tbuckley/cabot-search huggingface dataset:
A single-cell regulatory map of postnatal lung alveologenesis in humans and mice
Authors: Thu Elizabeth Duong, Yan Wu, Brandon Chin Sos, Weixiu Dong, Siddharth Limaye, Lauraine H. Rivier, Greg Myers, James S. Hagood, Kun Zhang
Journal: Cell Genomics (2022)

Ex-utero regulation of the lungs’ responses to breathing air and continued alveolar development shape adult respiratory health. Applying single-cell transposome hypersensitive site sequencing (scTHS-seq) to over 80,000 cells, we assembled the first regulatory atlas of postnatal human and mouse lung alveolar development. We defined regulatory modules and elucidated new mechanistic insights directing alveolar septation, including alveolar type 1 and myofibroblast cell signaling and differentiation, and a unique human matrix fibroblast population. Incorporating GWAS, we mapped lung function causal variants to myofibroblasts and identified a pathogenic regulatory unit linked to lineage marker FGF18, demonstrating the utility of chromatin accessibility data to uncover disease mechanism targets. Our regulatory map and analysis model provide valuable new resources to investigate age-dependent and species-specific control of critical developmental processes. Furthermore, these resources complement existing atlas efforts to advance our understanding of lung health and disease across the human lifespan.
IMPACT OF PHYSIOLOGICAL ASSESSMENT WITH QUANTITATIVE FLOW RATIO ON ARTERIAL GRAFT OCCLUSION IN PATIENTS UNDERGOING CORONARY ARTERY BYPASS GRAFTING: INSIGHTS FROM THE PRIDE-METAL REGISTRY
Authors: Keishiro Sugimoto, Kuniaki Takahashi, Mana Okune, Kosuke Fujita, Masafumi Ueno, Genichi Sakaguchi, Gaku Nakazawa
Journal: Journal of the American College of Cardiology (2022)
Fine Particulate Matter and Lung Function among Burning-Exposed <i>Deepwater Horizon</i> Oil Spill Workers
Authors: Dazhe Chen, Kaitlyn G. Lawrence, Gregory C. Pratt, Mark R. Stenzel, Patricia A. Stewart, Caroline P. Groth, Sudipto Banerjee, Kate Christenbury, Matthew D. Curry, W. Braxton Jackson, Richard K. Kwok, Aaron Blair, Lawrence S. Engel, Dale P. Sandler
Journal: Environmental Health Perspectives (2022)

Background: During the 2010 Deepwater Horizon (DWH) disaster, controlled burning was conducted to remove oil from the water. Workers near combustion sites were potentially exposed to increased fine particulate matter [with aerodynamic diameter ≤2.5μm (PM2.5)] levels. Exposure to PM2.5 has been linked to decreased lung function, but to our knowledge, no study has examined exposure encountered in an oil spill cleanup. Objective: We investigated the association between estimated PM2.5 only from burning/flaring of oil/gas and lung function measured 1–3 y after the DWH disaster. Methods: We included workers who participated in response and cleanup activities on the water during the DWH disaster and had lung function measured at a subsequent home visit (n=2,316). PM2.5 concentrations were estimated using a Gaussian plume dispersion model and linked to work histories via a job-exposure matrix. We evaluated forced expiratory volume in 1 s (FEV1; milliliters), forced vital capacity (FVC; milliliters), and their ratio (FEV1/FVC; %) in relation to average and cumulative daily maximum exposures using multivariable linear regressions. Results: We observed significant exposure–response trends associating higher cumulative daily maximum PM2.5 exposure with lower FEV1 (p-trend=0.04) and FEV1/FVC (p-trend=0.01). In comparison with the referent group (workers not involved in or near the burning), those with higher cumulative exposures had lower FEV1 [−166.8mL, 95% confidence interval (CI): −337.3, 3.7] and FEV1/FVC (−1.7, 95% CI: −3.6, 0.2). We also saw nonsignificant reductions in FVC (high vs. referent: −120.9, 95% CI: −319.4, 77.6; p-trend=0.36). Similar associations were seen for average daily maximum PM2.5 exposure. Inverse associations were also observed in analyses stratified by smoking and time from exposure to spirometry and when we restricted to workers without prespill lung disease. Conclusions: Among oil spill workers, exposure to PM2.5 specifically from controlled burning of oil/gas was associated with significantly lower FEV1 and FEV1/FVC when compared with workers not involved in burning. https://doi.org/10.1289/EHP8930
A RARE CASE OF EMBRYONIC DEXTROCARDIA: MULTIMODALITY IMAGING TO ASSIST IN PACEMAKER PLACEMENT FOR HIGH GRADE ATRIOVENTRICULAR BLOCK
Authors: Alex Cubberley, Gurjaspreet Bhattal, Rahul Sawhney, Ambarish Gopal, Samuel Woolbert, Aasim Afzal, David A. Rawitscher, Hafiza H. Khan
Journal: Journal of the American College of Cardiology (2022)
In Memoriam: Jeremiah Stamler, MD, 1919-2022
Authors: Philip Greenland, Donald M. Lloyd-Jones
Journal: JAMA Cardiology (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 Cardiology 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 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 Cardiology journal
Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers
Authors: Josephine R Giles, Sasikanth Manne, Elizabeth Freilich, Derek A Oldridge, Amy E Baxter, Sangeeth George, Zeyu Chen, Hua Huang, Lakshmi Chilukuri, Mary Carberry, Lydia Giles, Nan-Ping P Weng, Regina M Young, Carl H June, Lynn M Schuchter, Ravi K Amaravadi, Xiaowei Xu, Giorgos C Karakousis, Tara C Mitchell, Alexander C Huang, Junwei Shi, E John Wherry
Journal: Immunity (2022)
Corrigendum to ‘Targeting mammalian serine/threonine-protein kinase 4 through yes-associated protein/TEA domain transcription factor-mediated epithelial-mesenchymal transition ameliorates diabetic nephropathy orchestrated renal fibrosis [Metabolism Clinical and Experimental 108 (2020) 154258]
Authors: Tingting Yang, Cai Heng, Yi Zhou, Yinlu Hu, Shangxiu Chen, Haiyan Wang, Hao Yang, Zhenzhou Jiang, Sitong Qian, Yinan Wang, Jianyun Wang, Xia Zhu, Lei Du, Xiaoxing Yin, Qian Lu
Journal: Metabolism (2022)
LONG-TERM OUTCOMES OF POST-TAVR TRANSIENT LEFT BUNDLE BRANCH BLOCK: INSIGHTS FROM A MULTICENTER INTERNATIONAL STUDY
Authors: Takahiro Tsushima, Anthony Main, Sadeer G. Al-Kindi, Luis Augusto Palma Dallan, Heather Wheat, Cristian R. Baeza, Marc P. Pelletier, Mauricio Arruda, Judith A. Mackall, Sergio Thal, Yohei Ohno, Kyong-Hee Lee, Dimytri A. Siqueira, Tsuyoshi Kaneko, Morgan Harloff, Giuliano Costa, Marco Barbanti, Guilherme Attizzani
Journal: Journal of the American College of Cardiology (2022)
The effect of intravenous ferric carboxymaltose on right ventricular function – insights from the <scp>IRON‐CRT</scp> trial
Authors: Pieter Martens, Matthias Dupont, Jeroen Dauw, Petra Nijst, Philippe B Bertrand, W.H. Wilson Tang, Wilfried Mullens
Journal: European Journal of Heart Failure (2022)
THE VALUE OF PASSIVE LEG RAISE DURING RIGHT HEART CATHETERIZATION IN DIAGNOSING HEART FAILURE WITH PRESERVED EJECTION FRACTION
Authors: Arno A. van de Bovenkamp, Niels Wijkstra, Frank Oosterveer, Anton Vonk Noordegraaf, Harm Jan Bogaard, Albert C. van Rossum, Frances S. De Man, Barry Borlaug, M. Louis Handoko
Journal: Journal of the American College of Cardiology (2022)
Fluorescence Imaging of Neural Activity, Neurochemical Dynamics, and Drug-Specific Receptor Conformation with Genetically Encoded Sensors
Authors: Chunyang Dong, Yu Zheng, Kiran Long-Iyer, Emily C. Wright, Yulong Li, Lin Tian
Journal: Annual Review of Neuroscience (2022)

Recent advances in fluorescence imaging permit large-scale recording of neural activity and dynamics of neurochemical release with unprecedented resolution in behaving animals. Calcium imaging with highly optimized genetically encoded indicators provides a mesoscopic view of neural activity from genetically defined populations at cellular and subcellular resolutions. Rigorously improved voltage sensors and microscopy allow for robust spike imaging of populational neurons in various brain regions. In addition, recent protein engineering efforts in the past few years have led to the development of sensors for neurotransmitters and neuromodulators. Here, we discuss the development and applications of these genetically encoded fluorescent indicators in reporting neural activity in response to various behaviors in different biological systems as well as in drug discovery. We also report a simple model to guide sensor selection and optimization.
KETONE ESTER TREATMENT INCREASES CARDIAC KETONE UTILIZATION AND REDUCES CARDIAC INFLAMMATION IN A PORCINE MODEL OF ACUTE MYOCARDIAL INFARCTION
Authors: Salva Yurista, Aidan Welsh, William Jiang, Robert Eder, Shi Chen, Benjamin Bonner, Anna Foster, Jaume Coll-Font, Anthony Rosenzweig, Christopher Nguyen
Journal: Journal of the American College of Cardiology (2022)
Multi-arm RNA junctions encoding molecular logic unconstrained by input sequence for versatile cell-free diagnostics
Authors: Duo Ma, Yuexin Li, Kaiyue Wu, Zhaoqing Yan, Anli A. Tang, Soma Chaudhary, Zachary M. Ticktin, Jonathan Alcantar-Fernandez, José L. Moreno-Camacho, Abraham Campos-Romero, Alexander A. Green
Journal: Nature Biomedical Engineering (2022)

Abstract Applications of RNA-based molecular logic have been hampered by sequence constraints imposed on the input and output of the circuits. Here we show that the sequence constraints can be substantially reduced by appropriately encoded multi-arm junctions of single-stranded RNA structures. To conditionally activate RNA translation, we integrated multi-arm junctions, self-assembled upstream of a regulated gene and designed to unfold sequentially in response to different RNA inputs, with motifs of loop-initiated RNA activators that function independently of the sequence of the input RNAs and that reduce interference with the output gene. We used the integrated RNA system and sequence-independent input RNAs to execute two-input and three-input OR and AND logic in Escherichia coli , and designed paper-based cell-free colourimetric assays that accurately identified two human immunodeficiency virus (HIV) subtypes (by executing OR logic) in amplified synthetic HIV RNA as well as severe acute respiratory syndrome coronavirus-2 (via two-input AND logic) in amplified RNA from saliva samples. The sequence-independent molecular logic enabled by the integration of multi-arm junction RNAs with motifs for loop-initiated RNA activators may be broadly applicable in biotechnology.
Characterization of Internal Medicine Chief Resident Administrative, Educational, and Clinical Experiences
Authors: Megha Garg, Tejaswi Kompala, Michael Hurley, Lenny López
Journal: JAMA Network Open (2022)

The internal medicine (IM) chief residency is a position of leadership and honor common in IM programs, but the goals, responsibilities, and experiences of those who undertake it can be highly variable. Studies assessing the experience and impressions of the chief resident (CR) position from the viewpoint of the IM CRs are lacking.To describe the structure, responsibilities, and perceptions of the IM CR role across IM residency programs.A cross-sectional, simple descriptive electronic survey for current CRs was administered between April and June 2018 across US IM residency programs accredited by US Accreditation Council for Graduate Medical Education. A 2-step nonrandom sampling approach was used: first, snowball sampling was performed using the authors' professional networks, and second, the survey was sent to the Association of Program Directors in Internal Medicine (APDIM) CR listserv. Data analysis was performed from June 2020 to August 2020.Participation as a CR for an IM residency program in the 2017 to 2018 academic year.Descriptive CR personal and program characteristics and CR perceptions of administrative, clinical, and leadership experiences.Among 169 unique responses, 77 participants (46%) were female and 89 (53%) were White. The response rate was 57% (70 of 122 surveys) in the snowball sample and 12% (99 of 842 surveys) in the APDIM listserv. The 2 sampled groups were combined for analysis. Most respondents (125 CRs [74%]) were from academic or university-based programs. Common across CR responses was responsibility for administrative tasks, clinical work, and educational efforts. Most CRs (111 of 157 respondents [71%]) reported being the primary schedulers for the residency program. Clinical work differed widely across respondents. Only 70 of 156 respondents (45%) reported having an academic title associated with the CR role. CRs reported inconsistent evaluation throughout the year, with high percentages reporting never receiving feedback on teaching (34 respondents [23%]), clinical abilities (67 respondents [45%]), or leadership abilities (60 respondents [40%]). Most CRs (107 respondents [69%]) agreed that they find work as a CR fulfilling and 117 (74%) agreed they would do chief residency again.Despite its ubiquity in training programs across the US, the IM CR experience is very different across programs. Recommendations are provided to consider for improvement of the CR experience, including structured feedback opportunities, maximizing educational and clinical experiences, and standardizing policies.
FIVE-YEAR THROMBOEMBOLIC RISK AFTER A DIAGNOSIS OF PERIPARTUM CARDIOMYOPATHY: A PROPENSITY-MATCHED COHORT STUDY
Authors: Andreas P. Kalogeropoulos, Julia Dokko, Katherine Godfrey, Alan Abboud, Michelle Weisfelner Bloom, Hal A. Skopicki
Journal: Journal of the American College of Cardiology (2022)
PERCUTANEOUS INTERVENTION OR BYPASS GRAFT FOR LEFT MAIN CORONARY ARTERY DISEASE WITH LOW EJECTION FRACTION - A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Waqas Ullah, Tuoyo O. Mene-Afejuku, Hamza Zahidullah, Salman Zahid, Muhammad Shan Ul Abedin, Ramesha Mehreen, Ahmed Pasha, Abdul Mannan Khan Minhas, Muhammad Z. Khan, David L. Fischman
Journal: Journal of the American College of Cardiology (2022)
Characteristics and Adverse Events of Patients for Whom Nifurtimox Was Released Through CDC-Sponsored Investigational New Drug Program for Treatment of Chagas Disease — United States, 2001–2021
Authors: Andrew Abbott, Susan P. Montgomery, Rebecca J. Chancey
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

Chagas disease, or American trypanosomiasis, is caused by the parasite Trypanosoma cruzi. Chagas disease is endemic in rural areas of Latin America, but T. cruzi, triatomine vectors, infected mammalian reservoir hosts, and rare cases of autochthonous vector borne transmission have been reported in the United States (1). Possible modes of transmission include the following: vector borne via skin or mucosal contact with feces of infected triatomine bugs, congenital, blood transfusion, organ transplantation, or laboratory accident. Chagas disease can be treated with benznidazole (commercially available since May 14, 2018) or nifurtimox (2). Before January 25, 2021, nifurtimox (Lampit) had been exclusively available through CDC under an Institutional Review Board-approved Investigational New Drug (IND) treatment protocol, at which time it became reasonably accessible to health care providers outside of the program. This report summarizes CDC Drug Service reports for selected characteristics of and adverse events reported by 336 patients for whom nifurtimox was requested under the CDC IND program during January 1, 2001-January 25, 2021. Of the 336 patients, 34.2% resided in California. Median age of patients was 37 years (range = 1-78 years). Most patients were aged ≥18 (91.8%; 305 of 332) and Hispanic (93.2%; 290 of 311). Among the patients with available information, 91.4% (222 of 243) reported an adverse event. Among those with information about the severity of their adverse events, 20.5% reported a severe event. On August 7, 2020, the Food and Drug Administration (FDA) announced approval of a nifurtimox product, Lampit (Bayer), for treatment of Chagas disease in patients aged <18 years weighing ≥5.5 lbs (≥2.5 kg). Lampit became commercially available during October 2020. Physicians should take frequency of adverse events into consideration when prescribing nifurtimox and counseling patients.
Incomplete autophagy: Trouble is a friend
Authors: Qiang Zhang, Shijie Cao, Feng Qiu, Ning Kang
Journal: Medicinal Research Reviews (2022)

Abstract Incomplete autophagy is an impaired self‐eating process of intracellular macromolecules and organelles in which accumulated autophagosomes do not fuse with lysosomes for degradation, resulting in the blockage of autophagic flux. In this review, we summarized the literature over the past decade describing incomplete autophagy, and found that different from the double‐edged sword effect of general autophagy on promoting cell survival or death, incomplete autophagy plays a crucial role in disrupting cellular homeostasis, and promotes only cell death. What matters is that incomplete autophagy is closely relevant to the pathogenesis and progression of various human diseases, which, meanwhile, intimately linking to the pharmacologic and toxicologic effects of several compounds. Here, we comprehensively reviewed the latest progress of incomplete autophagy on molecular mechanisms and signaling pathways. Moreover, implications of incomplete autophagy for pharmacotherapy are also discussed, which has great relevance for our understanding of the distinctive role of incomplete autophagy in cellular physiology and disease. Consequently, targeting incomplete autophagy may contribute to the development of novel generation therapeutic agents for diverse human diseases.
Operative Autonomy of Surgical Residents and Patient Outcomes
Authors: Joshua Rabinowitz, Giordano Perin, Saba P. Balasubramanian
Journal: JAMA Surgery (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 Surgery 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 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 Surgery journal
Phase II single-arm study of nivolumab and ipilimumab (Nivo/Ipi) in previously treated classical Kaposi sarcoma (cKS)
Authors: A. Zer, O. Icht, L. Yosef, D. Avram, O. Jacobi, E. Fenig, N. Kurman, I. Peretz, S. Shamai, O. Merimsky, E. Ben-Ami, R. Shapira Frommer, A.E. Schwarzbach, H. Bernstine, R. Weitzen, O. Vornicova, G. Bar-Sela, S.M. Stemmer, M. Lotem
Journal: Annals of Oncology (2022)
Association Between Dexamethasone Treatment After Hospital Discharge for Patients With COVID-19 Infection and Rates of Hospital Readmission and Mortality
Authors: Cheng-Wei Huang, Albert S. Yu, Hubert Song, Joon S. Park, Stefanie S. Wu, Vang Kou Khang, Christopher C. Subject, Ernest Shen
Journal: JAMA Network Open (2022)

<h3>Importance</h3> Current guidelines recommend use of dexamethasone, 6 mg/d, up to 10 days or until discharge for patients hospitalized with COVID-19. Whether patients who received less than 10 days of corticosteroids during hospitalization for COVID-19 benefit from continuing treatment at discharge has not been determined. <h3>Objective</h3> To assess whether continuing dexamethasone treatment at discharge is associated with reduced all-cause readmissions or mortality postdischarge. <h3>Design, Setting, and Participants</h3> A retrospective cohort study was conducted at 15 medical centers within Kaiser Permanente Southern California. The population included adults who received less than 10 days of dexamethasone, 6 mg/d, until discharge during hospitalization for COVID-19 and were discharged alive between May 1 and September 30, 2020. <h3>Exposures</h3> Continued dexamethasone treatment at discharge. <h3>Main Outcomes and Measures</h3> All-cause readmissions or mortality within 14 days from discharge. <h3>Results</h3> A total of 1164 patients with a median age of 55 (IQR, 44-66) years were identified. Most patients were of Hispanic ethnicity (822 [70.6%]) and male (674 [57.9%]) and required oxygen support during hospitalization (1048 [90.0%]). Of the 1164 patients, 692 (59.5%) continued dexamethasone, 6 mg/d, at discharge. A balanced cohort was created using propensity score and inverse probability of treatment weighting. The adjusted odds ratio (OR) for readmissions or mortality within 14 days was 0.87 (95% CI, 0.58-1.30) for patients who continued dexamethasone therapy at discharge compared with those who did not. Similar results were produced by a sensitivity analysis that restricted the treatment group to those who received exactly 10 days of dexamethasone (OR, 0.89; 95% CI, 0.55-1.43) and by subgroup analyses stratified by the duration of dexamethasone treatment as an inpatient (1-3 days: OR, 0.71; 95% CI, 0.43-1.16; 4-9 days: OR, 1.01; 95% CI, 0.48-2.12), oxygen requirement at discharge (room air: OR, 0.91; 95% CI, 0.53-1.59; supplemental oxygen use: OR, 0.76; 95% CI, 0.42-1.37), and disease duration at discharge (≤10 days: OR, 0.81; 95% CI, 0.49-1.33; &gt;10 days: OR, 0.94; 95% CI, 0.48-1.86). <h3>Conclusions and Relevance</h3> In this cohort study of patients with COVID-19, continuing treatment with dexamethasone, 6 mg/d, at discharge was not associated with a reduction in 14-day all-cause readmission or mortality. This finding suggests that dexamethasone should not be routinely prescribed beyond discharge for individuals with COVID-19.
<i>TERT</i> promoter C228T mutation in neural progenitors confers growth advantage following telomere shortening <i>in vivo</i>
Authors: Shunichiro Miki, Tomoyuki Koga, Andrew M Mckinney, Alison D Parisian, Takahiro Tadokoro, Raghavendra Vadla, Martin Marsala, Robert F Hevner, Joseph F Costello, Frank Furnari
Journal: Neuro-Oncology (2022)

Heterozygous TERT (telomerase reverse transcriptase) promoter mutations (TPMs) facilitate TERT expression and are the most frequent mutation in glioblastoma (GBM). A recent analysis revealed this mutation is one of the earliest events in gliomagenesis. However, no appropriate human models have been engineered to study the role of this mutation in the initiation of these tumors.
Orthogonally induced differentiation of stem cells for the programmatic patterning of vascularized organoids and bioprinted tissues
Authors: Mark A. Skylar-Scott, Jeremy Y. Huang, Aric Lu, Alex H. M. Ng, Tomoya Duenki, Songlei Liu, Lucy L. Nam, Sarita Damaraju, George M. Church, Jennifer A. Lewis
Journal: Nature Biomedical Engineering (2022)