tbuckley/cabot-search huggingface dataset:
COVID-19 mRNA Vaccines During Pregnancy
Authors: Elyse O. Kharbanda, Gabriela Vazquez-Benitez
Journal: JAMA (2022)

Deshayne B. Fell, PhD; Tavleen Dhinsa, MSc; Gillian D. Alton, PhD; Eszter Török, PhD; Sheryll Dimanlig-Cruz, MSc; Annette K. Regan, PhD; Ann E. Sprague, PhD; Sarah A. Buchan, PhD; Jeffrey C. Kwong, MD; Sarah E. Wilson, MD; Siri E. Håberg, MD, PhD; Christopher A. Gravel, PhD; Kumanan Wilson, MD; Darine El-Chaâr, MD; Mark C. Walker, MD; Jon Barrett, MD; Shannon E. MacDonald, PhD; Nannette Okun, MD; Prakesh S. Shah, MD; Shelley D. Dougan, MSc; Sandra Dunn, PhD; Lise Bisnaire, PhD
Abstract P1-02-15: Predicting molecular subtypes of breast cancer using
Authors: Chi-Cheng Huang, Nam Nhut Phan, Ling-Ming Tseng
Journal: Cancer Research (2022)

Abstract Purpose: Breast cancer is a heterogeneously complex disease. A number of molecular subtypes with distinct biological features lead to different treatment responses and clinical outcomes. Traditionally, breast cancer is classified into subtypes based on gene expression profiles; these subtypes, namely intrinsic subtypes, include luminal A, luminal B, basal-like and HER2-enriched breast cancer. This molecular taxonomy, however, could only be appraised through transcriptome analyses. We aim to classify breast cancer intrinsic subtypes using un-annotated approach using deep learning models.Methods: 388 pathological whole slide images (WSIs) from TCGA-BRCA dataset were downloaded from TCGA-GDC portal. These WSIs underwent patches generation and normalization using PyHIST tool and Macenko algorithm, respectively. Laplacian algorithm was applied to remove patches with blurry areas and pixelated. The remaining patches (n = 1,833,889) were divided into 3 parts for training (70%), testing (5%) and validation (25%). We applied a 2-step transfer learning with 2 pre-trained models, namely ResNet50, ResNet101, Xception and VGG16, which have been trained on another in-house breast cancer pathological image dataset. Results: these four models shown promising classification results of 4 breast cancer intrinsic subtypes with accuracy ranged from 0.68 (ResNet50 model) to 0.78 (ResNet101 model) in both testing and validation sets. The average AUC score for these models were from 0.88 (ResNet50 model) to 0.94 (ResNet101 model), whereas ResNet101_imgnet with “imagenet” weight archived an accuracy of 0.73 and AUC of 0.92. The overall accuracy of patient-wise prediction even shown a higher average accuracy of 0.914. These models’ prediction visualization was also used to demonstrate that the process of model learning was based on pathological cells’ clusters. Conclusion: Our study demonstrated the feasibility and capability of the deep learning model in classifying breast cancer intrinsic subtypes without region of interest annotation, which wound facilitate the clinical applicability of proposed models. Citation Format: Chi-Cheng Huang, Nam Nhut Phan, Ling-Ming Tseng. Predicting molecular subtypes of breast cancer using [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-02-15.
Cardiovascular Disease Among Patients With AML and CHIP-Related Mutations
Authors: Oscar Calvillo-Argüelles, Alice Schoffel, José-Mario Capo-Chichi, Husam Abdel-Qadir, Andre Schuh, Montserrat Carrillo-Estrada, Shiying Liu, Vikas Gupta, Aaron D. Schimmer, Karen Yee, Liran I. Shlush, Pradeep Natarajan, Paaladinesh Thavendiranathan
Journal: JACC CardioOncology (2022)

Clonal hematopoiesis of indeterminate potential (CHIP) is a novel cardiovascular disease (CVD) risk factor in individuals without acute myeloid leukemia (AML). The aim of this study was to examine the association between mutations associated with CHIP (CHIP-related mutations) identified in patients at AML diagnosis and the risk for cardiovascular events (CVEs). This was a retrospective cohort study of 623 patients with AML treated between 2015 and 2018 who underwent DNA analysis. Cause-specific hazard regression models were used to study the associations between pathogenic mutations in common CHIP-related genes (DNMT3A, TET2, ASXL1, JAK2, TP53, SRSF2, and SF3B1) and the rate of CVEs (heart failure hospitalization, acute coronary syndrome, coronary artery revascularization, ischemic stroke, venous thromboembolism, and CVD death) and between CVE development and all-cause mortality. Patients were 64.6 ± 15.3 years of age, 265 (42.5%) were women, and 63% had at least 1 CHIP-related mutation. Those with CHIP-related mutations were older (69.2 ± 12.3 vs 56.6 ± 16.6 years; P < 0.001) and had a greater prevalence of CVD risk factors and CVD history. In adjusted analysis, the presence of any CHIP-related mutation was associated with a higher rate of CVEs (HR: 1.74; 95% CI: 1.03-2.93; P = 0.037) among intensively treated patients (anthracycline based) but not the whole cohort (HR: 1.26; 95% CI: 0.81-1.97; P = 0.31). TP53 (HR: 4.18; 95% CI: 2.07-8.47; P < 0.001) and ASXL1 (HR: 2.37; 95% CI: 1.21-4.63; P = 0.012) mutations were associated with CVEs among intensively treated patients. Interval development of CVEs was associated with all-cause mortality (HR: 1.99; 95% CI: 1.45-2.73; P < 0.001). Among patients with AML treated with intensive chemotherapy, mutations in CHIP-related genes were associated with an increased risk for developing incident CVEs after AML diagnosis.
CUT&amp;Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells
Authors: Derek H. Janssens, Dominik J. Otto, Michael P. Meers, Manu Setty, Kami Ahmad, Steven Henikoff
Journal: Genome biology (2022)

Abstract Cleavage Under Targets and Tagmentation (CUT&amp;Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells. We describe a modified CUT&amp;Tag protocol using a mixture of an antibody to the initiation form of RNA polymerase II (Pol2 Serine-5 phosphate) and an antibody to repressive Polycomb domains (H3K27me3) followed by computational signal deconvolution to produce high-resolution maps of both the active and repressive regulomes in single cells. The ability to seamlessly map active promoters, enhancers, and repressive regulatory elements using a single workflow provides a complete regulome profiling strategy suitable for high-throughput single-cell platforms.
Epithelial–Mesenchymal Plasticity in Tumor Immune Evasion
Authors: Riley D.Z. Mullins, Ananya Pal, Thomas F. Barrett, Molly E. Heft Neal, Sidharth V. Puram
Journal: Cancer Research (2022)

Epithelial-mesenchymal transition (EMT) is a fundamental process that occurs during embryogenesis and tissue repair. However, EMT can be hijacked by malignant cells, where it may promote immune evasion and metastasis. Classically considered a dichotomous transition, EMT in cancer has recently been considered a plastic process whereby malignant cells display and interconvert among hybrid epithelial/mesenchymal (E/M) states. Epithelial-mesenchymal plasticity (EMP) and associated hybrid E/M states are divergent from classical EMT, with unique immunomodulatory effects. Here, we review recent insights into the EMP-immune cross-talk, highlighting possible mechanisms of immune evasion conferred by hybrid E/M states and roles of immune cells in EMP.
Center for Medicare Director Envisions Holistic Approach to Health Care
Authors: Melissa Suran
Journal: JAMA (2022)

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 HomeNew OnlineCurrent IssueFor Authors 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Single-neuron projectome of mouse prefrontal cortex
Authors: Le Gao, Sang Liu, Lingfeng Gou, Yachuang Hu, Yanhe Liu, Li Deng, Danyi Ma, Haifang Wang, Qiaoqiao Yang, Zhaoqin Chen, Dechen Liu, Shou Qiu, Xiaofei Wang, Danying Wang, Xinran Wang, Biyu Ren, Qingxu Liu, Tianzhi Chen, Xiaoxue Shi, Haishan Yao, Chun Xu, Chengyu T. Li, Yangang Sun, Anan Li, Qingming Luo, Hui Gong, Ninglong Xu, Jun Yan
Journal: Nature Neuroscience (2022)
Electrocardiography Diagnostic Performance in the Assessment of Significant Coronary Artery Disease and its Anatomical site in Comparison with Coronary Angiography among Nigerians: A Pilot Study
Authors: Edafe Emmanuel Auchi, Dodiyi Manue, Sotonye Tamunobelema
Journal: Clinical Cardiology and Cardiovascular Interventions (2022)

Background: Coronary vessel dominance, defined by the coronary artery that supplies the posterior descending artery (PDA) and posterolateral branches, influences the relative contribution of the different coronary arteries to the total left ventricular blood flow. This work aimed to evaluate the prognostic value of coronary arterial dominance post primary PCI, during hospital stay and at 3-month follow-up, which include; cardiac mortality, heart failure, non-fatal myocardial infarction, re-vascularization, stroke/TIA and re-admission for ACS. Methods: This prospective observational study included 100 patients a with STEMI who underwent successful primary percutaneous coronary intervention with TIMI III flow and without procedural complications. Patients were divided into 3 groups according to coronary dominance: Right coronary dominant group (RCD), left coronary dominant group (LCD) and balanced coronary dominant group (BCD). All patients were subjected to transthoracic echocardiogram and coronary angiography and Primary percutaneous coronary intervention. Results: Ticagrelor and clopidogrel during hospital stay and on hospital discharge were significantly used more with RCA group than LCX group and LCX &amp; RCA group (P=0.021, 0.012), (P=0.018, 0.014), respectively. GPIIB/IIIA was significantly more used during hospital stay with RCA group than LCX group and LCX &amp; RCA group(P=0.014). Nitrates was significantly used more on hospital discharge with RCA group than LCX group and LCX &amp; RCA group (P&lt;0.001). Conclusions: Coronary arterial domi¬nance showed significant prognostic value in cases of myocardial Infarction after PCI, heart failure in LCX cases and in revascularization, heart failure, and stroke/TIA cases in RCA. Further, readmission for ACS was the most common outcome in all groups after 3-months follow-up.
ASSOCIATION BETWEEN SOLE E-CIGARETTE USE AND ENDOTHELIAL FUNCTION: THE VAPORSENDOTHELIAL FUNCTION STUDY (VAPORS-E)
Authors: Ngozi Osuji, S.M. Iftekhar Uddin, Olufunmilayo H. Obisesan, Albert Osei, John Erhabor, Ellen Boakye, Andrew P. DeFilippis, Michael Blaha
Journal: Journal of the American College of Cardiology (2022)
17P Driving NK cell immunotherapy against NSCLC, in the context of hypoxia, using tri-specific engagers
Authors: J.S. Miller, M. Felices, D.A. Vallera, B. Ettestad, C. Hallstrom, B. Kodal, D.A. Todhunter, U.S. Arvindam, S.K. Phung, Q. Kile, G. Berk, P.R. Kennedy
Journal: Annals of Oncology (2022)
Surface modification of titanium substrate via combining photothermal therapy and quorum-sensing-inhibition strategy for improving osseointegration and treating biofilm-associated bacterial infection
Authors: Jingwei Hu, Yao Ding, Bailong Tao, Zhang Yuan, Yulu Yang, Kun Xu, Xuan Li, Peng liu, Kaiyong Cai
Journal: Bioactive Materials (2022)
PERIOPERATIVE MANAGEMENT OF ANTICOAGULATION AFTER PULMONARY THROMBOENDARTERECTOMY IN PATIENTS WITH CHRONIC THROMBOEMBOLIC PULMONARY HYPERTENSION - A SINGLE CENTER EXPERIENCE
Authors: Khyati Somayaji, Rohit Maruthi, Yoshi Toyoda, Anjali Vaidya, Paul Forfia, Estefania Oliveros
Journal: Journal of the American College of Cardiology (2022)
PROGRESSION IN VALVULAR HEART DISEASE STAGES OVER SIX YEARS IN LATE-LIFE: THE ATHEROSCLEROSIS RISK IN COMMUNITIES (ARIC) STUDY
Authors: Khaled Shelbaya, Pranav Dorbala, Brian Claggett, Hicham Skali, Scott D. Solomon, Kunihiro Matsushita, Suma H. Konety, Thomas H. Mosley, Amil M. Shah
Journal: Journal of the American College of Cardiology (2022)
ZFP36L2 suppresses mTORc1 through a P53-dependent pathway to prevent peripartum cardiomyopathy in mice
Authors: Hidemichi Kouzu, Yuki Tatekoshi, Hsiang-Chun Chang, Jason S Shapiro, Warren A McGee, Adam De Jesus, Issam Ben-Sahra, Zoltan Arany, Jonathan Leor, Chunlei Chen, Perry J Blackshear, Hossein Ardehali
Journal: Journal of Clinical Investigation (2022)

Pregnancy is associated with substantial physiological changes of the heart, and disruptions in these processes can lead to peripartum cardiomyopathy (PPCM). The molecular processes that cause physiological and pathological changes in the heart during pregnancy are not well characterized. Here, we show that mTORc1 was activated in pregnancy to facilitate cardiac enlargement that was reversed after delivery in mice. mTORc1 activation in pregnancy was negatively regulated by the mRNA-destabilizing protein ZFP36L2 through its degradation of Mdm2 mRNA and P53 stabilization, leading to increased SESN2 and REDD1 expression. This pathway impeded uncontrolled cardiomyocyte hypertrophy during pregnancy, and mice with cardiac-specific Zfp36l2 deletion developed rapid cardiac dysfunction after delivery, while prenatal treatment of these mice with rapamycin improved postpartum cardiac function. Collectively, these data provide what we believe to be a novel pathway for the regulation of mTORc1 through mRNA stabilization of a P53 ubiquitin ligase. This pathway was critical for normal cardiac growth during pregnancy, and its reduction led to PPCM-like adverse remodeling in mice.
LEFT BUNDLE BRANCH AREA PACING IN HIGH-GRADE ATRIOVENTRICULAR BLOCK DUE TO LMNA MUTATION: A NOVEL STRATEGY IN PROGRESSIVE CARDIAC CONDUCTION DISEASE
Authors: Songyun Chu, Qin-Hui Sheng, Yu-Ling Wang, Yu-Long Xia, Chun-Yan Wang, Ying Yang, Jing Zhou
Journal: Journal of the American College of Cardiology (2022)
Late Recurrence Following Early Breast Cancer
Authors: Alexandra Thomas, Heather A. Parsons, Karen Lisa Smith
Journal: Journal of Clinical Oncology (2022)

The Oncology Grand Rounds series is designed to place original reports published in the Journal into clinical context. A case presentation is followed by a description of diagnostic and management challenges, a review of the relevant literature, and a summary of the authors' suggested management approaches. The goal of this series is to help readers better understand how to apply the results of key studies, including those published in the Journal of Clinical Oncology, to patients seen in their own clinical practice.
IMPACT OF SEX ON IN-HOSPITAL MORTALITY AND READMISSION RATES IN PATIENTS UNDERGOING TRANSCATHETER MITRAL VALVE REPLACEMENT (TMVR): A NATIONAL READMISSION DATABASE STUDY
Authors: Mahmoud Ismayl, Akshay Machanahalli Balakrishna, Abhishek Thandra, Fang Niu, Gauravpal S. Gill, Himanshu Agarwal, Ahmed Salah Ahmed Aboeata, Aiman Miloud Smer
Journal: Journal of the American College of Cardiology (2022)
3P Targeting pancreatic adenocarcinoma upregulated factor (PAUF) to treat pancreatic cancer (PC): In vivo efficacy and safety of PBP1510, a first in class monoclonal antibody (mAb)
Authors: S. Pradhan, Y.J. Kim, J. Park, S-Y. Jeong, S.S. Koh, K.D. Mandakhalikar, J. Kim, L. Jaison
Journal: Annals of Oncology (2022)
Decoding the diversity of killer immunoglobulin-like receptors by deep sequencing and a high-resolution imputation method
Authors: Saori Sakaue, Kazuyoshi Hosomichi, Jun Hirata, Hirofumi Nakaoka, Keiko Yamazaki, Makoto Yawata, Nobuyo Yawata, Tatsuhiko Naito, Junji Umeno, Takaaki Kawaguchi, Toshiyuki Matsui, Satoshi Motoya, Yasuo Suzuki, Hidetoshi Inoko, Atsushi Tajima, Takayuki Morisaki, Koichi Matsuda, Yoichiro Kamatani, Kazuhiko Yamamoto, Ituro Inoue, Yukinori Okada
Journal: Cell Genomics (2022)

The killer cell immunoglobulin-like receptor (KIR) recognizes human leukocyte antigen (HLA) class I molecules and modulates the function of natural killer cells. Despite its role in immunity, the complex genomic structure has limited a deep understanding of the KIR genomic landscape. Here we conduct deep sequencing of 16 KIR genes in 1,173 individuals. We devise a bioinformatics pipeline incorporating copy number estimation and insertion or deletion (indel) calling for high-resolution KIR genotyping. We define 118 alleles in 13 genes and demonstrate a linkage disequilibrium structure within and across KIR centromeric and telomeric regions. We construct a KIR imputation reference panel (nreference = 689, imputation accuracy = 99.7%), apply it to biobank genotype (ntotal = 169,907), and perform phenome-wide association studies of 85 traits. We observe a dearth of genome-wide significant associations, even in immune traits implicated previously to be associated with KIR (the smallest p = 1.5 × 10−4). Our pipeline presents a broadly applicable framework to evaluate innate immunity in large-scale datasets.
Correction to: Fresh and cryopreserved ovarian tissue transplantation for preserving reproductive and endocrine function: a systematic review and individual patient data meta-analysis
Authors: Hajra Khattak, Rosamund Malhas, Laurentiu Craciunas, Yousri Afifi, Christiani A Amorim, Simon Fishel, Sherman Silber, Debra Gook, Isabelle Demeestere, Olga Bystrova, Alla Lisyanskaya, Georgy Manikhas, Laura Lotz, Ralf Dittrich, Lotte Berdiin Colmorn, Kirsten Tryde Macklon, Ina Marie Dueholm Hjorth, Stine Gry Kristensen, Ioannis Gallos, Arri Coomarasamy
Journal: Human Reproduction Update (2022)

Hum Reprod Update, https://doi.org/10.1093/humupd/dmac003 Oxford University Press would like to apologies for errors in the annotation of authors' affiliations in the above article. The errors occurred during revision of the article proofs. The error does not affect any results, conclusions or other content of the article. The electronic version of the article has been updated at https://doi.org/10.1093/humupd/dmac003.
Neuropsychiatric and Cognitive Outcomes in Patients 6 Months After COVID-19 Requiring Hospitalization Compared With Matched Control Patients Hospitalized for Non–COVID-19 Illness
Authors: Vardan Nersesjan, Lise Fonsmark, Rune H. B. Christensen, Moshgan Amiri, Charlotte Merie, Anne-Mette Lebech, Terese Katzenstein, Lia E. Bang, Jesper Kjærgaard, Daniel Kondziella, Michael E. Benros
Journal: JAMA Psychiatry (2022)

Prolonged neuropsychiatric and cognitive symptoms are increasingly reported in patients after COVID-19, but studies with well-matched controls are lacking.To investigate cognitive impairment, neuropsychiatric diagnoses, and symptoms in survivors of COVID-19 compared with patients hospitalized for non-COVID-19 illness.This prospective case-control study from a tertiary referral hospital in Copenhagen, Denmark, conducted between July 2020 and July 2021, followed up hospitalized COVID-19 survivors and control patients hospitalized for non-COVID-19 illness, matched for age, sex, and intensive care unit (ICU) status 6 months after symptom onset.Hospitalization for COVID-19.Participants were investigated with the Mini-International Neuropsychiatric Interview, the Montreal Cognitive Assessment (MoCA), neurologic examination, and a semi-structured interview for subjective symptoms. Primary outcomes were total MoCA score and new onset of International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (ICD-10) psychiatric diagnoses. Secondary outcomes included specific psychiatric diagnoses, subjective symptoms, and neurologic examination results. All outcomes were adjusted for age, sex, ICU admission, admission length, and days of follow-up. Secondary outcomes were adjusted for multiple testing.A total of 85 COVID-19 survivors (36 [42%] women; mean [SD] age 56.8 [14] years) after hospitalization and 61 matched control patients with non-COVID-19 illness (27 [44%] women, mean age 59.4 years [SD, 13]) were enrolled. Cognitive status measured by total geometric mean MoCA scores at 6-month follow-up was lower (P = .01) among COVID-19 survivors (26.7; 95% CI, 26.2-27.1) than control patients (27.5; 95% CI, 27.0-27.9). The cognitive status improved substantially (P = .004), from 19.2 (95% CI, 15.2-23.2) at discharge to 26.1 (95% CI, 23.1-29.1) for 15 patients with COVID-19 with MoCA evaluations from hospital discharge. A total of 16 of 85 patients with COVID-19 (19%) and 12 of 61 control patients (20%) had a new-onset psychiatric diagnosis at 6-month follow-up, which was not significantly different (odds ratio, 0.93; 95% CI, 0.39-2.27; P = .87). In fully adjusted models, secondary outcomes were not significantly different, except anosmia, which was more common after COVID-19 (odds ratio, 4.56; 95% CI, 1.52-17.42; P = .006); but no longer when adjusting for multiple testing.In this prospective case-control study, cognitive status at 6 months was worse among survivors of COVID-19, but the overall burden of neuropsychiatric and neurologic signs and symptoms among survivors of COVID-19 requiring hospitalization was comparable with the burden observed among matched survivors hospitalized for non-COVID-19 causes.
BREAST ARTERIAL CALCIFICATION ON SCREENING MAMMOGRAPHY PREDICTS INCIDENT CORONARY ARTERY DISEASE EVENTS
Authors: Vinay Goel, William Cameron, Ella Spear, Udit Thakur, Nushrat Sultana, Jasmine Chan, Sean Tan, Yeong Chee Cheen, Adam J. Brown, Stephen J. Nicholls, Thomas H. Marwick, Nitesh Nerlekar
Journal: Journal of the American College of Cardiology (2022)