tbuckley/cabot-search huggingface dataset:
Current state of COVID-19 in children: 4 years on
Authors: Annabel A. Powell, Alexander C. Dowell, Paul Moss, Shamez N. Ladhani
Journal: Journal of Infection (2024)

Children have been disproportionately affected by the COVID-19 pandemic. Despite evidence of a very low risk of severe disease, children were subjected to extensive lockdown, restriction and mitigation measures, including school closures, to control the rapid spread of SARS-CoV-2 in most parts of the world. In this review we summarise the UK experience of COVID-19 in children four years into the largest and longest pandemic of this century. We address the risks of SARS-CoV-2 infection, immunity, transmission, severity and outcomes in children. We also assess the implementation, uptake, effectiveness and impact of COVID-19 vaccination, as well as the emergence, evolution and near disappearance of PIMS-TS (paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2) and current understanding of long COVID in children. This review consolidates current knowledge on childhood COVID-19 and emphasises the importance of continued research and the need for research-driven public health actions and policy decisions, especially in the context of new variants and future vaccines.
The Efficacy of Real-time Computer-aided Detection of Colonic Neoplasia in Community Practice: A Pragmatic Randomized Controlled Trial
Authors: Nikhil R. Thiruvengadam, Pejman Solaimani, Manish Shrestha, Seth Buller, Rachel Carson, Breanna Reyes-Garcia, Ronaldo D. Gnass, Bing Wang, Natalie Albasha, Paul Leonor, Monica Saumoy, Raul Coimbra, Arnold Tabuenca, Wichit Srikureja, Steve Serrao
Journal: Clinical Gastroenterology and Hepatology (2024)

The use of computer-aided detection (CADe) has increased the adenoma detection rates (ADRs) during colorectal cancer (CRC) screening/surveillance in randomized controlled trials (RCTs) but has not shown benefit in real-world implementation studies. We performed a single-center pragmatic RCT to evaluate the impact of real-time CADe on ADRs in colonoscopy performed by community gastroenterologists.
Innovative Biomaterials for Bone Tumor Treatment and Regeneration: Tackling Postoperative Challenges and Charting the Path Forward
Authors: Yu Wang, Huaiyuan Zhang, Huifen Qiang, Meigui Li, Yili Cai, Xuan Zhou, Yanlong Xu, Zhenzhen Yan, Jinhua Dong, Yuan Gao, Chengye Pan, Xiaojing Yin, Jie Gao, Tinglin Zhang, Zuochong Yu
Journal: Advanced Healthcare Materials (2024)

Abstract Surgical resection of bone tumors is the primary approach employed in the treatment of bone cancer. Simultaneously, perioperative interventions, particularly postoperative adjuvant anticancer strategies, play a crucial role in achieving satisfactory therapeutic outcomes. However, the occurrence of postoperative bone tumor recurrence, metastasis, extensive bone defects, and infection are significant risks that can result in unfavorable prognoses or even treatment failure. In recent years, there has been significant progress in the development of biomaterials, leading to the emergence of new treatment options for bone tumor therapy and bone regeneration. This progress report aims to comprehensively analyze the strategic development of unique therapeutic biomaterials with inherent healing properties and bioactive capabilities for bone tissue regeneration. These composite biomaterials, classified into metallic, inorganic non‐metallic, and organic types, are thoroughly investigated for their responses to external stimuli such as light or magnetic fields, internal interventions including chemotherapy or catalytic therapy, and combination therapy, as well as their role in bone regeneration. Additionally, an overview of self‐healing materials for osteogenesis is provided and their potential applications in combating osteosarcoma and promoting bone formation are explored. Furthermore, the safety concerns of integrated materials and current limitations are addressed, while also discussing the challenges and future prospects.
Persistent sex and race disparities in United States anaphylaxis mortality from 1999 to 2020
Authors: Ingrid Salciccioli, Padmanabh Bhatt, Joseph Shalhoub, Dominic Marshall, Justin Salciccioli, Kimberly Blumenthal
Journal: Allergy (2024)

The data that support the findings of this study are available in National Center for Health Statistics Mortality Data on CDC at https://wonder.cdc.gov/mcd.html, reference number 4. These data were derived from the following resources available in the public domain: CDC WONDER, https://wonder.cdc.gov/controller/datarequest/D176. Table S1. Table S2. Table S3. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
House dust mite <scp>SCIT</scp> reduces asthma risk and significantly improves long‐term rhinitis and asthma control—A <scp>RWE</scp> study
Authors: Marek Jutel, Ludger Klimek, Hartmut Richter, Bernd Brüggenjürgen, Christian Vogelberg
Journal: Allergy (2024)

Abstract Background The German Therapy Allergen Ordinance (TAO) triggered an ongoing upheaval in the market for house dust mite (HDM) allergen immunotherapy (AIT) products. Three HDM subcutaneous AIT (SCIT) products hold approval in Germany and therefore will be available after the scheduled completion of the TAO procedure in 2026. In general, data from clinical trials on the long‐term effectiveness of HDM AIT are rare. We evaluated real‐world data (RWD) in a retrospective, observational cohort study based on a longitudinal claims database including 60% of all German statutory healthcare prescriptions to show the long‐term effectiveness of one of these products in daily life. Aim of this analysis was to provide a per product analysis on effectiveness of mite AIT as it is demanded by international guidelines on AIT. Methods Subjects between 5 and 70 years receiving their first (index) prescription of SCIT with a native HDM product (SCIT group) between 2009 and 2013 were included. The exactly 3:1 matched control group received prescriptions for only symptomatic AR medication (non‐AIT group); the evaluation period for up to 6 years of follow‐up ended in February 2017. Study endpoints were the progression of allergic rhinitis (AR) and asthma, asthma occurrence and time to the onset of asthma after at least 2 treatment years. Results In total, 892 subjects (608 adults and 284 children/adolescents) were included in the SCIT group and 2676 subjects (1824 adults and 852 children/adolescents) in the non‐AIT group. During the follow‐up period after at least 2 years of SCIT, the number of prescriptions in the SCIT group was reduced by 62.8% ( p &lt; .0001) for AR medication and by 42.4% for asthma medication ( p = .0003). New‐onset asthma risk was significantly reduced in the SCIT vs non‐AIT group by 27.0% ( p = .0212). The asthma‐preventive effect of SCIT occurred 15 months after start of the treatment. In the SCIT group, the time to onset of asthma was prolonged compared to the non‐AIT group ( p = .0010). Conclusion In this first product based RWD analysis on SCIT with a native HDM product, patients aged 5 to 70 years benefited from AIT in the long term in terms of reduced progression of AR and asthma after at least 2 years of treatment. The effects seemed to last for up to 6 years after treatment termination. A significantly reduced risk of asthma onset was observed, starting after 15 months of treatment.
Real‐world evidence: Long‐term safety of deferiprone in a large cohort of patients with sickle cell disease enrolled in a registry for up to 10 years
Authors: Janet L. Kwiatkowski, Alexis A. Thompson, Fernando Tricta, Noemi Toiber Temin, Anna Rozova, Caroline Fradette, Sherif M. Badawy
Journal: American Journal of Hematology (2024)

Abstract Patients with sickle cell disease (SCD) and other anemias who receive blood transfusions are at risk of organ damage due to transfusional iron overload. Deferiprone is an iron chelator with a well‐established safety and efficacy profile that is indicated for the treatment of transfusional iron overload. Here, we report safety data from the large‐scale, retrospective Ferriprox® Total Care Registry, which involved all patients with SCD taking deferiprone following the 2011 approval of deferiprone in the United States through August 2020. A total of 634 patients who had initiated deferiprone treatment were included. The mean (SD) duration of deferiprone exposure in the registry was 1.6 (1.6) years (range 0 to 9.7 years). In the overall patient population ( N = 634), 64.7% ( n = 410) of patients reported a total of 1885 adverse events (AEs). In subgroup analyses, 54.6% ( n = 71) of pediatric patients and 67.3% ( n = 339) of adult patients reported AEs. The most common AEs reported in patients receiving deferiprone were sickle cell crisis (22.7%), nausea (12.1%), vomiting (8.7%), abdominal discomfort (5.4%), and fatigue (5.4%). Neutropenia was reported in four (0.6%) patients and severe neutropenia/agranulocytosis (defined as absolute neutrophil count &lt;0.5 × 10 9 /L) was reported in two (0.3%) patients. Of patients with evaluable data, all cases of neutropenia and severe neutropenia/agranulocytosis resolved with deferiprone discontinuation. Results from the nearly 10 years of real‐world data collected in the Ferriprox® Total Care Registry demonstrate that deferiprone is safe and well tolerated in patients with SCD or other anemias who have transfusional iron overload.
Metabolomic signatures of inflammation and metabolic dysregulation in relation to colorectal cancer risk
Authors: Alaina M Bever, Dong Hang, Dong Hoon Lee, Fred K Tabung, Tomotaka Ugai, Shuji Ogino, Jeffrey A Meyerhardt, Andrew T Chan, A Heather Eliassen, Liming Liang, Meir J Stampfer, Mingyang Song
Journal: JNCI Journal of the National Cancer Institute (2024)

Abstract Background Inflammation and metabolic dysregulation are associated with increased risk of colorectal cancer (CRC); the underlying mechanisms are not fully understood. We characterized metabolomic signatures of inflammation and metabolic dysregulation and evaluated the association of the signatures and individual metabolites with CRC risk. Methods Among 684 incident CRC cases and 684 age-matched controls in the Nurses’ Health Study (n = 818 women) and Health Professionals Follow-up Study (n = 550 men), we applied reduced rank and elastic net regression to 277 metabolites for markers of inflammation (C-reactive protein, interleukin 6, tumor necrosis factor receptor superfamily member 1B, and growth differentiation factor 15) or metabolic dysregulation (body mass index, waist circumference, C-peptide, and adiponectin) to derive metabolomic signatures. We evaluated the association of the signatures and individual metabolites with CRC using multivariable conditional logistic regression. All statistical tests were 2-sided. Results We derived a signature of 100 metabolites that explained 24% of variation in markers of inflammation and a signature of 73 metabolites that explained 27% of variation in markers of metabolic dysregulation. Among men, both signatures were associated with CRC (odds ratio [OR] = 1.34, 95% confidence interval [CI] = 1.07 to 1.68 per 1-standard deviation increase, inflammation; OR = 1.25, 95% CI = 1.00 to 1.55 metabolic dysregulation); neither signature was associated with CRC in women. A total of 11 metabolites were individually associated with CRC and biomarkers of inflammation or metabolic dysregulation among either men or women. Conclusion We derived metabolomic signatures and identified individual metabolites associated with inflammation, metabolic dysregulation, and CRC, highlighting several metabolites as promising candidates involved in the inflammatory and metabolic dysregulation pathways for CRC incidence.
KoNA: Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data
Authors: Gunhwan Ko, Jae Ho Lee, Young Mi Sim, Wangho Song, Byung-Ha Yoon, Iksu Byeon, Bang Hyuck Lee, Sang-Ok Kim, Jinhyuk Choi, Insoo Jang, Hyerin Kim, Jin Ok Yang, Kiwon Jang, Sora Kim, Jong-Hwan Kim, Jongbum Jeon, Jaeeun Jung, Seungwoo Hwang, Ji-Hwan Park, Pan-Gyu Kim, Seon-Young Kim, Byungwook Lee
Journal: Genomics Proteomics & Bioinformatics (2024)

Abstract During the last decade, the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges, including access to human data, as well as transfer, storage, and sharing of enormous amounts of data. To promote data-driven biological research, the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. Here, we introduce the Korean Nucleotide Archive (KoNA), a repository of nucleotide sequence data. As of July 2022, the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome projects. To ensure data quality and prepare for international alignment, a standard operating procedure was adopted, which is similar to that of the International Nucleotide Sequence Database Collaboration. The standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline, followed by manual examination. To ensure fast and stable data transfer, a high-speed transmission system called GBox is used in KoNA. Furthermore, the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called Bio-Express. This seamless coupling of KoNA, GBox, and Bio-Express enhances the data experience, including submission, access, and analysis of raw nucleotide sequences. KoNA not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in genomics. The KoNA is available at https://www.kobic.re.kr/kona/.
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search
Authors: Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou
Journal: Genomics Proteomics & Bioinformatics (2024)

Abstract Recent success of AlphaFold2 in protein structure prediction relied heavily on co-evolutionary information derived from homologous protein sequences found in the huge, integrated database of protein sequences (Big Fantastic Database). In contrast, the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search. Here, we built a comprehensive database by incorporating the non-coding RNA (ncRNA) sequences from RNAcentral, the transcriptome assembly and metagenome assembly from metagenomics RAST (MG-RAST), the genomic sequences from Genome Warehouse (GWH), and the genomic sequences from MGnify, in addition to the nucleotide (nt) database and its subsets in National Center of Biotechnology Information (NCBI). The resulting Master database of All possible RNA sequences (MARS) is 20-fold larger than NCBI’s nt database or 60-fold larger than RNAcentral. The new dataset along with a new split–search strategy allows a substantial improvement in homology search over existing state-of-the-art techniques. It also yields more accurate and more sensitive multiple sequence alignments (MSAs) than manually curated MSAs from Rfam for the majority of structured RNAs mapped to Rfam. The results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on MSAs. MARS is accessible at https://ngdc.cncb.ac.cn/omix/release/OMIX003037, and RNAcmap3 is accessible at http://zhouyq-lab.szbl.ac.cn/download/.
Remodeling Microenvironment for Implant‐Associated Osteomyelitis by Dual Metal Peroxide
Authors: Xin Guan, Siyuan Wu, Sixue Ouyang, Shuchen Ren, Naiqian Cui, Xiaohu Wu, Dayong Xiang, Wenting Chen, Bin Yu, Peng Zhao, Bowei Wang
Journal: Advanced Healthcare Materials (2024)

Abstract Implant‐associated osteomyelitis (IAOM) is characterized by bone infection and destruction; current therapy of antibiotic treatment and surgical debridement often results in drug resistance and bone defect. It is challenging to develop an antibiotic‐free bactericidal and osteogenic‐enhanced strategy for IAOM. Herein, an IAOM‐tailored antibacterial and osteoinductive composite of copper (Cu)–strontium (Sr) peroxide nanoparticles (CSp NPs), encapsulated in polyethylene glycol diacrylate (PEGDA) (CSp@PEGDA), is designed. The dual functional CSp NPs display hydrogen peroxide (H 2 O 2 ) self‐supplying and Fenton catalytic Cu 2+ ions’ release, generating plenty of hydroxyl radical ( • OH) in a pH‐responsive manner for bacterial killing, while the released Sr 2+ promotes the in vitro osteogenicity regarding cell proliferation, alkaline phosphatase activity, extracellular matrix calcification, and osteo‐associated genes expression. The integration of Cu 2+ and Sr 2+ in CSp NPs together with the coated PEGDA hydrogel ensures the stable and sustainable ion release during short‐ and long‐term periods. Benefitted from the injectablity and photo‐crosslink ability, CSp@PEGDA is able to thoroughly fill the infectious site and gelate in situ for bacterial elimination and bone regeneration, which is verified through in vivo evaluation using a clinical‐simulating IAOM mouse model. These favorable abilities of CSp@PEGDA precisely meet the multiple therapeutic needs and pave a promising way for implant‐associated osteomyelitis treatment.
Circulating biomarkers of inflammaging and Alzheimer’s disease to track age-related trajectories of dementia: Can we develop a clinically relevant composite combination?
Authors: Angela Marie Abbatecola, Angelica Giuliani, Leonardo Biscetti, Lucia Scisciola, Petronilla Battista, Michelangela Barbieri, Jacopo Sabbatinelli, Fabiola Olivieri
Journal: Ageing Research Reviews (2024)
Prevalence of Gastric Precursor Lesions in Countries With Differential Gastric Cancer Burden: A Systematic Review and Meta-analysis
Authors: Duco T. Mülder, Anne I. Hahn, Robert J. Huang, Margaret J. Zhou, Benjamin Blake, Omonefe Omofuma, John D. Murphy, Daniela S. Gutiérrez-Torres, Ann G. Zauber, James F. O’Mahony, M. Constanza Camargo, Uri Ladabaum, Jennifer M. Yeh, Chin Hur, Iris Lansdorp-Vogelaar, Reinier Meester, Monika Laszkowska
Journal: Clinical Gastroenterology and Hepatology (2024)
Microphysiological Blood‐Brain Barrier Systems for Disease Modeling and Drug Development
Authors: Atharva R. Mulay, Jihyun Hwang, Deok‐Ho Kim
Journal: Advanced Healthcare Materials (2024)

Abstract The blood‐brain barrier (BBB) is a highly controlled microenvironment that regulates the interactions between cerebral blood and brain tissue. Due to its selectivity, many therapeutics targeting various neurological disorders are not able to penetrate into brain tissue. Pre‐clinical studies using animals and other in vitro platforms have not shown the ability to fully replicate the human BBB leading to the failure of a majority of therapeutics in clinical trials. However, recent innovations in vitro and ex vivo modeling called organs‐on‐chips have shown the potential to create more accurate disease models for improved drug development. These microfluidic platforms induce physiological stressors on cultured cells and are able to generate more physiologically accurate BBBs compared to previous in vitro models. In this review, different approaches to create BBBs‐on‐chips are explored alongside their application in modeling various neurological disorders and potential therapeutic efficacy. Additionally, organs‐on‐chips use in BBB drug delivery studies is discussed, and advances in linking brain organs‐on‐chips onto multiorgan platforms to mimic organ crosstalk are reviewed.
Biventricular interaction and aortic function in adult patients with repaired tetralogy of Fallot: a two-dimensional–three-dimensional speckle-tracking echocardiographic study
Authors: Antonio Vitarelli, Lidia Capotosto, Fabio Miraldi, Khaled Mukred, Marco Francone, Nicola Galea, Enrico Mangieri, Gaetano Tanzilli, Nicola Viceconte, Massimo Mancone, Bich Lien Nguyen, Costantino Smaldone, Sulaiman Al-Kindy
Journal:  (2024)

Abstract Aims In patients late after correction of tetralogy of Fallot (TOF), the combined effects of pre-operative hypertrophy and hypoxia, ventricular interdependence, acquired post-operative lesions such as pulmonary or aortic regurgitation, and congenital vasculopathy may result in impaired right ventricular (RV) and left ventricular (LV) function. The aim of the present study was to investigate the interventricular interactions in repaired TOF (rTOF) and the impact of aortic function on biventricular performance using two-dimensional (2D-STE) and three-dimensional speckle-tracking echocardiography (3D-STE). Methods and results Twenty-five adult patients with rTOF and 25 age- and gender-matched healthy controls were studied. LV and RV volumes were determined by 3D-STE and cardiac magnetic resonance. LV and RV longitudinal strains (LVLS and RVLS) and LV and RV area strains (LVAS and RVAS) and LV twist/rotation were calculated by 3D-STE. Ascending aorta circumferential strain (AAo-CS) was obtained using 2D-STE. LV 3D-STE parameters were decreased in rTOF patients compared with controls even in patients with normal ejection fraction. AAo-CS was decreased (6.7 ± 1.9 vs. 10.1 ± 2.6, P = 0.003) in rTOF patients compared with controls even in the presence of normal aortic dimensions and correlated with AAo diameter (r = −0.69, P = 0.0001), LV twist (r = 0.54, P = 0.004), LVAS (r = −0.56, P = 0.003), and RVLS (r = −0.39, P = 0.036). LVAS and AAo-CS were associated with disease severity (peak oxygen consumption and arrhythmia occurrence). Significant improvement in global χ2 value was noted with RV 3D-STE parameters + LVAS + AAo-CS compared with RV dysfunction alone for detecting exercise capacity impairment (from 77.1 to 84.4 to 91.2, P = 0.003). Conclusion Speckle-tracking echocardiography revealed subtle LV and AAo dysfunction in adults with rTOF. A correlation was observed between LV and RV strain changes and between AAo strain impairment and LV/RV dysfunction. LV and AAo changes had an incremental value in evaluating disease severity.
Asparaginase completion among adults including older patients with acute lymphoblastic leukemia treated with a modified DFCI protocol
Authors: Maria Agustina Perusini, Claire Andrews, Atenafu G. Eshetu, Vikas Gupta, Dawn Maze, Karen W. L. Yee, Aniket Bankar, Marta B. Davidson, Guillaume Richard-Carpentier, Steven M. Chan, Aaron D. Schimmer, Jad Sibai, Salman Alharbi, Josephine A. Lucero, Swe Mar Linn, Mark D. Minden, Andre C. Schuh, Hassan Sibai
Journal: Leukemia (2024)