tbuckley/cabot-search huggingface dataset:
Longitudinal voice monitoring in a decentralized Bring Your Own Device trial for respiratory illness detection
Authors: Mar Santamaria, Yiorgos Christakis, Charmaine Demanuele, Yao Zhang, Pirinka Georgiev Tuttle, Fahimeh Mamashli, Jiawei Bai, Rogier Landman, Kara Chappie, Stefan Kell, John G Samuelsson, Kisha Talbert, Leonardo Seoane, W Mark Roberts, Edmond Kato Kabagambe, Joseph Capelouto, Paul Wacnik, Jessica Selig, Lukas Adamowicz, Sheraz Khan, Robert J Mather
Journal: npj Digital Medicine (2025)

The Acute Respiratory Illness Surveillance (AcRIS) Study was a low-interventional trial that examined voice changes with respiratory illnesses. This longitudinal trial was the first of its kind, conducted in a fully decentralized manner via a Bring Your Own Device mobile application. The app enabled social-media-based recruitment, remote consent, at-home sample collection, and daily remote voice and symptom capture in real-world settings. From April 2021 to April 2022, the trial enrolled 9151 participants, followed for up to eight weeks. Despite mild symptoms experienced by reverse transcription polymerase chain reaction (RT-PCR) positive participants, two machine learning algorithms developed to screen respiratory illnesses reached the pre-specified success criteria. Algorithm testing on independent cohorts demonstrated that the algorithm's sensitivity increased as symptoms increased, while specificity remained consistent. Study findings suggest voice features can identify individuals with viral respiratory illnesses and provide valuable insights into fully decentralized clinical trials design, operation, and adoption (study registered at ClinicalTrials.gov (NCT04748445) on 5 February 2021).
Classification of intracranial pressure epochs using a novel machine learning framework
Authors: Rohan Mathur, Sudha Yellapantula, Lin Cheng, Peter Dziedzic, Niteesh Potu, Eusebia Calvillo, Vishank Shah, Austen Lefebvre, Julian Bosel, Elizabeth K Zink, Susanne Muehlschlegel, Jose I Suarez
Journal: npj Digital Medicine (2025)

Patients with acute brain injuries are at risk for life threatening elevated intracranial pressure (ICP). External Ventricular Drains (EVDs) are used to measure and treat ICP, which switch between clamped and draining configurations, with accurate ICP data only available during clamped periods. While traditional guidelines focus on mean ICP values, evolving evidence indicates other waveform features may hold prognostic value. However, current machine learning models using ICP waveforms exclude EVD data due to a lack of digital labels indicating the clamped state, markedly limiting their generalizability. We introduce, detail, and validate CICL (Classification of ICP epochs using a machine Learning framework), a semi-supervised approach to classify ICP segments from EVDs as clamped, draining, or noise. This paves the way for multiple applications, including generalizable ICP crisis prediction, potentially benefiting tens of thousands of patients annually and highlights an innovate methodology to label large high frequency physiological time series datasets.
Neoadjuvant versus perioperative chemo-immunotherapy according to pathological response in resectable NSCLC: a reconstructed individual patient data meta-analysis
Authors: Antonio Nuccio, Fabio Salomone, Alberto Servetto, Biagio Ricciuti, Daniele Marinelli, Alessandra Bulotta, Giulia Veronesi, Marina Chiara Garassino, Valter Torri, Benjamin Besse, Giuseppe Viscardi, Roberto Ferrara
Journal: JNCI Journal of the National Cancer Institute (2025)

Abstract Neoadjuvant chemo-immunotherapy transformed early-stage non-small cell lung cancer (NSCLC) treatment. However, the prognostic value of different pathological responses and the impact of adjuvant immunotherapy within a chemo-immunotherapy perioperative strategy remains unclear. We estimated time-to-event outcomes by graphical reconstruction of event-free survival (EFS) curves by pathological response (pCR, MPR, no-MPR) reported in early-stage NSCLC neoadjuvant/perioperative chemo-immunotherapy trials. MPR 1-10% subgroup, previously unreported, was retrieved by removing patients achieving pCR from the MPR group. Survival analysis by pathological response and comparison between neoadjuvant/perioperative strategies within subgroups were assessed. A statistically significant EFS difference according to pathological response was found, showing a prognostic gradient shifting from pCR (good), MPR 1-10% (intermediate) and no-MPR (poor). There was no difference between neoadjuvant/perioperative strategies within subgroups, however a trend for EFS benefit with perioperative and neoadjuvant chemo-immunotherapy was observed in MPR 1-10% and no-MPR patients, respectively. In conclusio, a pathological response-based algorithm could better tailor early-stage NSCLC treatment.
Activation and maturation of antigen-specific B cells in nonectopic lung infiltrates are independent of germinal center reactions in the draining lymph node
Authors: Sarah-Sophie Schacht, Josefine Graffunder, Pawel Durek, Jonas Wehrenberg, Annette Siracusa, Charlotte Biese, Mir-Farzin Mashreghi, Kevin Thurley, Laura Bauer, Andreas Hutloff
Journal: Cellular and Molecular Immunology (2025)

Pulmonary T and B cells are important for protection of this mucosal barrier site. While viral infections lead to the development of ectopic lymphoid structures highly similar to those in germinal centers in secondary lymphoid organs, little is known about how T/B cooperation occurs in the unstructured, diffuse tissue infiltrates characteristic of autoimmune diseases and nonviral infections. Using a mouse model of interstitial lung inflammation, we found that naive B cells are directly activated in lung tissue. Despite the absence of any germinal center-like structures, the interaction of B cells with peripheral T helper cells results in efficient somatic hypermutation and class switching. As antigen-presenting cells, macrophages are critical for this process. Unique B-cell repertoires indicated that the lung response was autonomous from the lung-draining lymph node. Only lung GC-like B cells were switched to IgA and had a broader repertoire, making them ideal candidates for producing broadly neutralizing immunoglobulins against respiratory pathogens.
A working group report from the 2024 NCI/GCSC endometrial cancer clinical trials planning meeting: <i>refining the approach to endometrial cancer in the immunotherapy era</i>
Authors: Casey M Cosgrove, Dmitriy Zamarin, Jose R Conejo-Garcia, Kari E Hacker, Roberto Vargas, Panagiotis A Konstantinopoulos, Haider S Mahdi, Stephanie Gaillard, Stephanie Markovina, Elise C Kohn, Sarah F Adams
Journal: JNCI Journal of the National Cancer Institute (2025)

ABSTRACT Endometrial cancer (EC) is now the leading cause of gynecologic cancer death in the United States. Recognizing the urgent need to improve outcomes for patients diagnosed with EC, The National Cancer Institute (NCI) Gynecologic Cancer Steering Committee (GCSC) convened a Clinical Trials Planning Meeting (CTPM) on January 8th and 9th 2024, “Refining the Approach to Endometrial Cancer in the Immunotherapy Era.” Multi-disciplinary experts were charged with addressing critical challenges, to optimize treatment of EC in the new immunotherapy landscape. As part of the CTPM working groups were assembled to address several important aspects of clinical trial design. Working Group 1 (WG1) focused on translational science and was tasked with reviewing the scientific literature for data on validated discriminants of response to immunotherapy to inform trial concept development by the therapy-focused groups. The WG established that molecular subtyping of EC is now the standard approach for classifying endometrial tumors. Molecular subtyping for both prognostic and predictive applications should be considered when assessing biomarkers as well as therapeutic targets. Additionally, strategies to improve immune response like incorporation of radiation as well as therapy sequencing considerations should continue to be explored. A major key observation from WG1 was lack of validated discriminants for immunotherapy response beyond mismatch repair status and tumor mutational burden and exploration of additional discriminants of response and resistance will be critical with the increasing use of immunotherapy in EC.
Low-level shRNA Cytotoxicity Can Contribute to MYC-induced Hepatocellular Carcinoma in Adult Mice
Authors: Shelly Beer, David I. Bellovin, Joyce S. Lee, Kimberly Komatsubara, Lora S. Wang, Huishan Koh, Kathleen Börner, Theresa A. Storm, Corrine R. Davis, Mark A. Kay, Dean W. Felsher, Dirk Grimm
Journal: Molecular Therapy (2025)
Epicardial Metastases Causing Coronary Artery Compression and Myocardial Infarction on [18F]FDG PET-CT
Authors: Joshua Wilcox, Ankur Gulati, Elias Pintus, Andrew D’Silva, Manil Subesinghe
Journal: Clinical Nuclear Medicine (2025)

A 64-year-old woman with metastatic lung adenocarcinoma on immune checkpoint inhibitor (ICI) therapy suffered an acute coronary syndrome and underwent percutaneous coronary intervention (PCI). Despite PCI and anti-anginal therapy, she continued to experience angina. Cardiac magnetic resonance imaging (CMR) suggested a diagnosis of ICI myocarditis. However, refractory angina and non-resolving changes on CMR despite high-dose steroids prompted further evaluation with [ 18 F]FDG PET-CT; this yielded a final diagnosis of epicardial metastatic coronary artery compression with myocardial infarction. This case demonstrates the incremental diagnostic value of multimodality imaging in cardio-oncology.
The Impact of Comorbidities on Serum IgG Levels and Exacerbation Risk in Chronic Obstructive Pulmonary Disease
Authors: Hajime Fujimoto, Taro Yasuma, Corina N. D'Alessandro-Gabazza, Esteban C Gabazza, Osamu Hataji, Tetsu Kobayashi
Journal: American Journal of Respiratory and Critical Care Medicine (2025)
Overcoming Radiation-induced PD-L1 and Cox-2 Upregulation by Nitric Oxide Gas Nanogenerator to Sensitize Radiotherapy of Lung Cancer
Authors: Rui Hu, Xin Jiang, Lijie Zhu, Rui Meng, Rongbo Yang, Wenjie Sun, Zhenzhou Zhao, Yuehua Lyu, Ruoyuan Huang, Fei Xue, Mengke Shi, Zaigang Zhou, Jianliang Shen, Congying Xie
Journal: Biomaterials (2025)
HPV Genotypes affect the Efficacy of Hyperthermia Therapy for Plantar Warts: A Quality Improvement Study
Authors: Xu Han, Hui-Feng Wang Mm, Lei Ma, Ri-Xin Chen, Qiang Wang, Chun-Hong Zhang, Hai-Hong Zhang, Yue Han, Yang Yang, Hao Guo, Yun-Qiu Gao, Li Zhang, Hong-Wei Yan Pg, Shuai Qiao Pg, Yu Gao, Chun-Mei Shu, Li-Hao Pei, Hui Ma, Xiao-Dong Sun, Chun-Min Zhang, Hai-Jing Jiang, Xue-Qi Li, Ming-Ru Li, Gui-Feng Xu, Hong-Duo Chen, Rui-Qun Qi, Xing-Hua Gao
Journal: Journal of the American Academy of Dermatology (2025)
Genetic classification helps with precise sirolimus treatment in slow-flow vascular malformations: a prospective cohort study
Authors: Hongyuan Liu, Yuxi Chen, Xuanfeng Chen, Shih-Jen Chang, Yamin Rao, Xi Yang, Li Hu, Zian Xu, Hao Gu, Yajing Qiu, Chen Hua, Hui Chen, Xiaoxi Lin
Journal: Journal of the American Academy of Dermatology (2025)
Targeting Myeloid Cells with Platelet-Derived Extracellular Vesicles to Overcome Resistance of Immune Checkpoint Blockade Therapy
Authors: Chenlu Yao, Qingle Ma, Heng Wang, Bingbing Wu, Huaxing Dai, Jialu Xu, Jinyu Bai, Fang Xu, Admire Dube, Chao Wang
Journal: Biomaterials (2025)
Germination changes can restructure communities through priority effects
Authors: Vicky M Temperton
Journal: Trends in Ecology & Evolution (2025)

Priority effects caused by different species' arrival order can significantly influence community assembly and also plant community composition. Dawson-Glass et al. show for the first time in a multi-species setting, that warming-induced shifts in germination timing can restructure communities via seasonal priority effects that influence assembly and affect plant performance.
Advancing precision medicine in metabolic dysfunction-associated steatotic liver disease
Authors: Bryan A Priego-Parra, Rocío Gallego-Durán, Berenice M Román-Calleja, José Antonio Velarde-Ruiz Velasco, Manuel Romero-Gómez, Jordi Gracia-Sancho
Journal: Trends in Endocrinology and Metabolism (2025)
Performance of deep learning algorithm based on Xception in evaluating morphological characteristics reflecting the activity of vitiligo
Authors: Kyungho Paik, Bo Ri Kim, Sang Woong Youn, Hyun Jeong Ju, Jung Min Bae, Chong Won Choi
Journal: British Journal of Dermatology (2025)

We developed a dataset of 4133 cropped vitiligo patch images from 296 patients. Using this dataset, we trained a pre-trained Xception model to assess morphological characteristics of active or stable vitiligo. The deep learning algorithm achieved an area under the receiver operating characteristic curve of 0.96, an accuracy of 94%, a sensitivity of 92.63%, and a specificity of 94.60%. The deep learning algorithm demonstrated excellent performance in distinguishing lesions with morphological characteristics suggestive of active vitiligo from those indicative of a stable state.
Perinatal Exposures to Ambient Fine Particulate Matter and Outdoor Artificial Light at Night and Risk of Pediatric Papillary Thyroid Cancer
Authors: Nicole C. Deziel, Rong Wang, Joshua L. Warren, Catherine Dinauer, Jennifer Ogilvie, Cassandra J. Clark, Charlie Zhong, Joseph L. Wiemels, Libby Morimoto, Catherine Metayer, Xiaomei Ma
Journal: Environmental Health Perspectives (2025)

Pediatric thyroid cancer incidence has been increasing globally, with environmental exposures being a hypothesized risk factor. We evaluated the association between pediatric thyroid cancer risk and perinatal exposure to ambient fine particulate matter (PM2.5) and outdoor artificial light at night (O-ALAN). Both are considered environmental carcinogens with evidence of thyroid function disruption, reported associations with thyroid cancer in adults, and concerns of distributive inequity. O-ALAN may also serve as a proxy for other outdoor air pollutants or urbanization. We conducted a case-control study of papillary thyroid cancer nested within a California birth cohort that included 736 cases diagnosed at 0-19 years and born in 1982-2011 and 36,800 controls frequency-matched on birth year. We assigned individual-level exposures for residence at birth for ambient PM2.5 concentrations from a validated, ensemble-based prediction model and O-ALAN using the New World Atlas of Artificial Night Sky Brightness. We calculated odds ratios (OR) and 95% confidence intervals (CI) using logistic regression adjusting for potential confounders and stratified by age and race/ethnicity. We observed statistically significant associations between PM2.5 exposure and papillary thyroid cancer risk overall (OR per 10-µg/m3 increase in PM2.5=1.07, 95%CI: 1.01-1.14), among the 15-19 year age group (OR=1.08; 95%CI: 1.00-1.16), and among Hispanic children (OR=1.13; 95%CI: 1.02-1.24). For O-ALAN, we observed statistically significantly increased odds of papillary thyroid cancer in higher exposure tertiles compared to the reference tertile in the overall population (tertile 2: OR=1.25, 95%CI 1.04-1.50; tertile 3: OR=1.23, 95%CI: 1.02-1.50) and when modeled as a continuous variable (OR 1.07 per 1 mcd/m2). In age-stratified analyses, significant associations were observed among the 15-19-year-old age group, but not the 0-14-year-old group. No significant differences were found by race/ethnicity. This study provides new evidence suggesting associations between early-life exposure to PM2.5 and O-ALAN and pediatric papillary thyroid cancer. Given that O-ALAN may also represent other air pollutants or broader urbanization patterns, further research and refinements to exposure metrics are needed to disentangle these factors. https://doi.org/10.1289/EHP14849.
An unbiased genomewide screen uncovers 7 genes that drive hematopoietic stem cell fate from mouse embryonic stem cells
Authors: Luis Galan Palma, Gayathri M Kartha, Maria Maqueda, Mercedes Barrero, Eric Canton, Arnau Iglesias, Jessica Gonzalez Miranda, Patricia Herrero Molinero, Raul Torres-Ruíz, Bernhard Payer, Clara Bueno, Pablo Menendez, Lluis Espinosa, Anna Bigas
Journal: Blood (2025)
ZUMA-8: A Phase 1 Study of Brexucabtagene Autoleucel in Patients With Relapsed/Refractory Chronic Lymphocytic Leukemia
Authors: Matthew S. Davids, Saad S. Kenderian, Ian W. Flinn, Brian T. Hill, Michael B Maris, Paolo Ghia, Michael T. Byrne, Nancy L. Bartlett, John Pagel, Yan Zheng, Justyna Kanska, Wangshu Zhang, Enrique Granados, Javier Pinilla-Ibarz
Journal: Blood (2025)
Impact of quantitative radiological features of interstitial lung disease on immunomodulatory treatment response in three autoimmune interstitial lung disease cohorts
Authors: Scott M Matson, Grace Hyun J Kim, Stephen M Humphries, Michael D Roth, Jonathan Goldin, Donald P Tashkin, Mei Leng, Bryant R England, Joyce S Lee, Elizabeth R Volkmann
Journal: Thorax (2025)

Background The defining radiological features of autoimmune interstitial lung disease (ILD) are ground glass opacification (GGO) and fibrosis. The associations between these features and physiological response to immunomodulation remain unclear. Methods This study leveraged three autoimmune ILD cohorts: two with systemic sclerosis (SSc) and one with rheumatoid arthritis (RA) which were selected for inherent differences in fibrotic extents/patterns. Linear regression models examined associations between baseline quantitative GGO, fibrosis, their ratio and forced vital capacity (FVC)%-predicted changes after 12 months of immunomodulatory therapy. Results Patients with SSc-ILD (N=262) exhibited a higher GGO-to-fibrosis ratio compared with patients with RA-ILD (N=130) (mean ratio 3.0 vs 0.25). Increased GGO-to-fibrosis was not associated with improved FVC%-predicted in any cohort. Conversely, in patients with SSc-ILD treated with cyclophosphamide (CYC), increased fibrosis (estimate 0.17 (95% CI 0.003, 0.33); p=0.04) and increased GGO (estimate 0.15 (95% CI 0.004, 0.30); p=0.044) were both significantly associated with FVC% improvement. Given the negative direction of the estimate for GGO-to-fibrosis ratio (estimate −0.33 (95% CI −0.61, –0.06); p=0.016), CYC was associated with greater FVC% improvement in patients with a higher degree of fibrosis relative to GGO. No significant correlation was seen in patients with SSc-ILD treated with mycophenolate (N=56) or in patients with RA-ILD treated with immunomodulation (N=130). Discussion Increased quantitative GGO relative to fibrosis was not significantly associated with improved response to immunomodulation in patients with RA-ILD and SSc-ILD. However, increased quantitative fibrosis and GGO extent were associated with improved response to CYC in SSc-ILD. More research is needed to understand how to use radiological features to guide treatment selection in ILD.
Choice of colon capsule or colonoscopy versus default colonoscopy in FIT positive patients in the Danish screening programme: a parallel group randomised controlled trial
Authors: Gunnar Baatrup, Thomas Bjørsum-Meyer, Lasse Kaalby, Benedicte Schelde-Olesen, Morten Kobaek-Larsen, Anastasios Koulaouzidis, Rasmus Kroijer, Issam Al-Najami, Niels Buch, Anders Høgh, Niels Qvist, Marianne Kirstine Thygesen, Ulrik Deding
Journal: Gut (2025)

Background Colonoscopy is among the standard tests for colorectal cancer (CRC) screening. However, uptake varies, and alternatives such as colon capsule endoscopy (CCE) are available. The uptake and detection rate of clinically significant neoplasia with CCE, compared with colonoscopy, remain unclear in this setting. Objective The primary objective of this study was to compare the detection rates of advanced neoplasia between CCE and colonoscopy, using a pathway in which the study group could choose between the two procedures, while the control group was offered only colonoscopy. Design A randomised, intention-to-treat trial was conducted among Danish CRC screening participants who tested positive with a faecal immunochemical test (FIT). The trial compared the detection rate of advanced neoplasia (primary outcome) and the uptake rate of both approaches between the two arms. Results A total of 473 684 invitations were sent to 396 676 individuals, with 62.6% returning the test. Among them, 11 075 tests were positive (4.5%), with no significant differences between the two study groups. Among FIT-positive cases, the uptake for colonoscopy was 91.1% in the control arm and 91.7% in the study arm, where participants had a choice of methods. In the study arm, 45.8% preferred CCE, 11.4% preferred colonoscopy and 42.8% had no preference and underwent colonoscopy. Ultimately, 69.9% of patients who initially opted for CCE were later referred for colonoscopy. The rate of advanced neoplasia detection was similar between the groups: 0.67% in the study arm versus 0.64% in the control arm. Conclusion Offering CCE as an alternative to colonoscopy did not significantly alter the detection rate of advanced neoplasia, nor did it increase uptake in a screening programme with high adherence to colonoscopy following a positive FIT test. Instead, it led to a very high rate of secondary colonoscopies. Therefore, CCE cannot be recommended in this setting. Trial registration number NCT04049357 (ClinicalTrials.gov)
Insulin-Like Growth Factor-Binding Protein 7 and Cadmium-Induced Hepatorenal Fibrosis
Authors: Shuai-shuai Xie, Rui Hou, Li Gao, Qin Yang, Wei Li, Ze-hui Dong, Yu-hang Dong, Shuang-jian Li, Wen-xian Ma, Ying-ying Gao, Long Xu, Chao Li, Ying Chen, Ju-tao Yu, Jia-nan Wang, Ming-lu Ji, Ruo-bing He, Xiao-guo Suo, Ming-ming Liu, Juan Jin, Jia-gen Wen, Chen Yang, Xiao-ming Meng
Journal: Journal of the American Society of Nephrology (2025)

Background: Chronic cadmium exposure can induce the onset and progression of hepatorenal fibrosis; however, its molecular basis is unclear. Insulin-like growth factor-binding protein 7 (IGFBP7) is not only a biomarker of acute kidney injury (AKI), but also plays a functional role in promoting kidney injury and inflammation. Abnormal repair of AKI causes kidney fibrosis and chronic kidney disease. IGFBP7 has also been reported as a more sensitive biomarker for liver fibrosis. However, its role in hepatorenal fibrosis requires further investigation. Methods: IGFBP7 global and conditional knockout mice were used to determine the role of IGFBP7 in cadmium-induced hepatorenal fibrosis. Then, liquid chromatography-mass spectrometry, truncated mutants, co-immunoprecipitation, and microscale thermophoresis were employed to unravel the downstream mechanisms. Results: IGFBP7 expression was significantly elevated in kidney and liver tissues of mice subjected to chronic cadmium exposure. IGFBP7 deficiency attenuated cadmium-induced hepatorenal dysfunction and fibrosis, whereas restoration of IGFBP7 expression in IGFBP7-deficient mice reproduced hepatorenal fibrosis. Mechanistically, IGFBP7 interacted with alpha-enolase (ENO1) and inhibited its ubiquitination and degradation. Upregulated ENO1 further promoted glucose metabolic reprogramming and lactate accumulation. Conversely, lactate accumulation enhanced IGFBP7 transcription and expression through histone H3K18 lactylation. Importantly, therapy targeting IGFBP7 significantly ameliorated cadmium-induced hepatorenal fibrosis. Conclusions: IGFBP7 promoted cadmium-induced hepatorenal fibrosis by enhancing ENO1-driven abnormal glycolysis and lactate accumulation.