tbuckley/cabot-search huggingface dataset:
Optimizing surgical efficiency: a critical appraisal of machine learning in forecasting operative duration for metabolic and bariatric procedures
Authors: Cheng Guo, Qinghui Cai, Kai Liu
Journal: International Journal of Surgery (2024)

aComprehensive pediatrics & Pulmonary and Critical Care Medicine,Kunming Children's Hospital,No.28,Shulin Street,Kunming 650103,Yunnan Province,China bPediatric,Qionghai People's Hospital,No.33,Fuhai Road,Qionghai 571400,Hainan Province,China These authors contributed equally to the work: Cheng Guo,Qinghui Cai. Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article Published online ■ ■ *Corresponding author. Address: Comprehensive pediatrics & Pulmonary and Critical Care Medicine, Kunming Children's Hospital, Shulin Street 28, Kunming, China, 650103. E-mail address: [email protected] (K. Liu). 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. http://creativecommons.org/licenses/by/4.0/
Deep learning-based multi-model prediction for disease-free survival status of patients with clear cell renal cell carcinoma after surgery: a multicenter cohort study
Authors: Siteng Chen, Feng Gao, Tuanjie Guo, Liren Jiang, Ning Zhang, Xiang Wang, Junhua Zheng
Journal: International Journal of Surgery (2024)

Background: Although separate analysis of individual factor can somewhat improve the prognostic performance, integration of multimodal information into a single signature is necessary to stratify patients with clear cell renal cell carcinoma (ccRCC) for adjuvant therapy after surgery. Methods: A total of 414 patients with whole slide images, computed tomography images, and clinical data from three patient cohorts were retrospectively analyzed. The authors performed deep learning and machine learning algorithm to construct three single-modality prediction models for disease-free survival of ccRCC based on whole slide images, cell segmentation, and computed tomography images, respectively. A multimodel prediction signature (MMPS) for disease-free survival were further developed by combining three single-modality prediction models and tumor stage/grade system. Prognostic performance of the prognostic model was also verified in two independent validation cohorts. Results: Single-modality prediction models performed well in predicting the disease-free survival status of ccRCC. The MMPS achieved higher area under the curve value of 0.742, 0.917, and 0.900 in three independent patient cohorts, respectively. MMPS could distinguish patients with worse disease-free survival, with HR of 12.90 (95% CI: 2.443–68.120, P &lt;0.0001), 11.10 (95% CI: 5.467–22.520, P &lt;0.0001), and 8.27 (95% CI: 1.482–46.130, P &lt;0.0001) in three different patient cohorts. In addition, MMPS outperformed single-modality prediction models and current clinical prognostic factors, which could also provide complements to current risk stratification for adjuvant therapy of ccRCC. Conclusion: Our novel multimodel prediction analysis for disease-free survival exhibited significant improvements in prognostic prediction for patients with ccRCC. After further validation in multiple centers and regions, the multimodal system could be a potential practical tool for clinicians in the treatment for ccRCC patients.
The anatomic basis of leptomeningeal metastasis
Authors: Morgan E. Freret, Adrienne Boire
Journal: The Journal of Experimental Medicine (2024)

Leptomeningeal metastasis (LM), or spread of cancer to the cerebrospinal fluid (CSF)–filled space surrounding the central nervous system, is a fatal complication of cancer. Entry into this space poses an anatomical challenge for cancer cells; movement of cells between the blood and CSF is tightly regulated by the blood–CSF barriers. Anatomical understanding of the leptomeninges provides a roadmap of corridors for cancer entry. This Review describes the anatomy of the leptomeninges and routes of cancer spread to the CSF. Granular understanding of LM by route of entry may inform strategies for novel diagnostic and preventive strategies as well as therapies.
First report of gastric endoscopic intermuscular dissection
Authors: Edward J. Despott, Laura A. Lucaciu, Alberto Murino, Alessandro Rimondi, Kenneth Binmoeller
Journal: Endoscopy (2024)

Although endoscopic intermuscular dissection (EID) has been used successfully to treat rectal pathology [1], its application in stomach procedures has not been reported. EID involves the dissection of the circular layer from the longitudinal layer of the muscularis propria to achieve a clear vertical dissection margin [2] [3].
An Organ‐on‐Chip Platform for Simulating Drug Metabolism Along the Gut–Liver Axis
Authors: Mara Lucchetti, Kehinde Oluwasegun Aina, Léa Grandmougin, Christian Jäger, Pau Pérez Escriva, Elisabeth Letellier, Alexander S. Mosig, Paul Wilmes
Journal: Advanced Healthcare Materials (2024)

The human microbiome significantly influences drug metabolism through the gut-liver axis, leading to modified drug responses and potential toxicity. Due to the complex nature of the human gut environment, the understanding of microbiome-driven impacts on these processes is limited. To address this, a multiorgan-on-a-chip (MOoC) platform that combines the human microbial-crosstalk (HuMiX) gut-on-chip (GoC) and the Dynamic42 liver-on-chip (LoC), mimicking the bidirectional interconnection between the gut and liver known as the gut-liver axis, is introduced. This platform supports the viability and functionality of intestinal and liver cells. In a proof-of-concept study, the metabolism of irinotecan, a widely used colorectal cancer drug, is imitated within the MOoC. Utilizing liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), irinotecan metabolites are tracked, confirming the platform's ability to represent drug metabolism along the gut-liver axis. Further, using the authors' gut-liver platform, it is shown that the colorectal cancer-associated gut bacterium, Escherichia coli, modifies irinotecan metabolism through the transformation of its inactive metabolite SN-38G into its toxic metabolite SN-38. This platform serves as a robust tool for investigating the intricate interplay between gut microbes and pharmaceuticals, offering a representative alternative to animal models and providing novel drug development strategies.
Reply to D'Couto and Celi: Racial Physiology: A Dangerous Precedent
Authors: Naman S. Shetty, Valentina Giammatteo, Mokshad Gaonkar, Peng Li, Oluwaseun Akeju, Garima Arora, Lorenzo Berra, Pankaj Arora
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

"Reply to D'Couto and Celi: Racial Physiology: A Dangerous Precedent." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Pembrolizumab Versus Placebo as Adjuvant Therapy in Resected Stage IIB or IIC Melanoma: Final Analysis of Distant Metastasis-Free Survival in the Phase III KEYNOTE-716 Study
Authors: Jason J. Luke, Paolo A. Ascierto, Muhammad A. Khattak, Luis de la Cruz Merino, Michele Del Vecchio, Piotr Rutkowski, Francesco Spagnolo, Jacek Mackiewicz, Vanna Chiarion-Sileni, John M. Kirkwood, Caroline Robert, Jean-Jacques Grob, Federica de Galitiis, Dirk Schadendorf, Matteo S. Carlino, Xi Lawrence Wu, Mizuho Fukunaga-Kalabis, Clemens Krepler, Alexander M.M. Eggermont, Georgina V. Long
Journal: Journal of Clinical Oncology (2024)

Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported. Pembrolizumab adjuvant therapy was shown to significantly improve recurrence-free survival (RFS) and distant metastasis-free survival (DMFS) in patients with resected stage IIB or IIC melanoma in earlier analyses of the randomized, double-blind, phase III KEYNOTE-716 study (ClinicalTrials.gov identifier: NCT03553836 ). We report results of the protocol-specified final analysis of DMFS for KEYNOTE-716. Overall, 976 patients were randomly allocated to pembrolizumab (n = 487) or placebo (n = 489). As of January 4, 2023, median follow-up was 39.4 months (range, 26.0-51.4 months). The median DMFS was not reached in either treatment group, and the estimated 36-month DMFS was 84.4% for pembrolizumab and 74.7% for placebo (hazard ratio [HR], 0.59 [95% CI, 0.44 to 0.79]). The median RFS was not reached in either treatment group, and the estimated 36-month RFS was 76.2% for pembrolizumab and 63.4% for placebo (HR, 0.62 [95% CI, 0.49 to 0.79]). DMFS and RFS results were consistent across most prespecified subgroups, including stage IIB and stage IIC melanoma. The safety profile of pembrolizumab was manageable and consistent with previous reports. These results continue to support the use of pembrolizumab adjuvant therapy in patients with resected stage IIB or IIC melanoma.
Efficient Generation of Skin Organoids from Pluripotent Cells via Defined Extracellular Matrix Cues and Morphogen Gradients in a Spindle‐Shaped Microfluidic Device
Authors: Cristina Quílez, Eun Y. Jeon, Alberto Pappalardo, Pooja Pathak, Hasan E. Abaci
Journal: Advanced Healthcare Materials (2024)

Abstract Pluripotent stem cell‐derived skin organoids (PSOs) emerge as a developmental skin model that is self‐organized into multiple components, such as hair follicles. Despite their impressive complexity, PSOs are currently generated in the absence of 3D extracellular matrix (ECM) signals and have several major limitations, including an inverted anatomy (e.g., epidermis inside/dermis outside). In this work, a method is established to generate PSOs effectively in a chemically‐defined 3D ECM environment. After examining various dermal ECM molecules, it is found that PSOs generated in collagen ‐type I (COLI) supplemented with laminin 511 (LAM511) exhibit increased growth compared to conventional free‐floating conditions, but fail to induce complete skin differentiation due in part to necrosis. This problem is addressed by generating the PSOs in a 3D bioprinted spindle‐shaped hydrogel device, which constrains organoid growth longitudinally. This culture system significantly reduces organoid necrosis and leads to a twofold increase in keratinocyte differentiation and an eightfold increase in hair follicle formation. Finally, the system is adapted as a microfluidic device to create asymmetrical gradients of differentiation factors and improves the spatial organization of dermal and epidermal cells. This study highlights the pivotal role of ECM and morphogen gradients in promoting and spatially‐controlling skin differentiation in the PSO framework.
Deep Learning-based Segmentation of CT Scans Predicts Disease Progression and Mortality in IPF
Authors: Muhunthan Thillai, Justin M. Oldham, Alessandro Ruggiero, Fahdi Kanavati, Tom McLellan, Gauri Saini, Simon R. Johnson, Francois-Xavier Ble, Adnan Azim, Kristoffer Ostridge, Adam Platt, Maria Belvisi, Toby M. Maher, Philip L. Molyneaux
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

Despite evidence demonstrating a prognostic role for computed tomography (CT) scans in idiopathic pulmonary fibrosis (IPF), image-based biomarkers are not routinely used in clinical practice or trials.
Current State of Dermatology Mobile Applications With Artificial Intelligence Features
Authors: Shannon Wongvibulsin, Matthew J. Yan, Vartan Pahalyants, William Murphy, Roxana Daneshjou, Veronica Rotemberg
Journal: JAMA Dermatology (2024)

With advancements in mobile technology and artificial intelligence (AI) methods, there has been a substantial surge in the availability of direct-to-consumer mobile applications (apps) claiming to aid in the assessment and management of diverse skin conditions. Despite widespread patient downloads, these apps exhibit limited evidence supporting their efficacy.
Fitusiran prophylaxis in people with hemophilia A or B who switched from prior BPA/CFC prophylaxis (ATLAS-PPX)
Authors: Gili Kenet, Beatrice Nolan, Bulent Zulfikar, Bulent Antmen, Peter Kampmann, Tadashi Matsushita, Chur-Woo You, Kateryna Vilchevska, Catherine N. Bagot, Azizan Sharif, Flora Peyvandi, Guy Young, Claude Negrier, Jiarui Chi, Barbara Kittner, Christian Sussebach, Fadi Shammas, Baisong Mei, Shauna Andersson, Kaan Kavakli
Journal: Blood (2024)

Fitusiran, a subcutaneous investigational small interfering RNA therapeutic, targets antithrombin to rebalance hemostasis in people with hemophilia A or B (PwHA/B), irrespective of inhibitor status. This phase 3, open-label study evaluated the efficacy and safety of fitusiran prophylaxis in males aged ≥12 years with hemophilia A or B, with or without inhibitors, who received prior bypassing agent (BPA)/clotting factor concentrate (CFC) prophylaxis. Participants continued their prior BPA/CFC prophylaxis for 6 months before switching to once-monthly 80 mg fitusiran prophylaxis for 7 months (onset and efficacy periods). Primary end point was annualized bleeding rate (ABR) in the BPA/CFC prophylaxis and fitusiran efficacy period. Secondary end points included spontaneous ABR (AsBR) and joint ABR (AjBR). Safety and tolerability were assessed. Of 80 enrolled participants, 65 (inhibitor, n = 19; noninhibitor, n = 46) were eligible for ABR analyses. Observed median ABRs were 6.5 (interquartile range [IQR], 2.2-19.6)/4.4 (IQR, 2.2-8.7) with BPA/CFC prophylaxis vs 0.0 (IQR, 0.0-0.0)/0.0 (IQR, 0.0-2.7) in the corresponding fitusiran efficacy period. Estimated mean ABRs were substantially reduced with fitusiran by 79.7% (P = .0021) and 46.4% (P = .0598) vs BPA/CFC prophylaxis, respectively. Forty-one participants (63.1%) experienced 0 treated bleeds with fitusiran vs 11 (16.9%) with BPAs/CFCs. Median AsBR and AjBR were both 2.2 with BPA/CFC prophylaxis and 0.0 in the fitusiran efficacy period. Two participants (3.0%) experienced suspected or confirmed thromboembolic events with fitusiran. Once-monthly fitusiran prophylaxis significantly reduced bleeding events vs BPA/CFC prophylaxis in PwHA/B, with or without inhibitors, and reported adverse events were generally consistent with previously identified risks of fitusiran. This trial was registered at www.ClinicalTrials.gov as #NCT03549871.
Vector integration and fate in the hemophilia dog liver multiple years after AAV-FVIII gene transfer
Authors: Paul Batty, Sylvia Fong, Matteo Franco, Choong-Ryoul Sihn, Laura L. Swystun, Saira Afzal, Lorianne Harpell, David Hurlbut, Abbey Pender, Cheng Su, Hauke Thomsen, Christopher Wilson, Loubna Youssar, Andrew Winterborn, Irene Gil-Farina, David Lillicrap
Journal: Blood (2024)
Microfluidic Chip‐Assisted Upconversion Luminescence Biosensing Platform for Point‐of‐Care Virus Diagnostics
Authors: Yuan Liu, Xinyue Lao, Man‐Chung Wong, Menglin Song, Huang Lai, Pui Wang, Yingjin Ma, Lihua Li, Mo Yang, Honglin Chen, Jianhua Hao
Journal: Advanced Healthcare Materials (2024)

Epidemics caused by multiple viruses continue to emerge, which have brought a terrible impact on human society. Identification of viral infections with high sensitivity and portability is of significant importance for the screening and management of diseases caused by viruses. Herein, a microfluidic chip (MFC)-assisted upconversion luminescence biosensing platform is designed and fabricated for point-of-care virus detection. Upconversion nanoparticles with excellent stability are successfully synthesized as luminescent agents for optical signal generation in the portable virus diagnostic platform. The relevant investigation results illustrate that the MFC-assisted virus diagnostic platform possesses outstanding performance such as good integration, high sensitivity (1.12 pg mL-1), ease of use, and portability. In addition, clinical sample test result verifies its more prominent virus diagnostic properties than commercially available rapid test strips. All of these thrilling capabilities imply that the designed portable virus diagnostic platform has great potential for future virus detection applications.
Bronchiectasis–Chronic Obstructive Pulmonary Disease Overlap: A ROSE by Any Other Name?
Authors: David C. LaFon, Mark T. Dransfield
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

"Bronchiectasis-COPD Overlap: A ROSE by Any Other Name?." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Development of a liver disease–specific large language model chat interface using retrieval-augmented generation
Authors: Jin Ge, Steve Sun, Joseph Owens, Victor Galvez, Oksana Gologorskaya, Jennifer C. Lai, Mark J. Pletcher, Ki Lai
Journal: Hepatology (2024)

Background and Aims: Large language models (LLMs) have significant capabilities in clinical information processing tasks. Commercially available LLMs, however, are not optimized for clinical uses and are prone to generating hallucinatory information. Retrieval-augmented generation (RAG) is an enterprise architecture that allows the embedding of customized data into LLMs. This approach “specializes” the LLMs and is thought to reduce hallucinations. Approach and Results We developed “LiVersa,” a liver disease–specific LLM, by using our institution’s protected health information-complaint text embedding and LLM platform, “Versa.” We conducted RAG on 30 publicly available American Association for the Study of Liver Diseases guidance documents to be incorporated into LiVersa. We evaluated LiVersa’s performance by conducting 2 rounds of testing. First, we compared LiVersa’s outputs versus those of trainees from a previously published knowledge assessment. LiVersa answered all 10 questions correctly. Second, we asked 15 hepatologists to evaluate the outputs of 10 hepatology topic questions generated by LiVersa, OpenAI’s ChatGPT 4, and Meta’s Large Language Model Meta AI 2. LiVersa’s outputs were more accurate but were rated less comprehensive and safe compared to those of ChatGPT 4. Results: We evaluated LiVersa’s performance by conducting 2 rounds of testing. First, we compared LiVersa’s outputs versus those of trainees from a previously published knowledge assessment. LiVersa answered all 10 questions correctly. Second, we asked 15 hepatologists to evaluate the outputs of 10 hepatology topic questions generated by LiVersa, OpenAI’s ChatGPT 4, and Meta’s Large Language Model Meta AI 2. LiVersa’s outputs were more accurate but were rated less comprehensive and safe compared to those of ChatGPT 4. Conclusions: In this demonstration, we built disease-specific and protected health information-compliant LLMs using RAG. While LiVersa demonstrated higher accuracy in answering questions related to hepatology, there were some deficiencies due to limitations set by the number of documents used for RAG. LiVersa will likely require further refinement before potential live deployment. The LiVersa prototype, however, is a proof of concept for utilizing RAG to customize LLMs for clinical use cases.
How to model life’s trajectory from major diagnosis to death
Authors: Kamran Abbasi
Journal: BMJ (2024)

How do we model our lives from the time of a major diagnosis to death?Illness trajectories are one method, and they can help frame a conversation about what life will be like with a progressive illness.The three characteristic trajectories of decline are rapid (typically cancer), intermittent (declining organ function), and gradual (advanced frailty, neurological conditions, or major stroke).They can be used to inform person centred care and enable advance care planning.The trajectories may appear abstract, but the lives they describe are very real.
Does Radioactive Iodine Treatment Damage the Lacrimal System?
Authors: Ceren Gürez, Nurhan Ergül
Journal: Clinical Nuclear Medicine (2024)

Purpose In this prospective study, we aimed to make a quantitative assessment of the lacrimal glands before and after radioactive iodine (RAI) treatment in patients with hyperthyroidism and thyroid cancer. Methods The study included 80 eyes of 40 patients. There were 25 patients in group 1 (hyperthyroid group) and 15 patients in group 2 (thyroid cancer group). Group 1 has received low dose ( 131 I) and group 2 high dose ( 131 I). Before, and at the first and sixth month after RAI treatment, all patients underwent ophthalmological examinations, Schirmer tests, TBUT tests, tear osmolarity (TO), and ocular surface examinations. Results The age and sex characteristics of both groups were similar. Although no significant change was observed in tear film tests before and after treatment in group 1, a significant decrease in Schirmer and TBUT values and a significant increase in TO were observed in group 2 in the first month after treatment. These values returned to normal in the sixth month. Although no Schirmer test was observed lower than 10 mm in any patient before RAI treatment, the Schirmer test was measured 5 to 10 mm in 4 (10%) patients in group 2 in the first month after treatment. Again, in these patients, TBUT was below 10 seconds and TO was greater than 308 mOsm/L. Conclusions In this study, although no change was observed in tear function tests in patients receiving low doses of RAI, a decrease in tear secretion and an increase in TO were detected in patients receiving high doses in the early period.
Clinical outcomes and prognostic factors after HCV clearance with DAA in HIV/HCV-coinfected patients with advanced fibrosis/cirrhosis
Authors: Juan Berenguer, Teresa Aldámiz-Echevarría, Víctor Hontañón, Chiara Fanciulli, Carmen Quereda, Carmen Busca, Lourdes Domínguez, Cristina Hernández, Jorge Vergas, Gabriel Gaspar, Lucio J. García-Fraile, Cristina Díez, Marta De Miguel, José M. Bellón, Rafael Bañares, Juan González-García
Journal: Hepatology (2024)

Background and Aims: We assessed long-term clinical outcomes and prognostic factors for liver disease progression after sustained viral response with direct-acting antivirals in patients coinfected with HIV/HCV with advanced fibrosis or cirrhosis. Approach and Results: A total of 1300 patients who achieved sustained viral response with direct-acting antivirals from 2014 to 2017 in Spain were included: 1145 with compensated advanced chronic liver disease (384 advanced fibrosis and 761 compensated cirrhosis) and 155 with decompensated cirrhosis. The median follow-up was 40.9 months. Overall, 85 deaths occurred, 61 due to non-liver non-AIDS–related causes that were the leading cause of death across all stages of liver disease. The incidence (95% CI) of decompensation per 100 person-years (py) was 0 in patients with advanced fibrosis, 1.01 (0.68–1.51) in patients with compensated cirrhosis, and 8.35 (6.05–11.53) in patients with decompensated cirrhosis. The incidence (95% CI) of HCC per 100 py was 0.34 (0.13–0.91) in patients with advanced fibrosis, 0.73 (0.45–1.18) in patients with compensated cirrhosis, and 1.92 (1.00–3.70) per 100 py in patients with decompensated cirrhosis. Prognostic factors for decompensation in patients with compensated advanced chronic liver disease included serum albumin, liver stiffness measurement (LSM), and fibrosis 4. In this population, LSM and LSM-based posttreatment risk stratification models showed their predictive ability for decompensation and HCC. Conclusions: Non-liver non-AIDS–related events were the leading causes of morbidity and mortality after direct-acting antiviral cure among coinfected patients with advanced fibrosis/cirrhosis. Among those with compensated advanced chronic liver disease, baseline LSM and posttreatment LSM-based models helped to assess decompensation and HCC risk.