tbuckley/cabot-search huggingface dataset:
Biomarker Panels for Discriminating Risk of CKD Progression in Children
Authors: Jason H. Greenberg, Alison G. Abraham, Yunwen Xu, Jeffrey R. Schelling, Steven G. Coca, Sarah J. Schrauben, F. Perry Wilson, Sushrut S. Waikar, Ramachandran S. Vasan, Orlando M. Gutierrez, Michael G. Shlipak, Joachim H. Ix, Bradley A. Warady, Paul L. Kimmel, Joseph V. Bonventre, Chirag R. Parikh, Michelle Denburg, Susan Furth
Journal: Journal of the American Society of Nephrology (2025)

Background: We have previously studied biomarkers of tubular health (EGF), injury (KIM-1), dysfunction (alpha-1 microglobulin), and inflammation (TNFR-1, TNFR-2, MCP-1, YKL-40, suPAR), and demonstrated that plasma KIM-1, TNFR-1, TNFR-2 and urine KIM-1, EGF, MCP-1, urine alpha-1 microglobulin are each independently associated with CKD progression in children. In this study, we used bootstrapped survival trees to identify a combination of biomarkers to predict CKD progression in children. Methods: The CKiD Cohort Study prospectively enrolled children 6 months to 16 years old with an eGFR of 30-90 ml/min/1.73m 2 . We measured biomarkers in stored plasma and urine collected 5 months after study enrollment. The primary outcome of CKD progression was a composite of 50% eGFR decline or kidney failure. We constructed a regression tree-based model for predicting the time to the composite event, using a panel of clinically relevant biomarkers with empirically derived thresholds, in addition to conventional risk factors. Results: Of the 599 children included, the median age was 12 years [IQR, 8 - 15], 371 (62%) were male, baseline urine protein to creatinine ratio was 0.33 [IQR: 0.12 - 0.95] mg/mg, and baseline eGFR was 53 [IQR, 40 - 66] ml/min/1.73m 2 . Overall, 205 (34%) children reached the primary outcome of CKD. A single regression tree-based model using the most informative predictors with data driven biomarker thresholds suggested a final set of 4 prognosis groups. In the final model, urine albumin/creatinine was the variable with the highest importance, and along with urine EGF/creatinine identified the highest risk group of 24 children, 100% of whom developed CKD progression at a median time of 1.3 years [95% CI: 1.0, 1.7]. When the regression tree-derived risk group classifications were added to prediction models including the clinical risk factors, the C-statistic increased from 0.76 [95%CI: 0.71 - 0.80] to 0.85 [95%CI: 0.81 - 0.88]. Conclusions: Using regression tree-based methods, we identified a biomarker panel of urine albumin/creatinine, urine EGF/creatinine, plasma KIM-1, and eGFR which significantly improved discrimination for CKD progression.
Primary Antibody Deficiencies: Curation Of Gene-Disease Relationships Using A ClinGen Validation Framework
Authors: Alejandro Nieto-Patlán, Justyne Ross, Shruthi Mohan, Michelle K Paczosa, Rasha Soliman, Olga Sarmento, Ermal Aliu, Lavvina Thiyagarajan, Anita Chandra, Capucine Picard, Klaus Warnatz, Stephen Jolles, Harry Lesmana, Paul J Maglione, Craig D Platt, Anna Sediva, Kathleen E Sullivan, Kejian Zhang, Forum Raval, Stuart G Tangye, Roshini S Abraham
Journal: Journal of Allergy and Clinical Immunology (2025)
Revealing the Importance of a Multidisciplinary Approach to Reducing the Global Burden of SLD Through the COVID-19 Pandemic: Editorial on “Current Burden of Steatotic Liver Disease and Fibrosis among Adults in the United States, 2017-2023”
Authors: Jeayeon Park, Su Jong Yu
Journal: Clinical and Molecular Hepatology (2025)

Revealing the Importance of a Multidisciplinary Approach to Reducing the Global Burden of SLD Through the COVID-19 Pandemic: Editorial on "Current Burden of Steatotic Liver Disease and Fibrosis among Adults in the United States, 2017-2023"
Ileocecal stent placement for malignant obstruction using a side-viewing endoscope and a balloon-equipped overtube
Authors: Akihiro Maruyama, Makoto Kobayashi, Hirotaka Takeshima, Hiroshi Nakayabu, Hiroki Kato, Shintaro Tominaga, Motoyoshi Yano
Journal: Endoscopy (2025)

Ileocecal obstruction, particularly in malignant cases, presents unique procedural challenges in achieving optimal visualization and precise stent placement owing to the complex anatomy of this region [1] [2]. Traditional forward-viewing endoscopes often have limitations, and alternative endoscopic approaches yield better outcomes in complex gastrointestinal obstructions [3]. However, reports specifically addressing malignant ileocecal obstruction are limited. Herein, we describe a successful approach to managing procedural challenges in ileocecal obstruction.
A novel technique for colonic diverticular bleeding hemostasis using hemostatic forceps and the reopenable-clip over-the-line method
Authors: Junki Toyoda, Tatsuma Nomura, Takanobu Mitani, Yuto Ikadai, Tomohiro Sase, Tomonori Saito, Katsumi Mukai
Journal: Endoscopy (2025)

Colonic diverticular bleeding is the most common cause of acute lower gastrointestinal bleeding. Although colorectal endoscopic submucosal dissection has spread throughout the world, and hemostasis with hemostatic forceps for the vessels within the diverticulum has become common, the use of hemostatic forceps for diverticular bleeding is not common due to the risk of perforation [1]. We propose the use of a calibrated, small-caliber tip, transparent hood with a tapered 4-mm tip (CAST hood; TOP, Tokyo, Japan) to identify bleeding in small diverticula [2]. We report a novel method of closure for small diverticular bleeding in the ascending colon using the reopenable-clip over-the-line method (ROLM), which allows complete closure of the diverticulum after postoperative vascular coagulation with hemostatic forceps ([Fig. 1], [Video 1]) [3].
Intravaginal endoscopic vacuum therapy of a rectovaginal fistula: expanding boundaries
Authors: Renato Medas, Guilherme Macedo, Eduardo Rodrigues-Pinto
Journal: Endoscopy (2025)

A 36-year-old woman underwent anterior resection of the rectum owing to endometriosis. The procedure was complicated by a rectovaginal fistula, which needed several surgical reinterventions. Despite diversion colostomy and reconstruction of the posterior vaginal wall with a fasciocutaneous flap, the rectovaginal fistula persisted, with a 50-mm abscess interposed between the coloanal anastomosis and the neovagina. The patient was referred for endoscopic evaluation.
Donʼt be overconfident about the “cover” of a covered self-expandable metal stent in endoscopic ultrasound-guided hepaticogastrostomy
Authors: Masaki Miyazawa, Masahiro Yanagi, Masaki Nishitani, Tomoyuki Hayashi, Shinya Yamada, Hajime Takatori, Taro Yamashita
Journal: Endoscopy (2025)

The usefulness of endoscopic ultrasound-guided hepaticogastrostomy (EUS-HGS) for biliary obstruction has been widely reported in cases where a transpapillary approach is unsuitable or impossible [1] [2]. Covered self-expandable metal stents (CSEMSs) are often used for EUS-HGS, and the presence of the cover provides peace of mind that bile leakage will not occur, even if the CSEMS passes through the abdominal cavity [3]; however, we report here a case in which, despite successful EUS-HGS using a CSEMS, biliary peritonitis occurred immediately afterward owing to a broken "cover" ([Video 1]).
Treatment of thoracogastric–mediastinal–pleural–airway fistula with esophageal stent, vascular plug, and tissue glue
Authors: Yifan Li, Yahua Li, Binbin Ren, Zongming Li, Xinwei Han, Zhen Li, Kewei Ren
Journal: Endoscopy (2025)

Thoracogastric airway fistula is a rare and serious complication post-esophageal cancer surgery with an incidence of about 0.2% to 1.9% [1]. Due to the complexity of these fistulas, endoscopic and conservative treatments often fail. Most patients are too frail for surgery, making intervention-based closure therapy a crucial treatment option [2] [3].
Technical tip: endoscopic internalization by cutting the drainage tube after endoscopic ultrasound-guided naso-gallbladder drainage for acute cholecystitis
Authors: Noriyuki Hirakawa, Shuntaro Mukai, Takayoshi Tsuchiya, Reina Tanaka, Ryosuke Tonozuka, Takao Itoi
Journal: Endoscopy (2025)

Although a fully covered metal stent (FCMS) placed for malignant distal biliary obstruction can maintain long-term patency, it can obstruct the bifurcation of the cystic duct [1] [2]. Endoscopic ultrasound-guided naso-gallbladder drainage (EUS-NGBD) for acute cholecystitis caused by FCMS is reported to be effective [3] [4]. To prevent recurrence, it is recommended that internalization be performed by cutting the drainage tube in the stomach with a loop cutter after improvement of cholecystitis [5]. Here, we present a case of acute cholecystitis caused by FCMS placement in which EUS-NGBD was performed and endoscopic internalization was achieved using a reusable loop cutter.
Modelling the impact of environmental and social determinants on mental health using generative agents
Authors: Joseph Kambeitz, Andreas Meyer-Lindenberg
Journal: npj Digital Medicine (2025)

Abstract Mental health is shaped by socio-environmental determinants, yet traditional research approaches struggle to capture their complex interactions. This review explores the potential of generative agents, powered by large language models, to simulate human-like behaviour in virtual environments for mental health research. We outline potential applications including the modelling of adverse life events, urbanicity, climate change, discuss potential challenges and describe how generative agents could transform mental health research.
Inactivation of glutathione <i>S</i> -transferase alpha 4 blocks <i>Enterococcus faecalis</i> -induced bystander effect by promoting macrophage ferroptosis
Authors: Yuanyuan Ju, Chunhua Ma, Lin Huang, Yumei Tao, Tianqi Li, Haibo Li, Mark M. Huycke, Yonghong Yang, Xingmin Wang
Journal: Gut Microbes (2025)

Enterococcus faecalis-infected macrophages produce 4-hydroxynonenal (4-HNE) that mediates microbiota-induced bystander effect (MIBE) leading to colorectal cancer (CRC). Glutathione S-transferase alpha 4 (Gsta4), a specific detoxifying enzyme for 4-HNE, is overexpressed in human CRC and E. faecalis-induced murine CRC. However, the roles of Gsta4 in E. faecalis-induced colitis and CRC remain unclear. Herein, we demonstrate that Gsta4 is essential for MIBE by protecting macrophages from E. faecalis-induced ferroptosis. E. faecalis OG1RFSS was used to induce colitis in Gsta4-/- and Il10-/-/Gsta4-/- mice by orogastric gavage. Ferroptosis was assessed in Gsta4-deficient murine macrophages. We found that, unlike Il10-/- mice, Gsta4-/- and Il10-/-/Gsta4-/- mice colonized with E. faecalis failed to develop colitis or CRC. Immunofluorescent staining showed a reduction of macrophages in the lamina propria of E. faecalis-colonized Il10-/-/Gsta4-/- mice, as well as decreased Gpx4 expression, indicating the occurrence of ferroptosis. Ferroptosis was further confirmed in Gsta4-deficient murine macrophages infected with E. faecalis. Moreover, Gsta4 inactivation induced the upregulation of Hmox1 and phosphorylated c-Jun while blocked Nos2 expression, leading to the accumulation of intracellular ferrous iron, lipid peroxidation and, eventually, ferroptosis. Finally, Mapk8, as a ferroptosis driver, was remarkably elevated in E. faecalis-infected Gsta4-deficient macrophages. These results suggest that Gsta4 inactivation blocks MIBE by eliminating macrophages, thereby attenuates E. faecalis-induced colitis and CRC.
Correction: CD2AP deficiency aggravates Alzheimer’s disease phenotypes and pathology through p38 MAPK activation
Authors: Yan-Yan Xue, Zhe-Sheng Zhang, Rong-Rong Lin, Hui-Fen Huang, Ke-Qing Zhu, Dian-Fu Chen, Zhi-Ying Wu, Qing-Qing Tao
Journal: Translational Neurodegeneration (2025)
Appendicectomy versus antibiotics for acute uncomplicated appendicitis in children: an open-label, international, multicentre, randomised, non-inferiority trial
Authors: Shawn D St Peter, Janelle R Noel-MacDonnell, Nigel J Hall, Simon Eaton, Janne S Suominen, Tomas Wester, Jan F Svensson, Markus Almström, E Pete Muenks, Marianne Beaudin, Nelson Piché, Mary Brindle, Ali MacRobie, Richard Keijzer, Helene Engstrand Lilja, Ann-Marie Kassa, Tim Jancelewicz, Andreana Butter, Jacob Davidson, Erik Skarsgard, Yap Te-Lu, Shireen Nah, Andrew R Willan, Agostino Pierro
Journal: The Lancet (2025)
The end, and what comes after
Authors: Laura Salisbury, Dora Vargha, Debora Diniz, Luciana Brito, Osman Sankoh, Haja Ramatulai Wurie, Regina Mamidy Yillah, Sharifah Sekalala, Caroline Dubois, Emily Ying Yang Chan, Yureshya Perera, Ruth Ogden, Patricia Kingori
Journal: The Lancet (2025)
Long-term safety and efficacy of Oleogel-S10 (birch bark extract) in epidermolysis bullosa: 24-month results from the Phase III EASE Study
Authors: Dédée F Murrell, Christine Bodemer, Anna L Bruckner, Tracy Cunningham, Charles Davis, Mariá Florencia Fernández, Dimitra Kiritsi, Laura Maher, Eli Sprecher, Mauricio Torres Pradilla, Johannes S Kern
Journal: British Journal of Dermatology (2025)

Epidermolysis bullosa (EB) is a group of rare, severe, genetic disorders characterised by persistent skin fragility and open wounds. EB manifests as cutaneous and mucosal blistering, erosions and impaired wound healing. To determine the long-term efficacy, tolerability and safety of Oleogel-S10 (birch bark extract) in dystrophic (DEB) and junctional (JEB) EB in the 24-months open-label phase (OLP) of the EASE study. EASE was a double-blind, randomised, controlled, phase III study consisting of two phases: a 90-day double-blind phase (DBP), and a 24-month OLP. Patients from both former treatment groups in the DBP entered the single-arm OLP (n = 205). Patients received Oleogel-S10 on all EB partial thickness wounds. OLP endpoints included: incidence, severity/relatedness of adverse events (AEs), wound infection maximum severity, changes in body surface area percentage (BSAP) of wounds, EB Disease Activity and Scarring Index (EBDASI), pain, itch, disease severity and quality of life outcomes. The OLP data demonstrated Oleogel-S10 target wound treatment adherence was >99% and mean treatment duration was 584.7 days (±246.1 days). 71.7% of patients in the OLP were aged <18 years and 86.8% had DEB; recessive DEB predominated (78.0%). AEs were reported in 77.1% of patients and were typically mild-to-moderate. Severe and serious AEs were observed in 18.0% and 24.4% of patients, respectively. AEs resulted in the withdrawal of 7.8% of patients (n = 16), including three with treatment-related AEs. Nine deaths were reported: none attributable to treatment. Incidence of target wound infections was low (n = 7); five were mild-to-moderate and two severe. In patients treated with Oleogel-S10 throughout, mean (SD) BSAP changes from DBP baseline at 3, 12 and 24 months were -4.3% (8.1), P < 0.0001; -5.9% (8.6), P < 0.0001; -3.7% (9.0), P = 0.0026, respectively. Similarly, significant changes in EBDASI skin activity score from DBP baseline were observed: -3.9 (8.3), P < 0.0001; -5.1 (8.2), P < 0.0001; -3.0 (8.3), P = 0.0068, at 3, 12 and 24 months, respectively. These data support an encouraging long-term safety profile of Oleogel-S10, and a sustained reduction in wound burden over at least 24 months of Oleogel-S10 treatment.
Real-World Melanoma Miss-Rate In An NHS Hospital Dermatology Service. A Retrospective Study
Authors: Alexander D G Anderson, Hafsa F Shirwac, Hannah Morgan, Huw Greenish, Sarah Carswell, Victoria Owen, Harry Heath, James Koutsis, Pascale Guitera
Journal: British Journal of Dermatology (2025)

This retrospective study assessed the melanoma miss rate of dermatology clinicians working in a secondary care NHS hospital. Nine of 428 primary invasive melanomas (2.1%) diagnosed over a 2-year period had been dismissed as benign in the same service within the preceeding year (missed diagnosis) A further 4 cases (0.9%) were classed as possible misses and a final 4 (0.9%) as delayed diagnosis.
Computational Analysis of Intravascular OCT Images for Future Clinical Support: A Comprehensive Review
Authors: Juhwan Lee, Yazan Gharaibeh, Pengfei Dong, Luis A. P. Dallan, Gabriel T. R. Pereira, Justin N. Kim, Ammar Hoori, Linxia Gu, Hiram G. Bezerra, Bernardo Cortese, David L. Wilson
Journal: IEEE Reviews in Biomedical Engineering (2025)

Over the past two decades, intravascular optical coherence tomography (IVOCT) has emerged as a promising tool for planning percutaneous coronary interventions (PCI), studying coronary artery disease, and assessing treatments. With its nearhistological resolution and optical contrast, IVOCT uniquely evaluates coronary plaque characteristics, enhancing the guidance of interventional procedures. Artificial intelligence (AI) techniques have been widely applied to IVOCT imaging, providing fast and accurate automated interpretation. These techniques hold significant potential for both clinical and research purposes. Clinically, automated analysis offers comprehensive assessments of coronary plaques, leading to better treatment decisions during PCI. For research, automated interpretation of IVOCT opens new avenues to understand the pathophysiology of coronary atherosclerosis. However, these techniques face several limitations, including issues related to spatial resolution, challenges in manual assessments, and the additional time required for these analyses. This review covers recent advancements and applications of AI techniques and computational simulation methods in IVOCT image analysis, including vessel wall segmentation, plaque characterization, stent analysis, and their clinical applications. Furthermore, we discuss the potential of AI-enhanced IVOCT analysis to facilitate personalized decision-making, potentially improving short- and long-term patient outcomes.
Surveillance in inflammatory bowel disease: white light endoscopy with segmental re-inspection versus dye-based chromoendoscopy – a multi-arm randomised controlled trial (HELIOS)
Authors: Maarten te Groen, Anouk M Wijnands, Nathan den Broeder, Dirk J de Jong, Willemijn A van Dop, Marjolijn Duijvestein, Herma H Fidder, Fiona van Schaik, Meike M C Hirdes, Andrea E van der Meulen-de Jong, P W Jeroen Maljaars, Philip W Voorneveld, K H Nanne de Boer, Charlotte P Peters, Bas Oldenburg, Frank Hoentjen
Journal: Gut (2025)

Background It remains unclear if the increased colorectal neoplasia detection rate in inflammatory bowel disease (IBD) by high-definition (HD) dye-based chromoendoscopy compared with HD white-light endoscopy is due to enhanced contrast or increased inspection times. Longer withdrawal times may yield similar neoplasia detection rates as found by HD chromoendoscopy. Objective To compare colorectal neoplasia detection rates for HD white-light endoscopy with segmental re-inspection and HD chromoendoscopy, using single-pass HD white-light endoscopy as an additional control group. Design In a multicentre, randomised controlled trial, IBD patients aged ≥18 years without active disease and scheduled for endoscopic surveillance were included. Patients were 2:2:1 randomised to HD white-light endoscopy with segmental re-inspection of each colonic segment (double pass), HD chromoendoscopy or single-pass HD white-light endoscopy. The primary outcome was colorectal neoplasia detection rate. Assuming equal colorectal neoplasia rates (non-inferiority margin of 10%) between segmental re-inspection and chromoendoscopy and superiority of segmental re-inspection vs single-pass HD white-light endoscopy, a sample size of 566 patients was required. Results In total, 563 patients were analysed per-protocol. Colorectal neoplasia detection rates were 10.3% (n=24/234) for HD white-light endoscopy with segmental re-inspection and 13.1% (n=28/214) for HD chromoendoscopy. This confirmed non-inferiority to HD chromoendoscopy (Δ−2.8%, lower limit 95% CI −7.8, p&lt;0.01). In addition, the number of detected colorectal neoplasia per 10 min of withdrawal time was similar between HD white-light endoscopy with segmental re-inspection and HD chromoendoscopy (0.062 vs 0.058, p=0.83). Single-pass HD white-light endoscopy yielded a lower colorectal neoplasia rate (6.1%; n=7/115) than segmental re-inspection but this was not statistically significant (Δ4.1%, 95% CI −2.2:9.6%, p=0.19). Conclusions HD white-light endoscopy with segmental re-inspection was non-inferior to HD chromoendoscopy for colorectal neoplasia detection in IBD patients. It can therefore be assumed that the benefit of HD chromoendoscopy may be explained by the longer withdrawal time and not necessarily the enhanced contrast. However, re-inspection per se did not lead to a significantly higher colorectal neoplasia rate than single-pass HD white-light endoscopy alone.
Noninvasive Assessment of Myocardial Perfusion using Ultrafast Ultrasound: Clinical Study for Congenital Heart Disease
Authors: Minh B Nguyen, Naiyuan Zhang, Luc L Mertens, David Barron, Osami Honjo, Maelys Venet, Jerome Baranger, Olivier Villemain
Journal:  (2025)

Myocardial perfusion impacts cardiac function following surgical repair of critical congenital heart disease (CCHD). Temporal variation assessment of myocardial blood volume throughout the cardiac cycle can be a surrogate for perfusion. Ultrafast power Doppler (UPD) is an ultrasound imaging technique capable of noninvasively quantifying myocardial blood volume changes. The objective of this study is to demonstrate the feasibility of perioperative transthoracic UPD assessment and to determine if UPD reflects physiologic changes in myocardial perfusion. Five neonatal transposition of the great arteries (TGA) undergoing arterial switch operation (ASO), five hypoplastic left heart syndrome (HLHS) undergoing Stage 1 palliation (S1P), and five age/weight-matched controls were prospectively recruited. Transthoracic UPD acquisitions were performed before/after operations. Segmental perfusion in right/left ventricles (RV/LV) was assessed. The controls' myocardial perfusion patterns are visually similar to published human references for both ventricles. Systolic/diastolic myocardial perfusion differences were modified by ASO in the RV (P = 0.03) but not for LV (P = 0.99). For HLHS patients, no difference after S1P was observed in either the RV (P = 0.16) nor the LV (P = 0.51). For TGA patients, the perfusion profile of the myocardium seems to be directly influenced by the intracavitary pressure (directly driving coronary perfusion pressure), namely if it was the systemic or sub-pulmonary ventricle. Our data suggests that UPD could noninvasively quantify myocardial perfusion variation. Myocardial perfusion patterns change in CCHD according to their haemodynamic and surgical status. Correlation with clinical outcomes requires further study.