tbuckley/cabot-search huggingface dataset:
Itaconate modulates immune responses via inhibition of peroxiredoxin 5
Authors: Tomas Paulenda, Barbora Echalar, Lucie Potuckova, Veronika Vachova, Denis A Kleverov, Johannes Mehringer, Ekaterina Potekhina, Alex Jacoby, Devashish Sen, Chris Nelson, Rick Stegeman, Vladimir Sukhov, Danielle Kemper, Cheryl F Lichti, Nicholas J Day, Tong Zhang, Kamila Husarcikova, Monika Bambouskova, Daved H Fremont, Wei-Jun Qian, Sergej Djuranovic, Slavica Pavlovic-Djuranovic, Vsevolod V Belousov, Andrzej M Krezel, Maxim N Artyomov
Journal: Nature Metabolism (2025)
Executive summary of the KDIGO 2025 Clinical Practice Guideline for the Management of Nephrotic Syndrome in Children
Authors: Jürgen Floege, Keisha L Gibson, Marina Vivarelli, Adrian Liew, Jai Radhakrishnan, Ethan M Balk, Craig E Gordon, Gaelen Adam, Marcello Tonelli, Amy Earley, Brad H Rovin
Journal: Kidney International (2025)

The Kidney Disease: Improving Global Outcomes (KDIGO) Clinical Practice Guideline for the Management of Glomerular Diseases was last updated and published in 2021. KDIGO continues to be committed to the nephrology community to provide periodic updates, based on new developments for each of the glomerular diseases. For children with nephrotic syndrome, the updated guideline now contains a treatment algorithm on when to perform a kidney biopsy and/or genetic testing and which immunosuppressive therapy to use in children with a complete response to glucocorticoids (steroid sensitive), who subsequently become infrequent or frequent relapsers or even steroid dependent. If a glucocorticoid-sparing agent must be considered after failure of an initial glucocorticoid therapy to induce remission, the choice among a calcineurin inhibitor, oral cyclophosphamide, levamisole, mycophenolate mofetil, and rituximab is a decision that requires consideration of patient-related issues such as resources, adherence, adverse effects, and patient preferences. Herein, an executive summary of the most important changes in the KDIGO 2025 Clinical Practice Guideline for the Management of Nephrotic Syndrome in Children is provided as a quick reference.
GLP-1 receptor agonists and other incretin mimetics for diabetes and chronic kidney disease—a KDIGO commentary
Authors: Ian H de Boer, M Luiza Caramori, Juliana C N Chan, Hiddo J L Heerspink, Kamlesh Khunti, Adrian Liew, Erin D Michos, Sankar D Navaneethan, Wasiu A Olowu, Tami Sadusky, Nikhil Tandon, Katherine R Tuttle, Christoph Wanner, Katy G Wilkens, Sophia Zoungas, Peter Rossing
Journal: Kidney International (2025)
Helmholtz Health task force to strengthen prevention research and its translation globally
Authors: Eleftheria Zeggini, Ute Mons, Janine Krüger, Erika von Mutius, Anette-Gabriele Ziegler, Anja Braun, Michael Hoffmeister, Karen Steindorf, Stan A. Gorski, Markus Landthaler, Young-Ae Lee, Gabriele G. Schiattarella, N. Ahmad Aziz, Monique M. B. Breteler, Sarah Jewell, Birgit Grün, Carlos A. Guzman, Berit Lange, Fabian H. Leendertz, Sandra Hamann, Nadja Knauthe, Annette Peters
Journal: Nature Medicine (2025)
Description and comparison of national surveillance systems and response measures for Aedes-borne diseases in France, Italy and Portugal: a benchmarking study, 2023
Authors: Emmanouil Alexandros Fotakis, Berta Grau-Pujol, David Kelly, Pedro Pinto Leite, João Vieira Martins, Maria João Alves, Marco Di Luca, Giulietta Venturi, Federica Ferraro, Florian Franke, Clément Pietin, Clémentine Calba, Tanja Charles, Flavia Riccardo, Paula Vasconcelos, Lauriane Ramalli
Journal: Eurosurveillance (2025)

Background Regions of southern Europe are increasingly colonised by Aedes albopictus, with incidence of autochthonous dengue cases rising in recent years. Aim We describe and compare Aedes -borne disease (dengue, chikungunya and Zika) incidence from 2017 to 2023, and the surveillance systems and response measures operating in France, Italy and Portugal in 2023, to improve surveillance, prevention, preparedness and response in Europe. Methods We performed a benchmarking analysis to systematically capture the systems used in each country. We collected data from key-informant interviews, national guidelines, reports and scientific literature using a standardised questionnaire adapted from the European Centre for Disease Prevention and Control framework. Results All three countries have an integrated surveillance system for Aedes -borne diseases and share similarities in surveillance type, geographic coverage and case definitions. Differences entail mainly event-based and active surveillance activities. Geographic coverage of vector surveillance is national in France and Portugal but regional in Italy. In response to autochthonous transmission, all countries implement/foresee active case-finding and blood safety protocols, while France and Italy strongly rely on vector control. Upon vector detection in non-colonised areas, the three countries implement ad hoc entomological surveillance and vector control. Conclusions Surveillance systems and response measures in France, Italy and Portugal are broadly similar, with variations reflecting differences in healthcare system organisation (centralised in Portugal and France, regionalised in Italy), Ae. albopictus distribution and local transmission of Aedes- borne diseases. Risk-based surveillance, considering the national and cross-border epidemiological and entomological situations, can strengthen preparedness and early warning for Aedes -borne diseases in Europe.
Prevalence and risk factors for carriage of carbapenem-resistant Acinetobacter baumannii in post-acute care hospitals, Israel, 2021
Authors: Vered Schechner, Samira Masarwa, Gabrielle D Levi, Adi Cohen, Fadi Assi, Moshe Bechor, Elizabeth Temkin, Alona Keren-Paz, Mitchell J Schwaber, Yehuda Carmeli
Journal: Eurosurveillance (2025)

Background Post-acute care hospitals (PACH) may act as regional reservoirs for multidrug-resistant organisms. Aim We aimed to investigate the prevalence of carbapenem-resistant Acinetobacter baumannii (CRAB) carriers and identify risk factors for CRAB carriage in PACH. Methods We conducted a point prevalence survey in 18 PACH in Israel from June to December 2021. We screened patients in 55 wards of four types (mechanical ventilation, skilled nursing, sub-acute and rehabilitation) for CRAB carriage from skin, rectum and tracheostomy secretions (if applicable). We collected data on patient characteristics (including prior CRAB carriage) and ward and institution characteristics. We calculated the prevalence of CRAB carriers, the percentage of newly detected carriers, and assessed predictors of CRAB carriage using a mixed-effects logistic regression model. Results We screened 1,725 patients, with 385 (22%) testing positive for CRAB. The median prevalence of CRAB carriers was 48% (interquartile range (IQR): 33–70) in ventilation wards, 28% (IQR: 18–46) in skilled nursing wards, 8% (IQR: 6–13) in sub-acute wards and 0% (IQR: 0–3) in rehabilitation wards. Only 31% (118/385) had a known history of CRAB carriage. Individual risk factors for CRAB positivity included known CRAB carriage, bedsores and presence of a feeding tube. Modifiable ward-level risk factors included poor availability of alcohol-based hand rub (adjusted odds ratio (aOR) = 3.22; 95% confidence interval (CI): 1.52–6.81) and suctioning in common areas (aOR = 2.23; 95% CI: 1.30–3.85). Conclusions The hidden reservoir of CRAB carriers in Israeli ventilation and skilled nursing wards is large. We identified modifiable risk factors at ward level, highlighting areas for targeted intervention.
Increased incidence of human leptospirosis and the effect of temperature and precipitation, the Netherlands, 2005 to 2023
Authors: Ilja Obels, Lapo Mughini-Gras, Miriam Maas, Diederik Brandwagt, Nikita van den Berge, Daan W Notermans, Eelco Franz, Erika van Elzakker, Roan Pijnacker
Journal: Eurosurveillance (2025)

Background The incidence of leptospirosis, a zoonotic infection transmitted mainly by rodents, has increased in humans over the past decade in the Netherlands. Previous studies, mostly from countries with tropical climates, suggest that temperature and rainfall influence leptospirosis incidence. Aim We aimed to identify factors that could explain the increasing leptospirosis incidence in the Netherlands, including temperature and precipitation. Methods Epidemiological data of leptospirosis cases notified from 2005 to 2023 to the national surveillance system were analysed to identify changes over the years. Negative binomial regression models were used to assess associations between weather variables and leptospirosis incidence. Results From 2005 to 2023, 1,164 cases were notified. The annual number of cases increased 2.7-fold in the period of 2019–2023 compared with 2005–2009, and the number of autochthonous cases 4.1-fold. Data from 1,158 cases were included in the analyses, and 596 (51.5%) of these cases were autochthonous. Most cases were male (n = 927; 80.1%), needed hospital treatment (n = 861; 74.4%) and acquired the infection through contact with surface water and/or soil (n = 611, 72.6%). Higher mean winter (incidence rate ratio (IRR) = 1.27; 95% confidence interval (CI): 1.18–1.36) and summer (IRR = 1.38; 95% CI: 1.18–1.61) temperatures were significantly associated with increased leptospirosis incidence. Conclusion Leptospirosis incidence has increased over the past decades and may continue to increase due to climate change. Prevention should aim at advising the appropriate preventive measures to avoid exposure to Leptospira and increasing awareness about leptospirosis among clinicians to allow for timely diagnosis and treatment.
Seroprevalence of West Nile virus, Greece, 2020
Authors: Michalis Koureas, Asimina Nasika, Athanasios G Lianos, Alexandros Vontas, Maria A Kyritsi, Ioanna Voulgaridi, Alexia Matziri, Zacharoula Bogogiannidou, Fani Kalala, Varvara A Mouchtouri, Matthaios Speletas, Christos Hadjichristodoulou
Journal: Eurosurveillance (2025)

Background West Nile virus (WNV) is a growing public health concern in Europe. Greece is one of the most affected countries in Europe, with the highest annual incidences. Aim We aimed at assessing IgG antibodies to WNV in the Greek population and compared the results with a nationwide survey conducted in the period 2012–2013. Methods In a geographically stratified sampling, 4,416 serum samples were collected and analysed for WNV-specific IgG antibodies using ELISA. Samples positive for WNV IgG were further tested with a WNV serum neutralisation test to detect false positives. Results The weighted seroprevalence, adjusted for age, sex and region, was 2.83% (95% confidence interval (CI): 2.32–3.44) in the 4,416 samples tested, significantly higher than in the 2012–2013 survey (1.55%; 95% CI: 1.17–2.04). The seropositivity increased with age with the highest seroprevalence in persons aged ≥ 80 years (6.04%; 95% CI: 3.28–10.88). No significant differences in seropositivity were observed between sexes or regions. We estimated that 312 (95% CI: 256–379) persons had a WNV infection per a case of West Nile neuroinvasive disease (WNND). A certain degree of discordance was observed between areas with increased seroprevalence and those with an increased incidence of WNND. Conclusion Our study reveals a wider geographical spread of WNV infections in Greece compared with previous investigations. The nearly twofold increase in seroprevalence highlights the need for ongoing monitoring and preventive measures to mitigate the impact of WNV on public health in Greece.
Zero-shot evaluation reveals limitations of single-cell foundation models
Authors: Kasia Z Kedzierska, Lorin Crawford, Ava P Amini, Alex X Lu
Journal: Genome biology (2025)

Abstract Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of models in zero-shot settings is critical to applications that exclude the ability to fine-tune, such as discovery settings where labels are unknown. Our evaluation of the zero-shot performance of Geneformer and scGPT suggests that, in some cases, these models may face reliability challenges and could be outperformed by simpler methods. Our findings underscore the importance of zero-shot evaluations in development and deployment of foundation models in single-cell research.
Advances of Metal‐Based Nanomaterials in the Prevention and Treatment of Oral Infections
Authors: Junnan Qi, Chao Si, Haofeng Liu, Huen Li, Chunru Kong, Yawen Wang, Bei Chang
Journal: Advanced Healthcare Materials (2025)

The complicated environment of the oral cavity presents significant challenges to traditional antibacterial approaches, which has driven the exploration of novel therapeutic strategies. Metal-based nanomaterials (MNMs), with diverse antibacterial mechanisms (e.g., membrane disruption, oxidative stress) and evolution from empirical to theory-guided design, exhibit immense potential. This review introduces the pioneering Hierarchical Response Strategy Framework, systematically classifying MNM therapeutic systems into three progressive levels: Primary category, comprising MNMs that exert spontaneous antibacterial effects based on inherent physicochemical properties (e.g., ion release); Secondary category, including MNMs with precisely controlled antibacterial actions by microenvironmental or stimulus-responsive mechanisms (e.g., light-induced ROS); and Tertiary category, encompassing MNMs that integrate antibacterial and regenerative functions for multidimensional therapy (e.g., remineralization). Through this framework, the authors elucidate MNMs' transition from single-function to precision-controlled, multifunctional synergy, analyze the impact of metal elements and structural design on efficacy, and summarize their applications in dental caries, endodontic infections, and periodontal disease, etc. This framework offers a novel perspective on existing research and a theoretical foundation for the rational design of next-generation precise, smart, and comprehensive anti-infective materials.
Integrated proteomics identifies troponin I isoform switch as a regulator of a sarcomere-metabolism axis during cardiac regeneration
Authors: Timothy J Aballo, Jiyoung Bae, Wyatt G Paltzer, Emily A Chapman, Andrew J Perciaccante, Melissa R Pergande, Rebecca J Salamon, Dakota J Nuttall, Morgan W Mann, Ying Ge, Ahmed I Mahmoud
Journal: Cardiovascular Research (2025)

Abstract Aims Adult mammalian cardiomyocytes have limited regenerative potential, and after myocardial infarction (MI), injured cardiac tissue is replaced with fibrotic scar. In contrast, the neonatal mouse heart possesses a regenerative capacity governed by cardiomyocyte proliferation; however, a metabolic switch from glycolysis to fatty acid oxidation during postnatal development results in loss of this regenerative capacity. Interestingly, a sarcomere isoform switch also takes place during postnatal development where slow skeletal troponin I (ssTnI) is replaced with cardiac troponin I (cTnI). It remains unclear whether there is an interplay between sarcomere isoform switching, cardiac metabolism, and regeneration. Methods and results In this study, we employ proteomics, metabolomics and lipidomics, transgenic mice, MI models, and histological analysis to delineate the molecular and sarcomeric transitions that occur during cardiac maturation and regeneration. First, we utilize integrated quantitative bottom-up and top-down proteomics to comprehensively define the proteomic and sarcomeric landscape during postnatal heart maturation. By employing a cardiomyocyte-specific ssTnI transgenic mouse model, we discovered that ssTnI overexpression increased cardiomyocyte proliferation and the cardiac regenerative capacity of the postnatal heart following MI compared to control mice by histological analysis. Our global proteomic analysis of ssTnI transgenic mice following MI reveals that ssTnI overexpression induces a significant shift in the cardiac proteomic landscape. Additionally, our lipidomic analysis demonstrated a significant upregulation of lipid species in the transgenic mice. This proteomic shift is characterized by an upregulation of key proteins involved in glycolytic metabolism. Conclusions Collectively, our data suggest that the postnatal TnI isoform switch may play a role in the metabolic shift from glycolysis to fatty acid oxidation during postnatal maturation. This underscores the significance of a sarcomere-metabolism axis during cardiomyocyte proliferation and heart regeneration.
Reliable Harvest of Injectable Human Mesenchymal Stem Cell Sheets by Modulating Cell‐Substrate Adhesion Strength
Authors: Jemin Yeun, Seonghyeon Park, Younseong Song, Sung Hyun Yoon, Sang Yu Sun, Booseok Jeong, Minkyung Kim, Kyoung G. Lee, Sung Gap Im, Jieung Baek
Journal: Advanced Healthcare Materials (2025)

Abstract Cell sheet engineering has emerged as a promising scaffold‐free strategy in cell‐based therapeutics, preserving essential cell‐cell and cell‐extracellular matrix (ECM) interactions. To enable minimally invasive delivery, a key challenge relies on making the cell sheets compatible with injection‐based administration without subjecting sensitive cells to physical or thermal stresses. This study addresses a reliable method for controlling cell sheet dimensions by combining differential cell adhesion‐guided micropatterning along with an isothermal detachment method. The surface composition of a copolymer, poly(ethylene glycol dimethacrylate‐co‐hydroxyethyl methacrylate) is delicately controlled via initiated chemical vapor deposition to ensure intact cell adhesion and rapid cell detachment under isothermal condition. The optimized surface further allows hydrophobic microcontact printing for creating micron‐sized sheets. Human mesenchymal stem cell sheets harvested with this method show preserved ECM without compromising cell viability after both detachment and injection. Moreover, the injected cell sheets substantially enhance the angiogenic potential of human umbilical vein endothelial cells, demonstrating the sustained therapeutic activity of the cell sheet after injection. It is believed that this approach has great potential to broaden the scope of cell sheet engineering, serving as a robust platform for regenerative medicine.
Enhanced intracranial aneurysm development in a rat model of polycystic kidney disease
Authors: Anne F Cayron, Sandrine Morel, Maral Azam, Julien Haemmerli, Tomohiro Aoki, Philippe Bijlenga, Eric Allémann, Brenda R Kwak
Journal: Cardiovascular Research (2025)

Abstract Aim Polycystic kidney disease (PKD) patients have a high intracranial aneurysms (IAs) incidence and risk of rupture. The mechanisms that make PKD patients more vulnerable to IA disease are still not completely understood. The PCK rat is a well-known PKD model and has been extensively used to study cyst development and kidney damage. Here, we used this rat model to study IA induction and vulnerability. Methods and results IAs were induced in wild-type (WT) and PCK rats and their incidence was followed. Variation in the anatomy of the circle of Willis was studied in PCK rats and PKD patients. Immunohistochemistry was performed in rat IAs and in human ruptured and unruptured IAs from patients enrolled in the @neurIST observational cohort. An increased frequency of fatal aortic dissection was unexpectedly observed in PCK rats, which was due to modifications in the elastic architecture of the aorta in combination with the induced hypertension. Interestingly, IAs developed faster in PCK rats compared to WT rats. Variations in the anatomy of the circle of Willis were identified in PCK rats and PKD patients, a risk factor that may (in part) explain the higher IA incidence found in these groups. At 2-weeks after induction, the endothelium of IAs from PCK rats showed a decrease in the tight junction proteins zonula occludens-1 and claudin-5. Furthermore, the type III collagen content was lower in IAs of PCK rats at 4-weeks post-surgery. The decrease in tight junction proteins was also observed in the endothelium of human ruptured IAs compared to unruptured IAs. Conclusions Our study showed that PCK rats are more sensitive to IA induction. Variations in the anatomy of the circle of Willis and impaired regulation of tight junction proteins might put PCK rats and PKD patients more at risk of developing vulnerable IAs.
Reprogramming Glucose Metabolism of Macrophage for Acute Liver Failure Therapy with Itaconate Lipo‐Nanodrug
Authors: Chen Qiu, Wei Zhang, Yanan Zhao, Tian Han, Wende Yang, Yajing Liu, Peile Jin, Jifan Chen, Xintao Shuai, Jie Ren, Pintong Huang
Journal: Advanced Healthcare Materials (2025)

Abstract Acute liver failure (ALF) is a life‐threatening disease featuring comprehensive inflammatory response and metabolic disorders in which macrophages exert central roles. A glucose metabolism mediator of macrophages, itaconate, has demonstrated potent anti‐inflammatory efficacy in various diseases, implying that itaconate could work in treating ALF. However, systemic administration of itaconate may lead to immune disorder, making targeting the delivery of itaconate to the liver lesion area highly important. Herein, a liposomal nanodrug incorporating itaconate is developed, and its potential in treating acute liver failure in an ALF murine model established by LPS/D‐GalN administration is tested. The nanodrug shows preferential liver accumulation to effectively alleviate LPS/D‐GalN‐induced hepatic histopathological injury by decreasing oxidative stress. Moreover, it reprograms the glucose metabolism of macrophages, resulting in macrophage repolarization toward the anti‐inflammatory phenotype. Furthermore, western‐blot and immunohistochemical assays verifies that the nanodrug may inhibit aerobic glycolysis of macrophages in an NRF2 and STING‐dependent manner. These results underline the promise of the nanodrug for ALF treatment by reprogramming glucose metabolism.