tbuckley/cabot-search huggingface dataset:
Invasive fungal infections in patients with liver disease: immunological and clinical considerations for the intensive care unit
Authors: Oleg Epelbaum, Alice Gallo de Moraes, Jody C. Olson, Michail S. Lionakis
Journal: Intensive Care Medicine (2025)

Patients with liver disease in the intensive care unit (ICU) face a unique susceptibility to infection due to the complex immune dysfunction resulting from hepatic failure. Bacterial infections are commonly present in these patients upon arrival to the hospital, often being the primary reason for ICU admission. In contrast, invasive fungal infections (IFIs) afflict a smaller percentage of patients and are usually discovered in the course of the ICU stay. IFI diagnosis in the ICU, particularly in patients with liver disease, is often delayed or overlooked, contributing to the extremely high ICU mortality associated with IFI in these patients despite the availability of effective (and largely safe) antifungal therapy. Thus, to improve outcomes, it is crucial for intensive care clinicians to be vigilant for IFIs in patients with liver disease. This review aims to contribute to the intensive care literature in this regard. We begin with an overview of normal antifungal immunity followed by a summary of how it may become compromised in the setting of hepatic dysfunction. Next, a general discussion of IFIs in liver disease is presented and then the three most relevant fungal pathogens, namely Candida, Aspergillus, and Cryptococcus, are individually examined. This review concludes by highlighting key knowledge and practice gaps that require attention by the scientific and clinical communities in the coming years.
ESICM consensus-based recommendations for the management of very old patients in intensive care
Authors: Michael Beil, Laura Alberto, Richard S. Bourne, Nathan E. Brummel, Bas de Groot, Dylan W. de Lange, Paul Elbers, Marielle Emmelot-Vonk, Hans Flaatten, Yonathan Freund, Alessandro Galazzi, Ana Garcia-Martinez, Bertrand Guidet, Iva Holmerova, Jeremy M. Jacobs, Gavin M. Joynt, Susannah Leaver, Marc Leone, Bairbre McNicholas, David McWilliams, Victoria Metaxa, Christian H. Nickel, Daniele Poole, Chiara Robba, Kevin Roedl, Marc Romain, Anne-Françoise Rousseau, Sigal Sviri, Wojciech Szczeklik, Helene Vallet, James van Oppen, Christian Jung
Journal: Intensive Care Medicine (2025)
A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome
Authors: Shen-Ao Liang, Tianxin Ren, Jiayu Zhang, Jiahui He, Xuankai Wang, Xinrui Jiang, Yuan He, Rajiv C. McCoy, Qiaomei Fu, Joshua M. Akey, Yafei Mao, Lu Chen
Journal: Genome biology (2025)

Leveraging long-read sequencing technologies, the first complete human reference genome, T2T-CHM13, corrects assembly errors in previous references and resolves the remaining 8% of the genome. While studies on archaic admixture in modern humans have so far relied on the GRCh37 reference due to the availability of archaic genome data, the impact of T2T-CHM13 in this field remains unexplored. We remap the sequencing reads of the high-quality Altai Neanderthal and Denisovan genomes onto GRCh38 and T2T-CHM13. Compared to GRCh37, we find that T2T-CHM13 significantly improves read mapping quality in archaic samples. We then apply IBDmix to identify Neanderthal-introgressed sequences in 2504 individuals from 26 geographically diverse populations using different reference genomes. We observe that commonly used pre-phasing filtering strategies in public datasets substantially influence archaic ancestry determination, underscoring the need for careful filter selection. Our analysis identifies approximately 51 Mb of Neanderthal sequences unique to T2T-CHM13, predominantly in genomic regions where GRCh38 and T2T-CHM13 assemblies diverge. Additionally, we uncover novel instances of population-specific archaic introgression in diverse populations, spanning genes involved in metabolism, olfaction, and ion-channel function. Finally, to facilitate the exploration of archaic alleles and adaptive signals in human genomics and evolutionary research, we integrate these introgressed sequences and adaptive signals across all reference genomes into a visualization database, ASH ( www.arcseqhub.com ). Our study enhances the detection of archaic variations in modern humans, highlights the importance of utilizing the T2T-CHM13 reference, and provides novel insights into the functional consequences of archaic hominin admixture.
Improved prognosis of advanced-stage extranodal NK/T-cell lymphoma: results of the NKEA-Next study
Authors: Ayumi Fujimoto, Kana Miyazaki, Kimikazu Yakushijin, Takahiro Fujino, Wataru Munakata, Yasuo Ejima, Dai Maruyama, Nobuko Kubota, Takeshi Maeda, Jun Takizawa, Nobuhiro Hiramoto, Masahiro Takeuchi, Rika Sakai, Noriko Fukuhara, Senzo Taguchi, Naoko Asano, Motoko Yamaguchi, Ritsuro Suzuki
Journal: Leukemia (2025)

Abstract A retrospective study of extranodal natural killer/T-cell lymphoma (ENKL) patients diagnosed between 2014 and 2021 in Japan was conducted. Among 351 patients with sufficient data, 116 (33%) were in the advanced stage (5 in stage III and 111 in stage IV) at diagnosis, and were further analyzed. The median age was 60 years (range: 19–90), and 68 (59%) were male. Ninety-four (85%) of stage IV patients had two or more extranodal involvements. The most common first-line regimen was SMILE (steroid, methotrexate, ifosfamide, L-asparaginase, and etoposide; 52%). The 2-year overall survival (OS) for all patients was 38.5%, which was significantly improved after 2017 (25.2% for 2014–2017 vs. 50.7% for 2018–2021; P = 0.008). Patients treated with SMILE showed better OS than those treated with DeVIC or CHOP (2y-OS: 57.1%, 35.8%, and 0%, respectively; P &lt; 0.001). The prognosis was significantly better in patients who received hematopoietic stem cell transplantation (HSCT) than in those who did not (2-year OS: 68.3% vs. 17.6%, P &lt; 0.001). Multivariate analysis showed SMILE and HSCT were significant factors for OS. In conclusion, the prognosis of advanced-stage ENKL has improved in recent years. The L-asparaginase-containing chemotherapy and subsequent HSCT is considered the recommended strategy.
Multi-hole metal stent can prevent cystic and pancreatic duct obstruction during endoscopic ultrasound-guided antegrade stenting combined with hepaticogastrostomy
Authors: Takeshi Ogura, Yuki Uba, Takafumi Kanadani, Kimi Bessho, Hiroki Nishikawa
Journal: Endoscopy (2025)

Endoscopic ultrasound-guided biliary drainage (EUS-BD) is mainly indicated as an alternative to endoscopic retrograde cholangiopancreatography (ERCP) in patients with an inaccessible papilla. Recently, because of improved systemic chemotherapy including immune checkpoint inhibitors, a longer duration of stent patency has become very important even in EUS-BD. EUS-guided antegrade stenting (EUS-AS) combined with hepaticogastrostomy using a self-expandable metal stent (SEMS) can achieve longer-duration stent patency [1] [2]. In EUS-AS, to prevent stent dislocation, cholecystitis, and pancreatitis, an uncovered SEMS is usually selected. However, an uncovered SEMS has several disadvantages, such as easy tumor ingrowth, which could shorten its patency in comparison with a fully covered SEMS (FCSEMS). If, on the other hand, a fully covered SEMS is deployed antegradely, cystic duct or pancreatic duct obstruction can occur. Recently, a fully covered SEMS with side holes (Hanarostent Biliary Multi-hole NEO; M. I. Tech Co., Ltd., Pyeongtaek, South Korea) has become available (MHSEMS) ([Fig. 1]). This stent was designed to prevent stent migration by means of the small tissue ingrowths that form in the multiple small (1.8-mm) side holes along the covering membrane [3] [4]. Through this design, a MHSEMS can prevent the adverse events mentioned. Technical tips for EUS-AS combined with hepaticogastrostomy using a MHSEMS are presented here.
Most men choose eyebrows versus scalp hair: a response to “Evaluation of Eyebrow and Eyelash Regrowth and Patient Satisfaction in the Phase 3 THRIVE-AA2 Trial of Deuruxolitinib in Adult Patients with Alopecia Areata”
Authors: Austin J Coppinger, Carlos G Wambier
Journal: Journal of the American Academy of Dermatology (2025)
Technical failure of endoscopic ultrasound choledocoduodenostomy: Multicenter case-control study on rescue techniques, consequences and risk factors
Authors: Clara Beunon, Antoine Debourdeau, Marion Schaefer, Timothee Wallenhorst, Enrique Perez-Cuadrado-Robles, Arthur Belle, Jean-Michel Gonzalez, Marine Camus Duboc, Fabrice Caillol, Hervé-Pierre Toudic, Mathieu Pioche, Jean Baptiste Danset, Adrien Sportes, Bertrand Brieau, Emmanuel Ben Soussan, Mathilde Petiet, Antoine Martin, Sarra Oumrani, Frederique Maire, Arnaud Lemmers, Frederic Prat, Ludovic Caillo, Romain Gerard, Jérémie Albouys, Diane Lorenzo
Journal: Endoscopy (2025)

Background and study aims We aimed to identify risk factors and salvage technique for technical failures of endoscopic ultrasound-guided choledochoduodenostomy (EUS-CDS) and evaluate the short and long-term consequences in patients with biliary obstruction. Patients and methods This retrospective multicenter study included EUS-CDS from 2018 to 2024. Cases were defined as technical failure and classified as follow: type1 (digestive-flange mispositioned), type2 (biliary-flange mispositioned), type3 (stent deployment failure), type4 (catheter-LAMS through the bile duct), and type5 (others). Controls were successful EUS-CDS in the same center and period. The primary endpoint was to to identify risk factors for failure. Secondary endpoints were to describe the endoscopic rescue techniques to evaluate immediate and long-term consequences. Results Technical failures occurred in 7% (95%CI[5;9]). In 23 centers, 296 patients were included (53% male, 71±16 years): 100 cases (type1 [26%], type2 [41%], type3 [11%], type4 [6%], and type5 [16%]) and 196 controls. Risk factors in multivariate analysis for technical failures included CBD diameter ≤15mm, duodenal stenosis, Wired technique and low operator experience (≤10 LAMS). Endoscopic salvage was successful in 77% of cases, with 53% using a covered metal stent and 22% using a new LAMS. Early failures were mild in 50% of cases, but 12% resulted in death within 30 days. Immediate endoscopic salvage reduced severe clinical adverse event (p&lt;0.00001) and increased success rates (p&lt;0.0004). Conclusions EUS-CDS failures are not rare and are severe in half of the cases. Recognizing risk factors, identifying failures during the procedure, and knowing endoscopic salvage methods are crucial.
p52-ZER6/DAZAP1 axis promotes ferroptosis resistance and colorectal cancer progression via regulating SLC7A11 mRNA stabilization
Authors: Li Qiu, Wenfang Li, Lei Zhang, Xia Zhang, Hezhao Zhao, Makoto Miyagishi, Shourong Wu, Vivi Kasim
Journal: Acta Pharmaceutica Sinica B (2025)
Screw stent removal technique using a novel grasping device after inside plastic stent deployment for hilar biliary obstruction
Authors: Takeshi Ogura, Yuki Uba, Takafumi Kanadani, Kimi Bessho, Hiroki Nishikawa
Journal: Endoscopy (2025)

In cases of unresectable malignant hilar biliary obstruction, uncovered self-expandable metal stent (UCSEMS) deployment using a side-by-side or stent-in-stent technique may be recommended for the purpose of prolonging stent patency, according to a consensus statement and guideline [1] [2]. However, because of recent improvements in systemic chemotherapy, such as immune checkpoint inhibitors [3], the number of reinterventions required may have increased. If a UCSEMS is deployed, reintervention may be challenging, because the UCSEMS cannot be removed.
Colonic stenting plus vascular plug for malignant gastrocolonic fistula
Authors: Kewei Ren, Yahua Li, Zongming Li, Zeyi Yao, Bo Ma, Jianzhuang Ren, Xinwei Han
Journal: Endoscopy (2025)

A 48-year-old man visited our department with a 3-month history of intermediate abdominal pain. In the past 2 months, he had received two cycles of chemotherapy for gastric T-cell lymphoma with colon invasion. Seven days ago, he suffered diarrhea with food debris after a liquid diet. Abdominal computed tomography (CT), gastrointestinal radiography, and gastroscopy revealed the formation of a gastrocolonic fistula and transverse colonic stenosis ([Fig. 1]). Colonic stenting plus vascular plug placement was developed to solve this problem ([Video 1]).
In-hospital Mortality in Patients with Lower Gastrointestinal Bleeding: Development and Validation of a Prediction Score
Authors: Elton Dajti, Leonardo Frazzoni, Sílvia Castellet-Farrús, Jordi Guardiola, Emanuele Sinagra, Andrea Anderloni, Francesco Ferrara, Paraskevas Gkolfakis, Marine Camus Duboc, Francesco Vito Mandarino, Anahita Sadeghi, Vicente Lorenzo-Zúñiga, Sandra Perez, Konstantinos Triantafyllou, Maria Paula Curado, Antonio Facciorusso, Giulia Collatuzzo, Cesare Hassan, Franco Radaelli, Lorenzo Fuccio
Journal: Endoscopy (2025)

Background and study aims: Lower gastrointestinal bleeding (LGIB) is a common condition linked to increased morbidity, healthcare costs, and mortality. Currently, no prospectively validated prognostic model exists to predict mortality in LGIB patients. Our aim was to develop and validate a risk score that could accurately predict in-hospital mortality of patients admitted for LGIB. Patients and methods: Patient data from a nationwide cohort study in 15 centers in Italy (2019-2020) were used to derivate the risk score (Acute Lower gastrointestinal Bleeding and In-hospital mortality, ALIBI score); the model was then externally validated in a cohort of consecutive patients hospitalized for LGIB in 12 centers from six countries (Italy, Spain, France, Greece, Iran, Brazil) in 2020-2024. The main outcome was in-hospital mortality; we also reported rebleeding rates and in-hospital mortality rate stratified by risk score and timing of colonoscopy. Results: Among 1,198 patients in the derivation cohort, 105 (8.8%) rebled, 41 (3.4%) died. Age, Charlson Comorbidity Index (CCI), in-hospital onset, hemodynamic instability, and creatinine levels were independent predictors of in-hospital mortality. The model demonstrated excellent discrimination (AUROC=0.813, 95%-CI: 0.752-0.874) and calibration. In the validation cohort (n=752 patients), the model's good discrimination (AUROC=0.792, 95%-CI: 0.720-0.863) and calibration were confirmed. Patients were categorized as low (0-4 points, 1% mortality), intermediate (5-9 points, 4.6% mortality), or high risk (10-13 points, 19.1% mortality). Conclusions: A new validated score effectively predicts in-hospital mortality in LGIB patients, aiding in risk stratification and management.
Incidence of retinal vein occlusion and its association with mortality - results from the Gutenberg Health Study
Authors: A M Voigt, H Elbaz, E W Böhm, P S Wild, K J Lackner, M E Beutel, I Schmidtmann, O Tu Scher, J M Schattenberg, S V Konstantinides, N Pfeiffer, T Peto, A K Schuster
Journal: Ophthalmology (2025)
Editor’s Note: HHLA2, a New Immune Checkpoint Member of the B7 Family, Is Widely Expressed in Human Lung Cancer and Associated with EGFR Mutational Status
Authors: Haiying Cheng, Murali Janakiram, Alain Borczuk, Juan Lin, Wanglong Qiu, Huijie Liu, Jordan M. Chinai, Balazs Halmos, Roman Perez-Soler, Xingxing Zang
Journal: Clinical Cancer Research (2025)
Correction: Targeting the Phosphoinositide 3-Kinase p110-α Isoform Impairs Cell Proliferation, Survival, and Tumor Growth in Small Cell Lung Cancer
Authors: Anna Wojtalla, Barbara Fischer, Nataliya Kotelevets, Francesco A. Mauri, Jens Sobek, Hubert Rehrauer, Carlos Wotzkow, Mario P. Tschan, Michael J. Seckl, Uwe Zangemeister-Wittke, Alexandre Arcaro
Journal: Clinical Cancer Research (2025)
Publisher Correction: GPT-4 assistance for improvement of physician performance on patient care tasks: a randomized controlled trial
Authors: Ethan Goh, Robert J. Gallo, Eric Strong, Yingjie Weng, Hannah Kerman, Jason A. Freed, Joséphine A. Cool, Zahir Kanjee, Kathleen P. Lane, Andrew S. Parsons, Neera Ahuja, Eric Horvitz, Daniel Yang, Arnold Milstein, Andrew P. J. Olson, Jason Hom, Jonathan H. Chen, Adam Rodman
Journal: Nature Medicine (2025)
Population-Level Screening for Diabetes and Dyslipidemia After Pregnancies Complicated by Hypertension or Diabetes
Authors: Amy Y.X. Yu, Nathalie Auger, Longdi Fu, Anna Chu, Moira K. Kapral, Jodi D. Edwards, Sonia R. Dancey, Peter C. Austin, Manav V. Vyas, Kara A. Nerenberg
Journal: Circulation (2025)
Genes of the Fatty Acid Oxidation Pathway are Upregulated in Female as Compared to Male Cardiomyocytes
Authors: Maya Talukdar, Lukáš Chmátal, Linyong Mao, Daniel Reichart, Danielle S. Murashige, Helen Skaletsky, Daniel M. DeLaughter, Zoltan Arany, Jonathan G. Seidman, Christine E. Seidman, David C. Page
Journal: Circulation (2025)
Sex Chromosomes and Sex Hormones: Dissecting the Forces That Differentiate Female and Male Hearts
Authors: Annie Brong, Aikaterini Kontrogianni-Konstantopoulos
Journal: Circulation (2025)

The heart is a highly sex-biased organ, as sex shapes innumerable aspects of heart health and disease. Sex chromosomes and sex hormones —testosterone, progesterone, and estrogen— establish and perpetuate the division between male and female myocardium. Of these differentiating factors, the insulating effects of estrogen have been rigorously interrogated and reviewed, whereas the influence of sex chromosomes, testosterone, and progesterone remains in dispute or ill-defined. Here, we synthesize growing evidence that sex chromosomes and sex hormones substantially bias heart form, function, and dysfunction in a context-dependent fashion. The discrete protective functions ascribed to each of the 3 estrogen receptors are also enumerated. Subsequently, we overview obstacles that have historically discouraged the inclusion of female subjects in basic science such as the impact of the female estrus cycle and reproductive senescence on data reliability and reproducibility. Furthermore, we weigh the utility of several common strategies to intercept and rescue sex-specific protection. Last, we warn of common compounds in animal chow and cell culture that interfere with estrogen signaling. In sum, we survey the controversies and challenges that stem from sex-inclusive cardiovascular research, comparing the possible causes of cardiac sex bias, elucidating sex chromosome or hormone-dependent processes in the heart, describing common lapses that imperil female and male cell and animal work, and illuminating facets of the female heart yet unexplored or still uncertain.
Hypertension in Pregnancy and Postpartum: Current Standards and Opportunities to Improve Care
Authors: Malamo Countouris, Zainab Mahmoud, Jordana B. Cohen, Daniela Crousillat, Afshan B. Hameed, Colleen M. Harrington, Alisse Hauspurg, Michael C. Honigberg, Jennifer Lewey, Kathryn Lindley, Megan M. McLaughlin, Neha Sachdev, Amy Sarma, Kayle Shapero, Rachel Sinkey, Alan Tita, Kristen E. Wong, Eugene Yang, Leslie Cho, Natalie A. Bello
Journal: Circulation (2025)

Hypertension in pregnancy contributes substantially to maternal morbidity and mortality, persistent hypertension, and rehospitalization. Hypertensive disorders of pregnancy are also associated with a heightened risk of cardiovascular disease, and timely recognition and modification of associated risk factors is crucial in optimizing long-term maternal health. During pregnancy, there are expected physiologic alterations in blood pressure (BP); however, pathophysiologic alterations may also occur, leading to preeclampsia and gestational hypertension. The diagnosis and effective management of hypertension during pregnancy is essential to mitigate maternal risks, such as acute kidney injury, stroke, and heart failure, while balancing potential fetal risks, such as growth restriction and preterm birth due to altered uteroplacental perfusion. In the postpartum period, innovative and multidisciplinary care solutions that include postpartum maternal health clinics can help optimize short- and long-term care through enhanced BP management, screening of cardiovascular risk factors, and discussion of lifestyle modifications for cardiovascular disease prevention. As an adjunct to or distinct from postpartum clinics, home BP monitoring programs have been shown to improve BP ascertainment across diverse populations and to lower BP in the months after delivery. Because of concerns about pregnant patients being a vulnerable population for research, there is little evidence from trials examining the diagnosis and treatment of hypertension in pregnant and postpartum individuals. As a result, national and international guidelines differ in their recommendations, and more studies are needed to bolster future guidelines and establish best practices to achieve optimal cardiovascular health during and after pregnancy. Future research should focus on refining treatment thresholds and optimal BP range peripartum and postpartum and evaluating interventions to improve postpartum and long-term maternal cardiovascular outcomes that would advance evidence-based care and improve outcomes worldwide for people with hypertensive disorders of pregnancy.
Type 2 immunity in allergic diseases
Authors: Ismail Ogulur, Yasutaka Mitamura, Duygu Yazici, Yagiz Pat, Sena Ardicli, Manru Li, Paolo D’Avino, Carina Beha, Huseyn Babayev, Bingjie Zhao, Can Zeyneloglu, Oliva Giannelli Viscardi, Ozge Ardicli, Ayca Kiykim, Asuncion Garcia-Sanchez, Juan-Felipe Lopez, Li-li Shi, Minglin Yang, Stephan R. Schneider, Stephen Skolnick, Raja Dhir, Urszula Radzikowska, Abhijeet J. Kulkarni, Manal Bel Imam, Willem van de Veen, Milena Sokolowska, Mar Martin-Fontecha, Oscar Palomares, Kari C. Nadeau, Mubeccel Akdis, Cezmi A. Akdis
Journal: Cellular and Molecular Immunology (2025)
Multi-Site Retrospective Analysis of Diffusion and Perfusion MRI Correlates to Glioma Characteristics Derived from Radio-Pathomic Maps
Authors: Samuel A Bobholz, Daniel Aaronsen, Aleksandra Winiarz, Savannah R Duenweg, Allison K Lowman, Michael Flatley, Fitzgerald Kyereme, Jennifer Connelly, Kelly Mrachek, Max O Krucoff, Anjishnu Banerjee, Peter S LaViolette
Journal: Neuro-Oncology (2025)

Abstract Introduction This study determines the relationship between diffusion and perfusion-based MRI signatures and radio-pathomic maps of tumor pathology in a large, multi-site cohort. Methods This study included perfusion imaging from pre-surgical relative cerebral blood volume (rCBV) images from the UPenn-GBM dataset and pre-surgical arterial spin labeling (ASL) imaging from the UCSF-PDGM dataset. Diffusion imaging included fractional anisotropy (FA) estimates derived from diffusion tensor imaging (DTI) for each subject from each institution. A previously validated autopsy-based model was applied to the structural images from each patient to generate quantitative radio-pathomic maps of cell density and extracellular fluid (ECF). Mean cell density, ECF density, FA, rCBV calculated from DSC imaging, and rCBF calculated from ASL were computed for each patient and statistically compared within contrast-enhancement (CE) and the non-enhancing peritumor FLAIR hyperintensity (FH). Results Both rCBV and ASL showed positive correlation with cell density within CE (rCBV: R=0.280, p&amp;lt;0.001; ASL: R=0.117, p=0.023). However, both perfusion metrics also showed no association with cell density within the FH region at the group level (rCBV: R=0.0162, p=0.731; ASL: R=-0.020, p=0.652). Negative correlations were observed between FA and ECF density across both CE and FH in both the UPenn-GBM (CE: r = -0.204, p&amp;lt;0.001, FH: r=-0.332, p&amp;lt;0.001) and the UCSF-PDGM (CE:r=-0.179, p&amp;lt;0.001, FH:-0.355, p&amp;lt;0.001). Additionally, a positive ASL-cell density association per subject within FH was associated with worse survival prognosis (HR=5.58, p=0.022). Discussion These results suggest that radio-pathomic maps of tumor pathology provide complementary information to other MR signatures that reveal prognostically valuable signatures of the non-enhancing tumor margin.