cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r6m04
title: Data from: Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcoding

description: Freshwater fauna are particularly sensitive to environmental change and
 disturbance. Management agencies frequently use fish and amphibian
 biodiversity as indicators of ecosystem health and a way to prioritize and
 assess management strategies. Traditional aquatic bioassessment that
 relies on capture of organisms via nets, traps and electrofishing gear
 typically has low detection probabilities for rare species and can injure
 individuals of protected species. Our objective was to determine whether
 environmental DNA (eDNA) sampling and metabarcoding analysis can be used
 to accurately measure species diversity in aquatic assemblages with
 differing structures. We manipulated the density and relative abundance of
 eight fish and one amphibian species in replicated 206-L mesocosms.
 Environmental DNA was filtered from water samples, and six mitochondrial
 gene fragments were Illumina-sequenced to measure species diversity in
 each mesocosm. Metabarcoding detected all nine species in all treatment
 replicates. Additionally, we found a modest, but positive relationship
 between species abundance and sequencing read abundance. Our results
 illustrate the potential for eDNA sampling and metabarcoding approaches to
 improve quantification of aquatic species diversity in natural
 environments and point the way towards using eDNA metabarcoding as an
 index of macrofaunal species abundance.
description: MESO1.1.fastqMESO1.2.fastqMESO2.1.fastqMESO3.1.fastqMESO2.2.fastqMESO4.1.fastqMESO4.2.fastqMESO5.1.fastqMESO5.2.fastqMESO6.1.fastqMESO7.1.fastqMESO6.2.fastqMESO7.2.fastqMESO8.1.fastqMESO9.1.fastqMESO10.1.fastqMESO9.2.fastqMESO11.1.fastqMESO11.2.fastqMESO12.1.fastqMESO12.2.fastqMESO3.2.fastqMESO10.2.fastqMESO8.2.fastqOTUsReadmeOTU_Summary_Table
DOI: 10.5061/dryad.n9077
title: Data from: Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

description: DNA metabarcoding is promising for cost-effective biodiversity monitoring,
 but reliable diversity estimates are difficult to achieve and validate.
 Here we present and validate a method, called LULU, for removing erroneous
 molecular operational taxonomic units (OTUs) from community data derived
 by high-throughput sequencing of amplified marker genes. LULU identifies
 errors by combining sequence similarity and co-occurrence patterns. To
 validate the LULU method, we use a unique data set of high quality survey
 data of vascular plants paired with plant ITS2 metabarcoding data of DNA
 extracted from soil from 130 sites in Denmark spanning major environmental
 gradients. OTU tables are produced with several different OTU definition
 algorithms and subsequently curated with LULU, and validated against field
 survey data. LULU curation consistently improves α-diversity estimates and
 other biodiversity metrics, and does not require a sequence reference
 database; thus, it represents a promising method for reliable biodiversity
 estimation.
description: Illumina MiSeq data ITS2
 Vascular plantsContains 12 fastq files
 corresponding to R1 and R2 data from 6 Illumina MiSeq 250 bp PE sequencing
 libraries. 130 soil samples from Denmark were amplified with tagged
 primers (S2F and ITS4) and build into TruSeq PCR free libraries. Each
 sample was amplified in triplicates. Fastq files R1A and R1B contain reads
 from the first replicates, R2A and R2B from the second, etc. Data were
 produced as part of the Biowide (Biodiversity in width and depth),
 carryied out in Denmark from 2014-2018) supported by the Villum
 foundation. The vascular plant data included here was used in the
 validation of the LULU algorithm for post-clustering curation of OTU
 tables for reliable biodiversity metrics, as described in the publication.
 Tagging scheme and other information needed to demultiplex and analyse the
 data are accessible on the GitHub repository accompanying the
 publication/r-package.Vascular_Plants_ITS2_Denmark.tar.gz
DOI: 10.5061/dryad.h0h90
title: Data from: Hippocampus is place of interaction between unconscious and conscious memories

description: Recent evidence suggests that humans can form and later retrieve new
 semantic relations unconsciously by way of hippocampus—the key structure
 also recruited for conscious relational (episodic) memory. If the
 hippocampus subserves both conscious and unconscious relational
 encoding/retrieval, one would expect the hippocampus to be place of
 unconscious-conscious interactions during memory retrieval. We tested this
 hypothesis in an fMRI experiment probing the interaction between the
 unconscious and conscious retrieval of face-associated information. For
 the establishment of unconscious relational memories, we presented
 subliminal (masked) combinations of unfamiliar faces and written
 occupations (“actor” or “politician”). At test, we presented the former
 subliminal faces, but now supraliminally, as cues for the reactivation of
 the unconsciously associated occupations. We hypothesized that unconscious
 reactivation of the associated occupation—actor or politician—would
 facilitate or inhibit the subsequent conscious retrieval of a celebrity’s
 occupation, which was also actor or politician. Depending on whether the
 reactivated unconscious occupation was congruent or incongruent to the
 celebrity’s occupation, we expected either quicker or delayed conscious
 retrieval process. Conscious retrieval was quicker in the congruent
 relative to a neutral baseline condition but not delayed in the
 incongruent condition. fMRI data collected during subliminal
 face-occupation encoding confirmed previous evidence that the hippocampus
 was interacting with neocortical storage sites of semantic knowledge to
 support relational encoding. fMRI data collected at test revealed that the
 facilitated conscious retrieval was paralleled by deactivations in the
 hippocampus and neocortical storage sites of semantic knowledge. We assume
 that the unconscious reactivation has pre-activated overlapping relational
 representations in the hippocampus reducing the neural effort for
 conscious retrieval. This finding supports the notion of synergistic
 interactions between conscious and unconscious relational memories in a
 common, cohesive hippocampal-neocortical memory space.
description: fMRI_RT_datafMRI and reaction time data from an unconscoious relational memory paradigm. All data are prepared to be processed with SPM 8 for MATLAB. Additional information about the data structure, acquisition parameters and processing instructions are included in the downloadable package (zip format). Use an archive manager such as 7-zip, winrar or similar to access data.
DOI: 10.5061/dryad.pc548kj
title: Data from: A survey of digitized data from U.S. fish collections in the iDigBio data aggregator

description: Recent changes in institutional cyberinfrastructure and collections data
 storage methods have dramatically improved accessibility of specimen-based
 data through the use of digital databases and data aggregators. This
 analysis of digitized fish collections in the U.S. demonstrates how
 information from data aggregators, in this case iDigBio, can be extracted
 and analyzed. Data from U.S. institutional fish collections in iDigBio
 were explored through a strictly programmatic approach using the ridigbio
 package and fishfindR web application. iDigBio facilitates the aggregation
 of collections data on a purely voluntary fashion that requires collection
 staff to consent to sharing of their data. Not all collections are sharing
 their data with iDigBio, but the data harvested from 38 of the 143 known
 fish collections in the U.S. that are in iDigBio account for the majority
 of fish specimens housed in U.S. collections. In the 22 years since
 publication of the last survey providing information on these 38
 collections, 1,219,168 specimen records (lots), 15,225,744 specimens,
 3,192 primary types, and 32,868 records of secondary types have been
 added. This is an increase of 65.1% in the number of cataloged records and
 an increase of 56.1% in the number of specimens. In addition to providing
 specimen-based data for research, education, and various outreach
 activities, data that are accessible via data aggregators can be used to
 develop accurate, up-to-date reports of information on institutional
 collections. Such reports present collections data in an organized and
 accessible fashion and can guide targeted efforts by collections personnel
 to meet discipline-specific needs and make data more transparent to
 downstream users. Data from this survey will be updated and published
 regularly in a dynamic web application that will aid collections staff in
 communicating collections value while simultaneously giving stakeholders a
 way to explore collections holdings as they relate to the institutions in
 which they are housed. It is through this resource that collections will
 be able to leverage their data against those of similar collections to aid
 in the procurement of financial and institutional support.
description: Specimen Occurrence
 RecordsThese data are iDigBio
 specimen occurrence records downloaded from the iDigBio download API using
 the scripts found here:
 https://github.com/melanostomias/rstuff/tree/master/scripts Also found in
 this archive are intermediate data files used by the scripts to generate
 figures used in the preparation of this manuscript.data-raw.zip
DOI: 10.5061/dryad.5cp90
title: Data from: Mechanotransduction current is essential for stability of the transducing stereocilia in mammalian auditory hair cells

description: Mechanotransducer channels at the tips of sensory stereocilia of inner ear
 hair cells are gated by the tension of 'tip links'
 interconnecting stereocilia. To ensure maximal sensitivity, tip links are
 tensioned at rest, resulting in a continuous influx of Ca2+ into the cell.
 Here we show that this constitutive Ca2+ influx, usually considered as
 potentially deleterious for hair cells, is in fact essential for
 stereocilia stability. In the auditory hair cells of young postnatal mice
 and rats, a reduction in mechanotransducer current, via pharmacological
 channel blockers or disruption of tip links, leads to stereocilia shape
 changes and shortening. These effects occur only in stereocilia that
 harbor mechanotransducer channels, recover upon blocker washout or tip
 link regeneration, and can be replicated by manipulations of extracellular
 Ca2+ or intracellular Ca2+ buffering. Thus, our data provide the first
 experimental evidence for the dynamic control of stereocilia morphology by
 the mechanotransduction current.
description: Figure 1C 1D 1G and
 Figure 2 - Source DataScanning electron
 micrographsFigure 1E 1F - Source
 DataScanning electron
 micrographsFigure 3 - Source
 DataScanning electron
 micrographsFigure 4 and Figure 5 -
 Source DataScanning electron
 micrographsFigure 6 - Source
 DataScanning electron
 micrographsFigure 7 - Source
 DataScanning electron
 micrographs
DOI: 10.5061/dryad.7hj0j
title: Data from: Specific 50-kHz vocalizations are tightly linked to particular types of behavior in juvenile rats anticipating play

description: Rat ultrasonic vocalizations have been suggested to be either a byproduct
 of physical movement or, in the case of 50-kHz calls, a means to
 communicate positive affect. Yet there are up to 14 distinct types of
 50-kHz calls, raising issues for both explanations. To discriminate
 between these theories and address the purpose for the numerous 50-kHz
 call types, we studied single juvenile rats that were waiting to play with
 a partner, a situation associated with a high number of 50-kHz calls. We
 used a Monte-Carlo shuffling procedure to identify vocalization-behavior
 correlations that were statistically different from chance. We found that
 certain call types (“split”, “composite” and “multi-step”) were strongly
 associated with running and jumping while other call types (those
 involving “trills”) were more common during slower movements. Further,
 non-locomotor states such as resting and rearing were strongly predictive
 of a lack of vocalizations. We also found that the various sub-types of
 USVs can be clustered into 3–4 categories based on similarities in the way
 they are used. We did not find a one-to-one relationship between any
 movements and specific vocalizations, casting doubt on the motion
 byproduct theory. On the other hand, the use of specific calls during
 specific behaviors is problematic for the affect communication hypothesis.
 Based on our results, we suggest that ultrasonic calls may serve to
 coordinate moment-to-moment social interactions.
description: Vocalization Data -
 Testing Day 7 OnlyThese vocalization files
 are from the second set of data analysis where all data was taken from the
 last day (day 7) of data analysis. The files are named R_D_C. R for rat
 number, D for day of testing and C for the cohort the animal belonged to.
 These files match the videos uploaded.Vocalization Data -
 Assorted DaysThese vocalization files
 are from the first set of data analysis where all data was taken from
 assorted days of play anticipation and used for data analysis. The files
 are named R_D_C. R for rat number, D for day of testing and C for the
 cohort the animal belonged to. These files match the videos
 uploaded.Behavioural Data -Day 7
 OnlyThese video files are
 from the second set of data analysis where all data of anticipation of
 play was taken from the last day (day 7) for data analysis. The files are
 named R_D_C. R for rat number, D for day of testing and C for the cohort
 the animal belonged to. These files match the video files
 uploaded.Behavioural Data -
 Assorted DaysThese vocalization files
 are from the first set of data analysis where the data was taken from
 assorted days of anticipation of play for data analysis. The files are
 named R_D_C. R for rat number, D for day of testing and C for the cohort
 the animal belonged to. These files match the corresponding vocalization
 files uploaded.Data for Paper Publication -
 Video (2).zip
DOI: 10.5061/dryad.pc1q122
title: Data from: Inconspicuous echolocation in hoary bats (Lasiurus cinereus)

description: Echolocation allows bats to occupy diverse nocturnal niches. Bats almost
 always use echolocation, even when other sensory stimuli are available to
 guide navigation. Here, using arrays of calibrated infrared cameras and
 ultrasonic microphones, we demonstrate that hoary bats (Lasiurus cinereus)
 use previously unknown echolocation behaviors that challenge our current
 understanding of echolocation. We describe a novel call type (“micro”
 calls) that has three orders of magnitude less sound energy than other bat
 calls used in open habitats. We also document bats flying close to
 microphones (&lt; 3 m) without producing detectable echolocation
 calls. Acoustic modeling indicates that bats are not producing calls that
 exceed 70-75 dB at 0.1 m, a level that would have little or no known use
 for a bat flying in the open at speeds exceeding 7 m s-1. This indicates
 that hoary bats sometimes fly without echolocation. We speculate that bats
 reduce echolocation output to avoid eavesdropping by conspecifics during
 the mating season. These findings might partly explain why tens of
 thousands of hoary bats are killed at wind turbines each year. They also
 challenge the long-standing assumption that bats—model organisms for
 sensory specialization—are reliant on sonar for nocturnal navigation.
description: Overview of audio and
 video dataExcel spreadsheet giving
 filenames of audio and video files in the archiveAudioVideoData.xlsxREADMERead me filing giving descriptions of files in data archive3D_Tracks3D bat trajectoriesAudioDetectionsTime points of call detections in audio filesMatlabCodeMatlab code for 3D track generation and audio processingScenesMatlab files giving scene information for each recording night. Data include the positions of cameras (camXYZr), microphones (micsr), and 3D calibration data (easyWandData).AudioFilesOriginal Audio Files
DOI: 10.5061/dryad.p937t
title: Data from: Differential changes with age in multiscale entropy of electromyography signals from leg muscles during treadmill walking

description: Age-related gait changes may be due to the loss of complexity in the
 neuromuscular system. This theory is disputed due to inconsistent results
 from single-scale analyses. Also, behavioral adaptations may confound
 these changes. We examined whether EMG dynamics during gait is less
 complex in older adults over a range of timescales using the multiscale
 entropy method, and whether slower walking attenuates this effect. Surface
 EMG was measured from the left vastus lateralis (VL), biceps femoris (BF),
 gastrocnemius (GA), and tibialis anterior (TA) in 17 young and 18 older
 adults as they walked on a treadmill for 5 minutes at 0.8x-1.2x of
 preferred speed. Sample entropy (SE) and the complexity index (CI) of the
 EMG signals were calculated after successive coarse-graining to extract
 dynamics at timescales of 27 to 270 Hz, with m = 2 and r = 0.15 SD. SE and
 CI were lower across the timescales in older adults in VL and BF, but
 higher in GA (all p&lt;0.001); these results held for VL and GA even
 after accounting for longer EMG burst durations in older adults. CI was
 higher during slower walking speed in VL and BF (p&lt;0.001). Results
 were mostly similar for m = 3 and r = 0.01–0.35. Smaller r was more
 sensitive to age-related differences. The decrease in complexity with
 aging in the timescales studied was limited to proximal muscles,
 particularly VL. The increase in GA may be driven by other factors.
 Walking slower may reflect a behavioral adaptation that allows the nervous
 system to function with greater complexity.
description: Zip file part
 1File
 1 of 5 of the multi-part zip file. All 5 parts need to be downloaded and
 merged together before unzip. Readme is included as an Microsoft Excel
 file. Each folder inside has .mat files (MATLAB binary data) which
 contains 10 matrices, one for each data trial. Each matrix is of 4 muscles
 x 324000 data samples collected over 5 minutes at 1080
 Hz.emg-data-part.z01emg-data-part2see aboveemg-data-part.z02emg data part 3see aboveemg-data-part.z03emg-data-part4see aboveemg-data-part.z04emg data part 5 - zip portionpart 5 of 5emg-data-part.zip
DOI: 10.5061/dryad.8070m
title: Data from: Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated

description: Background: The accurate delimitation of species is essential to numerous
 areas of biological research. An unbiased assessment of the diversity,
 including the cryptic diversity, is of particular importance for the below
 ground fauna, a major component of global biodiversity. On the British
 Isles, the epigeic earthworm Lumbricus rubellus, which is a sentinel
 species in soil ecotoxicology, consists of two cryptic taxa that are
 differentiated in both the nuclear and the mitochondrial (mtDNA) genomes.
 Recently, several deeply divergent mtDNA lineages were detected in
 mainland Europe, but whether these earthworms also constitute cryptic
 species remains unclear. This information is important from an
 evolutionary perspective, but it is also essential for the interpretation
 and the design of ecotoxicological projects. In this study, we used
 genome-wide RADseq data to assess the reproductive isolation of the
 divergent mitochondrial lineages of L. rubellus that occur in sympatry in
 multiple localities in Central Europe. Results: We identified five
 divergent (up to 16 % net p-distance) mitochondrial lineages of
 L. rubellus in sympatry. Because the clustering of the RADseq data was
 according to the population of origin and not the mtDNA lineage,
 reproductive isolation among the mtDNA lineages was not likely. Although
 each population contained multiple mtDNA lineages, subdivisions within the
 populations were not observed for the nuclear genome. The lack of fixed
 differences and sharing of the overwhelming majority of nuclear
 polymorphisms between localities, indicated that the populations did not
 constitute allopatric species. The nucleotide diversity within the
 populations was high, 0.7–0.8 %. Conclusions: The deeply divergent mtDNA
 sympatric lineages of L. rubellus in Central Europe were not
 reproductively isolated groups. The earthworm L. rubellus, which is
 represented by several mtDNA lineages in continental Europe, apparently is
 a single highly polymorphic species rather than a complex of several
 cryptic species. This study demonstrated the critical importance of the
 use of multilocus nuclear data for the unbiased assessment of cryptic
 diversity and for the delimitation of species in soil invertebrates.
description: RADseq data for the
 earthworm Lumbricus rubellus sampled in PolandThe file includes RADseq
 data for Lumbricus rubellus earthworm, 100 individuals, sampled from four
 populations in Southern Poland. The data were generated with the double
 digest RADseq approach. The file includes output of the denovo_map.pl
 program of the Stacks software. Detailed description is available in the
 attached ReadMe file.Lrubellus_RADseq_Poland.zip
DOI: 10.5061/dryad.17m17
title: Data from: Airway bacteria drive a progressive COPD-like phenotype in mice with polymeric immunoglobulin receptor deficiency

description: Mechanisms driving persistent airway inflammation in chronic obstructive
 pulmonary disease (COPD) are incompletely understood. As secretory
 immunoglobulin A (SIgA) deficiency in small airways has been reported in
 COPD patients, we hypothesized that immunobarrier dysfunction resulting
 from reduced SIgA contributes to chronic airway inflammation and disease
 progression. Here we show that polymeric immunoglobulin receptor-deficient
 (pIgR−/−) mice, which lack SIgA, spontaneously develop COPD-like pathology
 as they age. Progressive airway wall remodelling and emphysema in pIgR−/−
 mice are associated with an altered lung microbiome, bacterial invasion of
 the airway epithelium, NF-κB activation, leukocyte infiltration and
 increased expression of matrix metalloproteinase-12 and neutrophil
 elastase. Re-derivation of pIgR−/− mice in germ-free conditions or
 treatment with the anti-inflammatory phosphodiesterase-4 inhibitor
 roflumilast prevents COPD-like lung inflammation and remodelling. These
 findings show that pIgR/SIgA deficiency in the airways leads to persistent
 activation of innate immune responses to resident lung microbiota, driving
 progressive small airway remodelling and emphysema.
description: commands_ML_BlackwellML_Blackwell_keepML_Blackwell_map_catML_Blackwell_mapparameters_core_diversityparameters_jackknifeML_Blackwell_97Supporting data analysis for Richmond et al., Nat Comm 2016Rawseqfiles
DOI: 10.15468/dl.5nkgwz
title: Occurrence Download

description: A dataset containing 80872 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "StateProvince is São Paulo",
 "TaxonKey is Fabaceae"
 ]
}

 The dataset includes 80872 records from 172 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000399-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.