cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m905qfv6m
title: Restoration and replication: a case study on the value of computational reproducibility assessment

description: Open science is vital to the interdisciplinary field of ecology due to its
 integrative nature and use of longitudinal datasets that build upon
 earlier data collections. To highlight the importance of open science in
 the rapidly growing discipline of restoration ecology, we conducted a
 'computational reproducibility’ assessment of a publication on a
 mining restoration program spanning several decades and over 250 km2 in a
 global biodiversity hotspot. Open data and code provided alongside the
 original publication were assessed for consistency with the results and
 conclusions of the original publication, as were potential limitations in
 findings due to the methodology. The impacts of inconsistencies and
 limitations were qualitatively assessed against the key findings from the
 publication and data were re-analysed where impacts were potentially
 significant. Of the six inconsistencies and limitations identified, two
 had a significant impact on five of the 11 key findings of the original
 publication, and one new key finding was made. The impact of this is of
 high ecological significance as the findings related to key restoration
 parameters: species richness (similarity of species richness between
 forest and 25-year-old restoration), functional diversity (correlation of
 species richness and functional diversity), and the restoration trajectory
 (long term trends and restored areas’ resilience to disturbance). These
 outcomes highlight the importance of open data and the value of detailed
 third-party data reviews, particularly in restoration ecology which relies
 on research findings to inform decision-making and policy and drive
 adaptive management.
DOI: 10.5061/dryad.np5hqbzzz
title: Landscape of Mast cell populations across organs in mice and humans

description: Mast cells (MCs) are tissue-resident immune cells which exhibit
 homeostatic and neuron-associated functions. Here we combined whole-tissue
 imaging and single-cell RNA sequencing datasets to generate a pan-organ
 analysis of MCs in mice and humans at steady state. In mice, we identify
 two mutually exclusive MC populations, MrgprB2+ connective tissue-type MCs
 and MrgprB2neg mucosal-type MCs, with specific transcriptomic core
 signatures. While MrgprB2+ MCs develop in-utero independently of the bone
 marrow, MrgprB2neg MCs develop after birth and are renewed by
 bone marrow progenitors. In humans, we unbiasedly identify 7 MC subsets
 (MC1 to 7) distributed across 12 organs with different transcriptomic core
 signatures. MC1 are preferentially enriched in the bladder, MC2 in the
 lungs, and MC4, MC6 and MC7 in the skin. Conversely, MC3 and MC5 are
 shared by most organs, but not skin. This comprehensive analysis offers
 valuable insights into the natural diversity of MC subtypes in both mice
 and humans.
description: Single cell datasets generated with 10X plateform at laboratory
 aggregated with publicly available datasets.
description: Tar archives contain raw sequencing data in fastq
 format. Rds file contains processed Seurat R
 objects.
DOI: 10.5061/dryad.63xsj3v7k
title: Data for: Antibiotic-degrading resistance changes bacterial community structure via species-specific responses

description: Some bacterial resistance mechanisms degrade antibiotics, potentially
 protecting neighbouring susceptible cells from antibiotic exposure. We do
 not yet understand how such effects influence bacterial communities of
 more than two species, which are typical in nature. Here, we used
 experimental multispecies communities to test the effects of clinically
 important pOXA-48-plasmid-encoded resistance on community-level responses
 to antibiotics. We found that resistance in one community member reduced
 antibiotic inhibition of other species, but some benefitted more than
 others. Further experiments with supernatants and pure-culture growth
 assays showed the susceptible species profiting most from detoxification
 were those that grew best at degraded antibiotic concentrations (greater
 than zero, but lower than the starting concentration). This pattern was
 also observed on agar surfaces, and the same species also showed
 relatively high survival compared to most other species during the initial
 high-antibiotic phase. By contrast, we found no evidence of a role for
 higher-order interactions or horizontal plasmid transfer in
 community-level responses to detoxification in our experimental
 communities. Our findings suggest carriage of an antibiotic-degrading
 resistance mechanism by one species can drastically alter community-level
 responses to antibiotics, and the identities of the species that profit
 most from antibiotic detoxification are predicted by their intrinsic
 ability to survive and grow at changing antibiotic concentrations.
DOI: 10.5061/dryad.ghx3ffbtw
title: Data from: Resolving a heated debate: the utility of prescribed burning as a management tool for biodiversity on lowland heath

description: We investigated the impact of prescribed burning and vegetation cutting on
 a chronisequence of heathland sites (107 in total) in the New Forest
 National Park, Hampshire, UK. We present data for vegetation cover, canopy
 active invertebrates collected with sweep nets and ground active
 invertebrates collected using pitfall traps. Using a multi-trophic
 approach, we compared the ecological impact of prescribed burning with two
 types of vegetation cutting (swiping and baling) as management tools for
 biodiversity outcomes for up to 20 years after management. Indicators
 included: Common Standards Monitoring assessment (CSM); vegetation species
 assemblage; invertebrate biodiversity; and available food resources for
 two characteristic heathland birds – the Dartford Warbler Sylvia undata
 and the Nightjar Caprimulgus europaeus. When compared with swiped sites,
 areas managed by prescribed burning resulted in: better habitat condition
 (assessed by CSM); higher cover of heathers; lower bracken cover; more
 areas of bare ground. We found no evidence that burning is detrimental for
 the investigated components of biodiversity. Cutting by swiping did not
 replicate the benefits of burning. Swiping supported grassland conditions
 that suit non-heathland species. Baling resulted in habitat conditions
 similar to prescribed burning but restricted replication of baled sites
 limited our conclusions. However, swiped sites supported high invertebrate
 abundance and diversity, including food resources for Dartford Warbler and
 Nightjar.
description: We present raw data. Data were collected from a 50 x 50 m area in
 the centre of each site. Two 50 m tapes were laid on the ground and
 location of sampling within this plot was randomised using a random number
 generator to select coordinates, we then paced to the selected locations.
 Here we have collated and present vegetation and invertebrate data
 collected as follows: Percentage cover of plant species was recorded in
 two 2x2 m quadrats per site; count data of canopy active invertebrates
 collected using 5 sweep net samples (each sweep presented separately),
 count data of ground active invertebrates where the data were pooled from
 six pitfall traps, count data of soil invertebrates where the data were
 pooled from six soil pits. 
description: The data are stored in one Excel workbook with multiple
 datasheets.
DOI: 10.5061/dryad.pzgmsbcsb
title: Supplementary materials for: Lost Loops: 19th century thermosiphon ventilation and its potential for heat recovery in buildings today

description: We investigate ventilation heat recovery with buoyancy flow, arranging
 interior spaces in an open thermal loop with heat exchange through
 partition walls. We draw inspiration from a Victorian-era thermosiphon
 scheme after finding it in Montreal’s former Royal Victoria Hospital and
 tracing the concept back to the original Centre Block of Canada’s
 Parliament Hill. We corroborate the archival evidence with analog models
 to visualize how the original hospital’s ventilation system worked. We use
 saline baths to verify how the siphon functioned and digital Schlieren to
 confirm how the full flow cycle worked with heat recovery. Then, to
 generalize these observations, we develop a mathematical model showing how
 heat recovery with buoyancy ventilation can work in simple room
 arrangements. We define a criterion for stable, unidirectional flow and a
 heat recovery efficiency limit of 50%. Finally, we validate the
 mathematical model experimentally, demonstrating stable, one-way flow
 close to the heat recovery limit.
DOI: 10.5061/dryad.wdbrv15tj
title: Ether lipid biosynthesis promotes lifespan extension and enables diverse prolongevity paradigms in Caenorhabditis elegans

description: Biguanides, including the world’s most prescribed drug for type 2
 diabetes, metformin, not only lower blood sugar but also promote longevity
 in preclinical models. Epidemiologic studies in humans parallel these
 findings, indicating favorable effects of metformin on longevity and on
 reducing the incidence and morbidity associated with aging-related
 diseases. Despite this promise, the full spectrum of molecular effectors
 responsible for these health benefits remains elusive. Through unbiased
 screening in C. elegans, we uncovered a role for genes necessary for ether
 lipid biosynthesis in the favorable effects of biguanides. We demonstrate
 that biguanides prompt lifespan extension by stimulating ether lipid
 biogenesis. Loss of the ether lipid biosynthetic machinery also mitigates
 lifespan extension attributable to dietary restriction, target of
 rapamycin (TOR) inhibition, and mitochondrial electron transport chain
 inhibition. A possible mechanistic explanation for this finding is that
 ether lipids are required for activation of longevity-promoting, metabolic
 stress defenses downstream of the conserved transcription factor
 skn-1/Nrf. In alignment with these findings, overexpression of a single,
 key, ether lipid biosynthetic enzyme, fard-1/FAR1, is sufficient to
 promote lifespan extension. These findings illuminate the ether lipid
 biosynthetic machinery as a novel therapeutic target to promote healthy
 aging.
description: Supplementary file 2 for Cedillo, L., Ahsan, F.M., et al., Ether
 Lipid Biosynthesis Promotes Lifespan Extension and Enables Diverse
 Prolongevity Paradigms in <em>Caenorhabditis
 elegans.</em> This file contains a dataset from
 the above manuscript in Microsoft Excel format where <em>C. elegans
 </em>nematodes (wild type and 3 mutants:
 <em>fard-1</em>, <em>ads-1</em>, and
 <em>acl-7</em>) were treated with vehicle or phenformin. Data
 on 3 biological replicates are included. The file has 3 tabs: 1) Raw mass
 counts for each identified ether lipid  2) Normalized mass counts for each
 identified ether lipid 3) Normalized and log10 transformed mass counts for
 each identified ether lipid The means by which data were normalized are
 described in the associated methods. 
description: This file can be opened in Microsoft Excel (all versions).
DOI: 10.5061/dryad.z8w9ghxj5
title: Data for: Thermal refugia and persistence of Texas horned lizards (Phrynosoma cornutum) in small towns

description: Vegetation loss is a primary cause of habitat degradation and results in a
 decline in reptile species abundance due to loss of refuge from predators
 and hot temperatures, and foraging opportunities. Texas horned lizards
 (Phrynosoma cornutum) have disappeared from many areas in Texas,
 especially from urbanized areas, probably in large part due to loss of
 suitable habitat. This species still occurs in some small towns in Texas
 that still contain suitable habitat. Long-term data from Kenedy and Karnes
 City, Texas indicate that when study sites experienced significant shrub
 and vegetation removal horned lizards declined by 79%. We hypothesize the
 decline was due to the degradation of the thermal landscape for these
 lizards. We determined the preferred temperature range (Tset25 −Tset75) of
 lizards at our study sites and took field measurements of body temperature
 (Tb). Temperature loggers were also placed in three microhabitats across
 our study sites. Shrubs and vegetation provided the highest quality
 thermal environment, especially for about 5 hours midday when temperatures
 in the open and buried under the surface in the open exceeded the lizards’
 critical maximum temperature (CTmax) or were above their preferred
 temperature range. Horned lizard density was positively related to the
 thermal quality of the habitat across our sites. Texas horned lizards in
 these towns require a heterogeneous mix of closely spaced microhabitats
 and especially thermal refugia, such as shrubs and vegetation along fence
 lines and in open fields. Maintaining thermal refugia is one of the most
 important and practical conservation actions that can be taken to help
 small ectotherms persist in modified human landscapes and cope with
 increasing temperatures due to climate change.
DOI: 10.5061/dryad.3n5tb2rp8
title: Data for: Positive in situ hybridization for ZIKV RNA in MFI tissues and gravid uteri slides

description: Zika virus (ZIKV) can be transmitted vertically from mother to fetus
 during pregnancy, resulting in a range of outcomes, including severe birth
 defects and fetal/infant death. Potential pathways of vertical
 transmission in utero have been proposed but remain undefined. Identifying
 the timing and routes of vertical transmission of ZIKV may help us
 identify when interventions would be most effective. Furthermore,
 understanding what barriers ZIKV overcomes to effect vertical transmission
 may help improve models for evaluating infection by other pathogens during
 pregnancy. The images included in this dataset belong to a study that
 aimed to determine the pathways of vertical transmission using a rhesus
 macaque model. Pregnant rhesus macaques were inoculated with
 104 plaque forming using (PFA) of an African-lineage ZIKV isolate
 (ZIKV-DAK) at gestational day 30 (term is 165 days). Maternal-fetal
 interface and gravid uteri were evaluated for ZIKV RNA using in situ
 hybridization (ISH). The included images are the maternal fetal interface
 tissues and coronal sections evaluated for ZIKV via ISH, areas were ZIKV
 RNA was detected have pink/red staining. The pattern of infection observed
 in the maternal-fetal interface provides evidence of vertical ZIKV
 transmission through the fetal membranes.
description: Detection of ZIKV RNA via in situ hybridization was conducted as
 previously described [Mohr EL et al. Ocular and uteroplacental pathology
 in a macaque pregnancy with congenital Zika virus infection. PLoS One
 2018;13:e0190617]. The ISH probes against the Zika virus genome were
 purchased commercially (Advanced Cell Diagnostics, Cat No. 468361, Newark,
 California, USA). Tissue sections were determined to be negative when ZIKV
 RNA was undetectable by RNAscope ISH, including instances when only a
 single, obviously non-cellular, focus of staining was observed. Imaging
 scanes were obtained with an Aperio Digital Pathology Slide Scanner (Leica
 Biosystems, Deer Park, IL, USA).
description: This dataset accompanies the manuscript "Vertical
 transmission of African-lineage Zika virus through the fetal membranes in
 a rhesus Macaque (<em>Macaca mulatta</em>)
 model". The .SVS files require Aperio ImageScope -
 Pathology Slide viewing software. This software is avialble for free from
 the Leica biosystems website. This software is only compatable with PCs.
 The remaining files do not require any specialized software/programs and
 can be opened with most image viewing software.
DOI: 10.5061/dryad.jm63xsjgx
title: Interspecific introgression and widespread intraspecific gene flow in a clade of tropical and subtropical seabirds

description: The mechanisms that restrict gene flow between populations and facilitate
 population differentiation and speciation vary across the tree of life. In
 systems where physical barriers to gene flow are dynamic over time and
 space, such as many marine species, genetic introgression may be a major
 factor in the speciation process. In sympatric species of seabirds,
 hybridization has been frequently observed but few studies have
 investigated patterns of introgression. We used whole-genome sequence data
 to test for interspecific introgression between five pairs of tropical and
 subtropical seabird species and to test for gene flow within species
 across major land mass barriers and ocean basins. We found evidence for
 introgression between: blue-footed (Sula nebouxii) and Peruvian boobies
 (S. variegata); masked (S. dactylatra) and Nazca boobies (S. granti); and
 blue-footed and Nazca boobies. We found no evidence of introgression
 between blue-footed and brown boobies (S. leucogaster), or masked and
 brown boobies, despite observed hybridization between these species. We
 also found evidence for gene flow across several major land masses in
 three pantropical species: red-footed (S. sula), brown, and masked
 boobies. Finally, we report mixed evidence for ancient introgression
 between brown boobies and the ancestor of blue-footed, Peruvian, masked,
 and Nazca boobies. Our work indicates (1) that interspecific introgression
 has shaped contemporary booby diversity in the eastern Pacific, and (2)
 that contemporary physical barriers to gene flow between booby colonies
 are not absolute. Our findings contribute novel insights to the growing
 body of evidence that introgression is a widespread evolutionary process.
description: # Interspecific introgression and widespread intraspecific gene flow in a
 clade of tropical and subtropical seabirds
 [https://doi.org/10.5061/dryad.jm63xsjgx](https://doi.org/10.5061/dryad.jm63xsjgx) We have made available the supplementary tables and figures. Raw sequence data can be found in the Sequence Read Archive (SRA) with BioProject ID: [PRJNA836623](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA836623). ## Description of the data and file structure Details of the methods involved can be found in the manuscript with the same name, which we have submitted to Systematic Biology. The code used to process this data can be found at the link below. ## Code/Software [https://github.com/dannyjackson/sula](https://github.com/dannyjackson/sula)
DOI: 10.5061/dryad.t4b8gtj6s
title: Data for: Developmental plasticity in anurans: meta-analysis reveals effects of larval environments on size at metamorphosis and timing of metamorphosis

description: Many anuran amphibians (frogs and toads) rely on aquatic habitats during
 their larval stage. The quality of this environment can significantly
 impact the overall lifetime fitness and dynamics of the population. Over
 450 studies have been published on the impact of the environment on anuran
 developmental plasticity, yet we lack a synthesis of these effects across
 different environments. We conducted a meta-analysis and used a
 comparative approach to understand whether developmental plasticity in
 response to different larval environments produces predictable changes in
 metamorphic phenotypes. We analyzed data from 124 studies spanning 80
 anuran species and six larval environments and showed that interspecific
 variation in mass at metamorphosis and the duration of the larval period
 is partly explained by the type of environment experienced during the
 larval period. Phylogenetic relationships among species were not
 associated with variation in mass at metamorphosis plasticity or duration
 of the larval period plasticity. Larval environments tended to reduce mass
 at metamorphosis relative to control conditions, with the degree of change
 depending on the identity and severity of environmental change. Higher
 temperatures and lower water levels shortened the duration of the larval
 period, whereas less food and higher densities increased the duration of
 the larval period. Our results provide a foundation for future studies on
 developmental plasticity, especially in response to global changes. This
 study provides motivation for additional work that links developmental
 plasticity with fitness consequences within and across life stages, as
 well as how the outcomes described here are altered in compounding
 environments.
DOI: 10.5061/dryad.b2rbnzsmt
title: Distribution of the Allium filidens group in Kyrgyzstan and Central Asia

description: On the basis of herbarium specimens and documented observations, a
 taxonomic confusion around Allium filidens s.l. (including A.
 filidentiforme) in Kyrgyzstan is resolved. The species status of A.
 filidentiforme is confirmed, and this species is classified in A. subsect.
 Crystallina, comb. nov. In Central Asia, the A. filidens group (A.
 subsect. Filidentia) includes species with whitish perianth colours (A.
 filidens s.str., A. karakense, A. ugami) and greenish perianth colours (A.
 mogianense, A. valentinae). The occurrence of A. filidens s.str. in
 Kyrgyzstan is confirmed. Allium valentinae is reported as new to
 Kyrgyzstan. The nomenclature of A. filidens is clarified, and its neotype
 is designated. The complete distributions of A. filidens, A.
 filidentiforme, A. mogianense, A. ugami and A. valentinae are mapped.
description: The dataset is based on herbarium specimens and documented
 observations. Herbarium collections from Kyrgyzstan were examined at the
 Institute of Biology, Bishkek, Kyrgyzstan (FRU), Komarov Botanical
 Institute, St.-Petersburg, Russia (LE) and Moscow State University, Russia
 (MW). Specimens were examined de visu (FRU, LE) or online (MW). Herbarium
 data were complemented with documented observations. Distribution maps
 were compiled on the basis of specimens examined and documented
 observations; when specimens and observations were largely unavailable,
 the occurrence data were borrowed from reliable treatments (Wendelbo
 1971). All records were georeferenced by the authors with the best
 precision available.
description: For this data format, Microsoft Excel is required.
DOI: 10.5061/dryad.vmcvdnczc
title: Food retail in remote Australia

description: This dataset documents food retail stores that service remote Indigenous
 communities in Australia. A seed list created by the National Indigenous
 Australians Agency (NIAA) was extended and validated, including reviews by
 experts and stakeholders, during 2022. Store location, contact
 information, management, and ownership/legal registration were identified
 along with the size of the community the store serves. A final dataset of
 233 remote or very remote stores was created.
description: A seed list from the National Indigenous Australians Agency
 (NIAA) was extended and validated. The dataset was extended using desk
 research with additional reviews by experts and stakeholders, during
 2022.
description: Data is stored in a single comma-delimited CSV. A data dictionary
 is provided in a separate CSV.