cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2j420
title: Data from: Ultra-fine scale spatially-integrated mapping of habitat and occupancy using structure-from-motion

description: Organisms respond to and often simultaneously modify their environment.
 While these interactions are apparent at the landscape extent, the driving
 mechanisms often occur at very fine spatial scales. Structure-from-Motion
 (SfM), a computer vision technique, allows the simultaneous mapping of
 organisms and fine scale habitat, and will greatly improve our
 understanding of habitat suitability, ecophysiology, and the
 bi-directional relationship between geomorphology and habitat use. SfM can
 be used to create high-resolution (centimeter-scale) three-dimensional
 (3D) habitat models at low cost. These models can capture the abiotic
 conditions formed by terrain and simultaneously record the position of
 individual organisms within that terrain. While coloniality is common in
 seabird species, we have a poor understanding of the extent to which dense
 breeding aggregations are driven by fine-scale active aggregation or
 limited suitable habitat. We demonstrate the use of SfM for fine-scale
 habitat suitability by reconstructing the locations of nests in a gentoo
 penguin colony and fitting models that explicitly account for conspecific
 attraction. The resulting digital elevation models (DEMs) are used as
 covariates in an inhomogeneous hybrid point process model. We find that
 gentoo penguin nest site selection is a function of the topography of the
 landscape, but that nests are far more aggregated than would be expected
 based on terrain alone, suggesting a strong role of behavioral aggregation
 in driving coloniality in this species. This integrated mapping of
 organisms and fine scale habitat will greatly improve our understanding of
 fine-scale habitat suitability, ecophysiology, and the complex
 bi-directional relationship between geomorphology and habitat use.
description: ElevationRaster (.tif) - Digital Surface Model of Port Lockroy on the Western Antarctic Peninsula. Created through Structure from Motion using Agisoft Photoscan. Projection EPSG: 3031 (Antarctic Stereographic).elevation.zipCost Distance RasterRaster (.tif) - Cost weighted distance from water for Port Lockroy. Cost of movement through each cell is given by slope of that cell. Projection EPSG: 3031 (Antarctic Stereographic).cost_distance.zipFlow AccumulationRaster (.tif) - Flow accumulation for Port Lockroy generated from SfM derived elevation, using ArcGIS. Projection EPSG: 3031 (Antarctic Stereographic).flow_acc_01.zipFlow Accumulation 4x scaleRaster (.tif) - Flow accumulation for Port Lockroy generated from SfM derived elevation, using ArcGIS at 4x scale. Projection EPSG: 3031 (Antarctic Stereographic).flow_acc_04.zipFlow Accumulation 16x scaleRaster (.tif) - Flow accumulation for Port Lockroy generated from SfM derived elevation, using ArcGIS at 16x scale. Projection EPSG: 3031 (Antarctic Stereographic).flow_acc_16.zipNest LocationsCSV - Locations of Gentoo nests at Port Lockroy, Western Antarctic Peninsula. Positions are given in EPSG:3031 (Antarctic Stereographic).nest_locations_EPSG3031.csv
DOI: 10.5061/dryad.b00f2
title: Data from: The action of stabilizing selection, mutation and drift on epistatic quantitative traits

description: For a quantitative trait under stabilizing selection, the effect of
 epistasis on its genetic architecture and on the changes of genetic
 variance caused by bottlenecking were investigated using theory and
 simulation. Assuming empirical estimates of the rate and effects of
 mutations and the intensity of selection, we assessed the impact of
 two-locus epistasis (synergistic/antagonistic) among linked or unlinked
 loci on the distribution of effects and frequencies of segregating loci in
 populations at the mutation-selection-drift balance. Strong pervasive
 epistasis did not modify substantially the genetic properties of the trait
 and, therefore, the most likely explanation for the low amount of
 variation usually accounted by the loci detected in genome-wide
 association analyses is that many causal loci will pass undetected. We
 investigated the impact of epistasis on the changes in genetic variance
 components when large populations were subjected to successive bottlenecks
 of different sizes, considering the action of genetic drift, operating
 singly (D), or jointly with mutation (MD) and selection (MSD). An initial
 increase of the different components of the genetic variance, as well as a
 dramatic acceleration of the between-line divergence, were always
 associated with synergistic epistasis but were strongly constrained by
 selection.
description: Avila_et_al_2014_EvolutionOutput files from simulations.
DOI: 10.5061/dryad.bs1q7
title: Data from: Body lift, drag and power are relatively higher in large-eared compared to small-eared bat species

description: Bats navigate the dark using echolocation. Echolocation is enhanced by
 external ears, but external ears increase the projected frontal area and
 reduce the streamlining of the animal. External ears are thus expected to
 compromise flight efficiency, but research suggests that very large ears
 may mitigate the cost by producing aerodynamic lift. Here we compare
 quantitative aerodynamic measures of flight efficiency of two bat species,
 one large-eared (Plecotus auritus) and one small-eared (Glossophaga
 soricina), flying freely in a wind tunnel. We find that the body drag of
 both species is higher than previously assumed and that the large-eared
 species has a higher body drag coefficient, but also produces relatively
 more ear/body lift than the small-eared species, in line with prior
 studies on model bats. The measured aerodynamic power of P. auritus was
 higher than predicted from the aerodynamic model, while the small-eared
 species aligned with predictions. The relatively higher power of the
 large-eared species results in lower optimal flight speeds and our
 findings support the notion of a trade-off between the acoustic benefits
 of large external ears and aerodynamic performance. The result of this
 trade-off would be the eco-morphological correlation in bat flight, with
 large-eared bats generally adopting slow-flight feeding strategies.
description: BatDataDATThe file contains velocity vector fields of the wakes of two bat species (Glossophaga soricina and Plecotus auritus) flying at various speeds in a wind tunnel. The data is in .dat format, organized in columns with spatial (x,y,z) coordinates followed by velocities (vx, vy, vz) in each of the dimensions. The coordinate system is right handed with z in the flow direction of the wind tunnel and y vertically upwards. Accompanying xls files associate each sequence with individual, flight speed and number of wing beats.
DOI: 10.5061/dryad.2p4t3
title: Data from: Scrimer: designing primers from transcriptome data

description: With the rise of next-generation sequencing methods, it has become
 increasingly possible to obtain genomewide sequence data even for nonmodel
 species. Such data are often used for the development of single nucleotide
 polymorphism (SNP) markers, which can subsequently be screened in a larger
 population sample using a variety of genotyping techniques. Many of these
 techniques require appropriate locus-specific PCR and genotyping primers.
 Currently, there is no publicly available software for the automated
 design of suitable PCR and genotyping primers from next-generation
 sequence data. Here we present a pipeline called Scrimer that automates
 multiple steps, including adaptor removal, read mapping, selection of SNPs
 and multiple primer design from transcriptome data. The designed primers
 can be used in conjunction with several widely used genotyping methods
 such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several
 reusable modules and an interactive bash workflow that connects these
 modules. Even the basic steps are presented, so the workflow can be
 executed in a step-by-step manner. The use of standard formats throughout
 the pipeline allows data from various sources to be plugged in, as well as
 easy inspection of intermediate results with visualization tools of the
 user's choice.
description: Luscinia transcriptome
 reads.A bzip2 archive
 containing reads in fastq fromat and sample and species assignment tables
 in tsv format.luscinia-mrna-454.tar.bz2
DOI: 10.5061/dryad.163mp
title: Data from: Rat retinal vasomotion assessed by laser speckle imaging

description: Vasomotion is spontaneous or induced rhythmic changes in vascular tone or
 vessel diameter that lead to rhythmic changes in flow. While the vascular
 research community debates the physiological and pathophysiological
 consequence of vasomotion, there is a great need for experimental
 techniques that can address the role and dynamical properties of
 vasomotion in vivo. We apply laser speckle imaging to study spontaneous
 and drug induced vasomotion in retinal network of anesthetized rats. The
 results reveal a wide variety of dynamical patterns. Wavelet-based
 analysis shows that (i) spontaneous vasomotion occurs in anesthetized
 animals and (ii) vasomotion can be initiated by systemic administration of
 the thromboxane analogue U-46619 and the nitric-oxide donor
 S-nitroso-acetylDL-penicillamine (SNAP). Although these drugs activate
 different cellular pathways responsible for vasomotion, our approach can
 track the dynamical changes they cause.
description: Retinal laser speckle
 dataThe data file contains 8
 blocks each representing a single experiment. In each experiment
 (recordings from one retina), several vessels were analyzed. In each block
 each individual vessel is marked with r. The data block representing each
 individual vessel contains a time series termed "lineTS" giving
 the speckle signal value averaged over the pixels in the center line. In
 addition there is a time series termed "vessel TS" containing
 the speckle signal value averaged over the pixels in the segmented vessel.
 These are the most important data. In total the following data are
 available: Alpha - estimated angle of the vessel in image axis; D -
 estimated diameter normalized by angle (double precision); Dleft - final
 estimation of the distance to the left vessel boundary from the center
 line; Dp - estimated diameter in pixels, not normalized by angle (integer
 precision); Dright - final estimation of the distance to the right vessel
 boundary from the center line; LineP - number of pixels in the center
 line; LineTS - Speckle signal value averaged over the pixels in the center
 line; MaskLine - binary mask used to select pixels which belong to the
 center line; MaskVessel - binary mask used to select pixels which belong
 to the vessel; Profile - average vessel profile in time; Rleft - first
 estimation of the distance to the left vessel boundary from the center
 line; Rright -first estimation of the distance to the right vessel
 boundary from the center line; VesselP - number of pixels in the
 recognized vessel segment; VesselTS - Speckle signal value averaged over
 the pixels in the segmented vessel; X1, X2, Y1, Y2 - coordinates of the
 segmentation region in the full -sized image. For further information
 please contact the corresponding author of the related
 paper.Retinal laser_speckle
 data.mat
DOI: 10.5061/dryad.4h49qg1
title: Data from: The UBR-1 ubiquitin ligase regulates glutamate metabolism to generate coordinated motor pattern in Caenorhabditis elegans

description: UBR1 is an E3 ubiquitin ligase best known for its ability to target
 protein degradation by the N-end rule. The physiological functions of UBR
 family proteins, however, remain not fully understood. We found that the
 functional loss of C. elegans UBR-1 leads to synchronized motor neuron
 activation, preventing body bending when animals generate reversal
 movements. This motor deficit is rescued by removing GOT-1, a transaminase
 that converts aspartate to glutamate. Both UBR-1 and GOT-1 are critically
 required in premotor interneurons of the reverse motor circuit to regulate
 the motor pattern. ubr-1 and got-1 mutants exhibit elevated and decreased
 glutamate level, respectively. These results raise an intriguing
 possibility that UBR proteins regulate glutamate metabolism.
description: A_MN_Calcium_ImagingA-type motor neuron Calcium imaging processed and summarized data for the entire dataset.Behaviour_AnalysisBehaviour assay processed and summarized data for the entire dataset.Amino_Acid_AnalysisHPLC and MS data for the entire dataset.AMN_Cal_Img_sample_hp684An example of a video recording for ubr-1(hp684) A-type motor neuron calcium imaging, and the corresponding processed data.Behaviour_assay_sample_hp684An example of a video recording for ubr-1(hp684) behaviour assay, and the corresponding processed data.AST_Activity_AssayGOT-1 enzyme activity assay data.
DOI: 10.34894/o3kafo
title: STED data for: CIP2A mediates mitotic recruitment of SLX4/MUS81/XPF to resolve replication stress-induced DNA lesions

description: Dataset of stimulated emission depletion (STED) microscopy images of CIP2A foci in mitotic cells, with labeling of CIP2A (WT, V5-tagged, or 1-876 mutant with V5 tag) together with TOPBP1, SLX4, ERCC1, MUS81, yH2AX, or EdU.&lt;br&gt;&lt;br&gt;

More information about the data is available in the readme.txt file.
DOI: 10.5061/dryad.6vj6n
title: Data from: Biomarker profiling in reef corals of Tonga's Ha'apai and Vava'u archipelagos

description: Given the significant threats towards Earth’s coral reefs, there is an
 urgent need to document the current physiological condition of the
 resident organisms, particularly the reef-building scleractinians
 themselves. Unfortunately, most of the planet’s reefs are understudied,
 and some have yet to be seen. For instance, the Kingdom of Tonga possesses
 an extensive reef system, with thousands of hectares of unobserved reefs;
 little is known about their ecology, nor is there any information on the
 health of the resident corals. Given such knowledge deficiencies, 59 reefs
 across three Tongan archipelagos were surveyed herein, and pocilloporid
 corals were sampled from approximately half of these surveyed sites; 10
 molecular-scale response variable were assessed in 88 of the sampled
 colonies, and 12 colonies were found to be outliers based on employment of
 a multivariate statistics-based aberrancy detection system. These outliers
 differed from the statistically normally behaving colonies in having not
 only higher RNA/DNA ratios but also elevated expression levels of three
 genes: 1) Symbiodinium zinc-induced facilitator-like 1-like, 2) host coral
 copper-zinc superoxide dismutase, and 3) host green fluorescent
 protein-like chromoprotein. Outliers were also characterized by
 significantly higher variation amongst the molecular response variables
 assessed, and the response variables that contributed most significantly
 to colonies being delineated as outliers differed between the two
 predominant reef coral species sampled, Pocillopora damicornis and P.
 acuta. These closely related species also displayed dissimilar temporal
 fluctuation patterns in their molecular physiologies, an observation that
 may have been driven by differences in their feeding strategies. Future
 works should attempt to determine whether corals displaying statistically
 aberrant molecular physiology, such as the 12 Tongan outliers identified
 herein, are indeed characterized by a diminished capacity for acclimating
 to the rapid changes in their abiotic milieu occurring as a result of
 global climate change.
description: Tonga pics for
 DryadZip file containing
 images of the majority of the coral reef sites surveyed, as well as
 whole-colony and "macro" images of the sampled colonies and
 their tissues/polyps, respectively.
DOI: 10.5061/dryad.fd3kj
title: Data from: Pleistocene climatic changes drive diversification across a tropical savanna

description: Spatial responses of species to past climate change depend on both
 intrinsic traits (climatic niche breadth, dispersal rates) and the scale
 of climatic fluctuations across the landscape. New capabilities in
 generating and analysing population genomic data, along with spatial
 modelling, have unleashed our capacity to infer how past climate changes
 have shaped populations, and by extension, complex communities. Combining
 these approaches, we uncover lineage diversity across four co-distributed
 lizards from the Australian Monsoonal Tropics and explore how varying
 climatic tolerances interact with regional climate history to generate
 common versus disparate responses to late Pleistocene change. We find more
 divergent spatial structuring and temporal demographic responses in the
 drier Kimberley region compared to the more mesic and consistently
 suitable Top End. We hypothesize that, in general, the effects of species’
 traits on sensitivity to climate fluctuation will be more evident in
 climatically marginal regions. If true, this points to the need in
 climatically marginal areas to craft more species- (or trait-) specific
 strategies for persistence under future climate change.
description: Comparative demographics
 of rainbow skinksThis is a compressed zip
 file of all the datasets and scripts used in this study grouped by
 analysis or dataset.Dryad Carlia
 2017.zip
DOI: 10.5061/dryad.r7g12
title: Data from: Genomic BLUP decoded: a look into the black box of genomic prediction

description: Genomic best linear unbiased prediction (BLUP) is a statistical method
 that uses relationships between individuals calculated from
 single-nucleotide polymorphisms (SNPs) to capture relationships at
 quantitative trait loci (QTL). We show that genomic BLUP exploits not only
 linkage disequilibrium (LD) and additive-genetic relationships, but also
 cosegregation to capture relationships at QTL. Simulations were used to
 study the contributions of those types of information to accuracy of
 genomic estimated breeding values (GEBVs), their persistence over
 generations without retraining, and their effect on the correlation of
 GEBVs within families. We show that accuracy of GEBVs based on
 additive-genetic relationships can decline with increasing training data
 size and speculate that modeling polygenic effects via pedigree
 relationships jointly with genomic breeding values using Bayesian methods
 may prevent that decline. Cosegregation information from half sibs
 contributes little to accuracy of GEBVs in current dairy cattle breeding
 schemes but from full sibs it contributes considerably to accuracy within
 family in corn breeding. Cosegregation information also declines with
 increasing training data size, and its persistence over generations is
 lower than that of LD, suggesting the need to model LD and cosegregation
 explicitly. The correlation between GEBVs within families depends largely
 on additive-genetic relationship information, which is determined by the
 effective number of SNPs and training data size. As genomic BLUP cannot
 capture short-range LD information well, we recommend Bayesian methods
 with t-distributed priors.
description: Simulated
 dataCompressed file of
 simulated data.GeneticsPublicationData.zip
DOI: 10.5061/dryad.7gt44
title: Data from: 8-way randomized controlled trial of doxylamine, pyridoxine and dicyclomine for nausea and vomiting during pregnancy: restoration of unpublished information

description: Objectives: We report information about an unpublished 1970s study
 (“8-way” Bendectin Study) that aimed to evaluate the relative therapeutic
 efficacy of doxylamine, pyridoxine, and dicyclomine in the management of
 nausea and vomiting during pregnancy. We are publishing the trial's
 findings according to the restoring invisible and abandoned trials (RIAT)
 initiative because the trial was never published. Design: Double blinded,
 multi-centred, randomized placebo-controlled study. Setting: 14 clinics in
 the United States. Participants: 2308 patients in the first 12 weeks of
 pregnancy with complaints of nausea or vomiting were enrolled.
 Interventions: Each patient was randomized to one of eight arms: placebo,
 doxylamine/pyridoxine/dicylcomine, doxylamine/pyridoxine,
 dicylomine/pyridoxine, doxylamine, dicyclomine/pyridoxine, pyridoxine and
 dicyclomine. Each patient was instructed to take 2 tablets at bedtime and
 1 additional tablet in the afternoon or morning if needed, for 7 nights.
 Outcomes: Reported outcomes included the number of hours of nausea
 reported by patients, the frequency of vomiting reported by patients and
 the overall efficacy of medication as judged by physicians. Results: Data
 from 1599 (69% of those randomized) participants were analyzed. Based on
 the available summary data of physician evaluation of symptoms and
 ignoring missing data and data integrity issues, the proportion of
 participants who were “evaluated moderate or excellent” was greater in
 each of the seven active treatment groups when compared with placebo
 (57%): doxylamine/pyridoxine/dicylcomine (14% absolute difference versus
 placebo; 95% CI: 4 to 24), doxylamine/pyridoxine (21; 95% CI 11 to 30),
 dicylomine/pyridoxine (21; 95% CI 11 to 30), doxylamine (20; 95% CI 10 to
 29), dicyclomine/pyridoxine (4; 95% CI -6 to 14), pyridoxine (9; 95% CI -1
 to 19) and dicyclomine (4; 95% CI -6 to 14). Based on incomplete
 information, the most common adverse events were apparently drowsiness and
 fatigue. There is a high risk of bias in these previously unpublished
 results given the high attrition rate in a 7 day trial, the lack of
 prespecified outcomes or analyses, and the exclusion of some data because
 of questionable data integrity. Conclusion: The available information
 about this “8-way Bendectin” trial indicates it should not be used to
 support the efficacy of doxylamine, pyridoxine or dicyclomine for the
 treatment of nausea and vomiting during pregnancy because of a high risk
 of bias.
description: F-Benedectin-Benedectin-Index to Benedecting DocumentIndex to fiches obtained from FDA.BendectinFichesFDACombinedAll FDA "fiche" files received. Some are not relevant.HealthCanadaA201100688_2012-11-19_09-21-37Partially redacted documents from Health CanadaA201100688_2012-11-19_09-21-37.pdf
DOI: 10.5281/zenodo.17754687
title: Elevation model and glacier displacements, Xinqingfeng ice cap, Tibet, related to glacier detachment of 1 November 2022

description: 2_1_sgm_dem.tif

Digital elevation model from WorldView satellite stereo data of 2 Jan 2023 over parts of the Xinqingfeng ice cap, Tibet.

disp.zip

Files YYYYMMDD_YYYYMMDD_disp.txt with displacements on the glaciers Bukadaban West and East, respectively, measured using image matching between repeat Sentinel-2 images of two dates YYYYMMDD. 

For details on methods, data, and use, seeKääb, A., Aga, J., Treichler, D. et al. Recent giant detachment of a glacier on the Tibetan plateau provoked by its frozen tongue. Commun Earth Environ 7, 74 (2026). https://doi.org/10.1038/s43247-025-03125-z
DOI: 10.5281/zenodo.17754686
title: Elevation model and glacier displacements, Xinqingfeng ice cap, Tibet, related to glacier detachment of 1 November 2022

description: 2_1_sgm_dem.tif

Digital elevation model from WorldView satellite stereo data of 2 Jan 2023 over parts of the Xinqingfeng ice cap, Tibet.

disp.zip

Files YYYYMMDD_YYYYMMDD_disp.txt with displacements on the glaciers Bukadaban West and East, respectively, measured using image matching between repeat Sentinel-2 images of two dates YYYYMMDD. 

For details on methods, data, and use, seeKääb, A., Aga, J., Treichler, D. et al. Recent giant detachment of a glacier on the Tibetan plateau provoked by its frozen tongue. Commun Earth Environ 7, 74 (2026). https://doi.org/10.1038/s43247-025-03125-z