tbuckley/cabot-search huggingface dataset:
Abstract PO-008: Federated learning on whole slide images using weakly supervised computational pathology
Authors: Ming Yang Lu, Dehan Kong, Jana Lipkova, Richard J. Chen, Rajendra Singh, Tiffany Y. Chen, Drew F. K. Williamson, Faisal Mahmood
Journal: Clinical Cancer Research (2021)

Abstract Deep learning has excelled in a wide range of tasks in computational pathology, including but not limited to the characterization of both common and rare morphological phenotypes and the prediction of molecular alterations from histology. However, large datasets of diverse, high-quality annotated training examples are often necessary in order to build robust and accurate deep learning-based models for real-world test scenarios. Pooling medical data from multiple institutions can alleviate this challenge but is constrained by privacy concerns associated with sharing sensitive patient information, in addition to the technical challenges of transferring and storing large whole slide image files at the terabyte or even petabyte scale. On the other hand, federated learning is a promising field of machine learning research that allows algorithms to learn from multiple decentralized data sources without requiring training data to be directly shared. We introduce a federated learning framework for computational pathology on whole slide images using attention-based multiple instance learning for weakly-supervised learning and random noise generation for preserving differential privacy. We evaluated our approach on two different classification problems using large multi-centric datasets, including renal cell carcinoma (RCC) histologic subtyping and invasive breast carcinoma (BRCA) histologic subtyping. We additionally demonstrate that our approach can be used for survival prediction and patient stratification from whole slide images. Our proposed privacy-preserving federated learning framework can be used to develop accurate, interpretable deep learning models from distributed data sources for both classification and survival prediction. Citation Format: Ming Yang Lu, Dehan Kong, Jana Lipkova, Richard J. Chen, Rajendra Singh, Tiffany Y. Chen, Drew F. K. Williamson, Faisal Mahmood. Federated learning on whole slide images using weakly supervised computational pathology [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-008.
Lung Cancer in the Netherlands
Authors: Lizza E.L. Hendriks, Anne-Marie C. Dingemans, Dirk K.M. De Ruysscher, Mieke J. Aarts, Lidia Barberio, Robin Cornelissen, Koen J. Hartemink, Michel van den Heuvel, Ed Schuuring, Hans J.M. Smit, Antonie J. van der Wekken, Egbert F. Smit
Journal: Journal of Thoracic Oncology (2021)
Resilience of the oral microbiome
Authors: William G. Wade
Journal: Periodontology 2000 (2021)

Abstract The human mouth harbors a complex microbiota, the composition of which is potentially influenced by a wide range of factors, including the intake of food and drink, the availability of endogenous nutrients, the host immune system, drug treatments, and systemic diseases. Despite these possible influences, the oral microbiota is remarkably resilient, particularly in comparison with the microbiota of the large intestine. Diet, with the exception of excessive and/or frequent consumption of fermentable carbohydrate or supplementation with nitrate, has minimal impact on the composition of the oral bacterial community. The common oral diseases dental caries and the periodontal diseases is associated with modification of the oral microbiota primarily as a result of the ecological changes induced by excessive acid production and inflammation, respectively. Systemically‐administered antimicrobials have only a small effect on the composition of the oral bacterial community, and while locally delivered antimicrobials can have some clinical benefits, the biofilm lifestyle of oral bacteria lends them substantial resistance to the agents used. Saliva plays an important role in oral microbial ecology, by supplying nutrients and providing protection against colonization by nonoral organisms. Dry mouth is one condition that has a major effect on the microbiota, resulting in increased colonization by opportunistic pathogens. Some systemic diseases do affect the oral microbiome, notably diabetes, in which raised levels of glucose in saliva and tissue impact on bacterial nutrition.
The dental plaque biofilm matrix
Authors: Nicholas S. Jakubovics, Steven D. Goodman, Lauren Mashburn‐Warren, Graham P. Stafford, Fabian Cieplik
Journal: Periodontology 2000 (2021)

Abstract The extracellular matrix is a critical component of microbial biofilms, such as dental plaque, maintaining the spatial arrangement of cells and coordinating cellular functions throughout the structure. The extracellular polymeric substances that comprise the matrix include carbohydrates, nucleic acids, proteins, and lipids, which are frequently organized into macromolecular complexes and/or are associated with the surfaces of microbial cells within the biofilm. Cariogenic dental plaque is rich in glucan and fructan polysaccharides derived from extracellular microbial metabolism of dietary sucrose. By contrast, the matrix of subgingival dental plaque is a complex mixture of macromolecules that is still not well understood. Components of the matrix escape from microbial cells during lysis by active secretion or through the shedding of vesicles and serve to anchor microbial cells to the tooth surface. By maintaining the biofilm in close association with host tissues, the matrix facilitates interactions between microorganisms and the host. The outcome of these interactions may be the maintenance of health or the development of dental disease, such as caries or periodontitis. The matrix affords microbial cells protection against chemical and physical insults and hinders the eradication of pathogenic dental plaque. Therefore, strategies to control the matrix are critical to maintain oral health. This review discusses recent advances in our understanding of the composition, origins, and function of the dental plaque matrix, with a focus on subgingival dental plaque. New strategies to control subgingival dental plaque based on targeting the biofilm matrix are also considered.
Acquisition and establishment of the oral microbiota
Authors: A. M. (Marije) Kaan, Dono Kahharova, Egija Zaura
Journal: Periodontology 2000 (2021)

Abstract Acquisition and establishment of the oral microbiota occur in a dynamic process over various stages and involve close and continuous interactions with the host and its environment. In the present review, we discuss the stages of this process in chronological order. We start with the prenatal period and address the following questions: ‘Is the fetus exposed to maternal microbiota during pregnancy?’ and ‘If so, what is the potential role of this exposure?’ We comment on recent reports of finding bacterial DNA in placenta during pregnancies, and provide current views on the potential functions of prenatal microbial encounters. Next, we discuss the physiological adaptations that take place in the newborn during the birth process and the effect of this phase of life on the acquisition of the oral microbiota. Is it really just exposure to maternal vaginal microbes that results in the difference between vaginally and Cesarian section‐born infants? Then, we review the postnatal phase, in which we focus on transmission of microbes, the intraoral niche specificity, the effects of the host behavior and environment, as well as the role of genetic background of the host on shaping the oral microbial ecosystem. We discuss the changes in oral microbiota during the transition from deciduous to permanent dentition and during puberty. We also address the finite knowledge on colonization of the oral cavity by microbes other than the bacterial component. Finally, we identify the main outstanding questions that limit our understanding of the acquisition and establishment of a healthy microbiome at an individual level.
Association of the clinical cell-cycle risk score with metastasis after radiation therapy and identification of men with prostate cancer who can forgo combined androgen deprivation therapy.
Authors: Jonathan David Tward, Constantine Mantz, Neal D. Shore, Paul Nguyen, Isla Garraway, Carl A Olsson, Steve Pai-hsun Lee, Arthur Hung, R Jonathan Henderson, Stanley L. Liauw, David Raben, Michael D. Fabrizio, Daniel R. Saltzstein, Paul Yonover, Hiram Alberto Gay, Daniel Joseph Albertson, Tatjana Antic, Lauren Lenz, Steven Stone, Todd Cohen
Journal: Journal of Clinical Oncology (2021)

195 Background: This study evaluated the ability of the combined clinical cell-cycle risk score (CCR) to prognosticate the risk of prostate cancer metastasis in men receiving dose-escalated radiation therapy (RT) with or without androgen deprivation therapy (ADT). Methods: The CCR score is a validated model that combines the cell cycle progression score (CCP) with the UCSF Cancer of the Prostate Risk Assessment score (CAPRA). The CCR score and a CCR-based multimodality threshold score (2.112) were evaluated in a retrospective, multi-institutional cohort of men with National Comprehensive Cancer Center (NCCN) intermediate- or high-risk localized disease (N = 741) who received single (RT) or multimodality therapy (ADT with RT). Effects of prognostic variables were analyzed using Kaplan-Meier and Cox regression methods. Results: Median follow-up was 5.9 years. CCR predicted metastasis [hazard ratio (HR) 2.21, 95% Confidence Interval (CI) 1.70-2.87, p &lt; 0.001]. The CCR score was a better prognosticator of metastasis (C-index 0.78) than either NCCN-risk group (C-index 0.70), CAPRA score (C-index 0.71), or CCP score (C-index 0.69) alone. In bivariate analyses, the CCR score remained highly prognostic for metastasis when comparing any ADT vs none (HR 2.19, 95% CI 1.62 to 2.97, p &lt; 0.001), ADT duration as a continuous variable (HR 2.05, 95% CI 1.54-2.72, p &lt; 0.001), or ADT use given as less than or at the recommended duration for each NCCN risk group (HR 2.22, 95% CI 1.71-2.88, p &lt; 0.001). Men with CCR scores either below or above the threshold (2.112) had a 10-year risk of metastasis of 4.2% and 25.3%, respectively. For men below the threshold receiving RT alone versus RT+ADT, the 10-year risk of metastasis was 4.2% and 3.9%, respectively. Conclusions: CCR is a highly precise and accurate predictor of metastasis in men undergoing dose-escalated RT, with or without ADT. CCR adds clinically actionable information relative to guideline recommended therapies that are based on NCCN risk groups or CAPRA alone. Men with scores below the multimodality threshold may not significantly reduce their 10-year risk of metastasis with the addition of ADT.
Abstract 15962: Physical Activity and Mortality Among Male Survivors of Myocardial Infarction
Authors: Laila Al-Shaar, Yanping Li, Eric B Rimm, Joann E Manson, Rosner Bernard, Frank Hu, Meir J Stampfer, Walter Willett
Journal: Circulation (2019)

Introduction: An inverse association between physical activity (PA) and risk of coronary heart disease has been seen in many studies, but evidence for benefits of PA after myocardial infarction (MI...
Rightsizing Treatment for Pneumonia in Children
Authors: Sharon V. Tsay, Adam L. Hersh, Katherine E. Fleming-Dutra
Journal: JAMA Pediatrics (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
Response to: ‘Correspondence on ‘Factors associated with COVID-19-related death in people with rheumatic diseases: results from the COVID-19 Global Rheumatology Alliance physician reported registry’’ by Mulhearn<i>et al</i>
Authors: Martin Schäfer, Anja Strangfeld, Kimme L Hyrich, Loreto Carmona, Milena Gianfrancesco, Saskia Lawson-Tovey, Elsa F Mateus, Laure Gossec, Philip C Robinson, Jinoos Yazdany, Pedro M Machado
Journal: Annals of the Rheumatic Diseases (2021)

undertreatment and development of GC-related adverse events (ie, give the GC for the shortest period of time and keep the dose as low as the level sufficient in order to achieve the required therapeutic effect in each individual patient). 5Finally, it should also be noted that patients on long-term GC therapy are at risk of GC-induced adrenal suppression and may therefore require GC supplementation in the context of major trauma, surgery or significant intercurrent infection, including COVID-19.
Phase II Study of the WEE1 Inhibitor Adavosertib in Recurrent Uterine Serous Carcinoma
Authors: Joyce F. Liu, Niya Xiong, Susana M. Campos, Alexi A. Wright, Carolyn Krasner, Susan Schumer, Neil Horowitz, Jennifer Veneris, Nabihah Tayob, Stephanie Morrissey, Gabriela West, Roxanne Quinn, Ursula A. Matulonis, Panagiotis A. Konstantinopoulos
Journal: Journal of Clinical Oncology (2021)

Uterine serous carcinoma (USC) is a distinct histologic subtype of endometrial cancer, with molecular characteristics suggesting frequent cell-cycle dysregulation paired with a high level of oncogene-driven replication stress. Adavosertib is a potent and selective oral inhibitor of the WEE1 kinase, a key regulator of the G2/M and S phase cell-cycle checkpoints. Because cells with impaired cell-cycle regulation and high replication stress may be vulnerable to WEE1 inhibition, we conducted this study to assess the activity of adavosertib monotherapy in women with recurrent USC.This was a single-arm two-stage phase II study with coprimary end points of objective response rate (ORR) and rate of progression-free survival at 6 months (PFS6). Women with recurrent USC were treated with adavosertib monotherapy at a starting dose of 300 mg orally once daily days 1 through 5 and 8 through 12 of a 21-day cycle until disease progression.In 34 evaluable patients, 10 total responses (one confirmed complete response, eight confirmed partial responses, and one unconfirmed partial response) were observed with adavosertib monotherapy, for an ORR of 29.4% (95% CI, 15.1 to 47.5). Sixteen patients were progression-free at 6 months, for a PFS6 rate of 47.1% (95% CI, 29.8 to 64.9). Median PFS was 6.1 months, and median duration of response was 9.0 months. Frequent treatment-related adverse events (AEs) included diarrhea (76.5%), fatigue (64.7%), nausea (61.8%), and hematologic AEs. No clear correlation of clinical activity with specific molecular alterations was observed in an exploratory biomarker analysis.Adavosertib monotherapy demonstrated encouraging and durable evidence of activity in women with USC, and further investigation of this agent in this cancer and biomarkers of activity are indicated.
Radiation Exposure From Cardiac Imaging Procedures: Do the Risks Outweigh the Benefits?⁎⁎Editorials published in the Journal of the American College of Cardiologyreflect the views of the authors and do not necessarily represent the views of JACCor the American College of Cardiology.
Authors: Matthew J. Budoff, Mohit Gupta
Journal: Journal of the American College of Cardiology (2010)
<i>APOE4</i> disrupts intracellular lipid homeostasis in human iPSC-derived glia
Authors: Grzegorz Sienski, Priyanka Narayan, Julia Maeve Bonner, Nora Kory, Sebastian Boland, Aleksandra A. Arczewska, William T. Ralvenius, Leyla Akay, Elana Lockshin, Liang He, Blerta Milo, Agnese Graziosi, Valeriya Baru, Caroline A. Lewis, Manolis Kellis, David M. Sabatini, Li-Huei Tsai, Susan Lindquist
Journal: Science Translational Medicine (2021)

The
Case 7-2021: A 19-Year-Old Man with Shock, Multiple Organ Failure, and Rash
Authors: Pavan K. Bendapudi, Michael J. Whalen, Manuella Lahoud-Rahme, Julian A. Villalba
Journal: New England Journal of Medicine (2021)

A 19-year-old man was admitted to the pediatric ICU because of shock, multiple organ failure, and rash. Twenty hours before admission, abdominal pain and nausea developed after he ate leftovers from a restaurant meal. Five hours before admission, purplish discoloration of the skin developed. Management decisions were made.
Abstract 19992: Left Ventricular Entropy and Scar Mass Predict Appropriate Device Therapy and End-Stage Heart Failure Outcome in Non-Ischemic Cardiomyopathy Patients Undergoing Primary Prevention Defibrillator
Authors: Rahul G Muthalaly, Raymond Y Kwong, Roy M John, William G Stevenson, Usha B Tedrow, Laurence M Epstein, Shinichi Tanigawa, Benjamin Schaeffer, Tomofumi Nakamura, Bruce A Koplan
Journal: Circulation (2017)

Introduction: Risk stratification in non ischemic cardiomyopathy (NICM) is imperfect. Late gadolinium enhancement (LGE) on cardiac magnetic resonance imaging (CMR) predicts arrhythmia events and en...
CAR T cells targeting CD13 controllably induce eradication of acute myeloid leukemia with a single domain antibody switch
Authors: Xin He, Zijie Feng, Jian Ma, Xuyao Zhang, Sunbin Ling, Yan Cao, Bowen Xing, Yuan Wu, Lei Wang, Bryson W. Katona, Carl H. June, Xianxin Hua
Journal: Leukemia (2021)
In Vivo Quantification of Nanoparticle Association with Immune Cell Subsets in Blood
Authors: Yih Rue Ong, Robert De Rose, Angus P. R. Johnston
Journal: Advanced Healthcare Materials (2021)

Abstract Nanoparticles offer great promise for more effective drug delivery. However, their particulate nature typically results in rapid systemic clearance by immune cells in blood. Currently, to understand these interactions, nanoparticle association is probed ex vivo with whole blood. While ex vivo assays give important information about the relative cell association, they do not consider changes in immune cell homeostasis or the complex mixing behavior that occurs in vivo. To address this, a nanoparticle in vivo immune‐cell association assay is developed to study the in vivo association of unmodified and poly(ethylene glycol) modified liposomes with immune cells, and compared this to the ex vivo association in static whole blood. In vivo, it is observed that neutrophils play a significantly greater role in nanoparticle binding than suggested by ex vivo assays. The increased influence of neutrophils in vivo is largely due to a significant increase in number of circulating neutrophils after intravenous injection. Conversely, the number of circulating monocytes significantly decreased after intravenous injection, leading to significantly less total association of liposomes to monocytes compared to ex vivo. This novel in vivo immune cell binding assay sheds new light on the fate of nanoparticles following intravenous delivery.
Use and Performance of the STOP-Bang Questionnaire for Obstructive Sleep Apnea Screening Across Geographic Regions
Authors: Bianca Pivetta, Lina Chen, Mahesh Nagappa, Aparna Saripella, Rida Waseem, Marina Englesakis, Frances Chung
Journal: JAMA Network Open (2021)

Obstructive sleep apnea (OSA) is a highly prevalent global health concern and is associated with many adverse outcomes for patients.To evaluate the utility of the STOP-Bang (snoring, tiredness, observed apnea, blood pressure, body mass index, age, neck size, gender) questionnaire in the sleep clinic setting to screen for and stratify the risk of OSA among populations from different geographical regions.MEDLINE, MEDLINE In-process, Embase, EmCare Nursing, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, PsycINFO, Journals@Ovid, Web of Science, Scopus, and CINAHL electronic databases were systematically searched from January 2008 to March 2020. This was done to identify studies that used the STOP-Bang questionnaire and polysomnography testing in adults referred to sleep clinics.Clinical and demographic data were extracted from each article independently by 2 reviewers. The combined test characteristics were calculated using 2 × 2 contingency tables. Random-effects meta-analyses and metaregression with sensitivity analyses were performed. The Preferred Reporting Items for Systematic Review and Meta-analyses (PRISMA) guideline was followed.The combined test characteristics and area under summary receiver operating characteristic curves (AUCs) were used to compare STOP-Bang questionnaire accuracy with polysomnography testing.A total of 47 studies with 26 547 participants (mean [SD] age, 50 [5] years; mean [SD] body mass index, 32 [3]; 16 780 [65%] men) met the criteria for the systematic review. Studies were organized in different geographic regional groups: North America, South America, Europe, Middle East, East Asia, and South or Southeast Asia. The prevalence rates for all OSA, moderate to severe OSA, and severe OSA were 80% (95% CI, 80%-81%), 58% (95% CI, 58%-59%), and 39% (95% CI, 38%-39%), respectively. A STOP-Bang score of at least 3 had excellent sensitivity (>90%) and high discriminative power to exclude moderate to severe and severe OSA, with negative predictive values of 77% (95% CI, 75%-78%) and 91% (95% CI, 90%-92%), respectively. The diagnostic accuracy of a STOP-Bang score of at least 3 to detect moderate to severe OSA was high (>0.80) in all regions except East Asia (0.52; 95% CI, 0.48-0.56).The results of this meta-analysis suggest that the STOP-Bang questionnaire can be used as a screening tool to assist in triaging patients with suspected OSA referred to sleep clinics in different global regions.