tbuckley/cabot-search huggingface dataset:
Identifying appropriate external control datasets in support of future glioblastoma clinical trials leveraging external data
Authors: Rifaquat Rahman, Steffen Ventz, Robert Redd, Geoffrey Fell, Yujue Tan, Peter Orio, Kirk Tanner, Patrick Y Wen, Lorenzo Trippa
Journal: Neuro-Oncology (2025)

Abstract Background Recent interest in leveraging external data for clinical trial design and analysis in glioblastoma has raised questions on the identification of appropriate data to use as external controls for future trials. We perform a comprehensive analysis assessing candidate sources of external data and comparing clinical trial and real-world datasets in newly diagnosed glioblastoma. Methods Individual patient-level data (PLD) from several clinical trials, a large academic institutional database and a registry (National Cancer Database) were used for analysis of patients receiving standard of care radiation with concurrent and adjuvant temozolomide. Data summaries from randomized trials 2012-2022 were analyzed to account for trials without available PLD. Multivariable modeling was employed to compare survival across datasets. Results In total, 8 datasets with PLD for 3061 patients with newly diagnosed glioblastoma treated with standard chemoradiation were analyzed. Patients on trials were younger (age&amp;lt;60:64% vs. 48%,p&amp;lt;0.001) and had higher KPS (KPS&amp;gt;90:58% vs. 48%,p&amp;lt;0.001) compared to non-trial patients. Patients in clinical trials exhibited inferior survival relative to non-trial patients (HR 1.30,95%CI 1.13-1.48,p&amp;lt;0.001) after adjustment for age, sex, KPS, extent of resection and MGMT methylation status. In assessment of data summaries of 19 randomized trials, there was no detectable time-trend toward improved outcomes 2012-2022. Conclusions In newly diagnosed glioblastoma patients treated with standard of care chemoradiation, there were significant differences between trial datasets and real-world datasets but no evidence of a trial effect benefit from trial participation. After adjustment of relevant covariates, there was no evidence of temporal drift of improved survival over the last decade.
Frequency and timing of multiple skin cancer development in five cohorts
Authors: Lee Wheless, Kai-Ping Liao, Siwei Zheng, Yao Li, Lydia Yao, Yaomin Xu, Christopher Madden, Jacqueline Ike, Isabelle T Smith, Dominique Mosley, Sarah Grossarth, Rebecca I Hartman, Otis Wilson, Adriana Hung, Mackenzie R Wehner
Journal: Journal of the American Academy of Dermatology (2025)
Impact of exercise on musculoskeletal pain and disability in the postpartum period: a systematic review and meta-analysis
Authors: Stephanie-May Ruchat, Nicole Beamish, Sophie Pellerin, Muhammad Usman, Sinead Dufour, Sarah Meyer, Allison Sivak, Margie H Davenport
Journal: British Journal of Sports Medicine (2025)

Abstract Objective To examine the impact of exercise on musculoskeletal pain (low back pain (LBP), pelvic girdle pain (PGP), lumbopelvic pain (LBPP) and bodily pain) and kinesiophobia during the postpartum period. Design Systematic review with random effects meta-analysis. Study eligibility criteria Online databases were searched from database inception to 12 January 2024. Studies of all designs (except case studies) of any publication date or language were included if they contained information on the population (women and people in the first year postpartum), intervention (subjective or objective measures of frequency, intensity, duration, volume or type of exercise, alone (‘exercise-only’) or in combination with other interventions (eg, electrotherapy, infrared irradiation, ultrasound; ‘exercise+cointervention’)), comparator (no exercise or different exercise measures) and outcome (symptom severity of LBP/PGP/LBPP, related disability, bodily pain and kinesiophobia). Results 37 studies (N=3769 participants) from 15 countries were included. Moderate certainty evidence showed that exercise-only interventions, including various strengthening exercises targeting the trunk muscles, were associated with a greater reduction in LBPP symptom severity (4 randomised controlled trials (RCTs), n=210; mean difference −2.21 points (on a 0–10 Visual Analogue Scale) 95% CI −3.33 to −1.08) and related disability (6 RCTs, n=296; standardised mean difference −1.17, 95% CI −1.92 to −0.43; large effect size) as compared with no exercise. Similar results were found for bodily pain (2 RCTs, n=318). Evidence was limited and inconclusive regarding the impact of exercise interventions on kinesiophobia. Conclusion Postnatal exercises, including a variety of muscular strengthening exercises targeting the trunk muscles, decrease the symptom severity of LBPP and related disability.
Prehospital care of suspected spine-injured lacrosse athletes: a systematic search, evidence review, and consensus recommendations
Authors: Thomas G Bowman, Richard J Boergers, Shane V Caswell, Darryl Conway, William J Mills, Margot Putukian, Mandy Merritt, Jason D Vescovi, Edward Strapp, Kellie Loehr, Jennifer Monnin, Rebecca Vozzo, Robert Hatch, Caroline Wesley Siler, Samantha E Scarneo-Miller
Journal: British Journal of Sports Medicine (2025)

Lacrosse has experienced significant growth in popularity worldwide and will return to the Summer Olympic Games in 2028. While there are published consensus recommendations for prehospital care of athletes with suspected spine injuries, there are currently no recommendations specific to lacrosse athletes with and without circulation, airway, or breathing (CAB) compromise. The document aims to determine evidence- and consensus-based best practices and provide implementation recommendations to guide healthcare professionals in the prehospital care of suspected spine-injured lacrosse athletes. We comprised a consensus group of 15 individuals with diverse clinical, research, and administrative experiences to ensure broad representation across lacrosse competition levels. Peer-reviewed scientific and medical research literature was systematically searched for articles on spine injury in lacrosse participants to derive evidence-based recommendations. Following a modified Delphi approach with three rounds of voting, the author panel developed ten consensus-based best practices and implementation recommendations related to the care of potentially spine-injured lacrosse athletes with and without CAB compromise. In addition, recommendations are provided to guide the implementation of key preparations before lacrosse participation, such as developing and distributing an emergency action plan, lacrosse-specific policies and procedures, and cardiopulmonary resuscitation and automated external defibrillator requirements. All recommendations obtained acceptable levels of agreeability, feasibility, and clarity from at least 80% of the panel. The recommendations provide prehospital care guidance for healthcare professionals and event organisers aimed at improving patient outcomes following suspected spine injury.
Insufficient evidence for a severe bottleneck in humans during the Early to Middle Pleistocene transition
Authors: Trevor Cousins, Arun Durvasula
Journal: Molecular Biology and Evolution (2025)

Abstract A recently proposed model suggests a severe bottleneck in the panmictic ancestral population of modern humans during the Early to Middle Pleistocene transition. Here, we show this model provides a worse fit to the data than a panmictic model without the bottleneck.
Controlled delivery of HIF-1α via extracellular vesicles with collagen-binding activity for enhanced wound healing
Authors: Sungmi Jeon, Seongeon Cho, Seongkyeong Yoo, Yeji Lee, Jiyoung Goo, Yu Jin Jeong, Gi-Hoon Nam, Hyun-Tae Shin, Jong-Wan Park, Cherlhyun Jeong, Sang Wha Kim, Iljin Kim, In-San Kim
Journal: Journal of Controlled Release (2025)
Improved patient satisfaction and overall experience in the post-operative period utilizing visual education on wound healing for primary closures: A prospective cohort study
Authors: Shirley Lin, Aaron Bao, Daniela Barata Herrera, Emanuelle Rizk, Chi Trinh, Luke Zhao, Calvin O'Donnell, Rachel De Armas, Erina Lie, Ashley Antony, Karina Paci, Elise Ng, Jeffrey Scott, Kristin Bibee
Journal: Journal of the American Academy of Dermatology (2025)
Advances in Nanotechnology for the Diagnosis and Management of Metabolic Dysfunction-associated Steatotic Liver Disease
Authors: Fenfen Li, Ruyan Yuan, Jiamin Zhang, Bing Su, Xiaolong Qi
Journal: Asian Journal of Pharmaceutical Sciences (2025)

Metabolic dysfunction-associated steatotic liver disease (MASLD) has a high global incidence and associated with increased lipid accumulation in hepatocytes, elevated hepatic enzyme levels, liver fibrosis, and hepatic carcinoma. Despite decades of research and significant advancements, the treatment of MASLD still faces formidable challenges. Nanoprobes for diagnostics and nanomedicine for targeted drug delivery to the liver present promising options for MASLD diagnosis and treatment, enhancing both imaging contrast and bioavailability. Here, we review recent advances in nanotechnology applied to MASLD diagnosis and treatment, specifically focusing on drug delivery systems targeting hepatocytes, hepatic stellate cells, Kupffer cells, and liver sinusoidal endothelial cells. This review aims to provide an overview of nanomedicine's potential in early MASLD diagnosis and therapeutic interventions, addressing related complications.
Characterisation of the antinociceptive effect of baricitinib in the collagen antibody-induced arthritis mouse model
Authors: Nils Simon, Resti Rudjito, Lydia Moll, Katalin Sandor, Juan Antonio Vazquez-Mora, Zerina Kurtović, Alexandra Kuliszkiewicz, Carlos E Morado Urbina, Sven David Arvidsson, Eduardo Mendoza-Sánchez, Giovanni E López-Delgado, Qing Luo, Qiaolin Deng, Arisai Martínez Martínez, Jens Gammeltoft Gerwien, Paul Karila, Venkatesh Krishnan, Juan Miguel Jiménez-Andrade, Camilla I Svensson
Journal: Annals of the Rheumatic Diseases (2025)

Many rheumatoid arthritis (RA) patients continue to experience persistent pain even after successful management of joint inflammation. Clinical data indicate that RA patients treated with the JAK inhibitor baricitinib consistently achieve pain relief that cannot be entirely attributed to its anti-inflammatory effects. In this study, we investigated the antinociceptive properties of baricitinib using the collagen antibody-induced arthritis (CAIA) model in which mechanical hypersensitivity persists long after resolution of joint inflammation. The effects of baricitinib, etanercept (tumour necrosis factor inhibitor), and LP-922761 (adaptor protein-2 (AP2) associated kinase 1 (AAK1) inhibitor) on pain-like behaviour in CAIA mice were examined. Tissue samples from the late, low-grade inflammatory phase were examined for the effect of the treatments. Additionally, in vitro experiments using dorsal root ganglion (DRG) cells were conducted to assess baricitinib's influence on neuronal excitability and cell morphology. Baricitinib reduced CAIA-induced joint inflammation, but its antinociceptive effects were most pronounced during the late phase when etanercept was ineffective. Administering baricitinib both early and late significantly decreased CAIA-induced bone loss, synovial innervation, and baseline STAT3 phosphorylation in ankle joints and DRGs. Unlike etanercept, baricitinib effectively reduced pain-like behaviour and synovial hyperinnervation when administered exclusively in the late phase. Additionally, baricitinib modulated glial cell morphology and neuronal excitability in vitro. Notably, it inhibited AAK1 signalling in DRGs, with AAK1 kinase activity blockade providing an antinociceptive effect in the CAIA model. Our data suggests that baricitinib has antinociceptive effects by targeting not only immune cells but also neurons and glia cells via inhibition of 2 signalling pathways linked to chronic pain.
IL-4 induces CD22 expression to restrain the effector program of virtual memory T cells
Authors: Bin Yang, Ophélie Piedfort, Guillem Sanchez-Sanchez, Arnaud Lavergne, Meijiao Gong, Garrie Peng, Ariel Madrigal, Georgios Petrellis, Brunette Katsandegwaza, Lucia Rodriguez Rodriguez, Alexis Balthazar, Sarah J. Meyer, Gert Van Isterdael, Julie Van Duyse, Fabienne Andris, Qiang Bai, Thomas Marichal, Bénédicte Machiels, Lars Nitschke, Hamed S. Najafabadi, Irah L. King, David Vermijlen, Benjamin G. Dewals
Journal: Science Immunology (2025)

Parasitic helminths induce the production of interleukin-4 (IL-4), which causes the expansion of virtual memory CD8+ T cells (TVM cells), a cell subset that contributes to the control of coinfection with intracellular pathogens. However, the mechanisms regulating IL-4-dependent TVM cell activation and expansion remain ill defined. Here, we used single-cell RNA sequencing of CD8+ T cells to identify pathways that control IL-4-dependent TVM cell responses. Gene signature analysis of CD8+ T cells identified a cell cluster marked by CD22, a canonical regulator of B cell activation, as a selective surface marker of IL-4-induced TVM cells. CD22+ TVM cells were enriched for interferon-γ and granzyme A and retained a diverse TCR repertoire while enriched in self-reactive CDR3 sequences. CD22 intrinsically regulated the IL-4-induced CD8+ T cell effector program, resulting in reduced responsiveness of CD22+ TVM cells and regulatory functions to infection and inflammation. Thus, helminth-induced IL-4 drives the expansion and activation of TVM cells that is counterinhibited by CD22.
Comparing self reported and physiological sleep quality from consumer devices to depression and neurocognitive performance
Authors: Samir Akre, Zachary D. Cohen, Amelia Welborn, Tomislav D. Zbozinek, Brunilda Balliu, Michelle G. Craske, Alex A. T. Bui
Journal: npj Digital Medicine (2025)

Abstract This study examines the relationship between self-reported and physiologically measured sleep quality and their impact on neurocognitive performance in individuals with depression. Using data from 249 participants with medium to severe depression monitored over 13 weeks, sleep quality was assessed via retrospective self-report and physiological measures from consumer smartphones and smartwatches. Correlations between self-reported and physiological sleep measures were generally weak. Machine learning models revealed that self-reported sleep quality could detect all depression symptoms measured using the Patient Health Questionnaire-14, whereas physiological sleep measures detected “sleeping too much” and low libido. Notably, only self-reported sleep disturbances correlated significantly with neurocognitive performance, specifically with processing speed. Physiological sleep was able to detect changes in self-reported sleep, medication use, and sleep latency. These findings emphasize that self-reported and physiological sleep quality are not measuring the same construct, and both are important to monitor when studying sleep quality in relation to depression.
First-Line Camrelizumab versus Placebo Plus Chemotherapy with or without Radiotherapy for Brain Metastases in Non-Small-Cell Lung Cancer: The CTONG 2003 Randomized Placebo-Controlled Trial
Authors: Yang-Si Li, Qitao Yu, Qing Bu, Lizhu Lin, Fangling Ning, Yun Zhao, Gang Wu, Gen Lin, Aimin Zang, Hao Sun, Jie Huang, Hai-Yan Tu, Shenglin Ma, Chengzhi Zhou, Anwen Liu, Cailian Wang, Yu Yao, Guang Han, Jun Zhao, Qing Zhou, Hong-Hong Yan, Si-Yang Maggie Liu, Mei-Mei Zheng, Jingye Lv, Fengzhuo Cheng, Zhongjiang Chen, Wen-Zhao Zhong, Yi Pan, Jin-Ji Yang, Yi-Long Wu
Journal: Journal of Thoracic Oncology (2025)
Safety, Pharmacokinetics, and Efficacy of TY-9591 (Deuterated Osimertinib Derivative) in Advanced EGFR-mutated Non-Small Cell Lung Cancer: A Phase 1 Dose-Escalation and Dose-Expansion Study
Authors: Baohui Han, Jie Liu, Lin Wu, Yanqiu Zhao, Wei Zhang, Bolin Chen, Jianbo He, Jianhua Shi, Yanqing Liu, Zhe Zhang, Xiugui Chen, Yusheng Wu
Journal: Journal of Thoracic Oncology (2025)
In vitro integration of a functional vasculature to model endothelial regulation of chemotherapy and T-cell immunotherapy in liver cancer
Authors: Jyothsna Vasudevan, Ragavi Vijayakumar, Jose Antonio Reales-Calderon, Maxine S Y Lam, Jin Rong Ow, Joey Aw, Damien Tan, Anthony Tanoto Tan, Antonio Bertoletti, Giulia Adriani, Andrea Pavesi
Journal: Biomaterials (2025)
Uncovering <i>de novo</i> polyamine biosynthesis in the gut microbiome and its alteration in inflammatory bowel disease
Authors: Xinwei Li, Xia Xiao, Shengnan Wang, Biyu Wu, Yixuan Zhou, Pan Deng
Journal: Gut Microbes (2025)

Polyamines are important gut microbial metabolites known to affect host physiology, yet the mechanisms behind their microbial production remain incompletely understood. In this study, we developed a stable isotope-resolved metabolomic (SIRM) approach to track polyamine biosynthesis in the gut microbiome. Viable microbial cells were extracted from fresh human and mouse feces and incubated anaerobically with [U-13C]-labeled inulin (tracer). Liquid chromatography-high resolution mass spectrometry analysis revealed distinct 13C enrichment profiles for spermidine (SPD) and putrescine (PUT), indicating that the arginine-agmatine-SPD pathway contributes to SPD biosynthesis in addition to the well-known spermidine synthase pathway (PUT aminopropylation). Species differences were observed in the 13C enrichments of polyamines and related metabolites between the human and mouse microbiome. By analyzing the fecal metabolomics and metatranscriptomic data from an inflammatory bowel disease (IBD) cohort, we found significantly higher polyamine levels in IBD patients compared to healthy controls. Further investigations using single-strain SIRM and in silico analyses identified Bacteroides spp. as key contributors to polyamine biosynthesis, harboring essential genes for this process and potentially driving the upregulation of polyamines in IBD. Taken together, this study expands our understanding of polyamine biosynthesis in the gut microbiome and will facilitate the development of precision therapies to target polyamine-associated diseases.
Genetic mechanisms and adaptive benefits of anthocyanin-red stigmas in a wind-pollinated tree
Authors: Wei-Hao Wang, Susanne S Renner, Hao-Sheng Liu, Liu-Feng Dai, Cai-Jin Chen, Yi Zhang, Bo-Wen Zhang, Da-Yong Zhang, Wei-Ning Bai
Journal: Molecular Biology and Evolution (2025)

Abstract Anthocyanin accumulation in leaves or flowers mitigates photooxidation damage from reactive oxygen species (ROS) and functions in plant/animal interactions. Among the most conspicuously anthocyanin-accumulating tissues are stigmas, especially in wind-pollinated trees. In the walnut genus (Juglans), yellow stigmas are ancestral, but a few species have dark red stigmas. We have used a natural F1 hybrid resulting from crosses between yellow stigma and red stigma species to investigate the genetic basis of the red stigmas. We found that a Copia transposable element (TE) insertion in the ubiquitin-protein ligase gene MIEL1 suppresses its expression in stigmas through RNA-directed DNA methylation and has gone to fixation in red stigma species. A younger Gypsy TE insertion fully inhibits MIEL1 expression, but is not fixed, explaining the color segregation in hybrid populations. Based on reference genomes and whole-genome sequencing data representing 20 of the 22 species of Juglans, we traced the evolution of MIEL1, finding the insertions in all consistently red stigma species. Red stigmas had lower levels of ROS than yellow stigmas, and population genetic data reveal strong positive selection on the TE-bearing MIEL1 allele. In combination, these results suggest that anthocyanin-accumulating stigma tissues support pollen germination and growth by protecting cells from ROS.
Cellular Proliferation Imaging With 18F-FMAU PET/CT as Adjunct to mpMRI in Image-Guided Biopsy of Suspected Prostate Cancer
Authors: Hossein Jadvar, Kai Chen, Passant Mohamed, Donya S. Jadvar, Andre Luis Abreu
Journal: Clinical Nuclear Medicine (2025)

Purpose We evaluated the potential diagnostic utility of PET with the cellular proliferation biomarker, 2′-deoxyl-2′-[ 18 F]fluoro-5-methyl-1-beta-D-arabinofuranosyluracil ( 18 F-FMAU), as an adjunct to multiparametric MRI (mpMRI), in localization of sites for image-guided biopsy in men with suspected prostate cancer. Patients and Materials Seventeen men with clinically suspected prostate cancer underwent standard mpMRI and investigational PET/CT with 18 F-FMAU. Results Tissue samples obtained from 22 image-guided biopsies were examined histologically. There were 11 benign, 6 ISUP grade 1, and 5 ISUP grade 2 tumors. The sensitivity for detection of ISUP 1 and ISUP 2 prostate cancer was 16.7% and 100% for mpMRI, and 50% and 60% for 18 F-FMAU PET/CT, respectively. Conclusions 18 F-FMAU PET/CT may be a useful adjunct to mpMRI in image-guided prostate biopsy.
Corrigendum to ‘The International Association for the Study of Lung Cancer Staging Project for Lung Cancer: Proposals for the Revision of the M Descriptors in the Forthcoming Ninth Edition of the TNM Classification for Lung Cancer’ [Journal of Thoracic Oncology, Volume 19 Issue 5 (2024) 786-802]
Authors: Kwun M Fong, Adam Rosenthal, Dorothy J Giroux, Katherine K Nishimura, Jeremy Erasmus, Yolande Lievens, Mirella Marino, Edith M Marom, Paul Martin Putora, Navneet Singh, Francisco Suárez, Ramon Rami-Porta, Frank Detterbeck, Wilfried E E Eberhardt, Hisao Asamura
Journal: Journal of Thoracic Oncology (2025)
Radiogenomics of intrahepatic cholangiocarcinoma predicts immunochemotherapy response and identifies therapeutic target
Authors: Gu-Wei Ji, Zheng-Gang Xu, Shuo-Chen Liu, Shu-Ya Cao, Chen-Yu Jiao, Ming Lu, Biao Zhang, Yue Yang, Qing Xu, Xiao-Feng Wu, Ke Wang, Yong-Xiang Xia, Xiang-Cheng Li, Xue-Hao Wang
Journal: Clinical and Molecular Hepatology (2025)

Identifying patients with intrahepatic cholangiocarcinoma (ICC) likely to benefit from immunochemotherapy, the new front-line treatment, remains challenging. We aimed to unveil a novel radiotranscriptomic signature that can facilitate treatment response prediction by multi-omics integration and multi-scale modelling. We analyzed bulk, single-cell and spatial transcriptomic data comprising 457 ICC patients to identify an immune-related score (IRS), followed by decoding its spatial immune context. We mapped radiomics profiles onto spatial-specific IRS using machine-learning to define a novel radiotranscriptomic signature, followed by multi-scale and multi-cohort validation covering 331 ICC patients. The signature was further explored for the potential therapeutic target from in vitro to in vivo. We revealed a novel 3-gene (PLAUR, CD40LG and FGFR4) IRS whose down-regulation correlated with better survival and improved sensitivity to immunochemotherapy. We highlighted functional IRS-immune interactions within tumor epithelium, rather than stromal compartment, irrespective of geospatial locations. Machine-learning pipeline identified the optimal 3-feature radiotranscriptomic signature that was well-validated by immunohistochemical assays in molecular cohort, exhibited favorable external prognostic validity with C-index over 0.64 in resection cohort, and predicted treatment response with an area under the curve of up to 0.84 in immunochemotherapy cohort. We also showed that anti-uPAR/PLAUR alone or in combination with anti-programmed cell death protein 1 therapy remarkably curbed tumor growth, using in vitro ICC cell lines and in vivo humanized ICC patient-derived xenograft mouse models. This proof-of-concept study sheds light on the spatially-resolved radiotranscriptomic signature to improve patient selection for emerging immunochemotherapy and high-order immunotherapy combinations in ICC.
Evaluating a Stock Inhaler Program in Chicago Public Schools: Using the RE-AIM Framework to Assess Impact
Authors: Andrea Pappalardo, Caroline Youssef, Paige Hardy, Danita Hingston, TaShunda Green, Jeannette White, J. Alyse Lodise, Jasmine Fowler, Nicole Wilson, Molly Martin
Journal: Journal of Allergy and Clinical Immunology (2025)