cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30621848.v1
title: Data files for Ba4SbRu3O12 Paper

description: This is supporting and included data for the published composition, Ba4SbRu3O12. Included is the following: raw XRD and NPD files, isothermal and DC magnetization raw data files, and supporting XRD and magnetization files for reference composition Ba4NbRu3O12.
DOI: 10.5281/zenodo.17507984
title: Documenting Italian libraries on Wikidata: From local projects to a multilayered national knowledge graph (dataset)

description: This dataset consists of:





“ICCU Library registry import.zip” contains three files, all licensed under CC0 (“20220830 biblioteche.json”, “20220830 indirizzi.csv”, “20220830 territorio.csv”), originally downloaded from https://anagrafe.iccu.sbn.it/it/open-data/ in June 2022




“ICCU Merged db.csv”: created by Davide Rolleri combining the data from the previous three between June and August 2022 and used to upload data about Italian libraries into Wikidata (cf. https://www.wikidata.org/wiki/Wikidata:Gruppo_Wikidata_per_Musei,_Archivi_e_Biblioteche/Anagrafe_ICCU)




“ICCU Imports June-August 2022 by P31.csv”: created by Davide Rolleri extracting the data from the Wikidata Query Service (https://query.wikidata.org/) between June and August 2022




“Sistema Cultura import.zip” contains seven files: three files were obtained from Regione Toscana, one on November 14, 2019 (“Library Network start file 2019-11-14.ods”) and two on January 10, 2020 (“Archives start file 2020-01-10 censored.ods”, “Libraries start file 2020-01-10 censored.ods”), licensed under CC BY, and were edited by Alessandro Marchetti to remove any personal data they contained; four files (“Archives end file NO YEARS.ods”, “Archives end file YEARS.ods”, “Libraries end file.ods”, “Library Network end file.ods”) were created by Alessandro Marchetti reviewing the data from the previous three between November 2019 and February 2020 and used to upload data about Tuscan library networks, archives and libraries into Wikidata (cf. https://www.wikidata.org/wiki/Wikidata:Sistema_Cultura)
DOI: 10.5281/zenodo.17507983
title: Documenting Italian libraries on Wikidata: From local projects to a multilayered national knowledge graph (dataset)

description: This dataset consists of:





“ICCU Library registry import.zip” contains three files, all licensed under CC0 (“20220830 biblioteche.json”, “20220830 indirizzi.csv”, “20220830 territorio.csv”), originally downloaded from https://anagrafe.iccu.sbn.it/it/open-data/ in June 2022




“ICCU Merged db.csv”: created by Davide Rolleri combining the data from the previous three between June and August 2022 and used to upload data about Italian libraries into Wikidata (cf. https://www.wikidata.org/wiki/Wikidata:Gruppo_Wikidata_per_Musei,_Archivi_e_Biblioteche/Anagrafe_ICCU)




“ICCU Imports June-August 2022 by P31.csv”: created by Davide Rolleri extracting the data from the Wikidata Query Service (https://query.wikidata.org/) between June and August 2022




“Sistema Cultura import.zip” contains seven files: three files were obtained from Regione Toscana, one on November 14, 2019 (“Library Network start file 2019-11-14.ods”) and two on January 10, 2020 (“Archives start file 2020-01-10 censored.ods”, “Libraries start file 2020-01-10 censored.ods”), licensed under CC BY, and were edited by Alessandro Marchetti to remove any personal data they contained; four files (“Archives end file NO YEARS.ods”, “Archives end file YEARS.ods”, “Libraries end file.ods”, “Library Network end file.ods”) were created by Alessandro Marchetti reviewing the data from the previous three between November 2019 and February 2020 and used to upload data about Tuscan library networks, archives and libraries into Wikidata (cf. https://www.wikidata.org/wiki/Wikidata:Sistema_Cultura)
DOI: 10.15468/dl.hrvu8j
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (USA.5.1_1, USA.5.7_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Rana boylii"
 ]
}

 The dataset includes 247 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033776-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30621835
title: Disruption of <i>TcGNBP3</i> via rna interference compromises antibacterial immunity in <i>tribolium castaneum</i>

description: Gram-negative bacteria binding proteins (GNBPs) serve as essential pattern recognition receptors in insect innate immunity, detecting pathogen-associated molecular patterns to activate downstream immune responses. This molecular recognition mechanism presents a promising target for pest control strategies. However, the immunological functions of <i>GNBP</i> family members in <i>Tribolium castaneum</i> remain poorly characterized, particularly for those with typical structural features. In this study, we identified and characterized a novel <i>GNBP3</i> (designated <i>TcGNBP3</i>) from the <i>T. castaneum</i> cDNA library. Structural analysis revealed that TcGNBP3 exhibits the typical domain architecture characteristic of the <i>GNBP</i> family, comprising an N-terminal carbohydrate-binding module 39 (CBM39) domain and a C-terminal glycoside hydrolase family 16 (GH16) domain. Spatiotemporal expression profiling demonstrated peak <i>TcGNBP3</i> transcript accumulation during early pupal and late adult developmental stages, with predominant localization in immune-related tissues including the fat body and hemolymph. Bacterial challenges (<i>Escherichia coli</i> or <i>Staphylococcus aureus</i>) induced significant upregulation of <i>TcGNBP3</i> expression from 6 to 72 h. Molecular docking and ELISA analyses demonstrated TcGNBP3’s binding affinity for lipopolysaccharide, peptidoglycan, and β-1,3-glucan, while functional assays confirmed its ability to bind and agglutinate five tested bacterial strains. RNAi-mediated silencing of <i>TcGNBP3</i> severely compromised the beetles’ immune response, suppressing immune-related genes (including transcription factors and antimicrobial peptides), disrupting prophenoloxidase cascade activation, and significantly reducing survival rates upon bacterial infection. These results identify <i>TcGNBP3</i> as a key immune regulator in <i>T. castaneum</i>, supporting its development as an RNAi-based pest control target.
DOI: 10.6084/m9.figshare.30621835.v1
title: Disruption of <i>TcGNBP3</i> via rna interference compromises antibacterial immunity in <i>tribolium castaneum</i>

description: Gram-negative bacteria binding proteins (GNBPs) serve as essential pattern recognition receptors in insect innate immunity, detecting pathogen-associated molecular patterns to activate downstream immune responses. This molecular recognition mechanism presents a promising target for pest control strategies. However, the immunological functions of <i>GNBP</i> family members in <i>Tribolium castaneum</i> remain poorly characterized, particularly for those with typical structural features. In this study, we identified and characterized a novel <i>GNBP3</i> (designated <i>TcGNBP3</i>) from the <i>T. castaneum</i> cDNA library. Structural analysis revealed that TcGNBP3 exhibits the typical domain architecture characteristic of the <i>GNBP</i> family, comprising an N-terminal carbohydrate-binding module 39 (CBM39) domain and a C-terminal glycoside hydrolase family 16 (GH16) domain. Spatiotemporal expression profiling demonstrated peak <i>TcGNBP3</i> transcript accumulation during early pupal and late adult developmental stages, with predominant localization in immune-related tissues including the fat body and hemolymph. Bacterial challenges (<i>Escherichia coli</i> or <i>Staphylococcus aureus</i>) induced significant upregulation of <i>TcGNBP3</i> expression from 6 to 72 h. Molecular docking and ELISA analyses demonstrated TcGNBP3’s binding affinity for lipopolysaccharide, peptidoglycan, and β-1,3-glucan, while functional assays confirmed its ability to bind and agglutinate five tested bacterial strains. RNAi-mediated silencing of <i>TcGNBP3</i> severely compromised the beetles’ immune response, suppressing immune-related genes (including transcription factors and antimicrobial peptides), disrupting prophenoloxidase cascade activation, and significantly reducing survival rates upon bacterial infection. These results identify <i>TcGNBP3</i> as a key immune regulator in <i>T. castaneum</i>, supporting its development as an RNAi-based pest control target.
DOI: 10.15468/dl.6wdrwr
title: Occurrence Download

description: A dataset containing 340953571 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is Europe"
 ]
}

 The dataset includes 340953571 records from 9089 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033732-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.68cxvd
title: Occurrence Download

description: A dataset containing 3253 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Corythucha arcuata (Say, 1832)"
 ]
}

 The dataset includes 3253 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013870-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3tx95x6fp
title: Rates of ascidian mediated nitrogen cycling

description: Large solitary ascidians, like Herdmania grandis (Heller), can dominate
 the benthic substrates of subtropical and temperate reefs, however their
 influence on nitrogen cycling, particularly nitrous oxide (N2O)
 production, is unknown. Here we incubated individual H. grandis and
 compared fluxes of dissolved inorganic and gaseous nitrogen species to
 fluxes from reef sediments. Nitrous oxide production rates per individual
 ascidian (21 ± 8 nmol ind h-1) are the highest reported for any marine
 invertebrate. An individual ascidian produced more N2O than a m2 of
 sediment (1.7 ± 1.7 nmol m-2 h-1). Ascidian mediated N2O production was
 found to occur under nutrient depleted conditions. While the addition of
 15N labelled organic material showed that H. grandis facilitates both
 nitrification and denitrification, the contribution of these pathways to
 N2O production could not be ascertained. As the ecology of temperate reefs
 change, any range expansion of H. grandis will increase coastal N2O
 production.
description: The Ascidian <em>Herdmania grandis</em> was collected
 from a subtropical reef on the east coast of Australia and incubated in
 sealed chambers. Some chambers received particulate organic nutrients
 (PON) and some received dissovled organic nutrients ((DON). Sediments were
 also incubated as a comparison. Rates of nitrogen processing were measured
 and this data has been collated. The data presented in this dataset are
 the calculated areal rates of nitrogen processing.
DOI: 10.5061/dryad.0cfxpnw1n
title: Temporal patterns of forest seedling emergence across different disturbance histories data

description: Forest ecosystems experience a myriad of natural and anthropogenic
 disturbances that shape ecological communities. Seedling emergence is a
 critical, preliminary stage in the recovery of forests post-disturbance
 and is triggered by a series of abiotic and biotic changes. However, the
 long-term influence of different disturbance histories on patterns of
 seedling emergence is poorly understood. Here, we address this research
 gap by using an 11-year dataset gathered between 2009 and 2020 to quantify
 the influence of different histories of natural (wildfire) and
 anthropogenic (clearcut and post-fire salvage logging) disturbances on
 emerging seedlings in early successional Mountain Ash forests in
 south-eastern Australia. We also describe patterns of seedling emergence
 across older successional forests varying in stand age (stands that
 regenerated in &lt;1900s, 1939, 1970-90 and 2007-11). Seedling
 emergence was highest in the first three years post-disturbance. Stand age
 and disturbance history significantly influenced the composition and
 abundance of plant seedlings. Specifically, in salvage logged forests,
 plant seedlings were the most different from similarly aged forests with
 other disturbance histories. For instance, relative to clearcut and
 unlogged, burnt forests of the same age, salvage logging had the lowest
 overall richness, the lowest counts of Acacia seedlings, and an absence of
 common species including Acacia obliquinervia, Acacia frigescens, Cassinia
 arcuealta, Olearia argophylla, Pimelea axiflora, Polyscias sambucifolia
 and Prosanthera melissifolia over the survey period. Synthesis: Our
 findings provide important new insights into the influence of different
 disturbance histories on regenerating forests and can help predict plant
 community responses to future disturbances, which may influence forest
 recovery under altered disturbance regimes.
description: Please see manuscript for detailed description of methods.
DOI: 10.5061/dryad.3xsj3txfw
title: DNA sequences employed in systematics of Lobelioideae (Campanulaceae): Review, phylogenetic and biogeographic analyses

description: Lobelioideae, the largest subfamily within Campanulaceae, includes 33
 genera and approximately1200 species. It is characterized by resupinate
 flowers with zygomorphic corollas and connate anthers and widely
 distributed across the world. The systematics of Lobelioideae has been
 quite challenging over the years, with different scholars postulating
 varying theories. To outline major progress and highlight the existing
 systematic problems in Lobelioideae, we conducted a literature review on
 this subfamily. Additionally, we conducted phylogenetic and biogeographic
 analyses for Lobelioideae using plastids and internal transcribed spacer
 regions. We found that former studies have reached agreement on the
 southern African origin of Lobelioideae, herbaceous habit and Asian origin
 of giant lobelioids, the convergent evolution of giant rosette lobelioids,
 and lastly, the multiple cosmopolitan and independent radiation of
 lobelioids in Africa, Pacific Basin, and the Hawaiian Islands. Also,
 Apetahia Baill., Sclerotheca A.DC., and Cyanea Gaudich. are paraphyletic,
 while Lobelia L., Pratia Gaudich., Centropogon C.Presl, Siphocampylus
 Pohl, and Isotoma Lindl. are polyphyletic. The taxonomy of these genera,
 especially Lobelia, is particularly quite frustrating. This calls for
 further reappraisals using both morphological and molecular data.
description: Nineteen loci were obtained, that is, eighteen plastid gene loci
 (atpB-rbcL spacer, atpB, atpF, atpF-atpH spacer, atpH, matK, ndhF,
 psbA-trnH spacer, psbA-trnK spacer, petD, rbcL, rpoC1, trnL-trnF spacer,
 trnT-trnL spacer, trnV-trnK spacer, trnK-matK spacer, rpl32-ndhF spacer,
 rpl16) and one nuclear gene, internal transcribed spacer (ITS). These
 sequences were generated using the NCBI ENTREZ UTILITY program (Accessed
 1ST April 2020) and double-checked manually at the GenBank database.
 Additionally, almost all available Campanulaceae complete plastid genomes
 were manually accessed from the GenBank. The respective plastid regions
 were extracted using NCBI BLASTN v. 2.9.0+ with default
 settings.
description: See ReadMe.txt file
DOI: 10.5061/dryad.rv15dv47h
title: Detecting genetic signals of selection in heavily bottlenecked reindeer populations by comparing parallel founder events

description: Founder populations are of special interest to both evolutionary and
 conservation biologists, but the detection of genetic signals of selection
 in these populations is challenging due to their demographic history.
 Geographically separated founder populations likely subjected to similar
 selection pressures provide an ideal but rare opportunity to overcome
 these challenges. Here we take advantage of such a situation generated
 when small, isolated founder populations of reindeer were established on
 the island of South Georgia, and using this system we look for empirical
 evidence of selection overcoming strong genetic drift. We generated a 70K
 ddRADseq SNP database for the two parallel reindeer founder populations
 and screened for signatures of soft sweeps. We find evidence for a genomic
 region under selection shared among the two populations, and support our
 findings with Wright-Fisher model simulations to assess the power and
 specificity of interpopulation selection scans – i.e. Bayescan, OutFLANK,
 PCadapt and a newly developed scan called Genome Wide Differentiation Scan
 (GWDS) – in the context of pairwise source-founder comparisons. Our
 simulations indicate that loci under selection in small founder
 populations are most likely detected by GWDS, and strengthen the
 hypothesis that the outlier region represents a true locus under
 selection. We explore possible, relevant functional roles for genes in
 linkage with the detected outlier locus.
description: SNP datasets containing genotype information for samples taken
 from the two introduced populations of reindeer
 (<em>Rangifer tarandus</em>) which occurred until recently on
 the south-Atlantic island South Georgia. The dataset also includes samples
 from their Norwegian source population. Sequencing libraries were
 generated with the ddRADseq protocol, and SNPs were subsequently called
 using the STACKS2.2 refmap pipeline, using the reindeer genome as
 reference. The data contains multiple SNPs per read pair. 
 The data is stored in PED and MAP format (plink format). Each
 population is represented by ~30 individuals, as specified in the popfile.
 'Busen' and 'Barff' are the names of the two
 peninsulas on which the two South Georgia reindeer populations
 occured. Also included in the download are read depth depth information
 files generated with vcftools.
description: The 'reindeer_commands.txt' file contains all the
 commands used to analyse the SNP dataset, to generate the main plots in
 the associated research article, and to perform simulations to test the
 performance of selection scans and the detectability of SNPs under
 selection. The commands make use of functions implemented in the R package
 SambaR, which can be downloaded from Github
 (https://github.com/mennodejong1986/SambaR).
DOI: 10.5061/dryad.931zcrjjm
title: Evidence that bottlenose dolphins can communicate with vocal signals to solve a cooperative task

description: Cooperation experiments have long been used to explore the cognition
 underlying animals' coordination towards a shared goal. While the
 ability to understand the need for a partner in a cooperative task has
 been demonstrated in a number of species, there has been far less focus on
 cooperation experiments that address the role of communication. In humans,
 cooperative efforts can be enhanced by physical synchrony, and
 coordination problems can be solved using spoken language. Indeed, human
 children adapt to complex coordination problems by communicating with
 vocal signals. Here, we investigate whether bottlenose dolphins can use
 vocal signals to coordinate their behaviour in a cooperative
 button-pressing task. The two dolphin dyads used in this study were
 significantly more likely to cooperate successfully when they used
 whistles prior to pressing their buttons, with whistling leading to
 shorter button press intervals and more successful trials. Whistle timing
 was important as the dolphins were significantly more likely to succeed if
 they pushed their buttons together after the last whistle, rather than
 pushing independently of whistle production. Bottlenose dolphins are well
 known for cooperating extensively in the wild, and while it remains to be
 seen how wild dolphins use communication to coordinate cooperation, our
 results reveal that at least some dolphins are capable of using vocal
 signals to facilitate the successful execution of coordinated, cooperative
 actions.  
description: Videos of the cooperative button-pressing task conducted with
 bottlenose dolphins (<em>Tursiops truncatus) </em>at the
 Dolphin Research Center, Florida Keys, USA.
DOI: 10.5061/dryad.t1g1jwt1r
title: Fossil-informed models reveal a Boreotropical origin and divergent evolutionary trajectories in the walnut family (Juglandaceae)

description: Temperate woody plants in the Northern Hemisphere have long been known to
 exhibit high species richness in East Asia and North America and
 significantly lower diversity in Europe, but the causes of this pattern
 remain debated. Here, we quantify the roles of dispersal, niche evolution,
 and extinction in shaping the geographic diversity of the temperate woody
 plant family Juglandaceae (walnuts and their relatives). Integrating
 evidence from molecular, morphological, fossil, and (paleo)environmental
 data, we find strong support for a Boreotropical origin of the family with
 contrasting evolutionary trajectories between the temperate subfamily
 Juglandoideae and the tropical subfamily Engelhardioideae. Juglandoideae
 rapidly evolved frost tolerance when the global climate shifted to
 ice-house conditions from the Oligocene, with diversification at high
 latitudes especially in Europe and Asia during the Miocene. Subsequent
 range contraction at high latitudes and high levels of extinction in
 Europe driven by global cooling led to the current regional disparity in
 species diversity. Engelhardioideae showed temperature conservatism while
 adapting to increased humidity, tracking tropical climates to low
 latitudes since the middle Eocene with comparatively little
 diversification, perhaps due to high competition in the tropical zone. The
 biogeographic history of Juglandaceae shows that the North Atlantic land
 bridge and Europe played more critical roles than previously thought in
 linking the floras of East Asia and North America, and showcases the
 complex interplay among climate change, niche evolution, dispersal, and
 extinction that shaped the modern disjunct pattern of species richness in
 temperate woody plants.
DOI: 10.5061/dryad.7pvmcvds1
title: The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size

description: Domestication and breeding have reshaped the genomic architecture of
 chicken, but the retention and loss of genomic elements during these
 evolutionary processes remain unclear. We present the first chicken
 pan-genome constructed using 664 individuals, which identified an
 additional ∼66.5 Mb sequences that are absent from the reference genome
 (GRCg6a). The constructed pan-genome encoded 20,491 predicated
 protein-coding genes, of which higher expression level are observed in
 conserved genes relative to dispensable genes. Presence/absence variation
 (PAV) analyses demonstrated that gene PAV in chicken was shaped by
 selection, genetic drift, and hybridization. PAV-based GWAS identified
 numerous candidate mutations related to growth, carcass composition, meat
 quality, or physiological traits. Among them, a deletion in the promoter
 region of IGF2BP1 affecting chicken body size is reported, which is
 supported by functional studies and extra samples. This is the first time
 to report the causal variant of chicken body size QTL located at
 chromosome 27 which was repeatedly reported. Therefore, the chicken
 pan-genome is a useful resource for biological discovery and breeding. It
 improves our understanding of chicken genome diversity and provides
 materials to unveil the evolution history of chicken domestication.