cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tx95x6b69
title: Data from: The genome of a globally invasive passerine, the common myna, Acridotheres tristis

description: In an era of global climate change, biodiversity conservation is receiving
 increased attention. Conservation efforts are greatly aided by genetic
 tools and approaches, which seek to understand patterns of genetic
 diversity and how they impact species health and their ability to persist
 under future climate regimes. Invasive species offer vital model systems
 in which to investigate questions regarding adaptive potential, with a
 particular focus on how changes in genetic diversity and effective
 population size interact with novel selection regimes. The common myna
 (Acridotheres tristis) is a globally invasive passerine and is an
 excellent model species for research both into the persistence of
 low-diversity populations and the mechanisms of biological invasion. To
 underpin research on the invasion genetics of this species, we present the
 genome assembly of the common myna. We describe the genomic landscape of
 this species, including genome wide allelic diversity, methylation,
 repeats, and recombination rate, as well as an examination of gene family
 evolution. Finally, we use demographic analysis to identify that some
 native regions underwent a dramatic population increase between the two
 most recent periods of glaciation, and reveal artefactual impacts of
 genetic bottlenecks on demographic analysis.
description: # The genome of a globally invasive passerine, the common myna,
 Acridotheres tristis This dryad upload contains the genome files that were
 generated for the myna genome
 ([https://doi.org/10.1093/dnares/dsae005](https://doi.org/10.1093/dnares/dsae005)). ## Description of the data and file structure ### List of uploaded files Assembly: AcTris_vAus2.0.fasta Matching annotation file: braker_gemoma_combined_katmanual_brakerforce_longestIsoform_transcripts.emapper.decorated.gff Tissue specific transcripts (raw fasta files): Heart.fa (heart tissue) Liver.fa (liver tissue) Test.fa (testies tissue) Repeat libraries and annotation: acridotheresTristis_combined_library.fasta (Earlgrey custom repeat library fasta file) allLTR_rename.lib (Maker custom repeat library fasta file) AcTris_vAus2.0.fasta.out (repeatmasker output of assembly repeat annotation) SNP based recombination track: recombination_rho_allchroms.txt Methylation track: AcTris_vAus_ALL_modbam2bed.out ### Raw Data and NCBI uploads BioProject [PRJNA928557](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA928557) * [10x short-reads](https://www.ncbi.nlm.nih.gov/sra/SRX22916976%5Baccn%5D) * [Nanopore long-reads](https://www.ncbi.nlm.nih.gov/sra/SRX22916973%5Baccn%5D) * [cDNA short-reads](https://www.ncbi.nlm.nih.gov/sra/SRX22916974%5Baccn%5D) NCBI assembly upload: [GCA_037013685.1](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA928557) ## Code/Software The associated code is available at [https://github.com/katarinastuart/At1_MynaGenome](https://github.com/katarinastuart/At1_MynaGenome)
DOI: 10.5061/dryad.73n5tb357
title: Data from: Meta-analytical evidence for frequency-dependent selection across the tree of life

description: Explaining the maintenance of genetic variation in fitness related traits
 within populations is a fundamental challenge in ecology and evolutionary
 biology. Frequency-dependent selection (FDS) is one mechanism that can
 maintain such variation, especially when selection favours rare variants
 (negative FDS). However, our general knowledge about the occurrence of
 FDS, its strength and direction remain fragmented, limiting general
 inferences about this important evolutionary process. We systematically
 reviewed the published literature on FDS and assembled a database of 747
 effect sizes from 101 studies to analyse the occurrence, strength, and
 direction of FDS, and the factors that could explain heterogeneity in FDS.
 Using a meta-analysis, we found that overall, FDS is more commonly
 negative, although not significantly when accounting for phylogeny. An
 analysis of absolute values of effect sizes, however, revealed the
 widespread occurrence of modest FDS. However, negative FDS was only
 significant in laboratory experiments and non-significant in mesocosms and
 field-based studies. Moreover, negative FDS was stronger in studies
 measuring fecundity and involving resource competition over studies using
 other fitness components or focused on other ecological interactions. Our
 study unveils key general patterns of FDS and points in future promising
 research directions that can help us understand a long-standing
 fundamental problem in evolutionary biology and its consequences for
 demography and ecological dynamics.
description: # Data from: Meta-analytical evidence for frequency-dependent selection
 across the tree of life
 [https://doi.org/10.5061/dryad.73n5tb357](https://doi.org/10.5061/dryad.73n5tb357) All the analyses and functions to replicate the study are in Code.R Data is found in Data_FDS.csv ## Description of the data and file structure metadata with the description of every variable is Metadata.csv NA = Not available
DOI: 10.5281/zenodo.18406809
title: Table 1 in Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae)

description: Table 1. Means and standard deviations of the rate (%) and duration (s) of motility in diluted curimba (P. lineatus) semen before freezing (toxicity test) using different antioxidants and water as activators (n=7). ns There were no significant difference between treatments (P>0.05). VE50: 50 µM, VE100: 100 µM and VE250: 250 µM of vitamin E; RG0.5: 0.5 mM, RG1.0: 1.0 mM and RG1.5: 1.5 mM of reduced glutathione.
TreatmentsRate (%)nsVariables Duration (s)nsControl94.17 ± 1.10128 ± 5VE5090.83 ± 1.27218 ± 69VE10093.33 ± 0.5085 ± 4VE25096.67 ± 2.8688 ± 22RG0.594.17 ± 1.1095 ± 17RG1.089.17 ± 2.44116 ± 2RG1.590.00 ± 1.85116 ± 3
description: Published as part of Paula, Daniella A. J., Andrade, Estefânia S., Murgas, Luis D. S., Felizardo, Viviane O., Winkaler, Elissandra U., Zeviani, Walmes & Freitas, Rilke T. F., 2012, Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae), pp. 663 in Neotropical Ichthyology 10 (3) on page 663, DOI: 10.1590/s1679-62252012005000016, http://zenodo.org/record/18406774
DOI: 10.5281/zenodo.18406808
title: Table 1 in Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae)

description: Table 1. Means and standard deviations of the rate (%) and duration (s) of motility in diluted curimba (P. lineatus) semen before freezing (toxicity test) using different antioxidants and water as activators (n=7). ns There were no significant difference between treatments (P>0.05). VE50: 50 µM, VE100: 100 µM and VE250: 250 µM of vitamin E; RG0.5: 0.5 mM, RG1.0: 1.0 mM and RG1.5: 1.5 mM of reduced glutathione.
TreatmentsRate (%)nsVariables Duration (s)nsControl94.17 ± 1.10128 ± 5VE5090.83 ± 1.27218 ± 69VE10093.33 ± 0.5085 ± 4VE25096.67 ± 2.8688 ± 22RG0.594.17 ± 1.1095 ± 17RG1.089.17 ± 2.44116 ± 2RG1.590.00 ± 1.85116 ± 3
description: Published as part of Paula, Daniella A. J., Andrade, Estefânia S., Murgas, Luis D. S., Felizardo, Viviane O., Winkaler, Elissandra U., Zeviani, Walmes & Freitas, Rilke T. F., 2012, Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae), pp. 663 in Neotropical Ichthyology 10 (3) on page 663, DOI: 10.1590/s1679-62252012005000016, http://zenodo.org/record/18406774
DOI: 10.5281/zenodo.18406811
title: Table 2 in Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae)

description: Table 2. Means and standard deviations of the rate (%) of semen motility (n = 7) and duration (s) of curimba (P. lineatus) semen after freeze-thaw (cryopreservation) using different antioxidants (n = 6) and using water and bicarbonate as semen activators. ns There were no significant differences in the duration of semen motility between treatments (P>0.05).* There were significant differences between the different activators (P<0.05). VE50: 50 µM, VE100: 100 µM and VE250: 250 µM of vitamin E; RG0.5:0.5 mM, RG1.0:1.0 mM and RG1.5: 1.5 mM of reduced glutathione.
TreatmentsRate of semen motility (%)Duration semen motility (s)ActivatorsActivators*WaternsBicarbonatensWaterBicarbonateControl65.71 ± 2.7867.86 ± 2.45164 ± 94b244 ± 70ªVE5070.00 ± 5.8170.71 ± 4.46156 ± 94b227 ± 59ªVE10076.86 ± 4.3065.00 ± 0.42177 ± 75b269 ± 52ªVE25072.14 ± 7.3374.29 ± 6.99176 ± 99b223 ± 52ªRG0.567.86 ± 4.8076.43 ± 6.39147 ± 86b246 ± 55ªRG1.067.14 ± 3.7064.29 ± 0.08156 ± 88b235 ± 64ªRG1.575.71 ± 9.8970.00 ± 3.96166 ± 92b255 ± 82ª
description: Published as part of Paula, Daniella A. J., Andrade, Estefânia S., Murgas, Luis D. S., Felizardo, Viviane O., Winkaler, Elissandra U., Zeviani, Walmes & Freitas, Rilke T. F., 2012, Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae), pp. 664 in Neotropical Ichthyology 10 (3) on page 664, DOI: 10.1590/s1679-62252012005000016, http://zenodo.org/record/18406774
DOI: 10.5281/zenodo.18406810
title: Table 2 in Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae)

description: Table 2. Means and standard deviations of the rate (%) of semen motility (n = 7) and duration (s) of curimba (P. lineatus) semen after freeze-thaw (cryopreservation) using different antioxidants (n = 6) and using water and bicarbonate as semen activators. ns There were no significant differences in the duration of semen motility between treatments (P>0.05).* There were significant differences between the different activators (P<0.05). VE50: 50 µM, VE100: 100 µM and VE250: 250 µM of vitamin E; RG0.5:0.5 mM, RG1.0:1.0 mM and RG1.5: 1.5 mM of reduced glutathione.
TreatmentsRate of semen motility (%)Duration semen motility (s)ActivatorsActivators*WaternsBicarbonatensWaterBicarbonateControl65.71 ± 2.7867.86 ± 2.45164 ± 94b244 ± 70ªVE5070.00 ± 5.8170.71 ± 4.46156 ± 94b227 ± 59ªVE10076.86 ± 4.3065.00 ± 0.42177 ± 75b269 ± 52ªVE25072.14 ± 7.3374.29 ± 6.99176 ± 99b223 ± 52ªRG0.567.86 ± 4.8076.43 ± 6.39147 ± 86b246 ± 55ªRG1.067.14 ± 3.7064.29 ± 0.08156 ± 88b235 ± 64ªRG1.575.71 ± 9.8970.00 ± 3.96166 ± 92b255 ± 82ª
description: Published as part of Paula, Daniella A. J., Andrade, Estefânia S., Murgas, Luis D. S., Felizardo, Viviane O., Winkaler, Elissandra U., Zeviani, Walmes & Freitas, Rilke T. F., 2012, Vitamin E and reduced glutathione in Prochilodus lineatus (curimba) semen cryopreservation (Characiformes: Prochilodontidae), pp. 664 in Neotropical Ichthyology 10 (3) on page 664, DOI: 10.1590/s1679-62252012005000016, http://zenodo.org/record/18406774
DOI: 10.5061/dryad.dv41ns26m
title: Attosecond impulsive stimulated x-ray raman scattering in liquid water

description: We report the measurement of impulsive stimulated x-ray Raman scattering
 in neutral liquid water. An attosecond pulse drives the excitations of an
 electronic wavepacket, which comprises two steps: a transition to
 core-excited states near the oxygen atoms accompanied by transition to a
 valence-excited states. Thus, the wavepacket is impulsively created at a
 specific atomic site within a few hundred attoseconds through a non-linear
 interaction between the water and the x-ray pulse. We observe this
 nonlinear signature in an intensity dependent Stokes Raman sideband at 526
 eV. Our measurements are supported by our state-of-the-art calculations
 based on the polarisation response of water dimers in bulk solvation and
 propagation of attosecond x-ray pulses at liquid density.
description: # Attosecond Impulsive Stimulated X-ray Raman Scattering in Liquid Water
 [https://doi.org/10.5061/dryad.dv41ns26m](https://doi.org/10.5061/dryad.dv41ns26m) Data from the Science Advances paper *"Attosecond Impulsive Stimulated X-ray Raman Scattering in Liquid Water"*. ## Description of the data and file structure All data is contained in .csv files, labelled with figure numbers corresponding to the figures in the assosciated paper and supplementary material. For the experimental data, the portion of the filename before the underscore identifies the figure, and the portion after the underscore identifies the data axis. The data files for theory plots, without underscore in their name, contain the data from the horizontal and vertical axis in the first and second columns, respectively, and when several datasets are represented in the same figure, they are stored in the subsequent columns. In the population-evolution data (Figs. 3B, S11, S12, S15, S21), the second column corresponds to the ground state, the third to eighth are the valence-excited states and the ninth to fifteenth are the core-excited states. In Fig S10, each line corresponds to a different state following the mentioned order. ## Code/Software The python notebook, *plot_exp_figures.ipynb*, plots all experimental data from the .csv files.
DOI: 10.5061/dryad.t1g1jwtb1
title: Mutant Harmonia axyridis raw sequencing data of CRISPR/Cas9 induced mutations in the genes laccase2 and scarlet

description: Harmonia axyridis (Pallas), commonly known as the Asian lady beetle, is a
 native insect species of Asia that has been intentionally introduced to
 various regions for biocontrol purposes. However, its widespread presence
 beyond its original release sites suggests a high degree of invasiveness.
 In this study, we utilized the CRISPR-Cas9 approach to achieve precise
 genome editing in H. axyridis. Specifically, we targeted two genes in H.
 axyridis, laccase2 and scarlet, knockdown of which orthologs in other
 insects showed visible phenotypic changes. The knockout laccase2 resulted
 in an early-detectable phenotype but also in lethality. However, we
 successfully established a viable and genetically stable mutant colony by
 disrupting the scarlet gene, resulting in beetles with white eyes. Our
 findings contribute to the expanding knowledge of genetic manipulation in
 H. axyridis and provide insights into its potential for future research
 and practical applications for biocontrol and invasive species management.
description: This dataset includes the raw sequencing data of the mutated
 <em>H. axyridis</em> as provided by the sequencing
 vendor.
description: # Mutant Harmonia axyridis raw sequencing data of CRISPR/Cas9 induced
 mutations in the genes laccase2 and scarlet
 [https://doi.org/10.5061/dryad.t1g1jwtb1](https://doi.org/10.5061/dryad.t1g1jwtb1) In this study, we have edited two genes in the Asian Ladybeetle, *Harmonia axyridis*, using CRISPR/Cas9 The two genes are: * Laccase2 - This gene is responsible for generating melanin. Its knockout resulted in white patches throughout the larvae's bodies, but it proved lethal when widespread. Homozygosity could not be achieved. * Scarlet - This gene codes for a portion of a pigment pump in insects' eyes. The phenotype was seen only in the eyes of adult beetles; no physiological effects were seen, and a stable line was generated. This dataset contains the sequence data as received from the sequencing provider. The sequences are divided into two groups. The first, "lac2," contains sequences obtained from *H. axyridis* with CRISPR-Cas9-induced mutation in the lac2 gene. The second group includes sequences obtained from mutants in the scarlet gene.  ## Description of the data and file structure The files are organized according to the figures, including supplementary.  File names are composed of the target gene for editing and a running serial number Each sequence has two file types: the chromatogram (trace) and a FASTA file representing the most likely sequence. The chromatogram files are in a .ab1 format and can be opened using many different programs, including FinchTV:  [https://digitalworldbiology.com/FinchTV](https://digitalworldbiology.com/FinchTV)
DOI: 10.5281/zenodo.18405944
title: Materiales complementarios del artículo "Análisis de la percepción del personal profesional de las bibliotecas públicas de Canarias sobre la práctica de la censura en las bibliotecas públicas españolas entre 2020 y 2024"

description: Materiales complementarios de un artículo científico publicado en la revista RIBES (Revista de Investigación sobre Bibliotecas, Educación y Sociedad), titulado "Análisis de la percepción del personal profesional de las bibliotecas públicas de Canarias sobre la práctica de la censura en las bibliotecas públicas españolas entre 2020 y 2024".

Se incluyen 3 archivos:

-1 PDF, consistente en el cuestionario con el que se ralizó la encuesta al personal profesional de las bibliotecas públicas de Canarias (España) para conocer su percepción sobre la cuestión de la censura en las bibliotecas españolas en el período comprendido entre 2020 y 2024  

-1 PDF, que incluye la relación de las bibliotecas públicas de Canarias (España) encuestadas para esta investigación

-1 archivo en formato xls, que recoge todas las respuestas de las bibliotecas públicas de Canarias (España) qur respondieron a la encuesta.

Los tres archivos, junto con el manuscrito del artículo, fueron remitidos a las personas revisoras para su verificación y réplica. Tras aceptar la revista RIBES su publicación, se incorporan a este repositorio de datos abiertos para su consultar y reutilización pública.__

Supplementary materials for a scientific article published in the journal RIBES (Journal of Research on Libraries, Education and Society), entitled ‘Analysis of the perception of professional staff in public libraries in the Canary Islands on the practice of censorship in Spanish public libraries between 2020 and 2024’.

Three files are included:

-1 PDF, consisting of the questionnaire used to survey professional staff at public libraries in the Canary Islands (Spain) to find out their perception of the issue of censorship in Spanish libraries in the period between 2020 and 2024.  

-1 PDF, which includes the list of public libraries in the Canary Islands (Spain) surveyed for this research.

-1 file in xls format, which contains all the responses from the public libraries in the Canary Islands (Spain) that responded to the survey.

The three files, together with the manuscript of the article, were sent to the reviewers for verification and replication. After the RIBES journal accepted their publication, they were added to this open data repository for public consultation and reuse.
DOI: 10.5281/zenodo.18405945
title: Materiales complementarios del artículo "Análisis de la percepción del personal profesional de las bibliotecas públicas de Canarias sobre la práctica de la censura en las bibliotecas públicas españolas entre 2020 y 2024"

description: Materiales complementarios de un artículo científico publicado en la revista RIBES (Revista de Investigación sobre Bibliotecas, Educación y Sociedad), titulado "Análisis de la percepción del personal profesional de las bibliotecas públicas de Canarias sobre la práctica de la censura en las bibliotecas públicas españolas entre 2020 y 2024".

Se incluyen 3 archivos:

-1 PDF, consistente en el cuestionario con el que se ralizó la encuesta al personal profesional de las bibliotecas públicas de Canarias (España) para conocer su percepción sobre la cuestión de la censura en las bibliotecas españolas en el período comprendido entre 2020 y 2024  

-1 PDF, que incluye la relación de las bibliotecas públicas de Canarias (España) encuestadas para esta investigación

-1 archivo en formato xls, que recoge todas las respuestas de las bibliotecas públicas de Canarias (España) qur respondieron a la encuesta.

Los tres archivos, junto con el manuscrito del artículo, fueron remitidos a las personas revisoras para su verificación y réplica. Tras aceptar la revista RIBES su publicación, se incorporan a este repositorio de datos abiertos para su consultar y reutilización pública.__

Supplementary materials for a scientific article published in the journal RIBES (Journal of Research on Libraries, Education and Society), entitled ‘Analysis of the perception of professional staff in public libraries in the Canary Islands on the practice of censorship in Spanish public libraries between 2020 and 2024’.

Three files are included:

-1 PDF, consisting of the questionnaire used to survey professional staff at public libraries in the Canary Islands (Spain) to find out their perception of the issue of censorship in Spanish libraries in the period between 2020 and 2024.  

-1 PDF, which includes the list of public libraries in the Canary Islands (Spain) surveyed for this research.

-1 file in xls format, which contains all the responses from the public libraries in the Canary Islands (Spain) that responded to the survey.

The three files, together with the manuscript of the article, were sent to the reviewers for verification and replication. After the RIBES journal accepted their publication, they were added to this open data repository for public consultation and reuse.
DOI: 10.5061/dryad.3n5tb2rsb
title: Terrestrial pollen and charcoal datasets for Emerald Swamp and laymuna paywuta, Bass Strait, Tasmania from 60,000 - 20,000 years

description: The nature of human influence on the landscape when they first arrived in
 Tasmania about 40,000 years ago remains speculative. We use pollen and
 charcoal records from Emerald Swamp and laymuna paywuta in Bass Strait,
 Tasmania to not only document the timing of Homo sapiens arrival in the
 region but also the first evidence of anthropogenic fire usage and
 terrestrial vegetation transformation upon arrival. The timing of human
 arrival in Tasmania is identified to be at least 41,000 years ago and
 people used fire to burn forested areas more than already open vegetation
 types. This provides a deeper understanding of Aboriginal land-use history
 in Tasmania, as they may have frequently used and managed forested
 landscapes more than previously thought. The pollen and charcoal records
 presented here include raw counts of pollen and charcoal, as well as
 sample depths and chronologies. Chronologies are based on the Bacon
 age-depth model, using the latest Southern Hemisphere calibration curve
 (ShCal20). Pollen records only include terrestrial taxa used in the study
 and are not inclusive of spores and aquatics.
description: Pollen processing follows standard protocol, which includes HCl,
 KOH, and acetolysis treatment. Charcoal samples were bleached with
 household bleach for ~16 hours, washed through a 125-um sieve, and counted
 manually under the stereoscope.
description: # Terrestrial pollen and charcoal datasets for Emerald Swamp and laymuna
 paywuta, Bass Strait, Tasmania from \~60,000 - 20,000 years
 [https://doi.org/10.5061/dryad.3n5tb2rsb](https://doi.org/10.5061/dryad.3n5tb2rsb) Access this dataset on Dryad DOI: 10.5061/dryad.3n5tb2rsb The dataset consists of raw counts of fossil pollen taxa and charcoal particles from Emerald Swamp and laymuna paywuta in Bass Strait, Tasmania. These datasets are used in the publication 'Landscape burning facilitated Aboriginal migration into Lutruwita/Tasmania 41,600 years ago'. They include raw counts of pollen and charcoal, as well as sample depths in cm and dates. Dates are based on the Bacon age-depth model, using the latest Southern Hemisphere calibration curve (ShCal20). Pollen records only include terrestrial taxa used in the study and are not inclusive of spores and aquatics.