tbuckley/cabot-search huggingface dataset:
Regulation of colonic neuropeptide Y expression by the gut microbiome in patients with ulcerative colitis and its association with anxiety- and depression-like behavior in mice
Authors: Min-Kyung Joo, Jae-Won Lee, Jeong-Hwa Woo, Hyo-Jong Kim, Dong-Hyun Kim, Jung-Hye Choi
Journal: Gut Microbes (2024)

Patients with inflammatory bowel disease (IBD), including ulcerative colitis (UC), show an increased incidence of anxiety and depression; however, the association between UC-associated psychiatric disorders and the gut microbiota is unclear. This study aimed to examine whether gut microbiota from patients with UC can alter colonic gene expression, leading to anxiety- and depression-like behavior in mice receiving fecal microbiota transplantation (FMT). RNA sequencing transcriptome analyses revealed a difference in colonic gene expression between mice receiving FMT from patients with UC (UC-FMT mice) and those receiving FMT from healthy controls (HC-FMT mice). Gene ontology analysis revealed the downregulation of neuropeptide signaling pathways, including neuropeptide Y (NPY) expression, in the colons of UC-FMT mice. The protein levels of NPY also decreased in the colon and plasma of UC-FMT mice compared to those in HC-FMT mice. The oral administration of
Immune signatures predict response to house dust mite subcutaneous immunotherapy in patients with allergic rhinitis
Authors: Nan Wang, Jia Song, Shi‐Ran Sun, Ke‐Zhang Zhu, Jing‐Xian Li, Zhi‐Chao Wang, Cui‐Lian Guo, Wen‐Xuan Xiang, Yun‐Long Tong, Ming Zeng, Heng Wang, Xiao‐Yan Xu, Yin Yao, Zheng Liu
Journal: Allergy (2024)

Identifying predictive biomarkers for allergen immunotherapy response is crucial for enhancing clinical efficacy. This study aims to identify such biomarkers in patients with allergic rhinitis (AR) undergoing subcutaneous immunotherapy (SCIT) for house dust mite allergy.
The astrocyte-produced growth factor HB-EGF limits autoimmune CNS pathology
Authors: Mathias Linnerbauer, Lena Lößlein, Oliver Vandrey, Anne Peter, Yanan Han, Thanos Tsaktanis, Emile Wogram, Maria Needhamsen, Lara Kular, Lisa Nagel, Julia Zissler, Marie Andert, Lisa Meszaros, Jannis Hanspach, Finnja Zuber, Ulrike J. Naumann, Martin Diebold, Michael A. Wheeler, Tobias Beyer, Lucy Nirschl, Ana Cirac, Frederik B. Laun, Claudia Günther, Jürgen Winkler, Tobias Bäuerle, Maja Jagodic, Bernhard Hemmer, Marco Prinz, Francisco J. Quintana, Veit Rothhammer
Journal: Nature Immunology (2024)

Central nervous system (CNS)-resident cells such as microglia, oligodendrocytes and astrocytes are gaining increasing attention in respect to their contribution to CNS pathologies including multiple sclerosis (MS). Several studies have demonstrated the involvement of pro-inflammatory glial subsets in the pathogenesis and propagation of inflammatory events in MS and its animal models. However, it has only recently become clear that the underlying heterogeneity of astrocytes and microglia can not only drive inflammation, but also lead to its resolution through direct and indirect mechanisms. Failure of these tissue-protective mechanisms may potentiate disease and increase the risk of conversion to progressive stages of MS, for which currently available therapies are limited. Using proteomic analyses of cerebrospinal fluid specimens from patients with MS in combination with experimental studies, we here identify Heparin-binding EGF-like growth factor (HB-EGF) as a central mediator of tissue-protective and anti-inflammatory effects important for the recovery from acute inflammatory lesions in CNS autoimmunity. Hypoxic conditions drive the rapid upregulation of HB-EGF by astrocytes during early CNS inflammation, while pro-inflammatory conditions suppress trophic HB-EGF signaling through epigenetic modifications. Finally, we demonstrate both anti-inflammatory and tissue-protective effects of HB-EGF in a broad variety of cell types in vitro and use intranasal administration of HB-EGF in acute and post-acute stages of autoimmune neuroinflammation to attenuate disease in a preclinical mouse model of MS. Altogether, we identify astrocyte-derived HB-EGF and its epigenetic regulation as a modulator of autoimmune CNS inflammation and potential therapeutic target in MS.
scGIST: gene panel design for spatial transcriptomics with prioritized gene sets
Authors: Mashrur Ahmed Yafi, Md. Hasibul Husain Hisham, Francisco Grisanti, James F. Martin, Atif Rahman, Md. Abul Hassan Samee
Journal: Genome biology (2024)

A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ hybridization, they are typically limited to panels of about a thousand genes. This constrains researchers to build panels from only the marker genes of different cell types and forgo other genes of interest, e.g., genes encoding ligand-receptor complexes or those in specific pathways. We propose scGIST, a constrained feature selection tool that designs sc-ST panels prioritizing user-specified genes without compromising cell type detection accuracy. We demonstrate scGIST's efficacy in diverse use cases, highlighting it as a valuable addition to sc-ST's algorithmic toolbox.
A comparison of marker gene selection methods for single-cell RNA sequencing data
Authors: Jeffrey M. Pullin, Davis J. McCarthy
Journal: Genome biology (2024)

Abstract Background The development of single-cell RNA sequencing (scRNA-seq) has enabled scientists to catalog and probe the transcriptional heterogeneity of individual cells in unprecedented detail. A common step in the analysis of scRNA-seq data is the selection of so-called marker genes, most commonly to enable annotation of the biological cell types present in the sample. In this paper, we benchmark 59 computational methods for selecting marker genes in scRNA-seq data. Results We compare the performance of the methods using 14 real scRNA-seq datasets and over 170 additional simulated datasets. Methods are compared on their ability to recover simulated and expert-annotated marker genes, the predictive performance and characteristics of the gene sets they select, their memory usage and speed, and their implementation quality. In addition, various case studies are used to scrutinize the most commonly used methods, highlighting issues and inconsistencies. Conclusions Overall, we present a comprehensive evaluation of methods for selecting marker genes in scRNA-seq data. Our results highlight the efficacy of simple methods, especially the Wilcoxon rank-sum test, Student’s t -test, and logistic regression.
Long-term outcomes by bone marrow B-cell depletion from the R2W trial of bortezomib with cyclophosphamide and rituximab in Waldenstrőm macroglobulinaemia
Authors: Ruth de Tute, Nicholas Counsell, Laura Clifton-Hadley, Shirley D’Sa, Guy Pratt, Gavin Campbell, Lauren Campbell, Ross Sadler, William Townsend, Bilyana Popova, Paul Smith, Oliver Schofield, Roger Owen, Rebecca Auer
Journal: Leukemia (2024)
Deciphering cancer cell state plasticity with single-cell genomics and artificial intelligence
Authors: Emily Holton, Walter Muskovic, Joseph E Powell
Journal: Genome Medicine (2024)

Abstract Cancer stem cell plasticity refers to the ability of tumour cells to dynamically switch between states—for example, from cancer stem cells to non-cancer stem cell states. Governed by regulatory processes, cells transition through a continuum, with this transition space often referred to as a cell state landscape. Plasticity in cancer cell states leads to divergent biological behaviours, with certain cell states, or state transitions, responsible for tumour progression and therapeutic response. The advent of single-cell assays means these features can now be measured for individual cancer cells and at scale. However, the high dimensionality of this data, complex relationships between genomic features, and a lack of precise knowledge of the genomic profiles defining cancer cell states have opened the door for artificial intelligence methods for depicting cancer cell state landscapes. The contribution of cell state plasticity to cancer phenotypes such as treatment resistance, metastasis, and dormancy has been masked by analysis of ‘bulk’ genomic data—constituted of the average signal from millions of cells. Single-cell technologies solve this problem by producing a high-dimensional cellular landscape of the tumour ecosystem, quantifying the genomic profiles of individual cells, and creating a more detailed model to investigate cancer plasticity (Genome Res 31:1719, 2021; Semin Cancer Biol 53: 48-58, 2018; Signal Transduct Target Ther 5:1-36, 2020). In conjunction, rapid development in artificial intelligence methods has led to numerous tools that can be employed to study cancer cell plasticity.
Covid-19: Two rare vaccine side effects detected in large global study
Authors: Jacqui Wise
Journal: BMJ (2024)

Covid-19: Two rare vaccine side effects detected in large global study Jacqui WiseThe largest vaccine safety study to date has identified two new, but very rare, side effects associated with covid-19 vaccines-transverse myelitis and acute disseminated encephalomyelitis.The Global Vaccine Data Network cohort study included 99 million vaccinated people from 10 sites across eight countries.Researchers compared the observed with expected rate for 13 neurological, blood, and heart related medical conditions. 1
Unravelling Immune‐Inflammatory Responses and Lysosomal Adaptation: Insights from Two‐Photon Excited Delayed Fluorescence Imaging
Authors: Xiang Wang, Gaona Shi, Shengnan Xu, Yuansheng Sun, Hailin Qiu, Qinghua Wang, Xiaowan Han, Qingyang Zhang, Tiantai Zhang, Hai‐Yu Hu
Journal: Advanced Healthcare Materials (2024)

Two-photon excitation (TPE) microscopy with near-infrared (NIR) emission has emerged as a promising technique for deep-tissue optical imaging. Recent developments in fluorescence lifetime imaging with long-lived emission probes have further enhanced the spatial resolution and precision of fluorescence imaging, especially in complex systems with short-lived background signals. In this study, two innovative lysosome-targeting probes, Cz-NA and tCz-NA, are introduced. These probes offer a combination of advantages, including TPE (λ
Delving Deeper Into Maternal COVID-19 Vaccination and Neonatal Outcomes
Authors: Tina Yi Jin Hsieh, James Cheng-Chung Wei
Journal: JAMA Pediatrics (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 Pediatrics 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 Pediatrics journal
Hospital and Physician Group Practice Participation in Prior and Next-Generation Value-Based Payment Programs
Authors: So-Yeon Kang, Gerard Anderson
Journal: JAMA Network Open (2024)

This cohort study examines whether prior direct or indirect participation in the Centers for Medicare &amp;amp;amp; Medicaid Innovation Bundled Payments for Care Improvement (BCPI) Initiative was associated with their participation in the next generation of the program.
Renal replacement therapy initiation strategies in comatose patients with severe acute kidney injury: a secondary analysis of a multicenter randomized controlled trial
Authors: Thomas Rambaud, David Hajage, Didier Dreyfuss, Saïd Lebbah, Laurent Martin-Lefevre, Guillaume Louis, Sébastien Moschietto, Dimitri Titeca-Beauport, Béatrice La Combe, Bertrand Pons, Nicolas De Prost, Sébastien Besset, Alain Combes, Adrien Robine, Marion Beuzelin, Julio Badie, Guillaume Chevrel, Julien Bohe, Elisabeth Coupez, Nicolas Chudeau, Saber Barbar, Christophe Vinsonneau, Jean-Marie Forel, Didier Thevenin, Eric Boulet, Karim Lakhal, Nadia Aissaoui, Steven Grange, Marc Leone, Guillaume Lacave, Saad Nseir, Florent Poirson, Julien Mayaux, Karim Ashenoune, Guillaume Geri, Kada Klouche, Guillaume Thiery, Laurent Argaud, Bertrand Rozec, Cyril Cadoz, Pascal Andreu, Jean Reignier, Jean-Damien Ricard, Jean-Pierre Quenot, Romain Sonneville, Stéphane Gaudry
Journal: Intensive Care Medicine (2024)
Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota
Authors: Huating Li, Lei Zhang, Jun Li, Qian Wu, Lingling Qian, Junsheng He, Yueqiong Ni, Petia Kovatcheva-Datchary, Rui Yuan, Shuangbo Liu, Li Shen, Mingliang Zhang, Bin Sheng, Ping Li, Kang Kang, Liang Wu, Qichen Fang, Xiaoxue Long, Xiaolin Wang, Yanli Li, Yaorui Ye, Jianping Ye, Yuqian Bao, Yueliang Zhao, Guowang Xu, Xinyu Liu, Gianni Panagiotou, Aimin Xu, Weiping Jia
Journal: Nature Metabolism (2024)

Abstract Emerging evidence suggests that modulation of gut microbiota by dietary fibre may offer solutions for metabolic disorders. In a randomized placebo-controlled crossover design trial (ChiCTR-TTRCC-13003333) in 37 participants with overweight or obesity, we test whether resistant starch (RS) as a dietary supplement influences obesity-related outcomes. Here, we show that RS supplementation for 8 weeks can help to achieve weight loss (mean −2.8 kg) and improve insulin resistance in individuals with excess body weight. The benefits of RS are associated with changes in gut microbiota composition. Supplementation with Bifidobacterium adolescentis , a species that is markedly associated with the alleviation of obesity in the study participants, protects male mice from diet-induced obesity. Mechanistically, the RS-induced changes in the gut microbiota alter the bile acid profile, reduce inflammation by restoring the intestinal barrier and inhibit lipid absorption. We demonstrate that RS can facilitate weight loss at least partially through B. adolescentis and that the gut microbiota is essential for the action of RS.
Psychotropic Medication Prescriptions and Large California Wildfires
Authors: Zachary S. Wettstein, Ambarish Vaidyanathan
Journal: JAMA Network Open (2024)

Wildfires, intensified by climate change, have known effects on physical health but their effects on mental health are less well characterized. It has been hypothesized that the residential proximity to a large wildfire can exacerbate underlying mental health conditions as evidenced by increased prescriptions of psychotropic medications.
Potential of Large Language Models as Tools Against Medical Disinformation
Authors: Lingxuan Zhu, Weiming Mou, Peng Luo
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
Delving Deeper Into Maternal COVID-19 Vaccination and Neonatal Outcomes—Reply
Authors: Sarah C. J. Jorgensen, Deshayne B. Fell, Jeffrey C. Kwong
Journal: JAMA Pediatrics (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 Pediatrics 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 Pediatrics journal
Treating Adolescent Opioid Use Disorder in Primary Care
Authors: Scott E. Hadland, William H. Burr, Kenneth Zoucha, Chloe A. Somberg, Deepa R. Camenga
Journal: JAMA Pediatrics (2024)

This survey study explores primary care pediatricians’ preparedness to counsel and treat adolescents with opioid use disorder (OUD) and perceived barriers to prescribing OUD medications.
Do My Children Have a Higher Risk of Epilepsy Because of My Epilepsy or Seizure Medications?
Authors: P. Emanuela Voinescu, Esther Bui
Journal: JAMA Network Open (2024)

Julie Werenberg Dreier, PhD; Jakob Christensen, DrMedSci; Jannicke Igland, PhD; Mika Gissler, PhD; Maarit K. Leinonen, PhD; Håkon Magne Vegrim, MD; Yuelian Sun, PhD; Torbjörn Tomson, PhD; Helga Zoega, PhD; Marte-Helene Bjørk, PhD; Rebecca L. Bromley, PhD
Targeting autophagy overcomes cancer‐intrinsic resistance to CAR‐T immunotherapy in B‐cell malignancies
Authors: Lu Tang, Huan Zhang, Fen Zhou, Qiuzhe Wei, Mengyi Du, Jianghua Wu, Chenggong Li, Wenjing Luo, Jie Zhou, Xindi Wang, Zhaozhao Chen, Yinqiang Zhang, Zhongpei Huang, Zhuolin Wu, Yuxi Wen, Huiwen Jiang, Danying Liao, Haiming Kou, Wei Xiong, Heng Mei, Yu Hu
Journal: Cancer Communications (2024)

Chimeric antigen receptor T (CAR-T) therapy has substantially revolutionized the clinical outcomes of patients with hematologic malignancies, but the cancer-intrinsic mechanisms underlying resistance to CAR-T cells remain yet to be fully understood. This study aims to explore the molecular determinants of cancer cell sensitivity to CAR-T cell-mediated killing and to provide a better understanding of the underlying mechanisms and potential modulation to improve clinical efficacy.
Cause of death by fibrosis stage in 959 patients with biopsy-proven NAFLD
Authors: Ying Shang, Camilla Akbari, Maja Dodd, Patrik Nasr, Johan Vessby, Fredrik Rorsman, Stergios Kechagias, Per Stål, Mattias Ekstedt, Hannes Hagström
Journal: Gut (2024)
Analysis of immunoglobulin/T‐cell receptor repertoires by high‐throughput RNA sequencing reveals a continuous dynamic of positive clonal selection in follicular lymphoma
Authors: Victor Bobée, Mathieu Viennot, Vinciane Rainville, Liana Veresezan, Fanny Drieux, Pierre‐Julien Viailly, Victor Michel, Vincent Sater, Marie‐Delphine Lanic, Elodie Bohers, Vincent Camus, Hervé Tilly, Fabrice Jardin, Philippe Ruminy
Journal: HemaSphere (2024)

Abstract Follicular lymphoma (FL) course is highly variable, making its clinical management challenging. In this incurable and recurring pathology, the interval between relapses tends to decrease while aggressiveness increases, sometimes resulting in the transformation to higher‐grade lymphoma. These evolutions are particularly difficult to anticipate, resulting from complex clonal evolutions where multiple subclones compete and thrive due to their capacity to proliferate and resist therapies. Here, to apprehend further these processes, we used a high‐throughput RNA sequencing approach to address simultaneously the B‐cell immunoglobulin repertoires and T‐cell immunoglobulin repertoires repertoires of lymphoma cells and their lymphoid microenvironment in a large cohort of 131 FL1/2‐3A patients. Our data confirm the existence of a high degree of intra‐clonal heterogeneity in this pathology, resulting from ongoing somatic hyper‐mutation and class switch recombination. Through the evaluation of the Simpson ecological‐diversity index, we show that the contribution of the cancerous cells increases during the course of the disease to the detriment of the reactive compartment, a phenomenon accompanied by a concomitant decrease in the diversity of the tumoral population. Clonal evolution in FL thus contrasts with many tumors, where clonal heterogeneity steadily increases over time and participates in treatment evasion. In this pathology, the selection of lymphoma subclones with proliferative advantages progressively outweighs clonal diversification, ultimately leading in extreme cases to transformation to high‐grade lymphoma resulting from the rapid emergence of homogeneous subpopulations.
Genome mining of sulfonated lanthipeptides reveals unique cyclic peptide sulfotransferases
Authors: Meng Wang, Wen-Wei Li, Zhe Cao, Jianong Sun, Jiang Xiong, Si-Qin Tao, Tinghong Lv, Kun Gao, Shangwen Luo, Shi-Hui Dong
Journal: Acta Pharmaceutica Sinica B (2024)

Although sulfonation plays crucial roles in various biological processes and is frequently utilized in medicinal chemistry to improve water solubility and chemical diversity of drug leads, it is rare and underexplored in ribosomally synthesized and post-translationally modiﬁed peptides (RiPPs). Biosynthesis of RiPPs typically entails modification of hydrophilic residues, which substantially increases their chemical stability and bioactivity, albeit at the expense of reducing water solubility. To explore sulfonated RiPPs that may have improved solubility, we conducted co-occurrence analysis of RiPP class-defining enzymes and sulfotransferase (ST), and discovered two distinctive biosynthetic gene clusters (BGCs) encoding both lanthipeptide synthetase (LanM) and ST. Upon expressing these BGCs, we characterized the structures of novel sulfonated lanthipeptides and determined the catalytic details of LanM and ST. We demonstrate that SslST-catalyzed sulfonation is leader-independent but relies on the presence of A ring formed by LanM. Both LanM and ST are promiscuous towards residues in the A ring, but ST displays strict regioselectivity toward Tyr5. The recognition of cyclic peptide by ST was further discussed. Bioactivity evaluation underscores the significance of the ST-catalyzed sulfonation. This study sets up the starting point to engineering the novel lanthipeptide STs as biocatalysts for hydrophobic lanthipeptides improvement.