tbuckley/cabot-search huggingface dataset:
ctDNA detection in cerebrospinal fluid and plasma and mutational concordance with the primary tumor in a multicenter prospective study of patients with glioma
Authors: S Cabezas-Camarero, R Pérez-Alfayate, V García-Barberán, M L Gandía-González, P García-Feijóo, I López-Cade, V Lorca, I Casado-Fariñas, M A Cerón, M Paz-Cabezas, M J Sotelo, M García Conde, H Roldán Delgado, Y Sánchez Medina, I Díaz-Millán, P Pérez-Segura
Journal: Annals of Oncology (2025)
Stewardship underpins sustainable foraging
Authors: Irene Teixidor-Toneu, Giulia Mattalia, Sophie Caillon, Abdullah Abdullah, Živa Fiser, Pål Karlsen, Shujaul Mulk Khan, Anneleen Kool, Gabriela Loayza, Anna Porcuna-Ferrer, Ismael Vaccaro, Christoph Schunko
Journal: Trends in Ecology & Evolution (2025)

Foraging wild plants and mushrooms can be both beneficial and detrimental to biodiversity. We examine the role of stewardship practices, which are grounded in care, knowledge, and agency, in fostering sustainable use of wild species. These practices are pervasive among foragers across social-ecological systems yet neglected in research and policymaking.
Novel “Hot Spring”-Mimetic Scaffolds for Sequential Neurovascular Network Reconstruction and Osteoporosis Reversion
Authors: Yanan Zhao, Jiawei Liu, Liangcong Hu, Xiaokang Yao, Rong Tu, Takashi Goto, Lianmeng Zhang, Xiaopei Wu, Guohui Liu, Honglian Dai
Journal: Biomaterials (2025)
Subtyping of Primary Aldosteronism by Adrenal Venous Sampling
Authors: Gian Paolo Rossi, Michele Battistel, Teresa Maria Seccia, Federico Bernardo Rossi, Giacomo Rossitto
Journal: Endocrine Reviews (2025)

Abstract Primary aldosteronism (PA), the most common cause of arterial hypertension, is surgically curable if a unilateral source of the hyperaldosteronism is discovered. To identify the patients who are curable, all current guidelines recommend adrenal venous sampling (AVS), a procedure which, albeit simple in principle, remains scarcely available and markedly under-utilized, because it is still perceived as technically challenging, invasive, and difficult to interpret. The lack of uniformly accepted standards for performance and interpretation of AVS, alongside the diffuse concerns that, albeit quite rarely, it can be complicated by adrenal vein rupture, contribute to the scant utilization of AVS. In the last decade, several major studies have contributed to a greater understanding of the use of AVS in PA patients, thus paving the way to a more rational and effective application that can allow to diagnose many more PA patients with a unilateral form of the disease to be referred for curative adrenalectomy. Moreover, microcatheters and androstenedione have been introduced to increase the success rate. This review provides updated information on the subtyping of PA by means of AVS and examines key issues on the selection and preparation of patients, the optimal performance of the procedure, and the interpretation of its results for diagnostic purposes, even in the most challenging cases. Situations when AVS can be omitted before surgery and alternative functional imaging techniques that have been proposed to identify unilateral surgical curable PA to circumvent the bottle-neck represented by the limited availability of AVS world-wide, are also discussed.
Association of Diabetic Ketoacidosis at Onset, Diabetes Technology Uptake, and Clinical Outcomes After 1 and 2 Years of Follow-up: A Collaborative Analysis of Pediatric Registries Involving 9,269 Children With Type 1 Diabetes From Nine Countries
Authors: Klemen Dovc, Vit Neuman, Gemulla Gita, Valentino Cherubini, G. Todd Alonso, Maria Fritsch, Claudia Boettcher, Carine de Beaufort, Reinhard W. Holl, Martin de Bock
Journal: Diabetes Care (2025)

OBJECTIVE This study examined the association between diabetic ketoacidosis (DKA) at type 1 diabetes diagnosis and long-term glycemic outcomes, insulin requirements, BMI SDS, and diabetes technology uptake in youth. RESEARCH DESIGN AND METHODS Data were from nine countries (Austria, Czechia, Germany, Italy, Luxembourg, New Zealand, Slovenia, Switzerland, and U.S. [Colorado]), including youth (0.5–15.9 years) diagnosed with type 1 diabetes in 2019–2020 and followed for 2 years thereafter. Participants were divided into three groups: no DKA, nonsevere, and severe DKA at diagnosis. HbA1c, insulin requirements, BMI SDS, and use of technology, including automated insulin delivery (AID), were assessed. RESULTS The analysis included 9,269 individuals (54.8% males, mean age 9.0 years). DKA at diagnosis was observed in 34.2% of participants and severe DKA in 12.8%. After 1 year, adjusted mean HbA1c was higher in the severe DKA group (7.41%) compared with nonsevere DKA (7.23%, P = 0.001) and no DKA groups (7.14, P &amp;lt; 0.001), and this difference persisted after 2 years (7.58% vs. 7.38% [P &amp;lt; 0.001] and vs. 7.32% [P &amp;lt; 0.001]). Higher BMI SDS was observed in both DKA groups compared with no DKA. The use of AID was associated with lower HbA1c levels compared with other treatment modalities and moderated differences between DKA groups after 2 years of follow-up (P = 0.072). CONCLUSIONS Severe and nonsevere DKA at type 1 diabetes diagnosis were both associated with persistently higher HbA1c and higher BMI SDS. AID use diminishes the association of DKA at diagnosis and higher HbA1c over time.
Exploring the Varied Clinical Presentation of Pediatric Asthma through the Metabolome
Authors: Kevin M. Mendez, Priyadarshini Kachroo, Nicole Prince, Mengna Huang, Margaret Cote, Su H. Chu, Yulu Chen, Rinku Sharma, Julian Hecker, Liang Chen, Robert Gerszten, Clary Clish, Lydiana Avila, Juan C. Celedón, Craig E. Wheelock, Scott T. Weiss, Michael McGeachie, David I Broadhurst, Rachel S Kelly, Stacey N Reinke, Jessica A. Lasky-Su
Journal: American Journal of Respiratory and Critical Care Medicine (2025)

Rationale: Pediatric asthma is heterogeneous, with varied clinical presentations and treatment responses. Metabolomic profiling may uncover shared and unique biological mechanisms across clinical traits that characterize pediatric asthma. Objectives: To characterize the varied clinical presentation of pediatric asthma by examining the metabolome's relationship with 22 clinical traits, categorized into 5 phenotypic domains: airway hyperresponsiveness (AHR), atopy, lung function (LF), blood eosinophil (B-EOS), and blood neutrophil (B-NEU). Methods: Metabolomic profiling was conducted on plasma samples from children in the Childhood Asthma Management Program (CAMP) (n=953) and the Genetic Epidemiology of Asthma in Costa Rica Study (GACRS) (n=1,155) studies. We identified domain-specific and multi-domain metabolites using a fixed-effect meta-analysis of generalized linear models between metabolites and 22 clinical traits. Metabolomic Risk Scores (MRSs) were developed to summarize the metabolic processes for each domain at the patient level. Measurements and Main Results: There were 154 unique metabolites significantly associated with at least one of 22 clinical traits (q-value<0.05). Histamine and kynurenine were significant across 4 domains, while 7 metabolites—12,13-diHOME, azelate, sebacate, PC(P-36:0)/PC(O-36:1), taurine, nudifloramide, and niacinamide—were significant across 3. Notable domain-specific metabolites include n-oleoyl dopamine for AHR, 9-cis-retinoic acid for lung function, phosphatidylcholines for B-EOS, and 2-hydroxybutyric acid for B-NEUT. We then applied the domain-specific MRSs to previously identified patient clusters, enabling a more comprehensive characterization of each endotype. Conclusion: This study demonstrated the power of the metabolome to capture the heterogeneity in the clinical presentation of pediatric asthma and to develop clinically relevant MRSs that inform our understanding of specific metabotypes to guide targeted treatment approaches.
Prenatal VEGF Nano-Delivery Reverses Congenital Diaphragmatic Hernia-associated Pulmonary Abnormalities
Authors: Stavros P. Loukogeorgakis, Federica Michielin, Noura Al-Juffali, Julio Jimenez, Soichi Shibuya, Jessica Allen-Hyttinen, Mary Patrice Eastwood, Ahmed S.N. Alhendi, Joseph Davidson, Eleonora Naldi, Panagiotis Maghsoudlou, Alfonso Tedeschi, Sahira Khalaf, Manuela Platé, Camila Fachin, Andre Dos Santos Dias, Nikhil Sindhwani, Dominic Scaglioni, Theodoros Xenakis, Neil Sebire, Monica Giomo, Simon Eaton, Jaan Toelen, Camilla Luni, Piero Pavan, Peter Carmeliet, Francesca Russo, Samuel Janes, Marko Z. Nikolic, Nicola Elvassore, Jan Deprest, Paolo De Coppi
Journal: American Journal of Respiratory and Critical Care Medicine (2025)

Congenital diaphragmatic hernia (CDH) results in lung hypoplasia. In severe cases, tracheal occlusion (TO) can be offered to promote lung growth. However the benefit is limited, and novel treatments are required to supplement TO. Vascular endothelial growth factor (VEGF) is downregulated in animal models of CDH and could be a therapeutic target, but its role in human CDH is not known. To investigate whether VEGF supplementation could be a suitable treatment for CDH-associated lung pathology. Fetal lungs from CDH patients were used to determine pulmonary morphology and VEGF expression. A novel human ex vivo model of fetal lung compression recapitulating CDH features was developed and used to determine the effect of exogenous VEGF supplementation. A nanoparticle-based approach for intra-pulmonary delivery of VEGF was developed by conjugating it on functionalized nanodiamonds (ND-VEGF) and was tested in experimental CDH in vivo. VEGF expression was downregulated in distal pulmonary epithelium of human CDH fetuses in conjunction with attenuated cell proliferation. The compression model resulted in impaired branching morphogenesis similar to CDH and downregulation of VEGF expression in conjunction with reduced proliferation of terminal bud epithelial progenitors; these could be reversed by exogenous supplementation of VEGF. Prenatal delivery of VEGF with the ND-VEGF platform in CDH fetal rats resulted in lung growth and pulmonary arterial remodelling that was complementary to that achieved by TO alone with appearances comparable to healthy controls. This innovative approach could have a significant impact on the treatment of CDH.
Alcohol Intake, Drinking Pattern, and Risk of Type 2 Diabetes in Three Prospective Cohorts of U.S. Women and Men
Authors: Xinyi Li, Jinhee Hur, Stephanie A. Smith-Warner, Mingyang Song, Liming Liang, Kenneth J. Mukamal, Eric B. Rimm, Edward L. Giovannucci
Journal: Diabetes Care (2025)

OBJECTIVE Although the adverse effects of excessive alcohol consumption are well established, the association between light to moderate alcohol consumption (≤30 g ethanol per day) and risk of type 2 diabetes (T2D) remains controversial and holds substantial public health implications. We aimed to examine the association of total alcohol intake and drinking pattern with T2D among three cohorts, Nurses’ Health Study (NHS), Nurses’ Health Study II (NHSII), and Health Professionals Follow-up Study (HPFS). RESEARCH DESIGN AND METHODS Former regular drinkers were excluded from baseline nondrinkers. Hazard ratios (HRs) and 95% CIs were estimated by Cox models. RESULTS Over 3 decades of follow-up, 20,551 T2D cases were documented among 200,969 participants. Total alcohol intake was associated with a lower risk of T2D, either using nondrinkers or 0.1–4.9 g/day as the reference. The association was robust to extended latency periods and alternative modeling of exposure. Drinking frequency was associated with a lower T2D risk. For example, compared with drinking 1–2 days per week, the HRs (95% CIs) for drinking 5–6 days were 0.73 (0.65, 0.83), 0.73 (0.62, 0.86), and 0.76 (0.67, 0.86) in the NHS, NHSII, and HPFS cohorts, respectively. When modeled jointly, the lower risk of T2D among drinkers was primarily driven by the drinking frequency. The inverse association began at drinking 1–2 days per week in women and 3–4 days per week in men and was strongest for ≥5 days per week, regardless of drinking &amp;lt;10 g or ≥30 g per drinking day. CONCLUSIONS Light to moderate alcohol consumption, especially regular light drinking, was associated with a lower risk of T2D in both men and women.
Multiomics analysis of immune correlatives in hepatocellular carcinoma patients treated with tremelimumab plus durvalumab
Authors: Yuta Myojin, Sepideh Babaei, Rajiv Trehan, Christoph Hoffman, Noemi Kedei, Benjamin Ruf, Mohamed-Reda Benmebarek, Kylynda C Bauer, Patrick Huang, Chi Ma, Cecilia Monge, Changqing Xie, Donna Hrones, Austin G Duffy, Paul Armstrong, Lorenz Kocheise, Fiona Desmond, Jemma Buchalter, Marie Galligan, Colin Cantwell, Ronan Ryan, Jeff McCann, Michele Bourke, Ross Mac Nicholas, Ray McDermott, Joy Awosika, Maggie Cam, Rosanna Krebs, Anuradha Budhu, Mahler Revsine, William D Figg, David E Kleiner, Bernadette Redd, Bradford J Wood, Xin Wei Wang, Firouzeh Korangy, Manfred Claassen, Tim F Greten
Journal: Gut (2025)

Background Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. The combination of tremelimumab and durvalumab is now a standard treatment option for advanced HCC. Objective To study immune responses in HCC patients treated with tremelimumab and durvalumab. Design We treated 28 HCC patients with durvalumab, tremelimumab and locoregional therapies. We performed a high-dimensional multiomics analysis including whole exome sequencing, single-cell RNA seq, CO-Detection by indEXing, flow cytometry and multiplex cytokine/chemokine analysis of patients’ blood and tumour samples and integrated this data to elucidate immune correlatives and response mechanisms. Mice with syngeneic HCC were treated with anti-PD-L1 plus anti-CTLA4 for hepatic lymphocytes, tumour-infiltrating lymphocytes and peripheral blood mononuclear cell analysis. Results The median overall survival was 19.2 months. Tumour tissue analysis revealed enhanced interferon responses, with stronger effects in responders. Gene set variation analysis indicated enhanced antigen presentation in responders. Spatial analysis revealed that non-responder tumours had higher numbers of Tregs located in neighbourhoods enriched with immune cells and expressed higher levels of ICOS and PD-1. Conversely, non-responder PD1+CD8+T in these Treg-enriched neighbourhoods expressed lower ICOS. Cell-communication analysis demonstrated that Treg-CD8+T interaction was enhanced in non-responder tissue. Peripheral blood analysis showed increased classical monocytes in responders and Tregs in non-responders. Treg-CD8+T interaction was confirmed in preclinical models. Finally, single-patient computational analysis from the all-across analysis was performed on 860 features, which led to the identification of multiomics feature sets including Treg features. Conclusion Our study provides a blueprint for in-depth analysis of immune correlates in immunotherapy studies and demonstrates the importance of Treg distribution in HCC. Trial registration numbers NCT02821754 and the EudraCT identifier: 2019-002767-98.
Body composition, exercise-related performance parameters and associated health factors of transgender women, cisgender women and cisgender men volleyball players
Authors: Leonardo Azevedo Alvares, Marcus VL dos Santos Quaresma, Fernanda Patti Nakamoto, Lívia Marcela Santos, Lucas Soglio Navarro, Giovanna Soglio Navarro, Bruno Marcos Mazoca Orozco, Beatriz Meconi Cardoso Sá, Gabriel Barasnevicius Achkar, Camila Guazzelli Marques, Renata Cleia Claudino Barbosa, Raphael Einsfeld Simões Ferreira
Journal: British Journal of Sports Medicine (2025)

Objective The inclusion of transgender athletes in competitive sports has promoted significant dialogue and controversy among exercise-related professionals. The objective of this study was to investigate body composition, exercise-related performance parameters and associated health-related factors of transgender women (TW), cisgender women (CW) and cisgender men (CM) amateur volleyball players. Methods This was a cross-sectional study comprising TW, CW and CM amateur volleyball players eligible with the following characteristics: ‘gender incongruent’ (for TW only); age between 18 and 35 years; body mass index (BMI) between 18.0 and 29.9 kg/m 2 ; ‘very active’ according to the International Physical Activity Questionnaire, and engaged in regular volleyball training for at least 1 year. All participants were assessed for body composition, blood biomarkers, handgrip strength, countermovement jump height (CMJ), squat jump height (SQJ) and maximum oxygen consumption (V̇O 2max ). Results 69 amateur volleyball players were initially evaluated, but only 23 met the inclusion criteria and were included in the study (7 TW, 8 CW and 8 CM). Age (p=0.07) and BMI (p=0.26) were similar between groups. Estradiol (p=0.47), total testosterone (p=1.00) and haemoglobin (p=1.00) levels did not differ between TW and CW. However, analysis not adjusted by confounding variables showed that CM presented higher testosterone levels (p&lt;0.001), haemoglobin levels (p=0.03), lean body mass (p=0.03), handgrip strength (p&lt;0.001), CMJ (p&lt;0.001), SQJ (p=0.012) and V̇O 2max (mL/min) (p=0.001) compared with TW. When adjusted by confounding variables, all p values were &lt;0.05, except for SQJ (p=0.062). Conclusion TW athletes displayed similar exercise performance and biomarkers compared with CW but lower results compared with CM.
TAOK1 suppression improves doxorubicin-induced cardiomyopathy by preventing cardiomyocyte death and dysfunction
Authors: Takaomi Suga, Tomoya Kitani, Masaya Kogure, Masatsugu Oishi, Fumiaki Ito, Atsushi Hoshino, Takehiro Ogata, Koji Ikeda, Satoaki Matoba
Journal: Cardiovascular Research (2025)

Abstract Aims Doxorubicin (DOX) is one of the most effective chemotherapeutic agents for various types of cancers. However, DOX often causes cardiotoxicity, which is referred to as DOX-induced cardiomyopathy (DIC). Despite extensive research, only a limited number of effective treatments are currently available. In this study, we aimed to identify a potential therapeutic target for DIC by preventing DOX-induced cell injury in cardiomyocytes. Methods and results We performed a kinome-wide CRISPR gene knockout screen in human cardiomyocytes derived from pluripotent stem cells (hPSC-CMs) and identified a member of the STE20 kinase family, thousand and one amino acid protein kinase 1 (TAOK1) as a potential regulator of DOX-induced cardiomyocyte death. Using CRISPR-mediated gene knockout and siRNA-mediated gene knockdown, we demonstrated that TAOK1 suppression improved DOX-induced cardiomyocyte death and dysfunction, including sarcomere disarray, contractile dysfunction, DNA damage, and mitochondrial dysfunction in hPSC-CMs. Transcriptome analysis using RNA-Seq also showed that DOX-induced mitochondrial dysfunction was attenuated by TAOK1 suppression. In contrast to the protective role of TAOK1 against DOX toxicity in cardiomyocytes, TAOK1 suppression did not induce DOX resistance in human cancer cell lines. DOX-induced activation of p38 MAPK was markedly attenuated in TAOK1-knockout hPSC-CMs. Furthermore, DOX-induced cardiomyocyte death and disruption of mitochondrial membrane potential were augmented by TAOK1 overexpression, which was partially attenuated by an inhibitor or knockdown of p38 MAPK or an apoptosis inhibitor. Finally, we demonstrated that TAOK1 suppression using AAV-mediated gene silencing attenuated DOX-induced myocardial damage, including myocardial fibrosis, apoptosis, and cardiomyocyte atrophy, resulting in improved cardiac function in a mouse model of DIC. Conclusion Our results indicate that TAOK1 suppression is a promising therapeutic approach for treating DIC in patients with cancer and highlight the advantages of hPSC-CMs as a platform to study drug-induced cardiotoxicity.
Construction and application of a large capacity VNAR library from the whitespotted bamboo shark (Chiloscyllium playgiosum)
Authors: Hao Li, Litong Liu, Xinyi Kang, Chuan-Wei Chen, Mengran Wang, Shaoqin Fu, Qingtong Zhou, Bo Zhao, Dehua Yang, Ming-Wei Wang
Journal: Acta Pharmaceutica Sinica B (2025)
Metagenomic analysis of microbial cell-free DNA from plasma of patients with suspected infections: performance and therapeutic impact in clinical routine
Authors: Jan Esse, Johannes Träger, Philipp Steininger, Karl Bihlmaier, Julia Fürst, Zsofia Bardonicsek-Depnering, Nora Naumann-Bartsch, Patrick Morhart, Ixchel Castellanos, Stefan W Krause, Larissa Herbst, Richard Strauß, Martin Chada, Klaus Korn, Giuseppe Valenza, Daniel Teschner, Christian Bogdan, Jürgen Held
Journal: Clinical Microbiology and Infection (2025)
Plasmacytoid dendritic cells alleviate allergic asthma via airway epithelial cells-dependent thymosin β4 expression
Authors: Yue Li, Zhengrong Chen, Miaomiao Han, Zhen Duan, Ruizhe Li, Xinyi Cui, Haiyan Ge, Yilai Shu, Huabin Li, Rui He
Journal: Journal of Allergy and Clinical Immunology (2025)
Detection of Treponema pallidum DNA for diagnosis, resistance identification, and treatment outcome prediction in early syphilis among men who have sex with men
Authors: Tzong-Yow Wu, Kuan-Yin Lin, Hsin-Yun Sun, Yu-Shan Huang, Wang-Da Liu, Li-Hsin Su, Wen-Chun Liu, Yi-Ching Su, Sui-Yuan Chang, Chien-Ching Hung
Journal: Clinical Microbiology and Infection (2025)
Wearable blood pressure sensors for cardiovascular monitoring and machine learning algorithms for blood pressure estimation
Authors: Seongwook Min, Jaehun An, Jae Hee Lee, Ji Hoon Kim, Daniel J. Joe, Soo Hwan Eom, Chang D. Yoo, Hyo-Suk Ahn, Jin-Young Hwang, Sheng Xu, John A. Rogers, Keon Jae Lee
Journal: Nature Reviews Cardiology (2025)
Post-Marketing Safety Surveillance of Adalimumab, Secukinumab, and Infliximab in Hidradenitis Suppurativa: An Analysis of the FDA Adverse Events Reporting System (FAERS) Database
Authors: Aditya Joshi, Lauren Gawey, Carissa Saadi, Pragna Naidoo, Jonathan W Rick, Song Y Park, Anna L Cogen, Steven D Daveluy, Jennifer L Hsiao, Vivian Y Shi
Journal: Journal of the American Academy of Dermatology (2025)
Persistent severe acute kidney injury is a major modifiable determinant of outcome during critical illness
Authors: Hernando Gómez, Xinlei Chen, John S. Minturn, Ivan E. Saraiva, Natsumi Hamahata, Arsalan Zaidi, Ankit Sakhuja, Chung-Chou H. Chang, Gilles Clermont, Alexander Zarbock, John A. Kellum
Journal: Intensive Care Medicine (2025)
KRASG12D-driven pentose phosphate pathway remodeling imparts a targetable vulnerability synergizing with MRTX1133 for durable remissions in PDAC
Authors: Xiangyan Jiang, Tao Wang, Bin Zhao, Haonan Sun, Yuman Dong, Yong Ma, Zhigang Li, Yuxia Wu, Keshen Wang, Xiaoying Guan, Bo Long, Long Qin, Wengui Shi, Lei Shi, Qichen He, Wenbo Liu, Mingdou Li, Lixia Xiao, Chengliang Zhou, Hui Sun, Jing Yang, Junhong Guan, Huinian Zhou, Zeyuan Yu, Zuoyi Jiao
Journal: Cell Reports Medicine (2025)