cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fj6q5740f
title: NGS data from: Predominant HDR-dependent genome editing and prevention of byproducts by DNA repair pathway choice

description: CRISPR-Cas9 genome editing has been widely adapted to cleave genomic DNA
 sequences of interest. Cellular repair of the CRISPR induced DNA
 double-strand breaks is dominated by error prone end joining pathways that
 outcompete inefficient homology-directed repair (HDR) that would allow
 precise introduction of a mutation present in a supplied synthetic DNA
 donor. To achieve predominant HDR, we studied the combinatory effect of
 inhibitory mutations in genes that are central to competing repair
 pathways.
DOI: 10.5061/dryad.wh70rxwsp
title: Multiple locus phylogeography to evaluate the diversity of the Cold Water Soft Coral Alcyonium spp. (Anthozoa, Octocorallia: Alcyonacea) between South America and West Antarctic Peninsula

description: The Antarctic marine environment has a unique geologic and climatic
 history that has contributed to the evolution of a diverse range of
 species. With the environment undergoing warming trends, it is critical to
 understand the history of Antarctic species to anticipate the effect of
 environmental changes on ecosystem functioning. Soft corals are a crucial
 component of the benthic marine assemblage of the Southern Ocean, which is
 recognized as a biodiversity hotspot. Nevertheless, our comprehension of
 the biogeographical patterns and distribution of this group in the
 Southern Ocean is insufficient. In this study, we used molecular
 phylogenetic reconstructions, divergence estimations, and species
 delimitations to examine the spatial patterns of genetic diversity in
 shallow-sea octocorals of the Alcyonium spp. in the Southern Ocean and
 adjacent regions, utilizing DNA sequences (mtMutS-COI and 28S) and Genomic
 Single Nucleotide Polymorphisms (SNPs) markers. The study revealed
 significant genetic differences between different populations, with a
 clear genetic break observed between SA and WAP populations. We also
 identified four putative species or evolutionary independent units (EIUs),
 with one putative species found in the West Antarctic Peninsula, one in
 the Patagonian region, and two found in Burdwood Bank and Falkland Island,
 respectively. The divergence time estimation indicated that the
 diversification process of Alcyonium began about 7.2 million years ago,
 with the initial separation occurring between WAP and SA populations.
 Furthermore, the study emphasized the critical role played by the Scotia
 Sea islands, especially Burdwood Bank, in the evolution of Southern Ocean
 biota. Overall, the findings provide evidence for the existence of
 multiple species within the genus Alcyonium and information on
 the evolutionary history of this group for the first time in the Southern
 Ocean.
description: Almost all collections were
 obtained through SCUBA diving, at depths varying between 5 m to 40 m on
 rocky substratum. In the case of BB sampling, a mini–Agassiz Trawl (AGT)
 with a mouth width of 1.25 m and a mesh size of 1 cm was used to collect
 specimens at a depth of 395 m. After collection, specimens were
 photographed in the laboratory. Subsequently, they were preserved in 70%
 ethanol for DNA analysis and fixed in 90% ethanol for taxonomic
 examination. Taxonomic description was done based on consistent
 differences observed in sclerite morphology and colony growth form, using
 the criteria described by (Van Ofwegen et al., 2007). For DNA analysis two
 molecular approaches were used: (1) Mito-nuclear genes and (2) Single
 Nucleotide Polymorphisms (SNPs).
description: dartR V.1.1.11 package
DOI: 10.5061/dryad.brv15dvdv
title: MicroCT scan of the nasal airway of a domestic short hair cat

description: The peripheral structures of mammalian sensory organs often serve to
 support their functionality, such as alignment of hair cells to the
 mechanical properties of the inner ear. Here, we examined the
 structure-function relationship for mammalian olfaction by creating an
 anatomically accurate computational nasal model for the domestic cat
 (Felis catus) based on high resolution microCT and sequential histological
 sections. Our results showed a distinct separation of respiratory and
 olfactory flow regimes, featuring a high-speed dorsal medial stream that
 increases odor delivery speed and efficiency to the ethmoid olfactory
 region without compromising the filtration and conditioning purpose of the
 nose. These results corroborated previous findings in other mammalian
 species, which implicates a common theme to deal with the physical size
 limitation of the head that confines the nasal airway from increasing in
 length infinitely as a straight tube. We thus hypothesized that these
 ethmoid olfactory channels function as parallel coiled chromatograph
 channels, and further showed that the theoretical plate number, a
 widely-used indicator of gas chromatograph efficiency, is more than 100
 times higher in the cat nose than an “amphibian-like” straight channel
 fitting the similar skull space, at restful breathing state. The parallel
 feature also reduces airflow speed within each coil, which is critical to
 achieving the high plate number, while feeding collectively from the
 high-speed dorsal medial stream so that total odor sampling speed is not
 sacrificed. The occurrence of ethmoid turbinates is an important step in
 the evolution of mammalian species that correlates to their expansive
 olfactory function and brain development. Our findings reveal novel
 mechanisms on how such structure may facilitate better olfactory
 performance, furthering our understanding of the successful adaptation of
 mammalian species, including F. catus, a popular pet, to diverse
 environments.
description: A domestic short hair cat cadaver was obtained, dissected, and
 fixed in 4% paraformaldehyde. Micro-CT scans of the head were then taken
 with contrast agent.
DOI: 10.5061/dryad.zw3r228cs
title: Latitudinal patterns of aquatic insect emergence driven by climate

description: Aim: Emerging aquatic insects link aquatic and terrestrial ecosystems
 across the Earth. Their diversity, abundance and functional importance
 mean their emergence is an important phenological event. Nevertheless,
 aquatic insect emergence is understudied at a global scale compared to
 other phenological events, despite changing phenology being one of the
 most significant ecological responses to climate change. Here, we
 quantitatively describe the global patterns, and key proposed drivers, of
 seasonal aquatic insect emergence, to further understand how these
 patterns might change in the future. Location: Global. Time period:
 1950–2018. Major taxa studied: Emerging aquatic insects. Methods: We
 extracted monthly emergence data from 86 studies across 163 sites to
 construct 1053 annual emergence curves. We parameterised the curves using
 two complementary metrics of seasonality, which were modelled against
 geographic and climatic variables to determine the direct and indirect
 relationships between them. Results: We found clear global trends in
 aquatic insect emergence patterns across latitude and underlying climates.
 Between-month variation and temporal restriction of emergence increased
 from the equator to the poles, going from small, aseasonal fluctuations in
 the warm, thermally stable tropics to large, seasonal peaks at cooler,
 thermally unstable higher latitudes. While emergence trends were
 associated with gradients of precipitation, temperature was the dominant
 climatic driver of the latitudinal trend. Main conclusions: These findings
 suggest that with climate warming, aquatic insects will emerge over longer
 periods, diluted in abundance and displaying less seasonal emergence
 patterns with smaller between-month fluctuations. This may result in
 disruption of ecosystem functions seasonally dependent on aquatic insects,
 such as riparian predation, pollination and disease transmission. The
 cross-ecosystem life cycle of aquatic insects means changes to their
 seasonal patterns of emergence will have impacts in both aquatic and
 terrestrial ecosystems. 
description: Further methodological details on data collection can be found
 within the published paper and its supplementary material.
description: This archive contains the dataset used for all modelling,
 analysis and plotting carried out in this paper. Please see the
 "ReadMe" for further descriptive information on the contents of
 the dataset and the units of each column. Any missing data are indicated
 by “NA”. All additional methodological details are present in the main and
 supplementary components of the published paper.
DOI: 10.25338/b8rd26
title: California subalpine forest post-fire conifer regeneration data

description: Wildfire may facilitate climate tracking of forest species moving upslope
 or north in latitude. For subalpine tree species, for which higher
 elevation habitat is limited, accelerated replacement by lower elevation
 montane tree species following fire may hasten their extinction risk. We
 used a dataset of post-fire tree regeneration spanning a broad geographic
 range to ask whether fire facilitated upslope movement of montane tree
 species at the montane-to-subalpine ecotone. We sampled tree seedling
 occurrence in 248 plots across a fire severity gradient (unburned to
 &gt;90% basal area mortality) and spanning ~500 km of latitude in
 Mediterranean-type subalpine forest in California, USA. We used logistic
 regression to quantify differences in postfire regeneration between
 resident subalpine species and the seedling-only range (interpreted as
 climate-induced range extension) of montane species. We tested our
 assumption of increasing climatic suitability for montane species in
 subalpine forest using the predicted difference in habitat suitability at
 study plots between 1990 and 2030. We found that postfire regeneration of
 resident subalpine species was uncorrelated or weakly positively
 correlated with fire severity. Regeneration of montane species, however,
 was roughly four times greater in unburned relative to burned subalpine
 forest. Although our overall results contrast with theoretical predictions
 of disturbance-facilitated range shifts, we found opposing postfire
 regeneration responses for montane species with distinct regeneration
 niches. Recruitment of shade-tolerant red fir declined with fire severity
 and recruitment of shade-intolerant Jeffrey pine increased with fire
 severity. Predicted climatic suitability increased 5% for red fir and 34%
 for Jeffrey pine. Differing postfire responses in newly climatically
 available habitat indicate that wildfire disturbance may only facilitate
 range extensions for species whose preferred regeneration conditions align
 with increased light and/or other postfire landscape characteristics.
description: Methods may be found in linked publication Brodie et al.,
 2023.
description: Data are in .csv format and may be opened with any program
 designed to view tabular data such as Microsoft Excel or Google
 Sheets.
DOI: 10.15468/dl.ascz86
title: Occurrence Download

description: A dataset containing 429702 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "DatasetKey is Waarnemingen.be - Bird occurrences in Flanders and the Brussels Capital Region, Belgium",
 "GadmGid is BEL.1.1.1_1",
 "License is one of (CC-BY 4.0, Pending, CC0 1.0)",
 "OccurrenceStatus is Present",
 "Year 2012-2026"
 ]
}

 The dataset includes 429702 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003408-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n8pk0p319
title: Data for: Plastic maternal effects of social density on reproduction and fitness in the least killifish, Heterandria formosa

description: Environmental parental effects, also known as transgenerational
 plasticity, are widespread in plants and animals. Less well known is
 whether those effects contribute to maternal fitness in the same manner in
 different populations. We carried out a multi-generational laboratory
 experiment with females drawn from two populations of the Least Killifish,
 Heterandria formosa, to assess transgenerational plasticity in
 reproductive traits in response to differences in social density and its
 effects on maternal fitness. In the first and second generations,
 increased density decreased reproductive rate and increased offspring size
 in females from both populations. There were complicated patterns of
 transgenerational plasticity on maternal fitness that differed between
 females from different populations. Females from a population with
 historically low densities whose mothers experienced lower density had
 higher fitness than females whose mothers experienced higher density,
 regardless of their own density. The opposite pattern emerged in females
 from the population with historically high densities: females whose
 mothers experienced higher density had higher fitness than females whose
 mothers experienced lower density. This transgenerational plasticity is
 not anticipatory but might be considered adaptive in both populations if
 providing those “silver spoons” enhances offspring fitness in all
 environments.
description: This dataset was generated for an experiment involving the least
 killifish, <em>Heterandria</em> <em>formosa</em>.
 We carried out a multi-generational laboratory experiment with females
 drawn from two populations of <em>H. formosa</em> to assess
 transgenerational plasticity in reproductive traits in response to
 differences in social density and its effects on maternal fitness. Fish
 were housed in high or low social density tanks, and each tank's
 reproductive output in terms of offspring mass and number was recorded
 daily for six weeks. These data contain each tank in each generation,
 offspring mass, and number across each week.
description: The data are available in Excel and could be imported into any
 number of statistical analysis programs.
DOI: 10.5061/dryad.ffbg79d0d
title: Process development and analyses for the co-production of 2-methyltetrahydrofuran and 1,4-pentanediol from lignocellulosic biomass

description: The development
 of technologies for utilizing biomass
 has attracted attention because biomass can be produced sustainably
 worldwide. Biomass-derived 2-methyltetrahydrofuran (MTHF), which is a
 promising alternative to gasoline, has great market potential
 and a growing demand. However, in conventional biomass
 conversion processes, the minimum selling price (MSP) of
 biochemicals is not economically acceptable. Co-production of
 biochemicals can increase the economics of biomass
 utilization. Herein, we developed a process
 for coproducing MTHF and 1,4-pentanediol (1,4-PDO) from
 lignocellulosic biomass. After biomass fractionation, cellulose and
 hemicellulose were converted to levulinic acid (LA),
 and lignin was used for heat and electricity
 generation. LA was then converted to
 γ-valerolactone (GVL). As a platform material for co-production,
 GVL was converted into MTHF and 1,4-PDO in each
 subsystem. The split ratio of GVL was controlled to
 efficiently produce MTHF and 1,4-PDO according to market conditions.
 Additionally, we performed a techno-economic and life-cycle
 assessment (TEA and LCA, respectively) for the developed process.
 The MSP of MTHF was calculated based on the TEA results,
 and the environmental impacts were quantitatively calculated based on the
 LCA results. We performed heat integration using pinch analysis
 and then reduced the energy requirement of the proposed process. The key
 cost drivers and environmental factors of the proposed process
 were identified via sensitivity
 analyses. Consequently, during
 the processing of 2,000 ton/day of corn stover
 (raw material of lignocellulose), the MSP of MTHF was calculated as
 $2.64/GGE (gasoline equivalent), and representative environmental impacts
 such as climate change and fossil
 depletion were calculated as -0.296 kg
 CO2 eq and -0.056 kg oil eq, respectively. As a
 result, we can increase the economics of commercial production of MTHF and
 1,4-PDO with environmental sustainability. The
 proposed process can serve as a potential solution to the growing demand
 for the need for more sustainable biomass utilization.
DOI: 10.5061/dryad.wdbrv15t7
title: DNA sequence data for two Roscoea species, R. stenophylla and R. australis (Zingiberaceae)

description: This dataset includes three genomic regions, nrITS (ITS1-5.8S–ITS2) and
 two chloroplast DNA (cpDNA) regions (psbA-trnH and trnL-F) for two Roscoea
 species R. stenophylla and R. australis (Zingiberaceae).
DOI: 10.7294/30984718
title: Range of Detection

description: The spotted lanternfly (<i>Lycorma delicatula</i>, SLF) poses a significant threat to U.S. agriculture, particularly vineyards, hops, and ornamental plants. Early detection of SLF egg masses is critical for limiting spread, yet current strategies are constrained by the availability of trained personnel and are extremely time-consuming. Detection dogs have shown strong potential for locating SLF egg masses with high accuracy, and training can be completed using devitalized samples, eliminating the risk of accidental release of this invasive insect. In a prior study, we demonstrated that participatory science teams, volunteer handlers with scent detection experience, could successfully train their companion dogs to detect devitalized SLF egg masses. This follow-up study evaluated whether selected teams from the original cohorts could perform under more complex, operationally relevant conditions. Specifically, we assessed detection accuracy and field performance across two experimental settings: (1) a range of detection (RoD) test to estimate reliable detection distance, and (2) a naturalistic field search in previously unsurveyed areas with unknown target presence, allowing comparison with human surveyors. In the RoD trials, dogs demonstrated the highest sensitivity (0.52) at 0–5 m, declining to 0.06 at 10–15 m, with overall precision ranging from 0.61 to 0.92 across distance bands where detections occurred. Several dogs also successfully generalized from devitalized training aids to naturally occurring, previously undetected SLF egg masses. In naturalistic searches, canine teams located more confirmed SLF egg mass sites than trained human searchers, highlighting their ability to detect cryptic targets under real-world conditions. Although not all canine alerts could be confirmed, the results indicate that trained community detection teams can effectively complement or enhance traditional survey methods. Overall, these findings support the operational feasibility of participatory science detection teams for SLF surveillance. Despite range limitations, trained community dog–handler teams can successfully detect SLF egg masses and, in some cases, outperform human searchers, offering a scalable, biosecure, and cost-effective approach to invasive species detection.
DOI: 10.7294/30984718.v1
title: Range of Detection

description: The spotted lanternfly (<i>Lycorma delicatula</i>, SLF) poses a significant threat to U.S. agriculture, particularly vineyards, hops, and ornamental plants. Early detection of SLF egg masses is critical for limiting spread, yet current strategies are constrained by the availability of trained personnel and are extremely time-consuming. Detection dogs have shown strong potential for locating SLF egg masses with high accuracy, and training can be completed using devitalized samples, eliminating the risk of accidental release of this invasive insect. In a prior study, we demonstrated that participatory science teams, volunteer handlers with scent detection experience, could successfully train their companion dogs to detect devitalized SLF egg masses. This follow-up study evaluated whether selected teams from the original cohorts could perform under more complex, operationally relevant conditions. Specifically, we assessed detection accuracy and field performance across two experimental settings: (1) a range of detection (RoD) test to estimate reliable detection distance, and (2) a naturalistic field search in previously unsurveyed areas with unknown target presence, allowing comparison with human surveyors. In the RoD trials, dogs demonstrated the highest sensitivity (0.52) at 0–5 m, declining to 0.06 at 10–15 m, with overall precision ranging from 0.61 to 0.92 across distance bands where detections occurred. Several dogs also successfully generalized from devitalized training aids to naturally occurring, previously undetected SLF egg masses. In naturalistic searches, canine teams located more confirmed SLF egg mass sites than trained human searchers, highlighting their ability to detect cryptic targets under real-world conditions. Although not all canine alerts could be confirmed, the results indicate that trained community detection teams can effectively complement or enhance traditional survey methods. Overall, these findings support the operational feasibility of participatory science detection teams for SLF surveillance. Despite range limitations, trained community dog–handler teams can successfully detect SLF egg masses and, in some cases, outperform human searchers, offering a scalable, biosecure, and cost-effective approach to invasive species detection.
DOI: 10.5061/dryad.2280gb5xj
title: Does the egg capsule protect against chronic UV-B radiation? A study based on encapsulated and decapsulated embryos of cuttlefish Sepia officinalis

description: Although the egg capsule plays a crucial role in the embryonic development
 of cephalopods, its ability to protect embryos from Ultraviolet (UV)
 radiation is unknown. Our study evaluated the photoprotection mechanisms
 of Sepia officinalis to UV-B radiation and estimated the ability of the
 black capsule to act as a physical shield against it. Embryos with (BC)
 and without capsule (WC) and juveniles were exposed to four experimental
 UVB conditions for 55 days. The effects of different UVB doses were
 evaluated in terms of morphological abnormalities and differences in gene
 expression between each group. We observed that the development might be
 severely impaired in embryos exposed to UVB without capsule protection and
 these effects were time- and UVB-dose-dependent. In addition, we found
 variations in gene expression levels (light-sensitive, stress response,
 and DNA repair) in different tissues as a function of UVB doses. We
 suggest a relationship between morphological abnormalities and the limit
 of molecular regulation. These results suggest that the quantitative
 differences in expression are essential for defining the survivability of
 the embryo face to UVB. Thus, we demonstrated that the egg capsule could
 ensure successful embryonic development of the cuttlefish S. officinalis
 even at high doses of UVB.
description: The present data are raw data obtained by digital PCR (in
 copies/microL). The data are classified by tissues and are presented for
 each treatment and treatment duration.
DOI: 10.15468/dl.84pxk7
title: Occurrence Download

description: A dataset containing 823 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyrrhulina australis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 823 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003523-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.