tbuckley/cabot-search huggingface dataset:
Clinical outcomes and care for spontaneous bacterial peritonitis: A national cohort study
Authors: Marina Serper, Helen Tang, Siqi Zhang, Alexadra McCullough, David E. Kaplan, Tamar H. Taddei, Nadim Mahmud
Journal: Hepatology (2025)

SBP leads to high rates acute kidney injury (AKI) -hepatorenal syndrome and mortality. Population-based studies on contemporary SBP epidemiology are needed to inform care. In a large, national cohort of patients diagnosed with SBP and confirmed by ascitic fluid criteria, we characterized ascitic fluid characteristics, in-hospital and 12-month mortality, AKI, and recurrent SBP. We investigated how individual and bundled quality measures for SBP associated with outcomes after multi-level adjustment for health-system, patient clinical factors and quality measures. Individual and bundled quality metrics were inpatient antibiotics within 48 hours, intravenous albumin, repeat paracentesis within 48 hours, recognition of SBP, and prophylactic antibiotics upon discharge. Among 4,330 patients with newly diagnosed SBP, in-hospital mortality was 15.5% and 12-month mortality was 56.6%. The incidence of Stage 1 AKI was 26.6%, 15.7% for Stage 2, and 22.8% for Stage 3. The cumulative incidence of recurrent SBP was 10.3%. Guideline-recommended albumin was the only individual metric associated with reduced in-hospital mortality (HR 0.73, 95%CI 0.59 - 0.91). Receipt of a higher number of metrics from the SBP bundle was associated with progressively lower 12-month post-discharge mortality: patients who received 3, 4, and 5 SBP bundle components had 20%, 38%, and 56% lower hazard of mortality, respectively, relative to those receiving 2 or fewer (all p<0.001). The SBP bundle was associated with lower incidence of Stage 3 versus Stage 0-2 AKI (OR 0.66, 95%CI 0.51-0.86). Prospective implementation of evidence-based SBP bundles may improve care outcomes and mortality in SBP.
Acquired Osteomalacia Associated with Autoantibodies against PHEX
Authors: Yoshitomo Hoshino, Kazuo Okamoto, Tomohiro Ogawa, Hajime Kato, Koki Irie, So Watanabe, Soichiro Kimura, Naoko Hidaka, Yuka Kinoshita, Hiroshi Kobayashi, Daisuke Hagiwara, Masakazu Kogawa, Hiroshi Takayanagi, Sakae Tanaka, Masaomi Nangaku, Noriko Makita, Peter D. Burbelo, Taku Saito, Nobuaki Ito
Journal: New England Journal of Medicine (2025)
Discovery of a MET-driven monogenic cause of steatotic liver disease
Authors: Filippo Pinto e Vairo, Michael T. Zimmermann, Jessica Wagenknecht, Salomão Doria Jorge, Shulan Tian, Robert A. Vierkant, Anthony C. Luehrs, Thiago Milech de Assunção, Angela Mathison, Paldeep S. Atwal, Yang Cao, Alina M. Allen, Eric W. Klee, Raul Urrutia, Konstantinos N. Lazaridis
Journal: Hepatology (2025)

Metabolic dysfunction-associated steatotic liver disease (MASLD) affects about a third of adults worldwide and is projected soon to be the leading cause of cirrhosis. It occurs when fat accumulates in hepatocytes and can progress to metabolic dysfunction-associated steatohepatitis (MASH), liver cirrhosis, and hepatocellular carcinoma. MASLD pathogenesis is believed to involve a combination of genetic and environmental risk factors. Single nucleotide polymorphisms have been implicated but non-syndromic monogenic causes are lacking. We identified a novel genetic variant in a familial case of MASH and performed deep variant functional analysis including protein modeling, dynamics, and cell-based assays to assess molecular mechanisms of dysfunction and altered cellular signaling. We analyzed exome sequencing data of 3,904 individuals with steatotic liver disease (SLD) to identify additional cases and establish the link between specific gene variants and SLD diagnosis. We discovered and functionally validated the NM_000245.4:c.3505A>T; p.(Ile1169Phe) variant in the MET (mesenchymal epithelial transition) kinase domain as a monogenic cause of SLD. Subsequently, we detected additional ultra-rare, previously un-interpreted, and likely deleterious variants in MET from screening sequencing data. Among individuals with confirmed SLD based on electronic record review, 1.1% (45/3,904) had rare predicted deleterious MET variants. Eight of 45 (17.7%) individuals had predicted deleterious variants in the MET kinase domain confirmed to be functionally like the familial case variant. We report the first germline non-malignant rare MET-driven disease, a monogenic form of SLD.
Endoscopic observation of acute appendiceal hemorrhage: A case report
Authors: Chenyang Jiao, Cuixia Liu, Zhen Yang, Haihua Zhou, Yiwei Fu
Journal: Endoscopy (2025)

A 24-year-old man manifested with bloody stools 10 times within 14 hours without obvious abdominal pain. A computed tomography (CT) scan showed no signs of appendicitis, but the enhanced CT scan revealed contrast agent leakage into the appendiceal lumen ([Fig. 1] a–c). An emergency colonoscopy showed fresh blood at the appendiceal orifice. The diagnosis of appendiceal bleeding was confirmed. However, the underlying cause remained unclear. An ultrathin gastroscope (GIF-XP290N; Olympus, Tokyo, Japan) was then inserted into the appendiceal lumen, revealing the formation of an ulcer with a blood clot at its center ([Video 1]). The patient underwent a laparoscopic appendectomy ([Fig. 2] a–d). After three months of follow-up, there was no recurrence of rectal bleeding, and hemoglobin levels returned to normal.
Frozen versus fresh embryo transfer in women with low prognosis for in vitro fertilisation treatment: pragmatic, multicentre, randomised controlled trial
Authors: Daimin Wei, Yun Sun, Han Zhao, Junhao Yan, Hong Zhou, Fei Gong, Aijun Zhang, Ze Wang, Lei Jin, Hongchu Bao, Shuyun Zhao, Zhuoni Xiao, Yingying Qin, Ling Geng, Linlin Cui, Yan Sheng, Mei Sun, Peihao Liu, Lingling Ding, Hong Liu, Keliang Wu, Yan Li, Yao Lu, Bufang Xu, Bei Xu, Luqing Zhang, Heping Zhang, Richard S Legro, Zi-Jiang Chen
Journal: BMJ (2025)

Abstract Objective To test the hypothesis that a freeze-all strategy would increase the chance of live birth compared with fresh embryo transfer in women with low prognosis for in vitro fertilisation (IVF) treatment. Design Pragmatic, multicentre, randomised controlled trial. Setting Nine academic fertility centres in China. Participants 838 women with a low prognosis for IVF treatment defined by ≤9 oocytes retrieved or poor ovarian reserve (antral follicle count &lt;5 or serum anti-Müllerian hormone level &lt;8.6 pmol/L). Interventions Eligible participants were randomised (1:1) to undergo either frozen embryo transfer or fresh embryo transfer on the day of oocyte retrieval. Participants in the frozen embryo transfer group had all of their embryos cryopreserved and underwent frozen embryo transfer later. Participants in the fresh embryo transfer group underwent fresh embryo transfer after oocyte retrieval. Main outcome measures The primary outcome was live birth, defined as the delivery of neonates with a heartbeat and respiration at ≥28 weeks’ gestation. Secondary outcomes were clinical pregnancy, singleton or twin pregnancy, pregnancy loss, ectopic pregnancy, birth weight, maternal and neonatal complications, and cumulative live birth after embryo transfers within one year after randomisation. Results In an intention-to-treat analysis, the rate of live birth was lower in the frozen embryo transfer group than in the fresh embryo transfer group (32% (132 of 419) v 40% (168 of 419); relative ratio 0.79 (95% confidence interval 0.65 to 0.94); P=0.009). The frozen embryo group had a lower rate of clinical pregnancy than the fresh embryo group (39% (164 of 419) v 47% (197 of 419); 0.83 (0.71 to 0.97)). The cumulative live birth rate was lower in the frozen embryo transfer group compared with the fresh embryo transfer group (44% (185 of 419) v 51% (215 of 419), 0.86 (0.75 to 0.99)). No difference was observed in birth weight, incidence of obstetric complications, or risk of neonatal morbidities. Conclusions Fresh embryo transfer may be a better choice for women with low prognosis in terms of live birth rate compared with a freeze-all strategy. The treatment strategies that prevent fresh embryo transfers, such as accumulating embryos with back-to-back cycles or performing routine preimplantation genetic testing for aneuploidy, warrant further studies in women with a low prognosis. Trial registration Chinese Clinical Trial Registry ChiCTR2100050168.
Low-coverage whole genome sequencing of low-grade dysplasia strongly predicts advanced neoplasia risk in ulcerative colitis
Authors: Ibrahim Al Bakir, Kit Curtius, George D Cresswell, Heather E Grant, Nadia Nasreddin, Kane Smith, Salpie Nowinski, Qingli Guo, Hayley L Belnoue-Davis, Jennifer Fisher, Theo Clarke, Christopher Kimberley, Maximilian Mossner, Philip D Dunne, Maurice B Loughrey, Ally Speight, James E East, Nicholas A Wright, Manuel Rodriguez-Justo, Marnix Jansen, Morgan Moorghen, Ann-Marie Baker, Simon J Leedham, Ailsa L Hart, Trevor A Graham
Journal: Gut (2025)

The risk of developing advanced neoplasia (AN; colorectal cancer and/or high-grade dysplasia) in ulcerative colitis (UC) patients with a low-grade dysplasia (LGD) lesion is variable and difficult to predict. This is a major challenge for effective clinical management. We aimed to provide accurate AN risk stratification in UC patients with LGD. We hypothesised that the pattern and burden of somatic genomic copy number alterations (CNAs) in LGD lesions could predict future AN risk. We performed a retrospective multicentre validated case-control study using n=270 LGD samples from n=122 patients with UC. Patients were designated progressors (n=40) if they had a diagnosis of AN in the ~5 years following LGD diagnosis or non-progressors (n=82) if they remained AN-free during follow-up. DNA was extracted from the baseline LGD lesion, low-coverage whole genome sequencing performed and data processed to detect CNAs. Survival analysis was used to evaluate CNAs as predictors of future AN risk. CNA burden was significantly higher in progressors than non-progressors (p=2×10-6 in discovery cohort) and was a very significant predictor of AN risk in univariate analysis (OR=36; p=9×10-7), outperforming existing clinical risk factors such as lesion size, shape and focality. Optimal risk prediction was achieved with a multivariate model combining CNA burden with the known clinical risk factor of incomplete LGD resection. Within-LGD lesion genetic heterogeneity did not confound risk prediction. Measurement of CNAs in LGD is an accurate predictor of AN risk in inflammatory bowel disease and is likely to support clinical management.
Author Correction: Enhanced control of a brain–computer interface by tetraplegic participants via neural-network-mediated feature extraction
Authors: Benyamin Haghi, Tyson Aflalo, Spencer Kellis, Charles Guan, Jorge A. Gamez de Leon, Albert Yan Huang, Nader Pouratian, Richard A. Andersen, Azita Emami
Journal: Nature Biomedical Engineering (2025)
The Critical Role of Commercial Analytical Reference Standards in the Control of Chemical Risks: The Case of PFAS and Ways Forward
Authors: Xenia Trier, Stefan P.J. van-Leeuwen, Gianfranco Brambilla, Roland Weber, Thomas F. Webster
Journal: Environmental Health Perspectives (2025)

Various countries have instituted risk governance measures to control and minimize the risks of chemicals at the national and international levels. Activities typically include risk assessment based on a) hazard and exposure assessments; b) setting limits on the production, use, and emissions of chemicals; c) enforcement of regulations; and d) monitoring the effectiveness of the measures taken. These steps largely depend on chemical analysis and access to pure chemical reference standards. However, except for specific highly regulated categories of chemicals, such reference standards often are not commercially available. This raises a critical question: Given the widespread lack of reference standards, is the current approach to governing chemicals adequate to protect humans and the environment from harm? If not, what measures could be taken to improve the situation? We outline how current chemical risk governance is hampered by the widespread lack of reference standards to produce the required scientific evidence. We also provide a list of recommendations for controlling chemical risks in the absence of reference standards. We use per- and polyfluoroalkyl substances (PFASs), specifically the chemical C6O4 [perfluoro ([5-methoxy-1,3-dioxolan-4-yl]oxy) acetic acid], to illustrate how companies that produce chemicals can prevent access to reference standards. We argue that the very limited availability of reference standards undermines the ability of scientists to produce independent scientific evidence needed for chemical risk governance and, thereby, prevents society from protecting people and the environment against chemical pollution and its harms. Possible ways to improve the situation include a) guaranteeing access to chemical reference standards by creating a reference standards repository, b) redefining the level of confidence sufficient for regulatory action, c) providing alternative options for chemical identification and quantification when reference standards are not available, and d) considering, when no reference standards are available, regulation of chemicals by class rather than individually. https://doi.org/10.1289/EHP12331.
Arginase-1-specific T cells target and modulate tumor-associated macrophages
Authors: Evelina Martinenaite, Inés Lecoq, Mia Aaboe-Jørgensen, Shamaila Munir Ahmad, Maria Perez-Penco, Hannah Jorinde Glöckner, Marion Chapellier, Lucía Lara de la Torre, Lars Rønn Olsen, Anne Mette Askehøj Rømer, Ayako Wakatsuki Pedersen, Mads Hald Andersen
Journal: Journal for ImmunoTherapy of Cancer (2025)

Arginase-1 (Arg1) expressing tumor-associated macrophages (TAMs) may create an immune-suppressive tumor microenvironment (TME), which is a significant challenge for cancer immunotherapy. We previously reported the existence of Arg1-specific memory T cells among peripheral blood mononuclear cells (PBMCs) and described that Arg-1-based immune modulatory vaccines (IMVs) control tumor growth and alter the M1/M2 macrophage ratio in murine models of cancer. In the present study, we investigated how Arg1-specific T cells can directly target TAMs and influence their polarization. Murine Arg1-specific CD4+T cells isolated from splenocytes of animals vaccinated with an Arg1-derived peptide in the adjuvant montanide were co-cultured with either in vitro M2-differentiated bone marrow-derived macrophages or ex vivo isolated F4/80+TAMs. Human Arg1-specific CD4+T cell clones were co-cultured with Arg1-expressing TAMs generated in vitro from either PBMC-derived CD14+cells or the myeloid cell lines MonoMac1 and THP-1. MHC class II-restricted Arg-1 peptide presentation by macrophages was confirmed by immunopeptidomics. T-cell-mediated changes in the macrophage immune phenotype and cytokine microenvironment were examined using flow cytometry, RT-qPCR and multiplex immunoassay. The effect of Arg1-derived peptide IMV on TAMs in vivo was assessed by multiplex gene analysis of F4/80+cells. We show that Arg1-based IMV-mediated tumor control was linked to a decrease in multiple immunosuppressive pathways in the TAM population of the treated animals. Tumor-conditioned media (TCM) derived from Arg1-vaccinated mice induced significantly higher upregulation of MHC-II on exposed myeloid cells compared with controls. Furthermore, murine CD4+Arg1-specific T cells were able to target TAMs and effectively reprogram their phenotype ex vivo by secreting IL2 and IFNγ. Next, we established that human Arg1+TAMs present Arg1-derived peptides and are directly recognized by proinflammatory CD4+Arg1-specific T cell clones. These CD4+Arg1-specific T cells were able to reprogram TCM-conditioned macrophages as observed by increased expression of CD80 and HLA-DR. TAMs may be directly targeted and modulated by Arg1-specific CD4+T cells. These findings provide a strong rationale for future clinical development of Arg1-based IMVs to alter the immune-suppressive TME by reprogramming TAMs and promoting a proinflammatory TME.
Hallmark discoveries in the biology of non-Wilms tumour childhood kidney cancers
Authors: Daniela Perotti, Maureen J. O’Sullivan, Amy L. Walz, Jonathan Davick, Reem Al-Saadi, Daniel J. Benedetti, Jack Brzezinski, Sara Ciceri, Nicholas G. Cost, Jeffrey S. Dome, Jarno Drost, Nicholas Evageliou, Rhoikos Furtwängler, Norbert Graf, Mariana Maschietto, Elizabeth A. Mullen, Andrew J. Murphy, Michael V. Ortiz, Justine N. van der Beek, Arnauld Verschuur, Jenny Wegert, Richard Williams, Filippo Spreafico, James I. Geller, Marry M. van den Heuvel-Eibrink, Andrew L. Hong
Journal: Nature Reviews Urology (2025)
The influence of familiarity between the surgeon and their assistant on patient outcomes: a prospective observational cohort study
Authors: Daniel R. Stelzl, Stephanie Polazzi, Jean-Christophe Lifante, Tanujit Dey, Antoine Duclos
Journal: International Journal of Surgery (2025)

Background: The inverse relationship between increased surgical team familiarity and reduced operative time is established, but its effect on patient outcomes remains uncertain. Materials and methods: A prospective cohort study including operations by attending surgeons between 1 November 2020 and 31 December 2021 across fourteen surgical departments from four French university hospitals. Surgical team familiarity was measured as the cumulative number of previous operations performed by the same dyad of attending and assisting surgeons. Composite of adverse events within 30 days of surgery encompassed major surgical complication, unplanned reoperation, extended ICU stay, and death. We used multivariable generally estimated equations to model the association between patient outcomes and surgical team familiarity, using a logarithmic function. The model considered the clustering of operations within surgeons. Results: Our analysis included 8546 operations by 1109 surgical team dyads, involving 45 attending surgeons and 369 assisting surgeons. We observed a significant inverse association between surgical team familiarity and composite adverse events odds ratio [OR] 0.92 (95% confidence interval [95% CI] 0.87–0.98), major surgical complications OR 0.93 (95% CI 0.88–0.99), and unplanned reoperations OR 0.88 (95% CI 0.78–0.99), with non-significant trends observed for extended ICU stays OR 0.88 (95% CI 0.75–1.04) and deaths OR 0.87 (95% CI 0.74–1.03). Within the first 15 collaborations, this was illustrated by a reduction in the occurrence of composite adverse events from 23.0% (95% CI 22.1%–24.0%) to 16.5% (95% CI 14.1%–18.8%), major surgical complications from 21.3% (95% CI 20.3%–22.2%) to 15.3% (95% CI 13.0%–17.5%), unplanned reoperations from 8.8% (95% CI 8.6%–9.1%) to 5.2% (95%CI 4.2%–6.1%), extended ICU stays from 4.3% (95% CI 4.1%–4.5%) to 3.1% (95% CI 2.0%–4.1%), and deaths from 2.3% (95% CI 2.1%–2.5%) to 1.4% (95% CI 0.9%–1.8%). Conclusions and relevance: This study emphasizes that heightened familiarity among surgical teams is associated with a significant reduction in major adverse events. Building stable operating room teams should be a management priority to enhance patient outcomes.
Retinal oculomics and risk of incident aortic aneurysm and aortic adverse events: a population-based cohort study
Authors: Cong Li, Yu Huang, Jian Chen, Guangyao Hua, Fan Yang, Dongqin Cai, Yu Kuang, Xue He, Yan Wang, Jianrong Jiang, Zhenchao Du, Jingyan Peng, Heng Li, Zhishen Peng, Tengda Huang, Yun Ren, Wenli Zhang, Lei Liu, Danli Shi, Jianfang Luo, Honghua Yu, Xiaohong Yang
Journal: International Journal of Surgery (2025)

Background: The asymptomatic onset and extremely high mortality rate of aortic aneurysm (AA) highlight the urgency of early detection and timely intervention. The alteration of retinal vascular features (RVFs) can reflect the systemic vascular properties, and be widely used as the biomarker for cardiovascular disease risk prediction. Therefore, we aimed to investigate associations of RVFs with AA and its progression. Methods: In this prospective population-based cohort study, participants with eligible fundus images and without a history of AA at recruitment were included for analysis. A fully automated Retina-based Microvascular Health Assessment System was used to quantify multidimensional RVFs including the branching angle, caliber, complexity, density, length, and tortuosity. Univariable and multivariable Cox regressions were used to estimate the association of RVFs with the incidence of AA and aortic adverse events (AAE). Furthermore, propensity score matching was performed to mitigate the confounding effects of baseline characteristics. Results: During a median follow-up of 11.0 years, 306 incident AA (164 with abdominal AA and 108 with thoracic AA) and 48 incident AAE were documented. In the fully adjusted model, the retinal arterial branching angle (hazard ratio [HR] 0.87, 95% confidence interval [CI] 0.77 to 0.99) and the central tendency and variability of minimum venular caliber were significantly associated with the risk of incident AA (HR 1.13-1.15), while the venular minimum angular asymmetry (0.48, 0.30 to 0.77) was significantly associated with the incidence of AAE. Moreover, specific alterations of RVFs were observed in different AA subtypes (caliber in abdominal AA [HR 1.21]; caliber [HR 1.21-1.28], complexity, length, and tortuosity [HR 0.77-0.82] in thoracic AA). Similar results were obtained after propensity score-matched analysis, confirming the stability of these associations. Conclusions: We identified a significant association of certain RVFs with incident AA and AAE, implying that noninvasive, and convenient fundus photography could be a promising tool to facilitate the early detection of AA and subsequent preventative interventions.
A commentary on “the efficacy of peritoneal flap fixation on symptomatic lymphocele formation following robotic-assisted laparoscopic radical prostatectomy with pelvic lymph node dissection: a systematic review and meta-analysis”
Authors: Wujie Chen, Dihao Lv, Yinglong Huang, Mingxia Ding
Journal: International Journal of Surgery (2025)

aDepartment of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan, China *Corresponding authors. Address: Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan, China. E-mail: [email protected] (M. Ding); [email protected] (Y. Huang). Wujie Chen and Dihao Lv equally contributed to the article. This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.