cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qg8dt
title: Data from: In vivo dynamics of skeletal muscle Dystrophin in zebrafish embryos revealed by improved FRAP analysis

description: Dystrophin forms an essential link between sarcolemma and cytoskeleton,
 perturbation of which causes muscular dystrophy. We analysed Dystrophin
 binding dynamics in vivo for the first time. Within maturing fibres of
 host zebrafish embryos, our analysis reveals a pool of diffusible
 Dystrophin and complexes bound at the fibre membrane. Combining modelling,
 an improved FRAP methodology and direct semi-quantitative analysis of
 bleaching suggests the existence of two membrane-bound Dystrophin
 populations with widely differing bound lifetimes: a stable, tightly bound
 pool, and a dynamic bound pool with high turnover rate that exchanges with
 the cytoplasmic pool. The three populations were found consistently in
 human and zebrafish Dystrophins overexpressed in wild-type or
 dmdta222a/ta222a zebrafish embryos, which lack Dystrophin, and in
 Gt(dmd-Citrine)ct90a that express endogenously-driven tagged zebrafish
 Dystrophin. These results lead to a new model for Dystrophin membrane
 association in developing muscle, and highlight our methodology as a
 valuable strategy for in vivo analysis of complex protein dynamics.
description: Datasets and FRAP
 analysisHere we provide the
 complete Dystrophin FRAP datasets used in Bajanca et al., 2015 eLife,
 together with the main FRAP analysis files and plots, and also
 instructions for free access to the software used to analyse cytoplasmic
 diffusion.Bajanca_et_al.zip
DOI: 10.5061/dryad.18b29
title: Data from: Characterization of Arabidopsis transcriptional responses to different aphid species reveals genes that contribute to host susceptibility and non-host resistance

description: Aphids are economically important pests that display exceptional variation
 in host range. The determinants of diverse aphid host ranges are not well
 understood, but it is likely that molecular interactions are involved.
 With significant progress being made towards understanding host responses
 upon aphid attack, the mechanisms underlying non-host resistance remain to
 be elucidated. Here, we investigated and compared Arabidopsis thaliana
 host and non-host responses to aphids at the transcriptional level using
 three different aphid species, Myzus persicae, Myzus cerasi and
 Rhopalosiphum pisum. Gene expression analyses revealed a high level of
 overlap in the overall gene expression changes during the host and
 non-host interactions with regards to the sets of genes differentially
 expressed and the direction of expression changes. Despite this overlap in
 transcriptional responses across interactions, there was a stronger
 repression of genes involved in metabolism and oxidative responses
 specifically during the host interaction with M. persicae. In addition, we
 identified a set of genes with opposite gene expression patterns during
 the host versus non-host interactions. Aphid performance assays on
 Arabidopsis mutants that were selected based on our transcriptome analyses
 identified novel genes contributing to host susceptibility, host defences
 during interactions with M. persicae as well to non-host resistance
 against R. padi. Understanding how plants respond to aphid species that
 differ in their ability to infest plant species, and identifying the genes
 and signaling pathways involved, is essential for the development of novel
 and durable aphid control in crop plants.
description: H2O2 production in
 NADPH-oxidase mutantsProduction of ROS in
 Arabidopsis NADPH-oxidase mutants upon aphid interactions. Confocal JPEG
 files and 8 bits ImageJ converted images. Leaves of Col-0, the atrbohD-3
 and atrbohF-3 mutant lines after exposure to aphids species Myzus persicae
 (Mp), M. cerasi (Mc) and Rhopalosihpum padi (Rp) and were collected after
 3 and 24 hours. 3 replicates, R1, R2 and R3.atrboh.zipH2O2 production in Col0Production of ROS in Col-0. Confocal JPEG files and 8 bits ImageJ converted images. Col-0 leaves after exposure to aphid species Myzus persicae (Mp), M. cerasi (Mc) and Rhopalosihpum padi (Rp) and collected after 3, 6,12 and 24 hours. 2 replicates, R1 and R2.Col0.zipH2O2 production in Col0 after aphid moult exposureProduction of ROS in Col-0. Confocal JPEG files and 8 bits ImageJ converted images. Col-0 leaves after exposure to aphid skin of Myzus persicae (Mp), M. cerasi (Mc) and Rhopalosihpum padi (Rp) and collected after 24 hours. .Skin.zip
DOI: 10.5281/zenodo.18380388
title: Code and data for the article "Do targeted, placed-based educational campaigns influence citizen engagement and violent crime? A quasi-experiment of the alert conscience technique of situational crime prevention"
DOI: 10.5281/zenodo.18380389
title: Code and data for the article "Do targeted, placed-based educational campaigns influence citizen engagement and violent crime? A quasi-experiment of the alert conscience technique of situational crime prevention"
DOI: 10.5061/dryad.6s48n
title: Data from: Waterjet and laser etching: the nonlinear inverse problem

description: In waterjet and laser milling, material is removed from a solid surface in
 a succession of layers to create a new shape, in a depth-controlled
 manner. The inverse problem consists of defining the control parameters,
 in particular, the two-dimensional beam path, to arrive at a prescribed
 freeform surface. Waterjet milling (WJM) and pulsed laser ablation (PLA)
 are studied in this paper, since a generic nonlinear material removal
 model is appropriate for both of these processes. The inverse problem is
 usually solved for this kind of process by simply controlling dwell time
 in proportion to the required depth of milling at a sequence of pixels on
 the surface. However, this approach is only valid when shallow surfaces
 are etched, since it does not take into account either the footprint of
 the beam or its overlapping on successive passes. A discrete adjoint
 algorithm is proposed in this paper to improve the solution. Nonlinear
 effects and non-straight passes are included in the optimization, while
 the calculation of the Jacobian matrix does not require large computation
 times. Several tests are performed to validate the proposed method and the
 results show that tracking error is reduced typically by a factor of two
 in comparison to the pixel-by-pixel approach and the classical raster path
 strategy with straight passes. The tracking error can be as low as 2–5%
 and 1–2% for WJM and PLA, respectively, depending on the complexity of the
 target surface.
description: RSOS
 PaperCompressed archive of
 all the Figures in the paper, the measurement data used to generate them
 and the beam path data files used in the experiments.
DOI: 10.5061/dryad.4sd51d4b
title: Data from: Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill

description: Benthic habitats harbour a significant (yet unexplored) diversity of
 microscopic eukaryote taxa, including metazoan phyla, protists, algae and
 fungi. These groups are thought to underpin ecosystem functioning across
 diverse marine environments. Coastal marine habitats in the Gulf of Mexico
 experienced visible, heavy impacts following the Deepwater Horizon oil
 spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity
 has precluded a thorough assessment of this disturbance. Using a marker
 gene and morphological approach, we present an intensive evaluation of
 microbial eukaryote communities prior to and following oiling around
 heavily impacted shorelines. Our results show significant changes in
 community structure, with pre-spill assemblages of diverse Metazoa giving
 way to dominant fungal communities in post-spill sediments. Post-spill
 fungal taxa exhibit low richness and are characterized by an abundance of
 known hydrocarbon-degrading genera, compared to prior communities that
 contained smaller and more diverse fungal assemblages. Comparative
 taxonomic data from nematodes further suggests drastic impacts; while
 pre-spill samples exhibit high richness and evenness of genera, post-spill
 communities contain mainly predatory and scavenger taxa alongside an
 abundance of juveniles. Based on this community analysis, our data suggest
 considerable (hidden) initial impacts across Gulf beaches may be ongoing,
 despite the disappearance of visible surface oil in the region.
description: Bik_etal_PLoSOne"Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill" This Dryad data packet contains: Raw Data Files - Pooled from 3 independent 454 Runs (GS FLX Titanium; 2 full plates, plus one 1/16 plate). Clustered OTU data - Raw data was demultiplexed and quality filtered in both the QIIME and OCTUPUS pipelines, and subsequently clustered at 99% pairwise sequence identity (two independent clustering runs carried out in uclust in QIIME and the octu.pl script in OCTUPUS). Taxonomy assignments - carried out using the Megablast algorithm against GenBank's non-redundant nucleotide database in Summer 2011. Alpha and beta diversity analyses (raw outputs with log files) - carried out in the QIIME pipeline.
DOI: 10.5061/dryad.1k8kq
title: Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

description: The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most
 divergent from the canonical laboratory strain N2 and has been widely used
 in developmental, population and evolutionary studies. To enhance the
 utility of the strain, we have generated a draft sequence of the CB4856
 genome, exploiting a variety of resources and strategies. The CB4856
 genome when compared against the N2 reference has 327,050 single
 nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels)
 that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing
 from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As
 previously reported, the density of SNVs varies along the chromosomes,
 with the arms of chromosomes showing greater average variation than the
 centers. In addition, we find 61 regions totaling 2.8 Mb, distributed
 across all six chromosomes, that have a greatly elevated SNV density,
 ranging from 2% to 16% SNVs. A survey of other wild isolates show that the
 two alternative haplotypes for each region are widely distributed,
 suggesting they have been maintained by balancing selection over long
 evolutionary times. These divergent regions contain an abundance of genes
 from large rapidly evolving families encoding F-box, MATH, BATH,
 seven-transmembrane G-coupled receptors, and nuclear hormone receptors
 suggesting that they provide selective advantages in natural environments.
 The draft sequence makes available a comprehensive catalog of sequence
 differences between the CB4856 and N2 strains that will facilitate the
 molecular dissection of their phenotypic differences. Our work also
 emphasizes the importance of going beyond simple alignment of reads to a
 reference genome when assessing differences between genomes.
description: File_S1_Celegans_N2_to_CB4856_lastz_alignment.txtLASTZ alignments between C. elegans N2 (WormBase version WS230) and C. elegans Hawaiian CB4856 (Genbank accession: JZEW00000000)
DOI: 10.5061/dryad.t9221
title: Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

description: Hybrid zones are a valuable tool for studying the process of speciation
 and for identifying the genomic regions undergoing divergence and the
 ecological (extrinsic) and non-ecological (intrinsic) factors involved.
 Here, we explored the genomic and geographic landscape of divergence in a
 hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome
 scan of 28,417 ddRAD SNPs, we identified genomic regions under possible
 selection and examined their distribution in the context of previously
 identified candidate genes for ecological adaptations. We showed that
 differentiation was genome-wide, including multiple candidate genes for
 ecological adaptations, particularly those involved in seasonal adaptation
 and host plant detoxification. The Z-chromosome and four autosomes showed
 a disproportionate amount of differentiation, suggesting genes on these
 chromosomes play a potential role in reproductive isolation. Cline
 analyses of significantly differentiated genomic SNPs, and of species
 diagnostic genetic markers, showed a high degree of geographic coincidence
 (81%) and concordance (80%) and were associated with the geographic
 distribution of a climate-mediated developmental threshold (length of the
 growing season). A relatively large proportion (1.3%) of the outliers for
 divergent selection were not associated with candidate genes for
 ecological adaptations and may reflect the presence of previously
 unrecognized intrinsic barriers between these species. These results
 suggest that exogenous (climate-mediated) and endogenous (unknown) clines
 may have become coupled and act together to reinforce reproductive
 isolation. This approach of assessing divergence across both the genomic
 and geographic landscape can provide insight about the interplay between
 the genetic architecture of reproductive isolation and endogenous and
 exogenous selection.
description: Associated
 MetadataIncludes CSV file with 4
 worksheets containing metadata for each specimen used in this
 studyScripts_for_processing_readsText document containing scripts used to process Illumina sequences, from raw reads to a vcf fileScripts_for_SNP_filtering_and_analysisText document containing scripts used to run all analyses (including scripts to prepare files for analyses)Rscripts_and_associated_filesREADME
DOI: 10.5061/dryad.0sj1q
title: Data from: Kinematic diversity suggests expanded roles for fly halteres

description: The halteres of flies are mechanosensory organs that provide information
 about body rotations during flight. We measured haltere movements in a
 range of fly taxa during free walking and tethered flight. We find a
 diversity of wing–haltere phase relationships in flight, with higher
 variability in more ancient families and less in more derived families.
 Diverse haltere movements were observed during free walking and were
 correlated with phylogeny. We predicted that haltere removal might
 decrease behavioural performance in those flies that move them during
 walking and provide evidence that this is the case. Our comparative
 approach reveals previously unknown diversity in haltere movements and
 opens the possibility of multiple functional roles for halteres in
 different fly behaviours.
description: Digitized traces of wing
 and haltere tip in flying fliesThese files contain
 two-dimensional coordinates for the tip and base of both the haltere and
 the wing in tethered flying flies.converted to
 cdata.zipWalking flies filmed
 with two camerasThese are
 two-dimensional coordinates of both halteres of walking flies as filmed
 with two cameras. The tip and base of each haltere is digitized, as well
 as the thorax (as a metric of body position) and one of the
 legs.digitized files for
 centipede.zipPerturbation
 videos
DOI: 10.5061/dryad.cn58f
title: Data from: A convex formulation for magnetic particle imaging x-space reconstruction

description: Magnetic Particle Imaging (MPI) is an emerging imaging modality with
 exceptional promise for clinical applications in rapid angiography, cell
 therapy tracking, cancer imaging, and inflammation imaging. Recent
 publications have demonstrated quantitative mpi across rat sized fields of
 view with x-space reconstruction methods. Critical to any medical imaging
 technology is the reliability and accuracy of image reconstruction.
 Because the average value of the mpi signal is lost during
 direct-feedthrough signal filtering, mpi reconstruction algorithms must
 recover this zero-frequency value. Prior x-space mpi recovery techniques
 were limited to 1d approaches which could introduce artifacts when
 reconstructing a 3d image. In this paper, we formulate x-space
 reconstruction as a 3d convex optimization problem and apply robust a
 priori knowledge of image smoothness and non-negativity to reduce
 non-physical banding and haze artifacts. We conclude with a discussion of
 the powerful extensibility of the presented formulation for future
 applications.
description: Experimental MPI Partial
 FOV DataExperimental magnetic
 particle imaging partial field of view data of a coronary artery phantom
 and a double helix phantom.mpiData.zip
DOI: 10.5061/dryad.6cv82g1
title: Data from: Heterochronic shifts and conserved embryonic shape underlie crocodylian craniofacial disparity and convergence

description: The distinctive anatomy of the crocodylian skull is intimately linked with
 dietary ecology, resulting in repeated convergence on blunt- and
 slender-snouted ecomorphs. These evolutionary shifts depend upon
 modifications of the developmental processes which direct growth and
 morphogenesis. Here we examine the evolution of cranial ontogenetic
 trajectories to shed light on the mechanisms underlying convergent snout
 evolution. We use geometric morphometrics to quantify skeletogenesis in an
 evolutionary context and reconstruct ancestral patterns of ontogenetic
 allometry to understand the developmental drivers of craniofacial
 diversity within Crocodylia. Our analyses uncovered a conserved embryonic
 region of morphospace (CER) shared by all non-gavialid crocodylians
 regardless of their eventual adult ecomorph. This observation suggests the
 presence of conserved developmental processes during early development
 (before Ferguson stage 20) across most of Crocodylia. Ancestral state
 reconstruction of ontogenetic trajectories revealed heterochrony,
 developmental constraint, and developmental systems drift have all played
 essential roles in the evolution of ecomorphs. Based on these
 observations, we conclude that two separate, but interconnected,
 developmental programs controlling craniofacial morphogenesis and growth
 enabled the evolutionary plasticity of skull shape in crocodylians.
description: Extant Crocodylian
 Dorsal Skull LandmarksA TPS file containing
 the landmark positions for all specimens included in the total ontogeny
 GMM analysis.Extant_Croc_Dorsal.tpsSkull images used in landmarkingZIP file containing a folder of all images used for landmarking in this analysis. Image names match those in the specimen list.Croc_HeterochronyMS_Skull_Images.zipSpecimen List CSVA CSV version of the specimen list table.HeterochronyMS_SpecimenList.csvSpecimen List PDFPDF table giving the specimen ID numbers, age, genus, species, and image filename used in the analysis.HeterochronyMS_SpecimenList.pdfMolecular Phylogeny FileNexus file containing the phylogeny following the molecular topology with branch lengths (after Oaks, 2016).Croc_Molecular_embryos.nexMorphology Phylogeny FileNexus file containing the phylogeny following the morphology topology and character matrix used to generate branch lengths (combination go Narvaez et al., 2016 & Brochu, 2010).Narvaez2016_Brochu2010_merged_embryos.nexLandmark WireframeFile containing the links connecting landmarks used in the analysis into a wireframe.14LM_Wireframe.csvCovariates spreadsheetCSV file containing covariate data associated with each specimen (i.e., species, ontogenetic period, clade, ecomorph shape).Extant_Croc_Covariates.csvR codeA ZIP file containing R package with code used for analysesCrocHeterochrony.zipList of CT scan parametersTable with scan parameters for all CT scans included in this analysis.Morris_Crocodylian_Embryo_CTScans_SI.pdf
DOI: 10.17172/nomad/2026.01.26-2
title: NOMAD dataset: Emergent superconductivity at optimal self-doping in La₂NiO₄:La₂XO₄ (X = Al, Ga, Sc) heterostructures.
DOI: 10.5061/dryad.4428s
title: Data from: Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections

description: Campylobacter jejuni and Campylobacter coli are the biggest causes of
 bacterial gastroenteritis in the developed world, with human infections
 typically arising from zoonotic transmission associated with infected
 meat. Because Campylobacter is not thought to survive well outside the
 gut, host-associated populations are genetically isolated to varying
 degrees. Therefore, the likely origin of most strains can be determined by
 host-associated variation in the genome. This is instructive for
 characterizing the source of human infection. However, some common
 strains, notably isolates belonging to the ST-21, ST-45 and ST-828 clonal
 complexes, appear to have broad host ranges, hindering source attribution.
 Here whole-genome sequencing has the potential to reveal fine-scale
 genetic structure associated with host specificity. We found that rates of
 zoonotic transmission among animal host species in these clonal complexes
 were so high that the signal of host association is all but obliterated,
 estimating one zoonotic transmission event every 1.6, 1.8 and 12 years in
 the ST-21, ST-45 and ST828 complexes, respectively. We attributed 89% of
 clinical cases to a chicken source, 10% to cattle and 1% to pig. Our
 results reveal that common strains of C. jejuni and C. coli infectious to
 humans are adapted to a generalist lifestyle, permitting rapid
 transmission between different hosts. Furthermore, they show that the weak
 signal of host association within these complexes presents a challenge for
 pinpointing the source of clinical infections, underlining the view that
 whole-genome sequencing, powerful though it is, cannot substitute for
 intensive sampling of suspected transmission reservoirs.
description: Dearlove et
 al_Genomes+IsolateListThis compressed folder
 contains assembled contig files for each isolate, the original alignments
 (one per clonal complex) and a list of all isolates
 used.