cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.43548
title: Data from: Trends in the sand: directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae)

description: Directional evolution is one of the most compelling evolutionary patterns
 observed in macroevolution. Yet, despite its importance, detecting such
 trends in multivariate data remains a challenge. In this study, we
 evaluate multivariate evolution of shell shape in 93 bivalved scallop
 species, combining geometric morphometrics and phylogenetic comparative
 methods. Phylomorphospace visualization described the history of
 morphological diversification in the group; revealing that taxa with a
 recessing life habit were the most distinctive in shell shape, and
 appeared to display a directional trend. To evaluate this hypothesis
 empirically, we extended existing methods by characterizing the mean
 directional evolution in phylomorphospace for recessing scallops. We then
 compared this pattern to what was expected under several alternative
 evolutionary scenarios using phylogenetic simulations. The observed
 pattern did not fall within the distribution obtained under multivariate
 Brownian motion, enabling us to reject this evolutionary scenario. By
 contrast, the observed pattern was more similar to, and fell within, the
 distribution obtained from simulations using Brownian motion combined with
 a directional trend. Thus, the observed data are consistent with a pattern
 of directional evolution for this lineage of recessing scallops. We
 discuss this putative directional evolutionary trend in terms of its
 potential adaptive role in exploiting novel habitats.
description: BMTrendAnalyses R
 scriptPhylogenetic simulation
 for calculating Mean Pairwise Angle to assess directional evolution in
 phylogenetic comparative datasets, in R.BMTrendAnalyses.rR data fileR environment file for 1000 simulated datasets under BM, and 1000 simulated datasets under BM with a trend (µ = 3).mu3.RDataShape DataSpecies average Procrustes residuals (202 landmarks in 3D) for 93 species of scallops.Shape.Data.csvPhylogenetic treePhylogenetic tree (time calibrated) for 93 species of scallop.tree.treGroup Classifier fileRelates species names in Shape.Data to phylogenetic tree and life habits.phylo.IDs.csvR source fileModified version of geiger's sim.char function that allows a vector of root values and modified µ.sim.char2.R
DOI: 10.5061/dryad.bh39282
title: Data from: Finite-element analysis of microwave scattering from a three-dimensional human head model for brain stroke detection

description: In this paper, a detailed analysis of microwave (MW) scattering from a
 three-dimensional (3D) anthropomorphic human head model is presented. It
 is the first time that the finite-element method (FEM) has been deployed
 to study the MW scattering phenomenon of a 3D realistic head model for
 brain stroke detection. A major contribution of this paper is to add
 anatomically more realistic details to the human head model compared with
 the literature available to date. Using the MRI database, a 3D numerical
 head model was developed and segmented into 21 different types through a
 novel tissue-mapping scheme and a mixed-model approach. The heterogeneous
 and frequency-dispersive dielectric properties were assigned to brain
 tissues using the same mapping technique. To mimic the simulation set-up,
 an eight-elements antenna array around the head model was designed using
 dipole antennae. Two types of brain stroke (haemorrhagic and ischaemic) at
 various locations inside the head model were then analysed for possible
 detection and classification. The transmitted and backscattered signals
 were calculated by finding out the solution of the Helmholtz wave equation
 in the frequency domain using the FEM. FE mesh convergence analysis for
 electric field values and comparison between different types of iterative
 solver were also performed to obtain error-free results in minimal
 computational time. At the end, specific absorption rate analysis was
 conducted to examine the ionization effects of MW signals to a 3D human
 head model. Through computer simulations, it is foreseen that MW imaging
 may efficiently be exploited to locate and differentiate two types of
 brain stroke by detecting abnormal tissues’ dielectric properties. A
 significant contrast between electric field values of the normal and
 stroke-affected brain tissues was observed at the stroke location. This is
 a step towards generating MW scattering information for the development of
 an efficient image reconstruction algorithm.
description: det_head_u2Zubal_Complete_Head_Reverse_ImageStack_Single_Mask_mphtxtZubal_Complete_Head_Reverse_ImageStack_Single_Mask.mphtxtZubal_Complete_Head_Reverse_ImageStack_Single_Mask_nasZubal_Complete_Head_Reverse_ImageStack_Single_Mask.nasZubal_Complete_Head_Reverse_ImageStack_Single_Mask_stlZubal_Complete_Head_Reverse_ImageStack_Single_Mask.stlZubal_Complete_Head_Solution_Hex_Finer_MeshZubal_Complete_Head_Solution_Hex_Finer.mphtxta_conductivity_output_3D_reverse_offset_omit_outside_1e+09a_permittivity_output_3D_reverse_offset_omit_outside_1e+09a_IDs_output_3D_reverse_offset_omit_zero_1e+09Import file for Matlab programming fileThis file is imported by Matlab programmed file to assign frequency-dispersive dielectric properties to Zubal head model tissues. This file provides the information of Zubal head model tissues' segmentation ids.det_head_u2med.dat
DOI: 10.5061/dryad.jv77v
title: Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

description: Unicellular, eukaryotic organisms (protists) play a key role in soil food
 webs as major predators of microorganisms. However, due to the
 polyphyletic nature of protists, no single universal barcode can be
 established for this group, and the structure of many protistean
 communities remains unresolved. Plasmodial slime moulds (Myxogastria or
 Myxomycetes) stand out among protists by their formation of fruit bodies,
 which allow for a morphological species concept. By Sanger sequencing of a
 large collection of morphospecies, this study presents the largest
 database to date of dark-spored myxomycetes and evaluate a partial 18S SSU
 gene marker for species annotation. We identify and discuss the use of an
 intraspecific sequence similarity threshold of 99.1% for species
 differentiation (OTU picking) in environmental PCR studies (ePCR) and
 estimate a hidden diversity of putative species, exceeding those of
 described morphospecies by 99%. When applying the identified threshold to
 an ePCR data set (including sequences from both NGS and cloning), we find
 64 OTUs of which 21.9% had a direct match (&gt;99.1% similarity) to
 the database and the remaining had on average 90.2 ± 0.8% similarity to
 their best match, thus thought to represent undiscovered diversity of
 dark-spored myxomycetes.
description: 502-705_S22_L001_R2_001Raw data, forward reads502-705_S22_L001_R2_001Raw data, reverse reads502705mapA mapping file to describe the barcode combinations for demultiplexing.cau demultiplexing scriptDemultiplexing script for the caucasus data. Requires uparse 7 and biopieces installed.cau.pypost-processing of caucasus data after demultiplexingpost-processing of caucasus data after demultiplexing. Requires uparse 7 including support scripts and NCBI blastpost-process.shcau_demultiplexedDemultiplexed fastq files produced by cau_fastq.pycau_demultiplexed_trimmedDemultiplexed fastq files with barcodes removed.cau_fastqScript for preprocessing raw miseq output data.S6_Scripts_ResubmissionSupplementary S6 from the manuscript. Contains scripts and commandlines necessary for reproducing the conclusions of the manuscriptREADMEREADME file for the dataDatabase_MAFFT_incl_outlier_20170725The database of Myxomycete sequences described in the paper.
DOI: 10.5061/dryad.8qv09
title: Data from: Awake fMRI reveals a specialized region in dog temporal cortex for face processing

description: Recent behavioral evidence suggests that dogs, like humans and monkeys,
 are capable of visual face recognition. But do dogs also exhibit
 specialized cortical face regions similar to humans and monkeys? Using
 functional magnetic resonance imaging (fMRI) in six dogs trained to remain
 motionless during scanning without restraint or sedation, we found a
 region in the canine temporal lobe that responded significantly more to
 movies of human faces than to movies of everyday objects. Next, using a
 new stimulus set to investigate face selectivity in this predefined
 candidate dog face area, we found that this region responded similarly to
 images of human faces and dog faces, yet significantly more to both human
 and dog faces than to images of objects. Such face selectivity was not
 found in dog primary visual cortex. Taken together, these findings: (1)
 provide the first evidence for a face-selective region in the temporal
 cortex of dogs, which cannot be explained by simple low-level visual
 feature extraction; (2) reveal that neural machinery dedicated to face
 processing is not unique to primates; and (3) may help explain dogs’
 exquisite sensitivity to human social cues.
description: Sample dataset for one
 dogIncludes: structural
 image, ROIs, condition timing files, concatenated raw fMRI scans,
 concatenated smoothed motion-corrected normalized fMRI scans, stats files.
 For use with AFNI.stella_faces.tar.gz
DOI: 10.5061/dryad.221mq23
title: Data from: Animal Sound Identifier (ASI): software for automated identification of vocal animals

description: Automated audio recording offers a powerful tool for acoustic monitoring
 schemes of bird, bat, frog and other vocal organisms, but the lack of
 automated species identification methods has made it difficult to fully
 utilise such data. We developed Animal Sound Identifier (ASI), a MATLAB
 software that performs probabilistic classification of species occurrences
 from field recordings. Unlike most previous approaches, ASI locates
 training data directly from the field recordings and thus avoids the need
 of pre‐defined reference libraries. We apply ASI to a case study on
 Amazonian birds, in which we classify the vocalisations of 14 species in
 194 504 one‐minute audio segments using in total two weeks of expert time
 to construct, parameterise, and validate the classification models. We
 compare the classification performance of ASI (with training templates
 extracted automatically from field data) to that of monitoR (with training
 templates extracted manually from the Xeno‐Canto database), the results
 showing ASI to have substantially higher recall and precision rates.
description: ASI_softwareZip file containing ASI software (Matlab scripts and functions).ASI manualPDF file containing the manual on how to use ASI softwareonline_example_audioZip folder containing the 100 audio files used to illustrate the use of ASI software, as described in the manual.online_example_outputsZip folder containing all output files generated by ASI for online example, as described in the manual.
DOI: 10.5061/dryad.12734
title: Data from: Projected population proximity indices (30km) for 2005, 2030 & 2050

description: This data package includes nine population proximity index layers for
 2005, 2030 and 2050, for rural, urban and total populations. The layers
 are distributed as 1km GeoTIFFs and GeoJPGss at 1km. The aim of these
 layers is to describe the population which may be likely to visit a
 specific locality where access is determined by Euclidean distance. By
 using the layers alongside other geographic datasets relating to disease
 risk it may help identify where people may come into contact with a
 disease. Human population layers are often used in models to identify risk
 areas where humans and viruses interact, however most pathogens are not
 restricted to areas of human habitation: many are found in lesser
 populated areas such as forests. This dataset will help identify less
 populated areas that may well still receive high visitor numbers. The
 layers have been projected to 2030 and 2050 to enable projections of
 human/disease interfaces in the medium-term which are required to inform
 policy makers at country and continental level. Urban and rural
 populations have been separated into individual layers as in some cases it
 is useful to distinguish between the behaviour and associated risks
 attributed to the different population segments. There may be a different
 risk of contacting diseases in rural habitats for rural workers than for
 than urban visitors.
description: Population Proximity
 LayersThis data package
 includes nine population proximity index layers for 2005, 2030 and 2050,
 for rural, urban and total populations. The layers are distributed as 1km
 GeoTIFFs and GeoJPGss at 1km.popproxv3.zip
DOI: 10.5061/dryad.r94k7
title: Data from: Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly

description: With advances in high-throughput sequencing technologies, de novo
 transcriptome sequencing and assembly has become a cost-effective method
 to obtain comprehensive genetic information of a species of interest,
 especially in non-model species with large genomes such as spiders.
 However, high-quality RNA is essential for successful sequencing and
 sample preservation conditions require careful consideration for the
 effective storage of field-collected samples. To this end, we report a
 streamlined feasibility study of various storage conditions and their
 effects on de novo transcriptome assembly results. The storage parameters
 considered include temperatures ranging from room temperature to -80°C;
 preservatives, including ethanol, RNAlater, TRIzol, and RNAlater-ICE; and
 sample submersion states. As a result, intact RNA was extracted and
 assembly was successful when samples were preserved at low temperatures
 regardless of the type of preservative used. The assemblies as well as the
 gene expression profiles were shown to be robust to RNA degradation, when
 30 million 150 bp paired-end reads are obtained. The parameters for sample
 storage, RNA extraction, library preparation, sequencing, and in silico
 assembly considered in this work provide a guideline for the study of
 field-collected samples of spiders.
description: Fasta file of COI
 sequence from all 24 samples and one reference assemblyThis fast file lists all
 COI sequences from all 24 samples and one reference assembly used in this
 work to confirm the species to be Parasteatoda
 tepidariorum.COI_all_comp.fastaFasta file of 18S rDNA sequences from all 24 samples and one reference assembly used in this workThis fast file lists all COI sequences from all 24 samples and one reference assembly used in this work to confirm the species to be Parasteatoda tepidariorum.18S_all_comp.fastaInput and Output Files for DEG analysis using edgeRInput count data (*_input.txt files, calculated by kallisto software) and output DEG analysis data (*_output.txt files, calculated by edgeR tool). 5M, 20M, or 30M indicates the number of subsampled reads used in the analysis. 1. Files with NO80_p[1-7]_[5|20|30]M_[input/output].txt or NO80_s[1-6]_[5|20|30]M_[input/output].txt These files were for the calculation of Fig. 2b, where NO80_p1_* NO80 vs RIN1.0, 2.2 NO80_p2_* NO80 vs RIN2.2, 3.8 NO80_p3_* NO80 vs RIN3.8, 5.3 NO80_p4_* NO80 vs RIN5.3, 6.3 NO80_p5_* NO80 vs RIN6.3, 7.1 NO80_p6_* NO80 vs RIN7.1, 8.0 NO80_p7_* NO80 vs RIN8.0, 9.0 NO80_s1_* NO80 vs RIN1.0, 2.2, 3.8 NO80_s2_* NO80 vs RIN2.2, 3.8, 5.3 NO80_s3_* NO80 vs RIN3.8, 5.3, 6.3 NO80_s4_* NO80 vs RIN5.3, 6.3, 7.1 NO80_s5_* NO80 vs RIN6.3, 7.1, 8.0 NO80_s6_* NO80 vs RIN7.1, 8.0, 9.0 2. Other files were used for the calculation of Table 3, where AE: Directly submerged in Ethanol AR: Directly submerged in RNAlater CE: Crushed and submerged in Ethanol CR: Crushed and submerged in RNAlater CT: Crushed and submerged in TRIzol NO: Flash-frozen in liquid nitrogenedgeR_OUT_IN_files.zip
DOI: 10.5061/dryad.h7j90
title: Data from: A model for simulating the active dispersal of juvenile sea turtles with a case study on western Pacific leatherback turtles

description: Oceanic currents are known to broadly shape the dispersal of juvenile sea
 turtles during their pelagic stage. Accordingly, simple passive drift
 models are widely used to investigate the distribution at sea of various
 juvenile sea turtle populations. However, evidence is growing that
 juveniles do not drift purely passively but also display some swimming
 activity likely directed towards favorable habitats. We therefore present
 here a novel Sea Turtle Active Movement Model (STAMM) in which juvenile
 sea turtles actively disperse under the combined effects of oceanic
 currents and habitat-driven movements. This model applies to all sea
 turtle species but is calibrated here for leatherback turtles (Dermochelys
 coriacea). It is first tested in a simulation of the active dispersal of
 juveniles originating from Jamursba-Medi, a main nesting beach of the
 western Pacific leatherback population. Dispersal into the North Pacific
 Ocean is specifically investigated. Simulation results demonstrate that,
 while oceanic currents broadly shape the dispersal area, modeled
 habitat-driven movements strongly structure the spatial and temporal
 distribution of juveniles within this area. In particular, these movements
 lead juveniles to gather in the North Pacific Transition Zone (NPTZ) and
 to undertake seasonal north-south migrations. More surprisingly, juveniles
 in the NPTZ are simulated to swim mostly towards west which considerably
 slows down their progression towards the American west coast. This
 increases their residence time, and hence the risk of interactions with
 fisheries, in the central and eastern part of the North Pacific basin.
 Simulated habitat-driven movements also strongly reduce the risk of
 cold-induced mortality. This risk appears to be larger among the juveniles
 that rapidly circulate into the Kuroshio than among those that first drift
 into the North Equatorial Counter Current (NECC). This mechanism might
 induce marked interannual variability in juvenile survival as the strength
 and position of the NECC are directly linked to El Niño activity.
description: Passive drift from
 Jamursba-MediSimulated 18-year-long
 trajectories of passive turtles emerging from Jamursba-Medi nesting beach
 (New Guinea, Indonesia) and drifting in the North Pacific. The file is in
 the self-described NetCDFformatpassive_dispersal_NPAC.ncActive dispersal from Jamursba-MediSimulated 18-year-long trajectories of actively swimming turtles emerging from Jamursba-Medi nesting beach (New Guinea, Indonesia) and drifting in the North Pacific. The file is in the self-described NetCDFformatactive_dispersal_NPAC.nc
DOI: 10.5061/dryad.20627
title: Data from: A social-ecological database to advance research on infrastructure development impacts in the Brazilian Amazon

description: Recognized as one of the world's most vital natural and cultural
 resources, the Amazon faces a wide variety of threats from natural
 resource and infrastructure development. Within this context, rigorous
 scientific study of the region's complex social-ecological system is
 critical to inform and direct decision-making toward more sustainable
 environmental and social outcomes. Given the Amazon's tightly linked
 social and ecological components and the scope of potential development
 impacts, effective study of this system requires an easily accessible
 resource that provides a broad and reliable data baseline. This paper
 brings together multiple datasets from diverse disciplines (including
 human health, socio-economics, environment, hydrology, and energy) to
 provide investigators with a variety of baseline data to explore the
 multiple long-term effects of infrastructure development in the Brazilian
 Amazon.
description: Hydrology
 DatasetsPoint data on river
 water level, river discharge/flow, and daily precipitation for the Amazon,
 Tocantins/Araguaia, Paraná, and Atlantic watersheds contained within the
 Brazilian Amazon.amazon
 hydrology.zipHealth
 DatasetsDisease incidence data
 by municipality of residence, including malaria, dengue fever, cutaneous
 leishmaniasis, and HIV/AIDS, for the Amazon region of
 Brazil.amazon
 health.zipEnvironment
 DatasetEnvironmental variables
 including mean monthly rainfall, dry season length, original forest cover,
 and surface water cover, aggregated by municipality in the Brazilian
 Amazon.Environment.csvSocio-economic DatasetsSocio-economic variables related to demography, education, income, work, agriculture, quality of life, poverty, and gold mining in Amazonian municipalities of Brazil.amazon socioecon.zipHydroelectric Dams DatasetInformation for operating large hydroelectric dams (&gt; 30 MW) in the Brazilian Amazon, including the following variables: dam name, affected river, construction start date, reservoir fill date, operation date, approved energy output, actual energy output, reservoir area, municipalities directly affected by the dam, and area of each municipality flooded by the dam.Base UHE-AMAZONIA.csvMunicipal Map (2010) for Brazilian AmazonOriginal 2010 digital municipal map shape files for the Brazilian Amazon states of Acre, Amapa, Amazonas, Maranhao, Mato Grosso, Para, Rondonia, Roraima, and Tocantins. Maps are produced by the Brazilian Institute of Geography and Statistics (Instituto Brasileira de Geografia e Estatistica - IBGE; www.ibge.gov.br). Downloads can be made by state from the ftp site: ftp://geoftp.ibge.gov.br/malhas_digitais/municipio_2010/.MunicipalMap2010.zipOriginal Health DatasetsOriginally downloaded health datasets for dengue fever, cutaneous leishmaniasis and HIV/AIDS.
DOI: 10.5061/dryad.0dg47
title: Data from: A nuclear magnetic resonance study of water in aggrecan solutions

description: Aggrecan, a highly charged macromolecule found in articular cartilage, was
 investigated in aqueous salt solutions with proton nuclear magnetic
 resonance. The longitudinal and transverse relaxation rates were
 determined at two different field strengths, 9.4 T and 0.5 T, for a range
 of temperatures and aggrecan concentrations. The diffusion coefficients of
 the water molecules were also measured as a function of temperature and
 aggrecan concentration, using a pulsed field gradient technique at 9.4 T.
 Assuming an Arrhenius relationship, the activation energies for the
 various relaxation processes and the translational motion of the water
 molecules were determined from temperature dependencies as a function of
 aggrecan concentration in the range 0–5.3% w/w. The longitudinal
 relaxation rate and inverse diffusion coefficient were approximately
 equally dependent on concentration and only increased by upto 20% from
 that of the salt solution. The transverse relaxation rate at high field
 demonstrated greatest concentration dependence, changing by an order of
 magnitude across the concentration range examined. We attribute this
 primarily to chemical exchange. Activation energies appeared to be
 approximately independent of aggrecan concentration, except for that of
 the low-field transverse relaxation rate, which decreased with
 concentration.
description: NMR data of Water in
 Aggrecan solutionsNMR data of water in
 Aggrecan solutions in raw data format from both Bruker NMR (Avance II) and
 Maran NMR. Range of concentrations on both instruments. A ReadMe file is
 contained within each dataset for additional guidance and
 identification.GAG
 data.zip