tbuckley/cabot-search huggingface dataset:
Epidemiology and Prognostic Significance of Cough in Fibrotic Interstitial Lung Disease
Authors: Yet H Khor, Kerri A Johannson, Veronica Marcoux, Jolene H Fisher, Deborah Assayag, Helene Manganas, Nasreen Khalil, Martin Kolb, Christopher J Ryerson
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

Rationale: Cough is a key symptom in patients with fibrotic interstitial lung disease (ILD). Objective: This study evaluated the prevalence, longitudinal change, associations, and prognostic significance of cough severity in patients with fibrotic ILD. Methods: We included consecutive patients with idiopathic pulmonary fibrosis (IPF) and non-IPF fibrotic ILD who completed the 100mm-Cough Severity Visual Analog Scale (VAS) from the prospective multi-center Canadian Registry for Pulmonary Fibrosis. Baseline cough severity and associations with patient demographics and clinical factors were determined. Relationships between baseline cough severity and health outcomes were evaluated. Measurements and Main Results: Patients with IPF (n=1061) had higher median baseline cough severity than those with non-IPF fibrotic ILD (n=2825) [24 vs 20mm, p<0.001], with worse cough associated with gastroesophageal reflux disease for both cohorts. Worse cough severity was independently associated with worse health-related quality of life at baseline, larger annualized decline in DLCO, development of disease progression, and reduced transplant-free survival in both IPF and non-IPF fibrotic ILD cohorts. The IPF cohort (2.2mm, 95% CI 1.6-2.9mm) had larger annualized increments in cough severity compared to the non-IPF fibrotic ILD cohort (1.1mm, 95% CI 0.8-1.4mm; p=0.004). There was no difference in worsening cough over time comparing those receiving and not receiving ILD-targeted therapy or with and without lung function decline. Conclusion: Cough is common in patients with IPF and non-IPF fibrotic ILD, with increasing cough severity over time irrespective of ILD-targeted therapy. Patient-reported cough severity has prognostic implications on health-related quality of life, disease progression, and survival in fibrotic ILD.
The Quest for a More Accurate Diagnosis of Cellulitis
Authors: David G. Li, Arash Mostaghimi
Journal: JAMA Dermatology (2024)

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 Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast Journals 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 2024 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 Dermatology journal
Sitting Time Reduction and Blood Pressure in Older Adults
Authors: Dori E. Rosenberg, Weiwei Zhu, Mikael Anne Greenwood-Hickman, Andrea J. Cook, Stefani Florez Acevedo, Jennifer B. McClure, David E. Arterburn, Julie Cooper, Neville Owen, David Dunstan, Stephen R. Perry, Laura Yarborough, Kayne D. Mettert, Beverly B. Green
Journal: JAMA Network Open (2024)

Importance Practical health promotion strategies for improving cardiometabolic health in older adults are needed. Objective To examine the efficacy of a sedentary behavior reduction intervention for reducing sitting time and improving blood pressure in older adults. Design, Setting, and Participants This parallel-group randomized clinical trial was conducted in adults aged 60 to 89 years with high sitting time and body mass index of 30 to 50 from January 1, 2019, to November 31, 2022, at a health care system in Washington State. Intervention Participants were randomized 1:1 to the sitting reduction intervention or a healthy living attention control condition for 6 months. Intervention participants received 10 health coaching contacts, sitting reduction goals, and a standing desk and fitness tracker to prompt sitting breaks. The attention control group received 10 health coaching contacts to set general healthy living goals, excluding physical activity or sedentary behavior. Main Outcomes and Measures The primary outcome, measured at baseline, 3 months, and 6 months, was sitting time assessed using accelerometers worn for 7 days at each time point. Coprimary outcomes were systolic and diastolic blood pressure measured at baseline and 6 months. Results A total of 283 participants (140 intervention and 143 control) were randomized (baseline mean [SD] age, 68.8 [6.2] years; 186 [65.7%] female; mean [SD] body mass index, 34.9 [4.7]). At baseline, 147 (51.9%) had a hypertension diagnosis and 97 (69.3%) took at least 1 antihypertensive medication. Sitting time was reduced, favoring the intervention arm, with a difference in the mean change of −31.44 min/d at 3 months (95% CI, −48.69 to −14.19 min/d; P &amp;amp;lt; .001) and −31.85 min/d at 6 months (95% CI, −52.91 to −10.79 min/d; P = .003). Systolic blood pressure change was lower by 3.48 mm Hg, favoring the intervention arm at 6 months (95% CI, −6.68 to −0.28 mm Hg; P = .03). There were 6 serious adverse events in each arm and none were study related. Conclusions and Relevance In this study of a 6-month sitting reduction intervention, older adults in the intervention reduced sedentary time by more than 30 min/d and reduced systolic blood pressure. Sitting reduction could be a promising approach to improve health in older adults. Trial Registration ClinicalTrials.gov Identifier: NCT03739762
Physical Activity and Incident Obesity Across the Spectrum of Genetic Risk for Obesity
Authors: Evan L. Brittain, Lide Han, Jeffrey Annis, Hiral Master, Andrew Hughes, Dan M. Roden, Paul A. Harris, Douglas M. Ruderfer
Journal: JAMA Network Open (2024)

Importance Despite consistent public health recommendations, obesity rates in the US continue to increase. Physical activity recommendations do not account for individual genetic variability, increasing risk of obesity. Objective To use activity, clinical, and genetic data from the All of Us Research Program (AoURP) to explore the association of genetic risk of higher body mass index (BMI) with the level of physical activity needed to reduce incident obesity. Design, Setting, and Participants In this US population–based retrospective cohort study, participants were enrolled in the AoURP between May 1, 2018, and July 1, 2022. Enrollees in the AoURP who were of European ancestry, owned a personal activity tracking device, and did not have obesity up to 6 months into activity tracking were included in the analysis. Exposure Physical activity expressed as daily step counts and a polygenic risk score (PRS) for BMI, calculated as weight in kilograms divided by height in meters squared. Main Outcome and Measures Incident obesity (BMI ≥30). Results A total of 3124 participants met inclusion criteria. Among 3051 participants with available data, 2216 (73%) were women, and the median age was 52.7 (IQR, 36.4-62.8) years. The total cohort of 3124 participants walked a median of 8326 (IQR, 6499-10 389) steps/d over a median of 5.4 (IQR, 3.4-7.0) years of personal activity tracking. The incidence of obesity over the study period increased from 13% (101 of 781) to 43% (335 of 781) in the lowest and highest PRS quartiles, respectively ( P = 1.0 × 10 −20 ). The BMI PRS demonstrated an 81% increase in obesity risk ( P = 3.57 × 10 −20 ) while mean step count demonstrated a 43% reduction ( P = 5.30 × 10 −12 ) when comparing the 75th and 25th percentiles, respectively. Individuals with a PRS in the 75th percentile would need to walk a mean of 2280 (95% CI, 1680-3310) more steps per day (11 020 total) than those at the 50th percentile to have a comparable risk of obesity. To have a comparable risk of obesity to individuals at the 25th percentile of PRS, those at the 75th percentile with a baseline BMI of 22 would need to walk an additional 3460 steps/d; with a baseline BMI of 24, an additional 4430 steps/d; with a baseline BMI of 26, an additional 5380 steps/d; and with a baseline BMI of 28, an additional 6350 steps/d. Conclusions and Relevance In this cohort study, the association between daily step count and obesity risk across genetic background and baseline BMI were quantified. Population-based recommendations may underestimate physical activity needed to prevent obesity among those at high genetic risk.
Targeted and Shallow Whole-Genome Sequencing Identifies Therapeutic Opportunities in p53abn Endometrial Cancers
Authors: Amy Jamieson, Juliana Sobral de Barros, Dawn R. Cochrane, J. Maxwell Douglas, Sameer Shankar, Branden J. Lynch, Samuel Leung, Spencer Martin, Janine Senz, Amy Lum, Yvette Drew, C. Blake Gilks, David G. Huntsman, Jessica N. McAlpine
Journal: Clinical Cancer Research (2024)

Abstract Purpose: Shallow whole-genome sequencing (sWGS) can detect copy-number (CN) aberrations. In high-grade serous ovarian cancer (HGSOC) sWGS identified CN signatures such as homologous recombination deficiency (HRD) to direct therapy. We applied sWGS with targeted sequencing to p53abn endometrial cancers to identify additional prognostic stratification and therapeutic opportunities. Experimental Design: sWGS and targeted panel sequencing was performed on formalin-fixed, paraffin-embedded p53abn endometrial cancers. CN alterations, mutational data and CN signatures were derived, and associations to clinicopathologic and outcomes data were assessed. Results: In 187 p53abn endometrial cancers, 5 distinct CN signatures were identified. Signature 5 was associated with BRCA1/2 CN loss with features similar to HGSOC HRD signature. Twenty-two percent of potential HRD cases were identified, 35 patients with signature 5, and 8 patients with BRCA1/2 somatic mutations. Signatures 3 and 4 were associated with a high ploidy state, and CCNE1, ERBB2, and MYC amplifications, with mutations in PIK3CA enriched in signature 3. We observed improved overall survival (OS) for patients with signature 2 and worse OS for signatures 1 and 3. Twenty-eight percent of patients had CCNE1 amplification and this subset was enriched with carcinosarcoma histotype. Thirty-four percent of patients, across all histotypes, had ERBB2 amplification and/or HER2 overexpression on IHC, which was associated with worse outcomes. Mutations in PPP2R1A (29%) and FBXW7 (16%) were among the top 5 most common mutations. Conclusions: sWGS and targeted sequencing identified therapeutic opportunities in 75% of patients with p53abn endometrial cancer. Further research is needed to determine the efficacy of treatments targeting these identified pathways within p53abn endometrial cancers.
Best Overall Response–Associated Signature to Doxorubicin in Soft Tissue Sarcomas: A Transcriptomic Analysis from ANNOUNCE
Authors: Jiangang Liu, David S. Moura, Robin L. Jones, Amit Aggarwal, Philip J. Ebert, Andrew J. Wagner, Jennifer Wright, Javier Martin-Broto, William D. Tap
Journal: Clinical Cancer Research (2024)

Abstract Purpose: This exploratory analysis evaluated the tumor samples of the patients treated with doxorubicin (with or without olaratumab) in a negative phase III ANNOUNCE trial to better understand the complexity of advanced soft tissue sarcomas (STS) and to potentially identify its predictive markers. Experimental Design: RNA sequencing was performed on pretreatment tumor samples (n = 273) from the ANNOUNCE trial to evaluate response patterns and identify potential predictive treatment markers for doxorubicin. A BOR-associated signature to doxorubicin (REDSARC) was created by evaluating tumors with radiographic response versus progression. An external cohort of doxorubicin-treated patients from the Spanish Group for Research on Sarcomas (GEIS) was used for refinement and validation. Results: A total of 259 samples from the trial were considered for analysis. Comparative analyses by the treatment arm did not explain the negative trial. However, there was an association between the BOR signature and histologic subtype (χ2P = 2.0e−7) and grade (P = 0.002). There were no associations between the BOR signature and gender, age, ethnicity, or stage. Applied to survival outcomes, REDSARC was also predictive for progression-free survival (PFS) and overall survival (OS). Using the GEIS cohort, a refined 25-gene signature was identified and applied to the ANNOUNCE cohort, where it was predictive of PFS and OS in leiomyosarcoma, liposarcoma, and other sarcoma subtypes, but not in undifferentiated pleomorphic sarcoma. Conclusions: The refined REDSARC signature provides a potential tool to direct the application of doxorubicin in sarcomas and other malignancies. Validation and further refinement of the signature in other potentially subtype specific prospective cohorts is recommended.
A Phase I Trial of Enzalutamide Plus Selective Glucocorticoid Receptor Modulator Relacorilant in Patients with Metastatic Castration-Resistant Prostate Cancer
Authors: Kunal B. Desai, Anthony V. Serritella, Walter M. Stadler, Peter H. O'Donnell, Randy F. Sweis, Russell Z. Szmulewitz
Journal: Clinical Cancer Research (2024)

The majority of patients with metastatic prostate cancer who receive androgen-deprivation therapy and androgen receptor (AR) signaling inhibitors (ARSI) progress. Activation of the glucocorticoid receptor (GR) is associated with ARSI resistance. This single-arm phase I trial assessed safety and pharmacokinetic (PK) feasibility of a combined AR antagonist (enzalutamide) and selective GR modulator (relacorilant) in patients with metastatic castration-resistant prostate cancer (mCRPC).
Fibrosis‐on‐Chip: A Guide to Recapitulate the Essential Features of Fibrotic Disease
Authors: Emma M. Streutker, Utku Devamoglu, Madelon C. Vonk, Wouter P. R. Verdurmen, Séverine Le Gac
Journal: Advanced Healthcare Materials (2024)

Fibrosis, which is primarily marked by excessive extracellular matrix (ECM) deposition, is a pathophysiological process associated with many disorders, which ultimately leads to organ dysfunction and poor patient outcomes. Despite the high prevalence of fibrosis, currently there exist few therapeutic options, and importantly, there is a paucity of in vitro models to accurately study fibrosis. This review discusses the multifaceted nature of fibrosis from the viewpoint of developing organ-on-chip (OoC) disease models, focusing on five key features: the ECM component, inflammation, mechanical cues, hypoxia, and vascularization. The potential of OoC technology is explored for better modeling these features in the context of studying fibrotic diseases and the interplay between various key features is emphasized. This paper reviews how organ-specific fibrotic diseases are modeled in OoC platforms, which elements are included in these existing models, and the avenues for novel research directions are highlighted. Finally, this review concludes with a perspective on how to address the current gap with respect to the inclusion of multiple features to yield more sophisticated and relevant models of fibrotic diseases in an OoC format.
Deep learning in cancer genomics and histopathology
Authors: Michaela Unger, Jakob Nikolas Kather
Journal: Genome Medicine (2024)

Abstract Histopathology and genomic profiling are cornerstones of precision oncology and are routinely obtained for patients with cancer. Traditionally, histopathology slides are manually reviewed by highly trained pathologists. Genomic data, on the other hand, is evaluated by engineered computational pipelines. In both applications, the advent of modern artificial intelligence methods, specifically machine learning (ML) and deep learning (DL), have opened up a fundamentally new way of extracting actionable insights from raw data, which could augment and potentially replace some aspects of traditional evaluation workflows. In this review, we summarize current and emerging applications of DL in histopathology and genomics, including basic diagnostic as well as advanced prognostic tasks. Based on a growing body of evidence, we suggest that DL could be the groundwork for a new kind of workflow in oncology and cancer research. However, we also point out that DL models can have biases and other flaws that users in healthcare and research need to know about, and we propose ways to address them.
Identification of SARS-CoV-2-specific T cell and its receptor
Authors: Qian Zhang, Qing Liang, Rui Zhang, Nan Wang, Xu Xiao, Jiahao Shao, Kejia Wang
Journal: Journal of Hematology & Oncology (2024)

Abstract The T-cell receptor (TCR) repertoires exhibits distinct signatures associated with COVID-19 severity. However, the precise identification of vaccine-induced SARS-CoV-2-specific TCRs and T-cell immunity mechanisms are unknown. We developed a machine-learning model that can differentiate COVID-19 patients from healthy individuals based on TCR sequence features with an accuracy of 95.7%. Additionally, we identified SARS-CoV-2-specific T cells and TCR in HLA-A*02 vaccinated individuals by peptide stimulation. The SARS-CoV-2-specific T cells exhibited higher cytotoxicity and prolonged survival when targeting spike-pulsed cells in vitro or in vivo. The top-performing TCR was further tested for its affinity and cytotoxic effect against SARS-CoV-2-associated epitopes. Furthermore, single-cell RNA sequencing (scRNA-seq), immune repertoire sequencing (IR-seq) and flow cytometry were used to access vaccine-induced cellular immunity, which demonstrated that robust T cell responses (T cell activation, tissue-resident memory T cell (Trm) generation, and TCR clonal expansion) could be induced by intranasal vaccination. In summary, we identified the SARS-CoV-2-associated TCR repertoires profile, specific TCRs and T cell responses. This study provides a theoretical basis for developing effective immunization strategies.
NPEPPS Is a Druggable Driver of Platinum Resistance
Authors: Robert T. Jones, Mathijs Scholtes, Andrew Goodspeed, Maryam Akbarzadeh, Saswat Mohapatra, Lily Elizabeth Feldman, Hedvig Vekony, Annie Jean, Charlene B. Tilton, Michael V. Orman, Shahla Romal, Cailin Deiter, Tsung Wai Kan, Nathaniel Xander, Stephanie P. Araki, Molishree Joshi, Mahmood Javaid, Eric T. Clambey, Ryan Layer, Teemu D. Laajala, Sarah J. Parker, Tokameh Mahmoudi, Tahlita C.M. Zuiverloon, Dan Theodorescu, James C. Costello
Journal: Cancer Research (2024)

There is an unmet need to improve the efficacy of platinum-based cancer chemotherapy, which is used in primary and metastatic settings in many cancer types. In bladder cancer, platinum-based chemotherapy leads to better outcomes in a subset of patients when used in the neoadjuvant setting or in combination with immunotherapy for advanced disease. Despite such promising results, extending the benefits of platinum drugs to a greater number of patients is highly desirable. Using the multiomic assessment of cisplatin-responsive and -resistant human bladder cancer cell lines and whole-genome CRISPR screens, we identified puromycin-sensitive aminopeptidase (NPEPPS) as a driver of cisplatin resistance. NPEPPS depletion sensitized resistant bladder cancer cells to cisplatin in vitro and in vivo. Conversely, overexpression of NPEPPS in sensitive cells increased cisplatin resistance. NPEPPS affected treatment response by regulating intracellular cisplatin concentrations. Patient-derived organoids (PDO) generated from bladder cancer samples before and after cisplatin-based treatment, and from patients who did not receive cisplatin, were evaluated for sensitivity to cisplatin, which was concordant with clinical response. In the PDOs, depletion or pharmacologic inhibition of NPEPPS increased cisplatin sensitivity, while NPEPPS overexpression conferred resistance. Our data present NPEPPS as a druggable driver of cisplatin resistance by regulating intracellular cisplatin concentrations.
TXA2 attenuates allergic lung inflammation through regulation of Th2, Th9, and Treg differentiation
Authors: Hong Li, J. Alyce Bradbury, Matthew L. Edin, Artiom Gruzdev, Huiling Li, Joan P. Graves, Laura M. DeGraff, Fred B. Lih, Chiguang Feng, Erin R. Wolf, Carl D. Bortner, Stephanie J. London, Matthew A. Sparks, Thomas M. Coffman, Darryl C. Zeldin
Journal: Journal of Clinical Investigation (2024)

In lung, thromboxane A2 (TXA2) activates the TP receptor to induce pro-inflammatory and bronchoconstrictor effects. Thus, TP receptor antagonists and TXA2 synthase inhibitors have been tested as potential asthma therapeutics in humans. Th9 cells play key roles in asthma and regulate the lung immune response to allergens. Herein, we found that TXA2 reduces Th9 cell differentiation during allergic lung inflammation. Th9 cells were decreased ~2-fold and airway hyperresponsiveness was attenuated in lungs of allergic mice treated with TXA2. Naïve CD4+ T cell differentiation to Th9 cells and IL-9 production was inhibited dose-dependently by TXA2 in vitro. TP receptor deficient mice had a ~2-fold increase in numbers of Th9 cells in lungs in vivo after OVA exposure compared to wild type (WT) mice. Naïve CD4+ T cells from TP deficient mice exhibited increased Th9 cell differentiation and IL-9 production in vitro compared to CD4+ T cells from WT mice. TXA2 also suppressed Th2 and enhanced Treg differentiation both in vitro and in vivo. Thus, in contrast to its acute, pro-inflammatory effects, TXA2 also has longer-lasting immunosuppressive effects that attenuate the Th9 differentiation that drives asthma progression. These findings may explain the paradoxical failure of anti-thromboxane therapies in the treatment of asthma.
MAP kinase phosphatase-1 inhibition of p38α within lung myofibroblasts is essential for spontaneous fibrosis resolution
Authors: Sean M. Fortier, Natalie M. Walker, Loka R. Penke, Jared D. Baas, Qinxue Shen, Jennifer M. Speth, Steven K. Huang, Rachel L. Zemans, Anton M. Bennett, Marc Peters-Golden
Journal: Journal of Clinical Investigation (2024)

Fibrosis following tissue injury is distinguished from normal repair by the accumulation of pathogenic and apoptosis-resistant myofibroblasts (MFs), which arise primarily by differentiation from resident fibroblasts. Endogenous molecular brakes that promote MF dedifferentiation and clearance during spontaneous resolution of experimental lung fibrosis may provide insights that could inform and improve treatment of progressive pulmonary fibrosis in patients. Mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP1) influences cellular phenotype and fate through precise and timely regulation of MAPK activity within various cell types and tissues, yet its role in lung fibroblasts and pulmonary fibrosis has not been explored. Utilizing gain- and loss-of-function studies, we found that MKP1 promoted lung MF dedifferentiation and restored their sensitivity to apoptosis — effects determined to be mainly dependent upon its dephosphorylation of p38α MAPK (p38α). Fibroblast-specific deletion of MKP1 following peak bleomycin-induced lung fibrosis largely abrogated its subsequent spontaneous resolution. Such resolution was restored by treating these transgenic mice with the p38α inhibitor VX-702. We conclude that MKP1 is a critical antifibrotic brake whose inhibition of pathogenic p38α in lung fibroblasts is necessary for fibrosis resolution following lung injury.