cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60493/4x92n-6m275
title: List of YouTube-Videos analysed in Schopper (2022): Zur Analyse von affektiven Atmosphären in audiovisuellen Medien: Kämpfe um Identität in extrem rechter Rap-Musik

description: File: schopper-2022-video-sources.csv
Description: List of YouTube-Videos analysed in Schopper, Tobias. 2022. "Zur Analyse von affektiven Atmosphären in audiovisuellen Medien: Kämpfe um Identität in extrem rechter Rap-Musik". Geographische Zeitschrift 110 (1): 2. https://doi.org/10.25162/gz-2021-0015. Please refer to the published article for details on methods and results.
DOI: 10.5061/dryad.8063
title: Data from: Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies

description: Most information about Chinook salmon genetic diversity and life history
 originates from studies from the west coast USA, western Canada, and
 Southeast Alaska; less is known about Chinook salmon from western and
 southcentral Alaska drainages. Populations in this large area are
 genetically distinct from populations to the south and represent an
 evolutionary legacy of unique genetic, phenotypic, and life history
 diversity. More genetic information is necessary to advance mixed stock
 analysis applications for studies involving these populations. We
 assembled a comprehensive, open-access baseline of 45 single nucleotide
 polymorphisms (SNPs) from 172 populations ranging from Russia to
 California. We compare SNP data from representative populations throughout
 the range with particular emphasis on western and southcentral Alaska. We
 grouped populations into major lineages based upon genetic and geographic
 characteristics, evaluated the resolution for identifying the composition
 of admixtures, and performed mixed stock analysis on Chinook salmon caught
 incidentally in the walleye pollock fishery in the Bering Sea. SNP data
 reveal complex genetic structure within Alaska and can be used in
 applications to address not only regional issues, but also migration
 pathways, bycatch studies on the high seas, and potential changes in the
 range of the species in response to climate change.
description: ChinookSNPGeno
DOI: 10.5061/dryad.fk558
title: Data from: "A reduced representation libraries approach for nuclear marker development via 454 sequencing applied on Tetramorium (Hymenoptera: Formicidae)" in Genomic Resources Notes Accepted 1 February 2015 to 31 March 2015

description: To clarify species boundaries in the cryptic Tetramorium caespitum/impurum
 ant species complex, a multi-disciplinary approach is necessary. Nuclear
 DNA markers constitute one important step in species delimitation. We
 established a reduced representation library (RRL) based on amplified
 fragment-length polymorphism (AFLP) PCR products of four species.
 Amplicons were size-selected by gel-electrophoresis, DNA-fragments
 recovered from the agarose gels, and 454 libraries constructed by a
 commercial provider. Pyrosequencing yielded 490,155 reads, from which we
 designed cross-species amplifying primer pairs for 28 loci. Wetlab
 procedures, bioinformatic pipeline, alignment statistics, and the
 developed primers are presented.
description: contigs+singletons.fastaMIRA contigs and singletons concatenated into a single fasta file or each libraryscripts+protocolPython scripts used for data handling, and a shellscript style bioinformatic protocolalignmentsAlignments of reads with matches that passed the Clustal stepdistance tableClustal based distance table used for selection of loci for subsequent primer design
DOI: 10.5061/dryad.64715
title: Data from: Unveiling the optimal parameters for cellulolytic characteristics of Talaromyces verruculosus SGMNPf3 and its secretory enzymes

description: AIMS: Elucidation of different physico-chemical parameters and the
 secretory enzymes released by Talaromyces verruculosus SGMNPf3 during
 cellulosic biomass degradation. METHODS AND RESULTS: We determined the
 optimal pH, temperature and time course parameters for the efficient
 degradation of different natural and commercial cellulosic substrates by
 T. verruculosus SGMNPf3, previously isolated from a forest soil. The
 optimal growth of the fungus and production of its cellulases were
 obtained when the culture condition was maintained at pH 3·3 and
 temperature 30°C. Activity of the crude cellulases was maximum at 60°C.
 Activity of cellulase enzymes produced on natural cellulose substrates was
 higher than that on commercial cellulose substrates. A continuous increase
 in cellulase activity at different time points indicated no apparent end
 product inhibition. This might be attributed to the high individual
 cellulases, notably β-glucosidase (316·1 μmol g(-1) ) production. Zymogram
 of extracellular crude proteins showed two dominant extracellular protein
 bands of molecular weight 72·3 and 61·4 kDa, indicating their cellulolytic
 nature. MALDI-TOF and LC-MS/MS analysis of the 2DE spots also identified
 several enzymes including β-glucosidase involved in the process of
 cellulose degradation. CONCLUSIONS: Based on its optimal parameters for
 cellulolytic activities, we suggest that the fungus is acido-mesophilic.
 There was apparently no end-product inhibition of the cellulase activity
 and this is attributed to the ability of the fungus to produce sufficient
 β-glucosidase. The dominant proteins secreted by the fungus were confirmed
 to be cellulases. SIGNIFICANCE AND IMPACT OF THE STUDY: The high
 individual cellulase activities, better cellulase production on natural
 substrates and apparent absence of end-product inhibition are
 characteristics of T. verruculosus SGMNPf3 for use in harvesting naturally
 endowed energy in cellulosic biomass.
description: Two Dimensional Gel
 Electrophoresis (2DE) of extracellular protein of Talaromyces verruculosus
 SGMNPf3The scientific data
 summarizes identified peptide spots from two dimensional gel
 electrophoresis. Identified spots are secretory products from the
 cellulolytic activity of Talaromyces verruculosus SGMNPf3. Peptide spots
 were identified by LC MS/MS and MALDI TOF-MS and detail characteristics of
 spots are provided.Table of 2D spots
 identified.pptx
DOI: 10.5061/dryad.52hj2
title: Data from: The genomes of two key bumblebee species with primitive eusocial organisation

description: Background: The shift from solitary to social behavior is one of the major
 evolutionary transitions. Primitively eusocial bumblebees are uniquely
 placed to illuminate the evolution of highly eusocial insect societies.
 Bumblebees are also invaluable natural and agricultural pollinators, and
 there is widespread concern over recent population declines in some
 species. High-quality genomic data will inform key aspects of bumblebee
 biology, including susceptibility to implicated population viability
 threats. Results: We report the high quality draft genome sequences of
 Bombus terrestris and Bombus impatiens, two ecologically dominant
 bumblebees and widely utilized study species. Comparing these new genomes
 to those of the highly eusocial honeybee Apis mellifera and other
 Hymenoptera, we identify deeply conserved similarities, as well as
 novelties key to the biology of these organisms. Some honeybee genome
 features thought to underpin advanced eusociality are also present in
 bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic
 detoxification and immune genes are similarly depauperate in bumblebees
 and honeybees, and multiple categories of genes linked to social
 organization, including development and behavior, show high conservation.
 Key differences identified include a bias in bumblebee chemoreception
 towards gustation from olfaction, and striking differences in microRNAs,
 potentially responsible for gene regulation underlying social and other
 traits. Conclusions: These two bumblebee genomes provide a foundation for
 post-genomic research on these key pollinators and insect societies.
 Overall, gene repertoires suggest that the route to advanced eusociality
 in bees was mediated by many small changes in many genes and processes,
 and not by notable expansion or depauperation.
description: RAD tag (SgrAI) derived
 SNPs from Bombus impatiensRAD tag (SgrAI) derived
 SNPs from Bombus impatiens from Sadd et al. (2015) "The genomes of
 two key bumblebee species with primitive eusocial
 organisation"Filtered_Bombus_imp_AEgenome.vcf
DOI: 10.15468/dl.b7spw3
title: Occurrence Download

description: A dataset containing 169469 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cheloniidae",
 "Year 2001-2026"
 ]
}

 The dataset includes 169469 records from 480 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001602-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kp328
title: Data from: New insights for Drosophila GAGA factor in larvae

description: GAGA factor plays important roles during Drosophila embryogenesis and its
 maternal contribution is essential for early development. Here, the role
 of GAGA factor was studied in 3rd instar larvae using depletion and
 overexpression conditions in wing disc and transcriptome analysis. We
 found that genes changing expression were different to those previously
 described using GAGA mutants in embryos. No apparent phenotypes on GAGA
 depletion could usually be observed at larval stages in imaginal discs but
 a strong effect on salivary gland polytene chromosomes was observed. In
 the adult, GAGA depletion produced many defects like abnormal cell
 proliferation in the wing, impaired dorsal closure and resulted in
 homeotic transformation of abdominal segment A5. Unexpectedly, no effects
 on Ultrabithorax expression were observed. Short overexpression of GAGA
 factor in 3rd instar larvae also resulted in activation of a set of genes
 not previously described to be under GAGA regulation, and in lethality at
 pupa. Our results suggest a little contribution of GAGA factor on gene
 transcription in wing discs and a change of the genes regulated in
 comparison with embryo. GAGA factor activity thus correlates with the
 global changes in gene expression that take place at the embryo-to-larva
 and, later, at the larva-to-pupa transitions.
description: normalized_data_batch2Microarray data of GAGA overexpression in wing disknormalized_data_batch3Microarray data of GAGA depleted wing disks
DOI: 10.5061/dryad.g6311
title: Data from: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

description: The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat
 of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four
 genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US
 soybean production from SCN. Whole-genome sequencing was performed, and
 PCR assays were developed to investigate allelic variation in sequence and
 copy number of the Rhg1 locus across a population of soybean germplasm
 accessions. Four distinct sequences of the 31.2-kb repeat unit were
 identified, and some Rhg1 alleles carry up to three different types of
 repeat unit. The total number of copies of the repeat varies from 1 to 10
 per haploid genome. Both copy number and sequence of the repeat correlate
 with the resistance phenotype, and the Rhg1 locus shows strong signatures
 of selection. Significant linkage disequilibrium in the genome outside the
 boundaries of the repeat allowed the Rhg1 genotype to be inferred using
 high-density single nucleotide polymorphism genotyping of 15 996
 accessions. Over 860 germplasm accessions were found likely to possess
 Rhg1 alleles. The regions surrounding the repeat show indications of
 non-neutral evolution and high genetic variability in populations from
 different geographic locations, but without evidence of fixation of the
 resistant genotype. A compelling explanation of these results is that
 balancing selection is in operation at Rhg1.
description: WGS_S1toS3.xlsxAnalyses-ready data for Fig. 3 (a pre-processed file that contains 18 accessions and nucleotide sequence within S1, S2, & S3 region).Infinium_1.5MbAnalyses-ready data in the PHYLIP format for Figs 4 & 5 (a pre-processed file that contains 19,548 accessions and concatenated sequence alignments within 1.5 Mb region).10SNPsAnalyses-ready data for Fig. 6 (a pre-processed file that contains 15,996 accessions and concatenated 10 nucleotide sequence alignments).NewickNewick format tree files for Figs 3c & 6. S1.nwk: Fig. 3c. S2.nwk: Fig. 3c. S3.nwk: Fig. 3c. 15996.nwk: Fig. 6.Perl scriptsPerl scripts used in this study.Scripts.zipRhg1_CNV.shA shell script to generate SAM/BAM/mpileup files.subpopulationAnalyses-ready data for Fig. 5. The list of accessions for each subpopulation.VCF filesVCF outputs from VarScanVCF.zip
DOI: 10.5061/dryad.vr7km
title: Data from: Biotic interactions govern genetic adaptation to toxicants

description: The genetic recovery of resistant populations released from pesticide
 exposure is accelerated by the presence of environmental stressors. By
 contrast, the relevance of environmental stressors for the spread of
 resistance during pesticide exposure has not been studied. Moreover, the
 consequences of interactions between different stressors have not been
 considered. Here we show that stress through intraspecific competition
 accelerates microevolution, because it enhances fitness differences
 between adapted and non-adapted individuals. By contrast, stress through
 interspecific competition or predation reduces intraspecific competition
 and thereby delays microevolution. This was demonstrated in mosquito
 populations (Culex quinquefasciatus) that were exposed to the pesticide
 chlorpyrifos. Non-selective predation through harvesting and interspecific
 competition with Daphnia magna delayed the selection for individuals
 carrying the ace-1R resistance allele. Under non-toxic conditions,
 susceptible individuals without ace-1R prevailed. Likewise, predation
 delayed the reverse adaptation of the populations to a non-toxic
 environment, while the effect of interspecific competition was not
 significant. Applying a simulation model, we further identified how
 microevolution is generally determined by the type and degree of
 competition and predation. We infer that interactions with other
 species—especially strong in ecosystems with high biodiversity—can delay
 the development of pesticide resistance.
description: Experimental
 DataExperimental data
 collected in the laboratory including a short overview of the experimental
 design. Population sizes, genotype and wing length from all collected
 individuals.Simulation
 ModelScript of the simulation
 model and associated functions written in R 3.1.2. Can be read in any
 normal text editor.
DOI: 10.5281/zenodo.18390870
title: A jet bent by a stellar wind in the black hole X-ray binary Cygnus X-1: jet model and final data products

description: In this repo, we provide the code used to model the jet bending in the paper titled 'A jet bent by a stellar wind in the black hole X-ray Cygnus X-1'. The repo also contains the model fit components fit to the archival VLBA and EVN datasets.
DOI: 10.5061/dryad.1607t
title: Data from: Development of the corticospinal and callosal tracts from extremely premature birth up to 2 years of age

description: White matter tracts mature asymmetrically during development, and this
 development can be studied using diffusion magnetic resonance imaging. The
 aims of this study were i. to generate dynamic population-averaged white
 matter registration templates covering in detail the period from 25 weeks
 gestational age to term, and extending to 2 years of age based on DTI and
 fractional anisotropy, ii. to produce tract-specific probability maps of
 the corticospinal tracts, forceps major and forceps minor using
 probabilistic tractography, and iii. to assess the development of these
 tracts throughout this critical period of neurodevelopment. We found
 evidence for asymmetric development across the fiber bundles studied, with
 the corticospinal tracts showing earlier maturation (as measured by
 fractional anisotropy) but slower volumetric growth compared to the
 callosal fibers. We also found evidence for an anterior to posterior
 gradient in white matter microstructure development (as measured by mean
 diffusivity) in the callosal fibers, with the posterior forceps major
 developing at a faster rate than the anterior forceps minor in this age
 range. Finally, we report a protocol for delineating callosal and
 corticospinal fibers in extremely premature cohorts, and make available
 population-averaged registration templates and a probabilistic tract atlas
 which we hope will be useful for future neonatal and infant white-matter
 imaging studies.
description: Probabilistic
 AtlasesNifty images containing
 population-averaged white matter atlases for 7 developmental time points
 in a preterm-born cohort. Each age group contains a mean fractional
 anisotropy (FA) map plus tract probability atlases for forceps major,
 forceps minor and corticospinal tracts. Age groups included are 25-28
 weeks gestational age (GA), 29-30 weeks GA, 31-32 weeks GA, 33-35 weeks
 GA, 39-42 weeks GA, 1-year and 2-years of age.Atlases.zip
DOI: 10.5281/zenodo.18390869
title: A jet bent by a stellar wind in the black hole X-ray binary Cygnus X-1: jet model and final data products

description: In this repo, we provide the code used to model the jet bending in the paper titled 'A jet bent by a stellar wind in the black hole X-ray Cygnus X-1'. The repo also contains the model fit components fit to the archival VLBA and EVN datasets.
DOI: 10.5061/dryad.g4mj2
title: Data from: Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

description: Background: High-throughput sequencing using targeted enrichment and
 transcriptomic methods enables rapid construction of phylogenomic data
 sets incorporating hundreds to thousands of loci. These advances have
 enabled access to an unprecedented amount of nucleotide sequence data, but
 they also pose new questions. Given that the loci targeted for enrichment
 are often highly conserved, how informative are they at different
 taxonomic scales, especially at the intraspecific / phylogeographic scale?
 We investigate this question using Australian scincid lizards in the
 Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid
 enriched loci for 43 individuals and mined 1650 exons (1648 loci) from
 transcriptomes (transcriptome mining) from 11 individuals, including
 multiple phylogeographic lineages within several species of Carlia,
 Lampropholis, and Saproscincus skinks. We assessed the phylogenetic
 information content of these loci at the intergeneric, interspecific, and
 phylogeographic scales. As a further test of the utility at the
 phylogeographic scale, we used the anchor hybrid enriched loci to infer
 lineage divergence parameters using coalescent models of isolation with
 migration. Results Phylogenetic analyses of both data sets inferred very
 strongly supported trees at all taxonomic levels. Further, AHE loci
 yielded estimates of divergence times between closely related lineages
 that were broadly consistent with previous population-level analyses.
 Conclusions Anchored-enriched loci are useful at the deep phylogeny and
 phylogeographic scales. Although overall phylogenetic support was high
 throughout the Australian Eugongylus group phylogeny, there were
 nonetheless some conflicting or unresolved relationships, especially
 regarding the placement of Pseudemoia, Cryptoblepharus, and the
 relationships amongst closely-related species of Tasmanian Niveoscincus
 skinks.
description: Eugongylus_Dryad_dataNucleotide data from transcriptome and anchored hybrid enriched loci, and scripts used in the analytical pipeline.
DOI: 10.5061/dryad.9d030
title: Data from: Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid

description: We performed a genetic analysis of sRNA abundance in flag leaf from an
 immortalized F2 (IMF2) population in rice. We identified 53,613,739 unique
 sRNAs and 165,797 sRNA expression traits (s-traits). A total of 66,649
 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs. By defining
 80,362 sRNA clusters, 22,263 sRNA cluster QTLs (scQTLs) were recovered for
 20,249 of all the 50,139 sRNA cluster expression traits (sc-traits). The
 expression levels for most of s-traits from the same genes or the same
 sRNA clusters were slightly positively correlated. While genetic
 co-regulation between sRNAs from the same mother genes and between sRNAs
 and their mother genes was observed for a portion of the sRNAs, most of
 the sRNAs and their mother genes showed little co-regulation. Some sRNA
 biogenesis genes were located in distant-sQTL hotspots and showed
 correspondence with specific length classes of sRNAs suggesting their
 important roles in the regulation and biogenesis of the sRNAs.
description: Reads of sRNAs in the
 four categories in the 104 libraries classified according to genome
 mapping to the SNP-replaced reference genomes of the
 parents.Reads of sRNAs in the
 four categories in the 104 libraries classified according to genome
 mapping to the SNP-replaced reference genomes of the
 parents.Supplementary file
 2.xlsSupplementary file
 3The
 identified s-traits.Supplementary file
 4The
 definition of sRNA clusters.Supplementary file
 5A
 summary of the mRNA sequencing data.Supplementary file
 6The
 genotype of the IMF2 population.Supplementary file
 9Information of sRNA
 biogenesis genes.Supplementary file
 14The
 crossing information of RILs to generate IMF2s.Supplementary file
 1The
 statistics of reads after quality filtering, size filtering, ncRNA
 filtering and genome mapping for redundant and distinct reads for 98
 crosses in the IMF2 population, the parents Zhenshan 97, Minghui 63 and
 their F1 hybrid.Supplementary file
 7The
 QTL analysis results of s-traits, sc-traits and
 e-traits.Supplementary file
 8Supplementary file
 10Supplementary file
 11Supplementary file
 12Supplementary file
 13Genetic effects of the
 sQTLs and scQTLs.