cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ht3564h
title: Data from: Decision and navigation in mouse parietal cortex

description: Posterior parietal cortex (PPC) has been implicated in navigation, in the
 control of movement, and in visually-guided decisions. To relate these
 views, we measured activity in PPC while mice performed a virtual
 navigation task driven by visual decisions. PPC neurons were selective for
 specific combinations of the animal's spatial position and heading
 angle. This selectivity closely predicted both the activity of individual
 PPC neurons, and the arrangement of their collective firing patterns in
 choice-selective sequences. These sequences reflected PPC encoding of the
 animal's navigation trajectory. Using decision as a predictor instead
 of heading yielded worse fits, and using it in addition to heading only
 slightly improved the fits. Alternative models based on visual or motor
 variables were inferior. We conclude that when mice use vision to choose
 their trajectories, a large fraction of parietal cortex activity can be
 predicted from simple attributes such as spatial position and heading.
description: Behavioral and
 two-photon imaging data for Krumin et al. eLife (2018)Krumin_etal_2018_eLife.mat
DOI: 10.5061/dryad.6p6k79p
title: Data from: Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

description: Eutrema salsugineum is a widely distributed species, which provide a good
 model to study long-distance dispersal and accumulation of deleterious
 mutations. Based on population genomic data, we clarified demographic
 history of E. salsugineum and showed how deleterious alleles accumulated.
description: Data for salt
 cressThe filtered SNP data
 and database for deletious mutationdata4salt_cress.rar
DOI: 10.5061/dryad.6rh3p
title: Data from: A Flippase-mediated GAL80/GAL4 intersectional resource for dissecting appendage development in Drosophila

description: Drosophila imaginal discs provide an ideal model to study processes
 important for cell signaling and cell specification, tissue
 differentiation, and cell competition during development. One challenge to
 understanding genetic control of cellular processes and cell interactions
 is the difficulty in effectively targeting a defined subset of cells in
 developing tissues in gene manipulation experiments. A recently developed
 Flippase-induced intersectional GAL80/GAL4 repression method incorporates
 several gene manipulation technologies in Drosophila to enable such
 fine-scale dissection in neural tissues. In particular, this approach
 brings together existing GAL4 transgenes, newly developed enhancer-trap
 flippase transgenes, and GAL80 transgenes flanked by Flippase recognition
 target sites. The combination of these tools enables gene
 activation/repression in particular subsets of cells within a GAL4
 expression pattern. Here, we expand the utility of a large collection of
 these enhancer-trap flippase transgenic insertion lines by characterizing
 their expression patterns in third larval instar imaginal discs. We
 screened 521 different enhancer-trap flippase lines and identified 28 that
 are expressed in imaginal tissues, including two transgenes that show
 sex-specific expression patterns. Using a line that expresses Flippase in
 the wing imaginal disc, we demonstrate the utility of this intersectional
 approach for studying development by knocking down gene expression of a
 key member of the planar cell polarity pathway. The results of our
 experiments show that these enhancer-trap flippase lines enable fine-scale
 manipulation in imaginal discs.
description: Imaginal disc
 Flp-induced expression patternsThis compressed file
 contains images from each of the ET-FLPx2 lines that show imaginal disc
 expression.Imaginal disc Flp expression
 patterns.zip
DOI: 10.5061/dryad.7dv96
title: Data from: Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

description: DNA metabarcoding is a powerful new tool allowing characterization of
 species assemblages using high-throughput amplicon sequencing. The utility
 of DNA metabarcoding for quantifying relative species abundances is
 currently limited by both biological and technical biases which influence
 sequence read counts. We tested the idea of sequencing 50/50 mixtures of
 target species and a control species in order to generate relative
 correction factors (RCFs) that account for multiple sources of bias and
 are applicable to field studies. RCFs will be most effective if they are
 not affected by input mass ratio or co-occurring species. In a model
 experiment involving three target fish species and a fixed control, we
 found RCFs did vary with input ratio but in a consistent fashion, and that
 50/50 RCFs applied to DNA sequence counts from various mixtures of the
 target species still greatly improved relative abundance estimates (e.g.
 average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for
 corrected estimates). To demonstrate the use of correction factors in a
 field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca
 vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these
 corrections to field-collected seal scats affected species percentages
 from individual samples (Δ 6.7 ± 6.6%) more than population-level species
 estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach
 is an effective tool for evaluating and correcting biases in DNA
 metabarcoding studies. The decision to apply correction factors will be
 influenced by the feasibility of creating tissue mixtures for the target
 species, and the level of accuracy needed to meet research objectives.
description: Model System
 DataPlease see ReadMe
 filePrey_Library_DataPlease see ReadMe fileSupplemental_FilesTissue mix sequence counts Custom BLAST database Model system species sequences
DOI: 10.5061/dryad.r2b1h
title: Data from: Testing adaptive hypotheses of convergence with functional landscapes: a case study of bone-cracking hypercarnivores

description: Morphological convergence is a well documented phenomenon in mammals, and
 adaptive explanations are commonly employed to infer similar functions for
 convergent characteristics. I present a study that adopts aspects of
 theoretical morphology and engineering optimization to test hypotheses
 about adaptive convergent evolution. Bone-cracking ecomorphologies in
 Carnivora were used as a case study. Previous research has shown that
 skull deepening and widening are major evolutionary patterns in convergent
 bone-cracking canids and hyaenids. A simple two-dimensional design space,
 with skull width-to-length and depth-to-length ratios as variables, was
 used to examine optimized shapes for two functional properties: mechanical
 advantage (MA) and strain energy (SE). Functionality of theoretical skull
 shapes was studied using finite element analysis (FEA) and visualized as
 functional landscapes. The distribution of actual skull shapes in the
 landscape showed a convergent trend of plesiomorphically low-MA and
 moderate-SE skulls evolving towards higher-MA and moderate-SE skulls; this
 is corroborated by FEA of 13 actual specimens. Nevertheless, regions exist
 in the landscape where high-MA and lower-SE shapes are not represented by
 existing species; their vacancy is observed even at higher taxonomic
 levels. Results highlight the interaction of biomechanical and
 non-biomechanical factors in constraining general skull dimensions to
 localized functional optima through evolution.
description: Computer Tomography data
 for Proteles cristata, J050607T02CT image data (DICOM
 format) of Proteles cristata scanned at University of California, Los
 Angeles Medical Center using Siemens Definition 64 CT scanner on 26
 October 2007.Proteles_cristata_J050607T02_CT.zipFinite element models of skulls of actual species analyzedThe zip file contains finite element models for the 13 species of hyaenids and canids analyzed in the paper. All models, except for Proteles cristata and Ictitherium sp., are derived from published papers cited in the text of the study. All models are in Strand7 format (*.st7). Additional formats are available upon request to the author.FE_models_actual.zipFinite element models of theoretical skull shapes based on Ictitherium sp.This zip file contains 36 finite element models of theoretical skull shapes modified from the skull of Ictitherium sp. All models were morphed (file names indicate model number, followed by percentage in width (w), depth (d), or rostral/skull length (r; held constant) relative to the original Ictitherium model) using Geomagic Studio. All models are in Strand7 format (*.st7). Additional formats are available upon request to the author.FE_models_theoretical.zip
DOI: 10.5061/dryad.9m6d2
title: Data from: Social conformity and propagation of information in collective u-turns of fish schools

description: Moving animal groups such as schools of fish or flocks of birds often
 undergo sudden collective changes of their travelling direction as a
 consequence of stochastic fluctuations in heading of the individuals.
 However, the mechanisms by which these behavioural fluctuations arise at
 the individual level and propagate within a group are still unclear. In
 the present study, we combine an experimental and theoretical approach to
 investigate spontaneous collective U-turns in groups of rummy-nose tetra
 (Hemigrammus rhodostomus) swimming in a ringshaped tank. U-turns imply
 that fish switch their heading between the clockwise and anticlockwise
 direction. We reconstruct trajectories of individuals moving alone and in
 groups of different sizes. We show that the group decreases its swimming
 speed before a collective U-turn. This is in agreement with previous
 theoretical predictions showing that speed decrease facilitates an
 amplification of fluctuations in heading in the group, which can trigger
 U-turns. These collective U-turns are mostly initiated by individuals at
 the front of the group. Once an individual has initiated a U-turn, the new
 direction propagates through the group from front to back without
 amplification or dampening, resembling the dynamics of falling dominoes.
 The mean time between collective U-turns sharply increases as the size of
 the group increases. We develop an Ising spin model integrating
 anisotropic and asymmetrical interactions between fish and their tendency
 to follow the majority of their neighbours nonlinearly (social
 conformity). The model quantitatively reproduces key features of the
 dynamics and the frequency of collective U-turns observed in experiments.
description: readmereadme file of the
 datasetExperiments
 metadatametadata.txt, a data
 frame that contains the metadata of the 57 experiments
 tracked.metadata.txtTrajectories for groups of 1 fish1.zipTrajectories for groups of 2 fish2.zipTrajectories for groups of 4 fish4.zipTrajectories for groups of 5 fish5.zipTrajectories for groups of 8 fish8.zipTrajectories for groups of 10 fish10.zipData for groups of 20 fishTime of individual and collective U-turns in groups of 20 fish.20.zip
DOI: 10.5061/dryad.f75730m
title: Data from: Convoluted nasal passages function as efficient heat exchangers in ankylosaurs (Dinosauria: Ornithischia: Thyreophora)

description: Convoluted nasal passages are an enigmatic hallmark of Ankylosauria.
 Previous research suggested that these convoluted nasal passages
 functioned as heat exchangers analogous to the respiratory turbinates of
 mammals and birds. We tested this hypothesis by performing a computational
 fluid dynamic analysis on the nasal passages of two ankylosaurs:
 Panoplosaurus mirus and Euoplocephalus tutus. Our models predicted that
 Panoplosaurus and Euoplocephalus would have required 833 and 1568 thermal
 calories, respectively, to warm a single breath of air by 20°C. Heat
 recovery during exhalation resulted in energy savings of 65% for
 Panoplosaurus and 84% for Euoplocephalus. Our results fell well within the
 range of values for heat and water savings observed in extant terrestrial
 amniotes. We further tested alternate airway reconstructions that removed
 nasal passage convolutions or reduced nasal vestibule length. Our results
 revealed that the extensive elaboration observed in the nasal vestibules
 of ankylosaurs was a viable alternative to respiratory turbinates with
 regards to air conditioning. Of the two dinosaurs tested, Euoplocephalus
 repeatedly exhibited a more efficient nasal passage than Panoplosaurus. We
 suggest that the higher heat loads associated with the larger body mass of
 Euoplocephalus necessitated these more efficient nasal passages. Our
 findings further indicate that the evolution of complicated airways in
 dinosaurs may have been driven by the thermal requirements of maintaining
 cerebral thermal homeostasis.
description: Ankylosaur Raw
 DataRaw data of airflow
 results during different airflow simulations in Euoplocephalus and
 Panoplosaurus. Data is in CGNS format.Ankylosaur_Airflow_Files.zipEuoplocephalus Supplement3D PDF of the skull and airway variants for Euoplocephalus tutus.Euoplocephalus_Supplement.pdfPanoplosaurus Supplement3D PDF of skull and airway variants for Panoplosaurus mirus.Panoplosaurus_Supplement.pdfSupplementary MovieMovie showing airflow and heat transfer in the nasal passages of Panoplosaurus and Euoplocephalus under the soft-tissue model.Supplementary_movie.mp4
DOI: 10.5061/dryad.bd4gs
title: Data from: Anxiety-like behavioural inhibition is normative under environmental threat-reward correlations

description: Behavioural inhibition is a key anxiety-like behaviour in rodents and
 humans, distinct from avoidance of danger, and reduced by anxiolytic
 drugs. In some situations, it is not clear how behavioural inhibition
 minimises harm or maximises benefit for the agent, and can even appear
 counterproductive. Extant explanations of this phenomenon make use of
 descriptive models but do not provide a formal assessment of its adaptive
 value. This hampers a better understanding of the neural computations
 underlying anxiety behaviour. Here, we analyse a standard rodent anxiety
 model, the operant conflict test. We harvest Bayesian Decision Theory to
 show that behavioural inhibition normatively arises as cost-minimising
 strategy in temporally correlated environments. Importantly, only if
 behavioural inhibition is aimed at minimising cost, it depends on
 probability and magnitude of threat. Harnessing a virtual computer game,
 we test model predictions in four experiments with human participants.
 Humans exhibit behavioural inhibition with a strong linear dependence on
 threat probability and magnitude. Strikingly, inhibition occurs before
 motor execution and depends on the virtual environment, thus likely
 resulting from a neural optimisation process rather than a pre-programmed
 mechanism. Individual trait anxiety scores predict behavioural inhibition,
 underlining the validity of this anxiety model. These findings put anxiety
 behaviour into the context of cost-minimisation and optimal inference, and
 may ultimately pave the way towards a mechanistic understanding of the
 neural computations gone awry in human anxiety disorder.
description: AAA_maindataBehavioural and SCR data from 4 experiments combined. Experiment scripts and a script for collection of individual data files into the repository are contained in AAA_metadata.zipAAA1_DATA.matAAA_MetadataAll experiment scripts, written in Matlab/Cogent 2000.
DOI: 10.5061/dryad.3v55m
title: Data from: Loci contributing to boric acid toxicity in two reference populations of Drosophila melanogaster

description: Populations maintain considerable segregating variation in the response to
 toxic, xenobiotic compounds. To identify variants associated with
 resistance to boric acid, a commonly-used household insecticide with a
 poorly understood mechanism of action, we assayed thousands of individuals
 from hundreds of strains. Using the Drosophila Synthetic Population
 Resource (DSPR), a multi-parental population (MPP) of inbred genotypes, we
 mapped six QTL to short genomic regions containing few protein-coding
 genes (3–188), allowing us to identify plausible candidate genes
 underlying resistance to boric acid toxicity. One interval contains
 multiple genes from the cytochrome P450 family, and we show that
 ubiquitous RNAi of one of these genes, Cyp9b2, markedly reduces resistance
 to the toxin. Resistance to boric acid is positively correlated with
 caffeine resistance. The two phenotypes additionally share a pair of QTL,
 potentially suggesting a degree of pleiotropy in the genetic control of
 resistance to these two distinct xenobiotics. Finally, we screened the
 Drosophila Genetic Reference Panel (DGRP) in an attempt to identify
 sequence variants within mapped QTL that are associated with boric acid
 resistance. The approach was largely unsuccessful, with only one QTL
 showing any associations at QTL-specific 20% False Discovery Rate (FDR)
 thresholds. Nonetheless, these associations point to a potential candidate
 gene that can be targeted in future validation efforts. Although the
 mapping data resulting from the two reference populations do not clearly
 overlap, our work provides a starting point for further genetic dissection
 of the processes underlying boric acid toxicity in insects.
description: Boric acid resistance R
 analysis scriptR script that, in
 conjuction with the files resulting from unpacking the
 "BoricAcidDSPR.tar" data package tarball, will allow the
 generation of boric acid resistance strain means. These were used in the
 associated study to map QTL for boric acid resistance. Script requires
 only R core commands. Instructions on how to run provided within
 file.DAM-BoricAcid_DSPR_AnalysisCode.txtDirectory of datafiles allowing measurement of boric acid resistanceThis is a tarball of a defined directory structure containing raw datafiles, that together with R scripts from "DAM-BoricAcid_DSPR_AnalysisCode.txt", can be used to generate boric acid resistance strain means used in the associated study for QTL mapping. We additionally give the actual analyzed datafiles generated by the authors so potential users can assure the code works correctly in their hands. Details of the directory structure and the various file types contained within can be found in the ReadMe.BoricAcidDSPR.tar
DOI: 10.5061/dryad.cg35k
title: Data from: Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network

description: The Drosophila embryo transiently exhibits a double segment periodicity,
 defined by the expression of seven "pair-rule" genes, each in a
 pattern of seven stripes. At gastrulation, interactions between the
 pair-rule genes lead to frequency doubling and the patterning of fourteen
 parasegment boundaries. In contrast to earlier stages of Drosophila
 anteroposterior patterning, this transition is not well understood. By
 carefully analysing the spatiotemporal dynamics of pair-rule gene
 expression, we demonstrate that frequency-doubling is precipitated by
 multiple coordinated changes to the network of regulatory interactions
 between the pair-rule genes. We identify the broadly expressed but
 temporally patterned transcription factor, Odd-paired (Opa/Zic), as the
 cause of these changes, and show that the patterning of the even-numbered
 parasegment boundaries relies on Opa-dependent regulatory interactions.
 Our findings indicate that the pair-rule gene regulatory network has a
 temporally-modulated topology, permitting the pair-rule genes to play
 stage-specific patterning roles.
description: Drosophila_PRG_double_FISH_dataThis archive contains 648 double channel TIFF images of wild-type Drosophila embryos that have undergone fluorescent in situ hybridisation for 32 pairwise combinations of pair-rule gene and segment-polarity gene transcripts. Most embryos are between mid-stage 5 and early stage 7. Images are 1024x1024 pixels, and were collected on a Leica SP5 confocal microscope. The unpacked archive is 5.15 GB.
DOI: 10.5061/dryad.r95dh
title: Data from: Relationships between spatial metrics and plant diversity in constructed freshwater wetlands

description: The diversity of plant species and their distribution in space are both
 thought to have important effects on the function of wetland ecosystems.
 However, knowledge of the relationships between plant species and spatial
 diversity remains incomplete. In this study, we investigated relationships
 between spatial pattern and plant species diversity over a five year
 period following the initial restoration of experimental wetland
 ecosystems. In 2003, six identical and hydrologically-isolated 0.18 ha
 wetland “cells” were constructed in former farmland in northeast Ohio. The
 systems were subjected to planting treatments that resulted in different
 levels of vascular plant species diversity among cells. Plant species
 diversity was assessed through annual inventories. Plant spatial pattern
 was assessed by digitizing low-altitude aerial photographs taken at the
 same time as the inventories. Diversity metrics derived from the
 inventories were significantly related to certain spatial metrics derived
 from the photographs, including cover type diversity and contagion. We
 found that wetlands with high cover type diversity harbor higher plant
 species diversity than wetlands with fewer types of patches. We also found
 significant relationships between plant species diversity and spatial
 patterning of patch types, but the direction of the effect differed
 depending on the diversity metric used. Links between diversity and
 spatial pattern observed in this study suggest that high-resolution aerial
 imagery may provide wetland scientists with a useful tool for assessing
 plant diversity.
description: Aerial
 PhotographsAerial photographs taken
 in the field and used for GIS analysis of vegetation spatial
 patternPlant Community
 SurveyData from plant
 community surveys used to calculate species diversity metrics and
 ground-truth aerial photographs for spatial pattern
 analysesSpecies
 DiversityCalculations of plant
 species diversity metricsSpatial
 PatternFRAGSTATS computations
 of spatial metrics
DOI: 10.15468/dl.dahnd4
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Oncidium luteopurpureum [GBIF Backbone Taxonomy])",
 "StateProvince is one of (Cundinamarca)"
 ]
 }
 ]
}

 The dataset includes 35 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000348-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.