{"_links":{"self":{"href":"/api/v2/search"},"first":{"href":"/api/v2/search"},"last":{"href":"/api/v2/search?page=3555"},"next":{"href":"/api/v2/search?page=2"}},"count":20,"total":71097,"_embedded":{"stash:datasets":[{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.gmsbcc34r"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.gmsbcc34r/versions"},"stash:version":{"href":"/api/v2/versions/449271"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.gmsbcc34r/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.gmsbcc34r","id":186653,"storageSize":1909044950,"relatedPublicationISSN":"0962-1083","title":"Summer rainfall drives adaptation with gene flow in a widespread butterfly","authors":[{"firstName":"Lily","lastName":"Durkee","email":"lilyfdurkee@gmail.com","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"orcid":"0000-0002-7328-0256","order":0},{"firstName":"Christen","lastName":"Bossu","email":"Christen.Bossu@colostate.edu","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":1},{"firstName":"Kristen","lastName":"Ruegg","email":"Kristen.Ruegg@colostate.edu","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"orcid":"0000-0001-5579-941X","order":2},{"firstName":"Ruth","lastName":"Hufbauer","email":"Ruth.Hufbauer@colostate.edu","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"orcid":"0000-0002-8270-0638","order":3}],"abstract":"\u003cp\u003eUnderstanding how environmental variation interacts with gene flow to shape population genomic patterns is a central goal in evolutionary biology. We investigated how geographic and environmental differences impact genomic variation in the clouded sulfur butterfly (\u003cem\u003eColias philodice eriphyle\u003c/em\u003e) by conducting whole-genome resequencing across replicated transects consisting of paired high- and low-elevation sites on both sides of a major mountain range. Despite sampling across steep environmental gradients, we found no evidence of discrete population structure, indicating high connectivity across the region. Nonetheless, significant isolation by distance – strongest in eastern populations – revealed that geographic distance still imposes limits on gene flow, and genetic diversity was also elevated in the east. Genotype-environment association analyses identified more than 16,000 loci associated with elevation, precipitation, and solar radiation. Our redundancy analysis identified precipitation as the strongest predictor of adaptive genomic differentiation, and candidate genes included those linked to melanization and thermoregulation (e.g., \u003cem\u003eTH\u003c/em\u003e and \u003cem\u003eyellow\u003c/em\u003e). These results demonstrate that even in a largely panmictic population, environmental variation can maintain regional-scale signals of local adaptation. Because insects are declining globally and remain underrepresented in genomic monitoring, conducting whole-genome analyses in a widespread species provides valuable context for assessing how insects today persist across such diverse landscapes and their potential for withstanding future environmental change.\u003c/p\u003e\n","funders":[{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"","awardDescription":"","awardTitle":"Graduate Research Fellowship Program","order":0},{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"","awardDescription":"","awardTitle":"Postdoctoral Research Fellowship in Biology","order":1}],"keywords":["whole genome resequencing","conservation genomics","colias philodice eriphyle","population structure ","local adaptation","Gene flow"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.64898/2025.12.12.694053"},{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1111/mec.70388"},{"relationship":"software","identifierType":"URL","identifier":"https://github.com/lilyd-csu/colias-gea/"}],"versionNumber":2,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"metadata_changed","publicationDate":"2026-06-24","lastModificationDate":"2026-06-24","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.gmsbcc34r","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.t1g1jwthm"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.t1g1jwthm/versions"},"stash:version":{"href":"/api/v2/versions/449276"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.t1g1jwthm/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.t1g1jwthm","id":183226,"storageSize":451033,"title":"Survey of Colorado beef and dairy cattle producers on perceptions of current barriers, opportunities, and technical solutions to reduce methane emissions from enteric and manure sources","authors":[{"firstName":"Sara","lastName":"Place","email":"sara.place@colostate.edu","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"orcid":"0000-0002-4033-3681"},{"firstName":"Kate","lastName":"Oviatt","email":"","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":1},{"firstName":"Rachel","lastName":"Lahoff","email":"","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":2},{"firstName":"Christina","lastName":"Herman","email":"","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":3},{"firstName":"Milagro","lastName":"Núñez-Solís","email":"","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":4},{"firstName":"Kimberly","lastName":"Stackhouse-Lawson","email":"","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":5},{"firstName":"John","lastName":"Ritten","email":"","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":6}],"abstract":"\u003cp\u003eObjective: Our objective was to assess Colorado beef and dairy cattle producers’ perceptions of the feasibility and current barriers to adopting enteric and manure methane reduction strategies.\u003c/p\u003e\n\u003cp\u003eMaterials and Methods: A survey was designed to assess Colorado beef and dairy cattle producers’ perceptions of the feasibility and barriers to technical solutions for reducing methane emissions from enteric and manure sources. Screening questions ensured the respondents were Colorado-located cow-calf or stocker, feedyard owner or operators, or dairy producers. Surveys were distributed electronically. Respondents received a series of 6-point Likert scale questions about the feasibility of methane reduction strategies. Survey questions included strategies common to all producer types and producer-specific methane reduction strategies. The survey included a final, open-ended question focused on identifying the most important consideration for implementing a potential methane reduction strategy.\u003c/p\u003e\n\u003cp\u003eResults and Discussion: A total of 110 complete responses were received. Across all producer types, vaccines were identified as the most feasible strategy followed by feed additives. For feed additives, dietary strategies, and modifying breeding/genetics, a greater proportion of respondents rated these strategies as “not at all” or “not very” feasible compared with “absolutely” or “very” feasible. Top barriers across common reduction strategies were cost associated with implementation and negative impacts on product quality. Top rated strategies varied by producer type; however, modifying breeding/genetics was consistently rated with the lowest feasibility across beef and dairy producers. Responses to the open-ended question indicated a general skepticism of the importance of reducing methane emissions, an emphasis on taking a more holistic view of the environmental benefits of cattle production, and concerns about the long-term implications of new methane reduction strategies such as vaccines and feed additives on animal welfare and productivity.\u003c/p\u003e\n\u003cp\u003eImplications and Applications: Feasibility of different methane reduction strategies varied by producer type, but concerns about implementation cost, logistics, and impacts on animal welfare, productivity, and product quality were consistent. These results indicate adoption of methane reduction strategies would benefit from context specific approaches that incorporate financial incentives. Further qualitative research would advance understanding of producer motivations, concerns, and contextual factors important to the adoption of methane reduction strategies.\u003c/p\u003e\n","funders":[{"organization":"Colorado Department of Agriculture","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":0}],"keywords":["Methane","Cattle","Producer perceptions","Mitigation","survey"],"fieldOfScience":"Earth and related environmental sciences","relatedWorks":[{"relationship":"article","identifierType":"DOI","identifier":"https://doi.org/10.1088/2515-7620/ad82b5"}],"versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-24","lastModificationDate":"2026-06-24","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.t1g1jwthm","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.vmcvdnd66"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.vmcvdnd66/versions"},"stash:version":{"href":"/api/v2/versions/449131"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.vmcvdnd66/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.vmcvdnd66","id":173743,"storageSize":356932211494,"title":"Multiphasic blood transcriptomic signatures of radioprotection by BIO 300, a synthetic genistein nanosuspension, in a nonhuman primate model of acute radiation syndrome","authors":[{"firstName":"Neetha Nanoth","lastName":"Vellichirammal","email":"","affiliation":"Henry M. Jackson Foundation","affiliationROR":"https://ror.org/04q9tew83","affiliations":[{"name":"Henry M. Jackson Foundation","ror_id":"https://ror.org/04q9tew83"}],"order":0},{"firstName":"Stephen Y.","lastName":"Wise","email":"","affiliation":"Uniformed Services University of the Health Sciences","affiliationROR":"https://ror.org/04r3kq386","affiliations":[{"name":"Uniformed Services University of the Health Sciences","ror_id":"https://ror.org/04r3kq386"},{"name":"Henry M. Jackson Foundation","ror_id":"https://ror.org/04q9tew83"}],"order":1},{"firstName":"Oluseyi O.","lastName":"Fatanmi","email":"","affiliation":"Uniformed Services University of the Health Sciences","affiliationROR":"https://ror.org/04r3kq386","affiliations":[{"name":"Uniformed Services University of the Health Sciences","ror_id":"https://ror.org/04r3kq386"}],"order":2},{"firstName":"Rachel C.","lastName":"Mingus","email":"","affiliation":"Uniformed Services University of the Health Sciences","affiliationROR":"https://ror.org/04r3kq386","affiliations":[{"name":"Uniformed Services University of the Health Sciences","ror_id":"https://ror.org/04r3kq386"},{"name":"Henry M. Jackson Foundation","ror_id":"https://ror.org/04q9tew83"}],"order":3},{"firstName":"Alana D.","lastName":"Carpenter","email":"","affiliation":"Uniformed Services University of the Health Sciences","affiliationROR":"https://ror.org/04r3kq386","affiliations":[{"name":"Uniformed Services University of the Health Sciences","ror_id":"https://ror.org/04r3kq386"},{"name":"Henry M. Jackson Foundation","ror_id":"https://ror.org/04q9tew83"}],"order":4},{"firstName":"Sarah A.","lastName":"Petrus","email":"","affiliation":"Uniformed Services University of the Health Sciences","affiliationROR":"https://ror.org/04r3kq386","affiliations":[{"name":"Uniformed Services University of the Health Sciences","ror_id":"https://ror.org/04r3kq386"},{"name":"Henry M. Jackson Foundation","ror_id":"https://ror.org/04q9tew83"}],"order":5},{"firstName":"Michael D.","lastName":"Kaytor","email":"","affiliation":"Humanetics Corporation (United States)","affiliationROR":"https://ror.org/002vxyf08","affiliations":[{"name":"Humanetics Corporation (United States)","ror_id":"https://ror.org/002vxyf08"}],"order":6},{"firstName":"Vijay K.","lastName":"Singh","email":"vijay.singh@usuhs.edu","affiliation":"Uniformed Services University of the Health Sciences","affiliationROR":"https://ror.org/04r3kq386","affiliations":[{"name":"Uniformed Services University of the Health Sciences","ror_id":"https://ror.org/04r3kq386"}],"orcid":"0000-0002-6631-3849","order":7}],"abstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eProphylactic radioprotectors for pre-exposure administration are notably absent, creating a critical gap in radiation emergency preparedness and ARS management. BIO 300, a wet nanomilled formulation of synthetic genistein, is in advanced development as a prophylactic radioprotector with demonstrated survival benefits in murine and nonhuman primate (NHP) models when administered prior to lethal radiation exposure. Longitudinal transcriptomic analysis enables characterization of the molecular mechanisms underlying radioprotective drug action and supports development of potential blood-based monitoring tools for clinical translation. We performed longitudinal blood transcriptome profiling in NHPs receiving 5.8 Gy total-body irradiation to characterize BIO 300's radioprotective mechanisms and identify candidate transcriptional biomarkers of drug activity.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eBIO 300 demonstrated multiphasic changes in the transcriptome spanning acute cellular preservation (Days 7 – 10), immune reconstitution (Day 21), and sustained recovery (Day 60), with peak protection spanning 745–865 genes at Days 7–10 and sustained late-phase protection of 558 genes at Day 60. Differential expression analysis revealed four distinct drug-related molecular mechanisms: direct cellular protection, active damage reversal, drug-specific therapeutic responses, and stress attenuation. A core set of 39 genes showing sustained or consistent differential expression was identified, of which 20 carry conventional gene symbols and are functionally interpretable; LOC-designated genes are excluded from functional annotation. Notable annotated genes include SOX2, AKAP11, TIMD4, BTNL10, VNN2, and CLEC1A, representing candidate exploratory transcriptional markers consistent with hematopoietic recovery and immune surveillance. Temporally orchestrated pathway signatures include neuroimmune modulation (Days 7), hemostatic recovery (Day 14), and immunometabolic reconstitution (Day 21).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eOur results show that BIO 300 provides multiphasic radioprotection across acute, immune reconstitution, and sustained recovery phases through four distinct mechanisms. Longitudinal transcriptomic signatures identified in this study represent potential blood-based monitoring tools for therapeutic efficacy assessment toward the continued development of BIO 300. \u003c/p\u003e\n","keywords":["Gamma radiation","Rhesus monkeys","Transcriptome analysis"],"fieldOfScience":"Biological sciences","versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-24","lastModificationDate":"2026-06-24","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.vmcvdnd66","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.r2280gbrw"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.r2280gbrw/versions"},"stash:version":{"href":"/api/v2/versions/449256"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.r2280gbrw/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.r2280gbrw","id":172569,"storageSize":387341667,"relatedPublicationISSN":"1095-9203","title":"Explaining building damage from wildfires in California","authors":[{"firstName":"Somnath","lastName":"Bar","email":"somnatb@uci.edu","affiliation":"University of California, Irvine","affiliationROR":"https://ror.org/04gyf1771","affiliations":[{"name":"University of California, Irvine","ror_id":"https://ror.org/04gyf1771"}],"orcid":"0000-0003-1679-6130","order":0},{"firstName":"Shu","lastName":"Li","email":"shul15@uci.edu","affiliation":"University of California, Irvine","affiliationROR":"https://ror.org/04gyf1771","affiliations":[{"name":"University of California, Irvine","ror_id":"https://ror.org/04gyf1771"}],"orcid":"0000-0003-1071-3496","order":1},{"firstName":"Tirtha","lastName":"Banerjee","email":"tirthab@uci.edu","affiliation":"University of California, Irvine","affiliationROR":"https://ror.org/04gyf1771","affiliations":[{"name":"University of California, Irvine","ror_id":"https://ror.org/04gyf1771"}],"orcid":"0000-0002-5153-9474","order":2}],"abstract":"\u003cp\u003eWildfires continue to devastate California's wildland-urban interface (WUI), where buildings intersect flammable landscapes. We present a physically interpretable, data-driven framework to elucidate causal interactions, model, and predict wildfire-induced building damage across California. Using over 100,000 damage inspection records (2013-2024), we identify the key environmental, structural, and exposure factors driving wildfire impacts on the built environment. Using Random Forest classifiers, building damage is modeled from static environmental variables (topography, vegetation, human footprint), dynamic weather inputs, and a Composite Building Flammability Rating (CBFR). Three model configurations were tested: (1) a comprehensive model integrating all variables, (2) an enviro-weather hybrid excluding CBFR, and (3) an environmental exposure model excluding both weather and CBFR. Applying a strict 200m spatial dead-zone constraint to eliminate local autocorrelation, the comprehensive model achieved 88% (±0.4%) accuracy, dropping to 82.9% (±0.6%) without CBFR and to 74.5% (±0.5%) without both weather and CBFR. Spatial grid-based cross-validation demonstrated a diverse accuracy of 68.0% (±17%), 66.0% (±16%), and 62.0% (±13%), respectively. Building flammability, dew point temperature, and near-surface wind vector were the most important predictors of damage. Causal analysis revealed spatially heterogeneous Conditional Average Treatment Effects, suggesting mitigation strategies should target specific environmental and anthropogenic gradients. We developed a 100-meter-resolution Wildfire Building Damage Risk Index (WBDRI) to highlight high-risk damage zones. Findings emphasize that wildfire impacts in the WUI result from a confluence of structural vulnerability, atmospheric dryness, and fuel exposure, offering scalable tools for risk forecasting, defensible space planning, and climate-resilient infrastructure development.\u003c/p\u003e\n","funders":[{"organization":"NASA Earth Science","identifierType":"ror","identifier":"https://ror.org/045s99b94","awardNumber":"80NSSC22K1911","awardDescription":"Technology Office","awardTitle":""},{"organization":"Division of Atmospheric and Geospace Sciences","identifierType":"ror","identifier":"https://ror.org/037gd6g64","awardNumber":"2146520","awardDescription":"","awardTitle":"CAREER: CONIFER: Role of Canopy Turbulence in Wildland Fire Behavior"},{"organization":"Office of International Science and Engineering","identifierType":"ror","identifier":"https://ror.org/01k638r21","awardNumber":"2114740","awardDescription":"","awardTitle":"AccelNet-Design: iFireNet: An international network of networks for prediction and management of wildland fires"},{"organization":"Division of Computer and Network Systems","identifierType":"ror","identifier":"https://ror.org/02rdzmk74","awardNumber":"2209695","awardDescription":"","awardTitle":"Collaborative Research:CPS:Medium:SMAC-FIRE: Closed-Loop Sensing, Modeling and Communications for WildFIRE"},{"organization":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","identifierType":"ror","identifier":"https://ror.org/0471zv972","awardNumber":"2318718","awardDescription":"","awardTitle":"ECO-CBET: Collaborative Research: Effect of surface-fuel attributes and forest-thinning patterns on wildfire, carbon storage, and advancing forest restoration"},{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"2536815","awardDescription":"","awardTitle":""},{"organization":"Division of Mathematical Sciences","identifierType":"ror","identifier":"https://ror.org/051fftw81","awardNumber":"2335847","awardDescription":"","awardTitle":"Collaborative Research: Planning: FIRE-PLAN: Advancing Wildland Fire Analytics for Actuarial Applications and Beyond"},{"organization":"University of California Office of the President","identifierType":"ror","identifier":"https://ror.org/00dmfq477","awardNumber":"UCOP-LFR-20-653572"},{"organization":"United States Department of Agriculture","identifierType":"ror","identifier":"https://ror.org/01na82s61","awardNumber":"NIFA 2021-67022-35908","awardDescription":"","awardTitle":""},{"organization":"United States Department of Agriculture","identifierType":"ror","identifier":"https://ror.org/01na82s61","awardNumber":"USDA-20- CR-11242306-072","awardDescription":"","awardTitle":""}],"keywords":["Wildfires","Building damage","Wild Urban Interface","Wildfire risk","California","spatial modeling","DINs"],"fieldOfScience":"Earth and related environmental sciences","relatedWorks":[{"relationship":"dataset","identifierType":"DOI","identifier":"https://doi.org/10.7280/D1B98J"}],"versionNumber":7,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.r2280gbrw","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.pc866t24z"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.pc866t24z/versions"},"stash:version":{"href":"/api/v2/versions/449250"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.pc866t24z/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.pc866t24z","id":186622,"storageSize":12848,"relatedPublicationISSN":"0021-8901","title":"Density-driven bottlenecks constrain restoration of macroalgal forests","authors":[{"firstName":"Aziz","lastName":"Mulla","email":"zeezyuk@gmail.com","affiliation":"Université Côte d'Azur","affiliationROR":"https://ror.org/019tgvf94","affiliations":[{"name":"Université Côte d'Azur","ror_id":"https://ror.org/019tgvf94"}],"orcid":"0000-0003-3957-7125"},{"firstName":"Anne-Marin","lastName":"Nisumaa-Comeau","email":"Anne-Marin.NISUMAA-COMEAU@univ-cotedazur.fr","affiliation":"Université Côte d'Azur","affiliationROR":"https://ror.org/019tgvf94","affiliations":[{"name":"Université Côte d'Azur","ror_id":"https://ror.org/019tgvf94"}],"order":1},{"firstName":"Erwin","lastName":"Reymondet","email":"Erwin.REYMONDET@univ-cotedazur.fr","affiliation":"Université Côte d'Azur","affiliationROR":"https://ror.org/019tgvf94","affiliations":[{"name":"Université Côte d'Azur","ror_id":"https://ror.org/019tgvf94"},{"name":"Laboratoire d’Océanographie de Villefranche","ror_id":"https://ror.org/05r5y6641"}],"order":2},{"firstName":"Joran","lastName":"de Gang","email":"jorandegang@blueseeds.org","affiliation":"Université Côte d'Azur","affiliationROR":"https://ror.org/019tgvf94","affiliations":[{"name":"Université Côte d'Azur","ror_id":"https://ror.org/019tgvf94"}],"order":3},{"firstName":"Florian","lastName":"Boyer","email":"florian.boyer1@etu.univ-cotedazur.fr","affiliation":"Université Côte d'Azur","affiliationROR":"https://ror.org/019tgvf94","affiliations":[{"name":"Université Côte d'Azur","ror_id":"https://ror.org/019tgvf94"}],"order":4},{"firstName":"Luisa","lastName":"Mangialajo","email":"luisa.mangialajo@univ.cotedazur.fr","affiliation":"Université Côte d'Azur","affiliationROR":"https://ror.org/019tgvf94","affiliations":[{"name":"Université Côte d'Azur","ror_id":"https://ror.org/019tgvf94"}],"order":5}],"abstract":"\u003cp\u003eLarge-scale restoration of Mediterranean macroalgal forests is set to accelerate under new policy commitments, yet many initiatives rely on high initial settlement densities despite limited understanding of how density regulates early recovery. If early demographic bottlenecks constrain survival, growth or reproduction, restoration strategies based on maximising numbers may undermine success. We experimentally manipulated initial settlement density of the canopy-forming brown alga \u003cem\u003eCystoseira compressa\u003c/em\u003e across four densities (10, 100, 250, and 500 individuals) spanning natural to highly elevated levels. Recruits were monitored every 3 months for 1 year in the field to quantify survival, growth, reproductive development and the timing and intensity of density-dependent bottlenecks. Survival declined across all densities but showed strong density dependence. The lowest density maintained high survival throughout the experiment, whereas intermediate and high densities experienced rapid early mortality. At the highest densities, survival collapsed within the first 2–3 months, indicating acute early bottlenecks rather than gradual mortality. Mean final densities at the end of the experiment ranged between 0.19 ind. cm \u003csup\u003e-2\u003c/sup\u003e and 0.44 ind. cm \u003csup\u003e-2\u003c/sup\u003e. Density strongly constrained individual growth. The lowest density rapidly progressed into larger size classes and were the only density where individuals reached reproductive maturity. Higher densities suppressed growth of surviving individuals, resulting in persistent confinement to small size classes and preventing reproductive development despite continued survival. Quantification of survival derivatives revealed that both the timing and intensity of bottlenecks scaled predictably with initial density. Bottlenecks were absent at lower densities, prolonged at intermediate densities and short but severe at the highest densities, demonstrating that early recovery trajectories were density-driven rather than time-dependent. This single-species and single-site experiment provides evidence that high-density restoration strategies accelerate mortality, suppress growth and delay reproduction, whereas low-density approaches promote faster demographic progression and resilience. Under the conditions tested here, focusing on growth and reproductive output, rather than maximising initial numbers, reduces the need for large propagule supply and extensive receptacle production, directly supporting the conservation of donor populations while maintaining restoration effectiveness.\u003c/p\u003e\n","funders":[{"organization":"British Ecological Society","identifierType":"ror","identifier":"https://ror.org/00n20jq68","awardNumber":"SR24\\1726","awardDescription":"","awardTitle":"","order":1},{"organization":"Agence Nationale de la Recherche","identifierType":"ror","identifier":"https://ror.org/00rbzpz17","awardNumber":"ANR-15-IDEX-01","awardDescription":"","awardTitle":"","order":0},{"organization":"BiodivERsA","identifierType":"ror","identifier":"https://ror.org/05cvqmv08","awardNumber":"Biodiversa+2021-134","awardDescription":"","awardTitle":"","order":2}],"keywords":["Ecology","Restoration ecology","Density"],"fieldOfScience":"Biological sciences","methods":"\u003ch5\u003e\n\u003ca href=\"#collection-site-and-culture\" aria-hidden=\"true\" class=\"anchor\" id=\"collection-site-and-culture\"\u003e\u003c/a\u003eCollection site and culture\u003c/h5\u003e\n\u003cp\u003eSaint-Jean-Cap-Ferrat is a rocky peninsula on the south-eastern French Mediterranean coast, located approximately 6 km east of Nice and 12 km west of Monaco (Figure 1 in associated manuscript). The collection site, Pointe du Colombier, is characterised by shallow subtidal rocky habitats (0.1–1 m depth) typical of Mediterranean \u003cem\u003eCystoseira\u003c/em\u003e forests, dominated by \u003cem\u003eCystoseira compressa\u003c/em\u003e, \u003cem\u003eEricaria crinita\u003c/em\u003e, \u003cem\u003eC. compressa\u003c/em\u003e \u003cem\u003ef. rosetta\u003c/em\u003e, and \u003cem\u003eE. amentacea\u003c/em\u003e.\u003c/p\u003e\n\u003cp\u003eApproximately 200 g of fertile branches of \u003cem\u003eC.compressa\u003c/em\u003e were collected from the donor population at Pointe du Colombier on 27 May 2024 (Figure 1a). As an ecosystem engineer, \u003cem\u003eC. compressa\u003c/em\u003e is an ideal model species for restoration experiments, being relatively tolerant, easy to work with it and has been shown to increase the chance of restoration success (Susini et al., 2007). To avoid inadvertently detaching individuals, the forest was approached by swimming (not walking) and branches were carefully removed using scissors. Branches were then transported to the laboratory at Université Côte d’Azur (Nice) in sealed plastic bags without seawater, placed in a cooler to maintain dark and cold conditions during transport. Upon arrival, fertile material was stored at ~4 °C for 15 h to promote zygote liberation following established protocols (see Cebrian et al., 2021). To assess natural settlement densities of \u003cem\u003eC. compressa\u003c/em\u003e at Pointe du Colombier, small experimental units (n = 10; area = 7.07 cm\u003csup\u003e2\u003c/sup\u003e; hereafter EU) were deployed beneath existing fertile canopies. Substrate was cleared using a wire brush and units were affixed to the rock using marine epoxy (IVEGOR Multi Putty) and left for 1 month.\u003c/p\u003e\n\u003cp\u003eExperimental aquaria were set up in a closed-circuit system supplied with filtered natural seawater (200 µm mesh) and continuously aerated using air pumps. Lighting conditions reflected the natural seasonal photoperiod, with large EUs (area = 36.5 cm\u003csup\u003e2\u003c/sup\u003e) exposed to ambient natural daylight. Temperature conditions were maintained between 18–20 °C. Fertile branches were evenly distributed across 16 tanks (internal dimensions: 18 × 24 × 12 cm; volume: 3.5 L), using a submerged mesh hammock positioned above two EUs per tank (12.5 g per tank; Figure 1b). Gamete release commenced on 28 May 2024 and continued until 31 May 2024. Following release, mesh hammocks were removed, branches discarded and EUs were placed into new tanks of filtered natural seawater. EUs used in the ex-situ field experiment (\u003cem\u003en\u003c/em\u003e = 20) were assigned to one of four predefined settlement densities; low density: 10 ind EU \u003csup\u003e-1\u003c/sup\u003e (hereafter LD), semi-intermediate density: 100 ind EU \u003csup\u003e-1\u003c/sup\u003e (hereafter SID), intermediate density 250 ind EU \u003csup\u003e-1\u003c/sup\u003e (hereafter ID) or high density: 500 ind EU \u003csup\u003e-1\u003c/sup\u003e (hereafter HD)) on 3 June 2024. Densities were manipulated under a stereomicroscope using fine forceps to selectively remove excess individuals until the target densities were achieved, while maintaining an even spatial distribution of remaining individuals across each unit to minimise clumping. Each unit was tagged and given a unique ID number. Following settlement, experimental units were maintained under stable conditions for three weeks, with seawater replaced every 3–4 days.\u003c/p\u003e\n\u003ch5\u003e\n\u003ca href=\"#study-site-and-monitoring\" aria-hidden=\"true\" class=\"anchor\" id=\"study-site-and-monitoring\"\u003e\u003c/a\u003eStudy site and monitoring\u003c/h5\u003e\n\u003cp\u003eThe Pointe du Colombier site and surrounding rockpools experience regular and intense grazing pressure, primarily from \u003cem\u003eSarpa salpa\u003c/em\u003e (Gianni et al., 2018). In addition, Saint-Jean-Cap-Ferrat is considered a tourist hotspot and shallow rocky habitats are subject to frequent physical disturbance through trampling. To minimise these external pressures an alternative monitoring site was selected.\u003c/p\u003e\n\u003cp\u003eCap d’Antibes is a rocky peninsula on the south-eastern French Mediterranean coast, located approximately 20 km southwest of Nice and 10 km east of Cannes (Figure 1c). The selected rockpool is semi-enclosed, while still permitting regular water exchange but protected from the threat grazing as to isolate and test the impact of density. The rockpool measures 7.71 m × 6.04 m and is relatively flat, with a water depth ranging between 0.2 and 0.5 m. The benthic community within the pool is dominated by \u003cem\u003eE. crinita\u003c/em\u003e and \u003cem\u003eC. foeniculacea\u003c/em\u003e, with \u003cem\u003eC. compressa\u003c/em\u003e and \u003cem\u003eE. amentacea\u003c/em\u003e present in the surrounding area.\u003c/p\u003e\n\u003cp\u003eEUs (\u003cem\u003en\u003c/em\u003e = 20) were deployed in the field using the same attachment method described above and were placed randomly within the rockpool on 24 June 2024. Monitoring was conducted over a 13-month period, from June 2024 to July 2025. To facilitate repeated monitoring, the rockpool and positions of each unit were mapped prior to the start of observations. Monitoring was conducted at three-month intervals to quantify the density, survival and growth of \u003cem\u003eC. compressa\u003c/em\u003e. Survival was assessed as the number of individuals present on each EU, while growth was quantified as the length (cm) of the longest axis of five randomly selected individuals per EU. Finally, reproductive activity was assessed by recording the presence and extent of receptacle development following the categorical protocol of Rindi et al. (2023). Individuals were classified as non-fertile (NF) or assigned to one of four fertility classes based on the proportion of branches bearing receptacles: \u0026lt; 25 % (F1), 25–50 % (F2), 50–75 % (F3), and \u0026gt; 75 % (F4).\u003c/p\u003e\n\u003ch5\u003e\n\u003ca href=\"#data-analysis\" aria-hidden=\"true\" class=\"anchor\" id=\"data-analysis\"\u003e\u003c/a\u003eData analysis\u003c/h5\u003e\n\u003cp\u003eSurvival was analysed using a binomial generalized linear mixed-effects model (GLMM) to quantify the influence of initial establishment density and time on post-settlement survival. Survival at each sampling time was expressed as the number of the individuals alive relative to the number initially established per EU. Initial densities (10, 100, 250, and 500 ind EU \u003csup\u003e-1\u003c/sup\u003e), time (sampling month) and their interaction were included as fixed effects to test whether survival trajectories differed among densities over time. EU ID was included as a random intercept to account for repeated measurements. Time was treated as a categorical variable to avoid imposing assumptions of linear decline. The initial sampling month (0) was excluded from the analysis as survival was fixed at 100 % by experimental design. Models were assessed using Type III Wald chi-square tests and where significant effects were detected, survival probabilities and 95 % confidence intervals were estimated. Pairwise comparisons among densities were conducted within each time point using odds ratio, with p values adjusted for multiple comparisons using the Holm method.\u003c/p\u003e\n\u003cp\u003eChanges in size among densities was assessed using non-parametric statistics. At each sampling time (3, 6, 9, 12 months), individual sizes (cm) were compared among densities (10, 100, 250, and 500 ind EU \u003csup\u003e-1\u003c/sup\u003e) using Kruskal-Wallis tests as size data violated assumptions of normality and homoscedasticity. When tests were significant, pairwise post-hoc comparisons between densities were conducted using Dunn’s tests with Holm correction for multiple comparisons. Growth rates (cm month \u003csup\u003e-1\u003c/sup\u003e) were calculated for each density between successive sampling times and analysed using a linear mixed-effects model with density, interval midpoint and their interaction as fixed effects and EU identity as a random intercept. Fixed effects were evaluated using Type III Wald chi-square tests and differences in density were assessed using Holm-adjusted pairwise comparisons of model-estimated marginal means.\u003c/p\u003e\n\u003cp\u003eTo quantify bottleneck timing and intensity, we analysed changes in survival over time using the numerical derivative of smoothed survival trajectories. Mean survival proportions were calculated for each density (10, 100, 250, and 500 ind EU \u003csup\u003e-1\u003c/sup\u003e) at each sampling time (3, 6, 9, 12 months). Generalised additive models (GAMs) were then fitted separately for each density, with time included as a smooth term, allowing for non-linear survival dynamics without imposing parametric assumptions on the shape of decline. The first derivative of survival with respect to time (dS/st) was estimated numerically for each density. This derivative represents the instantaneous rate of change in survival per month, with values close to zero indicating little mortality and increasingly negative values indicating faster rates of mortality. Bottlenecks were identified using a rule-based, two-step criteria. First, a minimum mortality threshold of −0.05 per month (equivalent to ≥ 5 % survival loss per month) was imposed to ensure that only ecologically meaningful mortality were considered. Bottlenecks were only classified when the most negative rate of survival exceeded this threshold. Second, for densities meeting this criterium, bottleneck window was defined as the period during which dS/dt remained below 50 % of the most negative slope. Bottleneck start and end times were identified as the upper and lower bounds of this period. This approach allowed for bottlenecks to be identified objectively and consistently across densities ensuring they reflected sustained periods of intense, density-dependent mortality rather than brief stochastic fluctuations or background decline.\u003c/p\u003e\n\u003cp\u003eAll statistical analyses were conducted in R (R Core Team, 2021). Survival proportions and growth rates were analysed using generalised and linear mixed-effects models fitted with package lme4. Estimated marginal means were obtained using the package emmeans. Differences in size distributions were evaluated using Kruskal–Wallis tests followed by Dunn post hoc tests with Holm correction. Density-dependent survival bottlenecks were quantified by fitting generalised additive models (GAMs) to smoothed survival trajectories (mgcv).\u003c/p\u003e\n","relatedWorks":[{"relationship":"software","identifierType":"DOI","identifier":"https://doi.org/10.5281/zenodo.20761763"}],"versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.pc866t24z","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.2bvq83c4f"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.2bvq83c4f/versions"},"stash:version":{"href":"/api/v2/versions/449264"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.2bvq83c4f/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.2bvq83c4f","id":173695,"storageSize":432658749,"relatedPublicationISSN":"2050-084X","title":"Data from: \u003cem\u003eSLC4A1\u003c/em\u003e mutations that cause distal renal tubular acidosis alter cytoplasmic pH and cellular autophagy","authors":[{"firstName":"Emmanuelle","lastName":"Cordat","email":"cordat@ualberta.ca","affiliation":"University of Alberta","affiliationROR":"https://ror.org/0160cpw27","affiliations":[{"name":"University of Alberta","ror_id":"https://ror.org/0160cpw27"}],"orcid":"0000-0001-9875-5804"},{"firstName":"Grace","lastName":"Essuman","email":"","affiliation":"University of Alberta","affiliationROR":"https://ror.org/0160cpw27","affiliations":[{"name":"University of Alberta","ror_id":"https://ror.org/0160cpw27"}]},{"firstName":"Midhat","lastName":"Rizvi","email":"","affiliation":"University of Alberta","affiliationROR":"https://ror.org/0160cpw27","affiliations":[{"name":"University of Alberta","ror_id":"https://ror.org/0160cpw27"}]},{"firstName":"Ensaf","lastName":"Almomani","email":"","affiliation":"Al-Balqa Applied University","affiliationROR":"https://ror.org/00qedmt22","affiliations":[{"name":"Al-Balqa Applied University","ror_id":"https://ror.org/00qedmt22"}]},{"firstName":"Shahid AK M","lastName":"Ullah","email":"","affiliation":"University of Alberta","affiliationROR":"https://ror.org/0160cpw27","affiliations":[{"name":"University of Alberta","ror_id":"https://ror.org/0160cpw27"}]},{"firstName":"Sarder MA","lastName":"Hasib","email":"","affiliation":"Saarland University","affiliationROR":"https://ror.org/01jdpyv68","affiliations":[{"name":"Saarland University","ror_id":"https://ror.org/01jdpyv68"}]},{"firstName":"Forough","lastName":"Chelangarimiyandoab","email":"","affiliation":"University of Alberta","affiliationROR":"https://ror.org/0160cpw27","affiliations":[{"name":"University of Alberta","ror_id":"https://ror.org/0160cpw27"}]},{"firstName":"Priyanka","lastName":"Mungara","email":"","affiliation":"University of Alberta","affiliationROR":"https://ror.org/0160cpw27","affiliations":[{"name":"University of Alberta","ror_id":"https://ror.org/0160cpw27"}]},{"firstName":"Manfred J","lastName":"Schmitt","email":"","affiliation":"Saarland University","affiliationROR":"https://ror.org/01jdpyv68","affiliations":[{"name":"Saarland University","ror_id":"https://ror.org/01jdpyv68"}]},{"firstName":"Marguerite","lastName":"Hureaux","email":"","affiliation":"Hôpital Européen Georges-Pompidou","affiliationROR":"https://ror.org/016vx5156","affiliations":[{"name":"Hôpital Européen Georges-Pompidou","ror_id":"https://ror.org/016vx5156"}]},{"firstName":"Rosa","lastName":"Vargas-Poussou","email":"","affiliation":"Hôpital Européen Georges-Pompidou","affiliationROR":"https://ror.org/016vx5156","affiliations":[{"name":"Hôpital Européen Georges-Pompidou","ror_id":"https://ror.org/016vx5156"}]},{"firstName":"Nicolas","lastName":"Touret","email":"","affiliation":"University of Alberta","affiliationROR":"https://ror.org/0160cpw27","affiliations":[{"name":"University of Alberta","ror_id":"https://ror.org/0160cpw27"}]}],"abstract":"\u003cjats:p\u003eDistal renal tubular acidosis (dRTA) is a disorder characterized by the inability of the collecting duct system to secrete acids during metabolic acidosis. The pathophysiology of dominant or recessive SLC4A1 variant related dRTA has been linked with the mis trafficking defect of mutant kAE1 protein. However, in vivo studies in kAE1 R607H dRTA mice and humans have revealed a complex pathophysiology implicating a loss of kAE1-expressing intercalated cells and intracellular relocation of the H+-ATPase in the remaining type-A intercalated cells. These cells also displayed accumulation of ubiquitin and p62 autophagy markers. The highly active transport properties of collecting duct cells require the maintenance of cellular energy and homeostasis, a process dependent on intracellular pH. Therefore, we hypothesized that the expression of dRTA variants affect intracellular pH and autophagy pathways. In this study, we report the characterization of newly identified dRTA variants and provide evidence of abnormal autophagy and degradative pathways in mouse inner medullary collecting duct cells and kidneys from mice expressing kAE1 R607H dRTA mutant protein. We show that reduced transport activity of the kAE1 variants correlated with increased cytosolic pH, reduced ATP synthesis, attenuated downstream autophagic pathways pertaining to the fusion of autophagosomes and lysosomes and/or lysosomal degradative activity. Our study elucidated a close relationship between the expression of defective kAE1 proteins, reduced mitochondrial activity and decreased autophagy and protein degradative flux.\u003c/jats:p\u003e","funders":[{"organization":"Canadian Institutes of Health Research","identifierType":"ror","identifier":"https://ror.org/01gavpb45","awardNumber":"PJT#168871","awardDescription":"","awardTitle":""},{"organization":"Natural Sciences and Engineering Research Council of Canada","identifierType":"ror","identifier":"https://ror.org/01h531d29","awardNumber":"RGPIN-2017-06432","awardDescription":"","awardTitle":""},{"organization":"Kidney Foundation of Canada","identifierType":"ror","identifier":"https://ror.org/019a0gk53","awardNumber":"2020KHRG-666615","awardDescription":"","awardTitle":""},{"organization":"Deutsche Forschungsgemeinschaft","identifierType":"ror","identifier":"https://ror.org/018mejw64","awardNumber":"IRTG1830","awardDescription":"","awardTitle":""},{"organization":"German Academic Exchange Service","identifierType":"ror","identifier":"https://ror.org/039djdh30","awardNumber":"PhD Scholarship","awardDescription":"","awardTitle":""},{"organization":"Canadian Institutes of Health Research","identifierType":"ror","identifier":"https://ror.org/01gavpb45","awardNumber":"PS165816","awardDescription":"","awardTitle":""},{"organization":"Natural Sciences and Engineering Research Council of Canada","identifierType":"ror","identifier":"https://ror.org/01h531d29","awardNumber":"RGPIN-2018-05783","awardDescription":"","awardTitle":""},{"organization":"University of Alberta","identifierType":"ror","identifier":"https://ror.org/0160cpw27","awardNumber":"Multiple Scholarships","awardDescription":"","awardTitle":""},{"organization":"Canadian Institutes of Health Research","identifierType":"ror","identifier":"https://ror.org/01gavpb45","awardNumber":"Canada Graduate Scholarship-Master's","awardDescription":"","awardTitle":""},{"organization":"Natural Sciences and Engineering Research Council of Canada","identifierType":"ror","identifier":"https://ror.org/01h531d29","awardNumber":"CREATE Graduate Studentship","awardDescription":"","awardTitle":""}],"keywords":["Kidneys","Acidosis","Cell biology"],"fieldOfScience":"Medical and health sciences","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.7554/elife.108253.2"}],"versionNumber":10,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.2bvq83c4f","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.gb5mkkx5c"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.gb5mkkx5c/versions"},"stash:version":{"href":"/api/v2/versions/449260"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.gb5mkkx5c/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.gb5mkkx5c","id":186593,"storageSize":78745540,"relatedPublicationISSN":"0022-3670","title":"Samoan Passage abyssal monitoring array 2012-2014","authors":[{"firstName":"Gunnar","lastName":"Voet","email":"gvoet@ucsd.edu","affiliation":"Scripps Institution of Oceanography","affiliationROR":"https://ror.org/04v7hvq31","affiliations":[{"name":"University of California San Diego","ror_id":"https://ror.org/0168r3w48"},{"name":"Scripps Institution of Oceanography","ror_id":"https://ror.org/04v7hvq31"}],"orcid":"0000-0003-1975-186X"},{"firstName":"Matthew","lastName":"Alford","email":"","affiliation":"Scripps Institution of Oceanography","affiliationROR":"https://ror.org/04v7hvq31","affiliations":[{"name":"University of California San Diego","ror_id":"https://ror.org/0168r3w48"},{"name":"Scripps Institution of Oceanography","ror_id":"https://ror.org/04v7hvq31"}],"order":1},{"firstName":"James","lastName":"Girton","email":"","affiliation":"University of Washington","affiliationROR":"https://ror.org/00cvxb145","affiliations":[{"name":"University of Washington","ror_id":"https://ror.org/00cvxb145"},{"name":"University of Washington Applied Physics Laboratory","ror_id":"https://ror.org/03d17d270"}],"order":2},{"firstName":"Glenn","lastName":"Carter","email":"","affiliation":"University of Hawaii at Hilo","affiliationROR":"https://ror.org/02mp2av58","affiliations":[{"name":"University of Hawaii at Hilo","ror_id":"https://ror.org/02mp2av58"}],"order":3}],"abstract":"\u003cp\u003eThis dataset comprises moored observations of the abyssal flow through the Samoan Passage, the major deep-water gateway into the North Pacific. Four moorings (M1–M4) were deployed in a cross-passage array at the entrance to the passage from July 2012 to February 2014 (~16 months), spanning the dense bottom layer below roughly 3700 m. Velocity (eastward and northward components, speed, and direction) was recorded by Aanderaa RCM8 rotor current meters and acoustic Doppler volume samplers, and temperature by the current meters together with Sea-Bird SBE39 and SBE37 recorders, at nominal depths between 3700 m and 5270 m. Velocities are given in m s⁻¹, temperatures in °C, and times in UTC.\u003c/p\u003e\n\u003cp\u003eThe data are organized into processed per-mooring time series (one MATLAB file per mooring) and a combined hourly array product that includes all instrument records plus the bathymetry of the mooring section. A derived abyssal volume transport time series, computed by integrating the objectively mapped velocity field below 4000 m, is provided in both MATLAB and netCDF formats together with the corresponding 1990s WOCE estimate for comparison; the time-mean transport over the well-constrained period is approximately 5.4 Sv (1 Sv = 10⁶ m³ s⁻¹). Raw instrument records, field clock-offset and recovery logs, and as-deployed and as-recovered mooring diagrams are also included for provenance.\u003c/p\u003e\n\u003cp\u003eThese data support studies of abyssal circulation, deep-water transport and its variability, the meridional overturning circulation, ocean mixing, and the multidecadal warming and weakening of the Pacific bottom limb, and are suitable for validating numerical models. The dataset contains only physical oceanographic measurements, with no human-subject, sensitive, or personally identifiable information, and is released into the public domain under a Creative Commons Zero (CC0 1.0) dedication, permitting unrestricted reuse.\u003c/p\u003e\n","funders":[{"organization":"Division of Ocean Sciences","identifierType":"ror","identifier":"https://ror.org/05wqqhv83","awardNumber":"1029268","awardDescription":"","awardTitle":"Collaborative Research:  Transport, Internal Waves and Mixing in the Samoan Passage","order":0}],"keywords":["Physical oceanography","Climate record","Pacific Ocean","Ocean circulation"],"fieldOfScience":"Earth and related environmental sciences","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1175/JPO-D-16-0063.1"}],"versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.gb5mkkx5c","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.w3r22817c"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.w3r22817c/versions"},"stash:version":{"href":"/api/v2/versions/449252"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.w3r22817c/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.w3r22817c","id":187087,"storageSize":81025,"relatedPublicationISSN":"0908-8857","title":"Data from: Hatching failure in an aerial insectivore, the tree swallow (\u003cem\u003eTachycineta bicolor\u003c/em\u003e), is driven by embryonic mortality, not infertility","authors":[{"firstName":"Hannah","lastName":"Tench","email":"hannah.tench@alumni.unbc.ca","affiliation":"University of Northern British Columbia","affiliationROR":"https://ror.org/025wzwv46","affiliations":[{"name":"University of Northern British Columbia","ror_id":"https://ror.org/025wzwv46"}],"orcid":"0009-0003-3951-5140"},{"firstName":"Nicola","lastName":"Hemmings","email":"n.hemmings@sheffield.ac.uk","affiliation":"University of Sheffield","affiliationROR":"https://ror.org/05krs5044","affiliations":[{"name":"University of Sheffield","ror_id":"https://ror.org/05krs5044"}],"orcid":"0000-0003-2418-3625","order":1},{"firstName":"Russell D.","lastName":"Dawson","email":"Russ.Dawson@unbc.ca","affiliation":"University of Northern British Columbia","affiliationROR":"https://ror.org/025wzwv46","affiliations":[{"name":"University of Northern British Columbia","ror_id":"https://ror.org/025wzwv46"}],"orcid":"0000-0002-7493-4645","order":2}],"abstract":"\u003cp\u003eEgg development is a crucial stage in the life cycle of birds, and across wild species, up to 17% of eggs fail to hatch under normal conditions. Hatching failure is due to either infertility or embryonic mortality; however, methods to distinguish between these two causes have been underused, partly due to an assumption that eggs had to be refrigerated and tested relatively quickly. In 2022 and 2023, we monitored 1090 eggs laid by tree swallows (\u003cem\u003eTachycineta bicolor\u003c/em\u003e) from 191 nests at three study sites in British Columbia, Canada. Using fluorescence microscopy to identify embryonic and sperm nuclei, we conservatively estimated that 98.3% – 100% of eggs were fertile, and most cases of hatching failure were therefore due to embryonic mortality, not infertility. Embryonic mortality was most likely to occur during early incubation, before development is usually macroscopically visible. We also used fluorescence microscopy to examine 114 eggs laid by tree swallows kept in long-term frozen storage and found that not only could fertility be assessed, but the fertility rate of these eggs was similarly close to 100%. To our knowledge, this study is the first to quantify fertility using embryonic nuclei in tree swallows, and provides the basis for further investigation into factors contributing to hatching failure in this species. Our success using frozen eggs for fertility testing is especially relevant for conservation groups and captive breeding facilities that may already have unhatched eggs stored in freezers, or are limited by capacity or funding and need to place eggs in long-term storage until resources are available for testing.\u003c/p\u003e\n","funders":[{"organization":"Natural Sciences and Engineering Research Council of Canada","identifierType":"ror","identifier":"https://ror.org/01h531d29","awardNumber":"","awardDescription":"","awardTitle":"","order":0},{"organization":"Canada Foundation for Innovation","identifierType":"ror","identifier":"https://ror.org/000az4664","awardNumber":"","awardDescription":"","awardTitle":"","order":1},{"organization":"Government of British Columbia","identifierType":"ror","identifier":"https://ror.org/011e3e176","awardNumber":"","awardDescription":"British Columbia Knowledge Development Fund","awardTitle":"","order":2},{"organization":"University of Northern British Columbia","identifierType":"ror","identifier":"https://ror.org/025wzwv46","awardNumber":"","awardDescription":"","awardTitle":"","order":3}],"keywords":["Aerial insectivores","fertility","Hatching success","tree swallows","breeding biology","Fluorescence microscopy"],"fieldOfScience":"Natural sciences","relatedWorks":[{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.22541/au.177128834.49461026/v1"}],"versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.w3r22817c","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.pvmcvdp1h"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.pvmcvdp1h/versions"},"stash:version":{"href":"/api/v2/versions/449066"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.pvmcvdp1h/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.pvmcvdp1h","id":184899,"storageSize":115283,"relatedPublicationISSN":"0022-1899","title":"Anopheles mosquitoes exposed to long-acting antimalarials via drug-spiked supplemented bloodmeal absorb drug but do not suffer fitness costs","authors":[{"firstName":"Morgan M.","lastName":"Goheen","email":"morgan.goheen@yale.edu","affiliation":"Yale University","affiliationROR":"https://ror.org/03v76x132","affiliations":[{"name":"Yale University","ror_id":"https://ror.org/03v76x132"}],"orcid":"0000-0003-2297-3295"},{"firstName":"Alessandra","lastName":"Orfanó","email":"","affiliation":"Yale University","affiliationROR":"https://ror.org/03v76x132","affiliations":[{"name":"Yale University","ror_id":"https://ror.org/03v76x132"}],"order":1},{"firstName":"S. Rodrigue","lastName":"Dah","email":"","affiliation":"Institut de Recherche en Sciences de la Santé","affiliationROR":"https://ror.org/05m88q091","affiliations":[{"name":"Institut de Recherche en Sciences de la Santé","ror_id":"https://ror.org/05m88q091"},{"name":"Nazi Boni University","ror_id":"https://ror.org/04cq90n15"}],"order":2},{"firstName":"Brian D.","lastName":"Foy","email":"","affiliation":"Colorado State University","affiliationROR":"https://ror.org/03k1gpj17","affiliations":[{"name":"Colorado State University","ror_id":"https://ror.org/03k1gpj17"}],"order":3},{"firstName":"Doug E.","lastName":"Brackney","email":"","affiliation":"Connecticut Agricultural Experiment Station","affiliationROR":"https://ror.org/02t7c5797","affiliations":[{"name":"Connecticut Agricultural Experiment Station","ror_id":"https://ror.org/02t7c5797"}],"order":4},{"firstName":"Fangyong","lastName":"Li","email":"","affiliation":"Yale University","affiliationROR":"https://ror.org/03v76x132","affiliations":[{"name":"Yale University","ror_id":"https://ror.org/03v76x132"}],"order":5},{"firstName":"Jean-Bosco","lastName":"Ouédraogo","email":"","affiliation":"Institut de Recherche en Sciences de la Santé","affiliationROR":"https://ror.org/05m88q091","affiliations":[{"name":"Institut de Recherche en Sciences de la Santé","ror_id":"https://ror.org/05m88q091"}],"order":6},{"firstName":"Dari F.","lastName":"Dah","email":"","affiliation":"Institut de Recherche en Sciences de la Santé","affiliationROR":"https://ror.org/05m88q091","affiliations":[{"name":"Institut de Recherche en Sciences de la Santé","ror_id":"https://ror.org/05m88q091"}],"order":7},{"firstName":"Roch K.","lastName":"Dabiré","email":"","affiliation":"Institut de Recherche en Sciences de la Santé","affiliationROR":"https://ror.org/05m88q091","affiliations":[{"name":"Institut de Recherche en Sciences de la Santé","ror_id":"https://ror.org/05m88q091"}],"order":8},{"firstName":"A. Fabrice","lastName":"Somé","email":"","affiliation":"Institut de Recherche en Sciences de la Santé","affiliationROR":"https://ror.org/05m88q091","affiliations":[{"name":"Institut de Recherche en Sciences de la Santé","ror_id":"https://ror.org/05m88q091"}],"order":9},{"firstName":"Amy K.","lastName":"Bei","email":"","affiliation":"Yale University","affiliationROR":"https://ror.org/03v76x132","affiliations":[{"name":"Yale University","ror_id":"https://ror.org/03v76x132"}],"order":10},{"firstName":"Sunil","lastName":"Parikh","email":"","affiliation":"Yale University","affiliationROR":"https://ror.org/03v76x132","affiliations":[{"name":"Yale University","ror_id":"https://ror.org/03v76x132"}],"order":11}],"abstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e The World Health Organization's recommendations for antimalarial chemoprevention and mass treatment use in endemic areas have greatly expanded, allowing more flexibility in demographic groups and regions targeted. An overlooked aspect of expanding human population-level drug exposure is the downstream impact of drug on the vector. \u003cem\u003eAnopheles\u003c/em\u003e mosquitoes re-feed often with ≥4 bloodmeals during their lifespan. This provides repeated opportunities for mosquitoes to ingest drug via bloodmeals taken from people with antimalarials in the bloodstream and raises questions as to drug impact on mosquitoes.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods:\u003c/strong\u003e We supplemented bloodmeals with physiologic levels of long-acting antimalarials to assess drug exposure impact on \u003cem\u003eAnopheles\u003c/em\u003e mosquito fitness and determine drug absorption extent.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults:\u003c/strong\u003e We did not observe any significant differences in mosquito feeding, behavior, fecundity, or viability after amodiaquine, desethylamodiaquine, piperaquine, and sulfadoxine-pyrimethamine ingestion in lab-reared \u003cem\u003eAn. gambiae\u003c/em\u003e or field-derived \u003cem\u003eAn. coluzzii\u003c/em\u003e mosquitoes. Interrogating drug distribution within mosquitoes utilizing LC-MS/MS, desethylamodiaquine, amodiaquine’s longer-acting active metabolite, was fed at half and twice C\u003csub\u003emax\u003c/sub\u003e concentrations, with drug then dose-dependently detected in pooled whole mosquitoes, midguts, and hemolymph. This was significant for whole mosquitoes harvested at 24hrs and 120hrs, and midguts harvested at 24hrs. Between 24 to 120hrs, drug decreased in midguts but increased in hemolymph.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions:\u003c/strong\u003e We show sustained biochemical evidence of antimalarial absorption into \u003cem\u003eAnopheles\u003c/em\u003e hemolymph following bloodmeal ingestion without fitness costs. These studies provide a foundation to next assess vector-stage antimalarial drug exposure impact on parasite development in infected mosquitoes, which could in turn have implications on transmission dynamics and drug resistance spread.  \u003c/p\u003e\n","funders":[{"organization":"Ambrose Monell Foundation","identifierType":"ror","identifier":"https://ror.org/022nw7x84","awardNumber":"","awardDescription":"","awardTitle":"Faculy Seed Grant","order":0},{"organization":"American Society of Tropical Medicine and Hygiene","identifierType":"ror","identifier":"https://ror.org/018eag955","awardNumber":"","awardDescription":"","awardTitle":"Centennial Travel Award in Basic Science Tropical Disease Research ","order":1},{"organization":"National Institute of Allergy and Infectious Diseases","identifierType":"ror","identifier":"https://ror.org/043z4tv69","awardNumber":"5T32AI007517-24","awardDescription":"","awardTitle":"Yale Infectious Diseases NIH T32","order":2},{"organization":"National Center for Advancing Translational Sciences","identifierType":"ror","identifier":"https://ror.org/04pw6fb54","awardNumber":"UL1 TR001863","awardDescription":"","awardTitle":"Yale Physician Scientist Development Award ","order":3},{"organization":"National Institute of Allergy and Infectious Diseases","identifierType":"ror","identifier":"https://ror.org/043z4tv69","awardNumber":"1K23AI193079-01","awardURI":"https://reporter.nih.gov/project-details/11215344","awardDescription":"","awardTitle":"Impact of Antimalarials on Parasite Selection Through the Mosquito Vector","order":4}],"keywords":["Mosquitoes","Malaria","Anopheles gambiae","Plasmodium","Antimalarials","Mass spectrometry","Pharmacokinetics","hemolymph"],"fieldOfScience":"Medical and health sciences","relatedWorks":[{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.1101/2025.11.13.688204"},{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1093/infdis/jiag300"}],"versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.pvmcvdp1h","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.cjsxksnnt"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.cjsxksnnt/versions"},"stash:version":{"href":"/api/v2/versions/449235"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.cjsxksnnt/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.cjsxksnnt","id":186951,"storageSize":127415,"relatedPublicationISSN":"2688-8319","title":"Data from: Trajectories and drivers of compositional and functional variation in sagebrush steppe restoration","authors":[{"firstName":"Sienna","lastName":"Wessel","email":"swessel1@uwyo.edu","affiliation":"University of Wyoming","affiliationROR":"https://ror.org/01485tq96","affiliations":[{"name":"University of Wyoming","ror_id":"https://ror.org/01485tq96"}],"orcid":"0000-0002-9660-5906"},{"firstName":"Laura","lastName":"Jones","email":"","affiliation":"National Park Service","affiliationROR":"https://ror.org/044zqqy65","affiliations":[{"name":"National Park Service","ror_id":"https://ror.org/044zqqy65"}],"order":1},{"firstName":"Erik","lastName":"Kramer","email":"","affiliation":"National Park Service","affiliationROR":"https://ror.org/044zqqy65","affiliations":[{"name":"National Park Service","ror_id":"https://ror.org/044zqqy65"}],"order":2},{"firstName":"Lauren","lastName":"Shoemaker","email":"","affiliation":"University of Wyoming","affiliationROR":"https://ror.org/01485tq96","affiliations":[{"name":"University of Wyoming","ror_id":"https://ror.org/01485tq96"}],"order":3},{"firstName":"Daniel","lastName":"Laughlin","email":"","affiliation":"University of Wyoming","affiliationROR":"https://ror.org/01485tq96","affiliations":[{"name":"University of Wyoming","ror_id":"https://ror.org/01485tq96"}],"order":4}],"abstract":"\u003cp\u003eRestoration outcomes are often variable and can fall short of targets due to poorly understood factors, especially in arid ecosystems. Identifying the drivers of variation during community assembly is critical for achieving restoration outcomes. Community trajectories and levels of recovery could be contingent on conditions at the time of establishment, a point at which practitioners may have the most control, though we currently lack a predictive understanding of these factors. Furthermore, it has been proposed that functional traits will respond more predictably than compositional metrics and could improve forecasts of restoration outcomes. Here, we use NMDS ordination and mixed effects models to evaluate sagebrush steppe restoration trajectories across 13 sites and 11 years. We compare the relative importance of time since restoration (age) and establishment conditions (soil, seed mix, establishment-year climate) to variation in restoration outcomes. Most compositional and trait metrics responded predictably through time, with sites converging with each other towards reference conditions despite differences at establishment. However, communities fell short of or overshot reference targets after 11 years, reaching a maximum 15 % compositional similarity and 69 % functional similarity compared to reference sites. Restored communities were dominated by native and exotic graminoid species, corresponding with a conservative and drought-tolerant composition of species with high leaf dry matter content and low turgor loss point. Restoration outcomes and convergence toward reference sites were contingent upon establishment year climate (year effects), soil sand content (site effects), and, to a lesser degree, seed mix design. These establishment effects on restoration trajectories often persisted or increased in strength over 11 years. Practical implication: Full restoration may require many more decades, but practitioners could speed success and increase control over outcomes by designing soil-specific seed mixes and scheduling seed sowing or post-seeding management to match short and long-term climate forecasts. When restoration efforts fall short of targets or lead to undesirable stable states, practitioners may improve recovery through actions such as supplemental targeted planting of desired shrub and forb species to redirect successional trajectories. Seed mixes with a higher proportion of forbs and shrubs to graminoids should be further tested.\u003c/p\u003e\n","funders":[{"organization":"Grand Teton National Park Foundation","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":0},{"organization":"Grand Teton National Park","identifierType":"ror","identifier":"https://ror.org/00vpxf870","awardNumber":"","awardDescription":"","awardTitle":"","order":1},{"organization":"University of Wyoming","identifierType":"ror","identifier":"https://ror.org/01485tq96","awardNumber":"","awardDescription":"","awardTitle":"","order":2},{"organization":"Wyoming Native Plant Society","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":4},{"organization":"Southwest Ecological Restoration Institutes","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":5}],"keywords":["vegetation dynamics","restoration success","Community assembly","functional traits","Ecological forecasting","contingency effects","sagebrush steppe"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"preprint","identifierType":"DOI","identifier":"https://doi.org/10.13140/RG.2.2.29164.23685"},{"relationship":"article","identifierType":"DOI","identifier":"https://doi.org/10.13140/RG.2.2.26870.36167"}],"versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.cjsxksnnt","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.cfxpnvxp2"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.cfxpnvxp2/versions"},"stash:version":{"href":"/api/v2/versions/449233"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.cfxpnvxp2/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.cfxpnvxp2","id":187216,"storageSize":771588,"relatedPublicationISSN":"0959-8138","title":"Data and code from: Acetic acid chromoendoscopy for the detection of neoplastic Barrett esophagus: a stepped wedge cluster randomized controlled trial (ACID-trial)","authors":[{"firstName":"Ilse","lastName":"Beaufort","email":"i.beaufort@antoniusziekenhuis.nl","affiliation":"University Medical Center Utrecht","affiliationROR":"https://ror.org/0575yy874","affiliations":[{"name":"St. Antonius Ziekenhuis","ror_id":"https://ror.org/01jvpb595"},{"name":"University Medical Center Utrecht","ror_id":"https://ror.org/0575yy874"}],"orcid":"0000-0002-5334-6609"},{"firstName":"Laura","lastName":"Boer","email":"l.s.boer-17@umcutrecht.nl","affiliation":"University Medical Center Utrecht","affiliationROR":"https://ror.org/0575yy874","affiliations":[{"name":"St. Antonius Ziekenhuis","ror_id":"https://ror.org/01jvpb595"},{"name":"University Medical Center Utrecht","ror_id":"https://ror.org/0575yy874"}],"order":1},{"firstName":"Anya","lastName":"Milne","email":"an.milne@antoniusziekenhuis.nl","affiliation":"St. Antonius Ziekenhuis","affiliationROR":"https://ror.org/01jvpb595","affiliations":[{"name":"St. Antonius Ziekenhuis","ror_id":"https://ror.org/01jvpb595"}],"order":2},{"firstName":"Yasser","lastName":"Alderlieste","email":"y.alderlieste@rivas.nl","affiliation":"Beatrix Hospital","affiliations":[{"name":"Beatrix Hospital"}],"order":3},{"firstName":"Judith","lastName":"Baars","email":"jbaars@amphia.nl","affiliation":"Amphia Ziekenhuis","affiliationROR":"https://ror.org/01g21pa45","affiliations":[{"name":"Amphia Ziekenhuis","ror_id":"https://ror.org/01g21pa45"}],"order":4},{"firstName":"Philip","lastName":"Bos","email":"bosp@zgv.nl","affiliation":"Ziekenhuis Gelderse Vallei","affiliationROR":"https://ror.org/03862t386","affiliations":[{"name":"Ziekenhuis Gelderse Vallei","ror_id":"https://ror.org/03862t386"}],"order":5},{"firstName":"Jordy","lastName":"Burger","email":"jburger@rijnstate.nl","affiliation":"Rijnstate Hospital","affiliationROR":"https://ror.org/0561z8p38","affiliations":[{"name":"Rijnstate Hospital","ror_id":"https://ror.org/0561z8p38"}],"order":6},{"firstName":"Nicoline","lastName":"van Heel","email":"n.van.heel@gelre.nl","affiliation":"Gelre Hospitals","affiliationROR":"https://ror.org/05275vm15","affiliations":[{"name":"Gelre Hospitals","ror_id":"https://ror.org/05275vm15"}],"order":7},{"firstName":"Michiel","lastName":"Ledeboer","email":"m.ledeboer@dz.nl","affiliation":"Deventer Ziekenhuis","affiliationROR":"https://ror.org/05w8df681","affiliations":[{"name":"Deventer Ziekenhuis","ror_id":"https://ror.org/05w8df681"}],"order":8},{"firstName":"Rob","lastName":"Lieverse","email":"roblieverse@live.nl","affiliation":"Ziekenhuis Groep Twente","affiliationROR":"https://ror.org/04grrp271","affiliations":[{"name":"Ziekenhuis Groep Twente","ror_id":"https://ror.org/04grrp271"}],"order":9},{"firstName":"Paul","lastName":"van de Meeberg","email":"p.van.de.meeberg@slingeland.nl","affiliation":"Slingeland Ziekenhuis","affiliationROR":"https://ror.org/00jw56w10","affiliations":[{"name":"Slingeland Ziekenhuis","ror_id":"https://ror.org/00jw56w10"}],"order":10},{"firstName":"Jan","lastName":"Meeuse","email":"j.meeuse@zrt.nl","affiliation":"Ziekenhuis Rivierenland","affiliationROR":"https://ror.org/03xwgfg33","affiliations":[{"name":"Ziekenhuis Rivierenland","ror_id":"https://ror.org/03xwgfg33"}],"order":11},{"firstName":"Ton","lastName":"Naber","email":"ahjnaber@hotmail.nl","affiliation":"Tergooi","affiliationROR":"https://ror.org/045nawc23","affiliations":[{"name":"Tergooi","ror_id":"https://ror.org/045nawc23"}],"order":12},{"firstName":"Hendrikus","lastName":"Pullens","email":"hjm.pullens@meandermc.nl","affiliation":"Meander Medisch Centrum","affiliationROR":"https://ror.org/04n1xa154","affiliations":[{"name":"Meander Medisch Centrum","ror_id":"https://ror.org/04n1xa154"}],"order":13},{"firstName":"Bob","lastName":"Scheffer","email":"b.scheffer@jbz.nl","affiliation":"Jeroen Bosch Ziekenhuis","affiliationROR":"https://ror.org/04rr42t68","affiliations":[{"name":"Jeroen Bosch Ziekenhuis","ror_id":"https://ror.org/04rr42t68"}],"order":14},{"firstName":"Marjolein","lastName":"Sikkema","email":"m.sikkema@etz.nl","affiliation":"Elisabeth-TweeSteden Ziekenhuis","affiliationROR":"https://ror.org/04gpfvy81","affiliations":[{"name":"Elisabeth-TweeSteden Ziekenhuis","ror_id":"https://ror.org/04gpfvy81"}],"order":15},{"firstName":"Mark","lastName":"Stolk","email":"m.stolk@antoniusziekenhuis.nl","affiliation":"St. Antonius Ziekenhuis","affiliationROR":"https://ror.org/01jvpb595","affiliations":[{"name":"St. Antonius Ziekenhuis","ror_id":"https://ror.org/01jvpb595"}],"order":16},{"firstName":"Romy","lastName":"Verbeek","email":"verbeekromy@gmail.com","affiliation":"Groene Hart Ziekenhuis","affiliationROR":"https://ror.org/0582y1e41","affiliations":[{"name":"Groene Hart Ziekenhuis","ror_id":"https://ror.org/0582y1e41"}],"order":17},{"firstName":"Marc","lastName":"Verhagen","email":"mverhagen@diakhuis.nl","affiliation":"Diakonessenhuis hospital","affiliationROR":"https://ror.org/01nrpzj54","affiliations":[{"name":"Diakonessenhuis hospital","ror_id":"https://ror.org/01nrpzj54"}],"order":18},{"firstName":"Wim","lastName":"van de Vrie","email":"w.vandevrie@asz.nl","affiliation":"Albert Schweitzer Ziekenhuis","affiliationROR":"https://ror.org/00e8ykd54","affiliations":[{"name":"Albert Schweitzer Ziekenhuis","ror_id":"https://ror.org/00e8ykd54"}],"order":19},{"firstName":"Marleen","lastName":"Willems","email":"m.willems@stjansdal.nl","affiliation":"St. Jansdal Hospital","affiliations":[{"name":"St. Jansdal Hospital"}],"order":20},{"firstName":"Henri","lastName":"van Werkhoven","email":"C.H.vanWerkhoven@umcutrecht.nl","affiliation":"University Medical Center Utrecht","affiliationROR":"https://ror.org/0575yy874","affiliations":[{"name":"University Medical Center Utrecht","ror_id":"https://ror.org/0575yy874"}],"order":21},{"firstName":"Bas","lastName":"Weusten","email":"b.l.a.weusten@umcutrecht.nl","affiliation":"University Medical Center Utrecht","affiliationROR":"https://ror.org/0575yy874","affiliations":[{"name":"St. Antonius Ziekenhuis","ror_id":"https://ror.org/01jvpb595"},{"name":"University Medical Center Utrecht","ror_id":"https://ror.org/0575yy874"}],"order":22}],"abstract":"\u003cp\u003eAcetic acid chromoendoscopy (AAC) is believed to be useful as a ‘red flag’ technique in Barrett esophagus (BE) surveillance, thereby improving the detection of dysplasia and esophageal adenocarcinoma (EAC). We assessed the added value of AAC in routine clinical practice. A total of 18 Dutch community hospitals participated in this stepped wedge cluster, randomized trial. Patients undergoing BE surveillance were eligible, excluding those with known or previously treated dysplasia. Hospitals randomly shifted from surveillance without AAC (control) to AAC (intervention) Targeted biopsies were obtained if lesions were present, before conducting random four-quadrant biopsies. Primary endpoint was the neoplasia detection rate, defined as the percentage of patients with low-grade dysplasia (LGD), high-grade dysplasia (HGD) and EAC in any biopsy. Secondary endpoints included neoplasia detection rate stratified by degree of dysplasia, neoplasia detection rate in targeted biopsies, and procedure time. We found that AAC-use did not increase the neoplasia detection rate. This also applied for the detection rate of LGD, and for HGD and EAC combined. More suspected lesions were detected in patients receiving AAC, yet the targeted neoplasia detection rate was not higher compared to patients in the control group. The total procedure time was longer during BE surveillance endoscopies when AAC was used. In addition, the increase of total procedure time was larger at the start of the AAC-guided surveillance compared to the AAC-guided endoscopies performed at the end of the trial. In a community hospital setting, characterized by procedures performed by non-expert BE endoscopists and a patient population at relatively low risk of EAC, AAC did not demonstrate added value.\u003c/p\u003e\n","funders":[{"organization":"St. Antonius Ziekenhuis","identifierType":"ror","identifier":"https://ror.org/01jvpb595","awardNumber":"","awardDescription":"","awardTitle":" Research Fund","order":0}],"keywords":["Clinical trials","Endoscopy","Gastroenterology and hepatology","Gastrointestinal tumors","Gastrointestinal tract"],"fieldOfScience":"Clinical medicine","hsiStatement":"The dataset contains coded data derived from human participants. Before deposition in Dryad, all direct identifiers were removed, and each record was assigned a randomly generated identification number. The published dataset is fully anonymized, and the random identifiers cannot be used to trace the data back to individual participants. Data sharing is consistent with the informed consent provided by participants and with approval from the relevant Medical Ethics Review Committee.","versionNumber":4,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"metadata_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.cfxpnvxp2","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.pnvx0k71c"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.pnvx0k71c/versions"},"stash:version":{"href":"/api/v2/versions/449198"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.pnvx0k71c/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.pnvx0k71c","id":167370,"storageSize":1150898,"relatedPublicationISSN":"1095-9203","title":"Sub-one-tenth exciton threshold lasers using stable self-charged perovskite quantum rods","authors":[{"firstName":"Jialu","lastName":"Li","email":"jialu-li@outlook.com","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"order":0},{"firstName":"Xue","lastName":"Han","email":"hanxuechn@163.com","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"order":1},{"firstName":"Wenjie","lastName":"Wang","email":"wangwenjie@tyut.edu.cn","affiliation":"Taiyuan University of Technology","affiliationROR":"https://ror.org/03kv08d37","affiliations":[{"name":"Taiyuan University of Technology","ror_id":"https://ror.org/03kv08d37"}],"order":2},{"firstName":"Jinhui","lastName":"Wang","email":"jinhui_wang2025@163.com","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"order":3},{"firstName":"Tingting","lastName":"Zhang","email":"20230000011@imut.edu.cn","affiliation":"Taiyuan University of Technology","affiliationROR":"https://ror.org/03kv08d37","affiliations":[{"name":"Taiyuan University of Technology","ror_id":"https://ror.org/03kv08d37"}],"order":4},{"firstName":"Yuting","lastName":"Wu","email":"wyt@njust.edu.cn","affiliation":"Nanjing University of Science and Technology","affiliationROR":"https://ror.org/00xp9wg62","affiliations":[{"name":"Nanjing University of Science and Technology","ror_id":"https://ror.org/00xp9wg62"}],"order":5},{"firstName":"Guofeng","lastName":"Zhang","email":"guofeng.zhang@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0000-0002-9030-0431","order":6},{"firstName":"Bin","lastName":"Li","email":"libin@sxnu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"order":7},{"firstName":"Changgang","lastName":"Yang","email":"changgang.yang@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"order":8},{"firstName":"Wenli","lastName":"Guo","email":"guowenlisx@163.com","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"order":9},{"firstName":"Mi","lastName":"Zhang","email":"z15034657487@163.com","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"order":10},{"firstName":"Ruiyun","lastName":"Chen","email":"chenry@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0000-0002-0037-856X","order":11},{"firstName":"Chengbing","lastName":"Qin","email":"chbqin@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0000-0002-6822-5113","order":12},{"firstName":"Jianyong","lastName":"Hu","email":"jyhu@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0009-0004-2245-3307","order":13},{"firstName":"Zhichun","lastName":"Yang","email":"yangzhichun@hust.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0000-0002-1613-5984","order":14},{"firstName":"Shao","lastName":"Liu","email":"liushaoding@tyut.edu.cn","affiliation":"Taiyuan University of Technology","affiliationROR":"https://ror.org/03kv08d37","affiliations":[{"name":"Taiyuan University of Technology","ror_id":"https://ror.org/03kv08d37"}],"order":15},{"firstName":"Yue","lastName":"Wang","email":"ywang@njust.edu.cn","affiliation":"Nanjing University of Science and Technology","affiliationROR":"https://ror.org/00xp9wg62","affiliations":[{"name":"Nanjing University of Science and Technology","ror_id":"https://ror.org/00xp9wg62"}],"orcid":"0000-0003-0098-5359","order":16},{"firstName":"Yunan","lastName":"Gao","email":"yngao@bjtu.edu.cn","affiliation":"Beijing Jiaotong University","affiliationROR":"https://ror.org/01yj56c84","affiliations":[{"name":"Beijing Jiaotong University","ror_id":"https://ror.org/01yj56c84"}],"orcid":"0000-0002-3131-7559","order":17},{"firstName":"Jie","lastName":"Ma","email":"mj@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0000-0003-4932-9205","order":18},{"firstName":"Liantuan","lastName":"Xiao","email":"xlt@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0000-0002-0104-8634","order":19},{"firstName":"Suotang","lastName":"Jia","email":"jggp@sxu.edu.cn","affiliation":"Shanxi University","affiliationROR":"https://ror.org/03y3e3s17","affiliations":[{"name":"Shanxi University","ror_id":"https://ror.org/03y3e3s17"}],"orcid":"0009-0003-7398-010X","order":20}],"abstract":"\u003cp\u003eColloidal quantum dots (QDs) are promising optical gain materials that require a reduction in the threshold to reach their full potential. While QD charging theoretically reduces the threshold to zero, its effectiveness has been limited by strong Auger recombination and unstable charging. In this study, we theoretically determine the optimal combination of charging number and Auger recombination to minimize the lasing threshold. Experimentally, we develop stable, self-charged perovskite quantum rods (QRs) as an alternative to QDs via state engineering and Mn-doping strategy. A two-order-of-magnitude reduction in nonradiative Auger recombination enables QRs to support a charging number of up to 6. We then achieve QR liquid lasing with a sub-one-tenth exciton threshold (an average of 0.098 excitons per QR) using 5-nanosecond pulse pumping. This threshold is exceptionally low among all reported QD lasers. These achievements demonstrate the potential of specially engineered QRs as excellent gain media and pave the way for their applications.\u003c/p\u003e\n","funders":[{"organization":"China Postdoctoral Science Foundation","identifierType":"ror","identifier":"https://ror.org/0426zh255","awardNumber":"2022M722006"},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"62325505","awardDescription":"","awardTitle":""},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"62222509","awardDescription":"","awardTitle":""},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"62274090","awardDescription":"","awardTitle":""},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"62205187","awardDescription":"","awardTitle":""},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"62305201","awardDescription":"","awardTitle":""},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"62405211","awardDescription":"","awardTitle":""},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"W2412024","awardDescription":"","awardTitle":""},{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"62375004","awardDescription":"","awardTitle":""},{"organization":"Shanxi Province Project 111","identifierType":"ror","identifier":"","awardNumber":"D18001","awardDescription":"","awardTitle":""}],"keywords":["liquid lasers","perovskite quantum rods","stable charging","nonradiative Auger recombination","near-zero lasing threshold"],"fieldOfScience":"Physical sciences","versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.pnvx0k71c","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.gf1vhhn37"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.gf1vhhn37/versions"},"stash:version":{"href":"/api/v2/versions/449248"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.gf1vhhn37/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.gf1vhhn37","id":174638,"storageSize":49916,"relatedPublicationISSN":"0962-8452","title":"Data from: Group recognition in the German cockroach, a subsocial omnivore, is based on fecal odor preference that is modulated by coprophagy, diet and learning","authors":[{"firstName":"Ayako","lastName":"Wada-Katsumata","email":"akatsum@ncsu.edu","affiliation":"North Carolina State University","affiliationROR":"https://ror.org/04tj63d06","affiliations":[{"name":"North Carolina State University","ror_id":"https://ror.org/04tj63d06"}],"orcid":"0000-0002-2895-1102"},{"firstName":"Jamora","lastName":"Hamilton","email":"jamora.hamilton.ext@envu.com","affiliation":"North Carolina State University","affiliationROR":"https://ror.org/04tj63d06","affiliations":[{"name":"North Carolina State University","ror_id":"https://ror.org/04tj63d06"}]},{"firstName":"Madhavi","lastName":"Kakumanu","email":"mlkakuma@ncsu.edu","affiliation":"North Carolina State University","affiliationROR":"https://ror.org/04tj63d06","affiliations":[{"name":"North Carolina State University","ror_id":"https://ror.org/04tj63d06"}],"orcid":"0000-0002-4325-3679"},{"firstName":"Coby","lastName":"Schal","email":"coby@ncsu.edu","affiliation":"North Carolina State University","affiliationROR":"https://ror.org/04tj63d06","affiliations":[{"name":"North Carolina State University","ror_id":"https://ror.org/04tj63d06"}],"orcid":"0000-0001-7195-6358"}],"abstract":"\u003cp\u003eFecal odors attract cockroaches to aggregations, where conspecific feces provide nutrients and seed the gut microbiota. Because these odors arise from the gut and fecal microbial communities, which are shaped by coprophagy and diet, discrete aggregations within a heterogeneous landscape can produce distinct fecal odor profiles. How such odor diversity influences recognition, group-affiliation and ultimately aggregation remains unclear. We manipulated coprophagy and then diet quality in gnotobiotic nymphs to generate groups with distinct fecal odor signatures, then raised them to the adult stage and collected their feces for behavioral assays. Naïve nymphs lacking coprophagy experience were equally attracted to fecal odors from all treatment groups, suggesting an innate attraction to conspecific feces. In contrast, experienced nymphs preferred the fecal odor of their natal group over foreign groups, suggesting learned group-specific recognition. In associative learning assays pairing a fecal odor with a glucose reward, nymphs preferentially aggregated with the conditioned odor over novel odors. These results show that aggregation in neonate cockroaches is mediated by both an innate attraction to conspecific fecal odor and learned preferences for specific odorants encountered during coprophagy soon after they hatch. We propose that these mechanisms guide neonates toward natal aggregations, facilitating acquisition of a locally adapted gut microbial community.\u003c/p\u003e\n","funders":[{"organization":"United States Department of Housing and Urban Development","identifierType":"ror","identifier":"https://ror.org/014a5gx79","awardNumber":"NCHHU0053-19","awardDescription":"Healthy Homes Program","awardTitle":"","order":0},{"organization":"United States Department of Housing and Urban Development","identifierType":"ror","identifier":"https://ror.org/014a5gx79","awardNumber":"NCHHU0081-24","awardDescription":"Healthy Homes Program","awardTitle":"","order":1},{"organization":"National Institute of Allergy and Infectious Diseases","identifierType":"ror","identifier":"https://ror.org/043z4tv69","awardNumber":"1R21AI187857-01","awardURI":"https://reporter.nih.gov/project-details/11035713","awardDescription":"","awardTitle":"Emerging Cockroach-associated Biocontaminants in Low-income Households","order":2},{"organization":"National Institute of Food and Agriculture","identifierType":"ror","identifier":"https://ror.org/05qx3fv49","awardNumber":"NC02639","awardDescription":"","awardTitle":"","order":3},{"organization":"National Pest Management Foundation","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":4},{"organization":"North Carolina State University","identifierType":"ror","identifier":"https://ror.org/04tj63d06","awardNumber":"","awardDescription":"Blanton J. Whitmire Endowment","awardTitle":"","order":5},{"organization":"North Carolina State University","identifierType":"ror","identifier":"https://ror.org/04tj63d06","awardNumber":"","awardDescription":"IH Initiative for Maximizing Student Diversity (IMSD)","awardTitle":"","order":6},{"organization":"Division of Graduate Education","identifierType":"ror","identifier":"https://ror.org/00whkrf32","awardNumber":"1746939","awardDescription":"","awardTitle":"Graduate Research Fellowship Program (GRFP)","order":7}],"keywords":["German cockroach","coprophagy","Aggregation","group recognition","olfactory learning","feces"],"fieldOfScience":"Biological sciences","methods":"\u003cp\u003eMETHODOLOGICAL INFORMATION\u003c/p\u003e\n\u003cp\u003e1. Description of methods used for collection/generation of data:\u003c/p\u003e\n\u003cp\u003eMaterials and Methods\u003c/p\u003e\n\u003cp\u003e(a) Insects\u003c/p\u003e\n\u003cp\u003eThe laboratory colony of \u003cem\u003eB. germanica\u003c/em\u003e (Orlando Normal strain, also known as American Cyanamid, collected in a Florida apartment in 1947) used in these experiments was reared on rodent diet (Purina 5001 Rodent Diet, PMI Nutrition International, St. Louis, MO, USA) and provided glass-distilled water in cotton-stoppered vials. The main colony and all cockroaches used in this study were maintained at 27 ± 1 °C, 40–70 % relative humidity, and a 12-h L : 12-h D photoperiod.\u003c/p\u003e\n\u003cp\u003e(b) Gnotobiotic first instar nymphs with axenic guts\u003c/p\u003e\n\u003cp\u003eThe German cockroach forms an ootheca (egg case) that houses ~40–45 fertilized eggs. The female carries the ootheca for a ~20-day embryonic development. Embryos that are close to hatching develop pigmented eyes and a prominent green spot representing yolk in the hindgut. When a “green line” was visible in the ootheca, the gravid female was briefly anesthetized with CO2 and the ootheca was gently removed with forceps. We sterilized the exterior surface of oothecae by washing them for 1 min in a 0.5 % bleach-water solution, then 70 % ethanol in water for 1 min, and three times with water for 1 min each. All solutions were made with autoclaved water. To determine if the sterilization process was effective to generate axenic first instar nymphs (henceforth, first instars), two surface-sterilized oothecae were plated on tryptic soy agar (TSA) and plate count agar (PCA). After 3 days of incubation at 28 °C, no colonies were visible in any of the treatments. This surface sterilization procedure resulted in gnotobiotic neonates that lacked a gut microbiome, but they retained their maternally provisioned endosymbionts, namely Blattabacterium. These gnotobiotic nymphs could be maintained on TSA plates for several weeks without any bacteria growth (data not shown), confirming that their guts were axenic.  \u003c/p\u003e\n\u003cp\u003eTo generate the experimental groups (200 nymphs/treatment), 20–30 surface-sterilized oothecae were placed in a sterile 15 ml conical centrifuge tube (Falcon-Corning, Corning, NY, USA) and kept in a rearing cage (18.7 x 13.3 x 9.5 cm, T-79, Althor Products, Windsor Locks, CT, USA) that had been sterilized with bleach and 95 % ethanol. To maintain moisture, sterilized glass test tubes containing autoclaved water were placed in the cage until the nymphs hatched. After hatching, the gnotobiotic first instars were randomly assigned to treatment groups.\u003c/p\u003e\n\u003cp\u003e(c) Three types of diets\u003c/p\u003e\n\u003cp\u003eTo obtain cockroach feces of different qualities and odor profiles for the aggregation bioassays, we used three non-sterile diets with variable protein, carbohydrate, lipid, and fiber contents: Rodent diet was the standard diet for our colony and it contained moderate protein (24 %), high carbohydrate (58 %), and low lipids (5 %) and fiber (5.2 %); Cat diet (Taste of the Wild Rocky Mountain Feline Recipe with roasted venison and smoked salmon, Schell \u0026amp; Kampeter Inc., Meta, MO, USA) contained high protein  (42%), low carbohydrate (21 %), moderate lipids (18 %) and low fiber (3 %); Rabbit diet (Oxbow Garden Select Adult Rabbit Food, Oxbow Enterprises Inc., Murdock, NE, USA) had low protein (12%), high carbohydrate (4 3%), low lipids (2.5 %) and high fiber (22–26 %). Each diet was crushed in a blender and placed into separate Ziploc bags. Sterilized rodent diet was prepared using gamma radiation at a dose of 10,000 Gy at the USDA-APHIS-PPQ S\u0026amp;T Otis Laboratory (Buzzards Bay, MA, USA). To verify the sterilization procedure, two samples of the irradiated diet were plated on TSA and PCA media using 4 plates per sample. After 3 days of incubation at 28 °C, no colonies or visible growth were detected in any of the diet and control plates.\u003c/p\u003e\n\u003cp\u003e(d) Generating three treatment groups\u003c/p\u003e\n\u003cp\u003eTo test the effects of bacteria sources and diet on aggregation preferences to fecal extracts, we generated three experimental groups. General procedures common to all three treatment groups were as follows. Gnotobiotic first instars (with axenic guts) were placed in a sterile rearing cage (100 nymphs/cage). Each cage contained an autoclaved egg carton shelter and autoclaved water in a sterilized glass test tube (25 x 150 mm, Fisherbrand, Fisher Scientific Company, Hanover Park, IL, USA). Each of the three experimental groups had two replicate cages. Routine maintenance every two weeks was conducted within a biosafety cabinet. The nymphs and their shelter were transferred without anesthesia to a new rearing cage to maintain a clean, sterile environment. Water and diets were replaced as needed. The first date that nymphs molted to the next development stage in each cage was recorded. The date of each adult emergence, the sex and body mass were recorded daily.\u003c/p\u003e\n\u003cp\u003eTo obtain fecal materials and first instars for bioassays, newly emerged adult males and females from each treatment group were transferred daily into sterile mating cages with sterile shelter, diet and water. Gravid females with a “green line” visible in their oothecae were then transferred to a sterile hatching cage with sterile shelter and water. Newly hatched gnotobiotic nymphs were used in bioassays. Thus, the adults were considered the end of the parental generation, and the offspring nymphs they produced were used in bioassays.\u003c/p\u003e\n\u003cp\u003eTo collect fresh feces from adult females, 20–50 females carrying oothecae were collected. We carefully dislodged their oothecae, which stimulated the females to initiate a new gonotrophic cycle of feeding, oocyte provisioning, and feces excretion. The females, along with a sterile shelter, diet and water were placed in a sterile cage with a screen (12 Mesh T316 Stainless, 0.58 mm wire diameter, 1.53 mm opening, TWP, Berkeley, CA, USA) at the bottom. We collected the feces that passed through the screen during one week. The diet was placed in a small Petri dish to prevent it from falling through the screen, but any diet debris were carefully removed from the feces under a microscope.\u003c/p\u003e\n\u003cp\u003eThe three treatment groups were defined as follows:\u003c/p\u003e\n\u003cp\u003eDifferent-Diets (no coprophagy). To evaluate the effect of diet on the development of gnotobiotic nymphs, one-day-old first instars with axenic guts received sterile water and one of three non-sterile diets (1 g of rodent, cat or rabbit diet, hereafter denoted D-Rodent, D-Cat and D-Rabbit, with “D” representing “Diet”) in a Petri dish (60 mm diameter, Falcon-Corning, Glendale, AZ, USA); they were not inoculated with fecal bacteria (no coprophagy). We expected their fecal odors to differentiate as their gut microbiomes diverged on the different diets and associated environmental bacteria during nymphal development.\u003c/p\u003e\n\u003cp\u003eCoprophagy \u0026amp; Different-Diets. To evaluate the effect of coprophagy on the development of gnotobiotic nymphs, one-day-old neonates with axenic guts received sterile water and non-sterile feces (0.5 g on a 60 mm Petri dish) excreted by virgin females from the laboratory colony; these females were maintained on non-sterile rodent diet. The nymphs were given 3 days to inoculate their guts with fecal bacteria. Then, the Petri dishes with feces were removed and groups of nymphs received one of three different non-sterile diets as in the “D” treatment above (hereafter denoted FD-Rodent, FD-Cat and FD-Rabbit, with “F” representing “Feces”). We expected the ingested fecal bacteria to inoculate all nymphs with a common gut microbiota, which would then be differentiated by the different diets and environmental bacteria during nymphal development, producing unique fecal odor profiles.\u003c/p\u003e\n\u003cp\u003eCoprophagy \u0026amp; sterilized-Rodent-diet. We expected cockroach groups raised on different diets to differ in their gut and fecal microbiomes and therefore in their fecal odors. To test whether inoculation with different fecal bacteria via coprophagy would impact the development and olfactory preferences of nymphs fed the same diet, one-day-old gnotobiotic neonates received sterile water and three different types of feces (from females in the FD-Rodent, FD-Cat or FD-Rabbit groups) for 3 days (0.5 g on a 60 mm Petri dish). After removing the Petri dishes with fecal inoculum, the nymphs were offered irradiated rodent diet. Hereafter, these treatments are denoted RoFD-stRodent, CaFD-stRodent and RaFD-stRodent, with RoF, CaF, and RaF representing rodent, cat, and rabbit feces, respectively, and stRodent representing sterilized rodent diet). Previous studies showed that diet quality strongly influenced and shaped gut bacterial communities. Therefore, we expected that gnotobiotic neonates inoculated with different bacteria from different fecal sources would develop divergent gut microbiota. At the same time, we expected that the common sterile diet throughout nymphal development and during the adult stage would converge digestion pathways and the gut environment and thus unify the gut bacterial communities of the three treatments.\u003c/p\u003e\n\u003cp\u003eWe also set up a single cage containing 100 nymphs to monitor development of gnotobiotic nymphs after a brief starvation period that mimicked the exposure to feces, followed by exposure to sterilized diet throughout nymphal development. These gnotobiotic neonates did not receive feces for one day (starved, no coprophagy) and then received irradiated rodent diet (No-coprophagy \u0026amp; sterilized-Rodent-diet).\u003c/p\u003e\n\u003cp\u003e(e) Bioassays using first instars\u003cbr\u003e\nFeces were collected from three groups of adult females fed the three non-sterile diets (i.e., rodent, cat or rabbit diets). The feces were weighed and homogenized (50 mg feces/ml sterile water) in a 1.5 ml Eppendorf tube. We vortexed the suspension for 3 min, then centrifuged (14,000 rpm for 1 min at 4 °C) and collected the supernatant in a 1.5-ml sterile Eppendorf tube. We defined the concentration of this initial extract as “1X” (50 μg feces-equivalents/μl).\u003c/p\u003e\n\u003cp\u003e1. Dose-response assays. Feces originating from the three different treatments varied in their effectiveness at stimulating aggregation. To standardize the stimuli used in two-choice aggregation assays, we estimated the Effective Concentration (EC) of each fecal extract using first instars that hatched from the respective diet treatment (i.e., offspring nymphs). Each of the fecal extracts from adult females fed different diets was diluted 10-fold (0.1X = 5 μg feces-equivalents/μl) and 100-fold (0.01X = 0.5 μg feces-equivalents/μl) with sterile water. Two accordion-style folded shelters (20 x 6.7 mm, Whatman #1, Pittsburgh, PA, USA) were placed at opposite edges of a Petri dish (60 mm). One shelter was treated with 1 μl of the fecal extract of the tested nymph’s own treatment group. The other shelter was treated as control with 1 μl of sterile water. A single first instar was allowed to walk onto an autoclaved wooden stick (140 x 5 mm, Eisco™ Wooden Splints, Fisherbrand) and guided to descend onto the center of the arena; thus no anesthesia was used. Bioassays were initiated during the photophase, when cockroaches normally aggregate, and the position of the nymph within the arena was recorded 2 hrs later. We conducted 20 to 60 assays per concentration. The EC50 (effective concentration) and EC70 were calculated from the resulting dose-response curve for each group. Based on these results, we used 3 μl of 5 μg feces-equivalents/μl fecal extract for all subsequent bioassays.\u003c/p\u003e\n\u003cp\u003e2. Two-choice aggregation assays. The experimental aggregation assays were identical to the dose-response assays, except we used 100 x 15 mm Petri dish arenas (Fisherbrand) and tent-shaped shelters (20 x 20 mm, Whatman #1). Based on the dose-response bioassays, Shelter 1 and Shelter 2 were treated with 3 μl of sterile water or fecal extract (5 μg feces-equivalents/μl). The overall response of nymphs was calculated as Response (%) = (100 × (# of nymphs choosing shelter 1 and shelter 2 / total # of tested nymphs)). A preference index was calculated as Preference (%) = (100 × (# of nymphs choosing either shelter 1 or shelter 2 / total # of nymphs that chose shelter 1 and shelter 2).\u003c/p\u003e\n\u003cp\u003e(f) Olfactory associative learning\u003cbr\u003e\nUsing gnotobiotic neonates, obtained by surface-sterilizing the oothecae of lab-colony females fed rodent diet, we generated five experimental groups. Newly hatched groups of approximately 200 gnotobiotic neonates with axenic guts were placed on a sterile filter paper strip (20 x 80 mm, Whatman #1) that served as a shelter in a sterile 50 ml conical centrifuge tube (Falcon-Corning, Corning, NY, USA) with sterile water in a 1.5 ml Eppendorf tube.\u003c/p\u003e\n\u003cp\u003e1. No-conditioning (N). Nymphs did not receive any conditioning.\u003c/p\u003e\n\u003cp\u003e2. Coprophagy-conditioning (F) (Fecal nutrient and fecal odors). To mimic natural coprophagy, nymphs received sterile water in a 1.5 ml Eppendorf tube and 0.2 g of non-sterile feces collected from females fed non-sterile rodent diet (FD-Rodent) moistened with 10 µl sterile water. In this paradigm, nymphs engaged in coprophagy while being exposed to fecal odor for either 1 day or 3 days.\u003c/p\u003e\n\u003cp\u003e3. Glucose-agar-conditioning (Glu) (Glucose nutrient only). Nymphs received 2 ml of a blue-colored glucose-agar mix (1 mol L–1 glucose, 1 % agar and 0.5 mmol L–1 erioglaucine). Erioglaucine, also known as Brilliant blue FCF, is a food-grade dye that is not toxic to cockroaches; it was used to confirm that the nymphs consumed the glucose-agar mix. Nymphs were exposed to the glucose-agar for either 1 day or 3 days but not to fecal odor other than their own feces.\u003c/p\u003e\n\u003cp\u003e4. Fecal odor-conditioning (FO) (Fecal odor only). Nymphs received fecal odor from 0.2 g of FD-Rodent female feces moistened with 10 µl sterile water. Feces were placed in a 1.5 ml Eppendorf tube capped with a piece of cheesecloth (Monarch, Knoxville, TN, USA). Thus, nymphs were exposed to fecal odor but prevented from contacting the feces for either 1 day or 3 days.\u003c/p\u003e\n\u003cp\u003e5. Glucose-agar \u0026amp; Fecal odor-conditioning (Glu+FO). Nymphs received 2 ml of blue-colored glucose-agar mix, as above, while being exposed to fecal odor, as above. Thus, nymphs were prevented from contacting the feces for either 1 day or 3 days but were exposed to fecal odor while eating glucose-agar.\u003c/p\u003e\n\u003cp\u003eFecal odor preferences of conditioned 1-day-old nymphs (1 day conditioning) and 3-day-old nymphs (3 days conditioning) were tested in two-choice aggregation assays using the fecal extracts of FD-Rodent, FD-Cat and FD-Rabbit (3 µl/shelter, 5 μg feces-equivalents/μl). We expected that nymphs in Experiment 1 (No conditioning) would be equally attracted to different fecal extracts, while nymphs in Experiment 2 (Coprophagy-conditioning) would prefer the FD-Rodent fecal odors over other fecal odors (FD-Cat and FD-Rabbit). If this fecal odor preference were due to associative olfactory learning during feeding, nymphs in Experiments 3 (Glucose nutrient only) and 4 (Fecal odor only) should not have a specific preference for FD-Rodent fecal odor. On the other hand, in Experiment 5 (Glucose-agar \u0026amp; Fecal odor-conditioning) nymphs were expected to prefer FD-Rodent fecal odors. The preference index was calculated using 30 replications of each assay.\u003c/p\u003e\n\u003cp\u003e(g) Data analysis\u003c/p\u003e\n\u003cp\u003eWe found no differences in the nymphal development periods between the two replicates within each treatment group. Therefore, we combined both replicates for the analysis of nymphal development times (adult emergence) and the bioassays that followed. The effects of diet and coprophagy on nymphal development and adult body mass (parental generation) of the Different-Diets group and Coprophagy \u0026amp; Different-Diets group were tested by two-way ANOVA (α = 0.05) followed by Tukey’s HSD, which enabled multiple comparisons of main (fixed) effects including development with vs. without coprophagy (Coprophagy main effect) across the three diets (Diet effect) and the interaction of these two factors (Coprophagy * Diet). Odor preferences of first instars (offspring generation) were assessed using a Chi-square test of independence (α = 0.05). All statistical analyses were performed in JMP (Student edition 18, Cary, NC, USA). Details of all statistical tests are shown in SI.\u003c/p\u003e\n\u003cp\u003e2. Methods for processing the data:\u003c/p\u003e\n\u003cp\u003eThe effects of diet and coprophagy on nymphal development and adult body mass (parental generation) of the Different-Diets group and Coprophagy \u0026amp; Different-Diets group were tested by two-way ANOVA (α = 0.05) followed by Tukey’s HSD, which enabled multiple comparisons of main (fixed) effects including development with vs. without coprophagy (Coprophagy main effect) across the three diets (Diet effect) and the interaction of these two factors (Coprophagy * Diet). Odor preferences of first instars (offspring generation) were assessed using a Chi-square test of independence (α = 0.05).\u003c/p\u003e\n\u003cp\u003e3. Instrument- or software-specific information (including package versions) needed to interpret the data:\u003c/p\u003e\n\u003cp\u003eAll statistical analyses were performed in JMP (Student edition 18, Cary, NC, USA).\u003c/p\u003e\n\u003cp\u003eattached base packages:\u003cbr\u003e\nN/A\u003c/p\u003e\n","versionNumber":8,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.gf1vhhn37","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":21,"downloads":4,"citations":0}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.prr4xgz2n"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.prr4xgz2n/versions"},"stash:version":{"href":"/api/v2/versions/449229"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.prr4xgz2n/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.prr4xgz2n","id":183465,"storageSize":8731662693,"relatedPublicationISSN":"2050-084X","title":"Spatiotemporal dynamics of bacterial biofilms in confined flows","authors":[{"firstName":"Massinissa","lastName":"Benbelkacem","email":"massinissa.benbelkacem@utoulouse.fr","affiliation":"Centre National de la Recherche Scientifique","affiliationROR":"https://ror.org/02feahw73","affiliations":[{"name":"Institut de Mécanique des Fluides de Toulouse","ror_id":"https://ror.org/025nmxp11"},{"name":"Laboratoire de Génie Chimique","ror_id":"https://ror.org/003jnac13"},{"name":"Université de Toulouse","ror_id":"https://ror.org/01ahyrz84"},{"name":"Centre National de la Recherche Scientifique","ror_id":"https://ror.org/02feahw73"},{"name":"Institut National Polytechnique de Toulouse","ror_id":"https://ror.org/033p9g875"}],"orcid":"0009-0004-5590-6720","order":0},{"firstName":"Gabriel","lastName":"Ramos","email":"","affiliation":"Centre National de la Recherche Scientifique","affiliationROR":"https://ror.org/02feahw73","affiliations":[{"name":"Institut de Mécanique des Fluides de Toulouse","ror_id":"https://ror.org/025nmxp11"},{"name":"Université de Toulouse","ror_id":"https://ror.org/01ahyrz84"},{"name":"Centre National de la Recherche Scientifique","ror_id":"https://ror.org/02feahw73"},{"name":"Institut National Polytechnique de Toulouse","ror_id":"https://ror.org/033p9g875"}],"order":2},{"firstName":"Fatima","lastName":"El Garah","email":"","affiliation":"Centre National de la Recherche Scientifique","affiliationROR":"https://ror.org/02feahw73","affiliations":[{"name":"Laboratoire de Génie Chimique","ror_id":"https://ror.org/003jnac13"},{"name":"Université de Toulouse","ror_id":"https://ror.org/01ahyrz84"},{"name":"Centre National de la Recherche Scientifique","ror_id":"https://ror.org/02feahw73"},{"name":"Institut National Polytechnique de Toulouse","ror_id":"https://ror.org/033p9g875"}],"order":3},{"firstName":"Yara","lastName":"Abidine","email":"yara.abidine@imft.fr","affiliation":"Centre National de la Recherche Scientifique","affiliationROR":"https://ror.org/02feahw73","affiliations":[{"name":"Institut de Mécanique des Fluides de Toulouse","ror_id":"https://ror.org/025nmxp11"},{"name":"Université de Toulouse","ror_id":"https://ror.org/01ahyrz84"},{"name":"Centre National de la Recherche Scientifique","ror_id":"https://ror.org/02feahw73"},{"name":"Institut National Polytechnique de Toulouse","ror_id":"https://ror.org/033p9g875"}],"order":4},{"firstName":"Christine","lastName":"Roques","email":"","affiliation":"Centre National de la Recherche Scientifique","affiliationROR":"https://ror.org/02feahw73","affiliations":[{"name":"Laboratoire de Génie Chimique","ror_id":"https://ror.org/003jnac13"},{"name":"Université de Toulouse","ror_id":"https://ror.org/01ahyrz84"},{"name":"Centre National de la Recherche Scientifique","ror_id":"https://ror.org/02feahw73"},{"name":"Institut National Polytechnique de Toulouse","ror_id":"https://ror.org/033p9g875"}],"order":5},{"firstName":"Yohan","lastName":"Davit","email":"yohan.davit@imft.fr","affiliation":"Centre National de la Recherche Scientifique","affiliationROR":"https://ror.org/02feahw73","affiliations":[{"name":"Institut de Mécanique des Fluides de Toulouse","ror_id":"https://ror.org/025nmxp11"},{"name":"Université de Toulouse","ror_id":"https://ror.org/01ahyrz84"},{"name":"Centre National de la Recherche Scientifique","ror_id":"https://ror.org/02feahw73"},{"name":"Institut National Polytechnique de Toulouse","ror_id":"https://ror.org/033p9g875"}],"orcid":"0000-0002-2234-9567","order":6}],"abstract":"\u003cp\u003eMost bacteria live in sessile biofilms that colonize the confined channels, pores and crevices of natural and engineered structures. In these environments, flow delivers nutrients necessary for growth while simultaneously generating mechanical stresses that cause detachment from surfaces. Bacteria, in turn, colonize flow passages, increasing hydraulic resistance and modifying transport properties. Although the importance of advective transport and hydrodynamic forces on bacterial populations is well established, the complex feedback mechanisms governing biofilm development in confined geometries remain poorly understood. Here, we study how couplings between flow and bacterial development control the spatiotemporal dynamics of \u003cem\u003ePseudomonas aeruginosa\u003c/em\u003e in microchannel flows. We demonstrate that nutrient availability primarily drives the longitudinal distribution of biomass along the channel, while competition between growth and flow-induced detachment controls the transverse distribution and temporal dynamics. We find that biofilms undergo successive cycles of sloughing and regrowth, causing persistent fluctuations in the hydraulic resistance and biomass that prevent the system from ever reaching a true steady state. Our results indicate that these self-sustained fluctuations are a signature effect in confined flows, originating from a pressure build-up as growing bacteria obstruct flow paths. We further show that the sloughing dynamics can be described as a jump stochastic process with gamma-distributed interevent times, analogous to other bursting events such as earthquakes or avalanches. This stochastic framework provides a quantitative approach to characterizing the inherent randomness and apparent irreproducibility of biofilm experiments, opening new avenues for predictive modeling of biofilms in confined systems.\u003c/p\u003e\n","funders":[{"organization":"European Research Council","identifierType":"ror","identifier":"https://ror.org/0472cxd90","awardNumber":"803074","awardDescription":"","awardTitle":"","order":0}],"keywords":["Bacterial biofilms","Fluid mechanics","Microfluidics","Pseudomonas ae"],"fieldOfScience":"Physical sciences","methods":"\u003ch6\u003e\n\u003ca href=\"#inoculation-and-flow-experiments\" aria-hidden=\"true\" class=\"anchor\" id=\"inoculation-and-flow-experiments\"\u003e\u003c/a\u003e\u003cstrong\u003eInoculation and flow experiments\u003c/strong\u003e\n\u003c/h6\u003e\n\u003cp\u003eBHI suspensions were adjusted at optical density at \u003cem\u003eOD\u003c/em\u003e\u003csub\u003e640\u003c/sub\u003e \u003cem\u003e\u003csub\u003enm\u003c/sub\u003e\u003c/em\u003e = 0.2 (10\u003csup\u003e8\u003c/sup\u003e \u003cem\u003eCF U\u003c/em\u003e/\u003cem\u003emL\u003c/em\u003e) and inoculated inside the microchannels from the outlet, up to approximately \u003csup\u003e3\u003c/sup\u003e/4 of the channel length in order to keep a clean inlet. The system was let at room temperature (25 °C) for 3 h under static conditions. Flow experiments were then performed at 0.02, 0.2, 2, 20 and 200 \u003cem\u003eμL\u003c/em\u003e/\u003cem\u003emin\u003c/em\u003e constant flow rates for 72h in the microchannels at room temperature. For the experiments at 0.2, 2, 20 and 200 \u003cem\u003eμL\u003c/em\u003e/\u003cem\u003emin\u003c/em\u003e, the fluidic system was based on a sterile culture medium reservoir pressurized by a pressure controller (Fluigent FlowEZ) and connected with a flow rate controller (Fluigent Flow unit). The flow rate was maintained constant by using a controller with a feedback loop adjusting the pressure in the liquid reservoir. The reservoir was connected to the chip using Tygon tubing (Saint Gobain Life Sciences Tygon\u003csup\u003eTM\u003c/sup\u003e ND 100-80) of 0.52 mm internal diameter and 1.52 mm external diameter, along with PEEK tubing (Cytiva Akta pure) with 0.25 mm inner diameter adapters for flow rate controller. The waste container was also pressurized by another independent pressure controller to reduce air bubble formation in the inlet part. For the experiments at 0.02 \u003cem\u003eμL\u003c/em\u003e/\u003cem\u003emin\u003c/em\u003e, we used an Harvard Phd2000 syringe pump for the flow.\u003c/p\u003e\n\u003ch6\u003e\n\u003ca href=\"#imaging-for-the-biofilm-experiment\" aria-hidden=\"true\" class=\"anchor\" id=\"imaging-for-the-biofilm-experiment\"\u003e\u003c/a\u003e\u003cstrong\u003eImaging for the biofilm experiment\u003c/strong\u003e\n\u003c/h6\u003e\n\u003cp\u003eBacterial development was imaged for a period of 72 hours with a timestep of 30 minutes at 25 °C on an inverted microscope (Ti-2E, Nikon) using a digital camera (back-illuminated PCO edge). Time-lapse images were acquired using brightfield and fluorescence microscopy (Sola light source 10% intensity with 30 ms exposure with 500 \u003cem\u003enm\u003c/em\u003e excitation and 513 \u003cem\u003enm\u003c/em\u003e emission combined with (FITC filter). Images were obtained with a focal plan at the glass/liquid interface. These images had dimensions of 30086 x 154 pixels obtained after multi position scanning using automatic Nikon platform and assembled by Nikon NIS software of single images with 0.65 µm/pixel using a 10X magnification Nikon objective (NA = 0.3).\u003c/p\u003e\n\u003ch6\u003e\n\u003ca href=\"#image-analysis-for-the-biofilm-distribution-in-the-longitudinal-direction\" aria-hidden=\"true\" class=\"anchor\" id=\"image-analysis-for-the-biofilm-distribution-in-the-longitudinal-direction\"\u003e\u003c/a\u003e\u003cstrong\u003eImage analysis for the biofilm distribution in the longitudinal direction\u003c/strong\u003e\n\u003c/h6\u003e\n\u003cp\u003eFluorescence images were loaded as a matrix (30086 x 154) in MATLAB (MathWorks). For each time acquisition, the signal was first integrated in the transverse direction to obtain a mean distribution in the longitudinal direction. In plotting curves to analyze the effect of nutrients, all timepoints were then averaged to obtain one dimensional curves of the mean longitudinal profile. For kymographs, one dimensional curves for each time point were stacked together to describe the spatiotemporal dynamics. The intensity values were normalized to the maximum values of each replicate over all times. For each flow and nutrient condition, three biological replicates were performed.\u003c/p\u003e\n\u003ch6\u003e\n\u003ca href=\"#image-analysis-for-the-biofilm-segmentation\" aria-hidden=\"true\" class=\"anchor\" id=\"image-analysis-for-the-biofilm-segmentation\"\u003e\u003c/a\u003e\u003cstrong\u003eImage analysis for the biofilm segmentation\u003c/strong\u003e\n\u003c/h6\u003e\n\u003cp\u003eTo estimate changes in channel colonization, GFP images were binarized using a machine learning software (Ilastik) (\u003ca href=\"https://elifesciences.org/reviewed-preprints/98292#c6\"\u003eBerg et al., 2019\u003c/a\u003e). Images were pre-treated with imageJ (\u003ca href=\"https://elifesciences.org/reviewed-preprints/98292#c68\"\u003eSchneider et al., 2012\u003c/a\u003e) by normalizing all pixel values between 0 and 65535 grayscale levels. In Ilastik, biofilm structures were first differentiated from the empty flow path using pixel-level manual labeling during pixel classification where visible patches of biofilm and empty channel were annotated manually by mouse cursor. Pixel classification workflow employs a Random Forest classifier, known for its generalization properties. Several samples of biofilm and background images were used to train the classifier by annotating pixels with corresponding labels, allowing the algorithm to learn and make predictions in real-time. The chosen features were color, intensity, edges, and texture. The generated probability maps indicating the likelihood of each class at every pixel were used for the object classification and were thresholded at a value of 0.6 with no size filter. Thresholding is a process involved in converting continuous probability maps generated from pixel classification into binary segmentation images by setting a threshold, where pixels above the threshold are classified as belonging to an object. The size, intensity, position and convexity of the biofilm objects was exported in .csv format and further analysed in matlab. Volumic fraction of biofilm in microchannel was calculated from the sum of the size of segmented objects divided by the interest growth area (non UVC irradiated central part of microchannel).\u003c/p\u003e\n","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.7554/eLife.98292.2"}],"versionNumber":3,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.prr4xgz2n","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.prr4xgxzq"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.prr4xgxzq/versions"},"stash:version":{"href":"/api/v2/versions/449021"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.prr4xgxzq/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.prr4xgxzq","id":158485,"storageSize":1474207446,"relatedPublicationISSN":"1741-2552","title":"Data from: Speech motor cortex enables BCI cursor control and click","authors":[{"firstName":"Tyler","lastName":"Singer-Clark","email":"tsingerclark@ucdavis.edu","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"orcid":"0000-0001-8636-5075"},{"firstName":"Xianda","lastName":"Hou","email":"","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"order":1},{"firstName":"Nicholas","lastName":"Card","email":"","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"order":2},{"firstName":"Maitreyee","lastName":"Wairagkar","email":"","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"order":3},{"firstName":"Carrina","lastName":"Iacobacci","email":"","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"order":4},{"firstName":"Hamza","lastName":"Peracha","email":"","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"order":5},{"firstName":"Leigh","lastName":"Hochberg","email":"","affiliation":"Brown University","affiliationROR":"https://ror.org/05gq02987","affiliations":[{"name":"Brown University","ror_id":"https://ror.org/05gq02987"},{"name":"Massachusetts General Hospital","ror_id":"https://ror.org/002pd6e78"},{"name":"Providence VA Medical Center","ror_id":"https://ror.org/041m0cc93"}],"order":6},{"firstName":"Sergey","lastName":"Stavisky","email":"","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"order":7},{"firstName":"David","lastName":"Brandman","email":"","affiliation":"University of California, Davis","affiliationROR":"https://ror.org/05rrcem69","affiliations":[{"name":"University of California, Davis","ror_id":"https://ror.org/05rrcem69"}],"order":8}],"abstract":"\u003cp\u003eOne human participant (T15) with four 64-channel microelectrode arrays (256 neural recording channels) implanted in his cortex performed brain-computer interface (BCI) 2-D cursor control tasks, i.e., he used his brain (no physical muscle movement) to move and click a cursor to select targets on a computer screen. T15's arrays were located in his ventral precentral gyrus (vPCG), canonically considered speech motor cortex. Nevertheless, T15's imagery while moving the cursor was motoric (either attempting hand movements, tongue movements, or generic \"intuition\" of where he wanted to move the cursor), not speech.\u003c/p\u003e\n\u003cp\u003eData streams in this dataset include task state (e.g., target position, cursor position) and neural features (threshold crossings, spike band power) for each recording channel, binned in 10 ms bins. Output from the neural decoders (predicted cursor velocities and click events) that was used online is also included.\u003c/p\u003e","funders":[{"organization":"United States Department of Defense","identifierType":"ror","identifier":"https://ror.org/0447fe631","awardNumber":"AL220043","awardDescription":"ALS Research Program","order":0},{"organization":"Searle Scholars Program","identifierType":"crossref_funder_id","identifier":"","awardNumber":"","awardDescription":"","order":1},{"organization":"U.S. National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"2152260","awardDescription":"NSF Research Traineeship NRT program","order":2},{"organization":"National Institute on Deafness and Other Communication Disorders","identifierType":"ror","identifier":"https://ror.org/04mhx6838","awardNumber":"1DP2DC021055","awardDescription":"DP2","order":3},{"organization":"Achievement Rewards for College Scientists Foundation","identifierType":"ror","identifier":"https://ror.org/054awkm93","awardNumber":"","awardDescription":"","order":4},{"organization":"Burroughs Wellcome Fund","identifierType":"ror","identifier":"https://ror.org/01d35cw23","awardNumber":"","awardDescription":"Career Award at the Scientific Interface","order":5},{"organization":"A.P. Giannini Foundation","identifierType":"ror","identifier":"https://ror.org/01e3cnp62","awardNumber":"","awardDescription":"","order":6},{"organization":"Amyotrophic Lateral Sclerosis Association","identifierType":"ror","identifier":"https://ror.org/00mwp5989","awardNumber":"24-AT-732‌","awardDescription":"Assistive Technology Grant","order":7}],"keywords":["Brain-Computer Interface","neural decoding","speech motor cortex","cursor control"],"fieldOfScience":"Medical engineering","hsiStatement":"These data recorded from a human participant have been anonymized and de-identified. They do not contain any personally identifiable information. The subject is referred to using a coded clinical trial identifier (also used in the associated publication). Raw neural data are not shared; only de-identified processed neural features. Behavioral data do not contain identifiable information. The participant has consented to the publication of this de-identified data in the public domain.","relatedWorks":[{"relationship":"primary_article","identifierType":"DOI","identifier":"https://doi.org/10.1088/1741-2552/add0e5"}],"versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.prr4xgxzq","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":94,"downloads":21,"citations":1}},{"_links":{"self":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.s7h44j1q5"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.s7h44j1q5/versions"},"stash:version":{"href":"/api/v2/versions/449238"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.s7h44j1q5/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.s7h44j1q5","id":187012,"storageSize":85365967805,"title":"Baleen whale whole-genome VCF data aligned to chromosome-level assemblies of Rice's whale (\u003cem\u003eBalaenoptera ricei\u003c/em\u003e) and blue whale (\u003cem\u003eB. musculus\u003c/em\u003e)","authors":[{"firstName":"Diana","lastName":"Aguilar-Gómez","email":"dianaguilr@gmail.com","affiliation":"University of California, Los Angeles","affiliationROR":"https://ror.org/046rm7j60","affiliations":[{"name":"University of California, Los Angeles","ror_id":"https://ror.org/046rm7j60"}],"orcid":"0000-0001-5930-3936","order":0},{"firstName":"Jacqueline","lastName":"Robinson","email":"jarobinson@princeton.edu","affiliation":"Princeton University","affiliationROR":"https://ror.org/00hx57361","affiliations":[{"name":"Princeton University","ror_id":"https://ror.org/00hx57361"}],"order":1},{"firstName":"Christopher","lastName":"Kyriazis","email":"ckyriazis@sdzwa.org","affiliation":"San Diego Zoo Institute for Conservation Research","affiliationROR":"https://ror.org/04fqe9p30","affiliations":[{"name":"San Diego Zoo Institute for Conservation Research","ror_id":"https://ror.org/04fqe9p30"}],"order":2},{"firstName":"Mallory","lastName":"Kenfield","email":"mkenfield3@gatech.edu","affiliation":"Georgia Institute of Technology","affiliationROR":"https://ror.org/01zkghx44","affiliations":[{"name":"Georgia Institute of Technology","ror_id":"https://ror.org/01zkghx44"}],"order":3},{"firstName":"Sergio","lastName":"Nigenda-Morales","email":"snigenda@csusm.edu","affiliation":"California State University, San Marcos","affiliationROR":"https://ror.org/01j8e0j24","affiliations":[{"name":"California State University, San Marcos","ror_id":"https://ror.org/01j8e0j24"}],"order":4},{"firstName":"Nicole","lastName":"Vollmer","email":"nicole.vollmer@noaa.gov","affiliation":"University of Miami","affiliationROR":"https://ror.org/02dgjyy92","affiliations":[{"name":"University of Miami","ror_id":"https://ror.org/02dgjyy92"}],"order":5},{"firstName":"Lynsey","lastName":"Wilcox Talbot","email":"lynsey.wilcox@noaa.gov","affiliation":"National Oceanic and Atmospheric Administration","affiliationROR":"https://ror.org/02z5nhe81","affiliations":[{"name":"National Oceanic and Atmospheric Administration","ror_id":"https://ror.org/02z5nhe81"}],"order":6},{"firstName":"Bernard","lastName":"Kim","email":"bernardkim@princeton.edu","affiliation":"Princeton University","affiliationROR":"https://ror.org/00hx57361","affiliations":[{"name":"Princeton University","ror_id":"https://ror.org/00hx57361"}],"order":7},{"firstName":"Ryan","lastName":"Hernandez","email":"ryan.hernandez@ucsf.edu","affiliation":"University of California, San Francisco","affiliationROR":"https://ror.org/043mz5j54","affiliations":[{"name":"University of California, San Francisco","ror_id":"https://ror.org/043mz5j54"}],"order":8},{"firstName":"Patricia","lastName":"Rosel","email":"phocoena4@gmail.com","affiliation":"National Oceanic and Atmospheric Administration","affiliationROR":"https://ror.org/02z5nhe81","affiliations":[{"name":"National Oceanic and Atmospheric Administration","ror_id":"https://ror.org/02z5nhe81"}],"order":9},{"firstName":"Phillip","lastName":"Morin","email":"philmor1964@gmail.com","affiliation":"National Oceanic and Atmospheric Administration","affiliationROR":"https://ror.org/02z5nhe81","affiliations":[{"name":"National Oceanic and Atmospheric Administration","ror_id":"https://ror.org/02z5nhe81"}],"order":10},{"firstName":"Kirk","lastName":"Lohmueller","email":"klohmueller@ucla.edu","affiliation":"University of California, Los Angeles","affiliationROR":"https://ror.org/046rm7j60","affiliations":[{"name":"University of California, Los Angeles","ror_id":"https://ror.org/046rm7j60"}],"order":11}],"abstract":"\u003cp\u003eThis dataset contains whole-genome sequencing data processed as variant call format (VCF) files for 37 baleen whale individuals representing six species: Rice's whale (\u003cem\u003eBalaenoptera ricei\u003c/em\u003e, n = 25), Bryde's whale (\u003cem\u003eB. edeni edeni\u003c/em\u003e, n = 2; \u003cem\u003eB. edeni brydei\u003c/em\u003e, n = 4), sei whale (\u003cem\u003eB. borealis\u003c/em\u003e, n = 1), blue whale (\u003cem\u003eB. musculus\u003c/em\u003e, n = 1), and fin whale (\u003cem\u003eB. physalus\u003c/em\u003e, n = 4). All individuals were mapped to two chromosome-level reference assemblies — the Rice's whale (\u003cem\u003eB. ricei\u003c/em\u003e) and blue whale (\u003cem\u003eB. musculus\u003c/em\u003e) — yielding two parallel VCF datasets for comparative genomic analyses. These data support phylogenomic and population genomic investigations of the Bryde's whale species complex, including assessment of species boundaries, mito-nuclear discordance, and the evolutionary distinctiveness of the critically endangered Rice's whale.\u003c/p\u003e\n","funders":[{"organization":"NOAA Office of Protected Resources","identifierType":"ror","identifier":"https://ror.org/03fy33a80","awardNumber":"","awardDescription":"","awardTitle":"","order":0},{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"5R35GM119856-10","awardURI":"https://reporter.nih.gov/project-details/11088866","awardDescription":"National Institute of General Medical Sciences","awardTitle":"Population genomics of the selective effects of new mutations","order":2},{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"5R35GM158240-02","awardURI":"https://reporter.nih.gov/project-details/11332843","awardDescription":"National Institute of General Medical Sciences","awardTitle":"Human evolution and the genetic architecture of complex traits","order":3},{"organization":"National Institute of General Medical Sciences","identifierType":"ror","identifier":"https://ror.org/04q48ey07","awardNumber":"5R01GM142112-04","awardURI":"https://reporter.nih.gov/project-details/10745276","awardDescription":"National Institute of General Medical Sciences","awardTitle":"Rarely Common: Uncovering the dominant role of rare variants in the genetic architecture of complex human traits.","order":4}],"keywords":["Genomics","DNA sequence analysis","Whales","Animal genetics"],"fieldOfScience":"Biological sciences","versionNumber":4,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.s7h44j1q5","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.70rxwdcdh"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.70rxwdcdh/versions"},"stash:version":{"href":"/api/v2/versions/449232"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.70rxwdcdh/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.70rxwdcdh","id":186130,"storageSize":4629777,"relatedPublicationISSN":"0030-1299","title":"Environmental data for modelling habitat suitability of the mosquito species \u003cem\u003eCulex modestus\u003c/em\u003e","authors":[{"firstName":"Susanna","lastName":"Cant","email":"susie.cant@ukhsa.gov.uk","affiliation":"UK Health Security Agency","affiliationROR":"https://ror.org/018h10037","affiliations":[{"name":"UK Health Security Agency","ror_id":"https://ror.org/018h10037"}],"orcid":"0009-0008-7003-8887"},{"firstName":"Owen","lastName":"Jones","email":"Owen.Jones@ukhsa.gov.uk","affiliation":"UK Health Security Agency","affiliationROR":"https://ror.org/018h10037","affiliations":[{"name":"UK Health Security Agency","ror_id":"https://ror.org/018h10037"}],"order":1},{"firstName":"Rob","lastName":"Paton","email":"Rob.Paton2@ukhsa.gov.uk","affiliation":"UK Health Security Agency","affiliationROR":"https://ror.org/018h10037","affiliations":[{"name":"UK Health Security Agency","ror_id":"https://ror.org/018h10037"}],"order":2}],"abstract":"\u003cp\u003eThis dataset contains environmental variables used for habitat suitability modelling of the mosquito species \u003cem\u003eCulex modestus\u003c/em\u003e. The data are provided in two comma-separated values (CSV) files: (1) a presence dataset containing environmental predictor values associated with observed occurrences of \u003cem\u003eCulex modestus\u003c/em\u003e, and (2) a distribution dataset containing environmental predictor values representing background  environmental conditions. The variables consist of satellite-derived environmental indices which capture ecological conditions relevant to mosquito habitat suitability. These data were compiled to support analyses of environmental drivers of species occurrence of \u003cem\u003eCulex modestus\u003c/em\u003e. The dataset is suitable for use in species distribution modelling and ecological analysis.\u003c/p\u003e\n","keywords":["Ecology","Habitability","Mosquitoes"],"fieldOfScience":"Earth and related environmental sciences","versionNumber":4,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.70rxwdcdh","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.zw3r228hp"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zw3r228hp/versions"},"stash:version":{"href":"/api/v2/versions/449061"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.zw3r228hp/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.zw3r228hp","id":142388,"storageSize":1282009,"relatedPublicationISSN":"0012-9658","title":"Data and codes from: Causes of interspecific variation in avian migration distance","authors":[{"firstName":"Neil","lastName":"Paprocki","email":"neilpaprocki@gmail.com","affiliation":"University of Idaho","affiliationROR":"https://ror.org/03hbp5t65","affiliations":[{"name":"University of Idaho","ror_id":"https://ror.org/03hbp5t65"}],"orcid":"0009-0005-2656-5506"},{"firstName":"Courtney","lastName":"Conway","email":"cconway@uidaho.edu","affiliation":"University of Idaho","affiliationROR":"https://ror.org/03hbp5t65","affiliations":[{"name":"University of Idaho","ror_id":"https://ror.org/03hbp5t65"}],"orcid":"0000-0003-0492-2953","order":1}],"abstract":"\u003cp\u003eMigration is an awe-inspiring behavior employed by a diverse suite of taxa throughout the animal kingdom. Avian migration is arguably the most well-known animal behavior and birds vary widely in how far they migrate, but the ecological mechanisms underlying interspecific variation in migration distance remain unclear. We developed a novel set of predictions deduced from seven mechanistic hypotheses proposed to explain interspecific variation in avian migration distance. We then used a Bayesian phylogenetic comparative analysis to test predictions from these seven hypotheses based on migration data and species traits from 446 species of migratory birds throughout the world based on data from animal-borne tracking technology. Body mass, seasonal food availability, and morphological/behavioral traits that improve flight efficiency explained significant interspecific variation in migration distance after controlling for absolute breeding latitude (which was positively correlated with migration distance). Specifically, we found migration distance was negatively correlated with body mass and seasonal food availability but positively correlated with hand-wing index (a measure of wing elongation and pointedness) and soaring flight. Moreover, the negative relationship between body mass and migration distance was not ubiquitous but rather depended on flight mode and intraspecific nonbreeding group size such that species employing flapping flight during migration and those overwintering in smaller intraspecific groups had the strongest negative relationships between body mass and migration distance. Within group-living birds, smaller bodied species may gain a foraging or thermoregulatory advantage that shortens migration distances while larger bodied species may gain an energetic advantage by using flock formations during migration that facilitate longer migrations to more suitable nonbreeding areas. From a life history perspective, maximum annual reproductive investment was negatively correlated with migration distance while minimum annual reproductive investment and adult annual survival were not correlated with migration distance. Overall, our results support flight efficiency, food limitation, and thermoregulatory-based hypotheses as causes of interspecific variation in migration distances in birds. Our results also help to refine the numerous and often ambiguous mechanisms underlying the negative relationship between body size and migration distance, and refute several hypotheses previously proposed to explain interspecific variation in avian migration distance.\u003c/p\u003e\n","funders":[{"organization":"National Science Foundation","identifierType":"ror","identifier":"https://ror.org/021nxhr62","awardNumber":"","awardDescription":"Graduate Research Fellowship Program","awardTitle":"","order":0}],"keywords":["phylogenetic comparative methods","Interspecific variation","migration distance"],"fieldOfScience":"Biological sciences","versionNumber":10,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.zw3r228hp","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.0zpc867cs"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.0zpc867cs/versions"},"stash:version":{"href":"/api/v2/versions/449072"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.0zpc867cs/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.0zpc867cs","id":187036,"storageSize":5296,"relatedPublicationISSN":"0269-8463","title":"Bioorganic fertilizer alleviated soil microbial C limitations, aggravated P limitations, and increased microbial C use efficiency in a degraded desert steppe","authors":[{"firstName":"Yao","lastName":"Zhou","email":"782421997@qq.com","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"orcid":"0000-0002-2603-0967"},{"firstName":"Wen","lastName":"Li","email":"18893813447@163.com","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"order":1},{"firstName":"Jing","lastName":"Ma","email":"majingstar@163.com","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"order":2},{"firstName":"Jinzhen","lastName":"Li","email":"12023131537@stu.nxu.edu.cn","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"order":3},{"firstName":"Haixin","lastName":"Jiang","email":"nxu_2022_jhx@163.com","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"order":4},{"firstName":"Guohui","lastName":"Wang","email":"wanggh2022@nxu.edu.cn","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"order":5},{"firstName":"Yan","lastName":"Shen","email":"nxshenyan@163.com","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"order":6},{"firstName":"Hongbin","lastName":"Wang","email":"ma_hb@nxu.edu.cn","affiliation":"Ningxia University","affiliationROR":"https://ror.org/04j7b2v61","affiliations":[{"name":"Ningxia University","ror_id":"https://ror.org/04j7b2v61"}],"order":7}],"abstract":"\u003cp\u003eBioorganic fertilizer (BOF), which integrates organic carbon sources, beneficial microorganisms, and essential nutrients, represents a distinctive approach to grassland restoration that differs fundamentally from conventional fertilization practices. Ecoenzymatic stoichiometry theory (EEST) provides a powerful framework for evaluating microbial nutrient limitation and carbon use efficiency (CUE) via analysis of the metabolic activities of extracellular enzymes involved in nutrient acquisition, supporting research on their responses to carbon-rich amendments and informing the optimization of restoration strategies.\u003c/p\u003e\n\u003cp\u003eIn this study, we investigated the responses of microbial metabolic limitations and CUE to different ecological restoration measures: bioorganic fertilizer (BOF), microbial fertilizer (MF), and super absorbent polymers (SAP), and a natural restoration control (CK). We quantified microbial metabolic limitation using three soil enzyme stoichiometry models (vector, vector-threshold (V-T), and threshold models), calculated microbial CUE across all treatments, and examined the regulatory effects of environmental factors on both microbial metabolic nutrient limitations and CUE.\u003c/p\u003e\n\u003cp\u003eDifferent restoration measures significantly affected soil physicochemical properties, microbial biomass, extracellular enzyme activities, and their stoichiometric characteristics. All three restoration measures altered stoichiometric imbalance: compared with CK, BOF, MF, and SAP treatments exhibited higher C:N imbalance but lower C:P and N:P imbalances. All three models consistently indicated the absence of soil microbial N limitation across all restoration measures, while confirming the presence of C and P limitations. Both vector and V-T models showed that BOF alleviated C limitations with no significant differences in P limitations among treatments, whereas the threshold model revealed that BOF relieved C limitations but exacerbated P limitations. Additionally, BOF improved CUE. Main factors that influenced C and P limitation were soil available resources. Meanwhile, soil microbial biomass was the main factor influencing CUE. This study demonstrates the utility of ecoenzymatic stoichiometry theory (EEST) in elucidating microbial resource ecology in degraded desert grasslands, providing a basis for targeted restoration measures in degraded ecosystems.\u003c/p\u003e\n","funders":[{"organization":"National Natural Science Foundation of China","identifierType":"ror","identifier":"https://ror.org/01h0zpd94","awardNumber":"","awardDescription":"","awardTitle":"","order":0},{"organization":"Ningxia Natural Science Foundation","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":1},{"organization":"Ningxia key research and development plan projects","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":2},{"organization":"National Guide Local Science and Technology Development Projects of Ningxia Province","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":3},{"organization":"First-Class Discipline Construction Project (Grassland Science Discipline) for the high school in Ningxia","identifierType":"ror","identifier":"","awardNumber":"","awardDescription":"","awardTitle":"","order":4}],"keywords":["Carbon use efficiency","ecoenzymatic stoichiometry model","microbial nutrient limitation","Desert steppe","ecological restoration measures"],"fieldOfScience":"Environmental engineering","versionNumber":5,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"metadata_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.0zpc867cs","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.v6wwpzh8s"},"stash:versions":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.v6wwpzh8s/versions"},"stash:version":{"href":"/api/v2/versions/448520"},"stash:download":{"href":"/api/v2/datasets/doi%3A10.5061%2Fdryad.v6wwpzh8s/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.v6wwpzh8s","id":170089,"storageSize":22216653,"relatedPublicationISSN":"2150-8925","title":"Blue oak landscape classification outputs based on multi-temporal satellite observations and species distribution models","authors":[{"firstName":"Miranda","lastName":"Rose","email":"mbrose@sdsu.edu","affiliation":"San Diego State University","affiliationROR":"https://ror.org/0264fdx42","affiliations":[{"name":"San Diego State University","ror_id":"https://ror.org/0264fdx42"}],"orcid":"0000-0001-5269-3759"}],"abstract":"\u003cp\u003eThis dataset contains spatial outputs from an approach that integrates vegetation resilience metrics with climate-based projections of future habitat suitability for blue oak (\u003cem\u003eQuercus douglasii\u003c/em\u003e) in California. The approach combines temporal mixture residual (TMR) analysis of multi-decadal satellite time series with species distribution models (SDMs) forecasting mid-21st century habitat suitability under a high-emissions climate scenario (RCP 8.5, 2040–2069), averaged for two global climate models (CNRM-CM5 and HadGEM2-ES).\u003c/p\u003e\n\u003cp\u003eData were generated for two conservation properties managed by The Nature Conservancy: Randall Preserve (Kern County) and Dye Creek Preserve (Tehama County).\u003c/p\u003e\n\u003cp\u003eThe outputs are provided as GeoTIFF raster files (.tif), grouped into two categories:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eLand classification rasters (4 files):\n\u003cul\u003e\n\u003cli\u003eLandsat-based classification for Randall Preserve\u003c/li\u003e\n\u003cli\u003eLandsat-based classification for Dye Creek Preserve\u003c/li\u003e\n\u003cli\u003eSentinel-2–based classification for Randall Preserve\u003c/li\u003e\n\u003cli\u003eSentinel-2–based classification for Dye Creek Preserve\u003cbr\u003e\nEach classification raster contains five discrete classes, representing combinations of historical vegetation resilience (derived from TMR residuals) and projected climatic suitability for blue oak habitat. These classes can be used to identify zones of high future potential, low stability, or mismatch between historical resilience and future climate suitability.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003eTemporal mixture residual (TMR) rasters (4 files):\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eLandsat-based TMR residuals for Randall Preserve\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eLandsat-based TMR residuals for Dye Creek Preserve\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eSentinel-2–based TMR residuals for Randall Preserve\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eSentinel-2–based TMR residuals for Dye Creek Preserve\u003c/p\u003e\n\u003cp\u003eThe TMR rasters provide continuous values that quantify deviations from expected multi-decadal vegetation dynamics. Higher residuals indicate greater instability in vegetation trajectories, while lower residuals indicate more stable, resilient vegetation dynamics.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eTogether, these datasets enable users to explore how historical vegetation resilience interacts with projected climate suitability at multiple spatial resolutions (30 m for Landsat, 10 m for Sentinel-2). They provide spatially explicit guidance for conservation planning and management in blue oak woodlands, highlighting areas where conservation investment may be most effective under future climate change.\u003c/p\u003e\n","funders":[{"organization":"NASA Earth Science","identifierType":"ror","identifier":"https://ror.org/045s99b94","awardNumber":"80NSSC25K7837","awardDescription":"","awardTitle":"","order":0},{"organization":"The Nature Conservancy","identifierType":"ror","identifier":"https://ror.org/0563w1497","awardNumber":"","awardDescription":"","awardTitle":"","order":1}],"keywords":["Temporal mixture models","species distribution models ","Remote sensing","oak woodlands","climate change adaptation"],"fieldOfScience":"Biological sciences","relatedWorks":[{"relationship":"dataset","identifierType":"DOI","identifier":"https://doi.org/10.5061/dryad.gf1vhhmw6"},{"relationship":"article","identifierType":"DOI","identifier":"https://doi.org/10.1111/geb.13618"}],"versionNumber":6,"versionStatus":"submitted","curationStatus":"Published","versionChanges":"files_changed","publicationDate":"2026-06-23","lastModificationDate":"2026-06-23","visibility":"public","sharingLink":"http://datadryad.org/dataset/doi:10.5061/dryad.v6wwpzh8s","license":"https://spdx.org/licenses/CC0-1.0.html","metrics":{"views":0,"downloads":0,"citations":0}}]}}