tbuckley/cabot-search huggingface dataset:
Systematic immune cell dysregulation and molecular subtypes revealed by single-cell RNA-seq of subjects with type 1 diabetes
Authors: Mohammad Amin Honardoost, Andreas Adinatha, Florian Schmidt, Bobby Ranjan, Maryam Ghaeidamini, Nirmala Arul Rayan, Michelle Gek Liang Lim, Ignasius Joanito, Quy Xiao Xuan Lin, Deepa Rajagopalan, Shi Qi Mok, You Yi Hwang, Anis Larbi, Chiea Chuen Khor, Roger Foo, Bernhard Otto Boehm, Shyam Prabhakar
Journal: Genome Medicine (2024)

Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting
EGFR Oncogenic Mutations in NSCLC Impair Macrophage Phagocytosis and Mediate Innate Immune Evasion Through Up-Regulation of CD47
Authors: Li-Yang Hu, Wei-Tao Zhuang, Mao-Jian Chen, Jun Liao, Dong-Fang Wu, Ya-Xiong Zhang, Lan-Lan Pang, Yi-Hua Huang, Tian-Qin Mao, Meng-Juan Yang, Pei-Jian Peng, Jin-Xia Liang, Liang Chen, Lin-Juan Zeng, Li Zhang, Wen-Feng Fang
Journal: Journal of Thoracic Oncology (2024)
Evaluation of safety and early efficacy of AAV gene therapy in mouse models of vanishing white matter disease
Authors: Jessica A Herstine, Pi-Kai Chang, Sergiy Chornyy, Tamara J Stevenson, Alex C Sunshine, Ksenia Nokhrina, Jessica Rediger, Julia Wentz, Tatyana A Vetter, Erika Scholl, Caleb Holaway, Nettie K Pyne, Anna Bratasz, Stewart Yeoh, Kevin M Flanigan, Joshua L Bonkowsky, Allison M Bradbury
Journal: Molecular Therapy (2024)
Anti-CD45 PBD-based antibody-drug conjugates are effective targeted conditioning agents for gene therapy and stem cell transplant
Authors: Jenny Yeung, Aiyin Liao, Matthew Shaw, Soraia Silva, Winston Vetharoy, Diego Leon Rico, Ian Kirby, Francesca Zammarchi, Karin Havenith, Lolke de Haan, Patrick H van Berkel, Neil Sebire, Olumide K Ogunbiyi, Claire Booth, H Bobby Gaspar, Adrian J Thrasher, Kerry A Chester, Persis J Amrolia
Journal: Molecular Therapy (2024)
Stuck in pandemic uncertainty: a review of the persistent effects of COVID-19 infection in immune-deficient people
Authors: Bevin Manuelpillai, Mackenzie Zendt, Emma Chang-Rabley, Emily E. Ricotta
Journal: Clinical Microbiology and Infection (2024)

Background Immune-deficient/disordered people (IDP) are underrepresented in COVID-19 studies. Specifically, there is limited research on post-SARS-CoV-2 infection outcomes, including viral persistence and long-term sequelae in these populations. Objectives This review aimed to examine the published literature on the occurrence of persistent SARS-CoV-2 positivity, relapse, reinfections, variant coinfection, and post-acute sequelae of COVID-19 in IDP. While the available literature largely centered on those with secondary immunodeficiencies, studies on people with inborn errors of immunity are also included. Sources PubMed was searched using Medical Subject Headings (MeSH) terms to identify relevant articles from the last four years. Articles on primary and secondary immunodeficiencies were chosen and a special emphasis was placed on including articles that studied people with inborn errors of immunity. The absence of extensive cohort studies including these individuals has limited most articles in this review to case reports, whereas the articles focusing on secondary immunodeficiencies include larger cohort, case-control, and cross-sectional studies. Articles focusing solely on HIV/AIDS were excluded. Content Scientific literature suggests that IDP of any age are more likely to experience persistent SARS-CoV-2 infections. While adult IDP exhibit a higher rate of post-acute sequelae of COVID-19 (PASC), milder COVID-19 infections in children may reduce their risk of experiencing PASC. Reinfections and coinfections may occur at a slightly higher rate in IDP than the general population. Implications While IDP experience increased viral persistence and inter-host evolution, it is unlikely that enough evidence can be generated at the population-level to support or refute the hypothesis that infections in IDP are significantly more likely to result in variants of concern than infections in the general population. Additional research on the relationship between viral persistence and the rate of long-term sequelae in IDP could inform the understanding of the immune response to SARS-CoV-2 in IDP and the general population.
From animal models to gut-on-chip: the challenging journey to capture inter-individual variability in chronic digestive disorders
Authors: Aicha Kriaa, Vincent Mariaule, Charlotte De Rudder, Amin Jablaoui, Harry Sokol, Paul Wilmes, Emmanuelle Maguin, Moez Rhimi
Journal: Gut Microbes (2024)

Chronic digestive disorders are of increasing incidence worldwide with expensive treatments and no available cure. Available therapeutic schemes mainly rely on symptom relief, with large degrees of variability in patients' response to such treatments, underlining the need for new therapeutic strategies. There are strong indications that the gut microbiota's contribution seems to be a key modulator of disease activity and patients' treatment responses. Hence, efforts have been devoted to understanding host–microbe interactions and the mechanisms underpinning such variability. Animal models, being the gold standard, provide valuable mechanistic insights into host–microbe interactions. However, they are not exempt from limitations prompting the development of alternative methods. Emerging microfluidic technologies and gut-on-chip models were shown to mirror the main features of gut physiology and disease state, reflect microbiota modification, and include functional readouts for studying host responses. In this commentary, we discuss the relevance of animal models in understanding host–microbe interactions and how gut-on-chip technology holds promises for addressing patient variability in responses to chronic digestive disease treatment.
Intuition-Guided Reinforcement Learning for Soft Tissue Manipulation with Unknown Constraints
Authors: Xian He, Shuai Zhang, Jian Chu, Tongyu Jia, Lantao Yu, Bo Ouyang
Journal: Cyborg and Bionic Systems (2024)

Intraoperative soft tissue manipulation is a critical challenge in autonomous robotic surgery. Furthermore, the intricate in vivo environment surrounding the target soft tissues poses additional hindrances to autonomous robotic decision-making. Previous studies assumed the grasping point was known and the target deformation could be achieved. The constraints were assumed to be constant during the operation, and there were no obstacles around the soft tissue. To address these problems, an intuition-guided deep reinforcement learning framework based on soft actor-critic (ID-SAC) was proposed for soft tissue manipulation under unknown constraints. The SAC algorithm is automatically activated upon encountering an obstacle, and the designed intuitive manipulation (IM) strategy is used to pull soft tissues toward the target shape directly when the obstacle is distant. A regulator factor is designed as an action within this framework to coordinate the IM approach and the SAC network. A reward function is designed to balance the exploration and exploitation of large deformations. Simultaneously, we proposed an autonomous grasp point selection neural network to prevent the impractical selection of grasp points, ensuring they can reach the target while avoiding grasping lesions and constrained areas. Successful simulation results confirmed that the proposed framework can manipulate the soft tissue while avoiding obstacles and adding new positional constraints. Compared with the SAC algorithm, the proposed framework can markedly increase the robotic soft tissue manipulation ability by automatically adjusting the regulator factors.
Adaptive Gait Training for a Lower Limb Rehabilitation Robot Using Human-Robot Interaction Force
Authors: Fuyang Yu, Yu Liu, Zhengxing Wu, Min Tan, Junzhi Yu
Journal: Cyborg and Bionic Systems (2024)

The existing fixed gait lower limb rehabilitation robots perform a predetermined walking trajectory for patients, ignoring their residual muscle strength. To enhance patient participation and safety in training, this paper aims to develop a lower limb rehabilitation robot with adaptive gait training capability relying on human-robot interaction force measurement. Firstly, a novel lower limb rehabilitation robot system with several active and passive driven joints is developed, and 2 face-to-face mounted cantilever beam force sensors are employed to measure the human-robot interaction forces. Secondly, a dynamic model of the rehabilitation training robot is constructed to estimate the driven forces of the human lower leg in a completely passive state. Thereafter, based on the theoretical moment from the dynamics and the actual joint interaction force collected by the sensors, an adaptive gait adjustment method is proposed to achieve the goal of adapting to the wearer's movement intention. Finally, interactive experiments are carried out to validate the effectiveness of the developed rehabilitation training robot system. The proposed rehabilitation training robot system with adaptive gaits offers great potential for future high-quality rehabilitation training, e.g., improving participation and safety.
Enhancing Brain–Computer Interface Performance by Incorporating Brain-to-Brain Coupling
Authors: Tianyu Jia, Jingyao Sun, Ciarán McGeady, Linhong Ji, Chong Li
Journal: Cyborg and Bionic Systems (2024)

Human cooperation relies on key features of social interaction in order to reach desirable outcomes. Similarly, human–robot interaction may benefit from integration with human–human interaction factors. In this paper, we aim to investigate brain-to-brain coupling during motor imagery (MI)-based brain–computer interface (BCI) training using eye-contact and hand-touch interaction. Twelve pairs of friends (experimental group) and 10 pairs of strangers (control group) were recruited for MI-based BCI tests concurrent with electroencephalography (EEG) hyperscanning. Event-related desynchronization (ERD) was estimated to measure cortical activation, and interbrain functional connectivity was assessed using multilevel statistical analysis. Furthermore, we compared BCI classification performance under different social interaction conditions. In the experimental group, greater ERD was found around the contralateral sensorimotor cortex under social interaction conditions compared with MI without any social interaction. Notably, EEG channels with decreased power were mainly distributed around the frontal, central, and occipital regions. A significant increase in interbrain coupling was also found under social interaction conditions. BCI decoding accuracies were significantly improved in the eye contact condition and eye and hand contact condition compared with the no-interaction condition. However, for the strangers’ group, no positive effects were observed in comparisons of cortical activations between interaction and no-interaction conditions. These findings indicate that social interaction can improve the neural synchronization between familiar partners with enhanced brain activations and brain-to-brain coupling. This study may provide a novel method for enhancing MI-based BCI performance in conjunction with neural synchronization between users.
Radiotherapy in younger patients with advanced aggressive B-cell lymphoma—long-term results from the phase 3 R-MegaCHOEP trial
Authors: Michael Oertel, Marita Ziepert, Fabian Frontzek, Nina Nacke, Bettina Altmann, Maike Nickelsen, Bertram Glass, Viola Poeschel, Christian Ruebe, Georg Lenz, Norbert Schmitz, Hans Theodor Eich
Journal: Leukemia (2024)

The role of consolidative radiotherapy (RT) for patients with aggressive B-cell lymphoma has not been fully elucidated. The R-MegaCHOEP trial investigated the use of high-dose chemotherapy and rituximab with subsequent autologous stem cell transplantations compared to conventional immunochemotherapy (R-CHOEP) for high-risk patients up to 60 years. The study protocol included RT for patients with bulky (maximum diameter ≥7.5 cm) or extranodal disease. Two-hundred sixty-one patients were analyzed, 120 of whom underwent RT. The most frequently irradiated regions were mediastinum (n = 50) and paraaortic (n = 27). Median RT dose was 36 Gray in median fractions of 1.8 Gray. Acute toxicities were mostly mild to moderate, with only 24 and 8 grade 3 and 4 toxicities reported during RT. Patients with bulky disease who received RT showed significantly better 10-year EFS, PFS and OS (EFS: 64% vs. 35%; p < 0.001; PFS 68% vs. 47%; p = 0.003; OS: 72% vs. 59%; p = 0.011). There was no significant increase in secondary malignancies with the use of RT. RT administered for consolidation of bulky disease after immunochemotherapy improved the prognosis of young high-risk patients with aggressive B-cell lymphoma and should be considered part of first-line therapy. The trial was registered with ClinicalTrials.gov, number NCT00129090.
Burden of disease and treatment patterns in patients with vitiligo: findings from a national longitudinal retrospective study in the UK
Authors: Viktoria Eleftheriadou, Carine Delattre, Shala Chetty-Mhlanga, Christopher Lee, Laura Girardat-Rotar, Iftekhar Khan, Amit Mathew, Andrew R Thompson
Journal: British Journal of Dermatology (2024)

UK studies examining vitiligo burden and vitiligo-related healthcare resource utilization (HCRU) are lacking.
Genetic and Phenotypic Features of Schizophrenia in the UK Biobank
Authors: Sophie E. Legge, Antonio F. Pardiñas, Grace Woolway, Elliott Rees, Alastair G. Cardno, Valentina Escott-Price, Peter Holmans, George Kirov, Michael J. Owen, Michael C. O’Donovan, James T. R. Walters
Journal: JAMA Psychiatry (2024)

Large-scale biobanks provide important opportunities for mental health research, but selection biases raise questions regarding the comparability of individuals with those in clinical research settings.
Mortality Among Individuals With Hypochondriasis
Authors: Robert Sigström
Journal: JAMA Psychiatry (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 Psychiatry 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 Psychiatry journal
Validation of a Multivariable Model to Predict Suicide Attempt in a Mental Health Intake Sample
Authors: Santiago Papini, Honor Hsin, Patricia Kipnis, Vincent X. Liu, Yun Lu, Kristine Girard, Stacy A. Sterling, Esti M. Iturralde
Journal: JAMA Psychiatry (2024)

Given that suicide rates have been increasing over the past decade and the demand for mental health care is at an all-time high, targeted prevention efforts are needed to identify individuals seeking to initiate mental health outpatient services who are at high risk for suicide. Suicide prediction models have been developed using outpatient mental health encounters, but their performance among intake appointments has not been directly examined.
Regular Use of Aspirin and Statins Reduces the Risk of Cancer in Individuals with Systemic Inflammatory Diseases
Authors: Jia-Run Lin, Duan-Duan Han, Wei Wei, Qin Zeng, Zi-Xuan Rong, Xue Bai, Yan-Pei Zhang, Jian Wang, Xiao-Ting Cai, Xu-Guang Rao, Si-Cong Ma, Zhong-Yi Dong
Journal: Cancer Research (2024)

Aspirin has shown potential for cancer prevention, but a recent large randomized controlled trial found no evidence for a reduction in cancer risk. Given the anti-inflammatory effects of aspirin, systemic inflammatory diseases (SID), such as osteoporosis, cardiovascular diseases, and metabolic diseases, could potentially modify the aspirin-cancer link. To investigate the impact of aspirin in people with SIDs, we conducted an observational study on a prospective cohort of 478,615 UK Biobank participants. Individuals with at least one of the 41 SIDs displayed a higher cancer risk than those without SIDs. Regular aspirin use showed protective effects exclusively in patients with SID, contrasting an elevated risk among their non-SID counterparts. Nonetheless, aspirin use demonstrated preventative potential only for 9 of 21 SID-associated cancer subtypes. Cholesterol emerged as another key mediator linking SIDs to cancer risk. Notably, regular statin use displayed protective properties in patients with SID but not in their non-SID counterparts. Concurrent use of aspirin and statins exhibited a stronger protective association in patients with SID, covering 14 common cancer subtypes. In summary, patients with SIDs may represent a population particularly responsive to regular aspirin and statin use. Promoting either combined or individual use of these medications within the context of SIDs could offer a promising chemoprevention strategy.
Safety of Pregnancy After Breast Cancer in <i>BRCA</i> Mutation Carriers
Authors: Lisa A. Newman, Emily Shippee Rockefeller, Cheng-Har Yip
Journal: JAMA Surgery (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 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 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 Surgery journal
Concerns Over Prediction of Kidney Discard and Nonrecovery
Authors: Fangjieyi Zheng, Kening Chen, Wenquan Niu
Journal: JAMA Surgery (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 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 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 Surgery journal
High-Dimensional Mass Cytometry Reveals Emphysema-associated Changes in the Pulmonary Immune System
Authors: Li Jia, Na Li, Tamim R.M. Abdelaal, Nannan Guo, Marieke E. IJsselstein, Vincent van Unen, Ciska Lindelauf, Qinyue Jiang, Yanling Xiao, M. Fernanda Pascutti, Pieter S. Hiemstra, Frits Koning, Jan Stolk, P. Padmini S. J. Khedoe
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

Chronic inflammation plays an important role in alveolar tissue damage in emphysema, but the underlying immune alterations and cellular interactions are incompletely understood.
The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood
Authors: Yideng Cai, Meng Luo, Wenyi Yang, Chang Xu, Pingping Wang, Guangfu Xue, Xiyun Jin, Rui Cheng, Jinhao Que, Wenyang Zhou, Boran Pang, Shouping Xu, Yu Li, Qinghua Jiang, Zhaochun Xu
Journal: Cancer Research (2024)

Abstract T cells recognize tumor antigens and initiate an anticancer immune response in the very early stages of tumor development, and the antigen specificity of T cells is determined by the T-cell receptor (TCR). Therefore, monitoring changes in the TCR repertoire in peripheral blood may offer a strategy to detect various cancers at a relatively early stage. Here, we developed the deep learning framework iCanTCR to identify patients with cancer based on the TCR repertoire. The iCanTCR framework uses TCRβ sequences from an individual as an input and outputs the predicted cancer probability. The model was trained on over 2,000 publicly available TCR repertoires from 11 types of cancer and healthy controls. Analysis of several additional publicly available datasets validated the ability of iCanTCR to distinguish patients with cancer from noncancer individuals and demonstrated the capability of iCanTCR for the accurate classification of multiple cancers. Importantly, iCanTCR precisely identified individuals with early-stage cancer with an AUC of 86%. Altogether, this work provides a liquid biopsy approach to capture immune signals from peripheral blood for noninvasive cancer diagnosis. Significance: Development of a deep learning–based method for multicancer detection using the TCR repertoire in the peripheral blood establishes the potential of evaluating circulating immune signals for noninvasive early cancer detection.
Telehealth Pulmonary Rehabilitation: A Call for Minimum Standards
Authors: Surya P. Bhatt, Richard Casaburi, Christopher L. Mosher, Carolyn L. Rochester, Chris Garvey
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

"Telehealth Pulmonary Rehabilitation: A Call for Minimum Standards." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Year-Over-Year Ventral Hernia Recurrence Rates and Risk Factors
Authors: Priya Bhardwaj, Maria T. Huayllani, Molly A. Olson, Jeffrey E. Janis
Journal: JAMA Surgery (2024)

Recurrence is one of the most challenging adverse events after ventral hernia repair as it impacts quality of life, utilization of resources, and subsequent need for re-repair. Rates of recurrence range from 30% to 80% after ventral hernia repair.