cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.50410
title: Data from: Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

description: To understand complex regulatory processes in multicellular organisms, it
 is critical to be able to quantitatively analyze protein movement and
 protein-protein interactions in time and space. During Arabidopsis
 development, the intercellular movement of SHORTROOT (SHR) and subsequent
 interaction with its downstream target SCARECROW (SCR) control root
 patterning and cell fate specification. However, quantitative information
 about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction
 is currently unavailable. Here, we quantify parameters including SHR
 mobility, oligomeric state, and association with SCR using a combination
 of Fluorescent Correlation Spectroscopy (FCS) techniques. We then
 incorporate these parameters into a mathematical model of SHR and SCR,
 which shows that SHR reaches a steady state in minutes, while SCR and the
 SHR-SCR complex reach a steady-state between 18 and 24 hours. Our model
 reveals the timing of SHR and SCR dynamics and allows us to understand how
 protein movement and protein-protein stoichiometry contribute to
 development.
description: Image files used for
 RICS and N&B analysis of 35S:GFP and UBQ10:mCherryImages used for RICS and
 N&B analysis of 35S:GFP and UBQ10:mCherry lines. Images were acquired
 using a Zeiss 710 or Zeiss 780 confocal microscope. Images can be viewed
 using the Zen imaging software. Images were analyzed using the SimFCS
 software.35SGFP and
 UBQ10mCherry.zipImage files used in RICS
 and N&B analysis of SHR:SHR-GFP, SHR:SHR-GFP in SCRi, SCR:SCR-GFP, and
 SHR:SHR-GFP/SCR:SCR-mCherryImages used for RICS and
 N&B analysis of SHR:SHR-GFP, SHR:SHR-GFP in SCRi, SCR:SCR-GFP, and
 SHR:SHR-GFP/SCR:SCR-mCherry lines. Images were acquired using a Zeiss 710
 or Zeiss 780 confocal microscope. Images can be viewed using the Zen
 imaging software. Images were analyzed using the SimFCS
 software.SHRSHRGFP, SCRSCRGFP,
 SHRSHRGFPxSCRSCRmCherry.zipImage files used for pCF
 analysisImage files used for pCF
 analysis of 35S:GFP, TMO5:3xGFP, SHR:SHR-GFP, SHR:SHR-GFP in SCRi, and
 SCR:SCR-GFP lines. Images were acquired using either a Zeiss 710 or Zeiss
 780 confocal microscope. Images can be viewed using the Zen imaging
 software. Images were analyzed using the SimFCS
 software.pCF.zipData tablesData tables for all images. All statistical analysis was performed using JMP software. The .csv files are formatted for easy import into the JMP software.Tables.zip
DOI: 10.5061/dryad.tj45p
title: Data from: Genome editing in butterflies reveals that spalt promotes and Distal-less represses eyespot colour patterns

description: Butterfly eyespot colour patterns are a key example of how a novel trait
 can appear in association with the co-option of developmental patterning
 genes. Little is known, however, about how, or even whether, co-opted
 genes function in eyespot development. Here we use CRISPR/Cas9 genome
 editing to determine the roles of two co-opted transcription factors that
 are expressed during early eyespot determination. We found that deletions
 in a single gene, spalt, are sufficient to reduce or completely delete
 eyespot colour patterns, thus demonstrating a positive regulatory role for
 this gene in eyespot determination. Conversely, and contrary to previous
 predictions, deletions in Distal-less (Dll) result in an increase in the
 size and number of eyespots, illustrating a repressive role for this gene
 in eyespot development. Altogether our results show that the presence,
 absence and shape of butterfly eyespots can be controlled by the activity
 of two co-opted transcription factors.
description: Wing
 imagesThis file is a .zip
 archive containing images of wings from butterflies with presumptive spalt
 and Distal-less mosaic gene deletion phenotypes. A reference table is
 included.Zhang&Reed_2016_Images.zip
DOI: 10.5281/zenodo.18385934
title: Identification of H1N1 and H3N2 Influenza A Virus Proteins as Druggable Targets for Phytochemicals using an in silico Computational Approach

description: Data associated with manuscript titled, "Identification of H1N1 and H3N2 Influenza A Virus Proteins as Druggable Targets for Phytochemicals using an in silico Computational Approach"
DOI: 10.5281/zenodo.18385933
title: Identification of H1N1 and H3N2 Influenza A Virus Proteins as Druggable Targets for Phytochemicals using an in silico Computational Approach

description: Data associated with manuscript titled, "Identification of H1N1 and H3N2 Influenza A Virus Proteins as Druggable Targets for Phytochemicals using an in silico Computational Approach"
DOI: 10.5061/dryad.524mc
title: Data from: Three-dimensional morphological analysis of a Parahaentzschelinia-like trace fossil

description: Serial grinding and three-dimensional reconstruction of aff.
 Parahaentzschelinia trace fossils from the Ordovician Winterhouse
 Formation reveals complex tiered network systems associated with more
 typical Parahaentzschelinia-like conical bundles of sub-vertical tubes.
 The morphological complexity of the burrow system is interpreted as an
 indication of the diverse behaviour of the trace-making organism. This
 organism is inferred to have exploited organic matter within the sand-rich
 event beds as well as in muddier beds above and below the sandstone beds
 using a variety of behaviours. Potential burrow irrigation and microbial
 cultivation associated with gardening behaviour is also inferred. The
 trace-making organism is unknown, but comparisons are drawn between the
 structures observed herein and those produced by both modern polychaetes
 and bivalves.
description: clip through
 network-like portionThe animation shows the
 movement of a clip plane orientated parallel to bedding documenting the
 network or Multina-like portion of the aff. Parahaentzschelinia burrow
 complexclip
 through network.aviSerial vertical cross
 sections of sample 1The video shows the
 complete series of vertical cross sections through sample 1 showing the
 Parahaentzschelinia burrows in the context of the host
 sedimentsample
 1.avisample 2 vertical cross
 sectionsComplete series of
 vertical cross sections through Sample 2 of
 Parahaentzschelinia.sample 2
 frontal.avibedding parallel cross
 sectionsComplete series of
 bedding parallel cross sections through aff. Parahaentzschelinia showing
 the endogenic radial mud-lined burrows.top down Bedding
DOI: 10.34740/kaggle/dsv/14637322
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.t6b05
title: Data from: Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

description: Biodiversity, phylogeography and population genetic studies will be
 revolutionized by access to large datasets thanks to next generation
 sequencing methods. In this study, we develop an easy and cost-effective
 protocol for in-solution enrichment hybridization capture of complete
 chloroplast genomes applicable at deep multiplexed levels. The protocol
 uses cheap in-house species-specific probes developed via long range PCR
 of the entire chloroplast. Barcoded libraries are constructed and
 in-solution enrichment of the chloroplasts is done using the probes. This
 protocol was tested and validated on six economically important West
 African crop species, namely African rice, pearl millet, three African yam
 species and fonio. For pearl millet, we also demonstrate the effectiveness
 of this protocol to retrieve 95% of the sequence of the whole chloroplast
 on 95 multiplexed individuals in a single MiSeq run at a success rate of
 95%. This new protocol allows whole chloroplast genomes to be retrieved at
 a modest cost and will allow unprecedented resolution for closely related
 species in phylogeography studies using plastomes.
description: replace95bam_and_ref95bam_and_ref.zipDe novo assembly Chloroplast of Dioscorea rotundataThe software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Dioscorea elephantipes (EF380353.1)cpRotundatav1_28itcp.fastaDe novo assembly Chloroplast of Digitaria excilisThe software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Pennisetum glaucumcpFONIO-18itv1.fastaDe novo assembly Chloroplast of Cenchrus americanusThe software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Zea mayscpmilv3100it.fastaRAM63_forward_500kThis file contain 500k forward reads Illumina TrueSeq v3 75 PE, from RAM63, an O. sativa ssp indica.These data have been used to validate the assembly method.RAM63_reverse_500k
DOI: 10.5061/dryad.4c039m4
title: Data from: Coasting in live-bearing fish: the drag penalty of being pregnant

description: Swimming performance of pregnant live-bearing fish is presumably
 constrained by the additional drag associated with the reproductive
 burden. Yet, it is still unclear how and to what extent the reproductive
 investment affects body drag of the females. We examined the effect of
 different levels of reproductive investment on body drag. The biggest
 measured increase in body volume due to pregnancy was about 43%, linked to
 a wetted area increase of about 16% and 69% for the frontal area. We
 printed three-dimensional models of live-bearing fish in a straight body
 posture representing different reproductive allocation (RA) levels. We
 measured the drag and visualized the flow around these models in a flow
 tunnel at different speeds. Drag grew in a power fashion with speed and
 exponentially with the increase of RA, thus drag penalty for becoming
 thicker was relatively low for low speeds compared to high ones. We show
 that the drag increase with increasing RA was most probably due to bigger
 regions of flow separation behind the enlarged belly. We suggest that the
 rising drag penalty with an increasing RA, possibly together with
 pregnancy-related negative effects on muscle- and abdominal bending
 performance, will reduce the maximum swimming speed.
description: Dryad_Drag_penalty_of_pregnancy
DOI: 10.5061/dryad.936p0df
title: Data from: A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila

description: Background: Population genetic theory predicts that rapid adaptation is
 largely driven by complex traits encoded by many loci of small effect.
 Because large-effect loci are quickly fixed in natural populations, they
 should not contribute much to rapid adaptation. Results: To investigate
 the genetic architecture of thermal adaptation — a highly complex trait —
 we performed experimental evolution on a natural Drosophila simulans
 population. Transcriptome and respiration measurements reveal extensive
 metabolic rewiring after only approximately 60 generations in a hot
 environment. Analysis of genome-wide polymorphisms identifies two
 interacting selection targets, Sestrin and SNF4Aγ, pointing to AMPK, a
 central metabolic switch, as a key factor for thermal adaptation.
 Conclusions: Our results demonstrate that large-effect loci segregating at
 intermediate allele frequencies can allow natural populations to rapidly
 respond to selection. Because SNF4Aγ also exhibits clinal variation in
 various Drosophila species, we suggest that this large-effect polymorphism
 is maintained by temporal and spatial temperature variation in natural
 environments.
description: Final_counts_DryadDsim_Portugal_Hot_bwa_mem_F0_F59_polymorphicDsim_Portugal_Hot_bowtie2_F0_F59_polymorphicDsim_Portugal_Hot_novoalign_F0_F59_polymorphic
DOI: 10.34810/data2942
title: Partitura i enregistrament [partitura y grabación]. Motete a 4 voces con acompañamiento instrumental, «Caro mea vere est cibus», ca. 1730, de Josep Picanyol (ca. 1700-1757?)

description: [CAT] Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical que està desenvolupant la UB i el CSIC, juntament amb el CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, el Grup per a l'Estudi del Patrimoni Musical (GEPAM), el Grup de Recerca Patrimoni Musical Històric de la Institució Milà i Fontanals d'Investigació en Humanitats del CSIC, l'Arquebisbat de Barcelona, la Catedral de Barcelona, l'Arxiu de l'Església de Santa Maria del Pi i l'Oratori de Sant Felip Neri de Barcelona, ha recuperat una peça musical de Josep Picanyol (ca. 1700- 1757?) que es troba al fons musical de la Catedral de Barcelona conservat a la Biblioteca de Catalunya, BC M-1618/10. Aquest conjunt de dades conté dos arxius:
- Transcripció del Motet a 4 amb acompanyament instrumental, ca. 1730, de , «Caro mea vere est cibus». 
- Enregistrament del so de la peça interpretada pel Cor Francesc Valls de la Catedral de Barcelona: Director: Pere Lluís Biosca. Sopranos: Maria Casado; Belen Barnaus; Laura Martínez Boj. Mezzos: Mariona Llobera; Miguel Gómez. Tenors: Carles Prat; Oriol Guimerà. Baixos: Joan Garcia; David Pastor. Acompanyament instrumental a càrrec de: Orgue: Joan Seguí. Violoncel: Clara Pouvreau. Violins: Sara Balasch; Ángela Moro. Oboès: Josep Domènech; Nina Alcanyiz. El vídeo es pot veure a: https://www.youtube.com/@GEPAM-UB
description: [ESP] El proyecto Estudio y Recuperación del Patrimonio Musical que desarrollan la UB y el CSIC, junto con el CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, el Grupo de Investigación Patrimonio Musical Histórico de la Institución Milá y Fontanals de Investigación en Humanidades del CSIC, la Archidiócesis de Barcelona, la Catedral de Barcelona, el Arxiu de l'Església de Santa Maria del Pi y el Oratorio de Sant Felip Neri de Barcelona, ha recuperado Patrimonio musical: una pieza musical de Josep Picanyol (ca. 1700- 1757?) del fondo musical de la Catedral de Barcelona conservado en la Biblioteca de Catalunya, BC M-1618/10. Este conjunto de datos contiene dos archivos:
- Transcripción del Motet a 4 amb acompanyament instrumental, ca. 1730, de , «Caro mea vere est cibus». 
- Grabación del sonido de la pieza interpretada por el coro Francesc Valls de la Catedral de Barcelona: Director: Pere Lluís Biosca. Sopranos: Maria Casado; Belen Barnaus; Laura Martínez Boj. Mezzos: Mariona Llobera; Miguel Gómez. Tenores: Carles Prat; Oriol Guimerà. Bajos: Joan Garcia; David Pastor. Acompañamiento instrumental a cargo de: Órgano: Joan Seguí. Violonchelo: Clara Pouvreau. Violines: Sara Balasch; Ángela Moro. Oboes: Josep Domènech; Nina Alcanyiz. El video se puede ver en: https://www.youtube.com/@GEPAM-UB.
DOI: 10.6084/m9.figshare.30913712
title: Dataset for: A case of invasive holobionts: invasive Ips typographus brings new fungal phytopathogens into the United Kingdom

description: Supplementary Files for 'A case of invasive holobionts: invasive Ips typographus brings new fungal phytopathogens into the United Kingdom'Files are:<br>The OTU x Sample tableFull Taxonomic Identifications for each OTU as determined by dnabarcoder and BLAST against UNITE and subsequent dynamic clusteringAn interactive KRONA plot showing taxonomy and abundance of OTUsRepresentative ITS2 sequences for all OTUs in FASTA formatOphiostomatales ITS2 sequences used for EPA-ng placementMicroascales ITS2 sequences used for EPA-ng placementOphiostomatales reference phylogeny with OTUs graftedMicroascales reference phylogeny with OTUs grafted<br>
DOI: 10.6084/m9.figshare.30913712.v2
title: Dataset for: A case of invasive holobionts: invasive Ips typographus brings new fungal phytopathogens into the United Kingdom

description: Supplementary Files for 'A case of invasive holobionts: invasive Ips typographus brings new fungal phytopathogens into the United Kingdom'Files are:<br>The OTU x Sample tableFull Taxonomic Identifications for each OTU as determined by dnabarcoder and BLAST against UNITE and subsequent dynamic clusteringAn interactive KRONA plot showing taxonomy and abundance of OTUsRepresentative ITS2 sequences for all OTUs in FASTA formatOphiostomatales ITS2 sequences used for EPA-ng placementMicroascales ITS2 sequences used for EPA-ng placementOphiostomatales reference phylogeny with OTUs graftedMicroascales reference phylogeny with OTUs grafted<br>
DOI: 10.6084/m9.figshare.30913712.v1
title: Dataset for: A case of invasive holobionts: invasive Ips typographus brings new fungal phytopathogens into the United Kingdom

description: Supplementary Files for 'A case of invasive holobionts: invasive Ips typographus brings new fungal phytopathogens into the United Kingdom' Llewellyn et al. (2025)Files are:<br>The OTU x Sample tableFull Taxonomic Identifications for each OTU as determined by dnabarcoder and BLAST against UNITE and subsequent dynamic clusteringAn interactive KRONA plot showing taxonomy and abundance of OTUsRepresentative ITS2 sequences for all OTUs in FASTA formatOphiostomatales ITS2 sequences used for EPA-ng placementMicroascales ITS2 sequences used for EPA-ng placementOphiostomatales reference phylogeny with OTUs graftedMicroascales reference phylogeny with OTUs grafted<br>
DOI: 10.5061/dryad.1h6h354
title: Data from: Multiple QTL underlie milk phenotypes at the CSF2RB locus

description: Background: Over many years, artificial selection has substantially
 improved milk production by cows. However, the genes that underlie milk
 production quantitative trait loci (QTL) remain relatively poorly
 characterised. Here, we investigate a previously reported QTL located at
 the CSF2RB locus on chromosome 5, for several milk production phenotypes,
 to better understand its underlying genetic and molecular causes. Results:
 Using a population of 29,350 taurine dairy cows, we conducted association
 analyses for milk yield and composition traits, and identified highly
 significant QTL for milk yield, milk fat concentration, and milk protein
 concentration. Strikingly, protein concentration and milk yield appear to
 show co-located yet genetically distinct QTL. To attempt to understand the
 molecular mechanisms that might be mediating these effects, gene
 expression data were used to investigate eQTL for 11 genes in the broader
 interval. This analysis highlighted genetic impacts on CSF2RB and NCF4
 expression that share similar association signatures to those observed for
 lactation QTL, strongly implicating one or both of these genes as
 responsible for these effects. Using the same gene expression dataset
 representing 357 lactating cows, we also identified 38 novel RNA editing
 sites in the 3′ UTR of CSF2RB transcripts. The extent to which two of
 these sites were edited also appears to be genetically co-regulated with
 lactation QTL, highlighting a further layer of regulatory complexity that
 involves the CSF2RB gene. Conclusions: This locus presents a diversity of
 molecular and lactation QTL, likely representing multiple overlapping
 effects that, at a minimum, highlight the CSF2RB gene as having a causal
 role in these processes.
description: rna-animals-357.vcfGenotypes for 357 RNAseq cows. Used for eQTL analyses.rna-animals-357-anon.vcf.gzht-phenosHerd test phenotypes for 29,350 cows. Used for milk phenotype association analyses.ht-phenos-namesColumn names for herd test phenotypes. These are in a separate file per the GCTA input format requirements.ht-phenos-anon-names.txtge-phenosGene expression phenotypes for 357 animals. Used for eQTL analyses.ge-phenos-namesColumn names for gene expression phenotypes. These are in a separate file per the GCTA input format requirements.ge-phenos-anon-names.txtHD.rna-animals-357.grmGZipped tar file containing the GRM for the 357 RNAseq animals in GCTA binary format. Based on Illumina BovineHD genotypes. Excludes chromosome 5 to enable MLMA-LOCO analyses.HD.milk-animals-29350.grmGZipped tar file containing the GRM for the 29,350 milk phenotype animals in GCTA binary format. Based on Illumina BovineHD genotypes. Excludes chromosome 5 to enable MLMA-LOCO analyses.milk-animals-29350.vcf.gzGenotypes for 29,350 herd test phenotype cows. Used for milk association analyses.READMEThe readme file describing this dataset.
DOI: 10.5061/dryad.83164r7v
title: Data from: Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats

description: The repetitive landscapes of mammalian genomes typically display high
 Class I (retrotransposon) transposable element (TE) content, usually
 around half of the genome. In contrast, the Class II (DNA transposon)
 contribution is typically small (&lt;3% in model mammals). Most
 mammalian genomes also exhibit a precipitous decline in Class II activity
 beginning roughly 40 million years ago (Ma). The first signs of more
 recently active mammalian Class II TEs were obtained from the little brown
 bat, Myotis lucifugus and are reflected by higher genome content (~5%). To
 aid in determining taxonomic limits and potential impacts of this elevated
 Class II activity, we performed 454 survey sequencing of a second Myotis
 species as well as four additional taxa within the family Vespertilionidae
 and an outgroup species from Phyllostomidae. Graph-based clustering
 methods were used to reconstruct the major repeat families present in each
 species and novel elements were identified in several taxa.
 Retrotransposons remained the dominant group with regard to overall genome
 mass. Elevated Class II TE composition (3-4%) was observed in all five
 vesper bats while less than 0.5% of the phyllostomid reads were identified
 as Class II derived. Differences in satellite DNA and Class I TE content
 are also described among vespertilionid taxa. These analyses present the
 first cohesive description of TE evolution across closely related mammals,
 revealing genome-scale differences in TE content within a single family.
description: Craf.454Lbor.454Maus.454Nhum.454Psub.454