tbuckley/cabot-search huggingface dataset:
Enhanced B cell and complement cascade gene signatures in patients with neuropsychiatric systemic lupus erythematosus
Authors: Dionysis Nikolopoulos, George Sentis, Iasonas Kitsios, Panagiotis Garantziotis, Noemin Kapsala, Antigone Pieta, Sofia Flouda, Theodora Manolakou, Myrto Nikoloudaki, Aggelos Banos, Katerina Chavatza, Ioannis Parodis, Anastasia Filia, George Bertsias, Antonis Fanouriakis, Dimitrios T Boumpas
Journal: Annals of the Rheumatic Diseases (2025)

The management of neuropsychiatric systemic lupus erythematosus (NPSLE) remains challenging because of clinical heterogeneity and the complexity of pathophysiologic mechanisms involved. We sought to determine the molecular signature of NPSLE and its endotypes towards novel biomarkers and targeted therapies. Whole-blood RNA sequencing from 308 patients with systemic lupus erythematosus (119 with NPSLE, 189 non-NPSLE) and 72-matched healthy controls (HCs) were performed. Supervised pathway enrichment analysis and unsupervised weighted gene coexpression network analysis were applied to distinguish clinically and molecularly defined NPSLE endotypes. Compared with HCs, patients with NPSLE demonstrated dysregulation of adaptive immune responses along with upregulation of interleukin (IL)-1, IL-6, IL-17, and IL-12/IL-23 signalling pathways. The comparison between NPSLE and non-NPSLE groups revealed a robust upregulation of complement cascade, DNA damage response, adaptive immunity, and IL-1 and IL-6 signalling. Furthermore, active NPSLE exhibited a strong autophagy signature. The B cell and complement cascade signatures exhibited a gradual upregulation across the non-NPSLE, inactive NPSLE, and active NPSLE subgroups. Within NPSLE, diffuse syndromes correlated positively with the oxidative phosphorylation module, while antiphospholipid antibody-positive NPSLE was not associated with specific signatures by unsupervised analysis. NPSLE endotypes such as cognitive dysfunction, seizures, psychosis, and optic neuritis were associated with distinct transcriptomic signatures namely IL-6 signalling and leukocyte migration, DNA damage response, inflammation, and type-I interferon, respectively. The clinical heterogeneity of NPSLE appears to be associated with molecular diversity, with certain endotypes or syndromes exhibiting distinct gene signatures. Upregulation of adaptive immune response and complement cascade suggests that complement inhibitors and B cell-targeted therapies could be further explored in NPSLE.
A Justice-First Approach to Ambient Intelligence in Healthcare
Authors: Jonathan Herington, Mildred K. Cho
Journal: The American Journal of Bioethics (2025)

Ambient intelligence systems (AIS) are increasingly deployed to provide persistent, artificially intelligent, monitoring and documentation of healthcare. AIS pose many ethical issues, including risks to the privacy of third parties, pernicious biases in predictive analytics, and intractable conflicts between the interests of patients, family members and care providers. In this paper we argue that these risks cannot be effectively navigated by applying a traditional bioethical framework. The traditional bioethical framework focuses heavily on protecting the autonomy and interests of a patient within the context of a single decision. An AIS, on the other hand, occupies a physical space and thus implicates multiple stakeholders, with interests that may conflict, in a setting where individually opting out of the interaction may be impractical or infeasible. Hence, we argue that, like many questions arising in the context of public health ethics, they should be dealt with through a "justice-first" approach to ethical theorizing.
RoCCY pilot study: A prospective cohort study on the safety of robotic-assisted laparoscopic colpectomy
Authors: Asra Vestering, Brechje L. Ronkes, Rik van Eekelen, Judith A. F. Huirne, Norah M. van Mello, Freek A. Groenman, Robert A. de Leeuw
Journal: International Journal of Transgender Health (2025)
The Impact of Allogeneic Hematopoietic Stem Cell Transplantation on Sickle Cell Retinopathy and Maculopathy: A Prospective, Observational Study
Authors: Rajani P. Brandsen, Elisabeth Dovern, Bart J. Biemond, Roselie M. H. Diederen, Erfan Nur
Journal: American Journal of Hematology (2025)
Prostate cancer clinicopathological presentation in South-East Africa during the 2010 decade
Authors: Sean M Patrick, Winstar Mokua Ombuki, Joan Ndambuki, Micah O Oyaro, Meshack Bida, Pamela X Y Soh, Gail S Prins, Maria Argos, Irene Barnhoorn, Daniel S Brewer, Raymond Campbell, Jenna Craddock, Rosalind A Eeles, Weerachai Jaratlerdsiri, Maphuti Tebogo Lebelo, Massimo Loda, Melanie Louw, Pavlo Lutsik, Ikenna C Madueke, Tumisang M N Mbeke, Daniel M Moreira, Shingai B A Mutambirwa, Muriuki Elias Nyaga, Martin Obida, Muvhulawa Obida, Willis Oyieko, Mulalo B Radzuma, Joyce Shirinde, Douglas I Walker, Edwin O O Walong, David C Wedge, Allan Yienya, Vanessa M Hayes, M S Riana Bornman, Peter Mungai Ngugi
Journal: JNCI Journal of the National Cancer Institute (2025)

Abstract Prostate cancer (PCa) is the leading cause of cancer-associated death amongst men across Sub-Saharan Africa, with Southern and East Africa ranking 1st and 5th globally. However, lack of coordinated National cancer registries has biased data towards single sourced, averaged or model estimates. Here, our retrospective study included 8,634 South-East African cases diagnosed between 2010-to-2019, which when compared with 71,694 Black and 322,356 White period-matched Americans, were over 3-fold more likely to present with aggressive disease (International Society of Urological Pathology grade groups ≥4: 45.38% vs 21.22% and 21.05%; Prostate Specific Antigen ≥20 ng/mL: 62.04% vs 17.29% and 11.17%, respectively; all two-sided P&amp;lt;0.0001). While East over Southern Africans are 1.5-times more likely to present with advanced disease, age was not a confounder. Supporting PCa as a major health concern for Africa, our data suggests underestimation in East Africa, while highlighting the need for accurate monitoring, increased awareness, and tailored screening criteria.
An attempt to evaluate the use of mixed reality in surgically treated pediatric oncology patients
Authors: Krzysztof Bronowicki, Justyna Antoniuk-Majchrzak, Iwona Malesza, Wiktor Możarowski, Agnieszka Szymborska, Bartosz Pachuta, Tomasz Walenta, Wojciech Jasica, Maciej Stanuch, Andrzej Skalski, Anna Raciborska
Journal: npj Digital Medicine (2025)
Extracellular Vesicles in Cancer Immunotherapy: Therapeutic, Challenges and Clinical Progress
Authors: Hamed Manoochehri, Anita S. La'ah, Ali Babaeizad, Mohsen Sheykhhasan, Mohadeseh Rostamipoor, Mahdiyeh Abbaspoor, Fariba Nikravesh, Samira Mozaffari Khosravi, Hanie Mahaki, Hamid Tanzadehpanah, Piao Yang
Journal: Asian Journal of Pharmaceutical Sciences (2025)
Liver Transplant is Associated with a Reduced Risk of Colorectal Dysplasia in patients with IBD and concomitant PSC
Authors: Nayantara Coelho-Prabhu, Ashwariya Ohri, Clara Benatzky, Nikitha Uma Baskaran, John E Eaton, Konstantinos N Lazaridis, Daniel Pratt, Ashwin N Ananthakrishnan
Journal: Clinical Gastroenterology and Hepatology (2025)
Significantly Enhanced Capture Efficiency of Cell-Imprinted Material for Circulating Tumor Cells via a Flexible and Ultra-Strong Double-Armed Phenylboronic Acid Design
Authors: Wenjing Sun, Xinmiao Zhao, Xinjia Zhao, Lingkai Meng, Mingliang Tang, Jiaqi Li, Yongxin Chang, Yuting Xiong, Hao Wang, Jinghua Chen, Guangyan Qing
Journal: Biomaterials (2025)
Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome
Authors: Anna Samarra, Simone Renwick, Aleksandr A. Arzamasov, Dmitry A. Rodionov, Kennedy Spann, Raul Cabrera-Rubio, Antia Acuna-Gonzalez, Cecilia Martínez-Costa, Lindsay Hall, Nicola Segata, Andrei L. Osterman, Lars Bode, MCarmen Collado
Journal: Gut Microbes (2025)

Breast milk, rich in human milk oligosaccharides (HMOs), supports the early-life colonization of beneficial bacteria such as bifidobacteria and lactobacilli, potentially reducing early-life antibiotic resistance. However, antibiotic treatment may interfere with the beneficial functions of HMO-degrading bacteria. This study investigated the metabolism of HMOs by bifidobacteria and lactobacilli isolated from human milk and mother-infant paired fecal samples, along with their antibiotic resistance profiles. Understanding these species- and sample-type-specific interactions will provide valuable insights into how bioactive components in human milk may shape the infant resistome during early life. A total of 39 Bifidobacterium and 14 Lactobacillaceae strains were isolated from paired mother-infant fecal and breast milk samples. Whole genome sequencing (WGS) allowed functional predictions on the HMO metabolism abilities and the resistance genotype of each strain. In vitro HMO utilization was assessed using growth kinetics assays combined with HMO glycoprofiling in culture supernatant. The minimum inhibitory concentration (MIC) was also determined for each strain. HMO metabolism by the bifidobacteria was species-specific. Bifidobacterium bifidum (B. bifidum) and Bifidobacterium longum subsp. infantis (B. infantis) exhibited the highest capacity for HMO degradation, consistent with genomic predictions. In contrast, lactobacilli were unable to degrade HMOs in vitro but were predicted to metabolize the by-products of HMO degradation. Phenotypic analysis revealed that B. bifidum strains had the lowest levels of antibiotic resistance, while Bifidobacterium animalis subsp. lactis (B. lactis) strains were resistant to most tested antibiotics. Overall, B. bifidum demonstrated the strongest HMO-degrading ability while remaining the most antibiotic-susceptible species. Early-life colonizing bifidobacterial species possess the essential machinery required to degrade HMOs and are highly susceptible to antibiotics. A better understanding of these dynamics could inform clinical strategies to protect and restore the infant gut microbiome, particularly in neonates exposed to antibiotics.
Expansion of functional human salivary acinar cell spheroids with reversible thermo-ionically crosslinked 3D hydrogels
Authors: Jose G Munguia-Lopez, Sangeeth Pillai, Yuli Zhang, Amatzia Gantz, Dimitria B Camasao, Showan N Nazhat, Joseph M Kinsella, Simon D Tran
Journal: International Journal of Oral Science (2025)
Profiling and functional characterization of long noncoding RNAs during human tooth development
Authors: Xiuge Gu, Wei Wei, Chuan Wu, Jing Sun, Xiaoshan Wu, Zongshan Shen, Hanzhang Zhou, Chunmei Zhang, Jinsong Wang, Lei Hu, Suwen Chen, Yuanyuan Zhang, Songlin Wang, Ran Zhang
Journal: International Journal of Oral Science (2025)
Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning
Authors: Sandipan Paul Arnab, Andre Luiz Campelo dos Santos, Matteo Fumagalli, Michael DeGiorgio
Journal: Molecular Biology and Evolution (2025)

Abstract Natural selection leaves detectable patterns of altered spatial diversity within genomes, and identifying affected regions is crucial for understanding species evolution. Recently, machine learning approaches applied to raw population genomic data have been developed to uncover these adaptive signatures. Convolutional neural networks (CNNs) are particularly effective for this task, as they handle large data arrays while maintaining element correlations. However, shallow CNNs may miss complex patterns due to their limited capacity, while deep CNNs can capture these patterns but require extensive data and computational power. Transfer learning addresses these challenges by utilizing a deep CNN pretrained on a large dataset as a feature extraction tool for downstream classification and evolutionary parameter prediction. This approach reduces extensive training data generation requirements and computational needs while maintaining high performance. In this study, we developed TrIdent, a tool that uses transfer learning to enhance detection of adaptive genomic regions from image representations of multilocus variation. We evaluated TrIdent across various genetic, demographic, and adaptive settings, in addition to unphased data and other confounding factors. TrIdent demonstrated improved detection of adaptive regions compared to recent methods using similar data representations. We further explored model interpretability through class activation maps and adapted TrIdent to infer selection parameters for identified adaptive candidates. Using whole-genome haplotype data from European and African populations, TrIdent effectively recapitulated known sweep candidates and identified novel cancer, and other disease-associated genes as potential sweeps.
Selenide‐Driven Reactive Oxygen Species Activation and Fe(II) Regeneration for Enhanced Nanocatalytic Antibacterial Therapeutics
Authors: Chenyao Wu, Yanling You, Dehong Yu, Ya‐Xuan Zhu, Han Lin, Jianlin Shi
Journal: Advanced Healthcare Materials (2025)

Abstract Fenton‐based nanocatalytic therapy has attracted widespread attention for its high efficiency and safety. Nevertheless, Fe 2+ regeneration, as the rate‐limiting step of Fenton reaction, hinders the ROS‐induced oxidative killing. Herein, a Fe 2+ auto‐regeneration strategy is exemplified by 2D FeSe 2 nanosheets to break the rate limitation of Fenton reaction and subsequently enhances the antibacterial oxidative damage via dual ROS generation pathways. To be specific, the Se species accelerate the Fe 3+ reduction to maintain high ·OH productivity of Fe 2+ ‐mediated Fenton reaction, which is accompanied by the production of H 2 Se in the presence of H + . The H 2 Se further converts O 2 into O 2 ·− and synergistically breaks the oxidative threshold of bacteria, leading to irreversible bacterial death with glutathione depletion, lipid peroxidation, and membrane destruction. In summary, the FeSe 2 ‐mediated Fe 2+ auto‐regeneration and ROS self‐production pathways largely elevate its oxidative killing capability, providing a potential ROS enhancement strategy for broad‐spectrum nonantibiotic bacterial disinfection.
Ultrasound‐Activated Selenium Nanocarrier: Bactericidal Enhancement and Osseointegration Promotion for Implant‐Associated Infections
Authors: Zhiying Cao, Renhao Xu, Wenyi Zheng, Li Ma, Yanni He, Tianfeng Chen, Hongmei Liu
Journal: Advanced Healthcare Materials (2025)

Abstract Implant‐associated infections (IAIs) are common and challenging complications of orthopedic surgery. The physical barrier formed by biofilms and the antioxidant defense system of bacteria shield them from attack by antimicrobial agents and immune cells, leading to irreversible bone loss and the failure of osseointegration. To address these challenges and enhance osseointegration in the presence of biofilm infections, a sequential therapy strategy is proposed using an ultrasound‐activated nanocarrier, PLGA@H/Se, designed to disrupt bacterial defenses and subsequently enhancing osteogenic differentiation. As expected, PLGA@H/Se, when activated by ultrasound, induces a cavitation effect that disrupts the outer barrier of the biofilm, while promoting the deep delivery of encapsulated SeNPs and the antimicrobial peptide HHC‐36. The SeNPs target the internal H₂S‐based antioxidant defense in bacteria, thereby synergistically enhancing the bactericidal effect of HHC‐36. Furthermore, the sustained release of SeNPs regulates selenoprotein expression, boosts antioxidant stress responses, and activates the Wnt/β‐catenin pathway, which helps restore the osteogenic differentiation potential of BMSCs impaired by oxidative damage, both in vitro and in vivo. Collectively, this ultrasound‐based sequential system facilitates functional osseointegration under pathological conditions, offering a practical and comprehensive strategy for treating IAIs.
Doubling of triazole resistance rates in invasive aspergillosis over a 10-year period, Belgium, 1 April 2022 to 31 March 2023
Authors: Lize Cuypers, Robina Aerts, Otto Van de gaer, Lore Vinken, Rita Merckx, Veerle Gerils, Greetje Vande Velde, Agustin Reséndiz-Sharpe, Johan Maertens, Katrien Lagrou
Journal: Eurosurveillance (2025)

Background Dutch national treatment guidelines for fungal infections have been adapted based on surveillance findings of triazole resistance rates &gt;10% in Aspergillus species isolates. In Belgium, nationwide resistance data have not been collected since 2011. Aim Our objective was to evaluate changes in antifungal susceptibility among Aspergillus species isolates from patients with invasive aspergillosis. Methods Laboratories across Belgium were invited to send all clinically relevant Aspergillus species isolates from patients diagnosed with invasive aspergillosis, collected between April 2022 and March 2023, to the National Reference Centre for Mycosis at UZ Leuven for identification and antifungal susceptibility testing. Results Overall, 29 clinical laboratories contributed 309 isolates from 297 patients. Median patient age was 66 years (range: 6 months–96 years). Among isolates, 61% (189/309) were from male patients. At species level, Aspergillus fumigatus isolates predominated (278/309, 90%), with a 9.7% (27/278) triazole resistance rate, compared to the 4.6% rate found in 2011. Of 27 resistant isolates, successful Cyp51A sequencing of 26 showed 20 with the TR 34 /L98H resistance mechanism. Across the country, local A. fumigatus triazole resistance rates varied. Among provinces in the Flanders region, Antwerp had the highest resistance rate (15.4%: 10/65; p = 0.082), Flemish Brabant (6/48) also had a rate &gt;10%, while Limburg (2/46) had the lowest rate. Conclusions Geographical differences in A. fumigatus triazole resistance rates stress the importance of implementing broad prospective surveillance initiatives, not limited to one region or one hospital. In Belgium, triazole resistance rates have doubled over 10 years, nearly attaining the 10% threshold, warranting re-evaluation of local empirical antifungal treatment regimen decisions.
Application of an updated methodology to estimate the burden of healthcare-associated infections in Italy, 2022
Authors: Costanza Vicentini, Valerio Bordino, Luca Bresciano, Stefania Di Giacomo, Fortunato D’Ancona, Carla Maria Zotti
Journal: Eurosurveillance (2025)

Background Accurate burden estimates are necessary to inform priority setting and rational resource allocation. Weighting prevalence inversely proportional to time-at-risk has been proposed as a solution for length-biased sampling, an important limitation affecting prevalence to incidence conversion for healthcare-associated infections (HAIs). Aim This study aimed to update Italian burden estimates by calculating HAI incidence, attributable mortality and disability-adjusted life years (DALYs). Further, we describe an adapted methodology for burden estimations. Methods We used data from the latest European Centre for Disease Prevention and Control (ECDC) point prevalence survey (PPS) of HAIs, conducted in Italy in November 2022, to calculate the burden of five major HAIs at national level. We adapted the Burden of Communicable Diseases in Europe (BCoDE) methodology to include inverse probability weighting and compared results of naïve and weighted calculations. Results The national sample included 18,397 patients. Overall, 564.8 DALYs per 100,000 general population resulted from weighted calculations (95% uncertainty interval (UI): 450.04–694.38), with an annual incidence of 685.42 cases per 100,000 general population (95% UI: 611.09–760.86) and 33.23 deaths per 100,000 general population per year (95% UI: 28.62–38.33). Concerning naïve estimates, overall 1,017.81 DALYs per 100,000 general population were calculated (95% UI: 855.16–1,190.59). In both calculations, healthcare-acquired bloodstream infections had the highest burden in terms of DALYs per 100,000 hospitalised and general population. Conclusion Our study confirmed the substantial burden of HAIs in Italy and renews the need to prioritise resources for infection prevention and control interventions.
Morphometric‐Assisted Prediction of Developmental Toxicity Using Stem Cell‐Based Embryo Models in Microwells
Authors: Vinidhra Shankar, Athanasia Zoi Pappa, Clemens van Blitterswijk, Erik Vrij, Stefan Giselbrecht
Journal: Advanced Healthcare Materials (2025)

Abstract Congenital abnormalities cause ≈3% of fetal defects and premature deaths in Europe, often due to maternal exposure to toxicants. To mitigate the ethical and logistical challenges of animal studies, stem cell‐based models are being exploredthat offer scalable readouts at various stages of embryogenesis. However, most current in vitro models are limited in complexity, throughput, automation compatibility or real‐time spatio‐temporal read‐outs. In this study, a scalable, automated platform capable of imaging and quantifying morphological features such as shape, size, texture, and marker intensity is presented. Using a microwell screening platform, XEn/EpiCs, a peri‐implantation stage embryo model that mimics eXtraembryonic Endoderm and Epiblast co‐development, is robustly generated and used to screen a library of 38 reported compounds. Unlike conventional cytotoxicity assays, this approach also evaluates development‐disrupting morphological changes, termed “morphotoxicity”, thereby offering complementary insights that may improve the prediction of developmental toxicity across cell types. This pilot study shows thathigh doses of compoundslike retinoic acid, caffeine, ampyrone, and dexamethasone, significantly disrupt XEn/EpiC development, causing morphotoxic effects with or without affecting cell viability. Together, thisstudy highlights the importance of complementing cytotoxicity assessments with morphotoxicity read‐outs, emphasizing its potential to enhance the evaluation of teratogenic risks in toxicity tests.