tbuckley/cabot-search huggingface dataset:
Multiple introductions of monkeypox virus to Ireland during the international mpox outbreak, May 2022 to October 2023
Authors: Gabriel Gonzalez, Michael Carr, Tomás M Kelleher, Emer O’Byrne, Weronika Banka, Brian Keogan, Charlene Bennett, Geraldine Franzoni, Patrice Keane, Cliona Kenna, Luke W Meredith, Nicola Fletcher, Jose Maria Urtasun-Elizari, Jonathan Dean, Ciaran Browne, Fiona Lyons, Brendan Crowley, Derval Igoe, Eve Robinson, Greg Martin, Jeff Connell, Cillian F De Gascun, Daniel Hare
Journal: Eurosurveillance (2024)

BackgroundMpox, caused by monkeypox virus (MPXV), was considered a rare zoonotic disease before May 2022, when a global epidemic of cases in non-endemic countries led to the declaration of a Public Health Emergency of International Concern. Cases of mpox in Ireland, a country without previous mpox reports, could reflect extended local transmission or multiple epidemiological introductions.AimTo elucidate the origins and molecular characteristics of MPXV circulating in Ireland between May 2022 and October 2023.MethodsWhole genome sequencing of MPXV from 75% of all Irish mpox cases (182/242) was performed and compared to sequences retrieved from public databases (n = 3,362). Bayesian approaches were used to infer divergence time between sequences from different subclades and evaluate putative importation events from other countries.ResultsOf 242 detected mpox cases, 99% were males (median age: 35 years; range: 15-60). All 182 analysed genomes were assigned to Clade IIb and, presence of 12 distinguishable subclades suggests multiple introductions into Ireland. Estimation of time to divergence of subclades further supports the hypothesis for multiple importation events from numerous countries, indicative of extended and sustained international spread of mpox. Further analysis of sequences revealed that 92% of nucleotide mutations were from cytosine to thymine (or from guanine to adenine), leading to a high number of non-synonymous mutations across subclades; mutations associated with tecovirimat resistance were not observed.ConclusionWe provide insights into the international transmission dynamics supporting multiple introductions of MPXV into Ireland. Such information supported the implementation of evidence-informed public health control measures.
Author Correction: IFNγ binding to extracellular matrix prevents fatal systemic toxicity
Authors: Josephine Kemna, Evelyne Gout, Leon Daniau, Jessica Lao, Kristoffer Weißert, Sandra Ammann, Ralf Kühn, Matthias Richter, Christine Molenda, Anje Sporbert, Dario Zocholl, Robert Klopfleisch, Anja Schütz, Hugues Lortat-Jacob, Peter Aichele, Thomas Kammertoens, Thomas Blankenstein
Journal: Nature Immunology (2024)
Cardiovascular imaging research and innovation in 2023
Authors: Andrea Barison, Ana Teresa Timoteo, Riccardo Liga, Sonia Borodzicz-Jazdzyk, Saloua El Messaoudi, Christina Luong, Giulia Elena Mandoli, Sara Moscatelli, Arti Anushka Ramkisoensing, Sarah Moharem-Elgamal, Gianluca Pontone, Danilo Neglia
Journal:  (2024)

Abstract In 2023, cardiovascular imaging has made significant advancements, in terms of technology, pathophysiology, and clinical application. In this review, the most recent research findings in the field of cardiovascular imaging are discussed. Artificial intelligence and large population cohorts, together with several technical improvements, have had a crucial impact on the technological advancements of echocardiography, cardiovascular magnetic resonance, computed tomography (CT), and nuclear medicine. In the field of ischaemic heart disease, it has been demonstrated that appropriate non-invasive imaging strategies improve patients’ management and reduce invasive procedures and the need for additional testing at follow-up. Moreover, improvements in plaque characterization with CT are an expanding field of research with relevant implications for the prediction of disease severity, evolution, and response to treatment. In the field of valvular heart disease, imaging techniques have advanced alongside improvements in transcatheter treatment for aortic stenosis, mitral, and tricuspid regurgitation. Finally, in the field of heart failure and cardiomyopathies, cardiovascular imaging has reinforced its crucial role in early diagnosis and risk evaluation, showcasing advanced techniques that outperform traditional methods in predicting adverse outcomes.
Author Correction: MEF2C regulates NK cell effector functions through control of lipid metabolism
Authors: Joey H. Li, Adalia Zhou, Cassidy D. Lee, Siya N. Shah, Jeong Hyun Ji, Vignesh Senthilkumar, Eddie T. Padilla, Andréa B. Ball, Qinyan Feng, Christian G. Bustillos, Luke Riggan, Alain Greige, Ajit S. Divakaruni, Fran Annese, Jessica A. Cooley Coleman, Steven A. Skinner, Christopher W. Cowan, Timothy E. O’Sullivan
Journal: Nature Immunology (2024)
New Insights Optimize Landing Strategies to Reduce Lower Limb Injury Risk
Authors: Datao Xu, Huiyu Zhou, Wenjing Quan, Xin Ma, Teo-Ee Chon, Justin Fernandez, Fekete Gusztav, András Kovács, Julien S. Baker, Yaodong Gu
Journal: Cyborg and Bionic Systems (2024)

Single-leg landing (SL) is often associated with a high injury risk, especially anterior cruciate ligament (ACL) injuries and lateral ankle sprain. This work investigates the relationship between ankle motion patterns (ankle initial contact angle [AICA] and ankle range of motion [AROM]) and the lower limb injury risk during SL, and proposes an optimized landing strategy that can reduce the injury risk. To more realistically revert and simulate the ACL injury mechanics, we developed a knee musculoskeletal model that reverts the ACL ligament to a nonlinear short-term viscoelastic mechanical mechanism (strain rate-dependent) generated by the dense connective tissue as a function of strain. Sixty healthy male subjects were recruited to collect biomechanics data during SL. The correlation analysis was conducted to explore the relationship between AICA, AROM, and peak vertical ground reaction force (PVGRF), joint total energy dissipation (TED), peak ankle knee hip sagittal moment, peak ankle inversion angle (PAIA), and peak ACL force (PAF). AICA exhibits a negative correlation with PVGRF ( r = −0.591) and PAF ( r = −0.554), and a positive correlation with TED ( r = 0.490) and PAIA ( r = 0.502). AROM exhibits a positive correlation with TED ( r = 0.687) and PAIA ( r = 0.600). The results suggested that the appropriate increases in AICA (30° to 40°) and AROM (50° to 70°) may reduce the lower limb injury risk. This study has the potential to offer novel perspectives on the optimized application of landing strategies, thus giving the crucial theoretical basis for decreasing injury risk.
Precise prediction of cerebrospinal fluid amyloid beta protein for early Alzheimer's disease detection using multimodal data
Authors: Jingnan Sun, Zengmai Xie, Yike Sun, Anruo Shen, Renren Li, Xiao Yuan, Bai Lu, Yunxia Li
Journal: MedComm (2024)

Abstract Alzheimer's disease (AD) constitutes a neurodegenerative disorder marked by a progressive decline in cognitive function and memory capacity. The accurate diagnosis of this condition predominantly relies on cerebrospinal fluid (CSF) markers, notwithstanding the associated burdens of pain and substantial financial costs endured by patients. This study encompasses subjects exhibiting varying degrees of cognitive impairment, encompassing individuals with subjective cognitive decline, mild cognitive impairment, and dementia, constituting a total sample size of 82 participants. The primary objective of this investigation is to explore the relationships among brain atrophy measurements derived from magnetic resonance imaging, atypical electroencephalography (EEG) patterns, behavioral assessment scales, and amyloid β‐protein (Aβ) indicators. The findings of this research reveal that individuals displaying reduced Aβ1‐42/Aβ‐40 levels exhibit significant atrophy in the frontotemporal lobe, alongside irregularities in various parameters related to EEG frequency characteristics, signal complexity, inter‐regional information exchange, and microstates. The study additionally endeavors to estimate Aβ1‐42/Aβ‐40 content through the application of a random forest algorithm, amalgamating structural data, electrophysiological features, and clinical scales, achieving a remarkable predictive precision of 91.6%. In summary, this study proposes a cost‐effective methodology for acquiring CSF markers, thereby offering a valuable tool for the early detection of AD.
TIM-3 <sup>+</sup> CD8 T cells with a terminally exhausted phenotype retain functional capacity in hematological malignancies
Authors: Simone A. Minnie, Olivia G. Waltner, Ping Zhang, Shuichiro Takahashi, Nicole S. Nemychenkov, Kathleen S. Ensbey, Christine R. Schmidt, Samuel R. W. Legg, Melissa Comstock, Julie R. Boiko, Ethan Nelson, Shruti S. Bhise, Alec B. Wilkens, Motoko Koyama, Madhav V. Dhodapkar, Marta Chesi, Stanley R. Riddell, Damian J. Green, Andrew Spencer, Scott N. Furlan, Geoffrey R. Hill
Journal: Science Immunology (2024)

Chronic antigen stimulation is thought to generate dysfunctional CD8 T cells. Here, we identify a CD8 T cell subset in the bone marrow tumor microenvironment that, despite an apparent terminally exhausted phenotype (T PHEX ), expressed granzymes, perforin, and IFN-γ. Concurrent gene expression and DNA accessibility revealed that genes encoding these functional proteins correlated with BATF expression and motif accessibility. IFN-γ + T PHEX effectively killed myeloma with comparable efficacy to transitory effectors, and disease progression correlated with numerical deficits in IFN-γ + T PHEX . We also observed IFN-γ + T PHEX within CD19-targeted chimeric antigen receptor T cells, which killed CD19 + leukemia cells. An IFN-γ + T PHEX gene signature was recapitulated in T EX cells from human cancers, including myeloma and lymphoma. Here, we characterize a T EX subset in hematological malignancies that paradoxically retains function and is distinct from dysfunctional T EX found in chronic viral infections. Thus, IFN-γ + T PHEX represent a potential target for immunotherapy of blood cancers.
RBM22 regulates RNA polymerase II 5′ pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5
Authors: Xian Du, Wenying Qin, Chunyu Yang, Lin Dai, Mingkui San, Yingdan Xia, Siyu Zhou, Mengyang Wang, Shuang Wu, Shaorui Zhang, Huiting Zhou, Fangshu Li, Fang He, Jingfeng Tang, Jia-Yu Chen, Yu Zhou, Rui Xiao
Journal: Genome biology (2024)

Abstract Background Splicing factors are vital for the regulation of RNA splicing, but some have also been implicated in regulating transcription. The underlying molecular mechanisms of their involvement in transcriptional processes remain poorly understood. Results Here, we describe a direct role of splicing factor RBM22 in coordinating multiple steps of RNA Polymerase II (RNAPII) transcription in human cells. The RBM22 protein widely occupies the RNAPII-transcribed gene locus in the nucleus. Loss of RBM22 promotes RNAPII pause release, reduces elongation velocity, and provokes transcriptional readthrough genome-wide, coupled with production of transcripts containing sequences from downstream of the gene. RBM22 preferentially binds to the hyperphosphorylated, transcriptionally engaged RNAPII and coordinates its dynamics by regulating the homeostasis of the 7SK-P-TEFb complex and the association between RNAPII and SPT5 at the chromatin level. Conclusions Our results uncover the multifaceted role of RBM22 in orchestrating the transcriptional program of RNAPII and provide evidence implicating a splicing factor in both RNAPII elongation kinetics and termination control.
When I use a word . . . Artificial languages and medicine
Authors: Jeffrey K Aronson
Journal: BMJ (2024)

No one knows how human language began, although there are many theories. However, we do know something about the linguistic roots of languages. English, for example, is one of a group of languages in the IndoEuropean group, all of which are thought to have arisen from a single language, proto-IndoEuropean. Semitic languages came from proto-Semitic, Slavonic languages from proto-Slavonic, and so on. Artificial languages, such as Esperanto, have mostly been based on existing natural languages, with some exceptions, such as Klingon. One artificial language, Interlingua, largely based on Latin, was for a time used to publish summaries of papers published in medical journals. It hasn't lasted, however. After all, we already have an international scientific language. It's called English.
Clot removAl with or without decompRessive craniectomy under ICP monitoring for supratentorial IntraCerebral Hemorrhage (CARICH): a randomized controlled trial
Authors: Chao Zhang, Shuixian Zhang, Yi Yin, Long Wang, Lan Li, Chuan Lan, Jiantao Shi, Zhouyang Jiang, Hongfei Ge, Xuegang Li, Zaiyong Ao, Shengli Hu, Jingyu Chen, Hua Feng, Rong Hu
Journal: International Journal of Surgery (2024)

Decompressive craniectomy (DC), a surgery to remove part of the skull and open the dura mater, maybe an effective treatment for controlling intracranial hypertension. It remains great interest to elucidate whether DC is beneficial to intracerebral hemorrhage (ICH) patients who warrant clot removal (CR) to prevent intracranial hypertension.
A commentary on ‘ChatGPT in medicine: prospects and challenges: a review article’ -correspondence
Authors: ArunSundar MohanaSundaram, Talha Bin Emran
Journal: International Journal of Surgery (2024)

aSchool of Pharmacy, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India bDepartment of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article. Published online ■ ■ *Corresponding author. Address: Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh, Cell: +88-01819942214. E-mail address: [email protected] (T.B. Emran). *Corresponding author. Address: School of Pharmacy, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India. Cell: +91 44 2450 3067. E-mail address: [email protected] (A.S. MohanaSundaram). This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0/
Letter to the Editor [“Long-term quality of life between duodenum-preserving pancreatic head resection and pancreatoduodenectomy: a systematic review and meta-analysis”]
Authors: Yong-Hui Sun, Nan Ding, Hai Lin, Kun Cheng, Hao Ding, Qi-Long Chen
Journal: International Journal of Surgery (2024)

Sun, Yong-Hui; Ding, Nan; Lin, Hai; Cheng, Kun; Ding, Hao; Chen, Qi-Long Author Information
The risk factors for postoperative temporary vocal cord paralysis after thyroid cancer surgery: an observational retrospective cohort study
Authors: Yujia Han, Yishen Zhao, Jiedong Kou, Jingting Li, Fang Li, Rui Du, Gianlorenzo Dionigi, Francesco Frattini, Nan Liang, Hui Sun
Journal: International Journal of Surgery (2024)

To analyze the potential factors influencing new-onset postoperative transient vocal cord paralysis (VCP) in thyroid cancer patients.
A commentary on “Circulating 25-hydroxyvitamin D concentration can predict bowel resection risk among individuals with inflammatory bowel disease in a longitudinal cohort with 13 years of follow-up”
Authors: Biao Liang, Yiheng Yang, Wang Zhenyi
Journal: International Journal of Surgery (2024)

Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article. Published online ■ ■ *Corresponding author. Address: Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China. Tel: +86 0216-5161782. E-mail address: [email protected] (Z. Wang). This is an open access article distributed under the Creative Commons Attribution-ShareAlike License 4.0, which allows others to remix, tweak, and build upon the work, even for commercial purposes, as long as the author is credited and the new creations are licensed under the identical terms. http://creativecommons.org/licenses/by-sa/4.0/
American Society for Gastrointestinal Endoscopy–European Society of Gastrointestinal Endoscopy guideline on primary endoscopic bariatric and metabolic therapies for adults with obesity
Authors: Pichamol Jirapinyo, Alia Hadefi, Vincent Huberty, Shelby Sullivan, Christopher C. Thompson, Árpád V. Patai, Rahul Pannala, Stefan K. Goelder, Vladimir Kushnir, Marc Barthet, Caroline M. Apovian, Ivo Boskoski, Christopher G. Chapman, Paul Davidson, Gianfranco Donatelli, Vivek Kumbhari, Bu Hayee, Janelle Esker, Tomas Hucl, Aurora D. Pryor, Roberta Maselli, Allison R. Schulman, Francois Pattou, Shira Zelber-Sagi, Paul A. Bain, Valérie Durieux, Konstantinos Triantafyllou, Nirav Thosani
Journal: Endoscopy (2024)

This joint ASGE-ESGE guideline provides an evidence-based summary and recommendations regarding the role of endoscopic bariatric and metabolic therapies (EBMTs) in the management of obesity. The document was developed using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) framework. It evaluates the efficacy and safety of EBMT devices and procedures that currently have CE mark or FDA-clearance/approval, or that had been approved within five years of document development. The guideline suggests the use of EBMTs plus lifestyle modification in patients with a BMI of ≥30 kg/m
Society for Immunotherapy of Cancer (SITC) recommendations on intratumoral immunotherapy clinical trials (IICT): from premalignant to metastatic disease
Authors: Jason J Luke, Diwakar Davar, Robert H Andtbacka, Nina Bhardwaj, Joshua D Brody, Jason Chesney, Robert Coffin, Thierry de Baere, Tanja D de Gruijl, Matthew Fury, Gregory Goldmacher, Kevin J Harrington, Howard Kaufman, Ciara M Kelly, Anuradha D Khilnani, Ke Liu, Sherene Loi, Georgina V Long, Ignacio Melero, Mark Middleton, Bart Neyns, David J Pinato, Rahul A Sheth, Stephen B Solomon, Philippe Szapary, Aurelien Marabelle
Journal: Journal for ImmunoTherapy of Cancer (2024)

Intratumorally delivered immunotherapies have the potential to favorably alter the local tumor microenvironment and may stimulate systemic host immunity, offering an alternative or adjunct to other local and systemic treatments. Despite their potential, these therapies have had limited success in late-phase trials for advanced cancer resulting in few formal approvals. The Society for Immunotherapy of Cancer (SITC) convened a panel of experts to determine how to design clinical trials with the greatest chance of demonstrating the benefits of intratumoral immunotherapy for patients with cancers across all stages of pathogenesis.
HDAC inhibitors as pharmacological treatment for Duchenne muscular dystrophy: a discovery journey from bench to patients
Authors: Chiara Mozzetta, Vittorio Sartorelli, Christian Steinkuhler, Pier Lorenzo Puri
Journal: Trends in Molecular Medicine (2024)

For personal reasons, Christian Steinkuhler requested to withdraw as author from the original review. All remaining authors of the review and the editor of Trends in Molecular Medicine have agreed on the withdrawal. This change does not affect the conclusions mentioned in the review. The authors apologize for any inconvenience this may cause. The updated author list and affiliations are as follows: Chiara Mozzetta,1 Vittorio Sartorelli,2 and Pier Lorenzo Puri3,* 1Institute of Molecular Biology and Pathology, National Research Council of Italy, Rome, Italy 2Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA 3Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA *Correspondence: [email protected] (P.L. Puri). The updated declaration of interests upon withdrawal of the author appears below. Declaration of interests The authors have no interests to declare. HDAC inhibitors as pharmacological treatment for Duchenne muscular dystrophy: a discovery journey from bench to patientsMozzetta et al.Trends in Molecular MedicineFebruary 25, 2024In BriefEarlier evidence that targeting the balance between histone acetyltransferases (HATs) and deacetylases (HDACs), through exposure to HDAC inhibitors (HDACis), could enhance skeletal myogenesis, prompted interest in using HDACis to promote muscle regeneration. Further identification of constitutive HDAC activation in dystrophin-deficient muscles, caused by dysregulated nitric oxide (NO) signaling, provided the rationale for HDACi-based therapeutic interventions for Duchenne muscular dystrophy (DMD). In this review, we describe the molecular, preclinical, and clinical evidence supporting the efficacy of HDACis in countering disease progression by targeting pathogenic networks of gene expression in multiple muscle-resident cell types of patients with DMD. Given that givinostat is paving the way for HDACi-based interventions in DMD, next-generation HDACis with optimized therapeutic profiles and efficacy could be also explored for synergistic combinations with other therapeutic strategies. Full-Text PDF
QDPR deficiency drives immune suppression in pancreatic cancer
Authors: Ji Liu, Xiaowei He, Shuang Deng, Sihan Zhao, Shaoping Zhang, Ziming Chen, Chunling Xue, Lingxing Zeng, Hongzhe Zhao, Yifan Zhou, Ruihong Bai, Zilan Xu, Shaoqiu Liu, Quanbo Zhou, Mei Li, Jialiang Zhang, Xudong Huang, Rufu Chen, Liqin Wang, Dongxin Lin, Jian Zheng
Journal: Cell Metabolism (2024)
Genome-first evaluation with exome sequence and clinical data uncovers underdiagnosed genetic disorders in a large healthcare system
Authors: Iain S. Forrest, Áine Duffy, Joshua K. Park, Ha My T. Vy, Louis R. Pasquale, Girish N. Nadkarni, Judy H. Cho, Ron Do
Journal: Cell Reports Medicine (2024)

Population-based genomic screening may help diagnose individuals with disease-risk variants. Here, we perform a genome-first evaluation for nine disorders in 29,039 participants with linked exome sequences and electronic health records (EHRs). We identify 614 individuals with 303 pathogenic/likely pathogenic or predicted loss-of-function (P/LP/LoF) variants, yielding 644 observations; 487 observations (76%) lack a corresponding clinical diagnosis in the EHR. Upon further investigation, 75 clinically undiagnosed observations (15%) have evidence of symptomatic untreated disease, including familial hypercholesterolemia (3 of 6 [50%] undiagnosed observations with disease evidence) and breast cancer (23 of 106 [22%]). These genetic findings enable targeted phenotyping that reveals new diagnoses in previously undiagnosed individuals. Disease yield is greater with variants in penetrant genes for which disease is observed in carriers in an independent cohort. The prevalence of P/LP/LoF variants exceeds that of clinical diagnoses, and some clinically undiagnosed carriers are discovered to have disease. These results highlight the potential of population-based genomic screening.