tbuckley/cabot-search huggingface dataset:
Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of <i>Gastrodia</i> (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera
Authors: Hanchen Wang, Deyi Wang, Bingyi Shao, Jingrui Li, Zhanghai Li, Mark W Chase, Jianwu Li, Yanlei Feng, Yingying Wen, Shiyu Qin, Binghua Chen, Zhiqiang Wu, Xiaohua Jin
Journal: Molecular Biology and Evolution (2025)

Abstract The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of “dispensable” chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g., plastome contraction) and specific (e.g., host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.
Exploring the mechanism of intestinal bacterial translocation after severe acute pancreatitis: the role of Toll-like receptor 5
Authors: Cheng Zhang, Shiyin Chen, Zhien Wang, Jian Zhang, Wenqiao Yu, Yanshuai Wang, Weiwei Si, Yuwei Zhang, Yun Zhang, Tingbo Liang
Journal: Gut Microbes (2025)

Severe acute pancreatitis (SAP)-induced intestinal bacterial translocation and enterogenic infection are among the leading causes of mortality in patients. However, the mechanisms by which SAP disrupted the intestinal barrier and led to bacterial translocation remained unclear. Therefore, we employed multi-omics analysis including microbiome, metabolome, epigenome, transcriptome, and mass cytometry (CyTOF) to identify potential targets, followed by functional validation using transgenic mice. The integrated multi-omics analysis primarily indicated overgrowth of intestinal flagellated bacteria, upregulation of intestinal Toll-like receptor 5 (TLR5) and acute inflammatory response, and increased infiltration of intestinal high-expressing TLR5 lamina propria dendritic cells (TLR5hi LPDC) after SAP. Subsequently, intestinal flagellin-TLR5 signaling was activated after SAP. Intestinal barrier disruption, bacterial translocation, and helper T cells (Th) differentiation imbalance caused by SAP were alleviated in TLR5 knocked out (Tlr5-/-) or conditionally knocked out on LPDC (Tlr5ΔDC) mice. However, TLR5 conditional knockout on intestinal epithelial cells (Tlr5ΔIEC) failed to improve SAP-induced bacterial translocation. Moreover, depletion of LPDC and regulatory T cells (Treg) ameliorated bacterial translocation after SAP. Our findings identify TLR5 on LPDC as a potential novel target for preventing or treating intestinal bacterial translocation caused by SAP.
Serum proteomic signatures prior to the diagnosis of rheumatoid arthritis demonstrate evolving biological pathways and identify specific periods of disease development
Authors: Samir Rachid Zaim, Adam K. Savage, Mark A. Gillespie, Jazmine Castillo, Christy Bennett, Troy R Torgerson, Lynne A. Becker, Michael Mahler, LauraKay Moss, Marie L. Feser, Jess D. Edison, Ted R. Mikuls, V. Michael Holers, Xiao‐jun Li, Kevin D. Deane
Journal: Arthritis & Rheumatology (2025)

Objective This longitudinal case‐control study evaluated serum proteomics prior to a clinical diagnosis of rheumatoid arthritis (i.e. pre‐RA) to evaluate biologic pathways of disease development and inform prediction of timing of onset of future disease. Methods Patients (cases, n=213) meeting the 1987 American College of Rheumatology (ACR) classification criteria for RA, and matched controls without RA (n=215) were identified in the Department of Defense Serum Repository. Serum samples from cases pre‐ and post‐RA diagnosis and controls were tested for RA‐related autoantibodies (anti‐cyclic citrullinated peptide [anti‐CCP3], rheumatoid factor [RF] isotypes immunoglobulin [Ig] M and A, and 197 proteins using a commercial platform (Olink). We applied linear mixed effect models to identify biomarkers distinguishing cases from controls prior to RA diagnosis and analyzed longitudinal patterns of enriched pathways; in addition, models were developed to classify the time of a sample in relationship to the time of RA diagnosis. Results Levels of anti‐CCP3, RFIgA, and RFIgM demonstrated the greatest differences between cases and controls ≤5 years prior to RA diagnosis. Longitudinal analyses identified 104 proteins that were differentially expressed between cases and controls; 60 were differentially expressed ≤5 years prior to diagnosis, 42 within and prior to 5 years of diagnosis, and 2 &gt;5 years prior. KEGG analyses identified that these proteins were associated with 32 pathways, including 21 pathways that were enriched ≤5 years prior to diagnosis. Within the ACPA positive samples from prior to RA diagnosis and controls, a set of features classified if that sample was from a period &lt;3 years prior to RA diagnosis with an area under the curve (AUC) of 0.78 [0.67, 0.89] in a training set, and 0.80 [0.68, 0.92] in a validation set. Conclusion Autoantibodies and protein signatures evolve in distinct stages prior to a diagnosis of RA. Furthermore, protein biomarkers may identify biologic pathways relevant to specific stages. These can be further explored to potentially improve prediction of disease onset and identify stage‐specific biological pathways to target with preventive interventions.
Reaching the unreached through an integrated communicable disease dashboard
Authors: Fukushi Morishita, Wei Su, James Kelley, Kiyohiko Izumi, Kalpeshsinh Rahevar, Kazim Hizbullah Sanikullah, Kyung Hyun Oh, Zoie Shui Yee Wong, Rajendra Prasad Yadav, Thi Giang Huong Tran
Journal: npj Digital Medicine (2025)
Comparative cardiovascular safety of medications for attention-deficit hyperactivity disorder in children, adolescents, and adults: a systematic review and network meta-analysis
Authors: Luis C Farhat, Alice Lannes, Cinzia Del Giovane, Valeria Parlatini, Miguel Garcia-Argibay, Edoardo G Ostinelli, Anneka Tomlison, Zheng Chang, Henrik Larsson, Cristiano Fava, François Montastruc, Andrea Cipriani, Alexis Revet, Samuele Cortese
Journal: The Lancet Psychiatry (2025)
Self-degradable “gemini-like” ionizable lipid-mediated delivery of siRNA for subcellular-specific gene therapy of hepatic diseases
Authors: Qiu Wang, Bin Wan, Yao Feng, Zimeng Yang, Dan Li, Fan Liu, Ya Gao, Chang Li, Yanhua Liu, Yongbing Sun, Zhonggui He, Cong Luo, Jin Sun, Qikun Jiang
Journal: Acta Pharmaceutica Sinica B (2025)
Achieving gender justice for global health equity: the Lancet Commission on gender and global health
Authors: Sarah Hawkes, Elhadj As Sy, Gary Barker, Frances Elaine Baum, Kent Buse, Angela Y Chang, Beniamino Cislaghi, Jocalyn Clark, Raewyn Connell, Morna Cornell, Gary L Darmstadt, Carmen Simone Grilo Diniz, Sharon Friel, Indrani Gupta, Sofia Gruskin, Sarah Hill, Amy Chiaying Hsieh, Renu Khanna, Jeni Klugman, Aaron Koay, Vivian Lin, Khadija T Moalla, Erica Nelson, Lynsey Robinson, Nina Schwalbe, Ravi Verma, Virginia Zarulli
Journal: The Lancet (2025)
Leveraging strain competition to address antimicrobial resistance with microbiota therapies
Authors: Danielle Barrios Steed, Dylan Koundakjian, Anthony D. Harris, Adriana E Rosato, Konstantinos T Konstantinidis, Michael H Woodworth
Journal: Gut Microbes (2025)

The enteric microbiota is an established reservoir for multidrug-resistant organisms that present urgent clinical and public health threats. Observational data and small interventional studies suggest that microbiome interventions, such as fecal microbiota products and characterized live biotherapeutic bacterial strains, could be an effective antibiotic-sparing prevention approach to address these threats. However, bacterial colonization is a complex ecological phenomenon that remains understudied in the context of the human gut. Antibiotic resistance is one among many adaptative strategies that impact long-term colonization. Here we review and synthesize evidence of how bacterial competition and differential fitness in the context of the gut present opportunities to improve mechanistic understanding of colonization resistance, therapeutic development, patient care, and ultimately public health.
Impact of Evolving <scp>WHO</scp> and <scp>ICC</scp> Classifications on Prognosis and Outcomes in <scp>AML</scp> Patients Undergoing Allogeneic Stem Cell Transplantation
Authors: Jacob Jendro, Jule Ussmann, Dominic Brauer, Donata Backhaus, Lara Bischof, Maximilian Merz, Vladan Vucinic, Georg‐Nikolaus Franke, Marco Herling, Klaus H. Metzeler, Uwe Platzbecker, Sebastian Schwind, Madlen Jentzsch
Journal: American Journal of Hematology (2025)
Shortening antibiotic therapy duration for hospital-acquired bloodstream infections in critically ill patients: a causal inference model from the international EUROBACT-2 database
Authors: Lena Gajdos, Niccolo Buetti, Alexis Tabah, Stephane Ruckly, Murat Akova, Frederik Sjöval, Kostoula Arvanti, Jan de Waele, Hendrik Bracht, Francois Barbier, Jean-François Timsit
Journal: Intensive Care Medicine (2025)
Implementation science in hemato‐oncology molecular diagnostics in France via the Groupe des Biologistes Moléculaire des Hémopathies Malignes (GBMHM)
Authors: Jean‐Michel Cayuela, Pierre Sujobert, Pascale Flandrin‐Gresta, Anne‐Sophie Alary, Carole Maute, Damien Luque‐Paz, Cédric Pastoret, Stéphanie Dulucq, Audrey Gauthier, Meryl Darlington, Isabelle Durand‐Zaleski, Olivier Kosmider, Elizabeth Macintyre
Journal: HemaSphere (2025)
Real-world experience with first-line CPX-351 treatment in patients with acute myeloid leukemia – long-term follow-up with focus on younger patients
Authors: Christina Rautenberg, Jan Moritz Middeke, Christoph Röllig, Matthias Stelljes, Verena Gaidzik, Oliver Kriege, Mareike Verbeek, Katrin Koch, Julia Marie Unglaub, Felicitas Thol, Stefan W Krause, Mathias Hänel, Charlotte Neuerburg, Vladan Vucinic, Christian-Friedrich Jehn, Maxi Wass, Michael Heuser, Lars Fransecky, Jens Chemnitz, Udo Holtick, Kerstin Schäfer-Eckart, Josephine Schröder, Sabrina Kraus, William Krüger, Ulrich Kaiser, Sebastian Scholl, Guido Kobbe, Paul Sebastian Jäger, Nael Alakel, Malte von Bonin, Katja Sockel, Maher Hanoun, Uwe Platzbecker, Tobias A W Holderried, Anke Morgner, Tim Sauer, Katharina S Götze, Eva Wagner-Drouet, Konstanze Döhner, Hartmut Döhner, Christoph Schliemann, Johannes Schetelig, Martin Bornhäuser, Ulrich Germing, Sara Flossdorf, Thomas Schroeder, Friedrich Stölzel
Journal: Blood Cancer Journal (2025)
MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles
Authors: Salvatore Milite, Giulio Caravagna, Andrea Sottoriva
Journal: Genome biology (2025)

High-throughput multi-omic molecular profiling allows the probing of biological systems at unprecedented resolution. However, integrating and interpreting high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving new biological insights with current methods is difficult because they are not rooted in biological principles but prioritise tasks like dimensionality reduction. Here, we introduce a framework that combines archetypal analysis, an approach grounded in biological principles, with deep learning. Using archetypes based on evolutionary trade-offs and Pareto optimality, MIDAA finds extreme data points that define the geometry of the latent space, preserving the complexity of biological interactions while retaining an interpretable output. We demonstrate that these extreme points represent cellular programmes reflecting the underlying biology. Moreover, we show that, compared to alternative methods, MIDAA can identify parsimonious, interpretable, and biologically relevant patterns from real and simulated multi-omics.
Detection of Cerebral Ischemia in Bone Scan
Authors: Léa Ghalyoun, Xavier Palard-Novello, Mehdi Mouheb, Allan Delaleux, Julie Faudemer
Journal: Clinical Nuclear Medicine (2025)

The current case involves a 68-year-old woman who was referred to the nuclear medicine department for a bone scan for suspected cardiac amyloidosis. Bone scan did not show any evidence of cardiac amyloidosis, but extraosseous cerebral 99m Tc-labeled diphosphonate analogs uptake was detected. Further questioning revealed that the patient has had left lower limb hemiparesis for the past 24 hours. Thus, she was admitted for an MRI the same day, which showed signs of a recent ischemic stroke. This case exhibits that cerebral uptake in bone scan may reflect acute ischemia and, thus, an MRI scan should be performed quickly.
18F-FDG PET/CT Findings in a Case of Plasmablastic Myeloma: A Rare Entity
Authors: Nivedita Kundu, Aparna Mahalik, Dikhra Khan, Rakesh Kumar
Journal: Clinical Nuclear Medicine (2025)

Plasmablastic myeloma (PBM) is an extremely rare variant of multiple myeloma, having morphologic, clinical, and radiologic overlap with plasmablastic lymphoma (PBL). Thus, distinguishing both becomes vital due to different treatment strategies. Due to limited literature on imaging findings in this rare entity, here we present a unique case of PBM developing in the setting of chronic light chain myeloma, with extensive extramedullary involvement and severe osteopenia, in addition to pleural deposits, pleural effusion, and perinephric fascial deposit. Thus, 18F-FDG PET/CT can be utilized as an important tool in distinguishing PBM and PBL on imaging, assessing disease extent, and identifying critical lesions requiring immediate intervention.
A Comparative Analysis of Glycemic Metrics Derived From Three Continuous Glucose Monitoring Systems
Authors: Guido Freckmann, Stephanie Wehrstedt, Manuel Eichenlaub, Stefan Pleus, Manuela Link, Nina Jendrike, Sükrü Öter, Derek Brandt, Cornelia Haug, Delia Waldenmaier
Journal: Diabetes Care (2025)

OBJECTIVE This study analyzed the differences in continuous glucose monitoring (CGM)-derived metrics among three current-generation systems and evaluated their impact on therapeutic decision-making. RESEARCH DESIGN AND METHODS Twenty-three participants wore the FreeStyle Libre 3, Dexcom G7, and Medtronic Simplera CGM systems for 14 days in parallel. CGM metrics were calculated for each participant and CGM system separately. RESULTS The apparent glucose profile was influenced by the used CGM system, resulting in substantially different glycemic metrics among the three systems. Agreement between FreeStyle Libre 3 and Dexcom G7 was higher than with Medtronic Simplera, which showed lower glucose levels, on average. There were marked intraparticipant discrepancies that would have resulted in different therapeutic recommendations. CONCLUSIONS The CGM systems indicated discordant glycemic metrics, which should be considered in diabetes therapy. Different CGM systems should provide the same glucose readings and CGM-derived metrics when used by the same person.
Winter Storm Uri, Mortality, and Health Care Use of Nursing Home Residents
Authors: Brian Downer, Alexandra Holland, Shuang Li, Huiwen Xu
Journal: JAMA Network Open (2025)

Importance Extreme weather events disproportionately affect vulnerable populations, particularly nursing home residents. In February 2021, Winter Storm Uri caused unprecedented power outages and water shortages across Texas. However, its impact on nursing home residents remains poorly understood. Objective To assess the association of power outages and water shortages during Winter Storm Uri with mortality and health care utilization among long-stay nursing home residents in Texas. Design, Setting, and Participants A retrospective cohort study of long-stay nursing home residents before and after Winter Storm Uri (February 14 to February 17, 2021) in Texas. Data analysis was conducted from March 2024 to January 2025. Exposure Residing in a nursing home that experienced a power outage or water shortage during Winter Storm Uri. Main Outcomes and Measures The outcome measures were weekly rates of mortality, clinician visits to nursing homes, emergency department (ED) visits, and hospitalizations among long-stay nursing home residents. Medicare claims were used to determine weekly mortality, clinician visits, ED visits, and hospitalizations 6 weeks before and 6 weeks after the storm. Differences-in-differences (DiD) analysis using 2-level logistic regression models estimated changes in outcomes associated with nursing home power or water loss. Results Of 1174 nursing homes, 231 (19.7%) reported power or water outages. The sample included 45 439 long-stay residents, with 8521 in facilities with outages (mean [SD] age, 80.07 [12.21] years; 5664 female [66.47%]) and 36 918 in facilities without outages (mean [SD] age, 80.42 [11.92] years; 12 705 female [65.59%]). DiD analysis found that residents of nursing homes with outages had a 0.13% (95% CI, 0.03% to 0.23%) higher mortality rate in the 3 to 5 weeks after the storm than those without outages. There were no significant differences in clinician visits (DiD, −0.31%; 95% CI, −1.08% to 0.47%), ED visits (DiD, 0.11%; 95% CI, −0.12% to 0.34%), or hospitalizations (DiD, 0.07%; 95% CI, −0.10% to 0.23%). Conclusions and Relevance In this cohort study of nursing home residents in Texas, power and water outages during Winter Storm Uri were associated with increased mortality but not ED visits or hospitalizations, highlighting the vulnerability of nursing home residents during extreme weather events.
Post–Intensive Care Syndrome and Caregiver Burden
Authors: Soojung Ahn, Marianna LaNoue, Han Su, Amanda C. Moale, Leslie P. Scheunemann, Amy L. Kiehl, Ivor S. Douglas, Matthew C. Exline, Michelle N. Gong, Babar A. Khan, Robert L. Owens, Margaret A. Pisani, Peter Rock, James C. Jackson, E. Wesley Ely, Timothy D. Girard, Leanne M. Boehm
Journal: JAMA Network Open (2025)

Importance Understanding the reciprocal association between post–intensive care syndrome (PICS) and caregiver burden is crucial for optimal care of patients and caregivers following critical illness. Objective To evaluate the associations between patient post–intensive care impairments and caregiver burden. Design, Setting, and Participants This secondary analysis of the MIND-USA study, a multicenter randomized clinical trial, which enrolled patients admitted to intensive care units (ICU) from 16 academic medical centers across the US (December 2011 to August 2017), included 148 patient-caregiver dyads. Patients were adults aged 18 years or older with ICU delirium randomized to receive haloperidol, ziprasidone, or placebo. A caregiver who provided unpaid assistance to the patient was identified at enrollment. PICS and caregiver burden were assessed at 3 months and 12 months after randomization. Statistical analysis was performed from March 2023 to April 2024. Main Outcomes and Measures ICU survivors were assessed for PICS domains, including physical and cognitive function, and posttraumatic stress disorder using the Katz Activities of Daily Living, the Functional Activities Questionnaire, the Telephone Interview for Cognitive Status, and the Posttraumatic Stress Disorder Checklist-Civilian version, respectively. Caregiver burden was assessed using the Zarit Burden Interview. The associations between patient PICS and caregiver burden at 3 and 12 months were examined using structural equation modeling. Results Of 148 patients included in this study with a median (IQR) age of 58 (48-65) years, the majority identified as male (79 patients [53.4%]), and there were 16 (10.8%) Black, 139 (93.9%) non-Hispanic, and 127 (85.8%) White patients. PICS and caregiver burden at 3-month follow-up was positively associated with these outcomes at 12-month follow-up (PICS: β = 0.69; 95% CI, 0.50 to 0.88; P &amp;amp;lt; .001; caregiver burden: β = 0.68; 95% CI, 0.53 to 0.82; P &amp;amp;lt; .001). However, contrary to the study hypotheses, significant associations between 3-month PICS and 12-month caregiver burden and between 3-month caregiver burden and 12-month PICS were not observed (PICS→caregiver burden: β = 0.82; 95% CI, −0.02 to 1.66; P = .09; caregiver burden→PICS: β = 0.00; 95% CI, −0.03 to 0.03; P = .95). There was significant covariance between PICS and caregiver burden at each time point. Conclusions and Relevance In this secondary analysis of a randomized clinical trial of ICU survivors and their caregivers, patient PICS and caregiver burden were associated at concurrent time points but were not associated with each other longitudinally. Trial Registration ClinicalTrials.gov Identifier: NCT01211522