{"_links":{"self":{"href":"/api/v2/search"},"first":{"href":"/api/v2/search"},"last":{"href":"/api/v2/search?page=3611"},"next":{"href":"/api/v2/search?page=2"}},"count":20,"total":72204,"_embedded":{"stash:datasets":[{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.vdncjsz57"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.vdncjsz57/versions"},"stash:version":{"href":"/api/v2/versions/462061"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.vdncjsz57/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.vdncjsz57","id":147704,"storageSize":41012,"relatedPublicationISSN":"0962-1083","title":"Data from: Evolution and organisation of MHC II genes in harbour porpoises: Insights from long-read cetacean genome assemblies, whole genome re-sequencing and locus-specific genotyping","authors":[{"firstName":"Enrique","lastName":"Celemin Amaro","email":"celeminamaro@uni-potsdam.de","affiliation":"University of Potsdam","affiliationROR":"https://ror.org/03bnmw459","affiliations":[{"name":"University of Potsdam","ror_id":"https://ror.org/03bnmw459"}],"orcid":"0000-0002-2232-3930"},{"firstName":"Nikolai","lastName":"Gusev","email":"","affiliation":"University of Potsdam","affiliationROR":"https://ror.org/03bnmw459","affiliations":[{"name":"University of Potsdam","ror_id":"https://ror.org/03bnmw459"},{"name":"Helmholtz Institute For One Health"}]},{"firstName":"Marisol","lastName":"Domínguez","email":"","affiliation":"University of Potsdam","affiliationROR":"https://ror.org/03bnmw459","affiliations":[{"name":"University of Potsdam","ror_id":"https://ror.org/03bnmw459"}]},{"firstName":"Katja","lastName":"Havenstein","email":"","affiliation":"University of Potsdam","affiliationROR":"https://ror.org/03bnmw459","affiliations":[{"name":"University of Potsdam","ror_id":"https://ror.org/03bnmw459"}]},{"firstName":"Per","lastName":"Berggren","email":"","affiliation":"Newcastle University","affiliationROR":"https://ror.org/01kj2bm70","affiliations":[{"name":"Newcastle University","ror_id":"https://ror.org/01kj2bm70"}]},{"firstName":"Mads-Peter","lastName":"Heide-Jorgensen","email":"","affiliation":"Grønlands Naturinstitut","affiliationROR":"https://ror.org/0342y5q78","affiliations":[{"name":"Grønlands Naturinstitut","ror_id":"https://ror.org/0342y5q78"}]},{"firstName":"Véronique","lastName":"Lesage","email":"","affiliation":"Fisheries and Oceans Canada","affiliationROR":"https://ror.org/02qa1x782","affiliations":[{"name":"Fisheries and Oceans Canada","ror_id":"https://ror.org/02qa1x782"}]},{"firstName":"Christina","lastName":"Lockyer","email":"","affiliation":"Age Dynamics","affiliations":[{"name":"Age Dynamics"}]},{"firstName":"Christophe","lastName":"Pampoulie","email":"","affiliation":"Marine and Freshwater Research Institute","affiliationROR":"https://ror.org/02c8sqt04","affiliations":[{"name":"Marine and Freshwater Research Institute","ror_id":"https://ror.org/02c8sqt04"}]},{"firstName":"Iwona","lastName":"Pawliczka","email":"","affiliation":"University of Gdańsk","affiliationROR":"https://ror.org/011dv8m48","affiliations":[{"name":"University of Gdańsk","ror_id":"https://ror.org/011dv8m48"}]},{"firstName":"Anna","lastName":"Roos","email":"","affiliation":"Swedish Museum of Natural History","affiliationROR":"https://ror.org/05k323c76","affiliations":[{"name":"Swedish Museum of Natural History","ror_id":"https://ror.org/05k323c76"}]},{"firstName":"Ursula","lastName":"Siebert","email":"","affiliation":"University of Veterinary Medicine Hannover, Foundation","affiliationROR":"https://ror.org/015qjqf64","affiliations":[{"name":"University of Veterinary Medicine Hannover, Foundation","ror_id":"https://ror.org/015qjqf64"}]},{"firstName":"Guðjón","lastName":"Sigurðsson","email":"","affiliation":"Marine and Freshwater Research Institute","affiliationROR":"https://ror.org/02c8sqt04","affiliations":[{"name":"Marine and Freshwater Research Institute","ror_id":"https://ror.org/02c8sqt04"}]},{"firstName":"Ayaka","lastName":"Öztürk","email":"","affiliation":"Istanbul University","affiliationROR":"https://ror.org/03a5qrr21","affiliations":[{"name":"Istanbul University","ror_id":"https://ror.org/03a5qrr21"}]},{"firstName":"Bayram","lastName":"Öztürk","email":"","affiliation":"Istanbul University","affiliationROR":"https://ror.org/03a5qrr21","affiliations":[{"name":"Istanbul University","ror_id":"https://ror.org/03a5qrr21"}]},{"firstName":"Ralph","lastName":"Tiedemann","email":"","affiliation":"University of Potsdam","affiliationROR":"https://ror.org/03bnmw459","affiliations":[{"name":"University of Potsdam","ror_id":"https://ror.org/03bnmw459"}],"orcid":"0000-0002-2604-6336"}],"abstract":"\u003cp\u003eThe Major Histocompatibility Complex (MHC) is a central element in the vertebrate immune system. While MHC genes are a common target of conservation genomic studies, it has been challenging to reliably amplify locus-specific alleles, which is especially problematic when studying endangered lineages, like some Harbour porpoise (\u003cem\u003ePhocoena phocoena\u003c/em\u003e) populations and subspecies. Here, we manually annotated all MHC II genes in the Harbour porpoise genome, and genotyped every exon 2 in 94 individuals spanning six geographical regions, including the endangered Black Sea porpoise subspecies (\u003cem\u003ePhocoena phocoena relicta\u003c/em\u003e) and the endangered Proper Baltic Sea population of the North Atlantic subspecies (\u003cem\u003eP. p. phocoena\u003c/em\u003e). We performed gene-wise analyses of diversity and selection, and put the results into perspective with 24 available Harbour porpoise genomes. Furthermore, we characterized all MHC II genes in 19 available long-read cetacean and terrestrial outgroups genomes to study the MHC II evolution across the cetacean diversification. From the 10 MHC II loci annotated in the Harbour porpoise genome, two (DRB1 and DQB) exhibited inflated allelic diversity and signatures of positive selection. Interestingly, DRB genes followed different evolutionary trajectories in mysticetes and odontocetes. Our results have significant conservation implications since we identified reduced MHC II diversity in the endangered Black Sea subspecies, and provide a case study for reliable MHC II genotyping in other species. Further, our study demonstrates the need for long-read genomes to understand the genomic architecture of MHC and to accurately assess its diversity and evolution.\u003c/p\u003e\n","funders":[{"organization":"University of Potsdam","identifierType":"ror","identifier":"https://ror.org/03bnmw459","awardDescription":"","order":0}],"keywords":["Genomics","Major histocompatibility complex","Cetacea"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.22541/au.172446843.30153751/v1"},{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1111/mec.70006"}],"versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-07","lastModificationDate":"2026-09-07","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.vdncjsz57","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.wpzgmsc40"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.wpzgmsc40/versions"},"stash:version":{"href":"/api/v2/versions/462065"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.wpzgmsc40/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.wpzgmsc40","id":181767,"storageSize":1586921730,"relatedPublicationISSN":"1362-4962","title":"Data from: Domain dynamics within the PriA DNA helicase regulate DNA replication restart","authors":[{"firstName":"Haley","lastName":"Deorio","email":"deorio@wisc.edu","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"orcid":"0000-0003-1364-027X"},{"firstName":"Alexander","lastName":"Duckworth","email":"aduckworth@wisc.edu","affiliation":"Morgridge Institute for Research","affiliationROR":"https://ror.org/05cb4rb43","affiliations":[{"name":"Morgridge Institute for Research","ror_id":"https://ror.org/05cb4rb43"}],"order":1},{"firstName":"Gavin","lastName":"Forsythe","email":"gavinrforsythe@gmail.com","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"order":2},{"firstName":"Andrew","lastName":"Sung","email":"andrew.sung@utsouthwestern.edu","affiliation":"The University of Texas Southwestern Medical Center","affiliationROR":"https://ror.org/05byvp690","affiliations":[{"name":"The University of Texas Southwestern Medical Center","ror_id":"https://ror.org/05byvp690"}],"order":3},{"firstName":"Tim","lastName":"Grant","email":"tim.grant@wisc.edu","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"order":4},{"firstName":"Steven","lastName":"Sandler","email":"ssandler@umass.edu","affiliation":"University of Massachusetts Amherst","affiliationROR":"https://ror.org/0072zz521","affiliations":[{"name":"University of Massachusetts Amherst","ror_id":"https://ror.org/0072zz521"}],"order":5},{"firstName":"James","lastName":"Keck","email":"jlkeck@wisc.edu","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"orcid":"0000-0002-5961-0220","order":6}],"abstract":"\u003cp\u003ePrematurely terminated DNA replication processes in bacteria must be restarted for successful genome duplication. In \u003cem\u003eEscherichia coli\u003c/em\u003e, the PriA DNA helicase orchestrates replication restart by assembling the PriA/PriB/DnaT preprimosome complex at abandoned DNA replication forks and reloading the replicative machinery. We show that the structure of the lagging strand—whether single- or double-stranded—influences the position of the cysteine-rich region in PriA (PriA\u003csup\u003eCRR\u003c/sup\u003e), thereby regulating PriA biochemical activity and preprimosome formation. When PriA binds to replication forks with a single-stranded lagging strand, the PriA\u003csup\u003eCRR\u003c/sup\u003e is found either in a state similar to free PriA or in a rotated position that encircles the lagging strand and allows PriB recruitment. Binding to a replication fork with a duplex lagging strand neither the PriA\u003csup\u003eCRR\u003c/sup\u003e position nor promotes PriB binding, suggesting PriA must unwind duplex lagging-strand DNA to trigger PriA\u003csup\u003eCRR\u003c/sup\u003e movement and subsequent preprimosome formation. PriA variants designed to destabilize the two PriA\u003csup\u003eCRR\u003c/sup\u003e positions differentially affect ATPase activity, helicase function, and PriB binding \u003cem\u003ein vitro\u003c/em\u003e, and PriA-mediated replication restart \u003cem\u003ein vivo\u003c/em\u003e. These results demonstrate that the PriA\u003csup\u003eCRR\u003c/sup\u003e functions as a regulatory switch that detects the structure of the lagging strand and controls the biochemical and cellular activities of PriA to restart DNA replication.\u003c/p\u003e\n","funders":[{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"5R01GM098885-12","awardURI":"https://reporter.nih.gov/project-details/11123170","awardDescription":"","awardTitle":"","order":0},{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"5T32GM140935-05","awardURI":"https://reporter.nih.gov/project-details/11123164","awardDescription":"","awardTitle":"","order":1},{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"2T32GM135066-06","awardURI":"https://reporter.nih.gov/project-details/11014514","awardDescription":"","awardTitle":"Biotechnology Training Program","order":2}],"keywords":["DNA replication","DNA helicases","DNA repair"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"software","identifierType":"URL","identifier":"https://github.com/AYSung/smoltools"}],"versionNumber":6,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-07","lastModificationDate":"2026-09-07","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.wpzgmsc40","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.44j0zpcwk"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.44j0zpcwk/versions"},"stash:version":{"href":"/api/v2/versions/462075"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.44j0zpcwk/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.44j0zpcwk","id":182483,"storageSize":1152512836,"relatedPublicationISSN":"1549-9618","title":"Data from: Molecular simulation and multistate analysis for efficient property estimation in polymeric systems: A case study on PIM-1","authors":[{"firstName":"Cassiano","lastName":"Gomes Aimoli","email":"aimoli@mit.edu","affiliation":"Massachusetts Institute of Technology","affiliationROR":"https://ror.org/042nb2s44","affiliations":[{"name":"Massachusetts Institute of Technology","ror_id":"https://ror.org/042nb2s44"},{"name":"Petrobras (Brazil)","ror_id":"https://ror.org/0235kyq22"}],"orcid":"0000-0003-4471-1579"},{"firstName":"Zachary","lastName":"Smith","email":"zpsmith@mit.edu","affiliation":"Massachusetts Institute of Technology","affiliationROR":"https://ror.org/042nb2s44","affiliations":[{"name":"Massachusetts Institute of Technology","ror_id":"https://ror.org/042nb2s44"}],"order":1}],"abstract":"\u003cp\u003eThis dataset contains the input files, simulation outputs, and analysis scripts associated with molecular simulations of CO\u003csub\u003e2\u003c/sub\u003e and CH\u003csub\u003e4\u003c/sub\u003e adsorption in the polymer of intrinsic microporosity PIM-1. The data were generated using molecular dynamics and Monte Carlo simulations performed with LAMMPS and analyzed using the Multistate Bennett Acceptance Ratio (MBAR) method to estimate thermodynamic properties across multiple thermodynamic states. The dataset includes simulation input scripts, force field parameters, initial molecular configurations, and output log files produced during the simulations. Post-processing scripts used to extract thermodynamic quantities and compute MBAR estimates are also provided. Processed data files containing averaged thermodynamic properties and uncertainty estimates are included to facilitate reproduction of the reported results. The directory structure reflects the simulation workflow, including folders for system preparation, production simulations, and analysis.\u003c/p\u003e\n","funders":[{"organization":"Petrobras (Brazil)","identifierType":"ror","identifier":"https://ror.org/0235kyq22","awardNumber":"","awardDescription":"","awardTitle":"","order":0}],"keywords":["Multistate Bennett Acceptance Ratio","PIM-1","molecular simulation"],"fieldOfScience":"Chemical engineering","versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-07","lastModificationDate":"2026-09-07","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.44j0zpcwk","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.95x69p91q"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.95x69p91q/versions"},"stash:version":{"href":"/api/v2/versions/462078"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.95x69p91q/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.95x69p91q","id":187667,"storageSize":6332118,"relatedPublicationISSN":"1558-5646","title":"Data and code from: Molecular characterization and cophylogenetic relationships between \u003cem\u003eCrassicauda\u003c/em\u003e spp. (Nematoda: Spirurida) and cetaceans of the Northwest Atlantic","authors":[{"firstName":"Jacquelyn M.","lastName":"Salguero","email":"jms2879@uncw.edu","affiliation":"University of North Carolina Wilmington","affiliationROR":"https://ror.org/02t0qr014","affiliations":[{"name":"University of North Carolina Wilmington","ror_id":"https://ror.org/02t0qr014"}],"orcid":"0009-0008-8041-7688","order":0},{"firstName":"Sebrina P.","lastName":"Brooks","email":"sebrinapbrooks@gmail.com","affiliation":"University of Colorado Boulder","affiliationROR":"https://ror.org/02ttsq026","affiliations":[{"name":"University of Colorado Boulder","ror_id":"https://ror.org/02ttsq026"}],"order":1},{"firstName":"Tiffany F.","lastName":"Keenan","email":"keenant@uncw.edu","affiliation":"University of North Carolina Wilmington","affiliationROR":"https://ror.org/02t0qr014","affiliations":[{"name":"University of North Carolina Wilmington","ror_id":"https://ror.org/02t0qr014"}],"order":2},{"firstName":"D. Ann","lastName":"Pabst","email":"pabsta@uncw.edu","affiliation":"University of North Carolina Wilmington","affiliationROR":"https://ror.org/02t0qr014","affiliations":[{"name":"University of North Carolina Wilmington","ror_id":"https://ror.org/02t0qr014"}],"order":3},{"firstName":"William A.","lastName":"McLellan","email":"mclellanw@uncw.edu","affiliation":"University of North Carolina Wilmington","affiliationROR":"https://ror.org/02t0qr014","affiliations":[{"name":"University of North Carolina Wilmington","ror_id":"https://ror.org/02t0qr014"}],"order":4},{"firstName":"D. Wilson","lastName":"Freshwater","email":"freshwaterw@uncw.edu","affiliation":"University of North Carolina Wilmington","affiliationROR":"https://ror.org/02t0qr014","affiliations":[{"name":"University of North Carolina Wilmington","ror_id":"https://ror.org/02t0qr014"}],"order":5},{"firstName":"Julia C.","lastName":"Buck","email":"buckj@uncw.edu","affiliation":"University of North Carolina Wilmington","affiliationROR":"https://ror.org/02t0qr014","affiliations":[{"name":"University of North Carolina Wilmington","ror_id":"https://ror.org/02t0qr014"}],"order":6}],"abstract":"\u003cp\u003eEvaluating the cophylogenetic relationships between hosts and parasites provides a valuable framework for investigating the evolutionary processes that shape biodiversity, including patterns of host specificity and parasite diversification. This study investigated the evolutionary relationships between cetaceans and their nematode parasites of the genus \u003cem\u003eCrassicauda\u003c/em\u003e. This genus was selected because it includes highly virulent species that may regulate host populations. Still, its diversity and evolutionary history remain poorly understood due to limitations in sampling these giant nematodes. To address this gap, we generated sequence data from 13 \u003cem\u003eCrassicauda\u003c/em\u003e specimens collected from five cetacean host species in the Northwest Atlantic using mitochondrial (\u003cem\u003ecox\u003c/em\u003e1) and nuclear (18S and ITS-2) genes, and combined these with homologous sequences from GenBank to characterize diversity within the genus and to delimit our putative species hypotheses. We assessed host-parasite cophylogenetic relationships by using complementary distance-based (PACo and ParaFit) and event-based (Jane) approaches. Phylogenetic analyses resolved 11 parasite species infecting 15 cetacean species, revealing potential cryptic and underreported diversity. Cophylogenetic analyses recovered significant cophylogenetic signal between host and parasite phylogenies, providing strong evidence that host-parasite associations are more structured than by chance. This signal was robust across multiple analytical parameters; distance-based analyses consistently recovered significant cophylogenetic signal in both consensus and posterior tree analyses. Although event-based reconciliation costs were significantly lower than expected under null models, inferred host-switching events exceeded cospeciation events, indicating incongruence between parasite and host phylogenies. Concordant results across independent methods, together with the known biology and ecology of both the hosts and parasites, support a long-term evolutionary association between \u003cem\u003eCrassicauda\u003c/em\u003e and cetaceans shaped by a combination of cospeciation, host-switching, failure-to-diverge, and other evolutionary processes.\u003c/p\u003e\n","funders":[{"organization":"National Oceanic and Atmospheric Administration","identifierType":"ror","identifier":"https://ror.org/02z5nhe81","awardNumber":"NA25NMFX439G0159","awardDescription":"","awardTitle":"John H. Prescott Marine Mammal Rescue Assistance Grant Program","order":0},{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"1945981","awardDescription":"Graduate Research Fellowship Program","awardTitle":"NSF GFRP","order":6},{"organization":"National Oceanic and Atmospheric Administration","identifierType":"ror","identifier":"https://ror.org/02z5nhe81","awardNumber":"NA22NMF4390241","awardDescription":"","awardTitle":"John H. Prescott Marine Mammal Rescue Assistance Grant Program","order":1},{"organization":"National Oceanic and Atmospheric Administration","identifierType":"ror","identifier":"https://ror.org/02z5nhe81","awardNumber":"NA21NMF4390398","awardDescription":"","awardTitle":"John H. Prescott Marine Mammal Rescue Assistance Grant Program","order":2},{"organization":"National Oceanic and Atmospheric Administration","identifierType":"ror","identifier":"https://ror.org/02z5nhe81","awardNumber":"NA20NMF4390119","awardDescription":"","awardTitle":"John H. Prescott Marine Mammal Rescue Assistance Grant Program","order":3},{"organization":"National Oceanic and Atmospheric Administration","identifierType":"ror","identifier":"https://ror.org/02z5nhe81","awardNumber":"NA18NMF4390033","awardDescription":"","awardTitle":"John H. Prescott Marine Mammal Rescue Assistance Grant Program","order":4},{"organization":"National Oceanic and Atmospheric Administration","identifierType":"ror","identifier":"https://ror.org/02z5nhe81","awardNumber":"NA17NMF4390085","awardDescription":"","awardTitle":"John H. Prescott Marine Mammal Rescue Assistance Grant Program","order":5}],"keywords":["Coevolution","Parasitology","Cetacea","Phylogenetics"],"fieldOfScience":"Biological sciences","versionNumber":2,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-07","lastModificationDate":"2026-09-07","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.95x69p91q","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.k6djh9wm8"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.k6djh9wm8/versions"},"stash:version":{"href":"/api/v2/versions/462025"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.k6djh9wm8/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.k6djh9wm8","id":169053,"storageSize":1930151,"relatedPublicationISSN":"2399-3642","title":"Developmental trajectories of somatostatin-positive interneurons in the human auditory cortex from migration to maturation","authors":[{"firstName":"Anjali","lastName":"Bind","email":"anjali233001@gmail.com","affiliation":"National Brain Research Centre","affiliationROR":"https://ror.org/022swbj46","affiliations":[{"name":"National Brain Research Centre","ror_id":"https://ror.org/022swbj46"}],"orcid":"0009-0007-9909-5132","order":0},{"firstName":"Arvind Singh","lastName":"Pundir","email":"arvind@nbrc.ac.in","affiliation":"National Brain Research Centre","affiliationROR":"https://ror.org/022swbj46","affiliations":[{"name":"National Brain Research Centre","ror_id":"https://ror.org/022swbj46"}],"order":1},{"firstName":"Bishan","lastName":"Radotra","email":"bishanradotra@gmail.com","affiliation":"Post Graduate Institute of Medical Education and Research","affiliationROR":"https://ror.org/009nfym65","affiliations":[{"name":"Post Graduate Institute of Medical Education and Research","ror_id":"https://ror.org/009nfym65"}],"order":2},{"firstName":"Kirti","lastName":"Gupta","email":"gupta.kirti@pgimer.edu.in","affiliation":"Post Graduate Institute of Medical Education and Research","affiliationROR":"https://ror.org/009nfym65","affiliations":[{"name":"Post Graduate Institute of Medical Education and Research","ror_id":"https://ror.org/009nfym65"}],"order":3},{"firstName":"Sudhir","lastName":"Gupta","email":"sgupta52001@yahoo.co.in","affiliation":"All India Institute of Medical Sciences","affiliationROR":"https://ror.org/02dwcqs71","affiliations":[{"name":"All India Institute of Medical Sciences","ror_id":"https://ror.org/02dwcqs71"}],"order":4},{"firstName":"Meenakshi","lastName":"Sharma","email":"specialmeenakshi@gmail.com","affiliation":"All India Institute of Medical Sciences","affiliationROR":"https://ror.org/02dwcqs71","affiliations":[{"name":"All India Institute of Medical Sciences","ror_id":"https://ror.org/02dwcqs71"}],"order":5},{"firstName":"Jhansi Lakshmi","lastName":"Mylapalli","email":"drjhansimylapalli.aiims@gmail.com","affiliation":"All India Institute of Medical Sciences","affiliationROR":"https://ror.org/02dwcqs71","affiliations":[{"name":"All India Institute of Medical Sciences","ror_id":"https://ror.org/02dwcqs71"}],"order":6},{"firstName":"Sanjeev","lastName":"Lalwani","email":"drsanjeevlalwani@gmail.com","affiliation":"All India Institute of Medical Sciences","affiliationROR":"https://ror.org/02dwcqs71","affiliations":[{"name":"All India Institute of Medical Sciences","ror_id":"https://ror.org/02dwcqs71"}],"order":7},{"firstName":"Soumya","lastName":"Iyengar","email":"soumya@nbrc.ac.in","affiliation":"National Brain Research Centre","affiliationROR":"https://ror.org/022swbj46","affiliations":[{"name":"National Brain Research Centre","ror_id":"https://ror.org/022swbj46"}],"orcid":"0000-0002-2060-6996","order":8}],"abstract":"\u003cp\u003eWe are interested in understanding morphological changes during development in the human auditory cortex and decided to focus on the development and maturation of inhibitory interneurons, particularly somatostatin (SOM+) interneurons that shape cortical circuits and regulate plasticity, which remains underexplored. The present study examines the development of SOM+ interneurons in the postmortem human auditory cortex from the prenatal period to adulthood, within primary and association auditory cortices. We find that there is an increase in SOM+ interneurons in the infragranular and subsequently supragranular cortical layers between prenatal development and childhood. Soma size and aspect ratio increase between the prenatal development and adulthood, of varying magnitudes across subtypes and cortical layers. Neurite complexity is highest during fetal and early postnatal stages and decreases during adolescence. The density of SOM+ interneurons peaks in layers 2 and 3 during childhood and adolescence and decreases in adulthood, coinciding with known periods of auditory plasticity. Our findings provide critical insights into the structural and spatial changes in SOM+ interneurons that likely regulate the sensitive period of the human auditory cortex. Since alterations in SOM+ interneuron density are linked to various neurodevelopmental disorders, our results provide an important baseline for future functional and clinical investigations.\u003c/p\u003e\n","funders":[{"organization":"Indian Council of Medical Research","identifierType":"ror","identifier":"https://ror.org/0492wrx28","awardNumber":"","awardDescription":"","awardTitle":"","order":0},{"organization":"Indian Council of Medical Research","identifierType":"ror","identifier":"https://ror.org/0492wrx28","awardNumber":"ICMR #2019-0155 (No. 51/4/2019-Ana/BMS)"}],"keywords":["Auditory cortex","Developmental neuroscience","Neuronal plasticity"],"fieldOfScience":"Biological sciences","hsiStatement":"We received explicit consent from the kin of the participants to publish the de-identified data in the public domain.  Other than the age and identification of the collaborating center where the data was collected from, the cases used in our study cannot be identified.","methods":"\u003cp\u003eAll procedures on post-mortem human brains used in this study have been approved by the Institutional Human Ethics committee at the National Brain Research Centre (BRIC - NBRC), Manesar, which are in accordance with international guidelines and those framed by the Indian Council of Medical Research and were also followed by collaborating institutes. All experiments were undertaken with the understanding and written consent of the next of kin or parents of each subject. Data regarding the identity of subjects and their case histories were anonymized and stored securely at BRIC - NBRC.\u003c/p\u003e\n\u003cp\u003eA total of 25 post-mortem human brain samples ranging from 30 gestational weeks to 45 years were used in this study (Supplementary Table 4). These cases were categorised into five groups based on age, namely, FE, PN, P, ADL, and AD. We ensured that the parents of the aborted fetuses were not suffering from any serious illness or psychological disorders and had no history of hearing or speech defects. Samples of the temporal lobe from the left hemisphere were collected only from those cases where there was no medical history of neurological or psychiatric disorders nor history of any hearing or speech deficits. We obtained sixteen of these samples (n = 2, Postnatal; n = 4, Pediatric; n = 5, Adolescence; n = 5, Adult) from the All India Institute of Medical Sciences (AIIMS), Delhi, and the remaining nine (n= 5, Fetal; n = 3, Postnatal; n = 1, Pediatric) from the Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh (Supplementary Table 4). Methods for dissecting formalin-fixed tissue and specifically, the human auditory cortex including the Heschl’s gyrus (area TC) and adjacent non-primary auditory areas (TA and TB) were performed as described by Pundir et al., (2012)\u003csup\u003e3\u003c/sup\u003e. Blocks containing TC, TA and TB were photographed in different orientations (dorsal, lateral, rostral, and caudal) to facilitate sectioning and identifying the locations of different auditory areas after staining. The blocks were kept in a cryoprotectant, that is, 30% sucrose in PBS at 4°C until they were completely immersed in the solution. Blocks were then frozen using dry ice and mounted in the optimal cutting temperature (OCT) media (Tissue Freezing Medium, Leica). This was followed by cryosectioning at -20ºC using a cryostat (Leica, CM3050 S) to obtain 7 sets of serial sections, each having a thickness of 50 µm\u003csup\u003e2,3\u003c/sup\u003e. The first set of these serial sections was used for Nissl staining to distinguish between different cortical layers and to delineate auditory areas based on cytoarchitecture\u003csup\u003e41\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eImmunohistochemistry\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eImmunohistochemistry was used to detect the presence of SOM\u003csup\u003e+\u003c/sup\u003e neurons in the auditory cortex (left hemisphere) from all ages used in our study. The sections were rinsed thrice using 0.01 M PBS and incubated in citrate buffer (pH 6.0) for 20 minutes at 80°C for antigen unmasking.  Sections were incubated in 2% H\u003csub\u003e2\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e with 0.3% Triton-X 100 for 20 minutes in the dark to quench endogenous peroxidase activity. After rinsing sections thrice in PBS, they were incubated for 1 hour in a blocking solution containing 5% normal goat serum (S-1000, Vector Laboratories, Burlingame, CA, USA), and 1% Bovine serum albumin (BSA; A7906, Sigma-Aldrich, USA). This was followed by incubating the sections overnight (for 15-17 hours) at 4ºC in a solution containing the primary antibody against SOM (made in rat; 1:200; Cat# ab30788, Abcam, RRID: AB_778010 or Cat# S5331, USBiological). The sections were again rinsed thrice in PBS and incubated for 2 hours in a secondary antibody solution (Biotinylated anti-rat antibody raised in goat; 1:250 dilution, BA-9400, Vector Laboratories, Burlingame, CA, USA) at RT. After this step, sections were rinsed in PBS three times and incubated in a solution containing the avidin-biotin complex (ABC reagent; PK-6100, Vectastain Elite ABC HRP kit, Vector Laboratories, USA) for 2 hours. This was followed by three rinses in PBS, after which the sections were developed in a solution containing the chromogen (NovaRED substrate kit, peroxidase; SK-4800, Vector Laboratories, USA) according to the manufacturer’s instructions. Finally, the sections were rinsed in PBS, mounted on gelatin-coated slides, and air-dried overnight before coverslipping with DPX. The same protocol and time durations was followed for each step of the staining procedure for all age groups used in our study. This ensured that variability due to staining duration was minimized across age groups. A negative control was also performed by incubating a section of the human auditory cortex in a solution containing the secondary antibody while omitting the primary antibody against SOM (Supplementary Fig. 17).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDouble labelling protocol\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe immunohistochemistry protocol used for SOM detection (detailed above) was followed by Nissl staining to visualize SOM\u003csup\u003e+\u003c/sup\u003e neurons in relation to their nuclei. Additionally, immunofluorescence staining was performed to show co-labelling of SOM\u003csup\u003e+\u003c/sup\u003e interneurons with the neuronal marker NeuN. For immunofluorescence, sections were rinsed, subjected to antigen unmasking and endogenous peroxidase quenching, as mentioned earlier. Sections were then blocked and incubated in the primary antibody against SOM, as described above. After this step, sections were incubated for 4 hours at room temperature in the dark with Alexa Fluor 488 anti-rat secondary antibody (raised in goat; 1:500; Cat#A11006; Invitrogen, USA). Following PBS rinses, sections were blocked for 1 hour in 5% normal horse serum (S-2000, Vector Laboratories, Burlingame, CA, USA) and then incubated overnight at 4°C with the NeuN antibody (raised in goat; 1:2000; Cat#PA5-143586, Invitrogen, RRID: AB_2942815). After rinsing in PBS, sections were incubated with Alexa Fluor 594 secondary antibody (Anti-goat, raised in donkey; 1:500; Cat#A11058; Invitrogen, USA) for 4 hours at room temperature. Finally, sections were rinsed thrice in PBS, mounted on gelatin-coated slides, air-dried, and coverslipped with Vectashield® Plus Antifade mounting medium containing DAPI nuclear stain (H-2000, Vector Laboratories, USA).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eQuantification of SOM\u003csup\u003e+\u003c/sup\u003e\u003c/strong\u003e \u003cstrong\u003eInterneurons\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSomatostatin-positive neurons at different stages of development were quantified using the optical fractionator method (Stereoinvestigator software; Microbrightfield, Williston, VT) attached to an Olympus microscope (BX51). This method employs stereology wherein Systematic Uniformly Random Sampling (SURS) is performed by placing uniform grids over the area of interest. A contour was drawn around the areas TA, TB, and TC of the auditory cortex in three serial sections at an interval of 7. The quantification of SOM\u003csup\u003e+\u003c/sup\u003e neurons was performed using a 40X objective, with the counting frame set at 150 μm × 150 μm, the sampling grid area set at 173 μm × 173 μm, and an optical disector height of 6 μm with 2 μm guard zones. The thickness of sections was measured at each counting site.\u003c/p\u003e\n\u003cp\u003eStaining intensity across ages and cortical layers in auditory areas was quantified from images acquired under identical conditions (light intensity, brightness, contrast, exposure). Images were converted to grayscale for analysis. Regions of the tissue lacking cells were marked as background, whereas individual SOM\u003csup\u003e+\u003c/sup\u003e neurons were outlined and categorized based on staining intensity as very light, intermediate (light to medium), or dark. Mean intensity values were measured for each category. Background staining had a mean intensity of 197 ± 15, whereas very lightly stained neurons had mean intensities of 166 ± 10 and were excluded from counts.\u003c/p\u003e\n\u003cp\u003eOnly those SOM\u003csup\u003e+\u003c/sup\u003e neurons which were darkly stained (85 ± 23) or demonstrated medium to low (135 ± 12) levels of staining compared to background staining, with one or more clearly distinguishable dendrites were counted and considered for analysis. Accordingly, all analyses were restricted to SOM\u003csup\u003e+\u003c/sup\u003e interneurons with low to high levels staining.**** Whereas the very lightly stained SOM\u003csup\u003e+\u003c/sup\u003e interneurons may represent a distinct category reflecting either developmental or functional differences, we decided to exclude them from our analyses to avoid introducing errors in the morphometric analysis that we performed. An estimated count using mean section thickness divided by estimated volume (Cavalieri method) was used to compare cell density across various age groups, layers, and areas\u003csup\u003e91,92\u003c/sup\u003e. For comparing the overall distribution of SOM\u003csup\u003e+\u003c/sup\u003e interneurons, digital images of sections stained for Nissl and somatostatin were acquired and adjusted for brightness and contrast but were not altered in any other way. \u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMorphometric Analysis of SOM\u003csup\u003e+\u003c/sup\u003e\u003c/strong\u003e \u003cstrong\u003eInterneurons\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eA three-dimensional reconstruction of SOM\u003csup\u003e+\u003c/sup\u003e interneurons at all developmental ages in each cortical layer and area was performed using Neurolucida and Neurolucida Explorer (Version:11, MBF Bioscience, USA) at a magnification of 100X. We specifically chose darkly stained neurons wherein the somata were clearly visible and possessed intact processes for reconstruction, all of which were considered as neurites. However, it is possible that some of the neurites may have extended into the sections above and below this plane. The morphometric analyses included changes in neurite branching and length (provided by the Neuron summary module) and a Sholl analysis was also performed to quantify neuronal complexity, using the Neurolucida Explorer software. For the Sholl analysis, concentric circles at a fixed interval (10 μm) were placed around the neuronal soma and the number of the points wherein neurites intersected these circles provided a measure of neuronal complexity. A statistical analysis was performed on data collected from the Sholl radius greater than 10 μm, to avoid errors in neuronal complexity, since the soma size of SOM\u003csup\u003e+\u003c/sup\u003e interneurons increased with age.\u003c/p\u003e\n\u003cp\u003e            Somatostatin-positive interneurons undergo significant physiological and functional maturation during the 2nd and 3rd postnatal weeks in the mouse cortex\u003csup\u003e93,94,95\u003c/sup\u003e, with axonal outgrowth being particularly prominent during the postnatal period following migration, when dendritic and axonal features become more distinguishable. Since we did not employ markers such as Ankyrin-G, TRIM46, MAP2, and Tau to differentiate axons and dendrites\u003csup\u003e96,97,98,99\u003c/sup\u003e, the difference between axons and dendrites was clear in some cases in our study and ambiguous in others. It was also not possible for us to use techniques such as filling individual neurons with neurobiotin\u003csup\u003e94\u003c/sup\u003e, since these techniques require fresh or very lightly fixed brain tissue. We therefore decided to label all processes visualized using immunohistochemistry as neurites and perform the morphological analysis, rather than erroneously classifying them as dendrites or axons. \u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eStatistics and reproducibility\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eStatistical analyses were performed on the density and morphometric data following quantification and three-dimensional reconstruction of SOM\u003csup\u003e+\u003c/sup\u003e interneurons using R (version 4.1.1) software. The data was tested to check whether it was normally distributed and possessed equal variance, using the Shapiro-Wilk and Levine tests, respectively. A One-Way ANOVA was used to compare developmental changes in the density and complexity of SOM\u003csup\u003e+\u003c/sup\u003e interneurons, for normally distributed data with equal variance. However, if the data was not normally distributed, a Kruskal-Wallis test was performed to judge statistical significance.  In both cases, the Tukey’s or Dunn’s post-hoc tests were performed for multiple comparisons.  A P-value of less than 0.05 was considered statistically significant for all statistical tests. All statistically significant and non-significant test values are provided as Supplementary Data 1.\u003c/p\u003e\n\u003cp\u003e            To assess the relationship between density and morphometric data with age, correlation analyses was performed. As the data were not normally distributed, MIC was used to detect non-linear and complex associations that may not be captured by simple linear correlation methods. The MIC values range from 0 to 1, with higher values indicating stronger associations between variables\u003csup\u003e100\u003c/sup\u003e. Therefore, MIC values below 0.3 were considered indicative of very weak associations, values between 0.3 to 0.6 as moderate associations, and values above 0.6 as very strong associations. The statistical significance of MIC was assessed using permutation-based tests, and the p-values were adjusted for multiple comparisons using the Benjamini-Hochberg procedure.\u003c/p\u003e\n","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1038/s42003-026-10120-3"}],"versionNumber":8,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-06","lastModificationDate":"2026-09-06","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.k6djh9wm8","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.73n5tb3cp"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.73n5tb3cp/versions"},"stash:version":{"href":"/api/v2/versions/462033"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.73n5tb3cp/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.73n5tb3cp","id":185343,"storageSize":361152,"relatedPublicationISSN":"0962-8436","title":"Face-to-face: The evolution and engineering of the LisH motif in plants","authors":[{"firstName":"Janet","lastName":"Solano Sanchez","email":"jsolanos@uw.edu","affiliation":"University of Washington","affiliationROR":"https://ror.org/00cvxb145","affiliations":[{"name":"University of Washington","ror_id":"https://ror.org/00cvxb145"}],"orcid":"0009-0009-2125-2550"},{"firstName":"Jennifer","lastName":"Nemhauser","email":"jn7@uw.edu","affiliation":"University of Washington","affiliationROR":"https://ror.org/00cvxb145","affiliations":[{"name":"University of Washington","ror_id":"https://ror.org/00cvxb145"}],"order":1}],"abstract":"\u003cp\u003eTranscriptional repression is a universal regulatory strategy that allows cells to fine-tune gene expression in response to developmental and environmental cues. In eukaryotes, corepressors are non–DNA-binding proteins that bridge transcription factors to repressor complexes. Plants have evolved a distinct repertoire of corepressors, including the LEUNIG/LEUNIG HOMOLOG family, the TOPLESS/TOPLESS-RELATED family, and HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15. A unifying feature among several plant and metazoan corepressors is the Lis1 Homology (LisH) domain, a short α-helical motif that mediates oligomerization and complex assembly. Here, we review the structure, conservation, and functional diversification of LisH-containing proteins in Arabidopsis, with a focus on how the first helix of the LisH domain provides a tunable interface for protein–protein interactions and intrinsic repression activity. We propose that the LisH domain represents an ancestral scaffold for assembling repression complexes, later co-opted to integrate chromatin remodeling, ubiquitin-mediated degradation, and environmental signaling in plants. Understanding how these modules evolved from shared ancestral architectures provides a conceptual framework for dissecting how eukaryotes diversified the molecular logic of transcriptional repression and offers design principles for engineering precise synthetic control of the transcriptome.\u003c/p\u003e\n","funders":[{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"","awardDescription":"","awardTitle":"","order":0},{"organization":"Andy Hill CARE Fund","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":1}],"keywords":["Arabidopsis thaliana","TOPLESS/TOPLESS-RELATED","LEUNIG/LEUNIG HOMOLOG","HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15","corepressor"],"fieldOfScience":"Natural sciences","versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-06","lastModificationDate":"2026-09-06","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.73n5tb3cp","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.2280gb641"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.2280gb641/versions"},"stash:version":{"href":"/api/v2/versions/462029"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.2280gb641/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.2280gb641","id":153475,"storageSize":199790700,"relatedPublicationISSN":"1742-464X","title":"Gut microbiome sequencing results in type 2 diabetes under p53 deficiency","authors":[{"firstName":"Zhiliang","lastName":"Xu","email":"xuzhiliang@wnmc.edu.cn","affiliation":"Wannan Medical College","affiliationROR":"https://ror.org/037ejjy86","affiliations":[{"name":"Wannan Medical College","ror_id":"https://ror.org/037ejjy86"}],"orcid":"0000-0003-0527-605X"}],"abstract":"\u003cp\u003eThe p53 protein has been identified as a critical regulator of metabolic processes in a variety of diseases, including obesity, diabetes, liver disease, and cardiovascular disease. However, the precise function and mechanism of action of p53 in the regulation of glucose-lipid metabolism through the enterohepatic axis remain to be fully elucidated.The present study investigated the effects of p53 deficiency on type 2 diabetic mice and demonstrated that p53 deficiency resulted in more severe impairment of glucose tolerance and insulin tolerance. Furthermore, the study revealed that p53 can influence hepatic glucose metabolism via the PI3K/AKT pathway. Additionally, p53 deletion has been observed to modify intestinal function and the intestinal microenvironment, thereby correlating with intestinal function and microbiota composition in T2DM mice. Specifically, p53 knockdown mice exhibited impaired ileal digestion, absorption, and colonic secretion after a HFD (HFD). Additionally, the richness and diversity of their intestinal flora were reduced, and these mice exhibited symptoms such as obesity, fat infiltration, defecation abnormalities, and severe abnormalities of glucose and insulin tolerance. The expression levels of β-catenin and c-Myc proteins were found to be elevated in mice fed a HFD, while the expression of these proteins was diminished in mice with p53 knockdown, compared to those on a normal diet. The experimental results suggest that p53 affects insulin secretion through PI3K/AKT signaling pathway and regulates the distribution of intestinal flora through Wnt signaling pathway, which in turn affects the development of type 2 diabetes mellitus.\u003c/p\u003e","funders":[{"organization":"Outstanding Youth Scientific Research Program for Universities in Anhui Province","identifierType":"ror","identifier":"","awardNumber":"2024AH020014","awardDescription":"","awardTitle":"","order":0}],"keywords":["16s DNA sequence","T2DM","Intestinal microorganisms"],"fieldOfScience":"Basic 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ocean circulation were much slower than ice-core records imply","authors":[{"firstName":"Xiyu","lastName":"Dong","email":"xiyu_dong@xjtu.edu.cn","affiliation":"Xi'an Jiaotong University","affiliationROR":"https://ror.org/017zhmm22","affiliations":[{"name":"Xi'an Jiaotong University","ror_id":"https://ror.org/017zhmm22"}],"orcid":"0000-0002-7611-0244","order":0},{"firstName":"Xu","lastName":"Zhang","email":"xuang@bas.ac.uk","affiliation":"British Antarctic Survey","affiliationROR":"https://ror.org/01rhff309","affiliations":[{"name":"British Antarctic Survey","ror_id":"https://ror.org/01rhff309"}],"orcid":"0000-0003-1833-9689","order":1},{"firstName":"Yuchen","lastName":"Sun","email":"yuchen.sun@awi.de","affiliation":"Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung","affiliationROR":"https://ror.org/032e6b942","affiliations":[{"name":"Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und 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Copenhagen","ror_id":"https://ror.org/035b05819"}],"orcid":"0000-0002-4177-3611","order":5},{"firstName":"Anders","lastName":"Svensson","email":"as@nbi.ku.dk","affiliation":"University of Copenhagen","affiliationROR":"https://ror.org/035b05819","affiliations":[{"name":"Niels Bohr Institute"},{"name":"University of Copenhagen","ror_id":"https://ror.org/035b05819"}],"orcid":"0000-0002-4364-6085","order":6},{"firstName":"Christo","lastName":"Buizert","email":"christo.buizert@oregonstate.edu","affiliation":"Oregon State University","affiliationROR":"https://ror.org/00ysfqy60","affiliations":[{"name":"Oregon State University","ror_id":"https://ror.org/00ysfqy60"}],"order":7},{"firstName":"Ashish","lastName":"Sinha","email":"asinha@csudh.edu","affiliation":"Xi'an Jiaotong University","affiliationROR":"https://ror.org/017zhmm22","affiliations":[{"name":"Xi'an Jiaotong University","ror_id":"https://ror.org/017zhmm22"}],"orcid":"0000-0001-5700-2451","order":8},{"firstName":"Stephen","lastName":"Barker","email":"barkers3@cf.ac.uk","affiliation":"Cardiff University","affiliationROR":"https://ror.org/03kk7td41","affiliations":[{"name":"Cardiff University","ror_id":"https://ror.org/03kk7td41"}],"orcid":"0000-0001-7870-6431","order":9},{"firstName":"Carlos","lastName":"Pérez-Mejías","email":"perezmegias@xjtu.edu.cn","affiliation":"Xi'an Jiaotong University","affiliationROR":"https://ror.org/017zhmm22","affiliations":[{"name":"Xi'an Jiaotong University","ror_id":"https://ror.org/017zhmm22"}],"orcid":"0000-0002-8370-9271","order":10},{"firstName":"Gregor","lastName":"Knorr","email":"Gregor.Knorr@awi.de","affiliation":"Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung","affiliationROR":"https://ror.org/032e6b942","affiliations":[{"name":"Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und 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Meeresforschung","affiliationROR":"https://ror.org/032e6b942","affiliations":[{"name":"Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung","ror_id":"https://ror.org/032e6b942"}],"orcid":"0000-0002-6473-0243","order":21},{"firstName":"Yongjin","lastName":"Wang","email":"yjwang@njnu.edu.cn","affiliation":"Nanjing Normal University","affiliationROR":"https://ror.org/036trcv74","affiliations":[{"name":"Nanjing Normal University","ror_id":"https://ror.org/036trcv74"}],"orcid":"0000-0001-6021-2724","order":22},{"firstName":"R. Lawrence","lastName":"Edwards","email":"edwar001@umn.edu","affiliation":"University of Minnesota","affiliationROR":"https://ror.org/017zqws13","affiliations":[{"name":"University of Minnesota","ror_id":"https://ror.org/017zqws13"}],"orcid":"0000-0002-7027-5881","order":23},{"firstName":"Hai","lastName":"Cheng","email":"cheng021@xjtu.edu.cn","affiliation":"Xi'an Jiaotong University","affiliationROR":"https://ror.org/017zhmm22","affiliations":[{"name":"Xi'an Jiaotong University","ror_id":"https://ror.org/017zhmm22"}],"orcid":"0000-0002-5305-9458","order":24}],"abstract":"\u003cp\u003eThis dataset includes four Excel files (Supplementary Data 1–4) and one MATLAB code file (Supplementary Code 1). Supplementary Data 1 contains absolute U-Th dates for five speleothems. Supplementary Data 2 provides δ\u003csup\u003e18\u003c/sup\u003eO time-series and annual lamina thickness data for speleothems Cherrapunji-2 and SX-1. Supplementary Data 3 contains Greenland ice-core records anchored to U-Th-based chronologies. Supplementary Data 4 includes stacked speleothem and ice-core records plus sensitivity test results. Supplementary Code 1 is the MATLAB script used for counting annual lamina.\u003c/p\u003e\n","funders":[{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"42488201","order":0},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"423B2204","order":1},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"42202218","order":2},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"42325705","order":3},{"organization":"Ministry of Science and Technology of the People's Republic of China","identifierType":"ror","identifier":"https://ror.org/027s68j25","awardNumber":"2023YFF0805201","awardDescription":"National Key Research and Development 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University","identifierType":"ror","identifier":"https://ror.org/017zhmm22","awardNumber":"xzy012026038","awardDescription":"","awardTitle":"Fundamental research funding for free exploration and innovation projects","order":15},{"organization":"Xi'an Jiaotong University","identifierType":"ror","identifier":"https://ror.org/017zhmm22","awardNumber":"","awardDescription":"","awardTitle":"Special fund for discipline development in global environmental change science (key project)","order":16},{"organization":"China Postdoctoral Science Foundation","identifierType":"ror","identifier":"https://ror.org/0426zh255","awardNumber":"2025M780387","awardDescription":"","awardTitle":"","order":14}],"keywords":["Paleoclimatology","Abrupt climate change","Atlantic Meridional Overturning Circulation","speleothem","ice core"],"fieldOfScience":"Earth and related environmental sciences","versionNumber":7,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.xgxd254wx","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.xgxd254z1"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.xgxd254z1/versions"},"stash:version":{"href":"/api/v2/versions/461826"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.xgxd254z1/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.xgxd254z1","id":192151,"storageSize":401717,"relatedPublicationISSN":"0021-8901","title":"Data from: Responses of protected groundwater-dependent vegetation communities to prolonged flooding along a lowland stream","authors":[{"firstName":"Paraskevi","lastName":"Manolaki","email":"pmanolaki@bio.au.dk","affiliation":"Aarhus University","affiliationROR":"https://ror.org/01aj84f44","affiliations":[{"name":"Aarhus University","ror_id":"https://ror.org/01aj84f44"}],"orcid":"0000-0003-3958-0199"},{"firstName":"Tenna","lastName":"Riis","email":"tenna.riis@bio.au.dk","affiliation":"Aarhus University","affiliationROR":"https://ror.org/01aj84f44","affiliations":[{"name":"Aarhus University","ror_id":"https://ror.org/01aj84f44"}],"order":2},{"firstName":"John","lastName":"Böhme Dybkjær","email":"jb@sg.dk","affiliation":"Silkeborg High School","affiliations":[{"name":"Silkeborg High School"}],"order":3},{"firstName":"Dagmar","lastName":"Kappel Andersen","email":"dagmarkappel@gmail.com","affiliation":"WSP Denmark","affiliations":[{"name":"WSP Denmark"}],"order":4},{"firstName":"Annette","lastName":"Baattrup-Pedersen","email":"abp@bio.au.dk","affiliation":"Aarhus University","affiliationROR":"https://ror.org/01aj84f44","affiliations":[{"name":"Aarhus University","ror_id":"https://ror.org/01aj84f44"}],"order":5}],"abstract":"\u003cp\u003eThis dataset contains vegetation, plant trait and groundwater data from a six-year field experiment conducted in three alkaline-rich fen sites along Kastbjerg Å in northern Denmark. The experiment comprised control plots and three treatments: prolonged flooding with stream floodwater, prolonged flooding with natural sandy sediment (NSS), and prolonged flooding with organic-enriched sediment (OES) from an agricultural catchment. In the dataset, treatment categories are coded as Control, Water, Coarse and Fine, corresponding respectively to control plots, prolonged flooding with stream floodwater, prolonged flooding with natural sandy sediment (NSS), and prolonged flooding with organic-enriched sediment (OES). The dataset includes baseline vegetation data, repeated plant species frequency data, plant functional and ecological trait information, and groundwater data. Species are represented by abbreviations in the vegetation data, and a separate lookup table is provided linking these abbreviations to the full species names. Species frequency was derived from occurrence within a fixed grid of 16 sub-quadrats and is expressed in the dataset as the proportion of occupied sub-quadrats (0–1). Plant trait variables include maximum canopy height, Grime CSR strategy components and Ellenberg indicator values for nutrients, light and moisture. Groundwater data include water-level measurements and concentrations of ammonium, nitrate and phosphate at different soil depths and sampling times. The data can be reused to investigate temporal vegetation dynamics, plant community responses to flooding and sediment deposition, recovery trajectories, responses of alkaline rich fen indicator species, and relationships between species composition and functional traits. They may also support comparative studies of wetland vegetation responses to hydrological disturbance, sedimentation and nutrient enrichment, as well as research on the conservation and restoration of alkaline rich fens. Prior to establishment of the experiment, verbal permission to conduct the fieldwork was obtained from Mariagerfjord Municipality, the relevant local authority, and from the landowner. As permission was granted verbally, no permit or license number was issued.\u003c/p\u003e\n","funders":[{"organization":"European Commission","identifierType":"ror","identifier":"https://ror.org/00k4n6c32","awardNumber":"603378","awardDescription":"","awardTitle":"European Union 7th Framework Project MARS ","order":0},{"organization":"Danish Council for Strategic Research","identifierType":"ror","identifier":"","awardNumber":"1305-00017B","awardDescription":"","awardTitle":"BUFFERTECH","order":1},{"organization":"European Commission","identifierType":"ror","identifier":"https://ror.org/00k4n6c32","awardNumber":"101036337","awardDescription":"Horizon 2020","awardTitle":"MERLIN – Mainstreaming Ecological Restoration of freshwater-related ecosystems in a Landscape context: INnovation, upscaling and transformation","order":2}],"keywords":["Alkaline rich fen","Sediment deposition","Hydromorphological processes","vegetation dynamics","Prolonged flooding","Plant functional traits","groundwater-dependent ecosystems","Eutrophication","nutrient enrichment","wetland vegetation","riparian vegetation","plant community composition"],"fieldOfScience":"Earth and related environmental sciences","versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.xgxd254z1","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.v6wwpzh8m"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.v6wwpzh8m/versions"},"stash:version":{"href":"/api/v2/versions/461801"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.v6wwpzh8m/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.v6wwpzh8m","id":169426,"storageSize":116716,"relatedPublicationISSN":"2045-7758","title":"Data from: The roles of contrasting host types on the environmental abundance of \u003cem\u003eAnaplasma phagocytophilum\u003c/em\u003e, an emerging zoonotic pathogen","authors":[{"firstName":"William","lastName":"McLellan","email":"2146238M@student.gla.ac.uk","affiliation":"University of Glasgow","affiliationROR":"https://ror.org/00vtgdb53","affiliations":[{"name":"University of Glasgow","ror_id":"https://ror.org/00vtgdb53"}],"orcid":"0009-0006-4998-5746"},{"firstName":"Sara","lastName":"Gandy","email":"sara.gandy@glasgow.ac.uk","affiliation":"University of Glasgow","affiliationROR":"https://ror.org/00vtgdb53","affiliations":[{"name":"University of Glasgow","ror_id":"https://ror.org/00vtgdb53"}],"orcid":"0000-0003-2579-4479","order":1},{"firstName":"Jaboury","lastName":"Ghazoul","email":"jaboury.ghazoul@env.ethz.ch","affiliation":"ETH Zurich","affiliationROR":"https://ror.org/05a28rw58","affiliations":[{"name":"ETH Zurich","ror_id":"https://ror.org/05a28rw58"}],"order":2},{"firstName":"Fanny","lastName":"Olsthoorn","email":"f.m.o.olsthoorn@gmail.com","affiliation":"ETH Zurich","affiliationROR":"https://ror.org/05a28rw58","affiliations":[{"name":"ETH Zurich","ror_id":"https://ror.org/05a28rw58"}],"order":3},{"firstName":"Livia","lastName":"May","email":"livia.may@gmx.ch","affiliation":"ETH Zurich","affiliationROR":"https://ror.org/05a28rw58","affiliations":[{"name":"ETH Zurich","ror_id":"https://ror.org/05a28rw58"}],"order":4},{"firstName":"Jude","lastName":"Eze","email":"jude.eze@sruc.ac.uk","affiliation":"Scotland's Rural College","affiliationROR":"https://ror.org/044e2ja82","affiliations":[{"name":"Scotland's Rural College","ror_id":"https://ror.org/044e2ja82"}],"order":5},{"firstName":"Mara","lastName":"Rocchi","email":"mara.rocchi@moredun.ac.uk","affiliation":"Moredun Research Institute","affiliationROR":"https://ror.org/047ck1j35","affiliations":[{"name":"Moredun Research Institute","ror_id":"https://ror.org/047ck1j35"}],"order":6},{"firstName":"Hein","lastName":"Sprong","email":"hein.sprong@rivm.nl","affiliation":"National Institute for Public Health and the Environment","affiliationROR":"https://ror.org/01cesdt21","affiliations":[{"name":"National Institute for Public Health and the Environment","ror_id":"https://ror.org/01cesdt21"}],"order":7},{"firstName":"Lucy","lastName":"Gilbert","email":"lucy.gilbert@glasgow.ac.uk","affiliation":"University of Glasgow","affiliationROR":"https://ror.org/00vtgdb53","affiliations":[{"name":"University of Glasgow","ror_id":"https://ror.org/00vtgdb53"}],"order":8}],"abstract":"\u003cp\u003eFundamental knowledge of the role of hosts in shaping vector-borne pathogen abundance is critical to understanding the ecology of these disease systems; yet the roles can be challenging to tease apart, especially for pathogens vectored by generalist feeders with multiple hosts. In this study, we aimed to quantify the relative contributions of hypothesised pathogen transmission hosts (deer and sheep) and non-transmission hosts (birds and rodents) on the environmental abundance of ecotypes I and II of \u003cem\u003eAnaplasma phagocytophilum\u003c/em\u003e, a zoonotic pathogen vectored by \u003cem\u003eIxodes ricinus\u003c/em\u003e ticks, that causes tick-borne fever in sheep and anaplasmosis in humans. Data on \u003cem\u003eA. phagocytophilum\u003c/em\u003e prevalence and hazard, deer space-use and sheep presence were collected from 40 sites, data on rodent space-use from 20 sites, and data on bird space-use from 10 sites in northwest Scotland 2018 – 2020.  As predicted, bird space-use was negatively associated with \u003cem\u003eA. phagocytophilum\u003c/em\u003e prevalence, indicating that birds may act as pathogen dilution hosts; deer were positively associated with \u003cem\u003eA. phagocytophilum\u003c/em\u003e prevalence and hazard, indicating their role as pathogen transmission hosts; and prevalences of \u003cem\u003eA. phagocytophilum\u003c/em\u003e and \u003cem\u003eB. burgdorferi\u003c/em\u003e s.l. were negatively correlated, supporting the hypothesis that each host has opposite roles for these pathogens. We did not find statistically significant associations between sheep presence or rodent space-use index with \u003cem\u003eA. phagocytophilum\u003c/em\u003e prevalence. Our results highlight the need to consider hosts that do not transmit the focal pathogen as well as potential trade-offs between different pathogens. Our findings have implications for conservation and disease mitigation in that land management practices that reduce deer density while increasing bird abundance may reduce \u003cem\u003eA. phagocytophilum\u003c/em\u003e prevalence and the risk it poses to humans and livestock.\u003c/p\u003e\n","funders":[{"organization":"Rural and Environment Science and Analytical Services","identifierType":"ror","identifier":"https://ror.org/02hrqhj53","awardNumber":"MRI-A2-10","awardDescription":"","awardTitle":"","order":0}],"keywords":["Deer","Birds","Rodents","Sheep","Ixodes ricinus"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"dataset","identifierType":"DOI","identifier":"https://doi.org/10.5061/dryad.jh9w0vtn0"},{"relationship":"article","identifierType":"DOI","identifier":"https://doi.org/10.1002/2688-8319.12403"},{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.32942/x2z671"}],"versionNumber":7,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.v6wwpzh8m","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.9w0vt4bx9"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.9w0vt4bx9/versions"},"stash:version":{"href":"/api/v2/versions/461715"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.9w0vt4bx9/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.9w0vt4bx9","id":188809,"storageSize":1106538483,"relatedPublicationISSN":"2692-8205","title":"Data from: Ultrafast venous and sagittal sinus constrictions in the brain driven by abdominal pressure","authors":[{"firstName":"Qingguang","lastName":"Zhang","email":"qzhang24@msu.edu","affiliation":"Michigan State University","affiliationROR":"https://ror.org/05hs6h993","affiliations":[{"name":"Pennsylvania State University","ror_id":"https://ror.org/04p491231"},{"name":"Michigan State University","ror_id":"https://ror.org/05hs6h993"}],"orcid":"0000-0003-4500-813X"},{"firstName":"C. Spencer","lastName":"Garborg","email":"","affiliation":"Pennsylvania State University","affiliationROR":"https://ror.org/04p491231","affiliations":[{"name":"Pennsylvania State University","ror_id":"https://ror.org/04p491231"}]},{"firstName":"Noah","lastName":"Frank","email":"","affiliation":"Pennsylvania State University","affiliationROR":"https://ror.org/04p491231","affiliations":[{"name":"Pennsylvania State University","ror_id":"https://ror.org/04p491231"}]},{"firstName":"Fatemeh","lastName":"Salehi","email":"","affiliation":"Pennsylvania State University","affiliationROR":"https://ror.org/04p491231","affiliations":[{"name":"Pennsylvania State University","ror_id":"https://ror.org/04p491231"}]},{"firstName":"Kevin","lastName":"Turner","affiliation":"Pennsylvania State University","affiliationROR":"https://ror.org/04p491231","affiliations":[{"name":"Pennsylvania State University","ror_id":"https://ror.org/04p491231"}]},{"firstName":"Patrick J.","lastName":"Drew","email":"","affiliation":"Pennsylvania State University","affiliationROR":"https://ror.org/04p491231","affiliations":[{"name":"Pennsylvania State University","ror_id":"https://ror.org/04p491231"}],"orcid":"0000-0002-7483-7378"}],"abstract":"\u003cp\u003eNearly all the blood supplying the cortex exits via the bridging veins (BVs) that drain into the superior sagittal sinus (SSS), making these vessels key chokepoints for cerebral blood flow. Using optical imaging in head-fixed mice, we found that the SSS and BVs exhibit ultrafast contractions (\u0026lt;0.1 s) at the onset of locomotion, following whisker stimulation, and upon awakening from sleep. Contractions of the BV and SSS were strongly correlated with abdominal muscle EMG activity and were tightly correlated with respiration at rest. The rapid decrease in blood volume caused by venous constrictions resulted in spurious increases in fluorescence in mice expressing fluorescent reporter proteins, creating artifacts that mimic functional signals. Venous contractions with the same amplitude and dynamics could be generated in anesthetized mice by abdominal pressure application, showing that these contractions were generated by mechanical coupling with the abdomen. Externally imposed abdominal pressures also drove a rapid but transient increase in blood flow. Unlike the pial and parenchymal microvasculature, whose diameters are controlled by local signals, the diameters of SSS/BV are dynamically controlled during behavior by abdominal muscle regulation of intracranial pressure, establishing a pathway for regulation of cerebral hemodynamics via mechanical coupling between the central nervous system and the viscera.\u003c/p\u003e\n","funders":[{"organization":"National Institute of Neurological Disorders and Stroke","identifierType":"ror","identifier":"https://ror.org/01s5ya894","awardNumber":"U19NS128613","awardDescription":"","awardTitle":""},{"organization":"National Institute of Neurological Disorders and Stroke","identifierType":"ror","identifier":"https://ror.org/01s5ya894","awardNumber":"R01NS078168","awardDescription":"","awardTitle":""},{"organization":"American Heart Association","identifierType":"ror","identifier":"https://ror.org/013kjyp64","awardNumber":"935961"},{"organization":"American Heart Association","identifierType":"ror","identifier":"https://ror.org/013kjyp64","awardNumber":"26BCDA1622705","awardDescription":"","awardTitle":"","order":1}],"keywords":["Neurovascular regulation","brain-body interaction","venous cotraction"],"fieldOfScience":"Health sciences","relatedWorks":[{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.64898/2026.05.02.722426"}],"versionNumber":8,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.9w0vt4bx9","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.ncjsxkt9w"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.ncjsxkt9w/versions"},"stash:version":{"href":"/api/v2/versions/461817"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.ncjsxkt9w/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.ncjsxkt9w","id":182074,"storageSize":77558,"relatedPublicationISSN":"1939-5582","title":"Data and code from: Trait-based assessment of fire regime risk to threatened fauna","authors":[{"firstName":"Victoria","lastName":"Reynolds","email":"victoria.reynolds@unimelb.edu.au","affiliation":"The University of Melbourne","affiliationROR":"https://ror.org/01ej9dk98","affiliations":[{"name":"The University of Melbourne","ror_id":"https://ror.org/01ej9dk98"}],"orcid":"0000-0002-6071-9303"},{"firstName":"Renée","lastName":"Woodward","email":"renee.woodward@dcceew.nsw.gov.au","affiliation":"The University of Melbourne","affiliationROR":"https://ror.org/01ej9dk98","affiliations":[{"name":"The University of Melbourne","ror_id":"https://ror.org/01ej9dk98"},{"name":"NSW Department of Climate Change, Energy, the Environment and Water","ror_id":"https://ror.org/038pwz535"}],"order":1},{"firstName":"Trent","lastName":"Penman","email":"trent.penman@unimelb.edu.au","affiliation":"The University of Melbourne","affiliationROR":"https://ror.org/01ej9dk98","affiliations":[{"name":"The University of Melbourne","ror_id":"https://ror.org/01ej9dk98"}],"order":2},{"firstName":"Ross","lastName":"Bradstock","email":"rossb@uow.edu.au","affiliation":"University of Wollongong","affiliationROR":"https://ror.org/00jtmb277","affiliations":[{"name":"University of Wollongong","ror_id":"https://ror.org/00jtmb277"}],"order":3}],"abstract":"\u003cp\u003eThis dataset contains expert-elicited and model-derived data used to assess fire regime risk to threatened fauna in New South Wales, Australia. It was developed to characterise how key components of fire regimes (time since fire, fire frequency, and fire severity) interact to influence species persistence in data-limited contexts.\u003c/p\u003e\n\u003cp\u003eSpecies were classified through expert elicitation into 18 trait-informed fire response groups (FRGs), representing shared patterns of survival, recovery, and post-fire abundance, and further synthesised into five broader fire response strategies. This dataset provides the expert-elicited fire-response curve data for each FRG, its trait-axis classification, and the derived optimal/minimal abundance coordinates used in the clustering of FRGs into fire response strategies.\u003c/p\u003e\n\u003cp\u003eData files are provided in unformatted, open-access CSV format, with accompanying documentation describing variable definitions, data structure, and processing steps.\u003c/p\u003e\n\u003cp\u003eThis dataset is accompanied by an R Markdown script that reproduces the fire response functional group (FRG) curve construction and the k-means clustering of FRGs into overarching fire response strategies (FRS) reported in the associated manuscript. Reference material on species-to-group assignments, curve construction rationale, and FRG/FRS definitions is published as Supplementary Information with the manuscript rather than included here.\u003c/p\u003e\n\u003cp\u003eThese data support reuse in ecological modelling, scenario analysis, and conservation planning, particularly for applications requiring generalisable representations of species responses to fire regimes. No sensitive or restricted data are included.\u003c/p\u003e\n","funders":[{"organization":"NSW Department of Climate Change, Energy, the Environment and Water","identifierType":"ror","identifier":"https://ror.org/038pwz535","awardNumber":"","awardDescription":"","awardTitle":"","order":0}],"keywords":["fire regimes","trait-based ecology","biodiversity risk","conservation planning","Functional groups"],"fieldOfScience":"Biological sciences","versionNumber":8,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.ncjsxkt9w","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.z8w9ghxw3"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.z8w9ghxw3/versions"},"stash:version":{"href":"/api/v2/versions/461811"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.z8w9ghxw3/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.z8w9ghxw3","id":191054,"storageSize":56145,"relatedPublicationISSN":"2045-7758","title":"Data and code from: Ontogenetic trophic differentiation in the Amur softshell turtle (\u003cem\u003ePelodiscus maackii\u003c/em\u003e) from a temperate large-river system","authors":[{"firstName":"XiaoChen","lastName":"Hou","email":"2357351973@qq.com","affiliation":"Tonghua Normal University","affiliationROR":"https://ror.org/05nq41m91","affiliations":[{"name":"Tonghua Normal University","ror_id":"https://ror.org/05nq41m91"}],"orcid":"0000-0001-5180-4461"}],"abstract":"\u003cp\u003eThe Amur softshell turtle (\u003cem\u003ePelodiscus maackii\u003c/em\u003e) has undergone severe population declines across northeastern China, yet its trophic ecology remains poorly understood. Because ontogenetic dietary shifts can generate size-structured functional roles within food webs, clarifying diet across life stages is critical for both ecological inference and conservation. We examined diet composition and ontogenetic trophic differentiation in a remnant population of \u003cem\u003eP. maackii\u003c/em\u003e from the midstream Ussuri River (China side) using stomach content analysis. Samples were obtained opportunistically from incidental fishery bycatch and market-derived remains collected between July 2022 and October 2025. Diet was quantified using frequency of occurrence and volumetric contribution of five functional prey categories and analysed with multivariate ordination and permutation-based tests, generalized additive models along a continuous body-mass gradient, and niche overlap indices. Across 41 individuals with non-empty stomachs, diet composition differed strongly among ontogenetic stages, whereas no sex-specific differences were detected after accounting for body mass. Juveniles exhibited diverse, invertebrate-dominated diets, particularly freshwater snails, while fish increased sharply with body size and dominated the diets of subadult and adult turtles. Dietary richness and within-group variability declined with ontogeny, and niche overlap was lowest between juveniles and adults but high among older stages. Together, these results demonstrate pronounced size-structured trophic differentiation in \u003cem\u003eP. maackii\u003c/em\u003e, indicating that population declines or size-selective losses may have disproportionate consequences for riverine food-web structure and function.\u003c/p\u003e\n","keywords":["Pelodiscus maackii","Amur softshell turtle","Diet","Trophic ecology","ontogeny","Stomach content analysis"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1002/ece3.74221"}],"versionNumber":4,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.z8w9ghxw3","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.dncjsxmfr"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.dncjsxmfr/versions"},"stash:version":{"href":"/api/v2/versions/461813"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.dncjsxmfr/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.dncjsxmfr","id":190215,"storageSize":5740695,"relatedPublicationISSN":"1523-7060","title":"Data from: Turbo Grignard-mediated distannylation of ester-functionalized quinoid heterocycles for narrow-bandgap polymer acceptors","authors":[{"firstName":"Shilong","lastName":"Dong","email":"shilong@g.ecc.u-tokyo.ac.jp","affiliation":"The University of Tokyo","affiliationROR":"https://ror.org/057zh3y96","affiliations":[{"name":"The University of Tokyo","ror_id":"https://ror.org/057zh3y96"}],"orcid":"0000-0003-3444-9511"},{"firstName":"Yi","lastName":"Zhang","email":"zhangyi@chnu.edu.cn","affiliation":"Huaibei Normal University","affiliationROR":"https://ror.org/03ek23472","affiliations":[{"name":"Huaibei Normal University","ror_id":"https://ror.org/03ek23472"}]}],"abstract":"\u003cp\u003eConventional lithiation of ester-substituted quinoid fluorinated thieno[3,4-b]thiophenes (FTT) induces irreversible carbonyl degradation. We report a kinetically controlled \u003cem\u003ei\u003c/em\u003e-PrMgCl·LiCl-mediated halogen–magnesium exchange that bypasses this limitation, enabling gram-scale synthesis of pure distannylated monomers. Stille polycondensation affords PY-FTT, a quinoid-enhanced polymer acceptor. All-polymer solar cells utilizing PY-FTT deliver an outstanding 12.4% power conversion efficiency. This mild stannylation protocol provides a robust paradigm for advanced narrow-bandgap conjugated materials.\u003c/p\u003e","keywords":["Turbo Grignard","Quinoid Heterocycles","fluorinated thieno[3","4-b]thiophenes","Narrow-Bandgap Polymer Acceptors"],"fieldOfScience":"Chemical sciences","methods":"\u003cp\u003eExperimental raw data including NMR spectra, high‑resolution mass spectrometry (HRMS), cyclic voltammetry (CV), UV‑Vis absorption spectra, and gel permeation chromatography (GPC) were acquired following standard synthetic and characterization protocols described in the associated manuscript. All raw spectral files were exported directly from corresponding instrument software without additional manual modification.\u003c/p\u003e","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1021/acs.orglett.6c03089"}],"versionNumber":9,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"metadata_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.dncjsxmfr","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.z8w9ghxjz"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.z8w9ghxjz/versions"},"stash:version":{"href":"/api/v2/versions/461791"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.z8w9ghxjz/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.z8w9ghxjz","id":117748,"storageSize":6275644956,"relatedPublicationISSN":"1544-9173","title":"Genetic, developmental and neural changes underlying evolving butterfly mate preference ","authors":[{"firstName":"Nicholas","lastName":"VanKuren","email":"nvankuren@uchicago.edu","affiliation":"University of Chicago","affiliationROR":"https://ror.org/024mw5h28","affiliations":[{"name":"University of Chicago","ror_id":"https://ror.org/024mw5h28"}],"orcid":"0000-0001-8633-8851"},{"firstName":"Nathan","lastName":"Buerkle","email":"nathan.p.buerkle@gmail.com","affiliation":"Yale University","affiliationROR":"https://ror.org/03v76x132","affiliations":[{"name":"Yale University","ror_id":"https://ror.org/03v76x132"}],"orcid":"0000-0002-2663-5472","order":1},{"firstName":"Wei","lastName":"Lu","email":"","affiliation":"University of Chicago","affiliationROR":"https://ror.org/024mw5h28","affiliations":[{"name":"University of Chicago","ror_id":"https://ror.org/024mw5h28"}],"order":2},{"firstName":"Erica","lastName":"Westerman","email":"","affiliation":"University of Arkansas at Fayetteville","affiliationROR":"https://ror.org/05jbt9m15","affiliations":[{"name":"University of Arkansas at Fayetteville","ror_id":"https://ror.org/05jbt9m15"}],"order":3},{"firstName":"Alexandria","lastName":"Im","email":"","affiliation":"University of Chicago","affiliationROR":"https://ror.org/024mw5h28","affiliations":[{"name":"University of Chicago","ror_id":"https://ror.org/024mw5h28"}],"order":4},{"firstName":"Laura","lastName":"Southcott","email":"","affiliation":"University of Chicago","affiliationROR":"https://ror.org/024mw5h28","affiliations":[{"name":"University of Chicago","ror_id":"https://ror.org/024mw5h28"}],"order":5},{"firstName":"Stephanie","lastName":"Palmer","email":"sepalmer@uchicago.edu","affiliation":"University of Chicago","affiliationROR":"https://ror.org/024mw5h28","affiliations":[{"name":"University of Chicago","ror_id":"https://ror.org/024mw5h28"}],"orcid":"0000-0001-6211-6293","order":6},{"firstName":"Marcus","lastName":"Kronforst","email":"mkronforst@uchicago.edu","affiliation":"University of Chicago","affiliationROR":"https://ror.org/024mw5h28","affiliations":[{"name":"University of Chicago","ror_id":"https://ror.org/024mw5h28"}],"order":7}],"abstract":"\u003cp\u003eMany studies have linked genetic variation to behavior, but the links between that variation and the neural circuits that drive behavior remain elusive. We investigated the architecture of mate choice behavior in \u003cem\u003eHeliconius\u003c/em\u003e butterflies, which use vision to identify preferred mates based on wing color patterns. We found that \u003cem\u003eHeliconius\u003c/em\u003e \u003cem\u003ecydno\u003c/em\u003e mate preference is associated with inter-photoreceptor inhibition of ultraviolet-sensitive photoreceptors (PRs) by long-wavelength sensitive PRs; identified a small number of genetic loci associated with preference variation; and began to link these multiple layers of behavior variation together through analyses of developmental gene networks. Our results support the idea that altered peripheral neural computations, driven by changes to underlying developmental genetic processes, can significantly and rapidly alter essential behaviors. \u003c/p\u003e\n\u003cp\u003eThis repository contains raw data, scripts, notebooks, and intermediate files that were used to perform and analyze genome-wide association studies, to analyze RNA-seq data, and to process and analyze electrophysiology data presented in the associated publication.\u003c/p\u003e\n","funders":[{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"1515295","awardDescription":"EAPSI","order":3},{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"GM131828","awardDescription":"R35","order":0},{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"1452648","awardDescription":"IOS","order":1},{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"1922624","awardDescription":"IOS","order":2}],"keywords":["RNA-seq","differential expression","genome assembly","Genome annotation","GWAS","Heliconius cydno","Electrophysiology","Photoreceptors"],"fieldOfScience":"Biological sciences","methods":"\u003cp\u003e\u003cstrong\u003eAnimals\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe used butterflies from four different taxa. The \u003cem\u003eH. c. alithea\u003c/em\u003e used in the preference and color GWA analyses were previously tested for courtship behavior in Ecuador in 2008 by Nicola Chamberlain and Durrell Kapan. These butterflies were tested for their preference, then the bodies stored in 100% ethanol at -80\u003csup\u003eo\u003c/sup\u003eC until genomic DNA extractions (see below) \u003ca href=\"https://paperpile.com/c/NyBjxn/ORVPO\"\u003e[1]\u003c/a\u003e. For all other experiments, butterflies were housed in greenhouse breeding colonies at the University of Chicago that were regularly supplemented with new individuals. Adults were fed Bird’s Choice artificial nectar ad libitum and supplied with blooming Lantana as an additional source of nectar and pollen. \u003cem\u003eHeliconius cydno galanthus\u003c/em\u003e and \u003cem\u003eH. melpomene\u003c/em\u003e pupae were obtained from El Bosque Nuevo in Costa Rica, and \u003cem\u003eH. c. alithea\u003c/em\u003e from \u003cem\u003eHeliconius\u003c/em\u003e Butterfly Works in Ecuador. Heliconius pachinus and F1 H. c. galanthus X \u003cem\u003eH. pachinus\u003c/em\u003e hybrids were bred in Panama and adults were transported to Chicago for experiments. Collection, rearing, import and export were done under permits from Ecuador, Panama, Costa Rica, and USA.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e\u003cstrong\u003eHeliconius cydno alithea\u003c/strong\u003e\u003c/em\u003e \u003cstrong\u003e(yellow) genome assembly and annotation\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe isolated DNA from thorax of a single adult yellow \u003cem\u003eH. cydno alithea\u003c/em\u003e female using the QIAGEN Genomic-tip 20/G following the manufacturer’s instructions with the following modifications: tissue was incubated at 50oC shaking at 800 rpm overnight in lysis buffer. We used 4 ug of this high molecular weight DNA as input to Oxford Nanopore Technologies (ONT) ligation library preparation kit SQK-LSK 110. We prepared libraries following the manufacturer’s instructions with modifications based on the protocol found here: \u003ca href=\"https://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-15-3-bp2l6n3kzgqe/v1\"\u003ehttps://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-15-3-bp2l6n3kzgqe/v1\u003c/a\u003e. This protocol differs from the manufacturer’s protocols in the following ways. End-repair was performed at 20\u003csup\u003eo\u003c/sup\u003eC for 1 hour, dA-tailing was performed for 30 minutes, ligation was performed for 1 hour at room temperature, and all bead elution steps were allowed to proceed for one hour at room temperature. We also used PacBio SRE XS kit to remove \u0026lt;10kb fragments in the final libraries.\u003c/p\u003e\n\u003cp\u003eFinal libraries were sequenced on an ONT MinION with version 9.4.1 flow cell. We performed basecalling using Guppy and the super accurate basecalling model in dna_r9.4.1_450bps_sup.cfg supplied with the basecaller. For the genome assembly, we adopted a similar strategy as \u003ca href=\"https://paperpile.com/c/NyBjxn/NIrw\"\u003e(Steward et al. 2021)\u003c/a\u003e. We generated the initial draft assembly using Flye 2.9 \u003ca href=\"https://paperpile.com/c/NyBjxn/7QWC\"\u003e[2]\u003c/a\u003e with estimated genome size of 282Mb (based on GenomeScope estimate \u003ca href=\"https://github.com/schatzlab/genomescope\"\u003ehttps://github.com/schatzlab/genomescope\u003c/a\u003e) and Shasta 0.10.0 (\u003ca href=\"https://github.com/chanzuckerberg/shasta\"\u003ehttps://github.com/chanzuckerberg/shasta\u003c/a\u003e) with default parameters. The Flye assembly and Shasta assembly were polished with two rounds of racon 1.5.0 (\u003ca href=\"https://github.com/isovic/racon\"\u003ehttps://github.com/isovic/racon\u003c/a\u003e) and one round of medaka 1.8.1 with ONT reads, and then purged to remove duplicate scaffolds (typically uncollapsed allelic variation) using purge_dups (\u003ca href=\"https://github.com/dfguan/purge_dups\"\u003ehttps://github.com/dfguan/purge_dups\u003c/a\u003e). Finally, the duplicate scaffolds were merged together with quickmerge (\u003ca href=\"https://github.com/mahulchak/quickmerge\"\u003ehttps://github.com/mahulchak/quickmerge\u003c/a\u003e) and purged using purge_dups.\u003c/p\u003e\n\u003cp\u003eTo simplify comparisons across species, we scaffolded \u003cem\u003eH. c. alithea\u003c/em\u003e contigs to the \u003cem\u003eHeliconius melpomene v2.5\u003c/em\u003e chromosome-level assembly using RagTag \u003ca href=\"https://paperpile.com/c/NyBjxn/uYkS\"\u003e[3]\u003c/a\u003e and renamed \u003cem\u003eH. c. alithea\u003c/em\u003e scaffolds to match. Finally, we identified and soft-masked repeat sequences using RepeatModeler and RepeatMasker \u003ca href=\"https://paperpile.com/c/NyBjxn/XU71+mSnW\"\u003e[4,5]\u003c/a\u003e. The genome sequence and annotation used in this study can be found in this repository z8w9ghxjz in the \u003ccode\u003egwas/data/genome/\u003c/code\u003e directory. The final genome assembly comprised 310 scaffolds spanning 294 Mb, with 287 Mb assigned to H. melpomene chromosomes. BUSCO v5 analysis showed the \u003cem\u003eH. c. alithea\u003c/em\u003e genome contained 97.7% complete (97.3% single-copy, 0.4% duplicated), 0.4% fragmented, and 1.9% missing OrthoDB v10 Endopteryogota (2,124 single-copy orthologs) SCOs. \u003c/p\u003e\n\u003cp\u003eWe annotated \u003cem\u003eH. c. alithea\u003c/em\u003e scaffolds using EvidenceModeler 1.1.1 \u003ca href=\"https://paperpile.com/c/NyBjxn/NVqsj\"\u003e[6]\u003c/a\u003e. We first assembled the \u003cem\u003eH. cydno\u003c/em\u003e transcriptome de novo using RNA-seq data generated by Walters et al. \u003ca href=\"https://paperpile.com/c/NyBjxn/IA1Uc\"\u003e[7]\u003c/a\u003e, Nallu et al. \u003ca href=\"https://paperpile.com/c/NyBjxn/WaIFc\"\u003e[8]\u003c/a\u003e, and Rossi et al. \u003ca href=\"https://paperpile.com/c/NyBjxn/HaLKh\"\u003e[9]\u003c/a\u003e using Trinity v2.10.0 \u003ca href=\"https://paperpile.com/c/NyBjxn/dHmK8\"\u003e[10]\u003c/a\u003e. RNA-seq data was also mapped to using STAR 2.6.1d \u003ca href=\"https://paperpile.com/c/NyBjxn/bXA90\"\u003e[11]\u003c/a\u003e, and the resulting alignments used to generate genome-guided assemblies using Trinity and StringTie 1.3.1 \u003ca href=\"https://paperpile.com/c/NyBjxn/YikrY\"\u003e[12]\u003c/a\u003e. We combined de novo and genome-guided assemblies using PASA \u003ca href=\"https://paperpile.com/c/NyBjxn/wqbqM\"\u003e[13]\u003c/a\u003e. Evidence for protein-coding regions came from mapping the UniProt/Swiss-Prot (2020_06) database and all Papilionoidea proteins available in NCBI’s GenBank nr protein database (downloaded 6/2020) using exonerate \u003ca href=\"https://paperpile.com/c/NyBjxn/uhK0P\"\u003e[14]\u003c/a\u003e. We identified high-quality multi-exon protein-coding PASA transcripts using TransDecoder (transdecoder.github.io), then used these models to train and run Genemark-ET 4 \u003ca href=\"https://paperpile.com/c/NyBjxn/niEPS\"\u003e[15]\u003c/a\u003e and GlimmerHMM 3.0.4 \u003ca href=\"https://paperpile.com/c/NyBjxn/GVwkw\"\u003e[16]\u003c/a\u003e. We also predicted gene models using Augustus 3.3.2 \u003ca href=\"https://paperpile.com/c/NyBjxn/KsGpm\"\u003e[17]\u003c/a\u003e, the supplied heliconius_melpomene1 parameter set, and hints derived from RNA-seq and protein mapping above. Augustus predictions with \u0026gt;90% of their length covered by hints were considered high-quality models. Transcript, protein, and ab initio data were integrated using EVM with the weights in table S8. \u003c/p\u003e\n\u003cp\u003eRaw EVM models were then updated twice using PASA to add UTRs and identify alternative transcripts. BUSCO v5 analysis of the final annotated protein set showed it contained 94.8% complete, 1.8% fragmented, and 3.4% missing OrthoDB v10 endopteryogta SCOs (n = 2124). Gene models derived from transposable element proteins were identified using BLASTp and removed from the annotation set. Functional annotations were applied to this annotation set using eggNOG mapper v5 \u003ca href=\"https://paperpile.com/c/NyBjxn/Z76Y\"\u003e[18]\u003c/a\u003e. The final annotation comprises 18,763 protein-coding genes and 30,325 transcripts. We identified 1:1 orthologs to \u003cem\u003eDrosophila melanogaster\u003c/em\u003e proteins using reciprocal BLASTp, assigning orthologs only to those genes where the top hit was identical between the two directions (i.e. Hca → Dmel AND Dmel → Hca). Gene annotations, eggNOG results, and \u003cem\u003eDrosophila\u003c/em\u003e orthologs are supplied in this repository z8w9ghxjz.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e\u003cstrong\u003eHeliconius cydno alithea\u003c/strong\u003e\u003c/em\u003e \u003cstrong\u003egenome re-sequencing and variant calling\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eGenomic DNA used for calling variants was isolated from thorax of 113 \u003cem\u003eH. c. alithea\u003c/em\u003e males studied by Chamberlain et al. \u003ca href=\"https://paperpile.com/c/NyBjxn/ORVPO\"\u003e[1]\u003c/a\u003e using chloroform extractions. These individuals were assessed for their mate preference in 2008, then stored in 100% ethanol at -80\u003csup\u003eo\u003c/sup\u003eC until gDNA extractions in 2015 - 2019. We re-sequenced all individuals with multiple courts, plus a number of males with just a single court, that produced high-quality genomic DNA, yielding a subset of 113 males from the original 175 included in the original study. Illumina paired-end libraries were constructed using the KAPA Hyper Prep Kit (KAPA Biosystems) or Nextera Library Prep Kit and sequenced to ~15X using 2x100 bp on an Illumina HiSeq2500 or 4000 at the University of Chicago Functional Genomics Facility. Raw data can be found in NCBI BioProject PRJNA802836.\u003c/p\u003e\n\u003cp\u003eLow-quality regions and adapters were trimmed from raw reads using Trimmomatic before mapping to the \u003cem\u003eH. c. alithea\u003c/em\u003e reference using bowtie2 v2.3.2 with default settings except --very-sensitive-local \u003ca href=\"https://paperpile.com/c/NyBjxn/JuwuN\"\u003e[19]\u003c/a\u003e. We then marked PCR duplicate reads with Picard and realigned around putative indels using the Genome Analysis Toolkit (GATK) 4.2 \u003ca href=\"https://paperpile.com/c/NyBjxn/1MVDe+mQ61S\"\u003e[20,21]\u003c/a\u003e. SNP and indel calling was performed using the HaplotypeCaller and GenotypeGVCFs module in GATK 4.3.0 with the heterozygosity priors set to 0.01 for both SNPs and indels. Scripts and variant calls in PLINK bed/bim/fam format can be found in this repository in \u003ccode\u003egwas/data/plink\u003c/code\u003e. \u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eRNA-sequencing data\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe aimed to collect RNA-sequencing data from retina, optic lobe, and brain tissue at seven developmental stages in \u003cem\u003eH. c. galanthus\u003c/em\u003e, white \u003cem\u003eH. c. alithea\u003c/em\u003e, and yellow \u003cem\u003eH. c. alithea\u003c/em\u003e males and females in triplicate. We used controlled crosses between \u003cem\u003eH. c. alithea\u003c/em\u003e males and females that were homozygous for the top wing color variant, thus ensuring that larvae and pupae from each cross would (if they were allowed to emerge) develop a single wing color. We identified appropriate adults for crosses by clipping a single leg from each individual that emerged from each shipment, extracting DNA from that leg using DNA ExtractALL reagents (Thermo), then performing a custom TaqMan genotyping assay for the wing color variant using the leg DNA. Only males and females that were homozygous for the yellow or white allele were used to set up “yellow” or “white” crosses. All H. c. galanthus individuals were used in \u003cem\u003eH. c. galanthus\u003c/em\u003e crosses. We set up crosses between multiple males and females in the UChicago greenhouse and provided ample host plants for egg lay. Caterpillars and pupae were maintained in separate small cages for each cross, and individuals were labeled upon pupation to track developmental timing. We collected tissues from one larval stage (final instar purple crawler, ~36h before pupation), five pupal stages (p0: 12 - 24 hours after pupation, p2: 48 - 60 hap, p4: 96 - 108 hap, p6: 144-156 hap, and p7: 168-180 hap), and one adult stage (ad: 24-48 hours after emergence). Pupal sex was determined using external pupal characteristics (\u003ca href=\"https://www.ucl.ac.uk/taxome/jim/Mim2/heliconius_pupa_sex_difference.html\"\u003ehttps://www.ucl.ac.uk/taxome/jim/Mim2/heliconius_pupa_sex_difference.html\u003c/a\u003e) as well as the presence/absence of testis, which are very prominent in butterflies. \u003c/p\u003e\n\u003cp\u003eWe collected head tissue from purple crawler and p0 pupae because the main neural tissues are small and difficult to separate. We collected retina, optic lobe, and central brain separately for all remaining stages. We dissected individuals in cold PBS and immediately placed dissected tissues into RNAlater (Ambion, USA). Tissues were stored in RNAlater at -80oC until RNA extraction using TRIzol (Ambion, USA). High quality (RIN \u0026gt; 7) RNA samples were treated with Turbo DNAse (Invitrogen, USA), then 1 ug was used as input for poly-A selection and RNA-seq library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext UltraII Directional RNA Prep Kit following the manufacturer’s instructions with minor modifications. RNA fragmentation was performed for 10 min at 94oC. We used the NEBNext Multiplex Oligos for Illumina dual-index adapters to uniquely barcode each sample. Double-sided selection was performed after adapter ligation to enrich for ~300 bp - 500 bp fragments. Final libraries were PCR amplified for 11 cycles. RNA-seq libraries were pooled and sequenced 2x100 bp on a NovaSeq 6000 at the University of Chicago Functional Genomics Facility. \u003c/p\u003e\n\u003cp\u003eAll raw RNA-seq data downloaded from NCBI BioProject PRJNA1019262. \u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePreliminary processing of RNA-seq data\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe quantified gene expression in each sample using the raw reads, the yellow \u003cem\u003eH. c. alithea\u003c/em\u003e transcriptome, and salmon v1.9.0 \u003ca href=\"https://paperpile.com/c/NyBjxn/Jl26J\"\u003e[31]\u003c/a\u003e. The whole genome sequence was included as the decoy, and sequence composition, GC, and positional bias corrections were used during quantification. Indexes and quantification used k-mer size 31. Quantifications, scripts for analysis, and other data objects can be found in this repository in the \u003ccode\u003ernaseq/\u003c/code\u003e directory.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eElectrophysiology methods\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eFor in vivo recordings, butterflies at least 3 days old were restrained in a custom built collar with heated beeswax. A small hole was cut in the dorsal eye to allow for electrode penetration along the dorsal-ventral axis of the eye and covered with silicone grease to prevent desiccation. A second small hole was cut near the mouthparts and a silver-chloride reference electrode was placed into the anterior portion of the head. The butterfly was then placed on a stage with the eye at the center of a Cardan arm perimeter device to allow for equivalent light stimulation at any spatial location.\u003c/p\u003e\n\u003cp\u003ePR responses were evoked using monochromatic stimuli from 310 to 700 nm in 10 nm increments (S12 Fig). Wavelengths above 630 nm were excluded from analysis because the output at those settings was not monochromatic, and the 580 and 660 nm settings were excluded because their intensity was at least an order of magnitude higher than the rest and could not be equalized with the neutral density filter. Thirty-eight wavelengths remain and the analyzed range is 310 to 630 nm. The light source was a dual Halogen-Deuterium lamp (DH-2000s, Ocean Optics), which was connected to a scanning monochromator (Monoscan-2000, Ocean Optics). Stimulus timing was controlled with an optical shutter (OZ Optics) and focused onto the butterfly eye using a collimator and lens (Edmund Optics). Every component was connected to each other using 1 mm fiber optic cables. Stimulus intensity was calibrated with a photodiode (Newport) and set to 1.5 x 10^15 photons/cm2/s using a variable neutral density filter in a rotational motor (Newport).  Recordings were amplified with a 0.1x headstage and high impedance amplifier (AxoClamp 900A, Molecular Devices) and digitized at 10 kHz (DigiData1550, Molecular Devices).\u003c/p\u003e\n\u003cp\u003ePRs were recorded intracellularly using sharp electrodes made from borosilicate glass on an electrode puller (P-97, Sutter Instruments). Electrodes were pulled to a resistance between 90 and 120 Mohm and filled with 3 M KCl. Recordings were made well away from the cut in the dorsal eye, and so exclusively from cells in the ventral half; the ventral third is the more likely extent. Cells were screened with white light on penetration, and only those responding with a depolarization of at least 30 mV were characterized further with monochromatic stimuli. A second criterion was applied to the monochromatic responses, retaining cells whose peak response reached at least 25 mV, relaxed to 15 mV for UV photoreceptors in order to better estimate the proportion of positive and negative tails within an individual. Response magnitude does not predict long wavelength inhibition and does not differ between males that preferentially court yellow females and those that do not.\u003c/p\u003e\n\u003cp\u003eStimuli were presented in fixed pseudo-random sequences. Seven sequences were generated in advance and reused across the study, ordered by light intensity rather than by wavelength to limit rotation of the variable neutral density filter. Four repeats per stimulus was the most common number but not the rule; repeats ranged from 1 to 24, with a mean of 3.6. Typically, responses were recorded at multiple intensity levels using neutral density filters (Thorlabs). After recording spectral responses, we also presented the wavelength that evoked the maximum response at twelve intensity levels that varied over 4 log units of attenuation: 0, 0.2, 0.4, 0.6, 1.0, 1.3, 1.6, 2.0, 2.5, 3.0, 3.5 and 4.0 log units. Where such a series was recorded, it was used to transform the isoquantal spectral responses of that PR to a spectral sensitivity curve using the  Naka-Rushton equation [109]. A series was obtained for 323 of the 508 PRs: 131 of 180 UV, 85 of 126 blue, 91 of 149 green and 16 of 33 red, and none of the 20 broadband. For the remaining cells the tuning curve is the normalized voltage response rather than a transformed sensitivity curve. The transform is undefined for responses at or below zero and floors there, so a transformed curve cannot represent a hyperpolarizing response; both kinds of curve appear in the deposited tables, and which kind a given cell holds is recorded per cell. The wavelength of peak sensitivity was estimated for each cell by fitting its responses with a standard rhodopsin tuning template [60].\u003c/p\u003e\n\u003cp\u003eTo measure response latency, we first measured the mean and standard deviation of the resting potential for 150 ms before the light flash. Onset latency was defined as the time for the response to exceed five times the standard deviation of this baseline. Latency could be measured only for cells recorded with a shutter TTL channel, from 2019 onward, which excludes the F1 hybrids.\u003c/p\u003e\n\u003cp\u003eFor experiments with the LED, we used green LEDs with peak tuning at 534 nm and a full width half maximum of 12 nm. Six LEDs were attached to the monochromatic source and had an intensity of 3.2 x 10^15 photons/cm2/s. Spectral responses were recorded from each cell before, during, and after turning on the LEDs. This intensity did not bleach PR responses, as the full response magnitude was typically recovered within seconds of turning off the LED. PRs that did not recover at least 80% of the original response were discarded.\u003c/p\u003e\n\u003cp\u003eWhen comparing physiology data across groups of butterflies (Figs 4B, 5I and 5J), we tested for significance using GLME models with a logit link function to account for repeated measures within single butterflies. For each model, butterfly identity was included as a random effect. For each analysis, we first computed significance using courtship preference (white, yellow, or equal) as a fixed effect, effectively grouping together taxa with similar behavior (e.g., F1 hybrids with white \u003cem\u003eH. c. alithea\u003c/em\u003e). We then conducted a series of models comparing white and yellow \u003cem\u003eH. c. alithea\u003c/em\u003e and all pairwise comparisons between \u003cem\u003eH. c. galanthus\u003c/em\u003e, \u003cem\u003eH. pachinus\u003c/em\u003e, and the F1 hybrid offspring of this pair. For models looking at long wavelength inhibition (Fig 5), we used the normalized response amplitude of a cell at 530 nm for UV cells and 590 nm for blue cells. Substituting presence or absence of inhibition as a binary fixed effect leaves the reported results and conclusions unchanged for courtship preference, for wing color in H. c. alithea, and for \u003cem\u003eH. c. galanthus\u003c/em\u003e against \u003cem\u003eH. pachinus\u003c/em\u003e. For \u003cem\u003eH. c. galanthus\u003c/em\u003e against the F1 hybrids the binary substitution gives p = 0.064 against p = 0.004 on amplitude. Figure 5I plots the proportion of cells classified as inhibited; the p-values reported for it are from the amplitude models.\u003c/p\u003e\n","relatedWorks":[{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.1101/2022.04.25.489404"},{"relationship":"dataset","identifierType":"URL","identifier":"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1019262"},{"relationship":"dataset","identifierType":"URL","identifier":"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA802836"},{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1371/journal.pbio.3002989"}],"versionNumber":12,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"metadata_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.z8w9ghxjz","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":162,"downloads":26,"citations":2}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.5tb2rbpjg"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.5tb2rbpjg/versions"},"stash:version":{"href":"/api/v2/versions/461833"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.5tb2rbpjg/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.5tb2rbpjg","id":179048,"storageSize":598813,"relatedPublicationISSN":"1466-822X","title":"Data from: Global patterns in body size and colour lightness diversity of swallowtail butterflies highlight biogeographical legacy over common environmental explanations","authors":[{"firstName":"Marvin","lastName":"Krampe","email":"marvinkrampe1999@web.de","affiliation":"Philipps University of Marburg","affiliationROR":"https://ror.org/01rdrb571","affiliations":[{"name":"Philipps University of Marburg","ror_id":"https://ror.org/01rdrb571"}],"order":0},{"firstName":"Ricarda","lastName":"Laumeier","email":"ricardalaumeier@gmail.com","affiliation":"Philipps University of Marburg","affiliationROR":"https://ror.org/01rdrb571","affiliations":[{"name":"Philipps University of Marburg","ror_id":"https://ror.org/01rdrb571"},{"name":"University of Applied Sciences Erfurt","ror_id":"https://ror.org/01hkc4630"}],"order":1},{"firstName":"Fabien L.","lastName":"Condamine","email":"fabien.condamine@gmail.com","affiliation":"Institut des Sciences de l'Evolution de Montpellier","affiliationROR":"https://ror.org/01cah1n37","affiliations":[{"name":"Institut des Sciences de l'Evolution de Montpellier","ror_id":"https://ror.org/01cah1n37"}],"order":2},{"firstName":"Nina","lastName":"Farwig","email":"farwig@staff.uni-marburg.de","affiliation":"Philipps University of Marburg","affiliationROR":"https://ror.org/01rdrb571","affiliations":[{"name":"Philipps University of Marburg","ror_id":"https://ror.org/01rdrb571"}],"order":3},{"firstName":"Stefan","lastName":"Pinkert","email":"StefanPinkert@posteo.de","affiliation":"Philipps University of Marburg","affiliationROR":"https://ror.org/01rdrb571","affiliations":[{"name":"Philipps University of Marburg","ror_id":"https://ror.org/01rdrb571"}],"orcid":"0000-0002-8348-2337","order":4}],"abstract":"\u003cp\u003eThis dataset includes data on species richness, range rarity, and functional diversity (body size and colour lightness dispersion) as well as mean annual temperature, mean annual productivity, and elevation across 10,611 (8,719 for FD) assemblages of swallowtail butterfly species (110 km × 110 km grid cells). Hotspots of species richness, range rarity, and functional diversity represent the top 10% grid cells of these metrics. In addition, assemblage-level mean colour lightness and body volume as well as their dispersion is provided.\u003c/p\u003e\n","funders":[{"organization":"Hessian Ministry for Science and the Arts","identifierType":"ror","identifier":"https://ror.org/00zd5gr55","awardNumber":"LOEWE/2/15/519/03/08.001(0002)/88","awardDescription":"LOEWE research cluster","awardTitle":"Tree-M","order":0},{"organization":"European Research Council","identifierType":"ror","identifier":"https://ror.org/0472cxd90","awardNumber":"851188","awardDescription":"European Union's Horizon 2020 research and innovation programme ","awardTitle":"GAIA","order":1},{"organization":"Agence Nationale de la Recherche","identifierType":"ror","identifier":"https://ror.org/00rbzpz17","awardNumber":"ANR-10-LABX-25-01","awardDescription":"Investissements d’Avenir","awardTitle":"CEBA","order":2}],"keywords":["Body size","butterfly biodiversity","colour lightness","ecogeographical rule","ecophysiological function","functional diversity ","Papilionidae","range size","Trait-environment relationship"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1111/geb.70306"}],"versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.5tb2rbpjg","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zcrjdfnvq"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zcrjdfnvq/versions"},"stash:version":{"href":"/api/v2/versions/461829"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zcrjdfnvq/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.zcrjdfnvq","id":192359,"storageSize":24002,"relatedPublicationISSN":"0909-6396","title":"Data from: Chronic wasting disease is associated with elevated cortisol concentrations in a white-tailed deer population","authors":[{"firstName":"Lisa","lastName":"Muller","email":"lmuller@utk.edu","affiliation":"University of Tennessee at Knoxville","affiliationROR":"https://ror.org/020f3ap87","affiliations":[{"name":"University of Tennessee at Knoxville","ror_id":"https://ror.org/020f3ap87"}],"orcid":"0000-0001-7833-2273","order":0},{"firstName":"Cameron","lastName":"Mitchell","email":"cmitch48@vols.utk.edu","affiliation":"University of Tennessee at Knoxville","affiliationROR":"https://ror.org/020f3ap87","affiliations":[{"name":"University of Tennessee at Knoxville","ror_id":"https://ror.org/020f3ap87"}],"order":1},{"firstName":"Jacob","lastName":"Wyrick","email":"qjl677@vols.utk.edu","affiliation":"University of Tennessee at Knoxville","affiliationROR":"https://ror.org/020f3ap87","affiliations":[{"name":"University of Tennessee at Knoxville","ror_id":"https://ror.org/020f3ap87"}],"order":2},{"firstName":"Justin","lastName":"Kosiewska","email":"jkosiews@vols.utk.edu","affiliation":"University of Tennessee at Knoxville","affiliationROR":"https://ror.org/020f3ap87","affiliations":[{"name":"University of Tennessee at Knoxville","ror_id":"https://ror.org/020f3ap87"}],"order":3},{"firstName":"Mark","lastName":"Wilber","email":"mwilber@utk.edu","affiliation":"University of Tennessee at Knoxville","affiliationROR":"https://ror.org/020f3ap87","affiliations":[{"name":"University of Tennessee at Knoxville","ror_id":"https://ror.org/020f3ap87"}],"orcid":"0000-0002-8274-8025","order":4},{"firstName":"Daniel","lastName":"Grove","email":"dgrove@utk.edu","affiliation":"University of Tennessee at Knoxville","affiliationROR":"https://ror.org/020f3ap87","affiliations":[{"name":"University of Tennessee at Knoxville","ror_id":"https://ror.org/020f3ap87"}],"order":5},{"firstName":"Dailee","lastName":"Metts","email":"daileeMetts12@gmail.com","affiliation":"University of Tennessee at Knoxville","affiliationROR":"https://ror.org/020f3ap87","affiliations":[{"name":"University of Tennessee at Knoxville","ror_id":"https://ror.org/020f3ap87"}],"order":6}],"abstract":"\u003cp\u003eWe tested whether cortisol concentrations were associated with CWD status by quantifying cortisol in hair from hunter-harvested deer. We supplemented this analysis with a small sample size (n=9) of serum from captured deer where CWD status was known within 30 days of capture due to mortality. Cortisol in hair is representative of long-term cortisol concentrations. In contrast, serum cortisol represents stress during capture and is highly variable by individual. In hair from hunter-harvested deer, cortisol concentrations were significantly higher in CWD+ animals (\u003cem\u003eP\u003c/em\u003e = 0.033). Cortisol concentrations in the hair of CWD+ deer were 1.3 pg/mg hair, (SE = 0.24) and for CWD non-detect (ND) were 0.79 pg/mg, (SE = 0.09). Despite small sample sizes, serum cortisol was still on average higher in CWD+ (mean = 5.9 mg/dl, SE = 1.6) compared to CWD ND deer (mean = 2.9 mg/dl, SE = 1.3), though this relationship was not significant (\u003cem\u003eP\u003c/em\u003e = 0.183). Combining these independent tests, there was significant evidence that cortisol concentrations differed between CWD+ and CWD non-detect animals (Fisher’s exact method: \u003cem\u003eP\u003c/em\u003e = 0.031).\u003c/p\u003e\n","funders":[{"organization":"Animal and Plant Health Inspection Service","identifierType":"ror","identifier":"https://ror.org/0599wfz09","awardNumber":"","awardDescription":"","awardTitle":"","order":0}],"keywords":["Cortisol","Chronic wasting disease","hair samples"],"fieldOfScience":"Biological sciences","methods":"\u003cp\u003e\u003cstrong\u003eHair sample collection\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe collected hair from 31 hunter-harvested deer at Ames REC during the regular hunting season. We collected additional samples from 1 collared deer mortality and 1 deer capture mortality (see below for capture description). We checked harvested deer at the Ames REC hunting club lodge where we collected samples and biometrics. We used Oster cordless hair clippers with #10 shears (Oster Professional Products, Sunbeam Products, Miami, FL, USA) to shave an approximate 10 x 10 cm section from the left rear hindquarter. Hair was collected on a paper plate and transferred to a manilla envelope that was stored at room temperature until analysis.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSerum sample collection from hunter-harvested and captured deer\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe used cardiac puncture for hunter-harvested deer to collect blood when available. We also collected blood from deer captured via helicopter with net guns (Helicopter Wildlife Services, Austin, TX, USA) and on the ground using baited Clover traps (Industrial Mechanical Inc., Watkinsville, GA, USA), baited Wildlife CaptureÒ magnetic drop nets (Wildlife Capture Services LLC, Flagstaff, AZ, USA), and by free-range darting from a baited ground blind. A Pneu-Dart G2 X-Caliber pneumatic air rifle and barbed 2ml Pneu-Dart transmitter darts were used for darting (Pneu-Dart Inc., Williamsport, PA, USA). Helicopter captured deer were hobbled, blindfolded, and placed in a sling for transport to a central processing station. Upon arrival at the processing station, deer were chemically immobilized. Deer captured with ground methods were chemically immobilized immediately. We used BAM (butorphanol-azaperone-medetomidine 17.3 mg/ ml butorphanol tartrate, 9.1 mg/ml azaperone, 10.9 mg/ml medetomidine; Wedgewood, Swedesboro, NJ, USA), or NalMed-A (40 mg/ml nalbuphine, 10 mg/ml azaperone, 10 mg/ml medetomidine, Wedgewood), or MKT (medetomidine (0.07 mg/kg, 20 mg/ml, Wedgewood), ketamine (1.5 mg/kg, 100 mg/ml, Covetrus, Ocala, FL, USA) and telazol (1.1 mg/kg, 100 mg/ml, Covetrus; Muller et al. 2012) before collecting a blood sample. For BAM or NalMed-A, we gave adult females 2 mls and males 3 mls. Once immobilized, we collected biological samples including blood from the jugular vein. We fitted LiteTrack Iridium Series GPS collars (Lotek Wireless, Newmarket, ON, Canada) on deer at this time. Animal temperature, pulse, and respiration were monitored during workup and supplemental oxygen was provided to anesthetized deer. Upon workup completion, deer were given appropriate antagonists and released (For BAM or NalMed-A, atipamezole (2 ml for every ml of BAM or NalMed-A, 25 mg/ml, Wedgewood) and 0.5 ml naltrexone (50 mg/ml, Wedgewood). For MKT, we used 0.35 mg/kg atipamezole (5 mg/ml, Covetrus)). We centrifuged (1775 G-force) all blood samples for 5 minutes to collect serum. We stored sera at -20 °C until analysis. We monitored collared deer for mortality signals using Lotek Web Service. Mortality alert signals were sent once collars had not moved for 6 hours. We collected mortalities as soon as possible once an alert was received. A licensed veterinarian (D. Grove) performed necropsies on deer that died when possible, including RPLN collection for CWD testing and evaluation of fat stores in body cavity and bone marrow.\u003c/p\u003e\n\u003cp\u003eOnly 9 live captured deer which died within 30 days after capture were used in the serum analysis because we required CWD status for the analysis close to the time of capture. These deer were tested for CWD at necropsy. We assumed within 30 days, the CWD status would be the same as the status during the time of capture. \u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCortisol assay\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe measured cortisol in hair and serum using cortisol ELISA kits (DetectX Cortisol ELISA Kits, Arbor Assays, Ann Arbor, MI, USA) at a temporary lab set up in West Tennessee to prevent potential contamination of CWD prions to our home lab in East Tennessee. For hair samples, we followed Arbor Assays hair protocol where 250 mg shaved hair was placed into 50 ml conical polypropylene centrifuge tubes with screw caps. We added 5 ml of isopropanol (Optima for HPLC, Fisher Chemical, Fisher Scientific, \u003ca href=\"http://www.fishersci.com\"\u003ewww.fishersci.com\u003c/a\u003e), mixed with the hair, and incubated for 5 minutes. The liquid was decanted and hair was washed 2 more times. The hair was dried on paper plates at room temperature. We ground the dried hair samples to a fine powder using a Retsch MM400 grinder mill with 50 ml steel screw-top canister and 25 mm grinding ball (Verder Scientific, Inc., Newtown, PA, USA). We weighed 50 mg of powdered hair into a 15 ml polypropylene centrifuge tube and added 1 ml methanol (Methanol (HPLC), Fisher Chemical). We placed the tubes with methanol on a rocker (Corning LSE Platform Rocker, Fisher Scientific) set to rotate 12-16 hours at 100 rpm. We centrifuged the tubes for 5 minutes (1775 G) and pipetted 0.5 ml of the methanol extract into a 1.5 ml centrifuge tube. The methanol was evaported using a Speedvac SPD1030 (Fisher Scientific) for 90 min at vacuum pressure 1 (heat time 30 min, temperature 40^^ °C). We reconstituted the dried extracts using 120 ul Assay Buffer in the cortisol kit. We measured parallelism using a higher concentration hair sample with dilutions from 120, 140, 150, 170, 190 ul buffer). All samples were measured between 20-89 % binding in the linear part of the curve. We reran any samples with CV \u0026gt; 20 % if possible. We measured extraction efficiency by comparing 2 samples with and without an added 5 ml of cortisol standard (32,000 pg/ml) to the spiked sample. We ran a pooled serum sample with every plate to evaluate interassay variability.\u003c/p\u003e\n\u003cp\u003eWe followed Arbor Assays protocol and tested parallelism in deer serum according to Grunwald et al. (2025). All samples were measured between 20-83 % binding in the linear part of the curve. Coefficient of variation was determined by (standard deviation/mean) *100 of replicates measured for each sample. We reran any samples with coefficient of variation (CV) \u0026gt; 20 %. \u003c/p\u003e\n","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1002/wlb3.01741"}],"versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.zcrjdfnvq","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.sn02v6xk5"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.sn02v6xk5/versions"},"stash:version":{"href":"/api/v2/versions/461834"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.sn02v6xk5/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.sn02v6xk5","id":174173,"storageSize":74048,"relatedPublicationISSN":"0929-1393","title":"Data from: Road salt application increases sodium levels in roadside plants and ants, reshaping tritrophic interactions","authors":[{"firstName":"Hiroki","lastName":"Terajima","email":"htrj2895choshi.jp@outlook.jp","affiliation":"Hirosaki University","affiliationROR":"https://ror.org/02syg0q74","affiliations":[{"name":"Hirosaki University","ror_id":"https://ror.org/02syg0q74"}],"order":0},{"firstName":"Youhei","lastName":"Kawase","email":"yohei.kawase@nikkawhisky.co.jp","affiliation":"Hirosaki University","affiliationROR":"https://ror.org/02syg0q74","affiliations":[{"name":"Hirosaki University","ror_id":"https://ror.org/02syg0q74"}],"order":1},{"firstName":"Akira","lastName":"Yamawo","email":"yamawo.aki@gmail.com","affiliation":"Kyoto University","affiliationROR":"https://ror.org/02kpeqv85","affiliations":[{"name":"Hirosaki University","ror_id":"https://ror.org/02syg0q74"},{"name":"Kyoto University","ror_id":"https://ror.org/02kpeqv85"}],"orcid":"0000-0003-2928-8151","order":2},{"firstName":"Nobuyuki","lastName":"Azuma","email":"azuma@hirosaki-u.ac.jp","affiliation":"Hirosaki University","affiliationROR":"https://ror.org/02syg0q74","affiliations":[{"name":"Hirosaki University","ror_id":"https://ror.org/02syg0q74"}],"order":3},{"firstName":"Kaori","lastName":"Noda","email":"kaolin@hirosaki-u.ac.jp","affiliation":"Hirosaki University","affiliationROR":"https://ror.org/02syg0q74","affiliations":[{"name":"Hirosaki University","ror_id":"https://ror.org/02syg0q74"}],"order":4},{"firstName":"Hiroshi","lastName":"Ikeda","email":"hiroikeda@g.ecc.u-tokyo.ac.jp","affiliation":"The University of Tokyo","affiliationROR":"https://ror.org/057zh3y96","affiliations":[{"name":"Hirosaki University","ror_id":"https://ror.org/02syg0q74"},{"name":"The University of Tokyo","ror_id":"https://ror.org/057zh3y96"}],"orcid":"0000-0002-3610-697X","order":5}],"abstract":"\u003cp\u003eIn areas with heavy snowfall and high levels of anthropogenic activity, a large amount of sodium chloride is applied in the winter as an antifreezing agent for the road surface. The effects of road salt application may be widespread among various plants and high-trophic-level organisms. Here, we examined the effects of road salt application on plants and omnivorous ants. Ten study sites were established along national route 7, which is the main road in the northwestern region of Japan. The concentrations of sodium in the soil, leaves of Japanese knotweed and white clover, the extrafloral nectar of Japanese knotweed, and ants increased closer to the national route in spring. Ants acclimated to high-sodium baits gathered at the low-sodium baits, indicating that road salt application changed the food preference of the ants and that the ants increasingly preferred low-sodium foods. The trophic level of ants was lower the closer they were to the national route in spring, suggesting that ants became more herbivorous near the national route, favouring lower-sodium food at lower trophic levels. Our study revealed that road salt application can change insect behaviour through sodium accumulation, leading to changes in biological interactions such as predator–prey relationships.\u003c/p\u003e\n","funders":[{"organization":"Nippon Life Insurance Foundation","identifierType":"ror","identifier":"https://ror.org/032jsmy36","awardNumber":"","awardDescription":"","awardTitle":"","order":0}],"keywords":["Ecology","Entomology","Chemical ecology"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1016/j.apsoil.2026.107417"}],"versionNumber":15,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.sn02v6xk5","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zpc866tnk"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zpc866tnk/versions"},"stash:version":{"href":"/api/v2/versions/461858"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zpc866tnk/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.zpc866tnk","id":167209,"storageSize":37477,"relatedPublicationISSN":"0008-7475","title":"Effects of nitrogen enrichment on wood decomposition","authors":[{"firstName":"Rylee","lastName":"Strassner","email":"rlstrassner@yahoo.com","affiliation":"Appalachian State University","affiliationROR":"https://ror.org/051m4vc48","affiliations":[{"name":"Appalachian State University","ror_id":"https://ror.org/051m4vc48"}],"orcid":"0009-0007-5337-286X"}],"abstract":"\u003cp\u003eNitrogen deposition supplements forest nutrient cycles, but levels vary with proximity to human activity. To assess its influence in remote Southern Appalachian forests, this study examined woody debris decomposition of \u003cem\u003eLiriodendron tulipifera\u003c/em\u003e and \u003cem\u003ePinus strobus\u003c/em\u003e under control and nitrogen enrichment (5 kg N ha⁻¹ yr⁻¹) treatments over one year. Logs (5 cm diameter) and sticks (\u0026lt; 5 cm diameter) were evaluated for mass and density changes, and logs were further analyzed for wood chemistry (lignin, cellulose, hemicellulose, C, and N). Wood species emerged as the dominant driver of early decomposition, with \u003cem\u003eL. tulipifera\u003c/em\u003e and \u003cem\u003eP. strobus\u003c/em\u003e differing in lignin and cellulose content. Nitrogen enrichment had little effect, except in one-year \u003cem\u003eL. tulipifera\u003c/em\u003e logs, which showed higher lignin concentrations—possibly reflecting delayed decay. These findings suggest that while wood chemistry dictates early-stage decomposition, low-level N additions may exert subtle, species-specific effects. Longer-term studies are needed to identify thresholds at which N enrichment alters decomposition, an important consideration as global change reshapes forest nutrient regimes and carbon storage potential.\u003c/p\u003e\n","funders":[{"organization":"Appalachian State University","identifierType":"ror","identifier":"https://ror.org/051m4vc48","awardNumber":"","awardDescription":"Office of Student Research","awardTitle":"OSR Research \u0026 Travel Grant","order":0},{"organization":"Appalachian State University","identifierType":"ror","identifier":"https://ror.org/051m4vc48","awardNumber":"","awardDescription":"","awardTitle":"James C. Greene Fellowship","order":1}],"keywords":["Nitrogen cycle","Decomposition","Temperate forests","Carbon cycle"],"fieldOfScience":"Biological sciences","versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-04","lastModificationDate":"2026-09-04","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.zpc866tnk","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.s7h44j1ph"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.s7h44j1ph/versions"},"stash:version":{"href":"/api/v2/versions/461553"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.s7h44j1ph/download"},"curies":[{"name":"stash","href":"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/link_relations.md#{rel}","templated":"true"}]},"identifier":"doi:10.5061/dryad.s7h44j1ph","id":180644,"storageSize":216876517929,"title":"Single-cell RNA sequencing of head and neck squamous cell carcinoma patient-derived xenografts treated with cetuximab","authors":[{"firstName":"Randall","lastName":"Kimple","email":"rkimple@wisc.edu","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"orcid":"0000-0001-8336-8000"},{"firstName":"Liliana","lastName":"Berube","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"orcid":"0000-0002-6673-2525","order":1},{"firstName":"Deric","lastName":"Wheeler","email":"dlwheeler@wisc.edu","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"order":2},{"firstName":"Justine","lastName":"Bruce","email":"jybruce@wisc.edu","affiliation":"University of Wisconsin–Madison","affiliationROR":"https://ror.org/01y2jtd41","affiliations":[{"name":"University of Wisconsin–Madison","ror_id":"https://ror.org/01y2jtd41"}],"order":3}],"abstract":"\u003cp\u003eCetuximab, an EGFR-targeting monoclonal antibody, benefits only a subset of patients with head and neck cancer (HNC), and the tumor-intrinsic programs distinguishing responders from non-responders remain incompletely defined. This dataset was generated as part of a single-site, single-arm, open-label window-of-opportunity study in which patients with HNC received two doses of preoperative cetuximab prior to surgical resection. Patient-derived xenografts (PDXs) were established from study biopsies, and single-cell RNA sequencing of cetuximab-treated xenograft tissue was used to compare tumors that were clinically sensitive versus resistant to cetuximab. Two PDX models are represented: UW-SCC-185 and UW-SCC-194.\u003c/p\u003e\n\u003cp\u003eTo capture biological heterogeneity within each model, tumors from multiple biological replicates were pooled prior to dissociation (n = 10 for UW-SCC-185; n = 12 for UW-SCC-194). Solid tumors were dissociated to single-cell suspensions, yielding suspensions with average viability exceeding 75%. Libraries were constructed using the PIPseq 3' Single Cell RNA Kit v4.0Plus (Fluent BioSciences/Illumina) — T20 for UW-SCC-185 and T2 for UW-SCC-194 — following the manufacturer's protocol, and sequenced on an Illumina NovaSeq X to a depth of at least 20,000 reads per cell. Reads were processed with PIPseeker against a combined human–mouse reference (GRCh38.p13 + GRCm39) to distinguish human tumor cells from murine stromal cells; quality control, normalization, clustering, and annotation were performed in [Seurat version 5.3.0]. After filtering and downsamples to 3000 cells for both UW-SCC-185 and UW-SCC-194.\u003c/p\u003e\n\u003cp\u003eAnalysis of these data indicated that cetuximab sensitivity is marked by broad transcriptional remodeling, whereas resistance is associated with stable HER-family signaling and elevated TAM receptor activity. Raw sequencing data are deposited here. This Dryad record contains the processed derivatives required to reproduce the published analyses: filtered gene–cell count matrices, per-cell metadata (model, species assignment, cluster and cell-type annotations).\u003c/p\u003e\n\u003cp\u003eThese data are reusable for studies of acquired and intrinsic EGFR-inhibitor resistance, AXL/TAM receptor signaling in solid tumors, comparative analysis of HNC tumor cell states across PDX models, and benchmarking of PIPseq chemistry and human–mouse read deconvolution.\u003c/p\u003e\n","funders":[{"organization":"National Institute of Dental and Craniofacial Research","identifierType":"ror","identifier":"https://ror.org/004a2wv92","awardNumber":"5P50DE026787-05","awardURI":"https://reporter.nih.gov/project-details/9988228","awardDescription":"","awardTitle":"","order":0},{"organization":"National Cancer Institute","identifierType":"ror","identifier":"https://ror.org/040gcmg81","awardNumber":"3R37CA255330","awardURI":"https://reporter.nih.gov/project-details/11211993","awardDescription":"","awardTitle":"Improving the translational value of head and neck cancer patient-in-mouse models","order":1}],"keywords":["Head and neck squamous cell carcinoma","chemotherapy resistance","cetuximab"],"fieldOfScience":"Medical and health sciences","hsiStatement":"The data in this record were generated from patient-derived xenograft (PDX) tissue, not from patient specimens directly. The PDX models represented here (UW-SCC-185 and UW-SCC-194) were established from tumor tissue obtained under a protocol approved by the University of Wisconsin–Madison Health Sciences Institutional Review Board, protocol #2018-1232 and registered at ClinicalTrials.gov (NCT03769311). All donors provided written informed consent for their tissue to be used to generate these models and for research use of data derived from them.\n\nNo patient-level data are included in this deposit. The record contains sequencing data and derived expression matrices from xenograft tumor tissue, annotated only by internal model identifiers (UW-SCC-185, UW-SCC-194). No names, medical record numbers, dates, geographic identifiers, or any other identifiers enumerated under the HIPAA Privacy Rule are present, and no clinical or demographic information about the tissue donors is included. The internal model identifiers carry no embedded donor information; any link between model identifier and donor is held separately by the study team under IRB-approved procedures and is neither included in nor derivable from this deposit.\nAll data in this data set is appropriate for unrestricted public sharing in Dryad, in accordance with the applicable consent, ethical approvals, and institutional requirements. No individual-level human genomic data are included in the submission.","methods":"\u003cp\u003eBiological replicates (n = 10 for UW-SCC 185, n = 12 for UW-SCC 194) were combined prior to dissociation to encompass biologic heterogeneity. Dissociation from solid tumor to single-cell suspension was performed as described previously (55). High quality cell suspensions were prepared with an average viability of over 75%. scRNA-seq libraries were constructed using the PIPseq 3’ Single Cell RNA Kit v4.0Plus (T20 for UW-SCC 185, T2 for UW-SCC 194), following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq X sequencer with a sequencing depth of at least 20,000 reads per cell.\u003c/p\u003e\n","versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-09-03","lastModificationDate":"2026-09-03","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.s7h44j1ph","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}}]}}