tbuckley/cabot-search huggingface dataset:
Prospective External Validation of the Esbenshade Vanderbilt Models Accurately Predicts Bloodstream Infection Risk in Febrile Non-Neutropenic Children With Cancer
Authors: Zhiguo Zhao, Pratik A. Patel, Leonora Slatnick, Anna Sitthi-Amorn, Kevin J. Bielamowicz, Farranaz A. Nunez, Alexandra M. Walsh, Jennifer Hess, Jenna Rossoff, Caitlin Elgarten, Regina Myers, Raya Saab, Maya Basbous, Meghan Mccormick, Catherine Aftandilian, Rebecca Richards, C. Nathan Nessle, Alison C. Tribble, Jessica K. Sheth Bhutada, Scott L. Coven, Daniel Runco, Jennifer Wilkes, Arun Gurunathan, Terri Guinipero, Jennifer A. Belsky, Karen Lee, Victor Wong, Megha Malhotra, Amy Armstrong, Lauren P. Jerkins, Shane J. Cross, Lyndsay Fisher, Madison T. Stein, Natalie L. Wu, Troy Yi, Etan Orgel, Gabrielle M. Haeusler, Joshua Wolf, Jenna M. Demedis, Tamara P. Miller, Adam J. Esbenshade
Journal: Journal of Clinical Oncology (2023)

PURPOSE The optimal management of fever without severe neutropenia (absolute neutrophil count [ANC] ≥500/µL) in pediatric patients with cancer is undefined. The previously proposed Esbenshade Vanderbilt (EsVan) models accurately predict bacterial bloodstream infections (BSIs) in this population and provide risk stratification to aid management, but have lacked prospective external validation. MATERIALS AND METHODS Episodes of fever with a central venous catheter and ANC ≥500/µL occurring in pediatric patients with cancer were prospectively collected from 18 academic medical centers. Variables included in the EsVan models and 7-day clinical outcomes were collected. Five versions of the EsVan models were applied to the data with calculation of C-statistics for both overall BSI rate and high-risk organism BSI (gram-negative and Staphylococcus aureus BSI), as well as model calibration. RESULTS In 2,565 evaluable episodes, the BSI rate was 4.7% (N = 120). Complications for the whole cohort were rare, with 1.1% (N = 27) needing intensive care unit (ICU) care by 7 days, and the all-cause mortality rate was 0.2% (N = 5), with only one potential infection-related death. C-statistics ranged from 0.775 to 0.789 for predicting overall BSI, with improved accuracy in predicting high-risk organism BSI (C-statistic 0.800-0.819). Initial empiric antibiotics were withheld in 14.9% of episodes, with no deaths or ICU admissions attributable to not receiving empiric antibiotics. CONCLUSION The EsVan models, especially EsVan2b, perform very well prospectively across multiple academic medical centers and accurately stratify risk of BSI in episodes of non-neutropenic fever in pediatric patients with cancer. Implementation of routine screening with risk-stratified management for non-neutropenic fever in pediatric patients with cancer could safely reduce unnecessary antibiotic use.
Ethnic variation in asthma phenotypic presentation and outcomes: a cross-sectional analysis of the UK Biobank
Authors: John Busby, P Jane McDowell, Paul E Pfeffer, Adel Hasan Mansur, Liam G Heaney
Journal: Thorax (2023)

Ethnic disparities exist within asthma; however, country of birth is rarely investigated. We described demographic and clinical characteristics by ethnicity and country of birth within the UK Biobank. Lung function and asthma hospitalisations were similar for white, black and North-East Asian participants, however, South-East (SE) Asians more commonly had an FEV 1 below the lower limits of normal (LLN; 53.8% vs 32.3%, p&lt;0.001), blood eosinophilia (38.6% vs 23.8%, p&lt;0.001) and asthma hospitalisation (12.5% vs 8.3%, p&lt;0.001) than white participants. First-generation SE Asian immigrants had poorer lung function (57.7% vs 27.7% FEV 1 below LLN, p&lt;0.001) than UK/Ireland born participants. These data demonstrate inter-ethnic and intra-ethnic disparities.
Taxanes for the treatment of breast cancer during pregnancy: an international cohort study
Authors: Ana S Ferrigno Guajardo, Bryan F Vaca-Cartagena, Erica L Mayer, Chayma Bousrih, Oke Oluchi, Cristina Saura, Fedro Peccatori, Wendy Muñoz-Montaño, Alvaro Cabrera-Garcia, Matteo Lambertini, Luis Corrales, Andrea Becerril-Gaitan, Tal Sella, Alexandra Bili Newman, Barbara Pistilli, Ashley Martinez, Carolina Ortiz, Laia Joval-Ramentol, Giovanna Scarfone, Barbara Buonomo, Fernando Lara-Medina, Jacqueline Sanchez, Luca Arecco, Allan Ramos-Esquivel, Snezana Susnjar, Gilberto Morgan, Cynthia Villarreal-Garza, Hatem A Azim
Journal: JNCI Journal of the National Cancer Institute (2023)

Abstract Introduction The addition of taxanes to anthracycline-based chemotherapy is considered standard of care in the treatment of breast cancer. However, there are insufficient data regarding the safety of taxanes during pregnancy. The aim of this study was to describe the incidence of obstetric and neonatal adverse events associated with the use of taxane-containing chemotherapy regimens for the treatment of breast cancer during pregnancy. Methods This is a multicenter, international cohort study of breast cancer patients treated with taxanes during pregnancy. A descriptive analysis was undertaken to synthetize available data. Results A total of 103 patients were included, most of whom were treated with paclitaxel and anthracyclines given in sequence during gestation (90.1%). The median gestational age at taxane initiation was 28 weeks (range = 12-37 weeks). Grade 3-4 adverse events were reported in 7 of 103 (6.8%) patients. The most common reported obstetric complications were intrauterine growth restriction (n = 8 of 94, 8.5%) and preterm premature rupture of membranes (n = 5 of 94, 5.3%). The live birth rate was 92 of 94 (97.9%), and the median gestational age at delivery was 37 weeks (range = 32-40 weeks). Admission to an intensive care unit was reported in 14 of 88 (15.9%) neonates, and 17 of 70 (24.3%) live births resulted in small for gestational age neonates. Congenital malformations were reported in 2 of 93 (2.2%). Conclusion Obstetric and neonatal outcomes after taxane exposure during pregnancy were generally favorable and did not seem to differ from those reported in the literature with standard anthracycline-based regimens. This study supports the use of taxanes during gestation when clinically indicated.
Physician and Patient Assessment of Extended Language Model Answers to Rheumatology Patient Inquiries: Doctor versus AI. Comment on the article by Ye et al
Authors: Hinpetch Daungsupawong, Viroj Wiwanitkit
Journal: Arthritis & Rheumatology (2023)

Disclosure form Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Implementation outcomes in psychosocial intervention studies for children and adolescents living in low- and middle-income countries: A systematic review
Authors: Caterina Ceccarelli, Eleonora Prina, Muhammad Alkasaby, Camilla Cadorin, Yashi Gandhi, Doriana Cristofalo, Yasser Abujamei, Orso Muneghina, Corrado Barbui, Mark J.D. Jordans, Marianna Purgato
Journal: Clinical Psychology Review (2023)
An end of year resolution: phase out fossil fuels
Authors: Kamran Abbasi
Journal: BMJ (2023)

As we approach the close of 2023, a hard, unforgiving year, consider this: the world, as we know it, is about to end.Life on Earth may not survive into the 22nd century; humanity has no more than 30 years.The window of opportunity to prevent both those extinction events is less than eight years, says doctor and climate activist Hugh
Encrypted federated learning for secure decentralized collaboration in cancer image analysis
Authors: Daniel Truhn, Soroosh Tayebi Arasteh, Oliver Lester Saldanha, Gustav Müller-Franzes, Firas Khader, Philip Quirke, Nicholas P. West, Richard Gray, Gordon G.A. Hutchins, Jacqueline A. James, Maurice B. Loughrey, Manuel Salto-Tellez, Hermann Brenner, Alexander Brobeil, Tanwei Yuan, Jenny Chang-Claude, Michael Hoffmeister, Sebastian Foersch, Tianyu Han, Sebastian Keil, Maximilian Schulze-Hagen, Peter Isfort, Philipp Bruners, Georgios Kaissis, Christiane Kuhl, Sven Nebelung, Jakob Nikolas Kather
Journal: Medical Image Analysis (2023)

Artificial intelligence (AI) has a multitude of applications in cancer research and oncology. However, the training of AI systems is impeded by the limited availability of large datasets due to data protection requirements and other regulatory obstacles. Federated and swarm learning represent possible solutions to this problem by collaboratively training AI models while avoiding data transfer. However, in these decentralized methods, weight updates are still transferred to the aggregation server for merging the models. This leaves the possibility for a breach of data privacy, for example by model inversion or membership inference attacks by untrusted servers. Somewhat-homomorphically-encrypted federated learning (SHEFL) is a solution to this problem because only encrypted weights are transferred, and model updates are performed in the encrypted space. Here, we demonstrate the first successful implementation of SHEFL in a range of clinically relevant tasks in cancer image analysis on multicentric datasets in radiology and histopathology. We show that SHEFL enables the training of AI models which outperform locally trained models and perform on par with models which are centrally trained. In the future, SHEFL can enable multiple institutions to co-train AI models without forsaking data governance and without ever transmitting any decryptable data to untrusted servers.
Segment anything model for medical images?
Authors: Yuhao Huang, Xin Yang, Lian Liu, Han Zhou, Ao Chang, Xinrui Zhou, Rusi Chen, Junxuan Yu, Jiongquan Chen, Chaoyu Chen, Sijing Liu, Haozhe Chi, Xindi Hu, Kejuan Yue, Lei Li, Vicente Grau, Deng-Ping Fan, Fajin Dong, Dong Ni
Journal: Medical Image Analysis (2023)
An Ancestral Major Histocompatibility Complex Organization in Cartilaginous Fish: Reconstructing MHC Origin and Evolution
Authors: Ana Veríssimo, L Filipe C Castro, Antonio Muñoz-Mérida, Tereza Almeida, Arnaud Gaigher, Fabiana Neves, Martin F Flajnik, Yuko Ohta
Journal: Molecular Biology and Evolution (2023)

Abstract Cartilaginous fish (sharks, rays, and chimeras) comprise the oldest living jawed vertebrates with a mammalian-like adaptive immune system based on immunoglobulins (Ig), T-cell receptors (TCRs), and the major histocompatibility complex (MHC). Here, we show that the cartilaginous fish “adaptive MHC” is highly regimented and compact, containing (i) a classical MHC class Ia (MHC-Ia) region containing antigen processing (antigen peptide transporters and immunoproteasome) and presenting (MHC-Ia) genes, (ii) an MHC class II (MHC-II) region (with alpha and beta genes) with linkage to beta-2-microglobulin (β2m) and bromodomain-containing 2, (iii) nonclassical MHC class Ib (MHC-Ib) regions with 450 million-year-old lineages, and (iv) a complement C4 associated with the MHC-Ia region. No MHC-Ib genes were found outside of the elasmobranch MHC. Our data suggest that both MHC-I and MHC-II genes arose after the second round of whole-genome duplication (2R) on a human chromosome (huchr) 6 precursor. Further analysis of MHC paralogous regions across early branching taxa from all jawed vertebrate lineages revealed that Ig/TCR genes likely arose on a precursor of the huchr9/12/14 MHC paralog. The β2m gene is linked to the Ig/TCR genes in some vertebrates suggesting that it was present at 1R, perhaps as the donor of C1 domain to the primordial MHC gene. In sum, extant cartilaginous fish exhibit a conserved and prototypical MHC genomic organization with features found in various vertebrates, reflecting the ancestral arrangement for the jawed vertebrates.
2023 American Thoracic Society BEAR Cage Winning Proposal. Endobronchial Optical Coherence Tomography: A Novel Imaging Technique for Early Microscopic Diagnosis and Monitoring of Interstitial Lung Disease
Authors: Sreyankar Nandy
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"2023 American Thoracic Society BEAR Cage Winning Proposal: Endobronchial Optical Coherence Tomography (EB-OCT): A Novel Imaging Technique for Early Microscopic Diagnosis and Monitoring of Interstitial Lung Disease." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Associations of combined phenotypic ageing and genetic risk with incidence of chronic respiratory diseases in the UK Biobank: a prospective cohort study
Authors: Ting Wang, Weiwei Duan, Xinying Jia, Xinmei Huang, Yi Liu, Fanqing Meng, Chunhui Ni
Journal: European Respiratory Journal (2023)

Background Accelerated biological ageing has been associated with an increased risk of several chronic respiratory diseases. However, the associations between phenotypic age, a new biological age indicator based on clinical chemistry biomarkers, and common chronic respiratory diseases have not been evaluated. Methods We analysed data from 308 592 participants at baseline in the UK Biobank. The phenotypic age was calculated from chronological age and nine clinical chemistry biomarkers, including albumin, alkaline phosphatase, creatinine, glucose, C-reactive protein, lymphocyte percent, mean cell volume, red cell distribution width and white blood cell count. Furthermore, phenotypic age acceleration (PhenoAgeAccel) was calculated by regressing phenotypic age on chronological age. The associations of PhenoAgeAccel with incident common chronic respiratory diseases and cross-sectional lung function were investigated. Moreover, we constructed polygenic risk scores and evaluated whether PhenoAgeAccel modified the effect of genetic susceptibility on chronic respiratory diseases and lung function. Results The results showed significant associations of PhenoAgeAccel with increased risk of idiopathic pulmonary fibrosis (IPF) (hazard ratio (HR) 1.52, 95% CI 1.45–1.59), COPD (HR 1.54, 95% CI 1.51–1.57) and asthma (HR 1.18, 95% CI 1.15–1.20) per 5-year increase and decreased lung function. There was an additive interaction between PhenoAgeAccel and the genetic risk for IPF and COPD. Participants with high genetic risk and who were biologically older had the highest risk of incident IPF (HR 5.24, 95% CI 3.91–7.02), COPD (HR 2.99, 95% CI 2.66–3.36) and asthma (HR 2.07, 95% CI 1.86–2.31). Mediation analysis indicated that PhenoAgeAccel could mediate 10∼20% of the associations between smoking and chronic respiratory diseases, while ∼10% of the associations between particulate matter with aerodynamic diameter &lt;2.5 µm and the disorders were mediated by PhenoAgeAccel. Conclusion PhenoAgeAccel was significantly associated with incident risk of common chronic respiratory diseases and decreased lung function and could serve as a novel clinical biomarker.
Nature-Based Interventions for Autistic Children
Authors: Myrian Sze Nga Fan, William Ho Cheung Li, Laurie Long Kwan Ho, Lophina Phiri, Kai Chow Choi
Journal: JAMA Network Open (2023)

Importance There is a gap in the evidence regarding nature-based interventions (NBIs) for children with autism spectrum disorder (ASD). Objective To systematically review and meta-analyze available evidence on the health-related outcomes in NBIs for children with ASD. Data Sources The Cumulative Index to Nursing and Allied Health Literature, Cochrane, Embase, Emcare, Education Resources Information Center, Global Health, MEDLINE, PsycInfo, SPORTDiscus, and Web of Science were searched from inception until May 2023. Google Scholar and references from included studies were searched for additional studies. Study Selection Included studies were randomized clinical trials (RCTs), controlled studies, and single-group before-and-after studies that reported health-related outcomes. Data Extraction and Synthesis This review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) reporting guidelines. Random-effects meta-analyses were used to synthesize the data. The findings of studies that were ineligible for meta-analysis were summarized according to the Synthesis Without Meta-analysis (SWIM) reporting guidelines. Main Outcomes and Measures The outcomes of interest were health-related outcomes (ie, social functioning, behavioral functioning, emotional functioning, sensory functioning) and the self-reported well-being of children with ASD. Results A total of 24 studies with 717 participants (mean age range, 5.3 to 17.8 years; 141 [21.9%] female) were included. A meta-analysis from 13 studies indicated a significant negative moderate association between NBIs and social communication (standardized mean difference [SMD], −0.59; 95% CI, −0.85 to −0.34). For behavioral functioning outcomes, NBIs showed a significant moderate association with reduced hyperactivity (SMD, −0.56; 95% CI, −0.86 to −0.26) and a small to moderate association with reduced irritability (SMD, −0.49; 95% CI, −0.79 to −0.19). For sensory functioning, NBIs were significantly associated with improved inattention and distractibility (SMD, 1.13; 95% CI, 0.67 to 1.60). Significant moderate associations were observed in sensory seeking (SMD, 0.77; 95% CI, 0.33 to 1.22; P &amp;amp;lt; .001; I 2 = 0%) and sensory sensitivity (SMD, 0.56; 95% CI, 0.12 to 1.00; P = .01; I 2 = 0%). Heterogeneity of the intervention effects was not high, and I 2 ranged from 0% to 67%. Conclusions and Relevance The findings of this systematic review and meta-analysis suggested an association of NBIs in group-based recreational therapy with experiential learning with positive short-term outcomes on sensory, social, and behavioral functioning for children with ASD. Future evidence using robust study design to aid the health and functional trajectories of children with ASD is recommended.
Opioid Prescribing by US Surgeons, 2016-2022
Authors: Jason Zhang, Jennifer F. Waljee, Thuy D. Nguyen, Amy S. Bohnert, Chad M. Brummett, Mark C. Bicket, Kao-Ping Chua
Journal: JAMA Network Open (2023)

This cross-sectional study investigates the rate and dosing of opioid prescriptions among US surgeons from 2016 to 2022.
Performance of Large Language Models on a Neurology Board–Style Examination
Authors: Marc Cicero Schubert, Wolfgang Wick, Varun Venkataramani
Journal: JAMA Network Open (2023)

Importance Recent advancements in large language models (LLMs) have shown potential in a wide array of applications, including health care. While LLMs showed heterogeneous results across specialized medical board examinations, the performance of these models in neurology board examinations remains unexplored. Objective To assess the performance of LLMs on neurology board–style examinations. Design, Setting, and Participants This cross-sectional study was conducted between May 17 and May 31, 2023. The evaluation utilized a question bank resembling neurology board-style examination questions and was validated with a small question cohort by the European Board for Neurology. All questions were categorized into lower-order (recall, understanding) and higher-order (apply, analyze, synthesize) questions based on the Bloom taxonomy for learning and assessment. Performance by LLM ChatGPT versions 3.5 (LLM 1) and 4 (LLM 2) was assessed in relation to overall scores, question type, and topics, along with the confidence level and reproducibility of answers. Main Outcomes and Measures Overall percentage scores of 2 LLMs. Results LLM 2 significantly outperformed LLM 1 by correctly answering 1662 of 1956 questions (85.0%) vs 1306 questions (66.8%) for LLM 1. Notably, LLM 2’s performance was greater than the mean human score of 73.8%, effectively achieving near-passing and passing grades in the neurology board–style examination. LLM 2 outperformed human users in behavioral, cognitive, and psychological–related questions and demonstrated superior performance to LLM 1 in 6 categories. Both LLMs performed better on lower-order than higher-order questions, with LLM 2 excelling in both lower-order and higher-order questions. Both models consistently used confident language, even when providing incorrect answers. Reproducible answers of both LLMs were associated with a higher percentage of correct answers than inconsistent answers. Conclusions and Relevance Despite the absence of neurology-specific training, LLM 2 demonstrated commendable performance, whereas LLM 1 performed slightly below the human average. While higher-order cognitive tasks were more challenging for both models, LLM 2’s results were equivalent to passing grades in specialized neurology examinations. These findings suggest that LLMs could have significant applications in clinical neurology and health care with further refinements.
Error in Grant Number
Journal: JAMA Network Open (2023)

Daniel B. Hoover, MD; P. Todd Korthuis, MD, MPH; Elizabeth Needham Waddell, PhD; Canyon Foot, BA; Caitlin Conway, BSN; Heidi M. Crane, MD, MPH; Peter D. Friedmann, MD, MPH; Vivian F. Go, PhD; Robin M. Nance, PhD; Mai T. Pho, MD; Milan F. Satcher, MD, MPH; Adams Sibley, MPH; Ryan P. Westergaard, MD, PhD, MPH; April M. Young, PhD, MPH; Ryan Cook, PhD, MSPH
Adult-onset idiopathic peripheral pulmonary artery stenosis
Authors: Yudai Tamura, Yuichi Tamura, Ayako Shigeta, Kazuya Hosokawa, Yu Taniguchi, Takumi Inami, Shiro Adachi, Ichizo Tsujino, Naohiko Nakanishi, Kimi Sato, Jiro Sakamoto, Nobuhiro Tanabe, Noriaki Takama, Kazuto Nakamura, Kayoko Kubota, Naohiro Komura, Shigehiko Kato, Jun Yamashita, Makoto Takei, Shuji Joho, Shunsuke Ishii, Ryo Takemura, Koichiro Sugimura, Koichiro Tatsumi
Journal: European Respiratory Journal (2023)

Background Peripheral pulmonary artery stenosis (PPS) refers to stenosis of the pulmonary artery from the trunk to the peripheral arteries. Although paediatric PPS is well described, the clinical characteristics of adult-onset idiopathic PPS have not been established. Our objectives in this study were to characterise the disease profile of adult-onset PPS. Methods We collected data in Japanese centres. This cohort included patients who underwent pulmonary angiography (PAG) and excluded patients with chronic thromboembolic pulmonary hypertension or Takayasu arteritis. Patient backgrounds, right heart catheterisation (RHC) findings, imaging findings and treatment profiles were collected. Results 44 patients (median (interquartile range) age 39 (29–57) years; 29 females (65.9%)) with PPS were enrolled from 20 centres. In PAG, stenosis of segmental and peripheral pulmonary arteries was observed in 41 (93.2%) and 36 patients (81.8%), respectively. 35 patients (79.5%) received medications approved for pulmonary arterial hypertension (PAH) and 22 patients (50.0%) received combination therapy. 25 patients (56.8%) underwent transcatheter pulmonary angioplasty. RHC data showed improvements in both mean pulmonary arterial pressure (44 versus 40 mmHg; p&lt;0.001) and pulmonary vascular resistance (760 versus 514 dyn·s·cm −5 ; p&lt;0.001) from baseline to final follow-up. The 3-, 5- and 10-year survival rates of patients with PPS were 97.5% (95% CI 83.5–99.6%), 89.0% (95% CI 68.9–96.4%) and 67.0% (95% CI 41.4–83.3%), respectively. Conclusions In this study, patients with adult-onset idiopathic PPS presented with segmental and peripheral pulmonary artery stenosis. Although patients had severe pulmonary hypertension at baseline, they showed a favourable treatment response to PAH drugs combined with transcatheter pulmonary angioplasty.
Effectiveness of Aerobic Exercise and Tai Chi Interventions on Sleep Quality in Patients With Advanced Lung Cancer
Authors: Naomi Takemura, Denise Shuk Ting Cheung, Daniel Yee Tak Fong, Anne Wing Mui Lee, Tai-Chung Lam, James Chung-Man Ho, Tsz Yeung Kam, Jeannie Yin Kwan Chik, Chia-Chin Lin
Journal: JAMA Oncology (2023)

Sleep disturbances prevalent among patients with advanced lung cancer can aggravate physical and psychological symptoms, contributing to decreased quality of life and survival.