tbuckley/cabot-search huggingface dataset:
Erythrocyte‐Membrane‐Camouflaged Magnetic Nanocapsules With Photothermal/Magnetothermal Effects for Thrombolysis
Authors: Liqiong Zhu, Weishuai Lian, Nuo Yu, Jialan Meng, Hongchun Zeng, Yue Wang, Xiao Wang, Mei Wen, Zhigang Chen
Journal: Advanced Healthcare Materials (2024)

Abstract Venous/arterial thrombosis poses significant threats to human health. However, drug‐enabled thrombolysis treatment often encounters challenges such as short half‐life and low bioavailability. To address these issues, the design of erythrocyte‐membrane (EM) camouflaged nanocapsules (USIO/UK@EM) incorporating ultra‐small iron oxide (USIO) and urokinase (UK) drug, which exhibits remarkable photothermal/magnetothermal effects and drug delivery ability for venous/arterial thrombolysis, is reported. USIO, UK, and EM are coextruded to fabricate USIO/UK@EM with average sizes of 103.7 nm. As USIO/UK@EM possesses wide photoabsorption and good magnetic properties, its solution demonstrates a temperature increase to 41.8–42.9 °C within 5 min when exposed to an 808 nm laser (0.33 mW cm −2 ) or alternating magnetic field (AMF). Such photothermal/magnetothermal effect along with UK confers impressive thrombolytic rates of 82.4% and 74.2%, higher than that (≈15%) achieved by UK alone. Further, the EM coating extends the circulating half‐life ( t 1/2 = 3.28 h). When USIO/UK@EM is administered to mice and rabbits, tail vein thrombus in mice and femoral artery thrombus in rabbits can be dissolved by the synergetic effect of thermothrombolysis and UK. Therefore, this study not only offers insights into the rational design of multifunctional biomimetic nanocapsules but also showcases a promising thrombolysis strategy utilizing nanomedicine.
Heterogeneous‐Structure‐Based AuNBs@TiO<sub>2</sub> Nano‐Photosensitizers for Computed Tomography Imaging Guided NIR‐II Photodynamic Therapy and Cancer Metastatic Prevention
Authors: Xinfeng Tang, Yi Wu, Yanqiong Shen, Zhiqi Huang, Wei Jiang, Yingming Zhao, Weifu Lv, Yanhua Zhu
Journal: Advanced Healthcare Materials (2024)

Photodynamic therapy (PDT) is a minimally invasive cancer treatment that, despite its significant attention, faces limitations in penetration depth, which restrict its effectiveness. Herein, it is found that gold nanobipyramid (AuNBs) coated with TiO
mi-Mic: a novel multi-layer statistical test for microbiota-disease associations
Authors: Oshrit Shtossel, Shani Finkelstein, Yoram Louzoun
Journal: Genome biology (2024)

mi-Mic, a novel approach for microbiome differential abundance analysis, tackles the key challenges of such statistical tests: a large number of tests, sparsity, varying abundance scales, and taxonomic relationships. mi-Mic first converts microbial counts to a cladogram of means. It then applies a priori tests on the upper levels of the cladogram to detect overall relationships. Finally, it performs a Mann-Whitney test on paths that are consistently significant along the cladogram or on the leaves. mi-Mic has much higher true to false positives ratios than existing tests, as measured by a new real-to-shuffle positive score.
Trends in Incidence of Hip Fracture and Hip Replacement in Denmark, 1996 to 2018
Authors: Troels Mygind Jensen, Jacob Krabbe Pedersen, Frans Boch Waldorff, Jens Søndergaard, Søren Overgaard, Kaare Christensen
Journal: JAMA Network Open (2024)

The past several decades have witnessed substantial changes in treatments that are particularly relevant for older patients.
ChatGPT’s ability to generate realistic experimental images poses a new challenge to academic integrity
Authors: Lingxuan Zhu, Yancheng Lai, Weiming Mou, Haoran Zhang, Anqi Lin, Chang Qi, Tao Yang, Liling Xu, Jian Zhang, Peng Luo
Journal: Journal of Hematology & Oncology (2024)

The rapid advancements in large language models (LLMs) such as ChatGPT have raised concerns about their potential impact on academic integrity. While initial concerns focused on ChatGPT's writing capabilities, recent updates have integrated DALL-E 3's image generation features, extending the risks to visual evidence in biomedical research. Our tests revealed ChatGPT's nearly barrier-free image generation feature can be used to generate experimental result images, such as blood smears, Western Blot, immunofluorescence and so on. Although the current ability of ChatGPT to generate experimental images is limited, the risk of misuse is evident. This development underscores the need for immediate action. We suggest that AI providers restrict the generation of experimental image, develop tools to detect AI-generated images, and consider adding "invisible watermarks" to the generated images. By implementing these measures, we can better ensure the responsible use of AI technology in academic research and maintain the integrity of scientific evidence.
Deep Learning–Based Assessment of Built Environment From Satellite Images and Cardiometabolic Disease Prevalence
Authors: Zhuo Chen, Jean-Eudes Dazard, Yassin Khalifa, Issam Motairek, Catherine Kreatsoulas, Sanjay Rajagopalan, Sadeer Al-Kindi
Journal: JAMA Cardiology (2024)

Importance Built environment plays an important role in development of cardiovascular disease. Large scale, pragmatic evaluation of built environment has been limited owing to scarce data and inconsistent data quality. Objective To investigate the association between image-based built environment and the prevalence of cardiometabolic disease in urban cities. Design, Setting, and Participants This cross-sectional study used features extracted from Google satellite images (GSI) to measure the built environment and link them with prevalence of cardiometabolic disease. Convolutional neural networks, light gradient-boosting machines, and activation maps were used to assess the association with health outcomes and identify feature associations with coronary heart disease (CHD), stroke, and chronic kidney disease (CKD). The study obtained aerial images from GSI covering census tracts in 7 cities (Cleveland, Ohio; Fremont, California; Kansas City, Missouri; Detroit, Michigan; Bellevue, Washington; Brownsville, Texas; and Denver, Colorado). The study used census tract-level data from the US Centers for Disease Control and Prevention’s 500 Cities project. The data were originally collected from the Behavioral Risk Factor Surveillance System that surveyed people 18 years and older across the country. Analyses were conducted from February to December 2022. Exposures GSI images of built environment and cardiometabolic disease prevalence. Main Outcomes and Measures Census tract-level estimated prevalence of CHD, stroke, and CKD based on image-based built environment features. Results The study obtained 31 786 aerial images from GSI covering 789 census tracts. Built environment features extracted from GSI using machine learning were associated with prevalence of CHD ( R 2 = 0.60), stroke ( R 2 = 0.65), and CKD ( R 2 = 0.64). The model performed better at distinguishing differences between cardiometabolic prevalence between cities than within cities (eg, highest within-city R 2 = 0.39 vs between-city R 2 = 0.64 for CKD). Addition of GSI features both outperformed and improved the model that only included age, sex, race, income, education, and composite indices for social determinants of health ( R 2 = 0.83 vs R 2 = 0.76 for CHD; P &amp;amp;lt;.001). Activation maps from the features revealed certain health-related built environment such as roads, highways, and railroads and recreational facilities such as amusement parks, arenas, and baseball parks. Conclusions and Relevance In this cross-sectional study, a significant portion of cardiometabolic disease prevalence was associated with GSI-based built environment using convolutional neural networks.
Errors in Byline
Journal: JAMA Network Open (2024)

Naveen Poonai, MD; Daniel M. Cohen, MD; Doug MacDowell, BA; Rakesh D. Mistry, MD, MS; Santiago Mintegi, MD, PhD; Simon Craig, MBBS; Damian Roland, MD; Michael Miller, PhD; Itai Shavit, MD; Paediatric Emergency Research Networks (PERN) PAINT Study Group ; Nishit Patel; Camilo Gutierrez; Emily Roben; Chris Pruitt; Kimberly S. Quayle; Alicia Rolin; Dan Kornfeld; Justin Davis; Jackie Grupp-Phelan; Amanda Bogie; Heather Territo; Eli Hershman; Jānis Kolbergs; Virginia Stanton; Sarah Sheedy; Steve Forester; Liz Binham; Laura Dell'Era; Assunta Tornesello; Yvette Wang; Alan Nager; Theodore Heyming; Rebekah Burns; Indi Trehan; Matthew Lipshaw; Carmen Sulton; Joyce Li; Aderonke Ojo; Susan Kelly; Matthew Thornton; Kerry Caperell; Iluonose Amoni; Anna Abrams; Myto Duong; Muhammad Wassem; Adrienne Davis; Jocelyn Gravel; Evelyne Doyon Trottier; Neta Bar Am; Graham Thompson; Vikram Sabhaney; Garth Meckler; Rini Jain; Samina Ali; Silvia Bressan; Tiziana Zangardi; Giovanna Villa; Martina Giacalone; Michelle Seiler; Cyril Sahyoun; Fabrizio Romano; Zsolt Bognar; Szofia Hajosi-Kalcakosz; Lisa Amir; Said Hachimi-Idrissi; Zanda Pucuka; Astra Zviedre; Emīlija Zeltiņa; Natalie Phillips; Meredith Borland; Sharon O'Brien; Jeanette Marchant; Amit Kochar; Shane George; Victoria Pennington; Mark Lyttle; Jen Browning; Anna McLoughlin; Stuart Hartshorn; Chaman Urooj; Lucy Johnston; Emily Walton; Deepika Subrahmanyam Puthucode; Phil Peacock; James Conroy; Rafael Marañon; Silvia Garcia; Nuria Cahís; Amaia Cámara-Otegui; Arantxa Gomez; Maria Carbonero; Carlos Angelats-Romero; Adriana Yock-Corrales; Gabriela Hualde; Fabian Spigariol; Alex Donas; Cinthia Gübeli Linné; Alessia Rocchi; Alessia Pedrazzini; Giorgio Cozzi; Dino Barbi; Laura Baggio; Giovana La Fauci; Angela Mauro; Matthew Steimle; Danilo Buonsenso; Irma Ugalde; Gaby Nieva; Charlotte Harper; Idanna Sforzi; Shobhit Jain
Adverse Pregnancy Outcomes and Subsequent First-Time Use of Psychiatric Treatment Among Fathers in Denmark
Authors: Frederik Christiansen, Janne Petersen, Ida Holte Thorius, Agnes Ladelund, Espen Jimenez-Solem, Merete Osler, Mikkel Zöllner Ankarfeldt
Journal: JAMA Network Open (2024)

Becoming a first-time parent is a major life-changing event and can be challenging regardless of the pregnancy outcome. However, little is known how different adverse pregnancy outcomes affect the father's risk of psychiatric treatment post partum.
Increasing equity in science requires better ethics training: A course by trainees, for trainees
Authors: Roshni A. Patel, Rachel A. Ungar, Alanna L. Pyke, Alvina Adimoelja, Meenakshi Chakraborty, Daniel J. Cotter, Malika Freund, Pagé Goddard, Justin Gomez-Stafford, Emily Greenwald, Emily Higgs, Naiomi Hunter, Tim M.G. MacKenzie, Anjali Narain, Tamara Gjorgjieva, Daphne O. Martschenko
Journal: Cell Genomics (2024)

Despite the profound impacts of scientific research, few scientists have received the necessary training to productively discuss the ethical and societal implications of their work. To address this critical gap, we-a group of predominantly human genetics trainees-developed a course on genetics, ethics, and society. We intend for this course to serve as a template for other institutions and scientific disciplines. Our curriculum positions human genetics within its historical and societal context and encourages students to evaluate how societal norms and structures impact the conduct of scientific research. We demonstrate the utility of this course via surveys of enrolled students and provide resources and strategies for others hoping to teach a similar course. We conclude by arguing that if we are to work toward rectifying the inequities and injustices produced by our field, we must first learn to view our own research as impacting and being impacted by society.
Management of Gallstone Pancreatitis
Authors: James McDermott, Lillian S. Kao, Jessica A. Keeley, Jeffry Nahmias, Christian de Virgilio
Journal: JAMA Surgery (2024)

Importance Gallstone pancreatitis (GSP) is the leading cause of acute pancreatitis, accounting for approximately 50% of cases. Without appropriate and timely treatment, patients are at increased risk of disease progression and recurrence. While there is increasing consensus among guidelines for the management of mild GSP, adherence to these guidelines remains poor. In addition, there is minimal evidence to guide clinicians in the treatment of moderately severe and severe pancreatitis. Observations The management of GSP continues to evolve and is dependent on severity of acute pancreatitis and concomitant biliary diagnoses. Across the spectrum of severity, there is evidence that goal-directed, moderate fluid resuscitation decreases the risk of fluid overload and mortality compared with aggressive resuscitation. Patients with isolated, mild GSP should undergo same-admission cholecystectomy; early cholecystectomy within 48 hours of admission has been supported by several randomized clinical trials. Cholecystectomy should be delayed for patients with severe disease; for severe and moderately severe disease, the optimal timing remains unclear. Preoperative endoscopic retrograde cholangiopancreatography (ERCP) is only useful for patients with suspected cholangitis or biliary obstruction, although the concomitance of these conditions in patients with GSP is rare. Modality of evaluation of the common bile duct to rule out concomitant choledocholithiasis varies and should be tailored to level of concern based on objective measures, such as laboratory results and imaging findings. Among these modalities, intraoperative cholangiography is associated with reduced length of stay and decreased use of ERCP. However, the benefit of routine intraoperative cholangiography remains in question. Conclusions and Relevance Treatment of GSP is dependent on disease severity, which can be difficult to assess. A comprehensive review of clinically relevant evidence and recommendations on GSP severity grading, fluid resuscitation, timing of cholecystectomy, need for ERCP, and evaluation and management of persistent choledocholithiasis can help guide clinicians in diagnosis and management.
Irritable bowel syndrome: low dose antidepressant improves symptoms
Authors: Helen Saul, Samantha Cassidy, Laura Swaithes, Alexander C Ford
Journal: BMJ (2024)

The study Ford AC, Wright-Hughes A, Alderson SL, et al. Amitriptyline at low-dose and titrated for irritable bowel syndrome as second-line treatment in primary care (ATLANTIS): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet 2023;402:1773-85. To read the full NIHR Alert, go to: https://evidence.nihr.ac.uk/alert/irritable-bowel-syndrome-low-dose-antidepressant-improves-symptoms/
Harnessing TME depicted by histological images to improve cancer prognosis through a deep learning system
Authors: Ruitian Gao, Xin Yuan, Yanran Ma, Ting Wei, Luke Johnston, Yanfei Shao, Wenwen Lv, Tengteng Zhu, Yue Zhang, Junke Zheng, Guoqiang Chen, Jing Sun, Yu Guang Wang, Zhangsheng Yu
Journal: Cell Reports Medicine (2024)

Spatial transcriptomics (ST) provides insights into the tumor microenvironment (TME), which is closely associated with cancer prognosis, but ST has limited clinical availability. In this study, we provide a powerful deep learning system to augment TME information based on histological images for patients without ST data, thereby empowering precise cancer prognosis. The system provides two connections to bridge existing gaps. The first is the integrated graph and image deep learning (IGI-DL) model, which predicts ST expression based on histological images with a 0.171 increase in mean correlation across three cancer types compared with five existing methods. The second connection is the cancer prognosis prediction model, based on TME depicted by spatial gene expression. Our survival model, using graphs with predicted ST features, achieves superior accuracy with a concordance index of 0.747 and 0.725 for The Cancer Genome Atlas breast cancer and colorectal cancer cohorts, outperforming other survival models. For the external Molecular and Cellular Oncology colorectal cancer cohort, our survival model maintains a stable advantage.
Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures
Authors: Venugopalan D. Nair, Hanna Pincas, Gregory R. Smith, Elena Zaslavsky, Yongchao Ge, Mary Anne S. Amper, Mital Vasoya, Maria Chikina, Yifei Sun, Archana Natarajan Raja, Weiguang Mao, Nicole R. Gay, Karyn A. Esser, Kevin S. Smith, Bingqing Zhao, Laurens Wiel, Aditya Singh, Malene E. Lindholm, David Amar, Stephen Montgomery, Michael P. Snyder, Martin J. Walsh, Stuart C. Sealfon, Joshua N. Adkins, Jose Juan Almagro Armenteros, Euan Ashley, Dam Bae, Marcas Bamman, Nasim Bararpour, Alexis Bennett, Bryan C. Bergman, Daniel H. Bessesen, Sue C. Bodine, Thomas W. Buford, Toby L. Chambers, Clarisa Chavez, Tiffany Cortes, Gary Cutter, Sara Espinoza, Facundo M. Fernández, Nicole Gagne, David A. Gaul, Bret H. Goodpaster, Chia-Jui Hung, Bailey E. Jackson, Catherine M. Jankowski, Christopher A. Jin, Wendy M. Kohrt, Kyle S. Kramer, Bridget Lester, Ana K. Lira, Sandy May, Nada Marjanovic, Edward L. Melanson, Samuel G. Moore, Kerrie L. Moreau, Nicolas Musi, Daniel Nachum, German Nudelman, Marco Pahor, Darpan Patel, Paul D. Piehowski, Wei-Jun Qian, Blake B. Rasmussen, Stas Rirak, Jessica L. Rooney, James A. Sanford, Evan M. Savage, Irene E. Schauer, Monica Serra, Cynthia L. Stowe, Anna Thalacker-Mercer, Todd A. Trappe, Scott Trappe, Nikolai G. Vetr, Elena Volpi, Matthew T. Wheeler, Si Wu, Navid Zebarjadi, Jimmy Zhen
Journal: Cell Genomics (2024)

Regular exercise has many physical and brain health benefits, yet the molecular mechanisms mediating exercise effects across tissues remain poorly understood. Here we analyzed 400 high-quality DNA methylation, ATAC-seq, and RNA-seq datasets from eight tissues from control and endurance exercise-trained (EET) rats. Integration of baseline datasets mapped the gene location dependence of epigenetic control features and identified differing regulatory landscapes in each tissue. The transcriptional responses to 8 weeks of EET showed little overlap across tissues and predominantly comprised tissue-type enriched genes. We identified sex differences in the transcriptomic and epigenomic changes induced by EET. However, the sex-biased gene responses were linked to shared signaling pathways. We found that many G protein-coupled receptor-encoding genes are regulated by EET, suggesting a role for these receptors in mediating the molecular adaptations to training across tissues. Our findings provide new insights into the mechanisms underlying EET-induced health benefits across organs.
The Role of Station 10 Lymph Nodes in D2 Dissection
Authors: Emily E. Stroobant, Aravind Sreeram, Vivian E. Strong
Journal: JAMA Surgery (2024)

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Serratus Anterior Plane Blocks for Early Rib Fracture Pain Management
Authors: Christopher Partyka, Stephen Asha, Melanie Berry, Ian Ferguson, Brian Burns, Katerina Tsacalos, Daniel Gaetani, Matthew Oliver, Georgina Luscombe, Anthony Delaney, Kate Curtis
Journal: JAMA Surgery (2024)

Importance Rib fractures secondary to blunt thoracic trauma typically result in severe pain that is notoriously difficult to manage. The serratus anterior plane block (SAPB) is a regional anesthesia technique that provides analgesia to most of the hemithorax; however, SAPB has limited evidence for analgesic benefits in rib fractures. Objective To determine whether the addition of an SAPB to protocolized care bundles increases the likelihood of early favorable analgesic outcomes and reduces opioid requirements in patients with rib fractures. Design, Setting, and Participants This multicenter, open-label, pragmatic randomized clinical trial was conducted at 8 emergency departments across metropolitan and regional New South Wales, Australia, between April 12, 2021, and January 22, 2022. Patients aged 16 years or older with clinically suspected or radiologically proven rib fractures were included in the study. Participants were excluded if they were intubated, transferred for urgent surgical intervention, or had a major concomitant nonthoracic injury. Data were analyzed from September 2022 to July 2023. Interventions Patients were randomly assigned (1:1) to receive an SAPB in addition to usual rib fracture management or standard care alone. Main Outcomes and Measures The primary outcome was a composite pain score measured 4 hours after enrollment. Patients met the primary outcome if they had a pain score reduction of 2 or more points and an absolute pain score of less than 4 out of 10 points. Results A total of 588 patients were screened, of whom 210 patients (median [IQR] age, 71 [55-84] years; 131 [62%] male) were enrolled, with 105 patients randomized to receive an SAPB plus standard care and 105 patients randomized to standard care alone. In the complete-case intention-to-treat primary outcome analysis, the composite pain score outcome was reached in 38 of 92 patients (41%) in the SAPB group and 18 of 92 patients (19.6%) in the control group (relative risk [RR], 0.73; 95% CI, 0.60-0.89; P = .001). There was a clinically significant reduction in overall opioid consumption in the SAPB group compared with the control group (eg, median [IQR] total opioid requirement at 24 hours: 45 [19-118] vs 91 [34-155] milligram morphine equivalents). Rates of pneumonia (6 patients [10%] vs 7 patients [11%]), length of stay (eg, median [IQR] hospital stay, 4.2 [2.2-7.7] vs 5 [3-7.3] days), and 30-day mortality (1 patient [1%] vs 3 patients [4%]) were similar between the SAPB and control groups. Conclusions and Relevance This randomized clinical trial found that the addition of an SAPB to standard rib fracture care significantly increased the proportion of patients who experienced a meaningful reduction in their pain score while also reducing in-hospital opioid requirements. Trial Registration http://anzctr.org.au Identifier: ACTRN12621000040864