cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bcc2fqzf6
title: Osmanthus plastid genome sequence for: Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae)

description: Species of Osmanthus are economically important ornamental trees, yet
 information regarding their plastid genomes (plastomes) has rarely been
 reported, thus hindering taxonomic and evolutionary studies of this small
 but enigmatic genus. Here, we performed comparative genomics and
 evolutionary analyses on plastomes of 16 of the 28 currently accepted
 species, with 11 plastomes newly sequenced. Phylogenetic studies
 identified four main lineages within the genus that are here designated:
 ‘Caucasian Osmanthus’ (corresponding to O. decorus), ‘Siphosmanthus’
 (corresponding to O. sect. Siphosmanthus), ‘O. serrulatus + O.
 yunnanensis’, and ‘Core Osmanthus’ (corresponding to O. sect. Osmanthus +
 O. sect. Linocieroides). Molecular clock analysis suggested that Osmanthus
 split from its sister clade c. 15.83 Ma. The estimated crown ages of the
 lineages were the following: genus Osmanthus at 12.66 Ma; ‘Siphosmanthus’
 clade at 5.85 Ma; ‘O. serrulatus + O. yunnanensis’ at 4.89 Ma; ‘Core
 Osmanthus’ clade at 6.2 Ma. Ancestral state reconstructions and trait
 mapping showed that ancestors of Osmanthus were spring-flowering and
 originated at lower elevations. Phylogenetic principal component analysis
 clearly distinguished spring-flowering species from autumn-flowering
 species, suggesting that flowering time differentiation is related to the
 difference in ecological niches. Nucleotide substitution rates of 80
 common genes showed a slow evolutionary pace and low nucleotide
 variations, all genes being subjected to purifying selection.
description: Total genomic DNA was isolated
 from fresh leaves of a single individual using the DNeasy Plant Mini Kit
 (Qiagen, Valencia, CA), and was used to prepare the shotgun library
 following the manufacturer’s protocol for Hiseq 4000 Sequencing System
 (Illumina, CA, USA). The library was sequenced by Nanjing Genepioneer
 Biotechnologies Inc. (Nanjing, China). Raw reads were obtained and trimmed
 using CLC Genomics Workbench v9 (CLC Bio, Aarhus, Denmark) with default
 parameters. The resultant clean reads were then employed to assemble the
 plastome using the program NOVOPlasty (Dierckxsens et al., 2017) with <em>O.
 fragrans</em> (GenBank: MG820121) (Duan et al., 2019) as the
 reference. The resultant genome was annotated by PGA (Qu et al., 2019).
 The plastomes generated in the present study are available in the NCBI
 Genbank database.
DOI: 10.5281/zenodo.17948920
title: Database experimental data (dataset 1 of 4) "Visualization and quantification of gas-liquid mass transfer in a sparger flow using a wire-mesh sensor", dataset 1 of 4, calibration series

description: ## DATABASE EXPERIMENTAL DATA (DATASET 1 OF 4) "VISUALIZATION AND QUANTIFICATION OF GAS-LIQUID MASS TRANSFER IN A SPARGER FLOW USING A WIRE-MESH SENSOR", DATASET 1 OF 4, CALIBRATION SERIESReference Open-Access journal publication: Alvaro Ramos Perez, Terttaliisa Lind, Victor Petrov, Annalisa Manera, Horst-Michael Prasser, Visualization and quantification of gas–liquid mass transfer in a sparger flow using a wire-mesh sensor, Chemical Engineering Science, Volume 320, Part A, 2026, 122360, ISSN 0009-2509, doi:10.1016/j.ces.2025.122360.

## THIS DATA CORRESPONDS TO THE DATASET 1 OF 4, CALIBRATION SERIES. THE ENTIRE DATASET LIST OF THE PUBLICATION IS:-DATASET 1 OF 4, CALIBRATION SERIES-DATASET 2 OF 4, TRACER SERIES-DATASET 3A+3B OF 4, CO2 SERIES-DATASET 4 OF 4, AIR SERIES

## WMS DATA"README_WMS.txt": Description of data matrix "WMS.csv" and data format "WMS.zip"
DOI: 10.5061/dryad.j0zpc86gv
title: A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues

description: Although cellular senescence drives multiple age-related co-morbidities
 through the senescence-associated secretory phenotype (SASP), in vivo
 senescent cell identification remains challenging. Here, we generated a
 gene set (SenMayo) and validated its enrichment in bone biopsies from two
 aged human cohorts. We further demonstrated reductions in SenMayo in bone
 following genetic clearance of senescent cells in mice and in adipose
 tissue from humans following pharmacological senescent cell clearance. We
 next used SenMayo to identify senescent hematopoietic or mesenchymal cells
 at the single cell level from human and murine bone marrow/bone scRNA-seq
 data. Thus, SenMayo identifies senescent cells across tissues and species
 with high fidelity. Using this senescence panel, we were able to
 characterize senescent cells at the single-cell level and identify key
 intercellular signaling pathways. SenMayo also represents a potentially
 clinically applicable panel for monitoring senescent cell burden with
 aging and other conditions as well as in studies of senolytic drugs.
description: Source Code Raw counts
DOI: 10.5061/dryad.cnp5hqc6g
title: Western Juniper Woodlands climate relations meta analysis

description: These data are based on tree-ring data from the internation tree ring data
 base and PRISM climate data.
description: Tree-ring data comes from 13 Western Juniper tree-ring studies
 from the International tree ring data base. Climate data comes from the
 PRISM climate group. Climate data has been aggregated into 4 month
 "seasons." All data has been standardized to a mean of 0 and an
 SD of 1.
DOI: 10.5061/dryad.jwstqjqbn
title: Replication data and code for: Environmental discourse exhibits consistency and variation across spatial scales on Twitter

description: Social media platforms, such as Twitter, are an increasingly important
 source of information and are forums for discourse within and between
 interest groups. Research highlights how social media communities have
 amplified movements such as the Arab Spring, #MeToo, and Black Lives
 Matter. But environmental digital discourse remains underexplored. In the
 present article, we apply automated text analysis to 200,000 Twitter users
 in several countries following leading environmental nongovernmental
 organizations. Some issues such as public action to decarbonize society or
 species conservation were discussed more intensely than agriculture or
 marine conservation. Our results illustrate where environmental discourse
 diverges and converges on Twitter across countries, states, and
 characteristics, such as political ideology. Using the coterminous United
 States as a case study, we observed that the prominence of issues varies
 across states and, in some cases, covaries with political ideology across
 counties. Our findings show paths forward to characterizing environmental
 priorities across many issues at unprecedented scale and extent. In this
 repository, we provide data and code to reproduce the results in the main
 text of this manuscript. This replication code and dataset accompany this
 manuscript: https://doi.org/10.1093/biosci/biac051
description: These data were scraped from Twitter. Please consult the README
 for more information.
description: Twitter data querying must comply with Twitter's Terms of
 Service. Researchers should obtain human ethics approval from their
 Institutional Review Board before scraping Twitter data.
DOI: 10.5061/dryad.fxpnvx0tv
title: Warming drives poleward range contractions of Beringian endemic plant species at high latitudes

description: Aim: Species are expected to disperse poleward in response to climate
 change. For species that are endemic to the high latitudes, this implies
 that many in the future would face a “no-where-to-go” situation as they
 are currently occupying the northernmost portion of the continent.
 Further, because endemism may arise from a combination of physical
 barriers, climate, and geological history, the persistence of many species
 may require spatial matching of multiple environmental factors within a
 limited dispersal space. Thus, it is not clear how endemic species might
 spatially adjust their distributions in response to climate change and
 whether there are future climate change refugia for these species.
 Location: Northwest North
 America                                Taxa: Plants Time period: Current and the future (2040) Methods: We used ensemble bioclimatic models to evaluate drivers and directional patterns of future change in the distributions of 66 North American Beringian and Amphi-Beringian species currently occurring in Alaska and the Yukon. We explored the spatial pattern of species richness, losses and climate change refugia across the region. Results: More than 80% of the species showed northward shifts in their latitudinal centroids under intermediate warming and are expected to shift their range northward by more than 140km on average by 2040. Additionally, more than 60% were projected to experience range contractions and up to 20% of the species would have the potential to expand their ranges by more than 100%. Main conclusions: Suitable habitat for endemic species in northwest North America is expected to decline significantly, especially for species occupying the Arctic tundra. Although the models identified several potential refugia from future climate change, especially at high latitude and elevation, whether the species would be able to colonize new habitats on their own and/or capitalize sufficiently on in situ refugia remains a pertinent conservation question.
DOI: 10.5061/dryad.vhhmgqnw3
title: Data from: Functional modularity and mechanical stress shape plastic responses during fish development

description: The adaptive potential of plastic phenotypes relies on combined
 developmental responses. Here, we investigated how manipulation of
 developmental conditions related to foraging mode in Megaleporinus
 macrocephalus fish induces plastic responses at different levels: 1)
 functional modularity of skull bones, 2) biomechanical properties of the
 chondrocranium using Finite Element Models, 3) bmp4 expression levels,
 used as a proxy for molecular pathways involved in bone responses to
 mechanical load. We identified new modules in the experimental groups,
 suggesting increased integration in head bone elements associated with the
 development of subterminal and upturned mouths, which are major features
 of Megaleporinus plastic morphotypes released in the lab. Plastic
 responses in head shape involved differences in the magnitude of
 mechanical stress, which seem restricted to certain chondrocranium
 regions. Three bones represent a ‘mechanical unit’ related to changes in
 mouth position induced by foraging mode, suggesting that functional
 modularity might be enhanced by specific regions responding to load.
 Differences in bmp4 expression levels between plastic morphotypes indicate
 associations between molecular signaling pathways and biomechanical
 responses to load. Our results offer a multilevel perspective of
 epigenetic factors involved in plastic responses, expanding our knowledge
 about mechanisms of developmental plasticity that originate novel complex
 phenotypes.
description: # Data from: Functional modularity and mechanical stress shape plastic
 responses during fish development Authors: Leandro Lofeu, Felipe
 Montefeltro, Monique Simon, Tiana Kohlsdorf. Description: The raw data are
 available here in a set of four xlsx Worksheet files into a zip file
 called "DATA_Lofeu et al.2022", as follows: * BMP4 QR values:
 with raw and Log10 transformed Quantitative Relation values for BMP4
 expression. * Von Misses values LS1: with raw and Log10 transformed values
 of Von Misses used to Compare mechanical stress magnitude and the Load
 space on Load Scenario 1. * Von Misses values LS2: with raw and Log10
 transformed values of Von Misses used to Compare mechanical stress
 magnitude and the Load space on Load Scenario 2. * Linear Distances: raw
 linear distance extracted from landmarks and used to build
 variation/covariation matrices used on Modularity tests. Experimental and
 Control groups: Bottom Complex- BC Bottom Simples- BS Surface Complex- SC
 Surface Simple- SS Lagoon (Control)- Lg
DOI: 10.5281/zenodo.18399959
title: Dataset for paper on Ab initio study on photocatalytic properties of PtSSe-WXY Janus heterostructures
DOI: 10.5061/dryad.m905qfv38
title: Patch-clamp dataset (SyncroPatch384PE) for control variants used in a calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome

description: Modern sequencing technologies have revolutionised our detection of gene
 variants. However, in most genes, including KCNH2, the majority
 of missense variants are currently classified as variants of
 uncertain significance (VUS). The aim of this study was to
 investigate the utility of an automated patch-clamp assay for aiding
 clinical variant classification in
 the KCNH2 gene. The assay was designed
 according to recommendations proposed by the ClinGen Sequence Variant
 Interpretation Working Group. Thirty-one variants (17 pathogenic/likely
 pathogenic, 14 benign/likely benign) were classified internally as variant
 controls. They were heterozygously expressed in Flp-In HEK293 cells for
 assessing the effects of variant on current density and channel gating in
 order to determine the sensitive and specificity of the assay. All 17
 pathogenic variant controls had reduced current density and 13/14 benign
 variant controls had normal current density, which enabled determination
 of normal and abnormal ranges for applying moderate or supporting evidence
 strength for VUS reclassification. Inclusion
 of KCNH2 functional assay evidence enabled us to
 reclassify 6 out of 44 VUS as likely pathogenic. The high-throughput patch
 clamp assay can provide moderate strength evidence for clinical
 interpretation of clinical KCNH2 variants
 and demonstrates the value of developing automated patch clamp
 assays for functional characterisation of ion channel gene variants.
description: The dataset was collected using the Nanion
 Syncropatch 384PE automated patch clamp system. Three voltage protocols
 were used to interrogate steady-state activation, steady-state
 deactivation (and recovery from inactivation) as well as rates of onset of
 inactivation. The raw data sets obtained from the PatchControl software
 (Nanion) are included in the ‘SyncroPatch_data.zip’ file, which contains
 additional variants that were not part of this study. The datasets
 obtained for variants that were investigated in this study after
 assessment for QC (seal resistances &gt; 300 MΩ, capacitance: 5-50 pF)
 are included as separate csv files ‘CSV_files.zip’.
description: The raw SyncroPatch datafiles (obtained after
 unzipping the SyncroPatch_data.zip file) can be opened using DataControl
 software (Nanion). Data can be reanalysed directly in DataControl or have
 been exported as csv files, which can be analysed using Python scripts
 available at
 https://git.victorchang.edu.au/projects/SADA/repos/syncropatch_automated_analysis/browse. The list of variants assayed on each plate are available in the “compound editor” tab of each dataset. This information is also provided in the excel spreadsheet: ‘variant locations.xlsx’ so that users can identify which plate dataset they need to open to look at specific variants.
DOI: 10.5281/zenodo.18399958
title: Dataset for paper on Ab initio study on photocatalytic properties of PtSSe-WXY Janus heterostructures
DOI: 10.5061/dryad.x3ffbg7mq
title: Colour polymorphism in the sea snake Emydocephalus annulatus

description: Evolutionary theory suggests that polymorphic traits can be maintained
 within a single population only under specific conditions, such as
 negative frequency-dependent selection or heterozygote advantage.
 Non-venomous turtle-headed sea snakes (Emydocephalus annulatus) living in
 shallow bays near Noumea in New Caledonia exhibit three colour morphs:
 black, black-and-white banded, and an intermediate (grey-banded) morph
 that darkens with age. We recorded morph frequencies during 18 consecutive
 years of surveys, and found that the numbers of recruits (neonates plus
 immigrants) belonging to each morph increased in years when that morph was
 unusually rare in the population, and decreased when that morph was
 unusually common. Thus, morph frequencies are maintained by negative
 frequency-dependent selection. We interpret the situation as Batesian
 mimicry of highly venomous sea snakes (Aipysurus, Hydrophis, Laticauda)
 that occur in the same bays, and range in colour from black-and-white
 banded to grey-banded. Consistent with the idea that mimicry may protect
 snakes from attack by large fish and sea eagles, behavioural studies have
 shown that smaller fish species in these bays flee from banded snakes but
 attack black individuals. As predicted by theory, mimetic (banded) morphs
 are less common than the cryptically-coloured melanic morph.
description: Three adjacent populaions were surveyed annually, in January,
 using mark-recapture methods. The colour phase of every individual was
 scored into one of three categories. The analyis looks at how the relative
 numbers of snakes of eachcolour morph changed through time in each
 population.
DOI: 10.5061/dryad.573n5tb9d
title: Epigenetic induction may speed up or slow down speciation with gene flow: code and data

description: Speciation is less likely to occur when there is gene flow between nascent
 species.  Natural selection can oppose gene flow and promote
 speciation if there is variation in ecological conditions among the
 nascent species' locations.  Previous theory on ecological
 speciation with gene flow has focused primarily on the role of genetic
 variation in ecological traits, largely neglecting the role of non-genetic
 inheritance or transgenerational plasticity.  Here we present the
 simulation code and data from models incorporating both genetic
 and epigenetic inheritance, the latter representing a form of non-genetic
 inheritance.  We investigate the rate of speciation for a
 population that inhabits two patches, connected by migration, and find
 that adaptively-biased epigenetic induction can speed up or slow down
 speciation, depending on the form of the map from genotype and epigenotype
 to phenotype. While adaptively-relevant epigenetic variation can speed up
 speciation by reducing the fitness of migrants and hybrids, it can also
 slow down speciation. This latter effect occurs when the epialleles are
 able to achieve adaptation faster than the genetic alleles, thereby
 weakening selection on the latter.
description: Please see the "README_description_of_data.pdf" file
 for description of data.
DOI: 10.5061/dryad.0k6djhb28
title: Ecological conditions predict the intensity of Hendra virus excretion over space and time from bat reservoir hosts

description: The ecological conditions experienced by wildlife reservoirs affect
 infection dynamics and thus the distribution of pathogen excreted into the
 environment, which have been hypothesized to shape risks of zoonotic
 spillover. However, few systems have data on both long-term ecological
 conditions and pathogen excretion to advance mechanistic understanding and
 test environmental drivers of spillover risk. We here analyze three years
 of Hendra virus data from nine Australian flying fox roosts with
 covariates derived from long-term studies of bat ecology. We show that the
 magnitude of winter pulses of viral excretion, previously considered
 idiosyncratic, are most pronounced after recent food shortages and in bat
 populations displaced to novel habitats. We further show that cumulative
 pathogen excretion over time is shaped by bat ecology and positively
 predicts spillover frequency. Our work emphasizes the role of reservoir
 host ecology in shaping pathogen excretion and provides a new approach to
 estimate spillover risk.
DOI: 10.5061/dryad.8w9ghx3ph
title: Sea-surface temperature anomalies mediate changes in fish richness and abundance in Western North Atlantic and Gulf of Mexico estuaries

description: Aim: Anthropogenic-driven warming of marine systems has resulted in a
 series of biological and physiological responses that are fundamentally
 altering ecosystem structure. Because estuaries exist at the land-ocean
 interface, they are particularly vulnerable to the effects of ocean
 warming as they can undergo rapid biogeochemical and hydrological shifts
 due to climate and land-use change. We explored how fish diversity
 structures—turnover, richness and abundance—have changed in the western
 North Atlantic and Gulf of Mexico estuaries through space and time and the
 drivers of change. Location: North Atlantic and Northern Gulf of Mexico
 Taxa: Fish Results: We found that species richness and abundance, turnover
 have increased in North Atlantic and northern Gulf of Mexico estuaries in
 the last 3 decades. These changes were mediated largely by sea-surface
 temperature anomalies, especially in more northern estuaries where warming
 has been relatively pronounced. There is also an indication that
 urbanization, perhaps through habitat fragmentation and/or fisheries
 activities may be contributing to the increase in fish richness in many of
 these estuaries. Main Conclusion: The increasing trajectory of turnover in
 many of the estuaries suggests that the fish communities have changed
 fundamentally from the baselines. A fundamental change in community
 composition can lead to an irreversible trophic imbalance or alternative
 stable states among other outcomes. Thus, predicting how shifting
 community structures might influence food webs, ecosystem stability and
 human resource use remains a pertinent task.
description: We compiled long-term (&gt;30 years),
 continent-wide fisheries independent trawl surveys conducted in
 estuaries—from the Gulf of Maine to the Gulf of Mexico (U.S. waters)—and
 combined these with climate and land-use-land-cover data to examine trends
 and ecological drivers of fish richness, abundance, and turnover using
 mixed-effect models.
DOI: 10.5061/dryad.5mkkwh77v
title: Molecular phylogeny reveals the past transoceanic voyages of drywood termites (Isoptera, Kalotermitidae)

description: Termites are major decomposers in terrestrial ecosystems and the second
 most diverse lineage of social insects. The Kalotermitidae form the
 second-largest termite family and are distributed across tropical and
 subtropical ecosystems, where they typically live in small colonies
 confined to single wood items inhabited by individuals with no foraging
 abilities. How the Kalotermitidae have acquired their global distribution
 patterns remains unresolved. Similarly, it is unclear whether foraging is
 ancestral to Kalotermitidae or was secondarily acquired in a few species.
 These questions can be addressed in a phylogenetic framework. We inferred
 time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial
 genomes of ~120 species, about 27% of kalotermitid diversity, including
 representatives of 21 of the 23 kalotermitid genera. Our mitochondrial
 genome phylogenetic trees were corroborated by phylogenies inferred from
 nuclear ultraconserved elements derived from a subset of 28 species. We
 found that extant kalotermitids shared a common ancestor 84 Mya (75–93 Mya
 95% HPD), indicating that a few disjunctions among early-diverging
 kalotermitid lineages may predate Gondwana breakup. However, most of the
 ~40 disjunctions among biogeographic realms were dated at less than 50
 Mya, indicating that transoceanic dispersals, and more recently
 human-mediated dispersals, have been the major drivers of the global
 distribution of Kalotermitidae. Our phylogeny also revealed that the
 capacity to forage is often found in early-diverging kalotermitid
 lineages, implying the ancestors of Kalotermitidae were able to forage
 among multiple wood pieces. Our phylogenetic estimates provide a platform
 for critical taxonomic revision and future comparative analyses of
 Kalotermitidae.