tbuckley/cabot-search huggingface dataset:
In Situ implantable, post-trauma microenvironment-responsive, ROS Depletion Hydrogels for the treatment of Traumatic brain injury
Authors: Feng Qian, Yuhan Han, Zhengzhong Han, Deyun Zhang, Long Zhang, Gang Zhao, Shanshan Li, Guoliang Jin, Rutong Yu, Hongmei Liu
Journal: Biomaterials (2021)
Estimates From Heterogeneous Studies of Opioid-Related Morbidity
Authors: Kao-Ping Chua, Chad M. Brummett, Amy Bohnert
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
Psychiatric Social Work
Journal: JAMA (1941)

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
Profiling Chromatin Accessibility at Single-Cell Resolution
Authors: Sarthak Sinha, Ansuman T. Satpathy, Weiqiang Zhou, Hongkai Ji, Jo A. Stratton, Arzina Jaffer, Nizar Bahlis, Sorana Morrissy, Jeff A. Biernaskie
Journal: Genomics Proteomics & Bioinformatics (2021)

Abstract How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity, and enable complex fate decisions are important open questions. One key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. Genome-wide chromatin accessibility measurements can impart insights into regulatory sequences (in)accessible to DNA-binding proteins at a single-cell resolution. This review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in a scalable fashion. It also covers joint profiling of chromatin with transcriptome/proteome measurements, computational strategies to integrate multi-omic measurements, and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic datasets. Methodological refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.
Epigenetic Remodeling in Innate Immunity and Inflammation
Authors: Qian Zhang, Xuetao Cao
Journal: Annual Review of Immunology (2021)

The innate immune response is a rapid response to pathogens or danger signals. It is precisely activated not only to efficiently eliminate pathogens but also to avoid excessive inflammation and tissue damage. cis-Regulatory element-associated chromatin architecture shaped by epigenetic factors, which we define as the epiregulome, endows innate immune cells with specialized phenotypes and unique functions by establishing cell-specific gene expression patterns, and it also contributes to resolution of the inflammatory response. In this review, we focus on two aspects: (a) how niche signals during lineage commitment or following infection and pathogenic stress program epiregulomes by regulating gene expression levels, enzymatic activities, or gene-specific targeting of chromatin modifiers and (b) how the programed epiregulomes in turn mediate regulation of gene-specific expression, which contributes to controlling the development of innate cells, or the response to infection and inflammation, in a timely manner. We also discuss the effects of innate immunometabolic rewiring on epiregulomes and speculate on several future challenges to be encountered during the exploration of the master regulators of epiregulomes in innate immunity and inflammation.
What Did We Learn from the Molecular Biology of Adrenal Cortical Neoplasia? From Histopathology to Translational Genomics
Authors: C. Christofer Juhlin, Jérôme Bertherat, Thomas J. Giordano, Gary D. Hammer, Hironobu Sasano, Ozgur Mete
Journal: Endocrine Pathology (2021)
Advances in peptide-mediated cytosolic delivery of proteins
Authors: Macarena Sánchez-Navarro
Journal: Advanced Drug Delivery Reviews (2021)

The number of protein-based drugs is exponentially increasing. However, development of protein therapeutics against intracellular targets is hampered by the lack of efficient cytosolic delivery strategies. In recent years, the use of cell-penetrating peptides has been proposed as a strategy to promote protein internalization. In this article, we provide the reader with a succinct update on the strategies exploited to enable peptide-mediated cytosolic delivery of proteins. First, we analyse the various methods available for delivery. We then describe the most popular and the in vitro assays designed to assess the intracellular distribution of protein cargo.
Efficacy and Safety of Tezepelumab in Adults and Adolescents with Severe, Uncontrolled Asthma: Results from the Phase 3 NAVIGATOR Study
Authors: Andrew Menzies-Gow, Jonathan Corren, Arnaud Bourdin, Geoffrey Chupp, Elliot Israel, Janet Griffiths, Åsa Hellqvist, Karin Bowen, Primal Kaur, Gun Almqvist, Sandhia Ponnarambil, Gene Colice
Journal: Journal of Allergy and Clinical Immunology (2021)
Cistanches Herba, from an endangered species to a big brand of Chinese medicine
Authors: Yuelin Song, Kewu Zeng, Yong Jiang, Pengfei Tu
Journal: Medicinal Research Reviews (2021)

Abstract Cistanches Herba (CH, Chinese name: Roucongrong ), is a very precious, tonic Chinese medicine. Cistanche deserticola and Cistanche tubulosa are the two commonly used species and authenticated in Chinese Pharmacopoeia. Due to the parasitic nature of Cistanche plants, the wild source was once endangered and listed in the Appendix II of Convention on International Trade in Endangered Species of Wild Fauna and Flora. However, after continuously struggling in the past decades, CH has grown up to a big brand of Chinese medicine featured with the cultivation area as 1.26 million mu, the annual output as 6000 tons, and the related industrial output value as more than 20 billion China Yuan, attributing to large‐scale cultivation and in‐depth phytochemical and pharmacological investigations. Noteworthily, great achievements have reached concerning the research and development of relevant products, such as modern drugs, traditional Chinese medicine prescriptions, and dietary supplements. The current review summarizes the research progresses concerning the distribution and cultivation, phytochemistry, pharmacology, metabolism and product development of CH in the past decades, and the emerging challenges and developing prospects are discussed as well.
m<sup>6</sup>A modification patterns and tumor immune landscape in clear cell renal carcinoma
Authors: Jiehui Zhong, Zezhen Liu, Chao Cai, Xiaolu Duan, Tuo Deng, Guohua Zeng
Journal: Journal for ImmunoTherapy of Cancer (2021)

Background Recent studies have focused on the correlation between N6-methyladenosine (m 6 A) modification and specific tumor-infiltrating immune cells. However, the potential roles of m 6 A modification in the tumor immune landscape remain elusive. Methods We comprehensively evaluated the m 6 A modification patterns and tumor immune landscape of 513 clear cell renal cell carcinoma (ccRCC) patients, and correlated the m 6 A modification patterns with the immune landscape. The m6Ascore was established using principal component analysis. Multivariate Cox regression analysis was performed to evaluate the prognostic value of the m6Ascore. Results We identified three m6Aclusters—characterized by differences in Th17 signature, extent of intratumor heterogeneity, overall cell proliferation, aneuploidy, expression of immunomodulatory genes, overall somatic copy number alterations, and prognosis. The m6Ascore was established to quantify the m 6 A modification pattern of individual ccRCC patients. Further analyses revealed that the m6Ascore was an independent prognostic factor of ccRCC. Finally, we verified the prognostic value of the m6Ascore in the programmed cell death protein 1 (PD-1) blockade therapy of patients with advanced ccRCC. Conclusions This study demonstrated the correlation between m 6 A modification and the tumor immune landscape in ccRCC. The comprehensive evaluation of m 6 A modification patterns in individual ccRCC patients enhances our understanding of the tumor immune landscape and provides a new approach toward new and improved immunotherapeutic strategies for ccRCC patients.
Abstract PO014: Clinicopathologic evaluation of <i>CTNNB1</i> gene mutations in high-intermediate risk endometrial cancer
Authors: Jennifer G. Haag, Rebecca J. Wolsky, Marisa R. Moroney, Jamie Sheren, Jeanelle Sheeder, Benjamin G. Bitler, Bradley R. Corr
Journal: Clinical Cancer Research (2021)

Abstract Background: CTNNB1 mutations convey increased risk of recurrence in low risk endometrioid endometrial cancers. However, sub-analyses of high-intermediate risk (HIR) endometrioid endometrial cancers in other cohorts have not demonstrated a clearly increased recurrence risk and have often been equivocal. The objective of this study is to perform a clinicopathologic evaluation of patients with HIR endometrioid endometrial cancer in relation to CTNNB1 mutational status. Methods: A single-institution chart review of patients diagnosed with endometrioid endometrial cancer between 2006 and 2018 was undertaken. Patients were classified as HIR according to GOG249 criteria. Mutational status was determined by Sanger sequencing of exon 3 of the CTNNB1 gene in primary tumor specimens. Immunohistochemical (IHC) analysis of B-catenin was performed to evaluate for the presence of nuclear staining. Factors associated with recurrence were assessed by logistic regression; recurrence-free (RFS) and overall survival (OS) were assessed by Kaplan-Meier survival analysis. Results: 93 cases of HIR endometrioid endometrial cancer were identified, of which 23 (24.7%) were CTNNB1 mutant and 70 (75.3%) were wild type. Median follow-up was 54.7 months. Recurrence occurred in 14/93 (15.1%) patients. Recurrence rates were not significantly different between patients with CTNNB1 mutant and wild type tumors (13.0% vs. 15.9%, p=0.76). In both univariable and multivariable analyses, RFS and OS were not significantly different (RFS HR 0.88, p=0.85, 95% CI 0.24 – 3.17; OS HR 0.20, p=0.12, 95% CI 0.03 – 1.54). Predicted oncogenic mutations comprised 87% of all identified mutations and were present in 100% of recurrent tumors and 85% of non-recurrent tumors (p=0.47). Nuclear B-catenin expression by IHC demonstrated a sensitivity of 87% and a specificity of 83% for CTNNB1 mutations. Conclusions: CTNNB1 mutations have a prevalence of 25% in HIR endometrioid endometrial cancer. In this single institution retrospective study, there were no differences in RFS or OS in patients with CTNNB1 mutant compared to wild-type tumors. Citation Format: Jennifer G. Haag, Rebecca J. Wolsky, Marisa R. Moroney, Jamie Sheren, Jeanelle Sheeder, Benjamin G. Bitler, Bradley R. Corr. Clinicopathologic evaluation of CTNNB1 gene mutations in high-intermediate risk endometrial cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference: Endometrial Cancer: New Biology Driving Research and Treatment; 2020 Nov 9-10. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(3_Suppl):Abstract nr PO014.
Effect of the p53 P72R Polymorphism on Mutant<i>TP53</i>Allele Selection in Human Cancer
Authors: Cristabelle De Souza, Jill Madden, Devin C Koestler, Dennis Minn, Dennis J Montoya, Kay Minn, Alan G Raetz, Zheng Zhu, Wen-Wu Xiao, Neeki Tahmassebi, Harikumara R Kathi, Nina Nelson, Anthony N Karnezis, Jeremy Chien
Journal: JNCI Journal of the National Cancer Institute (2021)

Abstract Background TP53 mutations occur in more than 50% of cancers. We sought to determine the effect of the intragenic P72R single nucleotide polymorphism (SNP; rs1042522) on the oncogenic properties of mutant p53. Methods P72R allelic selection in tumors was determined from genotype calls and a Gaussian distributed mixture model. The SNP effect on mutant p53 was determined in p53-negative cancer cell lines. RNA-sequencing, chromatin immunoprecipitation, and survival analysis were performed to describe the SNP effect. All statistical tests were 2-sided. Results Among 409 patients with germline heterozygous P72R SNP who harbored somatic mutations in TP53, we observed a selection bias against missense TP53 mutants encoding the P72 SNP (P = 1.64 x 10-13). Exogenously expressed hotspot p53 mutants with the P72 SNP were negatively selected in cancer cells. Gene expression analyses showed the enrichment of p53 pathway genes and inflammatory genes in cancer cells transduced with mutants encoding P72 SNP. Immune gene signature is enriched in patients harboring missense TP53 mutations with homozygous P72 SNP. These patients have improved overall survival as compared with those with the R72 SNP (P = .04). Conclusion This is the largest study demonstrating a selection against the P72 SNP. Missense p53 mutants with the P72 SNP retain partial wild-type tumor-suppressive functions, which may explain the selection bias against P72 SNP across cancer types. Ovarian cancer patients with the P72 SNP have a better prognosis than with the R72 SNP. Our study describes a previously unknown role through which the rs1042522 SNP modifies tumor suppressor activities of mutant p53 in patients.
Screening for Asymptomatic Carotid Artery Stenosis in the General Population
Authors: Janelle M. Guirguis-Blake, Elizabeth M. Webber, Erin L. Coppola
Journal: JAMA (2021)

US Preventive Services Task Force; Alex H. Krist, MD, MPH; Karina W. Davidson, PhD, MASc; Carol M. Mangione, MD, MSPH; Michael J. Barry, MD; Michael Cabana, MD, MA, MPH; Aaron B. Caughey, MD, PhD; Katrina Donahue, MD, MPH; Chyke A. Doubeni, MD, MPH; John W. Epling Jr, MD, MSEd; Martha Kubik, PhD, RN; Gbenga Ogedegbe, MD, MPH; Lori Pbert, PhD; Michael Silverstein, MD, MPH; Melissa A. Simon, MD, MPH; Chien-Wen Tseng, MD, MPH, MSEE; John B. Wong, MD
Implications of the COVID-19 Pandemic on Asthma Control and Socioeconomic Factors in Inner-City Cohort: A Rapid Online Cross-Sectional Survey
Authors: Thanaporn Ratchataswan, Christina Yee, Caroline Mortelliti, Amparito Cunningham, Lisa Bartnikas, Wanda Phipatanakul
Journal: Journal of Allergy and Clinical Immunology (2021)

The COVID-19 pandemic produced unprecedented disruption to many social determinants of health. We sought to explore the initial impact of the COVID-19 emergency on asthma control and health in school-age children and their families. We remotely surveyed the parents of children attending elementary school in a city in the Northeast, about their experiences from February-July 2020. We recorded demographic information about the children and their family members, COVID-19 associated illness and testing, asthma control, and socioeconomic factors related to health. The online survey was completed by 120 families. Seventy-four households (66.7%) had ≥1 adult working outside the home during the state of emergency. Two children (1.7%) had documented illness with SARS-CoV-2. Documented or suspected COVID-19-related illness was reported in ≥1 family member in 9.9% of households. Thirty-six children (30%) had asthma. During the initial period of the COVID-19 emergency, parents generally perceived their children's asthma as well-controlled (52.8%) or completely-controlled (41.7%). Most families reported good adherence to asthma medications (76%), though some (11.1%) expressed reluctance to access medical care during the outbreak. Nearly all children were offered online education during school closures. Many families reported that technical and/or logistical barriers limited participation. Notable proportions of families reported working outside the home and experiencing COVID-19-related illness during the first 4 months of the pandemic. Despite significant disruption to daily life, the situation tended to enhance protective factors on asthma control. Further studies are needed to better guide management of pediatric asthma and evaluate socioeconomic changes occurring during the COVID-19 emergency.
Repercussion of Maternal Diabetes and Post-Weaning High-Fat Diet Consumption in Laboratory Animals
Authors: Veronyca G. Paula, Yuri K. Sinzato, Rafaianne Q.M. Souza, Larissa L. Cruz, Eduardo Kloppel, Franciane Q. Gallego-Souza, Vinicius S. Barco, Carolina B. Saullo, Giovana Vesentini, Gustavo T. Volpato, Débora C. Damasceno
Journal: Metabolism (2021)
Abstract 19977: Idiopathic Pulmonary Fibrosis: What to Choose? Single or Double Lung Transplantation
Authors: Abul Kashem, Nazmus Sakib, Suresh Keshavamurthy, Stacey Brann, Jesus Gomez-Abraha, Kenji Minakata, Eros Leotta, Francis Cordova, Yoshiya Toyoda
Journal: Circulation (2017)

Introduction: Since the introduction of the new Lung Allocation Score (LAS), idiopathic pulmonary fibrosis (IPF) has become the most common indication for either single or double lung transplantati...
Impact of Broadening Trial Eligibility Criteria for Patients with Advanced Non–Small Cell Lung Cancer: Real-World Analysis of Select ASCO-<i>Friends</i> Recommendations
Authors: R. Donald Harvey, Suanna S. Bruinooge, Li Chen, Elizabeth Garrett-Mayer, Whitney Rhodes, Edward Stepanski, Thomas S. Uldrick, Gwynn Ison, Sean Khozin, Wendy S. Rubinstein, Caroline Schenkel, Robert S. Miller, George A. Komatsoulis, Richard L. Schilsky, Edward S. Kim
Journal: Clinical Cancer Research (2021)

Abstract Purpose: Cancer clinical trials often accrue slowly or miss enrollment targets. Strict eligibility criteria are a major reason. Restrictive criteria also limit opportunities for patient participation while compromising external validity of trial results. We examined the impact of broadening select eligibility criteria on characteristics and number of patients eligible for trials, using recommendations of the American Society of Clinical Oncology (ASCO) and Friends of Cancer Research. Experimental Design: A retrospective, observational analysis used electronic health record data from ASCO’s CancerLinQ Discovery database. Study cohort included patients with advanced non–small cell lung cancer treated from 2011 to 2018. Patients were grouped by traditional criteria [no brain metastases, no other malignancies, and creatinine clearance (CrCl) ≥ 60 mL/minute] and broadened criteria (including brain metastases, other malignancies, and CrCl ≥ 30 mL/minute). Results: The analysis cohort included 10,500 patients. Median age was 68 years, and 73% of patients were White. Most patients had stage IV disease (65%). A total of 5,005 patients (48%) would be excluded from trial participation using the traditional criteria. The broadened criteria, however, would allow 98% of patients (10,346) to be potential participants. Examination of patients included by traditional criteria (5,495) versus those added (4,851) by broadened criteria showed that the number of women, patients aged 75+ years, and those with stage IV cancer was significantly greater using broadened criteria. Conclusions: This analysis of real-world data demonstrated that broadening three common eligibility criteria has the potential to double the eligible patient population and include trial participants who are more representative of those encountered in practice. See related commentary by Giantonio, p. 2369
Safety review of Year 1 Oral Immunotherapy Clinic: Multifood Immunotherapy in Real-World setting
Authors: Antonella Cianferoni, Elizabeth Hanna, Megan Lewis, Maria Katerina Alfaro, Kristen Corrigan, Jill Buonanno, Rahul Datta, Terri Brown-Whitehorn, Jonathan Spergel
Journal: Journal of Allergy and Clinical Immunology (2021)
Associations of Aspirin and Non-Aspirin Non-Steroidal Anti-Inflammatory Drugs With Colorectal Cancer Mortality After Diagnosis
Authors: Jane C Figueiredo, Eric J Jacobs, Christina C Newton, Mark A Guinter, William G Cance, Peter T Campbell
Journal: JNCI Journal of the National Cancer Institute (2021)

Aspirin use reduces colorectal cancer (CRC) incidence, but there is limited evidence regarding associations of aspirin and non-aspirin non-steroidal anti-inflammatory drugs (NSAIDs) with CRC-specific survival.This prospective analysis includes women and men from the Cancer Prevention Study-II Nutrition Cohort who were cancer free at baseline (1992 or 1993) and diagnosed with CRC during incidence follow-up through 2015. Detailed information on aspirin and non-aspirin NSAID use was self-reported on questionnaires at baseline, in 1997, and every 2 years thereafter. Pre- and postdiagnosis data were available for 2686 and 1931 participants without distant metastases, respectively, among whom 512 and 251 died from CRC during mortality follow-up through 2016. Secondary analyses examined associations between prediagnosis aspirin use and stage at diagnosis (distant metastatic vs localized or regional). All statistical tests were 2-sided.Long-term regular use of aspirin (>15 times per month) before diagnosis was associated with lower CRC-specific mortality (multivariable-adjusted hazard ratio [HR] = 0.69, 95% confidence interval [CI] = 0.52 to 0.92). Postdiagnosis regular aspirin use was not statistically significantly associated with risk of CRC-specific mortality overall (HR = 0.82, 95% CI = 0.62 to 1.09), although participants who began regular aspirin use only after their diagnosis were at lower risk than participants who did not use aspirin at both the pre- and postdiagnosis periods (HR = 0.60, 95% CI = 0.36 to 0.98). Long-term aspirin use before diagnosis was also associated with lower odds of diagnosis with distant metastases (multivariable-adjusted odds ratio = 0.73, 95% CI = 0.53 to 0.99).Our results suggest that long-term aspirin use before a diagnosis of nonmetastatic colorectal cancer may be associated with lower CRC-specific mortality after diagnosis, consistent with possible inhibition of micrometastases before diagnosis.