tbuckley/cabot-search huggingface dataset:
A CT-based deep learning model predicts overall survival in patients with muscle invasive bladder cancer after radical cystectomy: a multicenter retrospective cohort study
Authors: Zongjie Wei, Yingjie Xv, Huayun Liu, Yang Li, Siwen Yin, Yongpeng Xie, Yong Chen, Fajin Lv, Qing Jiang, Feng Li, Mingzhao Xiao
Journal: International Journal of Surgery (2024)

Background: Muscle invasive bladder cancer (MIBC) has a poor prognosis even after radical cystectomy (RC). Postoperative survival stratification based on radiomics and deep learning algorithms may be useful for treatment decision-making and follow-up management. This study was aimed to develop and validate a deep learning (DL) model based on preoperative CT for predicting post-cystectomy overall survival in patients with MIBC. Methods: MIBC patients who underwent RC were retrospectively included from four centers, and divided into the training, internal validation and external validation sets. A deep learning model incorporated the convolutional block attention module (CBAM) was built for predicting overall survival using preoperative CT images. We assessed the prognostic accuracy of the DL model and compared it with classic handcrafted radiomics model and clinical model. Then, a deep learning radiomics nomogram (DLRN) was developed by combining clinicopathological factors, radiomics score (Rad-score) and deep learning score (DL-score). Model performance was assessed by C-index, KM curve, and time-dependent ROC curve. Results: A total of 405 patients with MIBC were included in this study. The DL-score achieved a much higher C-index than Rad-score and clinical model (0.690 vs. 0.652 vs. 0.618 in the internal validation set, and 0.658 vs. 0.601 vs. 0.610 in the external validation set). After adjusting for clinicopathologic variables, the DL-score was identified as a significantly independent risk factor for OS by the multivariate Cox regression analysis in all sets (all P &lt;0.01). The DLRN further improved the performance, with a C-index of 0.713 (95%CI: 0.627-0.798) in the internal validation set and 0.685 (95%CI: 0.586-0.765) in external validation set, respectively. Conclusions: A DL model based on preoperative CT can predict survival outcome of patients with MIBC, which may help in risk stratification and guide treatment decision-making and follow-up management.
Molecular mechanisms in MASLD/MASH-related HCC
Authors: Xiaobo Wang, Liang Zhang, Bingning Dong
Journal: Hepatology (2024)

Liver cancer is the third leading cause of cancer-related deaths and ranks as the sixth most prevalent cancer type globally. NAFLD or metabolic dysfunction-associated steatotic liver disease, and its more severe manifestation, NASH or metabolic dysfunction-associated steatohepatitis (MASH), pose a significant global health concern, affecting approximately 20%-25% of the population. The increased prevalence of metabolic dysfunction-associated steatotic liver disease and MASH is parallel to the increasing rates of obesity-associated metabolic diseases, including type 2 diabetes, insulin resistance, and fatty liver diseases. MASH can progress to MASH-related HCC (MASH-HCC) in about 2% of cases each year, influenced by various factors such as genetic mutations, carcinogen exposure, immune microenvironment, and microbiome. MASH-HCC exhibits distinct molecular and immune characteristics compared to other causes of HCC and affects both men and women equally. The management of early to intermediate-stage MASH-HCC typically involves surgery and locoregional therapies, while advanced HCC is treated with systemic therapies, including anti-angiogenic therapies and immune checkpoint inhibitors. In this comprehensive review, we consolidate previous research findings while also providing the most current insights into the intricate molecular processes underlying MASH-HCC development. We delve into MASH-HCC-associated genetic variations and somatic mutations, disease progression and research models, multiomics analysis, immunological and microenvironmental impacts, and discuss targeted/combined therapies to overcome immune evasion and the biomarkers to recognize treatment responders. By furthering our comprehension of the molecular mechanisms underlying MASH-HCC, our goal is to catalyze the advancement of more potent treatment strategies, ultimately leading to enhanced patient outcomes.
Diversifying the Physician Workforce—Reply
Authors: Utibe R. Essien, Victor Agbafe, Keith C. Norris
Journal: JAMA (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Outdoor air pollution exposure and uterine cancer incidence in the Sister Study
Authors: Jordyn A Brown, Jennifer L Ish, Che-Jung Chang, Deborah B Bookwalter, Katie M O’Brien, Rena R Jones, Joel D Kaufman, Dale P Sandler, Alexandra J White
Journal: JNCI Journal of the National Cancer Institute (2024)

Abstract Background Outdoor air pollution is a ubiquitous exposure that includes endocrine-disrupting and carcinogenic compounds that may contribute to the risk of hormone-sensitive outcomes such as uterine cancer. However, there is limited evidence about the relationship between outdoor air pollution and uterine cancer incidence. Methods We investigated the associations of residential exposure to particulate matter less than 2.5 µm in aerodynamic diameter (PM2.5) and nitrogen dioxide (NO2) with uterine cancer among 33 417 Sister Study participants with an intact uterus at baseline (2003-2009). Annual average air pollutant concentrations were estimated at participants’ geocoded primary residential addresses using validated spatiotemporal models. Cox proportional hazards models were used to estimate hazard ratios and 95% confidence intervals for the association between time-varying 12-month PM2.5 (µg/m3) and NO2 (parts per billion; ppb) averages and uterine cancer incidence. Results Over a median follow-up period of 9.8 years, 319 incident uterine cancer cases were identified. A 5-ppb increase in NO2 was associated with a 23% higher incidence of uterine cancer (hazard ratio = 1.23, 95% confidence interval = 1.04 to 1.46), especially among participants living in urban areas (hazard ratio = 1.53, 95% confidence interval = 1.13 to 2.07), but PM2.5 was not associated with increased uterine cancer incidence. Conclusion In this large US cohort, NO2, a marker of vehicular traffic exposure, was associated with a higher incidence of uterine cancer. These findings expand the scope of health effects associated with air pollution, supporting the need for policy and other interventions designed to reduce air pollutant exposure.
Reply: AGILE 3+ score, enhancing the diagnostic accuracy of advanced fibrosis in patients with nonalcoholic fatty liver disease
Authors: Rosa Lombardi, Andrea Dalbeni, Alessandro Mantovani, Federico Ravaioli
Journal: Hepatology (2024)

We would like to thank Bertot et al1 for their interest in our systematic review and meta-analysis assessing the diagnostic accuracy of the AGILE3+ score for diagnosing advanced fibrosis in patients with metabolic dysfunction–associated fatty liver disease.2 The concerns presented by the authors must be considered. Regarding the impact of obesity on the score's performance, we have highlighted how body mass index mildly impaired its capability in a ruling-out strategy, as it slightly lowered the test's sensitivity from 88% to 84%. Unfortunately, it has not been possible to perform a subanalysis for heterogeneity based on obese status, as obesity prevalence was not reported in all eligible studies. However, the pooled cohort of our analysis had a mean body mass index of 30.9 (SE: 2.3) kg/m2. Similarly, age mildly affected the performance of AGILE3+ in detecting advanced fibrosis. As suggested by Bertot et al,1 it would be interesting to evaluate AGILE3+ performance in an older metabolic dysfunction–associated fatty liver disease population (ie, >65 y) since age is included in its formula. Nevertheless, our meta-analysis reports data from middle-aged populations (mean age: 53 y [SE: 4.0]), and the percentage of subjects >65 years was not provided by eligible studies. Similarly, despite an intriguing aspect that could be the potential role of ethnicity in the model performance, based on the data available, we could not definitely determine the role of ethnicity on heterogeneity and AGILE3+ performance. In addition, we could not include the study by Arora et al3 published in December 2023 since we included papers published from inception to April 2023, as stated in the Methods section.2 Nonetheless, we are confident about the applicability of our findings to the Asian population since the cohorts already included in our analysis have a good representation of this subpopulation. Finally, given the few indeterminate results provided by AGILE3+, the authors point out how an accurate estimation of the pool prevalence of this indeterminate population, based on individual patient data, would reinforce our results. Nevertheless, as explained,2 based on the data we analyzed, we could not perform an individual patient data meta-analysis that would provide more robust evidence than an aggregate data meta-analysis.
Biogeographic Perspectives on Human Genetic Diversification
Authors: Tábita Hünemeier
Journal: Molecular Biology and Evolution (2024)

Abstract Modern humans originated in Africa 300,000 yr ago, and before leaving their continent of origin, they underwent a process of intense diversification involving complex demographic dynamics. Upon exiting Africa, different populations emerged on the four other inhabited continents, shaped by the interplay of various evolutionary processes, such as migrations, founder effects, and natural selection. Within each region, continental populations, in turn, diversified and evolved almost independently for millennia. As a backdrop to this diversification, introgressions from archaic species contributed to establishing different patterns of genetic diversity in different geographic regions, reshaping our understanding of our species’ variability. With the increasing availability of genomic data, it has become possible to delineate the subcontinental human population structure precisely. However, the bias toward the genomic research focused on populations from the global North has limited our understanding of the real diversity of our species and the processes and events that guided different human groups throughout their evolutionary history. This perspective is part of a series of articles celebrating 40 yr since our journal, Molecular Biology and Evolution, was founded (Russo et al. 2024). The perspective is accompanied by virtual issues, a selection of papers on human diversification published by Genome Biology and Evolution and Molecular Biology and Evolution.
Azithromycin for Prevention of Mortality in African Children
Authors: Chandy C. John, Ruth Namazzi, Jack G. Schneider
Journal: JAMA (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Optimizing Beneficence and Justice in Heart Transplant Allocation
Authors: Michelle M. Kittleson
Journal: JAMA (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Plant-Based Dietary Patterns and Incident Diabetes in the Atherosclerosis Risk in Communities (ARIC) Study
Authors: Valerie K. Sullivan, Hyunju Kim, Laura E. Caulfield, Lyn M. Steffen, Elizabeth Selvin, Casey M. Rebholz
Journal: Diabetes Care (2024)

OBJECTIVE Plant-based dietary patterns emphasize plant foods and minimize animal-derived foods. We investigated the association between plant-based dietary patterns and diabetes in a community-based U.S. sample of Black and White adults. RESEARCH DESIGN AND METHODS We included middle-aged adults from the Atherosclerosis Risk in Communities (ARIC) study without diabetes at baseline who completed a food-frequency questionnaire (n = 11,965). We scored plant-based diet adherence according to three indices: overall, healthy, and unhealthy plant-based diet indices. Higher overall plant-based diet index (PDI) scores represent greater intakes of all plant foods and lower intakes of animal-derived foods. Higher healthy plant-based diet index (hPDI) scores represent greater healthy plant food intake and lower intakes of animal-derived and unhealthy plant foods. Higher unhealthy plant-based diet index (uPDI) scores represent greater unhealthy plant food intake and lower intakes of animal-derived and healthy plant foods. We used Cox regression to estimate hazard ratios (HRs) for incident diabetes (defined according to self-reported diagnosis, medication use, or elevated blood glucose) associated with each index. RESULTS Over a median follow-up of 22 years, we identified 4,208 cases of diabetes among subjects. Higher PDI scores were associated with a lower risk of diabetes (quintile 5 vs. 1 HR 0.89 [95% CI 0.80, 0.98]; Ptrend = 0.01). hPDI scores were also inversely associated with diabetes risk (quintile 5 vs. 1 HR 0.85 [95% CI 0.77, 0.94]; Ptrend &amp;lt; 0.001). uPDI scores were not associated with diabetes risk. CONCLUSIONS A dietary pattern that minimizes animal-derived foods and emphasizes plant foods may reduce diabetes risk.
Liquid biopsy approach to monitor the efficacy and response to CAR-T cell therapy
Authors: Stephanie N Shishido, Olivia Hart, Sujin Jeong, Aidan Moriarty, Darren Heeke, John Rossi, Adrian Bot, Peter Kuhn
Journal: Journal for ImmunoTherapy of Cancer (2024)

Background Chimeric antigen receptor (CAR)-T cells are approved for use in the treatment of hematological malignancies. Axicabtagene ciloleucel (YESCARTA) and brexucabtagene autoleucel (TECARTUS) genetically modified autologous T cells expressing an anti-CD19 scFv based on the FMC63 clone have shown impressive response rates for the treatment of CD19+B cell malignancies, but there remain challenges in monitoring long-term persistence as well as the functional characterization of low-level persisting CAR-T cells in patients. Furthermore, due to CD19-negative driven relapse, having the capability to monitor patients with simultaneous detection of the B cell malignancy and persisting CAR-T cells in patient peripheral blood is important for ensuring timely treatment optionality and understanding relapse. Methods This study demonstrates the development and technical validation of a comprehensive liquid biopsy, high-definition single cell assay (HDSCA)-HemeCAR for (1) KTE-X19 CAR-T cell identification and analysis and (2) simultaneously monitoring the CD19-epitope landscape on neoplastic B cells in cryopreserved or fresh peripheral blood. Proprietary anti-CD19 CAR reagents, healthy donor transduced CAR-T cells, and patient samples consisting of malignant B cell fractions from manufacturing were used for assay development. Results The CAR-T assay showed an approximate limit of detection at 1 cell in 3 million with a sensitivity of 91%. Genomic analysis was additionally used to confirm the presence of the CAR transgene. This study additionally reports the successful completion of two B cell assays with multiple CD19 variants (FMC63 and LE-CD19) and a unique fourth channel biomarker (CD20 or CD22). In patient samples, we observed that CD19 isoforms were highly heterogeneous both intrapatient and interpatient. Conclusions With the simultaneous detection of the CAR-T cells and the B cell malignancy in patient peripheral blood, the HDSCA-HemeCAR workflow may be considered for risk monitoring and patient management.
Bile acids and coronavirus disease 2019
Authors: Xiaoru Huang, Xuening Liu, Zijian Li
Journal: Acta Pharmaceutica Sinica B (2024)

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been significantly alleviated. However, long-term health effects and prevention strategy remain unresolved. Thus, it is essential to explore the pathophysiological mechanisms and intervention for SARS-CoV-2 infection. Emerging research indicates a link between COVID-19 and bile acids, traditionally known for facilitating dietary fat absorption. The bile acid ursodeoxycholic acid potentially protects against SARS-CoV-2 infection by inhibiting the farnesoid X receptor, a bile acid nuclear receptor. The activation of G-protein-coupled bile acid receptor, another membrane receptor for bile acids, has also been found to regulate the expression of angiotensin-converting enzyme 2, the receptor through which the virus enters human cells. Here, we review the latest basic and clinical evidence linking bile acids to SARS-CoV-2, and reveal their complicated pathophysiological mechanisms.
Association Between Vonoprazan and the Risk of Gastric Cancer After Helicobacter pylori Eradication
Authors: Junya Arai, Atsushi Miyawaki, Tomonori Aoki, Ryota Niikura, Yoku Hayakawa, Hiroaki Fujiwara, Sozaburo Ihara, Mitsuhiro Fujishiro, Masato Kasuga
Journal: Clinical Gastroenterology and Hepatology (2024)
Hypercholesterolemia Is Associated With Dysregulation of Lipid Metabolism and Poor Prognosis in Primary Biliary Cholangitis
Authors: Linhua Zheng, Siyuan Tian, Chunmei Yang, Bo Li, Gui Jia, Yansheng Liu, Ruiqing Sun, Xiufang Wang, Juan Deng, Miao Zhang, Lina Cui, Changcun Guo, Xinmin Zhou, Patrick S.C. Leung, Christopher L. Bowlus, M. Eric Gershwin, Yulong Shang, Ying Han
Journal: Clinical Gastroenterology and Hepatology (2024)

Background and aims Hypercholesterolemia is frequently diagnosed in patients with primary biliary cholangitis (PBC). However, its association with the prognosis and lipid metabolism is unknown. In this study, we aimed to investigate the prognostic value of baseline total cholesterol (TC) levels in PBC and characterized the lipid metabolism. Methods Of note, 531 patients with PBC without prior cirrhosis-related complications were randomly divided into the derivation and validation cohorts at a ratio of 7:3. Complete clinical data were obtained and analyzed. The endpoints were defined as liver-related death, liver transplantation (LT) and cirrhosis-related complications. Untargeted lipidomics was performed in 89 patients and 28 healthy controls (HC). Results Baseline TC was independently associated with poor clinical outcomes and adjusted C-statistics were 0.8035 (95% confidence interval [CI]: 0.7372–0.8470) and 0.8754 (95% CI: 0.7777–0.9067) in the derivation and validation cohorts, respectively. The predictive ability of TC for disease outcomes was stable over the years and comparable to the Globe score. The 5.2 mmol/L cut-off optimally divided patients into low- and high-risk groups. A combination of TC and Globe score provided a more accurate stratification of patients into risk subgroups. Untargeted lipidomics indicated an upregulation of lipid families in high-risk patients. Pathway analysis of 66 upregulated lipids revealed the dysregulation of glycerophospholipid and sphingolipid metabolism in high-risk patients, which were associated with poor clinical outcomes. Conclusions Our results indicate that patients with PBC having baseline TC levels above 5.2 mmol/L have unique lipidome characteristics and are at a higher risk of poor clinical outcomes.
High tetracycline resistance percentages in Neisseria gonorrhoeae in Europe: is doxycycline post-exposure prophylaxis unlikely to reduce the incident gonorrhoea cases?
Authors: Magnus Unemo, Michelle J. Cole, Csaba Kodmon, Michaela Day, Susanne Jacobsson, Eszter Balla, Beatrice Bercot, Maria José Borrego, Dominique Caugant, Michelle Cole, Brendan Crowley, Michaela Day, Irith De Baetselier, Dagmar Heuer, Susanne Jacobsson, Csaba Kodmon, Vivi Miriagou, Beata Młynarczyk-Bonikowska, Peter Pavlik, Ivva Philipova, Stefanie Schindler, Daniel Schröder, Raquel Abad Torreblanca, Kairi Tõnsau, Magnus Unemo, Alje Van Dam, Francesca Vella, Polona Maver Vodičar, Hana Zákoucká
Journal: The Lancet Regional Health - Europe (2024)
Standardizing Extracted Data Using Automated Application of Controlled Vocabularies
Authors: Caroline Foster, Jessica Wignall, Samuel Kovach, Neepa Choksi, Dave Allen, Joanne Trgovcich, Johanna R. Rochester, Patricia Ceger, Amber Daniel, Jon Hamm, Jim Truax, Bevin Blake, Barry McIntyre, Vicki Sutherland, Matthew D. Stout, Nicole Kleinstreuer
Journal: Environmental Health Perspectives (2024)

Extraction of toxicological end points from primary sources is a central component of systematic reviews and human health risk assessments. To ensure optimal use of these data, consistent language should be used for end point descriptions. However, primary source language describing treatment-related end points can vary greatly, resulting in large labor efforts to manually standardize extractions before data are fit for use.