tbuckley/cabot-search huggingface dataset:
Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic
Authors: Philippe Colson, Hervé Chaudet, Jérémy Delerce, Pierre Pontarotti, Anthony Levasseur, Jacques Fantini, Bernard La Scola, Christian Devaux, Didier Raoult
Journal: Journal of Infection (2024)

ObjectivesThe SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center.MethodsWe analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance. Mutations frequencies were calculated using Nextclade, Microsoft Excel, and an in-house Python script.ResultsA total of 22,225 nucleotide mutations were identified, 220 (1.0%) being each at the root of ≥836 genomes, classifying mutations as 'hyperfertile'. Two seeded the European pandemic: P323L in RNA polymerase, associated with an increased mutation rate, and D614G in spike that improved fitness. Most 'hyperfertile' mutations occurred in areas not predicted with increased virulence. Their mean number was 8±6 (0-22) per 1,000 nucleotides per gene. They were 3.7-times more frequent in accessory than informational genes (13.9 versus 3.7/1,000 nucleotides). Particularly, they were 4.1-times more frequent in ORF8 than in the RNA polymerase gene. Interestingly, stop codons were present in 97 positions, almost only in accessory genes, including ORF8 (21/100 codons).Conclusionsmost 'hyperfertile' mutations did not predict emergence of a new epidemic, and some were stop codons indicating the existence of so-named 'non-virulence' genes.
Myeloperoxidase-specific antineutrophil cytoplasmic antibody-associated vasculitis
Authors: Sabrina Arnold, A Richard Kitching, Veronique Witko-Sarsat, Thorsten Wiech, Ulrich Specks, Sebastian Klapa, Sara Comdühr, Anja Stähle, Antje Müller, Peter Lamprecht
Journal: The Lancet Rheumatology (2024)

Myeloperoxidase (MPO)-specific antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (MPO-ANCA-associated vasculitis) is one of two major ANCA-associated vasculitis variants characterised by systemic necrotising vasculitis with few or no immune deposits. MPO-ANCA-associated vasculitis predominantly affects small blood vessels and, in contrast to its counterpart proteinase 3-ANCA-associated vasculitis, is generally not associated with granulomatous inflammation. The kidneys and lungs are the most commonly affected organs. The pathogenesis of MPO-ANCA-associated vasculitis is characterised by loss of tolerance to the neutrophil enzyme MPO. This loss of tolerance leads to a chronic immunopathological response where neutrophils become both the target and effector of autoimmunity. MPO-ANCA drives neutrophil activation, leading in turn to tissue and organ damage. Clinical trials have improved the therapeutic approach to MPO-ANCA-associated vasculitis. However, there remains substantial unmet need regarding relapse frequency, toxicity of current treatment, and long-term morbidity. In this Series paper, we present the current state of research regarding pathogenesis, diagnosis, and treatment of MPO-ANCA-associated vasculitis.
Early Outcomes From a Multicenter Transcatheter Self-Expanding Pulmonary Valve Replacement Registry
Authors: Bryan H. Goldstein, Doff B. McElhinney, Matthew J. Gillespie, Jamil A. Aboulhosn, Daniel S. Levi, Brian H. Morray, Allison K. Cabalka, Barry A. Love, Jeffrey D. Zampi, David T. Balzer, Mark A. Law, Mary D. Schiff, Arvind Hoskoppal, Athar M. Qureshi
Journal: Journal of the American College of Cardiology (2024)
The Effect of Using a Remote Patient Management Platform in Optimizing Guideline-Directed Medical Therapy in Heart Failure Patients
Authors: Darshan H. Brahmbhatt, Heather J. Ross, Mary O’Sullivan, Veronica Artanian, Brigitte Mueller, Kyle Runeckles, Chun-Po Steve Fan, Valeria E. Rac, Emily Seto
Journal: JACC Heart Failure (2024)

Guideline-directed medical therapy (GDMT) remains underutilized in patients with heart failure with reduced ejection fraction, leading to morbidity and mortality. The Medly Titrate (Use of Telemonitoring to Facilitate Heart Failure Mediation Titration) study was an open-label, randomized controlled trial to determine whether remote medication titration for patients with heart failure with reduced ejection fraction was more effective than usual care (UC). In this study, 108 patients were randomized to remote GDMT titration through the Medly heart failure program (n = 56) vs UC (n = 52). The primary outcome was the proportion of patients completing GDMT titration at 6 months. Secondary outcomes included the number of clinic visits and time required to achieve titration, patient health outcomes, and health care utilization, including urgent clinic/emergency department visits and hospitalization. At 6 months, GDMT titration was completed in 82.1% (95% CI: 71.2%-90.8%) of patients in the intervention arm vs 53.8% in UC (95% CI: 41.1%-67.7%; P = 0.001). Remote titration required fewer in-person (1.62 ± 1.09 vs 2.42 ± 1.65; P = 0.004) and virtual clinic visits (0.50 ± 1.08 vs 1.29 ± 1.86; P = 0.009) to complete titration. Median time to optimization was shorter with remote titration (3.42 months [Q1-Q3: 2.99-4.04 months] vs 5.47 months [Q1-Q3: 4.14-7.33 months]; P < 0.001). The number of urgent clinic/emergency department visits (incidence rate ratio of remote vs control groups: 0.90 [95% CI: 0.53-1.56]; P = 0.70) were similar between groups, with a reduction in all-cause hospitalization with remote titration (incidence rate ratio: 0.55 [95% CI: 0.31-0.97]; P = 0.042). Remote titration of GDMT in heart failure with reduced ejection fraction was effective, safe, feasible, and increased the proportion of patients achieving target doses, in a shorter period of time with no excess adverse events compared with UC. (Use of Telemonitoring to Facilitate Heart Failure Mediation Titration [Medly Titrate]; NCT04205513)
Multicentre phase II trial of cabozantinib in patients with hepatocellular carcinoma after immune checkpoint inhibitor treatment
Authors: Stephen L. Chan, Baek-Yeol Ryoo, Frankie Mo, Landon L. Chan, Jaekyung Cheon, Leung Li, Kwan H. Wong, Nicole Yim, Hyeyeong Kim, Changhoon Yoo
Journal: Journal of Hepatology (2024)
An innate immune response to adeno-associated virus genomes decreases cortical dendritic complexity and disrupts synaptic transmission
Authors: Christos M Suriano, Neerav Kumar, Jessica L Verpeut, Jie Ma, Caroline Jung, Connor E Dunn, Brigett V Carvajal, Ai Vy Nguyen, Lisa M Boulanger
Journal: Molecular Therapy (2024)

Recombinant adeno-associated viruses (AAVs) allow rapid and efficient gene delivery to the nervous system, are widely used in neuroscience research, and are the basis of FDA-approved neuron-targeting gene therapies. Here we find that an innate immune response to the AAV genome reduces dendritic length and complexity and disrupts synaptic transmission in mouse somatosensory cortex. Dendritic loss is apparent 3 weeks after injection of experimentally relevant viral titers, is not restricted to a particular capsid serotype, transgene, promoter, or production facility, and cannot be explained by responses to surgery or transgene expression. AAV-associated dendritic loss is accompanied by a decrease in the frequency and amplitude of miniature excitatory postsynaptic currents and an increase in the proportion of GluA2-lacking, calcium-permeable AMPA receptors. The AAV genome is rich in unmethylated CpG DNA, which is recognized by the innate immunoreceptor Toll-like receptor 9 (TLR9), and acutely blocking TLR9 preserves dendritic complexity and AMPA receptor subunit composition in AAV-injected mice. These results reveal unexpected impacts of an immune response to the AAV genome on neuronal structure and function and identify approaches to improve the safety and efficacy of AAV-mediated gene delivery in the nervous system.
In adults with post–COVID-19 conditions, a synbiotic preparation, SIM01, alleviated some symptoms at 6 mo
Authors: Deepa Gotur, Eleftherios Mylonakis
Journal: Annals of Internal Medicine (2024)

Source CitationLau RI, Su Q, Lau IS, et al. A synbiotic preparation (SIM01) for post-acute COVID-19 syndrome in Hong Kong (RECOVERY): a randomised, double-blind, placebo-controlled trial. Lancet Infect Dis. 2024;24:256-265. https://pubmed.ncbi.nlm.nih.gov/38071990/
In severe eosinophilic asthma controlled with benralizumab, tapering high-dose ICS reduced dose while maintaining control
Authors: Matthew B. Stanbrook
Journal: Annals of Internal Medicine (2024)

Source CitationJackson DJ, Heaney LG, Humbert M, et al; SHAMAL Investigators. Reduction of daily maintenance inhaled corticosteroids in patients with severe eosinophilic asthma treated with benralizumab (SHAMAL): a randomised, multicentre, open-label, phase 4 study. Lancet. 2024;403:271-281. https://pubmed.ncbi.nlm.nih.gov/38071986/
Impact of Postoperative Radiotherapy on the Prognosis of Early-Stage (pT1-2N0M0) Oral Tongue Squamous Cell Carcinoma
Authors: Qiaoying Tian, Lin Jiang, Dongjun Dai, Lihong Liu, Xiaomeng Shi, Yinglu Guo, Dang Wu, Jia Yang, Jing Xu, Zhuoying Cai, Zhimin Ye, Yun Xi, Zengguang Zheng, Huimin Li, Yongjie Shui, Yanming Liu, Jinbiao Shang, Shumei Wei, Qichun Wei
Journal: Journal of Clinical Oncology (2024)

To identify subgroups of patients with early-stage (pT1-2N0M0) oral tongue squamous cell carcinoma (OTSCC) who may benefit from postoperative radiotherapy (PORT).
Calcium Peroxide‐Based Hydrogel Patch with Sustainable Oxygenation for Diabetic Wound Healing
Authors: Na Li, Xiaohuan Lu, Yueying Yang, Shan Ning, Ye Tian, Mengyuan Zhou, Zheng Wang, Lin Wang, Jianfeng Zang
Journal: Advanced Healthcare Materials (2024)

Abstract Nonhealing diabetic wounds are predominantly attributed to the inhibition of angiogenesis, re‐epithelialization, and extracellular matrix (ECM) synthesis caused by hypoxia. Although oxygen therapy has demonstrated efficacy in promoting healing, its therapeutic impact remains suboptimal due to unsustainable oxygenation. Here, this work proposes an oxygen‐releasing hydrogel patch embedded with polyethylene glycol‐modified calcium peroxide microparticles, which sustainably releases oxygen for 7 days without requiring any supplementary conditions. The released oxygen effectively promotes cell migration and angiogenesis under hypoxic conditions as validated in vitro. The in vivo tests in diabetic mice models show that the sustainably released oxygen significantly facilitates the synthesis of ECM, induces angiogenesis, and decreases the expression of inflammatory cytokines, achieving a diabetic wound healing rate of 84.2% on day 7, outperforming the existing oxygen‐releasing approaches. Moreover, the proposed hydrogel patch is designed with porous, soft, antibacterial, biodegradable, and storage stability for 15 days. The proposed hydrogel patch is expected to be promising in clinics treating diabetic wounds.
The Challenge of Assessing Remission and Relapse in ANCA Kidney Disease
Authors: Silke R. Brix
Journal: Journal of the American Society of Nephrology (2024)

Renal, Transplantation and Urology Unit, Manchester University Hospitals NHS Foundation Trust, and Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, United Kingdom Correspondence: Dr. Silke R. Brix, email: [email protected] See related article, "Urinary CD4+ T Cells Predict Renal Relapse in ANCA-Associated Vasculitis," on pages 483–494.
Cover Image
Authors: Xiao-Tong Su, Jeremiah V. Reyes, Anne E. Lackey, Hasan Demirci, Sebastian Bachmann, Yujiro Maeoka, Ryan J. Cornelius, James A. McCormick, Chao-Ling Yang, Hyun Jun Jung, Paul A. Welling, Jonathan W. Nelson, David H. Ellison
Journal: Journal of the American Society of Nephrology (2024)

Immunofluorescence image of mouse kidney tissue expressing green fluorescent protein (green) in their nuclear envelope of distal convoluted tubule cells. To confirm the specificity of green fluorescent protein expression, the tissue was co-stained for NCC (red), a defining feature of the distal convoluted tubule. All nuclei are stained with 4',6-diamidino-2-phenylindole (blue) to visualize the tissue. In the accompanying study, the green nuclei were isolated from kidney tissue and profiled by singlenucleus RNA-sequencing to detail the molecular heterogeneity of distal convoluted tubule. Figure 1A from "Enriched Single-Nucleus RNA-Sequencing Reveals Unique Attributes of Distal Convoluted Tubule Cells" by Xiao-Tong Su, Jeremiah V. Reyes, Anne E. Lackey, Hasan Demirci, Sebastian Bachmann, Yujiro Maeoka, Ryan J. Cornelius, James A. McCormick, Chao-Ling Yang, Hyun Jun Jung, Paul A. Welling, Jonathan W. Nelson, and David H. Ellison. J Am Soc Nephrol. 2024;35(4):426–440. doi:10.1681/ASN.0000000000000297.
Secular Trends in Incidence of Treated Kidney Failure in the United States
Authors: Mallory L. Downie, Bethany J. Foster
Journal: Journal of the American Society of Nephrology (2024)

1Division of Nephrology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada 3Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada Correspondence: Dr. Bethany J. Foster, email: [email protected] See related article, "Age- and Race-Specific Changes in ESKD Incidence over Four Decades," on pages 456–465.
Low‐Cost Photoelectric Flow Rate Sensors Based on a Flexible Planar Curved Beam Structure for Clinical Treatments
Authors: Xinfang Cao, Qinlan Li, Shuang Li, Xinkai Xu, Liyang Wang, Mengjie Wang, Bo Ding, Shengwen Bao, Shugang Wang, Bao Sun, Jingqiang Cui, Guosheng Wang, Huiling Li, Yewang Su
Journal: Advanced Healthcare Materials (2024)

Abstract In clinical treatments, reliable flow rate measurements ensure accurate drug delivery during infusions, precise gas delivery during artificial ventilations, etc., thereby reducing patient morbidity and mortality. However, precise flow rate sensors are costly, so medical devices with limited budgets choose cheaper but unsatisfactory flow rate measurement approaches, leading to increased medical risks. Here, a photoelectric flow rate sensor based on a flexible planar curved beam structure (FPCBS) is proposed. The FPCBS ensures low out‐of‐plane stiffness of the sensitive sheet and allows large deformation in the elastic range, enabling the flow rate sensor to measure the flow rate with high sensitivity over a wide range. Meanwhile, the flow rate sensor can be mass‐produced using mature materials and manufacturing technology at less than $5 each. The flow rate sensors are integrated into a commercial infusion pump to measure drug infusion and a home ventilator to monitor respiration. The results are comparable to those measured by a commercial flow rate sensor, demonstrating the applicability of the sensor. Considering its proven outstanding performance at low cost, the flow rate sensor shows great potential in clinical treatment, medical diagnosis, and other medical fields.
A Rare False-Positive Whole-Body Scan in a Patient With Differentiated Thyroid Cancer
Authors: İlknur Ak Sivrikoz, Hakan Deveci, Nilgün Yıldırım
Journal: Clinical Nuclear Medicine (2024)

Abstract 131 I has been used effectively over the years in both diagnosis and therapy of differentiated thyroid cancer (DTC). Although whole-body scan with 131 I is a highly sensitive tool for detecting normal thyroid tissue and metastasis of DTC, it is not specific; therefore, false-positive images can be seen in clinical practice, and their recognition is critical for correct management. Evaluation of false-positive uptake is important because it may be confused with metastatic involvement. Here, we present a rare false-positive result of whole-body scan in a patient with DTC. To our knowledge, it is the first report on 131 I uptake of conjunctival concretions.
Intratumor microbiome-derived butyrate promotes lung cancer metastasis
Authors: Yi Ma, Haiming Chen, Haoran Li, Meiling Zheng, Xianglin Zuo, Wenxiang Wang, Shaodong Wang, Yiming Lu, Jun Wang, Yun Li, Jie Wang, Mantang Qiu
Journal: Cell Reports Medicine (2024)

Most recurrences of lung cancer (LC) occur within 3 years after surgery, but the underlying mechanism remains unclear. Here, we collect LC tissues with shorter (<3 years, recurrence group) and longer (>3 years, non-recurrence group) recurrence-free survival. By using 16S sequencing, we find that intratumor microbiome diversity is lower in the recurrence group and butyrate-producing bacteria are enriched in the recurrence group. The intratumor microbiome signature and circulating microbiome DNA can accurately predict LC recurrence. We prove that intratumor injection of butyrate-producing bacteria Roseburia can promote subcutaneous tumor growth. Mechanistically, bacteria-derived butyrate promotes LC metastasis by increasing expression of H19 in tumor cells through inhibiting HDAC2 and increasing H3K27 acetylation at the H19 promoter and inducing M2 macrophage polarization. Depletion of macrophages partially abolishes the metastasis-promoting effect of butyrate. Our results provide evidence for the cross-talk between the intratumor microbiome and LC metastasis and suggest the potential prognostic and therapeutic value of the intratumor microbiome.
FDG PET in Neurological Manifestations of COVID-19
Authors: Nikhil Seniaray, Ritu Verma, Rajeev Ranjan, Ethel Belho
Journal: Clinical Nuclear Medicine (2024)

Abstract Both the central and peripheral nervous systems can be affected in COVID-19. Although MRI is the primary investigative tool for neurological imaging, FDG PET may show additional areas of involvement in the brain in the form of regional hypometabolism or hypermetabolism, secondary to synaptic dysfunction and electrical or glial activation. We present a case series of 4 patients who had neurological symptoms attributable to COVID-19 infection with abnormalities in the brain FDG PET scan.
Multitarget Stool RNA Testing
Authors: Thomas F. Imperiale, Philip Lavin, David F. Ransohoff
Journal: JAMA (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 HomeNew OnlineCurrent IssueFor Authors 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Systemic and Neurosarcoidosis With Rare Involvement of the Extremities’ Peripheral Nerves
Authors: Fathima Fijula Palot Manzil, Joshua Eichhorn, Harleen Kaur
Journal: Clinical Nuclear Medicine (2024)

Abstract We present a case of sarcoidosis with a rare presentation of involvement of peripheral nerves of the lower limbs and subcutaneous nodules detected on 18 F-FDG PET/CT. The patient also had involvement of the spinal nerves and dura, histologically proven to be sarcoidosis. There were other manifestations of systemic sarcoidosis like metabolically active cervical and mediastinal lymphadenopathy. This case highlights the role of 18 F-FDG PET/CT in evaluating the uncommon sites of sarcoid involvement. Although many cases of sarcoid involvement of central nervous system have been reported, peripheral nerves involvement in the extremities was not found on a literature search.
Use of Recommended Neurodiagnostic Evaluation Among Patients With Drug-Resistant Epilepsy
Authors: Matthew Spotnitz, Cameron D. Ekanayake, Anna Ostropolets, Guy M. McKhann, Hyunmi Choi, Ruth Ottman, Alfred I. Neugut, George Hripcsak, Karthik Natarajan, Brett E. Youngerman
Journal: JAMA Neurology (2024)

Interdisciplinary practice parameters recommend that patients with drug-resistant epilepsy (DRE) undergo comprehensive neurodiagnostic evaluation, including presurgical assessment. Reporting from specialized centers suggests long delays to referral and underuse of surgery; however, longitudinal data are limited to characterize neurodiagnostic evaluation among patients with DRE in more diverse US settings and populations.
Multitarget Stool RNA Testing
Authors: Geoffrey Baird
Journal: JAMA (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 HomeNew OnlineCurrent IssueFor Authors 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Cooperation Between Medical and Correctional Stakeholders
Authors: Lawrence A. Haber, Brie A. Williams
Journal: JAMA Internal Medicine (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 Internal Medicine 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 Internal Medicine journal