tbuckley/cabot-search huggingface dataset:
Landscape of the gut mycobiome dynamics during pregnancy and its relationship with host metabolism and pregnancy health
Authors: Yuanqing Fu, Wanglong Gou, Ping Wu, Yuwei Lai, Xinxiu Liang, Ke Zhang, Menglei Shuai, Jun Tang, Zelei Miao, Jieteng Chen, Jiaying Yuan, Bin Zhao, Yunhaonan Yang, Xiaojuan Liu, Yayi Hu, An Pan, Xiong-Fei Pan, Ju-Sheng Zheng
Journal: Gut (2024)

Objective The remodelling of gut mycobiome (ie, fungi) during pregnancy and its potential influence on host metabolism and pregnancy health remains largely unexplored. Here, we aim to examine the characteristics of gut fungi in pregnant women, and reveal the associations between gut mycobiome, host metabolome and pregnancy health. Design Based on a prospective birth cohort in central China (2017 to 2020): Tongji-Huaxi-Shuangliu Birth Cohort, we included 4800 participants who had available ITS2 sequencing data, dietary information and clinical records during their pregnancy. Additionally, we established a subcohort of 1059 participants, which included 514 women who gave birth to preterm, low birthweight or macrosomia infants, as well as 545 randomly selected controls. In this subcohort, a total of 750, 748 and 709 participants had ITS2 sequencing data, 16S sequencing data and serum metabolome data available, respectively, across all trimesters. Results The composition of gut fungi changes dramatically from early to late pregnancy, exhibiting a greater degree of variability and individuality compared with changes observed in gut bacteria. The multiomics data provide a landscape of the networks among gut mycobiome, biological functionality, serum metabolites and pregnancy health, pinpointing the link between Mucor and adverse pregnancy outcomes. The prepregnancy overweight status is a key factor influencing both gut mycobiome compositional alteration and the pattern of metabolic remodelling during pregnancy. Conclusion This study provides a landscape of gut mycobiome dynamics during pregnancy and its relationship with host metabolism and pregnancy health, which lays the foundation of the future gut mycobiome investigation for healthy pregnancy.
The International Association for the Study of Lung Cancer Pleural Mesothelioma Staging Project: Proposal for Revision of the TNM Stage Groupings in the Forthcoming (Ninth) Edition of the TNM Classification for Pleural Mesothelioma
Authors: Anna K. Nowak, Dorothy J. Giroux, Megan Eisele, Adam Rosenthal, Andrea Bille, Ritu R. Gill, Hedy L. Kindler, Harvey I. Pass, David Rice, R Taylor Ripley, Andrea Wolf, Joseph Friedberg, Katherine Nishimura, Valerie W. Rusch
Journal: Journal of Thoracic Oncology (2024)
The International Association for the Study of Lung Cancer Mesothelioma Staging Project: Proposals for the “N” Descriptors in the Forthcoming Ninth Edition of the TNM Classification for Pleural Mesothelioma
Authors: Andrea Bille, R Taylor Ripley, Dorothy J Giroux, Ritu R Gill, Hedy L Kindler, Anna K Nowak, Isabelle Opitz, Harvey I Pass, Andrea Wolf, David Rice, Valerie W Rusch
Journal: Journal of Thoracic Oncology (2024)
Exclusive oral antibiotic treatment for hospitalized community-acquired pneumonia: a post-hoc analysis of a randomized clinical trial
Authors: Aurélien Dinh, Clara Duran, Jacques Ropers, Frédérique Bouchand, Laurène Deconinck, Morgan Matt, Olivia Senard, Aurore Lagrange, Guillaume Mellon, Ruxandra Calin, Sabrina Makhloufi, Victoire de Lastours, Emmanuel Mathieu, Jean-Emmanuel Kahn, Elisabeth Rouveix, Julie Grenet, Jennifer Dumoulin, Thierry Chinet, Marion Pépin, Véronique Delcey, Sylvain Diamantis, Daniel Benhamou, Virginie Vitrat, Marie-Christine Dombret, Bertrand Renaud, Yann-Erick Claessens, José Labarère, Jean-Pierre Bedos, Philippe Aegerter, Anne-Claude Crémieux, Julie Attal-Behar, Sébastien Beaune, None Thierry chinet, Tristan Cudennec, Marine de Laroche, Albane de Thezy, Jennifer Dumoulin, Caroline Dupont, Elise Fercot, Violaine Giraut, Ségolène Greffe, Julie Grenet, Caroline Guyot, Sylvie Labrune, Marie Lachatre, Sophie Moulias, Charlotte Naline, Marion Pépin, Elisabeth Rouveix, Marine Sahut-D'izarn, Abel Sefssafi, Laurent Teillet, Jean-Pierre Bru, Jacques Gaillat, Vincent Gautier, Cécile Janssen, Leonardo Pagani, Virginie Vitrat, Malika Abderrahmane, Juliette Camuset, Catherine Legall, Pascale Longuet-Flandres, Anne-Marie Menn, Victoire de Lastours, Gwenolée Prevost, Marie Lecronier, Charles Burdet, Ouda Derradji, Lelia Escaut, Etienne Hinglais, Philippe Lebras, Edouard Lefevre, Mathilde Noaillon, Pauline Rabier, Maurice Raphaël, Elina Teicher, Christiane Verny, Daniel Vittecoq, Benjamin Wyplosz, Michèle Ben Hayoun, Françoise Brun-Vezinet, Enrique Casalino, Christophe Choquet, Marie-Christine Dombret, Xavier Duval, Nadhira Houhou, Véronique Joly, Xavier Lescure, Manuela Pogliaghi, Christophe Rioux, Yazdan Yazdanpanah, Elsa Barros, Belinda Begga, Sébastien Boukobza, Houria Bouredji, Imad Chouahi, Isabelle Delacroix, Antoine Froissart, Valérie Garrait, Elsa Ngwem, Catherine Phlippoteau, Sepehr Salehabadi, Cécile Toper, Florent Vinas, Marie Amsilli, Olivier Epaulard, Patricia Pavese, Isabelle Pierre, Jean-Paul Stahl, Jérôme Aulagnier, Julie Celerier, Roxana Cojocariu, Jean-Emmanuel Kahn, Emmanuel Mathieu, Charlotte Rachline, Yoland Schoindre, Thomas Sene, Christelle Thierry, Caroline Aparicio, Véronique Delcey, Amanda Lopes, Marjolaine Morgand Pierre, None Sellier, Guy Simoneau, Catherine Chakvetadze, Sylvain Diamantis, Arnaud Gauthier, Kaoutar Jidar, Béatrice Jourdain, Jean-Francois Boitiaux, Patrick Deschamps, Edouard Devaud, Bruno Philippe, Ruxandra-Oana Calin, Tomasz Chroboczek, Benjamin Davido, Laurène Deconinck, Pierre de Truchis, Aurore Lagrange, Sabrina Makhloufi, Morgan Matt, Guillaume Mellon, Olivia Senard, Daniel Benhamou, Claire Chapuzet, Laure Chauffrey, Manuel Etienne, Luc-Marie Joly, Bérengère Obstoy, Mathieu Salaun, Luc Thiberville, Julie Tillon, Diane Bollens, Julie Bottero, Pauline Campa, Gäelle Cosqueric, Bénédicte Lefebvre, Zineb Ouazene, Jérôme Pacanowski, Dominique Pateron, Nadia Valin, Caroline Compain, Hugues Cordel, Benoit Doumenc, Elena Fois, Nicolas Gambier, Marie-Aude Khuong, Elisa Pasqualoni, Marie Poupard
Journal: Clinical Microbiology and Infection (2024)
Defining the subset of mutations in polymerase epsilon (POLE) associated with loss-of-proofreading (LOP) functionality
Authors: G. Maddalena, F.A. Zeineddine, S. Rivero-Hinojosa, V.N. Aushev, S. Chowdhury, M.A. Zeineddine, A.M. Yousef, T.A. Yap, A.C. EINaggar, M.C. Liu, M. White, M.J. Overman, S. Kopetz, J.P. Shen
Journal: Annals of Oncology (2024)
Staphylococcus aureus–specific skin resident memory T cells protect against bacteria colonization but exacerbate atopic dermatitis–like flares in mice
Authors: Camille Braun, Cédric Badiou, Aurélie Guironnet-Paquet, Masashi Iwata, Vanina Lenief, Amandine Mosnier, Charlotte Beauclair, Emilie Renucci, Pauline Bouschon, Roxane Cuzin, Yoann Briend, Vijaykumar Patra, Sabine Patot, Tiffany C. Scharschmidt, Willem van Wamel, Nicole Lemmens, Saeko Nakajima, François Vandenesh, Jean-François Nicolas, Gérard Lina, Audrey Nosbaum, Marc Vocanson
Journal: Journal of Allergy and Clinical Immunology (2024)
VP2-2024: Fuzuloparib with or without apatinib in HER2- metastatic breast cancer (mBC) patients (pts) with germline BRCA1/2 mutations (gBRCA1/2m): A randomized phase III trial
Authors: H. Li, J. Liu, Y. Liu, Q. Ouyang, S. Wang, Z. Tong, Y. Teng, T. Sun, X. Wang, J. Cheng, X. Zhou, L. Fanfan, M. Yan, J. Nie, C. Ye, Z-M. Shao, Y. Wang, X. Yang, E. Song
Journal: Annals of Oncology (2024)
Causal Inference About the Effects of Interventions From Observational Studies in Medical Journals
Authors: Issa J. Dahabreh, Kirsten Bibbins-Domingo
Journal: JAMA (2024)

Many medical journals, including JAMA, restrict the use of causal language to the reporting of randomized clinical trials. Although well-conducted randomized clinical trials remain the preferred approach for answering causal questions, methods for observational studies have advanced such that causal interpretations of the results of well-conducted observational studies may be possible when strong assumptions hold. Furthermore, observational studies may be the only practical source of information for answering some questions about the causal effects of medical or policy interventions, can support the study of interventions in populations and settings that reflect practice, and can help identify interventions for further experimental investigation. Identifying opportunities for the appropriate use of causal language when describing observational studies is important for communication in medical journals.
The role of oxidative stress in intervertebral disc degeneration: Mechanisms and therapeutic implications
Authors: Xianglong Chen, Anran Zhang, Kangcheng Zhao, Haiyang Gao, Pengzhi Shi, Yuhang Chen, Zhangrong Cheng, Wenjuan Zhou, Yukun Zhang
Journal: Ageing Research Reviews (2024)

Oxidative stress is one of the main driving mechanisms of intervertebral disc degeneration(IDD). Oxidative stress has been associated with inflammation in the intervertebral disc, cellular senescence, autophagy, and epigenetics of intervertebral disc cells. It and the above pathological mechanisms are closely linked through the common hub reactive oxygen species(ROS), and promote each other in the process of disc degeneration and promote the development of the disease. This reveals the important role of oxidative stress in the process of IDD, and the importance and great potential of IDD therapy targeting oxidative stress. The efficacy of traditional therapy is unstable or cannot be maintained. In recent years, due to the rise of materials science, many bioactive functional materials have been applied in the treatment of IDD, and through the combination with traditional drugs, satisfactory efficacy has been achieved. At present, the research review of antioxidant bioactive materials in the treatment of IDD is not complete. Based on the existing studies, the mechanism of oxidative stress in IDD and the common antioxidant therapy were summarized in this paper, and the strategies based on emerging bioactive materials were reviewed.
Hepatocyte-intrinsic SMN deficiency drives metabolic dysfunction and liver steatosis in spinal muscular atrophy
Authors: Damien Meng-Kiat Leow, Yang Kai Ng, Loo Chien Wang, Hiromi W.L. Koh, Tianyun Zhao, Zi Jian Khong, Tommaso Tabaglio, Gunaseelan Narayanan, Richard M. Giadone, Radoslaw M. Sobota, Shi-Yan Ng, Adrian Kee Keong Teo, Simon H. Parson, Lee L. Rubin, Wei-Yi Ong, Basil T. Darras, Crystal J.J. Yeo
Journal: Journal of Clinical Investigation (2024)

Spinal Muscular Atrophy (SMA) is typically characterized as a motor neuron disease, but extra-neuronal phenotypes are present in almost every organ in severely affected patients and animal models. Extra-neuronal phenotypes were previously underappreciated as patients with severe SMA phenotypes usually died in infancy; however, with current treatments for motor neurons increasing patient lifespan, impaired function of peripheral organs may develop into significant future comorbidities and lead to new treatment-modified phenotypes. Fatty liver is seen in SMA animal models , but generalizability to patients and whether this is due to hepatocyte-intrinsic Survival Motor Neuron (SMN) protein deficiency and/or subsequent to skeletal muscle denervation is unknown. If liver pathology in SMA is SMN-dependent and hepatocyte-intrinsic, this suggests SMN repleting therapies must target extra-neuronal tissues and motor neurons for optimal patient outcome. Here we showed that fatty liver is present in SMA and that SMA patient-specific iHeps were susceptible to steatosis. Using proteomics, functional studies and CRISPR/Cas9 gene editing, we confirmed that fatty liver in SMA is a primary SMN-dependent hepatocyte-intrinsic liver defect associated with mitochondrial and other hepatic metabolism implications. These pathologies require monitoring and indicate need for systematic clinical surveillance and additional and/or combinatorial therapies to ensure continued SMA patient health.
The effect of physical exercise interventions on insomnia: A systematic review and meta-analysis
Authors: Anuschka Riedel, Fee Benz, Peter Deibert, Friedrich Barsch, Lukas Frase, Anna F. Johann, Dieter Riemann, Bernd Feige
Journal: Sleep Medicine Reviews (2024)

6-10% of Europeans suffer from chronic insomnia. They have a higher risk to develop mental and cardiovascular diseases. Treatment of insomnia primarily recommended by the European guideline is cognitive behavioral therapy for insomnia (CBT-I). A quarter of patients treated with CBT-I do not respond sufficiently. The objective of this paper is to examine the influence of exercise interventions on insomnia by conducting a systematic review and meta-analysis. A database search was conducted, including randomized controlled trials (RCT) in which participants had received a diagnosis of insomnia or experienced symptoms thereof. Exercise interventions had to meet the definition of the World Health Organization (WHO), and their implementation was reported according to the FITT (Frequency, Intensity, Time and Type) principle. There was an inactive control and subjective or objective sleep parameters as outcomes. Nineteen studies were included. Results showed a significant improvement for objective (standardized mean difference, SMD=0.37; confidence interval, CI=[0.17; 0.57]) as well as subjective (SMD=0.90; CI=[0.61; 1.19]) sleep parameters. Meta-regression showed that the effect increased with intensity of intervention, mean age of participants and percentage of females, but showed high heterogeneity across studies. These results suggest great potential for treating insomnia. Conducting larger trials is advisable to provide precise recommendations.
Mitochondria regulate proliferation in adult cardiac myocytes
Authors: Gregory B. Waypa, Kimberly A. Smith, Paul T. Mungai, Vincent J. Dudley, Kathryn A. Helmin, Benjamin D. Singer, Clara Bien Peek, Joseph Bass, Lauren Nelson, Sanjiv J. Shah, Gaston Ofman, J. Andrew Wasserstrom, William A. Muller, Alexander V. Misharin, G.R. Scott Budinger, Hiam Abdala-Valencia, Navdeep S. Chandel, Danijela Dokic, Elizabeth Bartom, Shuang Zhang, Yuki Tatekoshi, Amir Mahmoodzadeh, Hossein Ardehali, Edward B. Thorp, Paul T. Schumacker
Journal: Journal of Clinical Investigation (2024)

Newborn mammalian cardiomyocytes quickly transition from a fetal to an adult phenotype that utilizes mitochondrial oxidative phosphorylation but loses mitotic capacity. We tested whether forced reversal of adult cardiomyocytes back to a fetal glycolytic phenotype would restore proliferative capacity. We deleted Uqcrfs1 (mitochondrial Rieske Iron-Sulfur protein, RISP) in hearts of adult mice. As RISP protein decreased, heart mitochondrial function declined, and glucose utilization increased. Simultaneously, they underwent hyperplastic remodeling during which cardiomyocyte number doubled without cellular hypertrophy. Cellular energy supply was preserved, AMPK activation was absent, and mTOR activation was evident. In ischemic hearts with RISP deletion, new cardiomyocytes migrated into the infarcted region, suggesting the potential for therapeutic cardiac regeneration. RNA-seq revealed upregulation of genes associated with cardiac development and proliferation. Metabolomic analysis revealed a decrease in alpha-ketoglutarate (required for TET-mediated demethylation) and an increase in S-adenosylmethionine (required for methyltransferase activity). Analysis revealed an increase in methylated CpGs near gene transcriptional start sites. Genes that were both differentially expressed and differentially methylated were linked to upregulated cardiac developmental pathways. We conclude that decreased mitochondrial function and increased glucose utilization can restore mitotic capacity in adult cardiomyocytes resulting in the generation of new heart cells, potentially through the modification of substrates that regulate epigenetic modification of genes required for proliferation.
Brief Report: Updated Data From IMscin001 Part 2, a Randomized Phase III Study of Subcutaneous Versus Intravenous Atezolizumab in Patients With Locally Advanced or Metastatic NSCLC
Authors: Mauricio Burotto, Zanete Zvirbule, Renzo Alvarez, Busayamas Chewaskulyong, Luis A Herraez-Baranda, Esther Shearer-Kang, Xiaoyan Liu, Nadia Tosti, Patrick Williams, Amparo Yovanna Castro Sanchez, James Zanghi, Enriqueta Felip
Journal: Journal of Thoracic Oncology (2024)
Effects of Thiopurine Withdrawal on Vedolizumab-Treated Patients With Ulcerative Colitis: A Randomized Controlled Trial
Authors: Aviv Pudipeddi, Sudarshan Paramsothy, Viraj Kariyawasam, Ramesh Paramsothy, Simon Ghaly, Craig Haifer, Yoon-Kyo An, Jakob Begun, Susan J. Connor, Crispin Corte, Mark G. Ward, Peter De Cruz, Caroline Lan-San Fung, Diane Redmond, Webber Chan, Fadi Mourad, Melissa Kermeen, Rupert W. Leong
Journal: Clinical Gastroenterology and Hepatology (2024)

The impact of thiopurine de-escalation while on vedolizumab versus continuing thiopurine therapy in ulcerative colitis (UC) is unclear. We aimed to determine the effect of thiopurine withdrawal for patients with UC in remission on vedolizumab.
Nasal solitary chemosensory cells govern daily rhythm in mouse model of allergic rhinitis
Authors: Haiman Xu, Lianxia Guo, Tingying Hao, Xiaocao Guo, Meiping Huang, Haobin Cen, Min Chen, Jiaxian Weng, Meixia Huang, Zicong Wu, Zifei Qin, Jing Yang, Baojian Wu
Journal: Journal of Allergy and Clinical Immunology (2024)
Baseline and end-of-treatment host serum biomarkers predict relapse in adults with pulmonary tuberculosis
Authors: Hygon Mutavhatsindi, Charles M Manyelo, Candice I Snyders, Ilana Van Rensburg, Martin Kidd, Kim Stanley, Gerard Tromp, Reynaldo Dietze, Bonnie Thiel, Paul D van Helden, John T Belisle, John L Johnson, W Henry Boom, Gerhard Walzl, Novel N Chegou
Journal: Journal of Infection (2024)
Identification of Clonal Hematopoiesis Driver Mutations through <i>In Silico</i> Saturation Mutagenesis
Authors: Santiago Demajo, Joan E. Ramis-Zaldivar, Ferran Muiños, Miguel L. Grau, Maria Andrianova, Núria López-Bigas, Abel González-Pérez
Journal: Cancer Discovery (2024)

Abstract Clonal hematopoiesis (CH) is a phenomenon of clonal expansion of hematopoietic stem cells driven by somatic mutations affecting certain genes. Recently, CH has been linked to the development of hematologic malignancies, cardiovascular diseases, and other conditions. Although the most frequently mutated CH driver genes have been identified, a systematic landscape of the mutations capable of initiating this phenomenon is still lacking. In this study, we trained machine learning models for 12 of the most recurrent CH genes to identify their driver mutations. These models outperform expert-curated rules based on prior knowledge of the function of these genes. Moreover, their application to identify CH driver mutations across almost half a million donors of the UK Biobank reproduces known associations between CH driver mutations and age, and the prevalence of several diseases and conditions. We thus propose that these models support the accurate identification of CH across healthy individuals. Significance: We developed and validated gene-specific machine learning models to identify CH driver mutations, showing their advantage with respect to expert-curated rules. These models can support the identification and clinical interpretation of CH mutations in newly sequenced individuals. See related commentary by Arends and Jaiswal, p. 1581
Examining the Associations Among Treatment Declination, Racial and Ethnic Inequities, and Breast Cancer Survival
Authors: Gregory S. Calip, Kent F. Hoskins, Jenny S. Guadamuz
Journal: JAMA Network Open (2024)

Jincong Q. Freeman, MPH, MS; James L. Li, BS; Susan G. Fisher, MS, PhD; Katharine A. Yao, MD; Sean P. David, MD, SM, DPhil; Dezheng Huo, MD, PhD
The COVID-19 Pandemic Period, SARS-CoV-2 Infection, and Perinatal Health
Authors: Shelley Jung, Emily F. Liu, Dana E. Goin, Kara E. Rudolph, Mahasin S. Mujahid, William H. Dow, Jennifer Ahern
Journal: JAMA Network Open (2024)

This cohort study assesses population-level associations of COVID-19 with birth parent and infant health, distinguishing the COVID-19 pandemic period from individual SARS-CoV-2 infection.
In Vivo Reactive Astrocyte Imaging in Patients With Schizophrenia Using Fluorine 18–Labeled THK5351
Authors: Minah Kim, Woori Choi, Sunah Choi, Harin Oh, Jongrak Kim, Jungha Lee, Su-Jin An, Jun Seo Hwang, Yun-Sang Lee, In Chan Song, Sun-Young Moon, Silvia Kyungjin Lho, Sang Soo Cho, Jun Soo Kwon
Journal: JAMA Network Open (2024)

Importance In vivo imaging studies of reactive astrocytes are crucial for understanding the pathophysiology of schizophrenia because astrocytes play a critical role in glutamate imbalance and neuroinflammation. Objective To investigate in vivo reactive astrocytes in patients with schizophrenia associated with positive symptoms using monoamine oxidase B (MAO-B)–binding fluorine 18 ([ 18 F])–labeled THK5351 positron emission tomography (PET). Design, Setting, and Participants In this case-control study, data were collected from October 1, 2021, to January 31, 2023, from the internet advertisement for the healthy control group and from the outpatient clinics of Seoul National University Hospital in Seoul, South Korea, for the schizophrenia group. Participants included patients with schizophrenia and age- and sex-matched healthy control individuals. Main Outcomes and Measures Standardized uptake value ratios (SUVrs) of [ 18 F]THK5351 in the anterior cingulate cortex (ACC) and hippocampus as primary regions of interest (ROIs), with other limbic regions as secondary ROIs, and the correlation between altered SUVrs and Positive and Negative Syndrome Scale (PANSS) positive symptom scores. Results A total of 68 participants (mean [SD] age, 32.0 [7.0] years; 41 men [60.3%]) included 33 patients with schizophrenia (mean [SD] age, 32.3 [6.3] years; 22 men [66.7%]) and 35 healthy controls (mean [SD] age, 31.8 [7.6] years; 19 men [54.3%]) who underwent [ 18 F]THK5351 PET scanning. Patients with schizophrenia showed significantly higher SUVrs in the bilateral ACC (left, F = 5.767 [false discovery rate (FDR)–corrected P = .04]; right, F = 5.977 [FDR-corrected P = .04]) and left hippocampus ( F = 4.834 [FDR-corrected P = .04]) than healthy controls. Trend-level group differences between the groups in the SUVrs were found in the secondary ROIs (eg, right parahippocampal gyrus, F = 3.387 [ P = .07]). There were positive correlations between the SUVrs in the bilateral ACC and the PANSS positive symptom scores (left, r = 0.423 [FDR-corrected P = .03]; right, r = 0.406 [FDR-corrected P = .03]) in patients with schizophrenia. Conclusions and Relevance This case-control study provides novel in vivo imaging evidence of reactive astrocyte involvement in the pathophysiology of schizophrenia. Reactive astrocytes in the ACC may be a future target for the treatment of symptoms of schizophrenia, especially positive symptoms.