cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fs728
title: Data from: Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

description: Amplicon based metabarcoding promises rapid and cost-efficient analyses of
 species composition. However, it is disputed whether abundance estimates
 can be derived from metabarcoding due to taxon specific PCR amplification
 biases. PCR-free approaches have been suggested to mitigate this problem,
 but come with considerable increases in workload and cost. Here, we
 analyze multilocus datasets of diverse arthropod communities, to evaluate
 whether amplification bias can be countered by (1) targeting loci with
 highly degenerate primers or conserved priming sites, (2) increasing PCR
 template concentration, (3) reducing PCR cycle number or (4) avoiding
 locus specific amplification by directly sequencing genomic DNA.
 Amplification bias is reduced considerably by degenerate primers or
 targeting amplicons with conserved priming sites. Surprisingly, a
 reduction of PCR cycles did not have a strong effect on amplification
 bias. The association of taxon abundance and read count was actually less
 predictable with fewer cycles. Even a complete exclusion of locus specific
 amplification did not exclude bias. Copy number variation of the target
 loci may be another explanation for read abundance differences between
 taxa, which would affect amplicon based and PCR free methods alike. As
 read abundance biases are taxon specific and predictable, the application
 of correction factors allows abundance estimates.
description: DNA_and_tissue_poolsTaxonomic composition of DNA and tissue pools and recovered read counts for all taxa.DNAPools.tarIllumina read files for the different markers and 16 DNA pools. Reads for the mitochondrial and nuclear markers are merged into each one file.PCRCycles.tarIllumina read files for the 23 DNA pools of the PCR cycle experiment. The number of PCR cycles for each sample is indicated in the file name.SingleSpecimens.tarIllumina read files of all 8 markers sequenced separately for each of the 43 taxa, which were used to prepare the DNA mock communities. Reads for all 8 markers are merged into single files.TissuePools.tarIllumina read files of the tissue pools. Each pool was sequenced twice, once using degraded DNA (L) and once using intact high molecular weight DNA (H).gDNA.tarIllumina read files of the sequenced genomic DNA pools. Due to low coverage, we merged the pools into one file, using equal read numbers from each file.
DOI: 10.5061/dryad.6k62p
title: Data from: Hydrospire morphology and implications for blastoid phylogeny

description: The external expression of hydrospires in blastoids has provided a basis
 for major and minor group classification in the clade for over a century.
 Unfortunately, the complete anatomy of the hydrospires has never been
 comprehensively studied. This study examined and described the internal
 hydrospires of six spiraculate species by digitally extracting hydrospire
 data from a legacy data set of serial acetate peels. Although only six
 models have been currently generated, hydrospire morphology is variable
 both within and between previously described spiraculate families.
 Hydrospires were found to possess novel characters that were incorporated
 into a phylogenetic analysis of the six digitally modeled species and
 several related species. The addition of internal morphology into the
 phylogenetic analysis provides further resolution between groupings of
 blastoids.
description: Bauer_SupplementalData1Supplemental Data 1. Brief character definitions and character states outlined. Numbers in first column refer to numbers utilized in the character matrix found in Supplemental Data 2. Internal character data denoted by an asterisk.Bauer_SupplementalData2Supplemental Data 2. Character matrix for the anatomically modeled species and several related taxa. Character number refer to the list of characters found in Supplemental Data 1. Outgroup species is denoted by an asterisk.Bauer_SupplementalData3Supplemental Data 3. Raw scanned peel data that were used in the reconstruction process for Cryptoblastus melo.Bauer_SupplementalData4Supplemental Data 4. Raw scanned peel data that were used in the reconstruction process for Deltoblastus permicus.Bauer_SupplementalData5Supplemental Data 5. Raw scanned peel data that were used in the reconstruction process for Diploblastus glaber.Bauer_SupplementalData6Supplemental Data 6. Raw scanned peel data that were used in the reconstruction process for Ellipicoblastus elliptica.Bauer_SupplementalData7Supplemental Data 7. Raw scanned peel data that were used in the reconstruction process for Monoschizoblastus rofei.Bauer_SupplementalData8Supplemental Data 8. Raw scanned peel data that were used in the reconstruction process for Pentremites godoni.
DOI: 10.5061/dryad.47n27
title: Data from: Nutrient-dependent growth underpinned the Ediacaran transition to large body size

description: Macroscale rangeomorph fossils, with characteristic branching fronds,
 appear (571 Myr ago) after the Gaskiers glaciation (580 Myr ago). However,
 biological mechanisms of size growth and potential connections to ocean
 geochemistry were untested. Using micro-computerized tomography and
 photographic measurements, alongside mathematical and computer models, we
 demonstrate that growth of rangeomorph branch internodes declined as their
 relative surface area decreased. This suggests that frond size and shape
 were directly responsive to nutrient uptake.
description: Micro-CT scan tiff
 images of Avalofractus abaculus (Rangeomorpha) cast ROM 63005 folder
 1Micro-CT tiff files.
 Original data suitable for reconstruction of a volume rendering. Folder
 1.CToriginal_tiffs_folder1.zipMicro-CT scan tiff images of Avalofractus abaculus (Rangeomorpha) cast ROM 63005 folder 2Micro-CT tiff files. Original data suitable for reconstruction of a volume rendering. Folder 2.CToriginal_tiffs_folder2.zipMicro-CT scan tiff images of Avalofractus abaculus (Rangeomorpha) cast ROM 63005 folder 3Micro-CT tiff files. Original data suitable for reconstruction of a volume rendering. Folder 3.CToriginal_tiffs_folder3.zipMicro-CT scan volume renderings of Avalofractus abaculus (Rangeomorpha) cast ROM 63005 and scan informationMicro-CT volume renderings generated with the program Drishti and CT scan information fileCTvolume_render_info.zip
DOI: 10.5061/dryad.7tv80
title: Data from: Evaluation of downscaled, gridded climate data for the conterminous United States

description: Weather and climate affect many ecological processes, making spatially
 continuous yet fine-resolution weather data desirable for ecological
 research and predictions. Numerous downscaled weather data sets exist, but
 little attempt has been made to evaluate them systematically. Here we
 address this shortcoming by focusing on four major questions: (1) How
 accurate are downscaled, gridded climate data sets in terms of temperature
 and precipitation estimates? (2) Are there significant regional
 differences in accuracy among data sets? (3) How accurate are their mean
 values compared with extremes? (4) Does their accuracy depend on spatial
 resolution? We compared eight widely used downscaled data sets that
 provide gridded daily weather data for recent decades across the United
 States. We found considerable differences among data sets and between
 downscaled and weather station data. Temperature is represented more
 accurately than precipitation, and climate averages are more accurate than
 weather extremes. The data set exhibiting the best agreement with station
 data varies among ecoregions. Surprisingly, the accuracy of the data sets
 does not depend on spatial resolution. Although some inherent differences
 among data sets and weather station data are to be expected, our findings
 highlight how much different interpolation methods affect downscaled
 weather data, even for local comparisons with nearby weather stations
 located inside a grid cell. More broadly, our results highlight the need
 for careful consideration among different available data sets in terms of
 which variables they describe best, where they perform best, and their
 resolution, when selecting a downscaled weather data set for a given
 ecological application.
description: Weather station
 recordsRaw GHCN weather station
 records (1981-2010) for stations used in the paper.Station_Data.zipIndependent weather station analysisData for follow-up analysis of gridded weather products with an independent set of weather stations.Independent_Data.zipCPC GriddedData for primary analysis, both gridded data and the corresponding observed dataCPC_Gridded.zipDAYMET_GriddedData for primary analysis, both gridded data and the corresponding observed dataLIVNEH_GriddedData for primary analysis, both gridded data and the corresponding observed dataMAURER_GriddedData for primary analysis, both gridded data and the corresponding observed dataNLDAS2_GriddedData for primary analysis, both gridded data and the corresponding observed dataPRISM_GriddedData for primary analysis, both gridded data and the corresponding observed dataTOPOWX_GriddedData for primary analysis, both gridded data and the corresponding observed dataUIDAHO_GriddedData for primary analysis, both gridded data and the corresponding observed data
DOI: 10.5061/dryad.40877s4
title: Data from: Upper atmosphere heating from ocean-generated acoustic wave energy

description: Colliding sea surface waves generate the ocean microbarom, an acoustic
 signal that may transmit significant energy to the upper atmosphere.
 Previous estimates of acoustic energy flux from the ocean microbarom and
 mountain/wind interactions are on the order of 0.01 to 1 mW/m2, heating
 the thermosphere by tens of degrees Kelvin per day. We captured up going
 ocean microbarom waves with a balloon borne infrasound microphone; the
 maximum acoustic energy flux was approximately 0.05 mW/m2. This is about
 half the average value reported in previous ground-based microbarom
 observations spanning eight years. The acoustic flux from the microbarom
 episode described here may have heated the thermosphere by several degrees
 Kelvin per day while the source persisted. We suggest that ocean wave
 models could be used to parameterize acoustically-generated heating of the
 upper atmosphere based on sea state.
description: File 1Archive file 1 of 9. All
 of the files need to be downloaded, then the data can be extracted via:
 cat uldb.tar.gza* | (tar -xz)uldb.tar.gzaaFile 2File 2 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzabFile 3File 3 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzacFile 4File 4 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzadFile 5File 5 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzaeFile 6File 6 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzafFile 7File 7 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzagFile 8File 8 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzahFile 9File 9 of 9. All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)uldb.tar.gzai
DOI: 10.5061/dryad.6907h
title: Data from: Evolutionary stability of antibiotic protection in a defensive symbiosis

description: The increasing resistance of human pathogens severely limits the efficacy
 of antibiotics in medicine, yet many animals, including solitary beewolf
 wasps, successfully engage in defensive alliances with
 antibiotic-producing bacteria for millions of years. Here, we report on
 the in situ production of 49 derivatives belonging to three antibiotic
 compound classes (45 piericidin derivatives, 3 streptochlorin derivatives,
 and nigericin) by the symbionts of 25 beewolf host species and subspecies,
 spanning 68 million years of evolution. Despite a high degree of
 qualitative stability in the antibiotic mixture, we found consistent
 quantitative differences between species and across geographic localities,
 presumably reflecting adaptations to combat local pathogen communities.
 Antimicrobial bioassays with the three main components and in silico
 predictions based on the structure and specificity in polyketide synthase
 domains of the piericidin biosynthesis gene cluster yield insights into
 the mechanistic basis and ecoevolutionary implications of producing a
 complex mixture of antimicrobial compounds in a natural setting.
description: HPLC-MS/MS Philanthus
 spp. TurkeyHPLC-MS/MS runs of MeOH
 extracts of single Philanthus specimen antennae from
 TurkeyTurkey
 samples.7zHPLC-MS/MS Philanthus
 spp. South AfricaHPLC-MS/MS runs of MeOH
 extracts from single Philanthus specimen antennae collected in South
 AfricaSouth
 Africa samples.7zHPLC-MS/MS Philanthus
 spp. GermanyHPLC-MS/MS runs of MeOH
 extracts from single Philanthus triangulum specimen antennae and cocoons
 collected in GermanyGermany
 samples.7zHPLC-MS/MS Philanthus
 gibbosus cocoonsHPLC-MS/MS runs of MeOH
 extracts from single Philanthus gibbosus cocoons reared in
 GermanyPgibbosus
 cocoons.7zmanual MS2
 scansmanual MS2 scans to
 obtaine fragmentation patterns for compounds not obtained by automatic MS2
 scansHPLC-MS/MS Trachypus
 boharti Brazil 1HPLC-MS/MS runs of MeOH
 extracts from single Trachypus boharti specimen antennae collected in
 Brazil - first halfBrazil samples
 1.7zHPLC-MS/MS Trachypus
 boharti Brazil 2HPLC-MS/MS runs of MeOH
 extracts from single Trachypus boharti specimen antennae collected in
 Brazil - second halfBrazil samples
 2.7zHPLC-MS/MS Trachypus
 spp. BrazilHPLC-MS/MS runs of MeOH
 extracts from single Trachypus spp. specimen antennae & cocoons
 collected in BrazilBrazil samples
 3.7zHPLC-MS/MS pooled
 samplesHPLC-MS/MS runs of
 pooled MeOH extracts from Philanthus, Trachyous and Philanthunus specimen
 antennae and cocoonspooled
 samples.7z
DOI: 10.5061/dryad.ck54h
title: Data from: Peripheral sensory coding through oscillatory synchrony in weakly electric fish

description: Adaptations to an organism's environment often involve sensory system
 modifications. In this study, we address how evolutionary divergence in
 sensory perception relates to the physiological coding of stimuli.
 Mormyrid fishes that can detect subtle variations in electric
 communication signals encode signal waveform into spike-timing differences
 between sensory receptors. In contrast, the receptors of species
 insensitive to waveform variation produce spontaneously oscillating
 potentials. We found that oscillating receptors respond to electric pulses
 by resetting their phase, resulting in transient synchrony among receptors
 that encodes signal timing and location, but not waveform. These receptors
 were most sensitive to frequencies found only in the collective signals of
 groups of conspecifics, and this was correlated with increased behavioral
 responses to these frequencies. Thus, different perceptual capabilities
 correspond to different receptor physiologies. We hypothesize that these
 divergent mechanisms represent adaptations for different social
 environments. Our findings provide the first evidence for sensory coding
 through oscillatory synchrony.
description: B brachyistius receptor
 recordingsAll data and metadata
 related to receptor recordings in Brienomyrus
 brachyistius.Behavioral
 playbackAll data and metadata
 related to behavioral playback experiments in Petrocephalus tenuicauda and
 Petrocephalus microphthalmus.EOD
 waveformsAll electric organ
 discharge (EOD) waveforms analyzed in this manuscript.EODs.zipGroup tank and single fish IPI recordingsRecordings of interpulse intervals (IPIs) produced by single fish and a group of fish in the species Petrocephalus tenuicauda and Petrocephalus microphthalmusP soudanensis receptor recordingsAll data and metadata related to receptor recordings in Petrocephalus soudanensis.P tenuicauda rosette photosAll photos taken of rosettes in a single Petrocephalus tenuicauda. These photos contributed to Fig. 2A.P_tenuicauda_rosette_photos.zipB niger receptor recordingsAll data and metadata related to receptor recordings from Brevimyrus niger.B_niger_receptor_recordings.zipP adspersus receptor recordingsAll data and metadata related to receptor recordings from Pollimyrus adspersus.P_adspersus_receptor_recordings.zipP tenuicauda receptor recordingsAll data and metadata related to receptor recordings from Petrocephalus tenuicauda.P_tenuicauda_receptor_recordings.zipData analysis toolsAll Matlab files used for data analysisdata analysis tools.zipP microphthalmus receptor recordingsAll data and metadata related to receptor recordings from Petrocephalus microphthalmus.P_microphthalmus_receptor_recordings.zip
DOI: 10.15139/s3/2fokix
title: Data Management and Sharing Plan for: Coronavirus Genome Replication

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.sk6s0
title: Data from: X-ray microtomography for ant taxonomy: an exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from Madagascar

description: We explore the potential of x-ray micro computed tomography (μCT) for the
 field of ant taxonomy by using it to enhance the descriptions of two
 remarkable new species of the ant genus Terataner: T. balrog sp. n. and T.
 nymeria sp. n.. We provide an illustrated worker-based species
 identification key for all species found on Madagascar, as well as
 detailed taxonomic descriptions, which include diagnoses, discussions,
 measurements, natural history data, high-quality montage images and
 distribution maps for both new species. In addition to conventional
 morphological examination, we have used virtual reconstructions based on
 volumetric μCT scanning data for the species descriptions. We also include
 3D PDFs, still images of virtual reconstructions, and 3D rotation videos
 for both holotype workers and one paratype queen. The complete μCT
 datasets have been made available online (Dryad, https://datadryad.org)
 and represent the first cybertypes in ants (and insects). We discuss the
 potential of μCT scanning and critically assess the usefulness of
 cybertypes for ant taxonomy.
description: Cybertype_Terataner
 balrog_CASENT0472559_holotype worker_1Cybertype dataset for
 Terataner balrog (CASENT0472559) holotype worker 1: complete micro-CT
 scanning raw dataset in DICOM format (993 slices)Cybertype_Terataner
 balrog_CASENT0472559_holotype worker_2Cybertype dataset for
 Terataner balrog (CASENT0472559) holotype worker 2: 3D PDF, 3D rotation
 video in mpg format, and montage photos (full-face view, body in profile,
 and dorsal view of body) in tif formatCybertype_Terataner
 balrog_CASENT0426614_paratype queen_1Cybertype dataset for
 Terataner balrog (CASENT0426614) paratype queen 1: complete micro-CT
 scanning raw dataset in DICOM format (993 slices)Cybertype_Terataner
 balrog_CASENT0426614_paratype queen_2Cybertype dataset for
 Terataner balrog (CASENT0426614) paratype queen 2: 3D PDF, 3D rotation
 video in mpg format, and montage photos (full-face view, body in profile,
 and dorsal view of body) in tif formatCybertype_Teratener
 nymeria_CASENT0053630_holotype worker_1Cybertype dataset for
 Terataner nymeria (CASENT0053630) holotype worker 1: complete micro-CT
 scanning raw dataset in DICOM format (993 slices)Cybertype_Teratener
 nymeria_CASENT0053630_holotype worker_2Cybertype dataset for
 Terataner nymeria (CASENT0053630) holotype worker 2: 3D PDF, 3D rotation
 video in mpg format, and montage photos (full-face view, body in profile,
 and dorsal view of body) in tif format
DOI: 10.5061/dryad.1db5500
title: Data from: Rev7 and 53BP1/Crb2 prevent RecQ helicase-dependent hyper-resection of DNA double-strand breaks

description: Poly(ADP ribose) polymerase inhibitors (PARPi) target cancer cells
 deficient in homology-directed repair of DNA double-strand breaks (DSBs).
 In preclinical models, PARPi resistance is tied to altered nucleolytic
 processing (resection) at the 5' ends of a DSB. For example, loss of
 53BP1 or Rev7/MAD2L2/FANCV derepresses resection to drive PARPi
 resistance, although the mechanisms are poorly understood. Long-range
 resection can be catalyzed by two machineries: the exonuclease Exo1, or
 the combination of a RecQ helicase and Dna2. Here, we develop a single
 cell microscopy assay that allows the distinct phases and machineries of
 resection to be interrogated simultaneously in living S. pombe cells.
 Using this assay, we find that the 53BP1 orthologue and Rev7 specifically
 repress long-range resection through the RecQ helicase-dependent pathway,
 thereby preventing hyper-resection. These results suggest that
 'rewiring' of BRCA1-deficient cells to employ an
 Exo1-independent hyper-resection pathway is a driver of PARPi resistance.
description: Leland_King_2018_eLife_Rev7_EndResection_ImageUploadRaw images and ImageJ1 code for all figures
DOI: 10.5061/dryad.4f92n
title: Data from: Optimizing the detection of wakeful and sleep-like states for future electrocorticographic brain computer interface applications

description: Previous studies suggest stable and robust control of a brain-computer
 interface (BCI) can be achieved using electrocorticography (ECoG).
 Translation of this technology from the laboratory to the real world
 requires additional methods that allow users operate their ECoG-based BCI
 autonomously. In such an environment, users must be able to perform all
 tasks currently performed by the experimenter, including manually
 switching the BCI system on/off. Although a simple task, it can be
 challenging for target users (e.g., individuals with tetraplegia) due to
 severe motor disability. In this study, we present an automated and
 practical strategy to switch a BCI system on or off based on the cognitive
 state of the user. Using a logistic regression, we built probabilistic
 models that utilized sub-dural ECoG signals from humans to estimate in
 pseudo real-time whether a person is awake or in a sleep-like state, and
 subsequently, whether to turn a BCI system on or off. Furthermore, we
 constrained these models to identify the optimal anatomical and spectral
 parameters for delineating states. Other methods exist to differentiate
 wake and sleep states using ECoG, but none account for practical
 requirements of BCI application, such as minimizing the size of an ECoG
 implant and predicting states in real time. Our results demonstrate that,
 across 4 individuals, wakeful and sleep-like states can be classified with
 over 80% accuracy (up to 92%) in pseudo real-time using high gamma (70–110
 Hz) band limited power from only 5 electrodes (platinum discs with a
 diameter of 2.3 mm) located above the precentral and posterior superior
 temporal gyrus.
description: SubA_Sleep1SubA_Sleep2_part1SubA_Sleep2_part2SubA_Wake1_part1SubA_Wake1_part2SubA_Wake2_part1SubA_Wake2_part2SubB_Sleep1SubB_Sleep2_part1SubB_Sleep2_part2SubB_Wake1SubB_Wake2_part1SubB_Wake2_part2SubC_Sleep1SubC_Sleep2_part1SubC_Sleep2_part2SubC_Wake_1SubC_Wake2SubD_Sleep1_part1SubD_Sleep1_part2SubD_Sleep2SubD_Wake1SubD_Wake2