electron microscopy include the ability to image cells and tissues without any preparation that could kill or alter them, providing a more accurate representation of the specimen. After scanning the specimen, acoustic signals are merged into an image on the basis of changes in the impedance mismatch between the immersion fluid and the specimens. The acoustic parameters determining the image quality are absorption and scattering. Surface scans can assess surface characteristics of the specimen. SAM is also capable of elastography, that is, studying elastic properties to discern differences between healthy and affected tissues. SAM has significant potential for detection/analysis in research and clinical studies.
Replay and Ripples in Humans
Authors: Jinbo Zhang, Jianxin Ou, Yunzhe Liu
Journal: Annual Review of Neuroscience (2025)

During rest and sleep, the brain processes information through replay, reactivating neural patterns linked to past events and facilitating the exploration of potential future scenarios. This review summarizes recent advances in understanding human replay and its biomarker, sharp-wave ripples (SPW-Rs). We explore detection methods and connect insights from rodent studies. The review highlights unique aspects of human replay in internal cognition such as prioritizing past experiences for offline learning, generating hypothesized solutions to current problems, and factorizing structural representations for future generalization. We also examine the characteristics of SPW-Rs in humans, including their distribution along the hippocampal longitudinal axis, their widespread brain activations, and their influence on internal cognitive processes. Finally, we emphasize the need for improved methodologies and technologies to advance our understanding of cognitive processes during rest and sleep.
The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification
Authors: Lingxia Qiao, Ali Khalilimeybodi, Nathaniel J. Linden-Santangeli, Padmini Rangamani
Journal: Annual Review of Biomedical Engineering (2025)

Understanding interaction mechanisms within cells, tissues, and organisms is crucial for driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating such biological systems. Building on experiments, mechanistic models are widely used to describe small-scale intracellular networks. The development of sequencing techniques and computational tools has recently enabled multiscale models. Combining such larger scale network modeling with mechanistic modeling provides us with an opportunity to reveal previously unknown disease mechanisms and pharmacological interventions. Here, we review systems biology models from mechanistic models to multiscale models that integrate multiple layers of cellular networks and discuss how they can be used to shed light on disease states and even wellness-related states. Additionally, we introduce several methods that increase the certainty and accuracy of model predictions. Thus, combining mechanistic models with emerging mathematical and computational techniques can provide us with increasingly powerful tools to understand disease states and inspire drug discoveries.
Replicating Host–Microbiome Interactions: Harnessing Organ-on-a-Chip and Organoid Technologies to Model Vaginal and Lung Physiology
Authors: Jade Coxon, Emily Linder, Caden Sweet, Scott Magness, Leopold Green
Journal: Annual Review of Biomedical Engineering (2025)

Organ-on-a-chip (OOC) and organoid technologies are at the forefront of developing sophisticated in vitro systems that replicate complex host–microbiome interactions, including those associated with vaginal health and lung infection. We explore how these technologies provide insights into host–microbiome and host–pathogen interactions and the associated immune responses. Integrating omics data and high-resolution imaging in analyzing these models enhances our understanding of host–microbiome interactions' temporal and spatial aspects, paving the way for new diagnostic and treatment strategies. This review underscores the potential of OOC and organoid technologies in elucidating the complexities of vaginal health and lung disease, which have received less attention than other organ systems in recent organoid and OCC studies. Yet, each system presents notable characteristics, rendering them ideal candidates for these designs. Additionally, this review describes the key factors associated with each organ system and how to choose the technology setup to replicate human physiology.
Therapeutic Ultrasound for Multimodal Cancer Treatment: A Spotlight on Breast Cancer
Authors: Zehra E.F. Demir, Natasha D. Sheybani
Journal: Annual Review of Biomedical Engineering (2025)

Cancer remains a leading cause of mortality worldwide, and the demand for improved efficacy, precision, and safety of management options has never been greater. Focused ultrasound (FUS) is a rapidly emerging strategy for nonionizing, noninvasive intervention that holds promise for the multimodal treatment of solid cancers. Owing to its versatile array of bioeffects, this technology is now being evaluated across preclinical and clinical oncology trials for tumor ablation, therapeutic delivery, radiosensitization, sonodynamic therapy, and enhancement of tumor-specific immune responses. Given the breadth of this burgeoning domain, this review places a spotlight on recent advancements in breast cancer care to exemplify the multifaceted role of FUS technology for oncology indications—outlining physical principles of FUS-mediated thermal and mechanical bioeffects, giving an overview of results from recent preclinical and clinical studies investigating FUS with and without adjunct therapeutics in primary or disseminated breast cancer settings, and offering perspectives on the future of the field.
Anesthetics as Treatments for Depression: Clinical Insights and Underlying Mechanisms
Authors: Macauley Smith Breault, Sirma Orguc, Ohyoon Kwon, Gloria H. Kang, Bryan Tseng, David R. Schreier, Emery N. Brown
Journal: Annual Review of Neuroscience (2025)

Major depressive disorder and treatment-resistant depression are significant worldwide health problems that need new therapies. The success of the anesthetic ketamine as an antidepressant is well known. It is less widely known that several other anesthetic agents have also shown antidepressant effects. These include nitrous oxide, propofol, isoflurane, sevoflurane, dexmedetomidine, and xenon. We review clinical and basic science investigations that have studied the therapeutic value of these anesthetics for treating depression. We propose potential neurophysiological mechanisms underlying the antidepressant effects of anesthetics by combining our understanding of how anesthetics modulate brain dynamics to alter arousal states, current theories of depression pathophysiology, and findings from other depression treatment modalities.
Harnessing Implementation Science in Clinical Psychology: Past, Present, and Future
Authors: Rinad S. Beidas, Meredith Boyd, Elizabeth Casline, Kelli Scott, Zabin Patel-Syed, Chynna Mills, Brian Mustanski, Simone Schriger, Faith Summersett Williams, Claire Waller, Sarah A. Helseth, Sara J. Becker
Journal: Annual Review of Clinical Psychology (2025)

Implementation science aspires to equitably accelerate the uptake of clinical research into practice to improve population health. The focus of implementation science includes individual behavior change mechanisms that are similar to those that drive the field of clinical psychology. For this reason, clinical psychologists are well-suited to take up implementation science methods in pursuit of improving the quality of behavioral health care. To do so, clinical psychologists must expand beyond individual behavior change to include a focus on organizations and systems. In this review, we reflect on ways that clinical psychologists can lead in the integration of implementation science principles and approaches into clinical psychology research and practice. We discuss the role clinical psychologists play in closing know–do gaps in behavioral health and describe how clinical psychologists can build implementation science competencies. We end with current controversies and opportunities for innovation to further improve the quality of behavioral health care.
A digital heat early warning system for older adults
Authors: Mehak Oberai, Zhiwei Xu, Aaron Bach, Connor Forbes, Ella Jackman, Fergus O’Connor, Isabella Ennever, Sebastian Binnewies, Steven Baker, Shannon Rutherford
Journal: npj Digital Medicine (2025)

Abstract Extreme heat events lead to considerable health burden and are becoming more severe and frequent, calling for the development of effective population-based and individualised heat early warning systems. We developed an individualised heat early warning system and tested it in 78 older adults’ ( ≥ 65 years) homes in Southeast Queensland, Australia. Quantitative and qualitative data from this proof-of-concept testing study showed that the Ethos system performed well on a standard usability scale (mean score of 78 on the System Usability Scale). Following a summer-time use of this early warning system, there were increases in heat preparedness ( P &lt; 0.001, marginal homogeneity tests) but no significant increases in heat health risk perception or the uptake of low-cost cooling measures (e.g., hand/forearm bath, fans). This proof-of-concept research demonstrated the usability of this tailored, actionable, real-time digital heat early warning system, although the effectiveness of the system remains to be evaluated in a robust trial design.
Immunogenic Cuproptosis in Cancer Immunotherapy via an In Situ Cuproptosis-Inducing System
Authors: Jiehan Li, Ge Zhang, Zhao Sun, Meimei Jiang, Guiyun Jia, Hao Liu, Nannan Liu, Liyang Shi, Lingling Zhang, Liming Nie, Yingjie Zhang, Yang Fu
Journal: Biomaterials (2025)
Exploring the Temporal Interplay of Allergic Sensitization and Asthma via Graph and Manifold Analysis
Authors: Alex Cucco, Angela Simpson, Clare Murray, Adnan Custovic, Sara Fontanella
Journal: Journal of Allergy and Clinical Immunology (2025)

The association between allergic sensitization and asthma is well-documented, but its precise role in asthma remains uncertain. Component-resolved diagnostics allows detailed assessment of IgE-sensitization to multiple allergenic molecules (c-sIgE). We applied advanced network embedding techniques to investigate the dynamics of temporal development of multiple c-sIgE and identify networks associated with asthma. In a population-based birth cohort, we measured c-sIgE to 112 proteins using multiplex array at 6 time-points from infancy to adolescence. We built weighted co-occurrence networks between c-sIgEs to investigate connectivity structures at different ages. To identify critical periods where networks are similar/divergent, we applied Graph embedding and dimensionality reduction techniques. We then compared network development structure between subjects with and without asthma at different ages, and analyzed topological features to compare network structures. c-sIgEs sensitization networks across ages revealed significant changes and a continuous evolution rather than abrupt shifts, with networks at ages 5 and 8 being very similar. Individuals with asthma consistently exhibited more complex and interconnected networks of c-sIgEs, which became more pronounced with age. Graph embedding showed that while profiles of those with and without asthma were distinct and the separation persisted across ages. A specific set of c-sIgEs and their interactions was responsible for this distinction. Topological features of networks which distinguished between sensitized individuals with and without asthma were age dependent. The differences in c-sIgE networks between subjects with and without asthma are consistently observed throughout childhood. Age needs to be considered when developing interpretation algorithms for asthma diagnosis/prediction.
Molecular mimicry-driven autoimmunity in chronic rhinosinusitis with nasal polyps
Authors: Tomoaki Asamori, Hiroto Katoh, Mikiya Takata, Daisuke Komura, Miwako Kakiuchi, Itaru Hashimoto, Madoka Sakurai, Asami Yamamoto, Takeshi Tsutsumi, Takahiro Asakage, Yasushi Ota, Shumpei Ishikawa
Journal: Journal of Allergy and Clinical Immunology (2025)

The pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) remains a subject of discussion. Although both microbial infection and autoimmunity have been proposed as potential contributors to CRSwNP pathobiology, their respective roles and intricate interactions in disease progression remain unclear owing to the limited knowledge regarding dysregulated humoral immunity in CRSwNP. To deepen our understanding of CRSwNP, we sought to identify the precise humoral antigens targeted by dominant B-cell clones within the disease environments. Immunoglobulin repertoire sequencing was performed to identify dominant B-cell clones in CRSwNP tissues. These immunoglobulin clones were reconstructed as antibodies, which were then used in immunoprecipitation and antigen array experiments for hypothesis-free global antigen profiling of auto- and exogenous antigens. From the analysis of 13 CRSwNP patients, 31 antibodies were reconstructed from dominant B-cell clones identified in nine patients. Seven novel protein autoantigens were identified, five of which were nucleic acid-binding proteins, and all were associated with autoimmune diseases. Additionally, nine microbial antigens, including various viruses, bacteria, and fungi, were discovered. Notably, two antibodies demonstrated dual reactivity, simultaneously recognizing both microbial and human proteins. For example, one antibody targeted CMV, Clostridium tetani, and human plectin (PLEC), while another recognized Aspergillus niger and human dihydrolipoamide S-acetyltransferase (DLAT), through molecular mimicry of shared amino acid homologies. Our data indicate the possibility that the pathobiology of CRSwNP involves autoreactive humoral immunity, with a subset of cases potentially exhibiting molecular mimicry-driven autoimmune features triggered by microbial infections. Nevertheless, this hypothesis requires further investigation.