tbuckley/cabot-search huggingface dataset:
Orchestrating explainable artificial intelligence for multimodal and longitudinal data in medical imaging
Authors: Aurélie Pahud de Mortanges, Haozhe Luo, Shelley Zixin Shu, Amith Kamath, Yannick Suter, Mohamed Shelan, Alexander Pöllinger, Mauricio Reyes
Journal: npj Digital Medicine (2024)

Abstract Explainable artificial intelligence (XAI) has experienced a vast increase in recognition over the last few years. While the technical developments are manifold, less focus has been placed on the clinical applicability and usability of systems. Moreover, not much attention has been given to XAI systems that can handle multimodal and longitudinal data, which we postulate are important features in many clinical workflows. In this study, we review, from a clinical perspective, the current state of XAI for multimodal and longitudinal datasets and highlight the challenges thereof. Additionally, we propose the XAI orchestrator, an instance that aims to help clinicians with the synopsis of multimodal and longitudinal data, the resulting AI predictions, and the corresponding explainability output. We propose several desirable properties of the XAI orchestrator, such as being adaptive, hierarchical, interactive, and uncertainty-aware.
BCL7A inhibits the progression and drug-resistance in acute myeloid leukemia
Authors: Tushuai Li, Renjie Gao, Kaiwen Xu, Pengpeng Pan, Congcong Chen, Daokuan Wang, Keyi Zhang, Jilei Qiao, Yue Gu
Journal: Drug Resistance Updates (2024)

This study aimed to elucidate the biological roles and regulatory mechanisms of B-cell lymphoma 7 protein family member A (BCL7A) in acute myeloid leukemia (AML), particularly its interaction with polypyrimidine tract binding protein 1 (PTBP1) and the effects on cancer progression and drug resistance.
Safety and efficacy studies of CRISPR-Cas9 treatment of sickle cell disease highlights disease-specific responses
Authors: Giacomo Frati, Megane Brusson, Gilles Sartre, Bochra Mlayah, Tristan Felix, Anne Chalumeau, Panagiotis Antoniou, Giulia Hardouin, Jean-Paul Concordet, Oriana Romano, Giandomenico Turchiano, Annarita Miccio
Journal: Molecular Therapy (2024)

Fetal hemoglobin (HbF) reactivation expression through CRISPR-Cas9 is a promising strategy for the treatment of sickle cell disease (SCD). Here, we describe a genome editing strategy leading to reactivation of HbF expression by targeting the binding sites (BSs) for the lymphoma-related factor (LRF) repressor in the γ-globin promoters. CRISPR-Cas9 treatment in healthy donor (HD) and patient-derived HSPCs resulted in a high frequency of LRF BS disruption and potent HbF synthesis in their erythroid progeny. LRF BS disruption did not impair HSPC engraftment and differentiation but was more efficient in SCD than in HD cells. However, SCD HSPCs showed a reduced engraftment and a myeloid bias compared with HD cells. We detected off-target activity and chromosomal rearrangements, particularly in SCD samples (likely because of the higher overall editing efficiency) but did not impact the target gene expression and HSPC engraftment and differentiation. Transcriptomic analyses showed that the editing procedure results in the up-regulation of genes involved in DNA damage and inflammatory responses, which was more evident in SCD HSPCs. This study provides evidence of efficacy and safety for an editing strategy based on HbF reactivation and highlights the need of performing safety studies in clinically relevant conditions, i.e., in patient-derived HSPCs. Fetal hemoglobin (HbF) reactivation expression through CRISPR-Cas9 is a promising strategy for the treatment of sickle cell disease (SCD). Here, we describe a genome editing strategy leading to reactivation of HbF expression by targeting the binding sites (BSs) for the lymphoma-related factor (LRF) repressor in the γ-globin promoters. CRISPR-Cas9 treatment in healthy donor (HD) and patient-derived HSPCs resulted in a high frequency of LRF BS disruption and potent HbF synthesis in their erythroid progeny. LRF BS disruption did not impair HSPC engraftment and differentiation but was more efficient in SCD than in HD cells. However, SCD HSPCs showed a reduced engraftment and a myeloid bias compared with HD cells. We detected off-target activity and chromosomal rearrangements, particularly in SCD samples (likely because of the higher overall editing efficiency) but did not impact the target gene expression and HSPC engraftment and differentiation. Transcriptomic analyses showed that the editing procedure results in the up-regulation of genes involved in DNA damage and inflammatory responses, which was more evident in SCD HSPCs. This study provides evidence of efficacy and safety for an editing strategy based on HbF reactivation and highlights the need of performing safety studies in clinically relevant conditions, i.e., in patient-derived HSPCs.
A systematic review of immunosuppressive protocols used in AAV gene therapy for monogenic disorders
Authors: Besarte Vrellaku, Ilda Sethw Hassan, Rebecca Howitt, Christopher P. Webster, Eli Harriss, Fraser McBlane, Corinne Betts, Jorge Schettini, Mattia Lion, John E. Mindur, Michael Duerr, Pamela J. Shaw, Janine Kirby, Mimoun Azzouz, Laurent Servais
Journal: Molecular Therapy (2024)
Efficacy and safety of robotic surgery versus open surgery for hilar cholangiocarcinoma: a systematic review and meta-analysis
Authors: Manqin Hu, Dingwei Xu, Yan Zhang, Ao Li, Xincheng Li, Jie Huang
Journal: International Journal of Surgery (2024)

Objective: The aim is to assess and contrast the effectiveness and safety of employing robotic surgery versus traditional open surgery in managing cases of hilar cholangiocarcinoma. Methods: Computer searches were conducted in PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Infrastructure (CNKI), and Wanfang Database to identify case-control studies comparing robotic surgery with traditional open surgery in the treatment of hilar cholangiocarcinoma from inception until July 2023. References from retrieved articles were reviewed to broaden the search. This review was prospectively registered in the PROSPERO database (PROSPERO ID: CRD42024527511) and reported in line with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) and AMSTAR (Assessing the methodological quality of systematic reviews) Guidelines.The primary outcome measures included operation time, intraoperative blood transfusion rate, R0 resection rate, lymph node metastasis rate, incidence of postoperative complications, and postoperative hospital stay. Data analysis was performed using RevMan 5.4 software, calculating combined odds ratios (OR), mean differences (MD), and 95% confidence intervals (95% CI). Results: A total of 4 studies encompassing 267 patients diagnosed with hilar cholangiocarcinoma (177 males and 90 females, mean age of (58.8±5.7) years) were included in this analysis. Among these, 165 patients underwent open surgery, while 102 patients underwent robotic surgery. The results of the meta-analysis demonstrated comparable outcomes between the two groups. Specifically, the operation time between the robotic surgery and open surgery cohorts did not significantly differ ( MD =−103.96, 95% CI : −216.90 to 8.98, P = 0.070 ). Additionally, the intraoperative blood transfusion rate ( OR =1.32, 95% CI : 0.43 to 4.07, P =0.630), R0 resection rate ( OR =1.41, 95% CI : 0.71 to 2.81, P=0.330 ), and lymph node metastasis rate ( OR =1.62, 95% CI : 0.46 to 5.63, P=0.450 ) showed no significant differences between the groups. Similarly, there were no statistically significant disparities observed in the incidence of postoperative complications (OR=0.60, 95% CI : 0.28 to 1.31, P=0.200 ) and postoperative hospital stay ( MD =2.17, 95% CI : −11.56 to 15.90, P=0.760 ). Conclusion: In the treatment of hilar cholangiocarcinoma, robotic surgery demonstrates comparable safety and feasibility to traditional open surgery. However, due to the limited quantity and quality of the included studies, these conclusions warrant validation through additional high-quality investigations.
Extracorporeal shock wave therapy modulates miRNA expression, reduces inflammation, and improves liposome retention in a rat model of cyclophosphamide induced cystitis-experimental studies
Authors: Zong-Sheng Wu, Wei-Chia Lee, Michael B. Chancellor, Hung-Jen Wang, Chao-Cheng Huang, Yao-Chi Chuang
Journal: International Journal of Surgery (2024)

Wu, Zong-Sheng; Lee, Wei-Chia; Chancellor, Michael B.; Wang, Hung-Jen; Huang, Chao-Cheng; Chuang, Yao-Chi Author Information
Predictors for low rates of surgical resection in elderly patients with resectable pancreatic ductal adenocarcinoma: a retrospective case-control study
Authors: Chunjing Li, Jiahao Chen, Liting Zhao, Xiao Hu, Hongfei Yao, Zhiwei Cai, Chongyi Jiang
Journal: International Journal of Surgery (2024)

Li, Chunjing MD; Chen, Jiahao MD; Zhao, Liting MD; Hu, Xiao MD; Yao, Hongfei MD; Cai, Zhiwei MD; Jiang, Chongyi MD, PHD Author Information
Proteomic signatures improve risk prediction for common and rare diseases
Authors: Julia Carrasco-Zanini, Maik Pietzner, Jonathan Davitte, Praveen Surendran, Damien C. Croteau-Chonka, Chloe Robins, Ana Torralbo, Christopher Tomlinson, Florian Grünschläger, Natalie Fitzpatrick, Cai Ytsma, Tokuwa Kanno, Stephan Gade, Daniel Freitag, Frederik Ziebell, Simon Haas, Spiros Denaxas, Joanna C. Betts, Nicholas J. Wareham, Harry Hemingway, Robert A. Scott, Claudia Langenberg
Journal: Nature Medicine (2024)

For many diseases there are delays in diagnosis due to a lack of objective biomarkers for disease onset. Here, in 41,931 individuals from the United Kingdom Biobank Pharma Proteomics Project, we integrated measurements of ~3,000 plasma proteins with clinical information to derive sparse prediction models for the 10-year incidence of 218 common and rare diseases (81-6,038 cases). We then compared prediction models developed using proteomic data with models developed using either basic clinical information alone or clinical information combined with data from 37 clinical assays. The predictive performance of sparse models including as few as 5 to 20 proteins was superior to the performance of models developed using basic clinical information for 67 pathologically diverse diseases (median delta C-index = 0.07; range = 0.02-0.31). Sparse protein models further outperformed models developed using basic information combined with clinical assay data for 52 diseases, including multiple myeloma, non-Hodgkin lymphoma, motor neuron disease, pulmonary fibrosis and dilated cardiomyopathy. For multiple myeloma, single-cell RNA sequencing from bone marrow in newly diagnosed patients showed that four of the five predictor proteins were expressed specifically in plasma cells, consistent with the strong predictive power of these proteins. External replication of sparse protein models in the EPIC-Norfolk study showed good generalizability for prediction of the six diseases tested. These findings show that sparse plasma protein signatures, including both disease-specific proteins and protein predictors shared across several diseases, offer clinically useful prediction of common and rare diseases.
Effect of Cash Benefits on Health Care Utilization and Health
Authors: Sumit D. Agarwal, Benjamin Lê Cook, Jeffrey B. Liebman
Journal: JAMA (2024)

Importance Poverty is associated with greater barriers to health care and worse health outcomes, but it remains unclear whether income support can improve health. Objective To examine the effect of cash benefits on health care utilization and health. Design, Setting, and Participants The City of Chelsea, Massachusetts, a low-income community near Boston, randomly assigned individuals by lottery to receive cash benefits. Participants’ medical records were linked across multiple health systems. Outcomes were assessed during the intervention period from November 24, 2020, to August 31, 2021. Intervention Cash benefits via debit card of up to $400 per month for 9 months. Main Outcomes and Measures The primary outcome was emergency department visits. Secondary outcomes included specific types of emergency department visits, outpatient use overall and by specialty, COVID-19 vaccination, and biomarkers such as cholesterol levels. Results Among 2880 individuals who applied for the lottery, mean age was 45.1 years and 77% were female. The 1746 participants randomized to receive the cash benefits had significantly fewer emergency department visits compared with the control group (217.1 vs 317.5 emergency department visits per 1000 persons; adjusted difference, −87.0 per 1000 persons [95% CI, −160.2 to −13.8]). This included reductions in emergency department visits related to behavioral health (−21.6 visits per 1000 persons [95% CI, −40.2 to −3.1]) and substance use (−12.8 visits per 1000 persons [95% CI, −25.0 to −0.6]) as well as those that resulted in a hospitalization (−27.3 visits per 1000 persons [95% CI, −53.6 to −1.1]). The cash benefit had no statistically significant effect on total outpatient visits (424.3 visits per 1000 persons [95% CI, −118.6 to 967.2]), visits to primary care (−90.4 visits per 1000 persons [95% CI, −308.1 to 127.2]), or outpatient behavioral health (83.5 visits per 1000 persons [95% CI, −182.9 to 349.9]). Outpatient visits to other subspecialties were higher in the cash benefit group compared with the control group (303.1 visits per 1000 persons [95% CI, 32.9 to 573.2]), particularly for individuals without a car. The cash benefit had no statistically significant effect on COVID-19 vaccination, blood pressure, body weight, glycated hemoglobin, or cholesterol level. Conclusions and Relevance In this randomized study, individuals who received a cash benefit had significantly fewer emergency department visits, including those related to behavioral health and substance use, fewer admissions to the hospital from the emergency department, and increased use of outpatient subspecialty care. Study results suggest that policies that seek to alleviate poverty by providing income support may have important benefits for health and access to care.
DNA methylation urine test in the diagnosis of upper tract urothelial carcinoma: a systematic review and meta-analysis
Authors: Jianjun Ye, Xiaoli Wang, Xinyang Liao, Ye Chen, Zeyu Chen, Qihao Wang, Jianzhong Ai, Qiang Wei, Yige Bao
Journal: International Journal of Surgery (2024)

Objective: The DNA methylation urine test, a non-invasive early detection method for upper tract urothelial carcinoma (UTUC), is currently in full swing. This study aimed to systematically assess its diagnostic performance on UTUC. Materials and methods: PubMed, Scopus, Embase, and Cochrane were our main databases when searching articles published from January 2000 to December 2023. Sensitivity and specificity were study primary endpoints. I 2 was used to evaluated heterogeneity, meanwhile subgroup and meta-regression analyses were adopted to investigated the source of heterogeneity. Sensitivity analysis was performed to evaluate the result robustness, while Deeks’ funnel plot asymmetry test was for the publication bias. Results: Nine studies with 1326 patients were included. The pooled sensitivity was 0.89 (95% confidence interval (CI), 0.83-0.93) and specificity were 0.91 (95% CI, 0.83-0.96). The area under the receiver operating characteristic curve was 0.96 (95% CI, 0.93-0.97). Substantial heterogeneity was found during the data synthesis, whereas the pooled results remained robust in the sensitivity analysis. None of the potential covariates—urine sample collection method, population, country, methylation test method, or tumor grade—could account for the heterogeneity. Conclusion: DNA methylation urine test is a promising method with high efficiency for UTUC early detection. Nevertheless, owing to the significant heterogeneity, more well-organized studies are warranted to further explore its diagnostic efficiency and application context.
Intraoperative goal-directed fluid management and postoperative brain edema in patients having high-grade gliomas resections: a randomized trial
Authors: Xiaoyuan Liu, Xingyue Zhang, Yifang Fan, Bo Wang, Jie Wang, Min Zeng, Shu Li, Mi Shen, Wei Zhang, Daniel I. Sessler, Yuming Peng
Journal: International Journal of Surgery (2024)

Introduction: Patients with high-grade gliomas often have severe brain edema. Goal-directed fluid management protects neurological function, but whether reduces postoperative brain edema remains unknown. Methods: Patients having elective resection of supratentorial malignant gliomas were randomly assigned to goal-directed versus routine fluid management. Patients assigned to goal-directed management group were given 3 mL kg -1 hydroxyethyl starch solution when stroke volume variation exceeded 15% for 5 minutes. Fluid was managed per routine by attending anesthesiologists in reference patients. The primary outcome was cerebral edema volume after surgery as assessed by computerized tomography. Results: A total of 480 eligible patients were randomly assigned to the goal-directed (n = 240) or the routine fluid management group (n = 240). The amounts of crystalloid (5.4 vs. 7.0 ml kg -1 hour -1 , P &lt; 0.001), colloid (1.1 vs. 1.7 ml kg -1 hour -1 , P &lt; 0.001), and overall fluid balance (0.3 vs. 1.9 ml kg -1 hour -1 , P &lt; 0.001) were significantly lower in goal-directed fluid management. There was no significant difference in postoperative brain edema volume between groups (36.0 cm 3 vs. 38.9 cm 3 , mean difference: 0.18cm 3 , 95% CI: -5.7 to 5.9). Goal-directed patients had lower intraoperative dural tension (risk ratio: 0.63, 95% CI: 0.50 to 0.80, P &lt; 0.001). There was no significant difference in Karnofsky Performance Status between the two groups at 30 days after surgery. Conclusions: Goal-directed fluid therapy substantially reduced intravenous fluid volumes, but did not reduce postoperative brain edema in patients having brain tumor resections.
Development and validation of a novel predictive model for postpancreatectomy hemorrhage using lasso-logistic regression: an international multicenter observational study of 9,631 pancreatectomy patients
Authors: Yunjie Duan, Yongxing Du, Yongrun Mu, Xiao Guan, Jin He, Jianwei Zhang, Zongting Gu, Chengfeng Wang
Journal: International Journal of Surgery (2024)

Background: Hemorrhage following pancreatectomy represents a grave complication, exerting a significant impact on patient prognosis. The formulation of a precise predictive model for postpancreatectomy hemorrhage risk holds substantial importance in enhancing surgical safety and improving patient outcomes. Materials and Methods: This study utilized the patient cohort from the American College of Surgeons National Surgical Quality Improvement Program database, who underwent pancreatectomy between 2014 and 2017 (n=5779), as the training set to establish the Lasso-logistic model. For external validation, a patient cohort (n=3852) from the Chinese National Multicenter Database of Pancreatectomy Patients, who underwent the procedure between 2014 and 2020, was employed. A predictive nomogram for postpancreatectomy hemorrhage was developed, and polynomial equations were extracted. The performance of the predictive model was assessed through the receiver operating characteristic curve, calibration curve, and decision curve analysis. Results: In the training and validation cohorts, 9.0% (520/5779) and 8.5% (328/3852) of patients, respectively, experienced postpancreatectomy hemorrhage. Following selection via lasso and logistic regression, only nine predictive factors were identified as independent risk factors associated with postpancreatectomy hemorrhage. These included five preoperative indicators (BMI, ASA ≥3, preoperative obstructive jaundice, chemotherapy within 90 days before surgery, and radiotherapy within 90 days before surgery), two intraoperative indicators (total operation time, vascular resection), and two postoperative indicators (postoperative septic shock, pancreatic fistula). The new model demonstrated high predictive accuracy, with an area under the receiver operating characteristic curve of 0.87 in the external validation cohort. Its predictive performance significantly surpassed that of the previous five postpancreatectomy hemorrhage risk prediction models ( P &lt;0.001, likelihood ratio test). Conclusion: The Lasso-logistic predictive model we developed, constructed from nine rigorously selected variables, accurately predicts the risk of PPH. It has the potential to significantly enhance the safety of pancreatectomy surgeries and improve patient outcomes.
Standardization and clinical applications of retinal imaging biomarkers for cardiovascular disease: a Roadmap from an NHLBI workshop
Authors: Emily Y Chew, Stephen A Burns, Alison G Abraham, Mathieu F Bakhoum, Joshua A Beckman, Toco Y P Chui, Robert P Finger, Alejandro F Frangi, Rebecca F Gottesman, Maria B Grant, Henner Hanssen, Cecilia S Lee, Michelle L Meyer, Damiano Rizzoni, Alicja R Rudnicka, Joel S Schuman, Sara B Seidelmann, W H Wilson Tang, Bishow B Adhikari, Narasimhan Danthi, Yuling Hong, Diane Reid, Grace L Shen, Young S Oh
Journal: Nature Reviews Cardiology (2024)
Outcomes of clinical decision support systems in real-world perioperative care: A systematic review and meta-analysis
Authors: JianWen Cai, Peiyi Li, Weimin Li, Tao Zhu
Journal: International Journal of Surgery (2024)

Background: Although clinical decision support systems (CDSS) have been developed to enhance the quality and efficiency of surgeries, little is known regarding the practical effects in real-world perioperative care. Objective: To systematically review and meta-analyze the current impact of CDSS on various aspects of perioperative care, providing evidence support for future research on CDSS development and clinical implementation. Methods: This systematic review and meta-analysis followed the Cochrane Handbook and PRISMA statement guidelines, searching databases up to February 2, 2024, including MEDLINE, PubMed, Embase, Cochrane, and Web of Science. It included studies on the effectiveness of CDSS in assisting perioperative decision-making, involving anaesthesiologists, doctors, or surgical patients, and reporting at least one outcome such as complications, mortality, length of stay, compliance, or cost. Results: Forty studies met inclusion criteria, analyzing outcomes from 408,357 participants, predominantly in developed countries. Most perioperative CDSS use was associated with improved guideline adherence, decreased medication errors, and some improvements in patient safety measures such as reduced postoperative nausea and vomiting and myocardial injury. However, reported results varied widely, and no significant improvement in postoperative mortality was observed. Conclusion: The preliminary findings of this review offer an overview of the potential use of CDSS in real-world perioperative situations to enhance patient and anaesthesiologist outcomes, but further researches with broader outcome dimensions, involving more stakeholders, and with longer follow-up periods are warranted for the critical evaluation of CDSS and then in better facilitate clinical adoption.
A new pragmatic classification system for thymoma associated myasthenia gravis: a retrospective cohort study
Authors: Yongqiang Ao, Jiahao Jiang, Junjie Miao, Jian Gao, Xinyu Yang, Yuansheng Zheng, Fei Liang, Shuai Wang, Jihong Dong, Jianyong Ding
Journal: International Journal of Surgery (2024)

The management and outcomes of patients with thymoma associated with myasthenia gravis (TAMG) are heterogeneous. Here, we propose a novel classification system based on Masaoka stage and Myasthenia Gravis Foundation of America (MGFA) classification, aiming to guide surgical decisions and perioperative management for these patients. Considering both oncological and neurological factors, this novel TAMG classification provides valuable information on outcome stratification and clinical decision-making for TAMG.