tbuckley/cabot-search huggingface dataset:
LETSmix: a spatially informed and learning-based domain adaptation method for cell-type deconvolution in spatial transcriptomics
Authors: Yangen Zhan, Yongbing Zhang, Zheqi Hu, Yifeng Wang, Zirui Zhu, Sijing Du, Xiangming Yan, Xiu Li
Journal: Genome Medicine (2025)

Spatial transcriptomics (ST) enables the study of gene expression in spatial context, but many ST technologies face challenges due to limited resolution, leading to cell mixtures at each spot. We present LETSmix to deconvolve cell types by integrating spatial correlations through a tailored LETS filter, which leverages layer annotations, expression similarities, image texture features, and spatial coordinates to refine ST data. Additionally, LETSmix employs a mixup-augmented domain adaptation strategy to address discrepancies between ST and reference single-cell RNA sequencing data. Comprehensive evaluations across diverse ST platforms and tissue types demonstrate its high accuracy in estimating cell-type proportions and spatial patterns, surpassing existing methods (URL: https://github.com/ZhanYangen/LETSmix ).
Assessment of the effectiveness of West Nile virus screening by analysing suspected positive donations among blood donors, Germany, 2020 to 2023
Authors: Stefano Orru', Annette Reissinger, Angela Filomena, Anna Heitmann, Markus Benedikt Funk, Jonas Schmidt-Chanasit, Julia Kreß, Heinrich Scheiblauer, Dániel Cadar, Sarah Anna Fiedler
Journal: Eurosurveillance (2025)

Background The first autochthonous human West Nile virus (WNV)-positive cases in Germany were confirmed in 2019. Risk minimisation measures (RMM) were introduced in 2020; no WNV transfusion-transmitted infections have been reported to date. Aim To analyse German suspected WNV-positive blood donations during annual seasons 2020–23 to review donor testing requirements. Methods WNV look-back procedures were initiated as per German regulations and additional donor data were collected. Blood samples were analysed by metagenomic next-generation sequencing (mNGS), individual donor nucleic acid amplification technique (ID-NAT)-based testing and antibody (Ab) testing. Results Seventy-four cases were followed up after WNV-positive donor mini-pool screening. Forty-five (83%) of 54 samples tested with the cobas WNV assay and 14 (29%) of 49 samples tested with the RealStar WNV assay showed a reactive ID-NAT-based result; the viral load ranged between 70,251 IU/mL and values below quantification limits. Fifteen (23%) of 64 samples serologically tested were reactive with at least one of the three Ab tests performed; the previous WNV-negative donation was nearly always documented &gt; 28 days before. Of 73 samples sequenced, mNGS detected WNV in 26 (36%) and other flaviviruses in 14 (19%) cases. Conclusion In some suspected cases where a WNV infection was not confirmed, mNGS demonstrated a cross-reaction with other flaviviruses. Ab testing could only detect WNV in late stages of infection. A NAT-based WNV donor screening with a detection limit of at least 120 IU/mL seems to be a sufficiently effective RMM at present. However, a continuous re-evaluation of test strategy is always required.
COVID-19 vaccine effectiveness in the paediatric population aged 5–17 years: a multicentre cohort study using electronic health registries in six European countries, 2021 to 2022
Authors: Patrícia Soares, Ausenda Machado, Nathalie Nicolay, Susana Monge, Chiara Sacco, Christian Holm Hansen, Hinta Meijerink, Iván Martínez-Baz, Susanne Schmitz, James Humphreys, Massimo Fabiani, Aitziber Echeverria, Ala’a AlKerwi, Anthony Nardone, Alberto Mateo-Urdiales, Jesús Castilla, Esther Kissling, Baltazar Nunes
Journal: Eurosurveillance (2025)

Background During the first year of the COVID-19 pandemic, vaccination programmes targeted children and adolescents to prevent severe outcomes of SARS-CoV-2 infection. Aim To estimate COVID-19 vaccine effectiveness (VE) against hospitalisation due to COVID-19 in the paediatric population, among those with and without previously documented SARS-CoV-2 infection. Methods We established a fixed cohort followed for 12 months in Denmark, Norway, Italy, Luxembourg, Navarre (Spain) and Portugal using routine electronic health registries. The study commenced with paediatric COVID-19 vaccination campaign at each site between June 2021 and January 2022. The outcome was hospitalisation with a laboratory-confirmed SARS-CoV-2 infection or COVID-19 as the main diagnosis. Using Cox proportional hazard models, VE was estimated as 1 minus the confounder-adjusted hazard ratio of COVID-19 hospitalisation between vaccinated and unvaccinated. A random-effects meta-analysis was used to pool VE estimates. Results We included 4,144,667 5–11-year-olds and 3,861,841 12–17-year-olds. In 12–17-year-olds without previous infection, overall VE was 69% (95% CI: 40 to 84). VE declined with time since vaccination from 77% ≤ 3 months to 48% 180–365 days after immunisation. VE was 94% (95% CI: 90 to 96), 56% (95% CI: 3 to 80) and 41% (95% CI: −14 to 69) in the Delta, Omicron BA.1/BA.2 and BA.4/BA.5 periods, respectively. In 12–17-year-olds with previous infection, one dose VE was 80% (95% CI: 18 to 95). VE estimates were similar for 5–11-year-olds but with lower precision. Conclusion Vaccines recommended for 5–17-year-olds provided protection against COVID-19 hospitalisation, regardless of a previously documented infection of SARS-CoV-2, with high levels of protection in the first 3 months of the vaccination.
Discovery of metabolites prevails amid in-source fragmentation
Authors: Yasin El Abiead, Adriano Rutz, Simone Zuffa, Bashar Amer, Shipei Xing, Corinna Brungs, Robin Schmid, Mario S. P. Correia, Andres Mauricio Caraballo-Rodriguez, Amir Zarrinpar, Helena Mannochio-Russo, Michael Witting, Ipsita Mohanty, Tomáš Pluskal, Wout Bittremieux, Rob Knight, Andrew D. Patterson, Justin J. J. van der Hooft, Sebastian Böcker, Warwick B. Dunn, Roger G. Linington, David S. Wishart, Jean-Luc Wolfender, Oliver Fiehn, Nicola Zamboni, Pieter C. Dorrestein
Journal: Nature Metabolism (2025)
Rapid brain tumor classification from sparse epigenomic data
Authors: Björn Brändl, Mara Steiger, Carolin Kubelt, Christian Rohrandt, Zhihan Zhu, Maximilian Evers, Gaojianyong Wang, Bernhard Schuldt, Ann-Kristin Afflerbach, Derek Wong, Amy Lum, Skarphedinn Halldorsson, Luna Djirackor, Henning Leske, Svetlana Magadeeva, Romualdas Smičius, Claudia Quedenau, Nils O. Schmidt, Ulrich Schüller, Einar O. Vik-Mo, Martin Proescholdt, Markus J. Riemenschneider, Gelareh Zadeh, Ole Ammerpohl, Stephen Yip, Michael Synowitz, Alena van Bömmel, Helene Kretzmer, Franz-Josef Müller
Journal: Nature Medicine (2025)

Abstract Although the intraoperative molecular diagnosis of the approximately 100 known brain tumor entities described to date has been a goal of neuropathology for the past decade, achieving this within a clinically relevant timeframe of under 1 h after biopsy collection remains elusive. Advances in third-generation sequencing have brought this goal closer, but established machine learning techniques rely on computationally intensive methods, making them impractical for live diagnostic workflows in clinical applications. Here we present MethyLYZR, a naive Bayesian framework enabling fully tractable, live classification of cancer epigenomes. For evaluation, we used nanopore sequencing to classify over 200 brain tumor samples, including 10 sequenced in a clinical setting next to the operating room, achieving highly accurate results within 15 min of sequencing. MethyLYZR can be run in parallel with an ongoing nanopore experiment with negligible computational overhead. Therefore, the only limiting factors for even faster time to results are DNA extraction time and the nanopore sequencer’s maximum parallel throughput. Although more evidence from prospective studies is needed, our study suggests the potential applicability of MethyLYZR for live molecular classification of nervous system malignancies using nanopore sequencing not only for the neurosurgical intraoperative use case but also for other oncologic indications and the classification of tumors from cell-free DNA in liquid biopsies.
The role of masks and respirators in preventing respiratory infections in healthcare and community settings
Authors: C Raina MacIntyre, Abrar A Chughtai, Mohana Kunasekaran, Essa Tawfiq, Trish Greenhalgh
Journal: BMJ (2025)

Abstract The covid-19 pandemic saw frequent changes and conflicts in mask policies and politicization of masks. On reviewing the evidence, including studies published after the pandemic, the data suggest respirators are more effective than masks in healthcare, but must be continuously worn to be protective. Healthcare and aged care settings amplify outbreaks, so protection of patients and staff is paramount. Most guidelines assume risk is only present during close contact or aerosol generating procedures, but studies show intermittent use of respirators is not protective. New research in aerosol science confirms the risk of infection is widespread in health facilities. In community settings, any mask use is protective during epidemics, especially if used early, when combined with hand hygiene, and if wearers are compliant. Community use of N95 respirators is more protective than surgical masks, which are more protective than cloth masks, but even cloth masks provide some protection. Mask guidelines should be adaptable to the specific context and should account for rising epidemic activity, and whether a pathogen has asymptomatic transmission. The main rationale for universal masking during pandemics is asymptomatic transmission, which means risk of transmission cannot be self-identified. The precautionary principle should be applied during serious emerging infections or pandemics when transmission mode is not fully understood, or vaccines and drugs are not available. If respirators are not available, medical or cloth masks could be used as a last resort. Data exist to support extended use and reuse of masks and respirators during short supply. In summary, extensive evidence generated during the covid-19 pandemic confirms the superiority of respirators and supports the use of masks and respirators in the community during periods of high epidemic activity. Some gaps in research remain, including economic analyses, research in special population groups for whom masking is challenging, and research on countering disinformation.
CAR-mediated target recognition limits TCR-mediated target recognition of TCR- and CAR-dual-receptor-edited T cells
Authors: Tassilo L A Wachsmann, Teuntje Poortvliet, Miranda H Meeuwsen, Dennis F G Remst, Marijke F Toes, Anne K Wouters, Renate S Hagedoorn, J H Frederik Falkenburg, Mirjam H M Heemskerk
Journal: Molecular Therapy (2025)
A VSV-based oral rabies vaccine was sentineled by Peyer's patches and induced a timely and durable immune response
Authors: Shen Wang, Zhenshan Wang, Weiqi Wang, Hongyu Sun, Na Feng, Yongkun Zhao, Jianzhong Wang, Tiecheng Wang, Xianzhu Xia, Feihu Yan
Journal: Molecular Therapy (2025)
A novel scheme for non-invasive drug delivery with a magnetically controlled drug delivering capsule endoscope
Authors: Weijun Wang, Kun Zhang, Fanhua Ming, Biao Chen, Hao Zhang, Zhe Wang, Xin Jiang, Hang Zhang, Guochen Shang, Yuhui Bao, Hangyu Peng, Shanshan Liu, Xin Ling, Wenhao Li, Huanpeng Zhu, Yurui Zhang, Sicheng Cai, Zhen Ding, Rong Lin
Journal: Journal of Controlled Release (2025)
CTLA-4 inhibitors are associated with a higher risk of cardiovascular events than PD-1 inhibitors in Patients with Melanoma
Authors: Ching-Chung Chang, Shao-Wei Lo, Hua-Ching Chang, Junmin Song, Yu-Cheng Chang, Kevin Yang, Kuan-Yu Chi, Yu Chang, Cho-Hung Chiang, Cho-Han Chiang
Journal: Journal of the American Academy of Dermatology (2025)
NIR-II AIEgen Nanocomplex with Suppressed Nonradiative Decay and Intersystem Crossing for High-Contrast Mesenteric Vascular Imaging
Authors: Jianlin Liu, Wenjing Liu, Guanghui Liu, Rongfeng Wang, Jing Liu, Xiaogang Zhang, Heping Shi, Xiuqing Dong, Jing Zhao, Dan Ding, Guorui Jin
Journal: Biomaterials (2025)
FDG-PET/CT for Effective Staging of Disseminated Blastomycosis
Authors: Yousif A. Lucinian, Nuzha B. Noorah, Peter George Maliha, Marc-André Morin
Journal: Clinical Nuclear Medicine (2025)

We present the case of a 67-year-old man undergoing immunosuppressive therapy with known pulmonary blastomycosis who presented with knee swelling and fever. FDG-PET/CT performed to exclude septic arthritis revealed increased uptake within the right epididymis and multiple osteoarticular, cutaneous, and subcutaneous sites. Cultures obtained from bronchoalveolar lavage, urine, right knee arthrocentesis, and subcutaneous tissue all demonstrated Blastomyces dermatitidis , compatible with disseminated blastomycosis (DB). To the best of our knowledge, this is the first case of DB in a human subject documented by FDG-PET. This case showcases FDG-PET as a potentially sensitive imaging modality in staging blastomycosis multiorgan involvement, aiding in identifying culture sites by revealing clinically and radiologically unsuspected foci of infection.
Rare Metastatic Clear Cell Renal Cell Carcinoma to Pancreas Revealed by 68Ga-FAPI PET/CT
Authors: Yunuan Liu, Yan Zhao, Fenglian Jing, Xinming Zhao, Jingmian Zhang
Journal: Clinical Nuclear Medicine (2025)

A 56-year-old woman underwent surgery for clear cell renal cell carcinoma (ccRCC) 8 years ago. The patient incidentally discovered 2 foci in the body and tail of the pancreas by abdominal ultrasound during follow-up. MRI disclosed lesions with central inhomogeneous enhancement and restricted diffusion. The 2 lesions showed no 18F-FDG uptake but had mild to moderate 68Ga-FAPI accumulation in the PET/CT images. Postoperative pathology and immunohistochemical analysis confirmed metastatic ccRCC to the pancreas. 68Ga-FAPI PET/CT might be a useful tool in the diagnosis and staging of ccRCC.
Radiotracer Accumulation in the Pyelocaliceal System of Transplanted Kidney: A Potential Pitfall in Lymphoscintigraphy of Pelvic Malignancies
Authors: Amin Saber Tanha, Haniye Elahifard, Faeze Rabani, Nasrin Raeisi, Ramin Sadeghi
Journal: Clinical Nuclear Medicine (2025)

A 34-year-old woman with a history of renal transplantation and cervical cancer underwent lymphoscintigraphy using 99m Tc-phytate before surgery. Initial planar images revealed multiple foci of uptake, which were later precisely localized using SPECT/CT imaging. Notably, uptakes in the right lower quadrant were attributed to the pyelocalyceal system of the transplanted kidney, highlighting a potential pitfall in patients with ectopic or transplanted kidneys. This case report emphasizes the importance of recognizing the limitations of lymphoscintigraphy in patients with complex anatomy and the value of hybrid imaging in ensuring accurate sentinel lymph node localization.
Transfer learning method for prenatal ultrasound diagnosis of biliary atresia
Authors: Fujiao He, Gang Li, Zhichao Zhang, Chaoran Yang, Zeyu Yang, Hao Ding, Dan Zhao, Wei Sun, Yu Wang, Kaihui Zeng, Xian Li, Mingming Shao, Jiao Yin, Jia Yao, Boxuan Hong, Zhibo Zhang, Zhengwei Yuan, Zongjie Weng, Luyao Zhou, Mo Zhang, Lizhu Chen
Journal: npj Digital Medicine (2025)

Biliary atresia (BA) is a rare and severe congenital disorder with a significant challenge for prenatal diagnosis. This study, registered at the Chinese Clinical Trial Registry (ChiCTR2200059705), aimed to develop an intelligent model to aid in the prenatal diagnosis of BA. To develop and evaluate this model, fetuses from 20 hospitals across China and infants sourced from public database were collected. The transfer-learning model (TLM) demonstrated superior diagnostic performance compared to the basic deep-learning model, with higher area under the curves of 0.906 (95%CI: 0.872–0.940) vs 0.793 (0.743–0.843), 0.914 (0.875–0.953) vs 0.790 (0.727–0.853), and 0.907 (0.869–0.945) vs 0.880 (0.838–0.922) for the three independent test cohorts. Furthermore, when aided by the TLM, diagnostic accuracy surpassed that of individual sonologists alone. The TLM achieved satisfactory performance in predicting fetal BA, providing a low-cost, easily accessible, and accurate diagnostic tool for this condition, making it an effective aid in clinical practice.
Mirrored Metastatic Neuroendocrine Tumor in a Mother-Daughter Duo With Mutations in the MEN1 Gene
Authors: Piyush Aggarwal, Gurjeet Kaur, Sanjay Kumar Bhadada, Rajender Kumar, Somit Pandey, Ashwani Sood, Bhagwant Rai Mittal
Journal: Clinical Nuclear Medicine (2025)

Multiple endocrine neoplasia (MEN) 1 syndrome may present with either of any or all neuroendocrine tumors (NETs), parathyroid and pituitary adenoma. There is a paucity of data on the intronic and exonic mutations in the MEN1 gene associated with the MEN1 syndrome. We present an interesting study of a mother-daughter duo of MEN1 who had a similar lesions distribution of metastatic NET and underwent genetic analysis to reveal a rare mutation in the MEN1 gene and both first-degree relatives presented with metastatic NET without any other syndromic manifestation of MEN1 syndrome. Both patients received peptide receptor radionuclide therapy.
Frizzled-7-targeting antibody-derived bifunctional protein retargets NK cells against triple-negative breast cancer cells via MICA-NKG2D axis
Authors: Chenyue Wang, Lisha Wu, Xingxing Li, Shuyang Mao, Zitong Wang, Haiyan Xie, Jing Xu, Danfang Li, Hao Yang, Tong Wang, Qingqing Huang, Lin Yang, Xiaofei Zhang, Yuxia Liu, Jin Wang, Gang Huang, Wei Xie
Journal: Journal for ImmunoTherapy of Cancer (2025)

Background Hypoxia is associated with the evasion of triple-negative breast cancer (TNBC) from immune surveillance. Hypoxia increases the subpopulation of putative TNBC stem-like cells (TNBCSCs) through activating Wnt/β-Catenin signaling. The shedding of MHC class I-related chain A (MICA) is particularly noteworthy in cancer stem cells (CSCs), promoting the resistance of CSCs to natural killer (NK) cell cytotoxicity. To reestablish MICA/NKG2D-mediated immunosurveillance, we proposed the design of a fusion protein (SHH002-hu1-MICA) which consists of Frizzled-7 (Fzd7)-targeting antibody and MICA, serving as an engager retargeting NK cells against TNBCs, especially TNBCSCs. Methods Opal multicolor immunohistochemistry staining was used to validate the expression of membrane MICA (mMICA) and existence of NK cells in TNBC tumors; flow cytometry (FCM) assay was used to detect the expression of Fzd7/mMICA on TNBCs. Biolayer interferometry (BLI) and surface plasmon resonance (SPR) assays were executed to assess the affinity of SHH002-hu1-MICA towards rhFzd7/rhNKG2D; near-infrared imaging assay was used to evaluate the targeting capability. A cytotoxicity assay was conducted to assess the effects of SHH002-hu1-MICA on NK cell-mediated killing of TNBCs, and FCM assay to analyze the effects of SHH002-hu1-MICA on the degranulation of NK cells. Finally, TNBC cell-line-derived xenografts were established to evaluate the anti-tumor activities of SHH002-hu1-MICA in vivo. Results The expression of mMICA is significantly downregulated in hypoxic TNBCs and TNBCSCs, leading to the evasion of immune surveillance exerted by NK cells. The expression of Fzd7 is significantly upregulated in TNBCSCs and exhibits a negative correlation with the expression of mMICA and infiltration level of NK cells. On accurate assembly, SHH002-hu1-MICA shows a strong affinity for rhFzd7/rhNKG2D, specifically targets TNBC tumor tissues, and disrupts Wnt/β-Catenin signaling. SHH002-hu1-MICA significantly enhances the cytotoxicity of NK cells against hypoxic TNBCs and TNBCSCs by inducing the degranulation of NK cells and promotes the infiltration of NK cells in CD44 high regions within TNBC xenograft tumors, exhibiting superior anti-tumor activities than SHH002-hu1. Conclusions SHH002-hu1-MICA maintains the targeting property of SHH002-hu1, successfully activates and retargets NK cells against TNBCs, especially TNBCSCs, exhibiting superior antitumor activities than SHH002-hu1. SHH002-hu1-MICA represents a promising new engager for NK cell-based immunotherapy for TNBC.
Letter to the editor: radiomics signature for dynamic monitoring of tumor-inflamed microenvironment and immunotherapy response prediction
Authors: Yuhao Dong, Shuixing Zhang
Journal: Journal for ImmunoTherapy of Cancer (2025)

We read with great interest the article by Bernatowicz et al . Despite the promising findings, we would like to highlight several concerns regarding the methodology and interpretation of the results that warrant further discussion, including the stability of radiomic features across pan-cancer types, the optimal threshold for CT-TIME (tumor immune microenvironment) scores, the biological interpretability of radiomic models, and the survival tail effect of immunotherapy responses.
Safety of colchicine on fertility, pregnancy, and lactation: a systematic review and meta-analysis informing the EULAR/PReS recommendations for familial Mediterranean fever
Authors: Teresa Otón, Erdal Sağ, Loreto Carmona, Seza Ozen
Journal: Annals of the Rheumatic Diseases (2025)

To summarise the evidence of colchicine's effects on fertility, pregnancy, and lactation in the treatment of patients with familial Mediterranean fever (FMF). Two reviewers and a methodologist conducted the systematic review. Together with an expert in FMF, they established the protocol and the PICOt questions. Medline via PubMed, Embase, and the Cochrane Library were searched from inception until August 23, 2023. All clinical trials, cohort studies, or case series focused on the safety of colchicine in FMF, concerning reproductive issues or breastfeeding, and involving at least 5 patients were eligible. The risk of bias in the studies was assessed using the Newcastle-Ottawa Scale. Meta-analysis was planned for at least 2 homogeneous studies with fixed-effect models using the Mantel-Haenszel method to obtain the pooled risk ratio (RR) and 95% CI. Twenty-five studies were included overall of moderate to low quality. The RR of miscarriage or foetal loss with colchicine in FMF was 0.87 (95% CI, 0.67-1.12), showing a heterogeneity of 31%. The percentage of birth defects in the exposed group ranged from 0.6% to 4.0%, not very different, comparable to the rates of women with FMF without exposure to colchicine. Regarding fertility, there were no apparent differences between colchicine-exposed and nonexposed groups, neither among women nor men (sperm assessment). Only 1 study reported breastfeeding data, showing no growth differences among exposed and nonexposed babies. Colchicine appears to have a good risk-benefit profile regarding reproductive safety. Ideally, higher-quality studies should be performed, especially regarding male fertility.
Author Correction: Five ways to enhance the diversity and quality of health data
Authors: Paola Quattroni, Ash Routen, Joe Alderman, Claire Argent, Samuel Cusworth, Hajira Dambha-Miller, Rose Drummond, Alastair Denniston, Poushali Ganguli, Nicola Hamilton, Uwaye Ideh, Sara Khalid, Aden Kwok, Elinor Laws, Xiaoxuan Liu, Vahe Nafilyan, Jo Palmer, Marta Pineda-Moncusi, Alexia Sampri, Holly Tibble, Fatemeh Torabi, Jonathan Valabhji, Diana Withrow, Claire Welsh, Angela M. Wood, Ashley Akbari, Kamlesh Khunti
Journal: Nature Medicine (2025)