cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mt57r
title: Data from: Brain – endocast relationship in the Australian lungfish, Neoceratodus forsteri, elucidated from tomographic data (Sarcopterygii: Dipnoi)

description: Although the brains of the three extant lungfish genera have been
 previously described, the spatial relationship between the brain and the
 neurocranium has never before been fully described nor quantified. Through
 the application of virtual microtomography (μCT) and 3D rendering
 software, we describe aspects of the gross anatomy of the brain and
 labyrinth region in the Australian lungfish, Neoceratodus forsteri and
 compare this to previous accounts. Unexpected characters in this specimen
 include short olfactory peduncles connecting the olfactory bulbs to the
 telencephalon, and an oblong telencephalon. Furthermore, we illustrate the
 endocast (the mould of the internal space of the neurocranial cavity) of
 Neoceratodus, also describing and quantifying the brain-endocast
 relationship in a lungfish for the first time. Overall, the brain of the
 Australian lungfish closely matches the size and shape of the endocast
 cavity housing it, filling more than four fifths of the total volume. The
 forebrain and labyrinth regions of the brain correspond very well to the
 endocast morphology, while the midbrain and hindbrain do not fit so
 closely. Our results cast light on the gross neural and endocast anatomy
 in lungfishes, and are likely to have particular significance for
 palaeoneurologists studying fossil taxa.
description: Supplementary
 Information 1: Surface mesh distance scriptThe script surf_dist.py
 computes the surface-to-surface distance between two aligned STL models
 and displays the result as color-coded distance maps. It also computes the
 mean absolute distance (MAD), the root-mean square (RMS) distance, and the
 max absolute (Hausdorff) distance between the models and writes the
 resulting distance values to a text file.surf_dist.zipSupplementary Information 2: Surface mesh distance animationSurface mesh distance animation, showing Endocast, Brain, Overlay, Signed Distance Map and Unsigned Distance Map of the Australian lungfish, Neoceratodus.S2_movie.m4v
DOI: 10.5061/dryad.s4945
title: Data from: Resource specialists lead local insect community turnover associated with temperature – analysis of an 18-year full-seasonal record of moths and beetles

description: Insect responses to recent climate change are well documented, but the
 role of resource specialization in determining species vulnerability
 remains poorly understood. Uncovering local ecological effects of
 temperature change with high-quality, standardized data provides an
 important first opportunity for predictions about responses of resource
 specialists, and long-term time series are essential in revealing these
 responses. Here, we investigate temperature-related changes in local
 insect communities, using a sampling site with more than a quarter-million
 records from two decades (1992–2009) of full-season, quantitative light
 trapping of 1543 species of moths and beetles. We investigated annual as
 well as long-term changes in fauna composition, abundance and phenology in
 a climate-related context using species temperature affinities and local
 temperature data. Finally, we explored these local changes in the context
 of dietary specialization. Across both moths and beetles, temperature
 affinity of specialists increased through net gain of hot-dwelling species
 and net loss of cold-dwelling species. The climate-related composition of
 generalists remained constant over time. We observed an increase in
 species richness of both groups. Furthermore, we observed divergent
 phenological responses between cold- and hot-dwelling species, advancing
 and delaying their relative abundance, respectively. Phenological advances
 were particularly pronounced in cold-adapted specialists. Our results
 suggest an important role of resource specialization in explaining the
 compositional and phenological responses of insect communities to local
 temperature increases. We propose that resource specialists in particular
 are affected by local temperature increase, leading to the distinct
 temperature-mediated turnover seen for this group. We suggest that the
 observed increase in species number could have been facilitated by
 dissimilar utilization of an expanded growing season by cold- and
 hot-adapted species, as indicated by their oppositely directed
 phenological responses. An especially pronounced advancement of
 cold-adapted specialists suggests that such phenological advances might
 help minimize further temperature-induced loss of resource specialists.
 Although limited to a single study site, our results suggest several local
 changes in the insect fauna in concordance with expected change of
 larger-scale temperature increases.
description: Raw data from light trap
 catchThis file contains the
 raw data from the light trapping study ordered by: order
 (Lepidoptera/Coleoptera), family, name (species), year, date1 (start),
 date2 (end) and no. individualsThomsen_Jørgensen_et_al._JAE_All_data_1992-2009.csv
DOI: 10.5061/dryad.j8227
title: Data from: Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States

description: Greenhouse gas (GHG) emissions from soils are a key sustainability metric
 of cropping systems. During crop establishment, disruptive land-use change
 is known to be a critical, but under reported period, for determining GHG
 emissions. We measured soil N2O emissions and potential environmental
 drivers of these fluxes from a three-year establishment-phase bioenergy
 cropping systems experiment replicated in southcentral Wisconsin (ARL) and
 southwestern Michigan (KBS). Cropping systems treatments were annual
 monocultures (continuous corn, corn–soybean–canola rotation), perennial
 monocultures (switchgrass, miscanthus, and poplar), and perennial
 polycultures (native grass mixture, early successional community, and
 restored prairie) all grown using best management practices specific to
 the system. Cumulative three-year N2O emissions from annuals were 142%
 higher than from perennials, with fertilized perennials 190% higher than
 unfertilized perennials. Emissions ranged from 3.1 to 19.1 kg N2O-N ha−1
 yr−1 for the annuals with continuous corn &gt; corn–soybean–canola
 rotation and 1.1 to 6.3 kg N2O-N ha−1 yr−1 for perennials. Nitrous oxide
 peak fluxes typically were associated with precipitation events that
 closely followed fertilization. Bayesian modeling of N2O fluxes based on
 measured environmental factors explained 33% of variability across all
 systems. Models trained on single systems performed well in most
 monocultures (e.g., R2 = 0.52 for poplar) but notably worse in
 polycultures (e.g., R2 = 0.17 for early successional, R2 = 0.06 for
 restored prairie), indicating that simulation models that include N2O
 emissions should be parameterized specific to particular plant
 communities. Our results indicate that perennial bioenergy crops in their
 establishment phase emit less N2O than annual crops, especially when not
 fertilized. These findings should be considered further alongside yield
 and other metrics contributing to important ecosystem services.
description: Aggregate Annual
 FluxesDaily fluxes were
 aggregated at the plot level over a calendar year. Details of aggregation
 are given in the paper.agg_out.txtGas concentrationsThis dataset contains time series of concentrations of CO2, CH4, and N2O in static chambers. The data were used to calculate soil fluxes.conc_out.txtDaily FluxesThis dataset contains single-day N2O flux measurements at the plot level and concurrent ancillary measurements of soil properties. These data were used to generate Tables 1-2 and Figures 2-4. Details of flux estimation are given in the paper.flux_out.txt
DOI: 10.5061/dryad.2k27f
title: Data from: Can observation skills of citizen scientists be estimated using species accumulation curves?

description: Volunteers are increasingly being recruited into citizen science projects
 to collect observations for scientific studies. An additional goal of
 these projects is to engage and educate these volunteers. Thus, there are
 few barriers to participation resulting in volunteer observers with
 varying ability to complete the project’s tasks. To improve the quality of
 a citizen science project’s outcomes it would be useful to account for
 inter-observer variation, and to assess the rarely tested presumption that
 participating in a citizen science projects results in volunteers becoming
 better observers. Here we present a method for indexing observer
 variability based on the data routinely submitted by observers
 participating in the citizen science project eBird, a broad-scale
 monitoring project in which observers collect and submit lists of the bird
 species observed while birding. Our method for indexing observer
 variability uses species accumulation curves, lines that describe how the
 total number of species reported increase with increasing time spent in
 collecting observations. We find that differences in species accumulation
 curves among observers equates to higher rates of species accumulation,
 particularly for harder-to-identify species, and reveals increased species
 accumulation rates with continued participation. We suggest that these
 properties of our analysis provide a measure of observer skill, and that
 the potential to derive post-hoc data-derived measurements of participant
 ability should be more widely explored by analysts of data from citizen
 science projects. We see the potential for inferential results from
 analyses of citizen science data to be improved by accounting for observer
 skill.
description: eBird checklist
 summaries for six BCR regionsChecklists_no_species.zip
DOI: 10.5061/dryad.nr6bb
title: Data from: Development and preliminary evaluation of a genome-wide single-nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)

description: Recent advances in high-throughput sequencing technologies have offered
 the possibility to generate genome-wide sequence data to delineate
 previously unidentified genetic structure, obtain more accurate estimates
 of demographic parameters, and to evaluate potential adaptive divergence.
 Here, we identified 27 556 single-nucleotide polymorphisms for the small
 yellow croaker (Larimichthys polyactis) using restriction-site-associated
 DNA (RAD) sequencing of 24 individuals from two populations. Significant
 sources of genetic variation was identified, with an average nucleotide
 diversity (π) of 0.00105 ± 0.000425 across individuals and long-term
 effective population size was thus estimated to range between 26 172 and
 261 716. According to the results, no differentiation between the two
 populations was detected based on the SNP dataset of top quality score per
 contig or neutral loci. However, the two analyzed populations were highly
 differentiated based on SNP dataset of both top FST value per contig and
 the outlier SNPs. Moreover, local adaptation was highlighted by an
 FST-based outlier tests implemented in LOSITAN and a total of 538
 potentially locally selected SNPs were identified. BLAST2GO annotation of
 contigs containing the outlier SNPs yielded hits for 37 (66%) of 56
 significant BLASTX matches. Candidate genes for local adaptation
 constituted a wide array of biological functions, including cellular
 response to oxidative stress, actin filament binding, ion transmembrane
 transport and synapse assembly. The generated SNP resources in the present
 study provided a valuable tool for future population genetics and genomics
 studies of L. polyactis.
description: XHY_small_yellow_croaker_SNPSingle-nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) were identified using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations in China on an Illumina Hi-Seq 2500 platform.XHY_small_yellow_croaker_reference_sequence_assemblyOne small yellow croaker (Larimichthys polyactis) individual from the sampled populations was sequenced with the greatest amount of data (approximately 5 whole-genome coverage for this reference individual)as the reference assembly assembled from pair-end reads sequencing on Illumina Hi-Seq 2500 platformXHY_small_yellow_croaker_sequence_assembly.zipXHY_small_yellow_croaker_SNP_summary_statisticsSummary information on individual SNP (IDs, allele frequencies, Fst et al) was provided for the small yellow croaker (Larimichthys polyactis)XHY_small_yellow_croaker_SNP_statistics.zipAdmixture_Lositan_input_filesInput files of ADMIXTURE and LOSITAN analysis were provided for the small yellow croaker (Larimichthys polyactis)
DOI: 10.5061/dryad.gg8g5
title: Data from: Retracted: Biomechanical characteristics of hand coordination in grasping activities of daily living

description: THIS ARTICLE HAS BEEN RETRACTED Hand coordination can allow humans to have
 dexterous control with many degrees of freedom to perform various tasks in
 daily living. An important contributing factor to this important ability
 is the complex biomechanical architecture of the human hand. However,
 drawing a clear functional link between biomechanical architecture and
 hand coordination is challenging. It is not understood which biomechanical
 characteristics are responsible for hand coordination and what specific
 effect each biomechanical characteristic has. To explore this link, we
 first inspected the characteristics of hand coordination during daily
 tasks through a statistical analysis of the kinematic data, which were
 collected from thirty right-handed subjects during a multitude of grasping
 tasks. Then, the functional link between biomechanical architecture and
 hand coordination was drawn by establishing the clear corresponding
 causality between the tendinous connective characteristics of the human
 hand and the coordinated characteristics during daily grasping activities.
 The explicit functional link indicates that the biomechanical
 characteristic of tendinous connective architecture between muscles and
 articulations is the proper design by the Creator to perform a multitude
 of daily tasks in a comfortable way. The clear link between the structure
 and the function of the human hand also suggests that the design of a
 multifunctional robotic hand should be able to better imitate such basic
 architecture.
description: Motion data of hand
 during the daily grasping tasksData.zip
DOI: 10.5061/dryad.p2g11
title: Data from: A stochastic vision based model inspired by the collective behaviour of zebrafish in heterogeneous environments

description: Collective motion is one of the most ubiquitous behaviours displayed by
 social organisms and has led to the development of numerous models. Recent
 advances in the understanding of sensory system and information processing
 by animals impels one to revise classical assumptions made in decisional
 algorithms. In this context, we present a model describing the
 three-dimensional visual sensory system of fish that adjust their
 trajectory according to their perception field. Furthermore, we introduce
 a stochastic process based on a probability distribution function to move
 in targeted directions rather than on a summation of influential vectors
 as is classically assumed by most models. In parallel, we present
 experimental results of zebrafish (alone or in group of 10) swimming in
 both homogeneous and heterogeneous environments. We use these experimental
 data to set the parameter values of our model and show that this
 perception-based approach can simulate the collective motion of species
 showing cohesive behaviour in heterogeneous environments. Finally, we
 discuss the advances of this multilayer model and its possible outcomes in
 biological, physical and robotic sciences.
description: Zebrafish_Positions_dataThe files contain the positions of the zebrafish in different environments (homogeneous or heterogeneous) for one hour. As indicated by the headers, the first column is the time (in s) while the others are the X and Y coordinates (in m) of the different fish in the tank. There are 10 replicates for each group size (1 or 10) and each environment (homogeneous or heterogeneous) for a total of 40 files.
DOI: 10.5061/dryad.33vn1
title: Data from: Functional advantages of conserved intrinsic disorder in RNA-binding proteins

description: Proteins form large macromolecular assemblies with RNA that govern
 essential molecular processes. RNA-binding proteins have often been
 associated with conformational flexibility, yet the extent and functional
 implications of their intrinsic disorder have never been fully assessed.
 Here, through large-scale analysis of comprehensive protein sequence and
 structure datasets we demonstrate the prevalence of intrinsic structural
 disorder in RNA-binding proteins and domains. We addressed their
 functionality through a quantitative description of the evolutionary
 conservation of disordered segments involved in binding, and investigated
 the structural implications of flexibility in terms of conformational
 stability and interface formation. We conclude that the functional role of
 intrinsically disordered protein segments in RNA-binding is two-fold:
 first, these regions establish extended, conserved electrostatic
 interfaces with RNAs via induced fit. Second, conformational flexibility
 enables them to target different RNA partners, providing
 multi-functionality, while also ensuring specificity. These findings
 emphasize the functional importance of intrinsically disordered regions in
 RNA-binding proteins.
description: Nucleic acid binding
 sequence dataThis is the sequence
 data in FASTA format that underlies the analysis.sequence_data.tar.gz
DOI: 10.5281/zenodo.15692228
title: 3D ED raw data for "When Reality Defies Prediction: Polymorphism, Twinning, and Accordion Crystals"

description: 3D ED data for the crystal structure in the title publication  (https://www.doi.org/10.1021/jacs.5c22213). Data were collected using continuous rotation in selected area mode. The table below summarizes generic data collection parameters for the data collection.

 




Collection site
University of Southampton, NCS/NEDF


Sample label(s)
2024NCS0773


Crystal structure deposit
CSD 2465455


 
 


Instrumental
 


Instrument
Rigaku XtaLAB Synergy-ED, electron diffractometer


Radiation source
LaB6


Accelerating voltage [kV]
200


Wavelength [Å]
0.0251


Probe type
Parallel beam (SAED)


Beam convergence
Parallel beam


Detector
Rigaku HyPix-ED, hybrid pixel array detector


Number of pixels in the image
775 x 385


Pixel size [µm]
100


Hardware binning
1


 
 


Sample description
 


Name
DBS-CONHNH2 


Chemical composition
C22H27N4O8.5


Sample source
Synthesis


Grid
laceycarbon coated copper grid, 200 mesh (Agar Scientific)


Sample preparation
Sample ground between glass slides, grid dabbed, cryo transfer @ 175 K


Sample holder
GATAN Elsa cryo-transfer holder 698


 
 


Experimental
 


Data type
Electron diffraction data - 3D ED


Data collection method
Continuous rotation  - cRED


Collection temperature [K]
175


 
 


Software
 


Software used for the data collection
CrysAlisPro 1.171.44.78a


Software used for processing
CrysAlisPro 1.171.44.79a


 
 


Files and data formats
 


Image folders
./frames/xxx.rodhypix./frames/TIFF/xxx.tiff


Image format
.rodhypix.tiff (converted with CrysAlisPro)


Additional files


 

CrysAlisPro files:

./expinfo/./expinfo/exp_XXXX_datacoll.ini

./plots_dc.plots_dc/exp_XXX_hypix.dat.plots_dc/exp_XXX_Jeol_MicroED.dat.plots_dc/exp_XXX_primarybeam.dat.plots_dc/exp_XXX_primarybeam_0.jpg

./CrysalisExpSettings.ini./exp_XXX.par./exp_XXX.run./new.ccd

 

Grain snapshots files:

./exp_XXXX_microed_grain_snapshot.rodhypix./exp_XXXX_microed_grain_snapshot.tiff
DOI: 10.5281/zenodo.15692229
title: 3D ED raw data for "When Reality Defies Prediction: Polymorphism, Twinning, and Accordion Crystals"

description: 3D ED data for the crystal structure in the title publication  (https://www.doi.org/10.1021/jacs.5c22213). Data were collected using continuous rotation in selected area mode. The table below summarizes generic data collection parameters for the data collection.

 




Collection site
University of Southampton, NCS/NEDF


Sample label(s)
2024NCS0773


Crystal structure deposit
CSD 2465455


 
 


Instrumental
 


Instrument
Rigaku XtaLAB Synergy-ED, electron diffractometer


Radiation source
LaB6


Accelerating voltage [kV]
200


Wavelength [Å]
0.0251


Probe type
Parallel beam (SAED)


Beam convergence
Parallel beam


Detector
Rigaku HyPix-ED, hybrid pixel array detector


Number of pixels in the image
775 x 385


Pixel size [µm]
100


Hardware binning
1


 
 


Sample description
 


Name
DBS-CONHNH2 


Chemical composition
C22H27N4O8.5


Sample source
Synthesis


Grid
laceycarbon coated copper grid, 200 mesh (Agar Scientific)


Sample preparation
Sample ground between glass slides, grid dabbed, cryo transfer @ 175 K


Sample holder
GATAN Elsa cryo-transfer holder 698


 
 


Experimental
 


Data type
Electron diffraction data - 3D ED


Data collection method
Continuous rotation  - cRED


Collection temperature [K]
175


 
 


Software
 


Software used for the data collection
CrysAlisPro 1.171.44.78a


Software used for processing
CrysAlisPro 1.171.44.79a


 
 


Files and data formats
 


Image folders
./frames/xxx.rodhypix./frames/TIFF/xxx.tiff


Image format
.rodhypix.tiff (converted with CrysAlisPro)


Additional files


 

CrysAlisPro files:

./expinfo/./expinfo/exp_XXXX_datacoll.ini

./plots_dc.plots_dc/exp_XXX_hypix.dat.plots_dc/exp_XXX_Jeol_MicroED.dat.plots_dc/exp_XXX_primarybeam.dat.plots_dc/exp_XXX_primarybeam_0.jpg

./CrysalisExpSettings.ini./exp_XXX.par./exp_XXX.run./new.ccd

 

Grain snapshots files:

./exp_XXXX_microed_grain_snapshot.rodhypix./exp_XXXX_microed_grain_snapshot.tiff