tbuckley/cabot-search huggingface dataset:
Peroral cholangioscopy-guided lithotripsy using a novel thin cholangioscope under balloon enteroscopy for Roux-en-Y anastomosis
Authors: Yuki Tanisaka, Masafumi Mizuide, Akashi Fujita, Takahiro Shin, Kei Sugimoto, Ryuhei Jinushi, Shomei Ryozawa
Journal: Endoscopy (2024)

Stone extraction using endoscopic retrograde cholangiopancreatography (ERCP) is less invasive than surgical procedures. However, stone extraction in patients with surgically altered anatomy, such as those who have undergone a Roux-en-Y procedure, is challenging. Although balloon enteroscopy is useful for such cases, there is still room for improvement [1] [2]. Peroral cholangioscopy (POCS)-guided lithotripsy can aid in the extraction of stones that are difficult to remove [3] [4]. However, performing POCS-guided lithotripsy under balloon enteroscopy is difficult because cholangioscopes have an approximate diameter of 10 Fr and cannot pass through the forceps channel of the balloon enteroscope. This report describes a patient with a Roux-en-Y anastomosis who was successfully treated with POCS-guided lithotripsy using a novel thin cholangioscope under balloon enteroscopy.
Pull-back myotomy to prevent mucosal injury during peroral endoscopic myotomy for jackhammer esophagus
Authors: Jun Nakamura, Takuto Hikichi, Minami Hashimoto, Tsunetaka Kato, Takumi Yanagita, Tadayuki Takagi, Hiromasa Ohira
Journal: Endoscopy (2024)

Mucosal injury is a notable perioperative complication of peroral endoscopic myotomy (POEM), occurring in 1.6%–25.8% of procedures [1] [2] [3]. Esophageal perforation caused by mucosal injury can lead to leakage of contents into the mediastinum, potentially resulting in mediastinitis [4]. Jackhammer esophagus is a hypercontractile esophageal motility disorder diagnosed using high-resolution manometry (HRM), necessitating extended myotomy in POEM [5]. Additionally, heightened caution is warranted when the length of the submucosal tunnel exceeds 13 cm, as it is associated with an elevated risk of mucosal injury [2]. Therefore, the POEM for jackhammer esophagus should be approached cautiously, considering the potential risk of mucosal injury.
Kill two birds with one stone: Flexible cholangioscopy for treatment of common bile duct stone and identification of suspicious gallbladder wall thickening
Authors: Ruixin Zhang, Tao Yu, Rui Ji
Journal: Endoscopy (2024)

A 76-year-old man suffered from recurrent abdominal pain and distention. The contract-enhanced computed tomography (CT) and endoscopic ultrasound (EUS) exams revealed the presence of a stone in common bile duct (CBD) ([Fig. 1] a) and concerning evidence of gallbladder wall thickening, suggestive of either gallbladder adenomyosis or gallbladder carcinoma ([Fig. 1] b, c). In order to distinguish benign adenomyosis from malignant carcinoma, together with treatment of the CBD stone, we sequentially performed endoscopic basket retrieval and target biopsies of the gallbladder.
Difficult management of pancreatic pseudocyst drainage in a 4-year-old child
Authors: Jingqing Zeng, Zhaohui Deng, Sheng Ding
Journal: Endoscopy (2024)

A 4-year-old boy with acute lymphoblastic leukemia had recurrent pancreatitis with pancreatic pseudocyst formation following asparaginase chemotherapy. At 6 months after stent drainage of the pancreatic duct, computed tomography (CT) revealed an enlarged pancreatic pseudocyst ([Fig. 1]).
Environmental impact of small-bowel capsule endoscopy
Authors: Mathieu Pioche, Joao A Cunha Neves, Heiko Pohl, Minh-Quyen Lê, Raphaelle Grau, Xavier Dray, Clara Yzet, Mikael Mochet, Jérémie Jacques, Timothée Wallenhorst, Jérôme Rivory, Nadège Siret, Anne-Laure Peillet, Jean-Baptiste Chevaux, François Mion, Ulriikka Chaput, Philippe Jacob, Daniel Grinberg, Jean-Christophe Saurin, Robin Baddeley, Enrique Rodriguez de Santiago, Pierre-Jean Cottinet
Journal: Endoscopy (2024)

The environmental impact of endoscopy, including small-bowel capsule endoscopy (SBCE), is a topic of growing attention and concern. This study aimed to evaluate the greenhouse gas (GHG) emissions (kgCO
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
Authors: João Dourado Santos, Daniel Sobral, Miguel Pinheiro, Joana Isidro, Carlijn Bogaardt, Miguel Pinto, Rodrigo Eusébio, André Santos, Rafael Mamede, Daniel L. Horton, João Paulo Gomes, Laurent Bigarré, Jovita Fernández-Pinero, Ricardo J. Pais, Maurilia Marcacci, Ana Moreno, Tobias Lilja, Øivind Øines, Artur Rzeżutka, Elisabeth Mathijs, Steven Van Borm, Morten Rasmussen, Katja Spiess, Vítor Borges
Journal: Genome Medicine (2024)

Abstract Background Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. Results The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a “generic” build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime , a tool aimed at reducing costs and the time between sample reception and diagnosis. Conclusions The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
The effect of using a large language model to respond to patient messages
Authors: Shan Chen, Marco Guevara, Shalini Moningi, Frank Hoebers, Hesham Elhalawani, Benjamin H Kann, Fallon E Chipidza, Jonathan Leeman, Hugo J W L Aerts, Timothy Miller, Guergana K Savova, Jack Gallifant, Leo A Celi, Raymond H Mak, Maryam Lustberg, Majid Afshar, Danielle S Bitterman
Journal: The Lancet Digital Health (2024)
Randomised controlled trials evaluating artificial intelligence in clinical practice: a scoping review
Authors: Ryan Han, Julián N Acosta, Zahra Shakeri, John P A Ioannidis, Eric J Topol, Pranav Rajpurkar
Journal: The Lancet Digital Health (2024)

This scoping review of randomised controlled trials on artificial intelligence (AI) in clinical practice reveals an expanding interest in AI across clinical specialties and locations. The USA and China are leading in the number of trials, with a focus on deep learning systems for medical imaging, particularly in gastroenterology and radiology. A majority of trials (70 [81%] of 86) report positive primary endpoints, primarily related to diagnostic yield or performance; however, the predominance of single-centre trials, little demographic reporting, and varying reports of operational efficiency raise concerns about the generalisability and practicality of these results. Despite the promising outcomes, considering the likelihood of publication bias and the need for more comprehensive research including multicentre trials, diverse outcome measures, and improved reporting standards is crucial. Future AI trials should prioritise patient-relevant outcomes to fully understand AI's true effects and limitations in health care.
Data challenges for international health emergencies: lessons learned from ten international COVID-19 driver projects
Authors: Sally Boylan, Catherine Arsenault, Marcos Barreto, Fernando A Bozza, Adalton Fonseca, Eoghan Forde, Lauren Hookham, Georgina S Humphreys, Maria Yury Ichihara, Kirsty Le Doare, Xiao Fan Liu, Edel McNamara, Jean Claude Mugunga, Juliane F Oliveira, Joseph Ouma, Neil Postlethwaite, Matthew Retford, Luis Felipe Reyes, Andrew D Morris, Anne Wozencraft
Journal: The Lancet Digital Health (2024)

The COVID-19 pandemic highlighted the importance of international data sharing and access to improve health outcomes for all. The International COVID-19 Data Alliance (ICODA) programme enabled 12 exemplar or driver projects to use existing health-related data to address major research questions relating to the pandemic, and developed data science approaches that helped each research team to overcome challenges, accelerate the data research cycle, and produce rapid insights and outputs. These approaches also sought to address inequity in data access and use, test approaches to ethical health data use, and make summary datasets and outputs accessible to a wider group of researchers. This Health Policy paper focuses on the challenges and lessons learned from ten of the ICODA driver projects, involving researchers from 19 countries and a range of health-related datasets. The ICODA programme reviewed the time taken for each project to complete stages of the health data research cycle and identified common challenges in areas such as data sharing agreements and data curation. Solutions included provision of standard data sharing templates, additional data curation expertise at an early stage, and a trusted research environment that facilitated data sharing across national boundaries and reduced risk. These approaches enabled the driver projects to rapidly produce research outputs, including publications, shared code, dashboards, and innovative resources, which can all be accessed and used by other research teams to address global health challenges.
Chronic respiratory disease in Indigenous peoples: a framework to address inequity and strengthen respiratory health and health care globally
Authors: Anne B Chang, Tom Kovesi, Gregory J Redding, Conroy Wong, Gonzalo G Alvarez, Rebecca Nantanda, Edgar Beltetón, Maynor Bravo-López, Maree Toombs, Paul J Torzillo, Diane M Gray
Journal: The Lancet Respiratory Medicine (2024)
Effectiveness of a universal, school-based, online programme for the prevention of anxiety, depression, and substance misuse among adolescents in Australia: 72-month outcomes from a cluster-randomised controlled trial
Authors: Maree Teesson, Louise Birrell, Tim Slade, Louise R Mewton, Nick Olsen, Leanne Hides, Nyanda McBride, Mary Lou Chatterton, Steve Allsop, Ainsley Furneaux-Bate, Zachary Bryant, Rhiannon Ellem, Megan J Baker, Annalise Healy, Jennifer Debenham, Julia Boyle, Marius Mather, Cathrine Mihalopoulos, Catherine Chapman, Nicola C Newton
Journal: The Lancet Digital Health (2024)

The CSC study found that the universal delivery of a school-based, online programme for the prevention of mental health and substance use disorders among adolescents resulted in improvements in mental health and substance use outcomes at 30-month follow-up. We aimed to compare the long-term effects of four interventions-Climate Schools Combined (CSC) mental health and substance use, Climate Schools Substance Use (CSSU) alone, Climate Schools Mental Health (CSMH) alone, and standard health education-on mental health and substance use outcomes among adolescents at 72-month follow-up into early adulthood.
Machine learning to understand risks for severe COVID-19 outcomes: a retrospective cohort study of immune-mediated inflammatory diseases, immunomodulatory medications, and comorbidities in a large US health-care system
Authors: Qi Wei, Philip J Mease, Michael Chiorean, Lulu Iles-Shih, Wanessa F Matos, Andrew Baumgartner, Sevda Molani, Yeon Mi Hwang, Basazin Belhu, Alexandra Ralevski, Jennifer Hadlock
Journal: The Lancet Digital Health (2024)

In the context of immune-mediated inflammatory diseases (IMIDs), COVID-19 outcomes are incompletely understood and vary considerably depending on the patient population studied. We aimed to analyse severe COVID-19 outcomes and to investigate the effects of the pandemic time period and the risks associated with individual IMIDs, classes of immunomodulatory medications (IMMs), chronic comorbidities, and COVID-19 vaccination status.
Measuring fairness preferences is important for artificial intelligence in health care
Authors: Anatol-Fiete Näher, Ivar Krumpal, Esther-Maria Antão, Erika Ong, Marina Rojo, Fred Kaggwa, Felix Balzer, Leo Anthony Celi, Katarina Braune, Lothar H Wieler, Louis Agha-Mir-Salim
Journal: The Lancet Digital Health (2024)
Isatuximab, carfilzomib, lenalidomide, and dexamethasone in patients with newly diagnosed, transplantation-eligible multiple myeloma (SKylaRk): a single-arm, phase 2 trial
Authors: Elizabeth O'Donnell, Clifton Mo, Andrew J Yee, Omar Nadeem, Jacob Laubach, Jacalyn Rosenblatt, Nikhil Munshi, Shonali Midha, Diana Cirstea, Pavlina Chrysafi, Nora Horick, Paul G Richardson, Noopur Raje
Journal: The Lancet Haematology (2024)
Endoscopic sutured purse-string resection: a novel technique for resection of large gastric subepithelial lesions
Authors: Olaolu Olabintan, Theodoros Voulgaris, Homira Ayubi, Sri Thrumurthy, Amyn Haji, Bu'Hussain Hayee
Journal: Endoscopy (2024)

Subepithelial lesions (SELs) in the gastrointestinal (GI) tract are common and often necessitate removal, particularly when >20 mm [1] [2]. The choice of endoscopic resection depends on various factors, including lesion characteristics, location, and evidence of deeper tissue involvement [2] [3]. Challenges in achieving full-thickness resection have driven the development of innovative over-the-scope devices [4]. However, these devices are typically restricted to lesions <30 mm, and their size and rigidity often hinder passage beyond the pharynx. We present here a novel technique for accomplishing full-thickness resection of SELs, known as endoscopic sutured purse-string resection (ESPR). ESPR employs the Overstitch device (Apollo Endosurgery, Austin, Texas, USA), a well-established tool for placing full-thickness endoscopic sutures. It involves creating a purse-string configuration around the lesion ([Fig. 1]) before resection, enabling the safe and complete removal of even larger lesions.
AI-assisted capsule endoscopy reading in suspected small bowel bleeding: a multicentre prospective study
Authors: Cristiano Spada, Stefania Piccirelli, Cesare Hassan, Clarissa Ferrari, Ervin Toth, Begoña González-Suárez, Martin Keuchel, Marc McAlindon, Ádám Finta, András Rosztóczy, Xavier Dray, Daniele Salvi, Maria Elena Riccioni, Robert Benamouzig, Amit Chattree, Adam Humphries, Jean-Christophe Saurin, Edward J Despott, Alberto Murino, Gabriele Wurm Johansson, Antonio Giordano, Peter Baltes, Reena Sidhu, Milan Szalai, Krisztina Helle, Artur Nemeth, Tanja Nowak, Rong Lin, Guido Costamagna
Journal: The Lancet Digital Health (2024)

Capsule endoscopy reading is time consuming, and readers are required to maintain attention so as not to miss significant findings. Deep convolutional neural networks can recognise relevant findings, possibly exceeding human performances and reducing the reading time of capsule endoscopy. Our primary aim was to assess the non-inferiority of artificial intelligence (AI)-assisted reading versus standard reading for potentially small bowel bleeding lesions (high P2, moderate P1; Saurin classification) at per-patient analysis. The mean reading time in both reading modalities was evaluated among the secondary endpoints.
Tunable ciprofloxacin delivery through personalized electrospun patches for tympanic membrane perforations
Authors: Shivesh Anand, Alessandra Fusco, Cemre Günday, Nazende Günday-Türeli, Giovanna Donnarumma, Serena Danti, Lorenzo Moroni, Carlos Mota
Journal: Bioactive Materials (2024)

Approximately 740 million symptomatic patients are affected by otitis media every year. Being an inflammatory disease affecting the middle ear, it is one of the primary causes of tympanic membrane (TM) perforations, often resulting in impaired hearing abilities. Antibiotic therapy using broad-spectrum fluoroquinolones, such as ciprofloxacin (CIP), is frequently employed and considered the optimal route to treat otitis media. However, patients often get exposed to high dosages to compensate for the low drug concentration reaching the affected site. Therefore, this study aims to integrate tissue engineering with drug delivery strategies to create biomimetic scaffolds promoting TM regeneration while facilitating a localized release of CIP. Distinct electrospinning (ES) modalities were designed in this regard either by blending CIP into the polymer ES solution or by incorporating nanoparticles-based co-ES/electrospraying. The combination of these modalities was investigated as well. A broad range of release kinetic profiles was achieved from the fabricated scaffolds, thereby offering a wide spectrum of antibiotic concentrations that could serve patients with diverse therapeutic needs. Furthermore, the incorporation of CIP into the TM patches demonstrated a favorable influence on their resultant mechanical properties. Biological studies performed with human mesenchymal stromal cells confirmed the absence of any cytotoxic or anti-proliferative effects from the released antibiotic. Finally, antibacterial assays validated the efficacy of CIP-loaded scaffolds in suppressing bacterial infections, highlighting their promising relevance for TM applications.
Nutritional Support for Moderate-to-Late–Preterm Infants — A Randomized Trial
Authors: Tanith Alexander, Sharin Asadi, Michael Meyer, Jane E. Harding, Yannan Jiang, Jane M. Alsweiler, Mariana Muelbert, Frank H. Bloomfield
Journal: New England Journal of Medicine (2024)

Most moderate-to-late-preterm infants need nutritional support until they are feeding exclusively on their mother's breast milk. Evidence to guide nutrition strategies for these infants is lacking.
Specificity of CRISPR-Cas9 Editing in Exagamglogene Autotemcel
Authors: Angela Yen, Zachary Zappala, Rebecca S Fine, Timothy D Majarian, Parin Sripakdeevong, David Altshuler
Journal: New England Journal of Medicine (2024)

The autologous cellular therapy exagamglogene autotemcel is generated by editing an erythroid-specific enhancer of BCL11A. Could another site be edited unintentionally? This study gauged the likelihood of off-target editing.
The AMR brain drain
Authors: None The Lancet Microbe
Journal: The Lancet Microbe (2024)

"The AMR field has been steadily losing vital scientific and research talent for more than two decades." That was the overall message from the Leaving The Lab report published by the AMR Industry Alliance on Feb 8. Using publicly available data, the report outlines the number and output of research and development (R&D) professionals in the AMR field since the late 1980s, estimating that 3000 researchers are currently active, a seemingly modest figure given the global problem of AMR. The research output of these professionals has been steadily decreasing, with a peak of 586 studies on antimicrobials in 1995 compared with 216 in 2022; unsurprisingly, the number of AMR R&D-associated authors has also declined over this period.
CAR as Booster to Launch Allogeneic Transplantation in Refractory Leukemia
Authors: Didier Blaise
Journal: New England Journal of Medicine (2024)

Chimeric antigen receptor (CAR) T-cell therapies have revolutionized the treatment landscape for patients with relapsed or refractory B-cell lymphoid cancers.1 With studies showing that more than 50% of patients had an objective response and that half these patients had sustained disease-free survival, up to 10 distinct CAR T-cell products have received regulatory approval worldwide2,3 for various indications and disease stages of non-Hodgkin's lymphoma, acute lymphoblastic leukemia, and multiple myeloma for approximately 10,000 patients treated each year.3,4 Current research efforts aim to introduce CAR T-cell therapy in earlier disease stages to potentially enhance long-term disease control. A disease that until recently . . .
Exagamglogene Autotemcel for Severe Sickle Cell Disease
Authors: Haydar Frangoul, Franco Locatelli, Akshay Sharma, Monica Bhatia, Markus Mapara, Lyndsay Molinari, Donna Wall, Robert I. Liem, Paul Telfer, Ami J. Shah, Marina Cavazzana, Selim Corbacioglu, Damiano Rondelli, Roland Meisel, Laurence Dedeken, Stephan Lobitz, Mariane de Montalembert, Martin H. Steinberg, Mark C. Walters, Michael J. Eckrich, Suzan Imren, Laura Bower, Christopher Simard, Weiyu Zhou, Fengjuan Xuan, Phuong Khanh Morrow, William E. Hobbs, Stephan A. Grupp
Journal: New England Journal of Medicine (2024)

Exagamglogene autotemcel (exa-cel) is a nonviral cell therapy designed to reactivate fetal hemoglobin synthesis by means of ex vivo clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 gene editing of autologous CD34+ hematopoietic stem and progenitor cells (HSPCs) at the erythroid-specific enhancer region of
Oral Simnotrelvir for Adult Patients with Mild-to-Moderate Covid-19
Authors: Carlee B Moser, Jonathan Z Li, Michael D Hughes
Journal: New England Journal of Medicine (2024)

open fractures, given that surgical fixation with wound closure (e.g., with skin grafts and flaps, procedures that were performed in 5.0% of the patients in iodine group and in 4.4% of those in the chlorhexidine group with open fractures) is usually more complex and time-consuming than closed fixation.Thus, the lack of adjustment for surgical duration as an independent risk factor for surgical-site infection may have led to bias in the investigators' findings.