cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gh830j7
title: Data from: Evaluating NGS methods for routine monitoring of wild bees: metabarcoding, mitogenomics or NGS barcoding

description: Implementing cost-effective monitoring programs for wild bees remains
 challenging due to the high costs of sampling and specimen identification.
 To reduce costs, next generation sequencing (NGS)-based methods have
 lately been suggested as alternatives to morphology-based identifications.
 To provide a comprehensive presentation of the advantages and weaknesses
 of different NGS-based identification methods, we assessed three of the
 most promising ones, namely metabarcoding, mitogenomics and NGS barcoding.
 Using a regular monitoring dataset (723 specimens identified using
 morphology), we found that NGS barcoding performed best for both species
 presence/absence and abundance data, producing only few false positives
 (3.4%) and none false negatives. In contrast, the proportion of false
 positive and false negative was higher using metabarcoding and
 mitogenomics. Although strong correlations were found between biomass and
 read numbers, abundance estimates significantly skewed the communities’
 composition in these two techniques. NGS barcoding recovered the same
 ecological patterns as morphology. Ecological conclusions based on
 metabarcoding and mitogenomics were similar to those based on morphology
 when using presence/absence data, but different from when using abundance
 data. In terms of workload and cost, we show that metabarcoding and NGS
 barcoding can compete with morphology, but not mitogenomics which was
 consistently more expensive. Based on these results, we advocate that NGS
 barcoding is currently the seemliest NGS method for monitoring of wild
 bees. Furthermore, this method has the advantage of potentially linking
 DNA sequences with preserved voucher specimens, which enable morphological
 re-examination and will thus produce verifiable records which can be fed
 into faunistic databases.
description: Absolute abundance
 community matrixCommunity matrix for all
 identification methods.Community_matrix_all_identification_methods_AbsAbund.txtMPS raw dataBarcodes and primer sequences are available in the mapping file formatted for QIIME1MPS_raw_data.7zMetadataMetadata containing information on ID and code for each specimens. The file also contains metadata on the different flower strips sampled (e.g. plant species richness)Meta_data_DRYAD.xlsxMG raw dataRaw data of the mitogenomic run. The names of the communities are included into the file names.MG_raw_data.7zMB raw dataBarcodes and primer sequences are available in the mapping file formatted for QIIME1.MB_raw_data.7z
DOI: 10.35079/hbm646.rksl.674
title: Visium (no probes) data from the ovary (right) of a 30-year-old white female
DOI: 10.5061/dryad.37bj2
title: Data from: Effects of working-memory training on striatal dopamine release

description: Updating of working memory has been associated with striato-frontal brain
 regions and phasic dopaminergic neurotransmission. We assessed raclopride
 binding to striatal dopamine (DA) D2 receptors during a letter-updating
 task and a control condition before and after 5 weeks of updating
 training. Results showed that updating affected DA activity before
 training and that training further increased striatal DA release during
 updating. These findings highlight the pivotal role of transient neural
 processes associated with D2 receptor activity in working memory.
description: MEMTRAIN1_CognitiveDataCognitive test resultsMEMTRAIN1_MRIDATAT1 structural MRI data in Nifti format (defaced) for each participantC0001PET1_DICOMPET data of single scanC0001PET2_DICOMPET data of single scanC0002PET1_DICOMPET data of single scanC0002PET2_DICOMPET data of single scanC0003PET1_DICOMPET data of single scanC0003PET2_DICOMPET data of single scanC0005PET1_DICOMPET data of single scanC0005PET2_DICOMPET data of single scanC0006PET1_DICOMPET data of single scanC0006PET2_DICOMPET data of single scanC0007PET1_DICOMPET data of single scanC0007PET2_DICOMPET data of single scanC0008PET1_DICOMPET data of single scanC0008PET2_DICOMPET data of single scanC0009PET1_DICOMImage data from single PET scanC0009PET2_DICOMImage data from single PET scanC0010PET1_DICOMImage data from single PET scanC0010PET2_DICOMImage data from single PET scanC0011PET1_DICOMImage data from single PET scanC0011PET2_DICOMImage data from single PET scanC0012PET1_DICOMImage data from single PET scanC0012PET2_DICOMImage data from single PET scanC0013PET1_DICOMImage data from single PET scanC0013PET2_DICOMImage data from single PET scanC0015PET1_DICOMImage data from single PET scanC0015PET2_DICOMImage data from single PET scanC0016PET1_DICOMImage data from single PET scanC0016PET2_DICOMImage data from single PET scanC0017PET1_DICOMImage data from single PET scanC0017PET2_DICOMImage data from single PET scanC0018PET1_DICOMImage data from single PET scanC0018PET2_DICOMImage data from single PET scanC0019PET1_DICOMImage data from single PET scanC0019PET2_DICOMImage data from single PET scanC0020PET1_DICOMImage data from single PET scanC0020PET2_DICOMImage data from single PET scanC0021PET1_DICOMImage data from single PET scanC0021PET2_DICOMImage data from single PET scanC0022PET1_DICOMImage data from single PET scanC0022PET2_DICOMImage data from single PET scan
DOI: 10.15468/dl.88xsg2
title: Occurrence Download

description: A dataset listing the 10 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Material citation",
 "GadmGid is COL",
 "OccurrenceStatus is Present",
 "TaxonKey is Chironomidae"
 ]
}

 The dataset's 10 records were derived from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000405-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.35079/hbm245.lzbz.879
title: Visium (no probes) data from the uterus of a 30-year-old white female
DOI: 10.5061/dryad.ff4fs
title: Data from: Genotyping-in-Thousands by sequencing (GT-seq): a cost effective SNP genotyping method based on custom amplicon sequencing

description: Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses
 next-generation sequencing of multiplexed PCR products to generate
 genotypes from relatively small panels (50–500) of targeted
 single-nucleotide polymorphisms (SNPs) for thousands of individuals in a
 single Illumina HiSeq lane. This method uses only unlabelled oligos and
 PCR master mix in two thermal cycling steps for amplification of targeted
 SNP loci. During this process, sequencing adapters and dual barcode
 sequence tags are incorporated into the amplicons enabling thousands of
 individuals to be pooled into a single sequencing library. Post
 sequencing, reads from individual samples are split into individual files
 using their unique combination of barcode sequences. Genotyping is
 performed with a simple perl script which counts amplicon-specific
 sequences for each allele, and allele ratios are used to determine the
 genotypes. We demonstrate this technique by genotyping 2068 individual
 steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP
 markers in a single library sequenced in a single Illumina HiSeq lane.
 Genotype data were 99.9% concordant to previously collected TaqMan™
 genotypes at the same 192 loci, but call rates were slightly lower with
 GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were
 genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped
 in &lt;70% of samples. This study demonstrates amplicon sequencing
 with GT-seq greatly reduces the cost of genotyping hundreds of targeted
 SNPs relative to existing methods by utilizing a simple library
 preparation method and massive efficiency of scale.
description: GTseq_DataCompressed folder (.zip) containing sequencing data and input files necessary for genotyping using the GTseq method described in the manuscript.
DOI: 10.35079/hbm789.vhtr.333
title: Visium (no probes) data from the uterus of a 30-year-old white female
DOI: 10.5061/dryad.hr431
title: Data from: Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus

description: The Coral Triangle is widely considered the most important centre of
 marine biodiversity in Asia while areas on its periphery such as the South
 China Sea, have received much less interest. Here, we demonstrate that a
 small population of the knobbly sea star Protoreaster nodosus in Singapore
 has similarly high levels of genetic diversity as comparable Indonesian
 populations from the Coral Triangle. The high genetic diversity of this
 population is remarkable because it is maintained despite decades of
 continued anthropogenic disturbance. We postulate that it is probably due
 to broadcast spawning which is likely to maintain high levels of
 population connectivity. To test this, we analysed 6140 genome-wide single
 nucleotide polymorphism (SNP) loci for Singapore's populations and
 demonstrate a pattern of near panmixia. We here document a second case of
 high genetic diversity and low genetic structure for a broadcast spawner
 in Singapore, which suggests that such species have high resilience
 against anthropogenic disturbances. The study demonstrates the feasibility
 and power of using genome-wide SNPs for connectivity studies of marine
 invertebrates without a sequenced genome.
description: Bash command to remove
 potential chimerasThese bash commands were
 used to search for and remove any read containing the EcoRI and MspI
 recognition sites, which are potential chimeric sites formed during
 ligation.20151206_rem_potchimeras_PNOD_pub.shDemultiplexed ddRADseq fastq files per specimenThis zip file contains the individual fastq files for each sea star in which ddRADseq was performed. The data was demultiplexed in STACKS as described in the manuscript.Pnodosus_ddRADseq_files.zip
DOI: 10.5061/dryad.h1v85
title: Data from: Joint analysis of cortical area and thickness as a replacement for the analysis of the volume of the cerebral cortex

description: Cortical surface area is an increasingly used brain morphology metric that
 is ontogenetically and phylogenetically distinct from cortical thickness
 and offers a separate index of neurodevelopment and disease. However, the
 various existing methods for assessment of cortical surface area from
 magnetic resonance images have never been systematically compared. We show
 that the surface area method implemented in FreeSurfer corresponds closely
 to the exact, but computationally more demanding, mass-conservative
 (pycnophylactic) method, provided that images are smoothed. Thus, the data
 produced by this method can be interpreted as estimates of cortical
 surface area, as opposed to areal expansion. In addition, focusing on the
 joint analysis of thickness and area, we compare an improved, analytic
 method for measuring cortical volume to a permutation-based nonparametric
 combination (NPC) method. We use the methods to analyze area, thickness
 and volume in young adults born preterm with very low birth weight, and
 show that NPC analysis is a more sensitive option for studying joint
 effects on area and thickness, giving equal weight to variation in both of
 these 2 morphological features.
description: Supplementary
 MaterialThis is the
 Supplementary Material associated with the paper "Joint analysis of
 cortical area and thickness as a replacement for the analysis of the
 volume of the cerebral cortex", published in Cerebral Cortex. A
 pre-print is on biorXiv: http://dx.doi.org/10.1101/074666. To open,
 download and untar the file, and then open the "index.html" in
 any web browser.Winkler_etal_CerebralCortex.tar
DOI: 10.35079/hbm672.bhmr.926
title: Visium (no probes) data from the uterus of a 30-year-old white female
DOI: 10.5061/dryad.m5pr3
title: Data from: Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation

description: Global climate change and other anthropogenic stressors have heightened
 the need to rapidly characterize ecological changes in marine benthic
 communities across large scales. Digital photography enables rapid
 collection of survey images to meet this need, but the subsequent image
 annotation is typically a time consuming, manual task. We investigated the
 feasibility of using automated point-annotation to expedite cover
 estimation of the 17 dominant benthic categories from survey-images
 captured at four Pacific coral reefs. Inter- and intra- annotator
 variability among six human experts was quantified and compared to semi-
 and fully- automated annotation methods, which are made available at
 coralnet.ucsd.edu. Our results indicate high expert agreement for
 identification of coral genera, but lower agreement for algal functional
 groups, in particular between turf algae and crustose coralline algae.
 This indicates the need for unequivocal definitions of algal groups,
 careful training of multiple annotators, and enhanced imaging technology.
 Semi-automated annotation, where 50% of the annotation decisions were
 performed automatically, yielded cover estimate errors comparable to those
 of the human experts. Furthermore, fully-automated annotation yielded
 rapid, unbiased cover estimates but with increased variance. These results
 show that automated annotation can increase spatial coverage and decrease
 time and financial outlay for image-based reef surveys.
description: Data package for the
 Line Islands.This is a .zip
 compressed data archive of size 754MB. See README.txt for content
 details.line_islands.zipPart 1(2) of the data package for Nanwan Bay.This is a .zip compressed data archive, split using the linux "split" command. The full size of the merged .zip archive is 1.8GB. See README.txt for content details.nanwan_bay.zip.part01Part 2(2) of the data package for Nanwan Bay.nanwan_bay.zip.part02Part 1(6) of the data package for Heron Reef.This is a .zip compressed data archive, split using the linux "split" command. The full size of the merged .zip archive is 5.5GB. See README.txt for content details.heron_reef.zip.part01Part 2(6) of the data package for Heron Reef.heron_reef.zip.part02Part 3(6) of the data package for Heron Reef.heron_reef.zip.part03Part 4(6) of the data package for Heron Reef.heron_reef.zip.part04Part 5(6) of the data package for Heron Reef.heron_reef.zip.part05Part 6(6) of the data package for Heron Reef.heron_reef.zip.part06Data package for Moorea.This is a .zip compressed data archive of size 2.0GB. See README.txt for content details. The data is hosted on an external server. Please use doi:[doi:10.6073/pasta/8e09736f3c37c3554af349f21184b2a8] to lookup the download url.
DOI: 10.35079/hbm826.wvbx.975
title: Visium (no probes) data from the uterus of a 30-year-old white female
DOI: 10.5061/dryad.rq0pj53
title: Data from: Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?

description: Many tropical fruit-feeding nymphalid butterflies are associated with
 either the forest canopy or the understory, however, the exceptions offer
 insights into the origins of tropical diversity. As it occurs in both
 habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon
 is one such exception. We compared patterns of occurrence of A. demophon
 in the canopy and understory and population genomic variation for evidence
 of ecological and genetic differentiation between habitats. We found that
 butterfly occurrences in the canopy were largely uncorrelated with
 occurrences in the understory at both localities, indicating independent
 demographic patterns in the two habitats. We also documented modest,
 significant genome-level differentiation at both localities. Genetic
 differentiation between habitat types (approximately 20m in elevation)
 were comparable to levels of differentiation between sampling locations
 (approximately 1500km). We conclude that canopy and understory populations
 of A. demophon represent incipient independent evolutionary units. These
 findings support the hypothesis that divergence between canopy and
 understory-associated populations might be a mechanism generating insect
 diversity in the tropics.
description: canopy_ecuador_part1.tarIndividual .fastq files for canopy Ecuador samples, part 1.canopy_ecuador_part2.tarIndividual .fastq files for canopy Ecuador samples, part 2.canopy_ecuador_part3.tarIndividual .fastq files for canopy Ecuador samples, part 3.canopy_peru.tarIndividual .fastq files for canopy Peru samples.understory_ecuador_part1.tarIndividual .fastq files for understory Ecuador samples, part 1.understory_ecuador_part2.tarIndividual .fastq files for understory Ecuador samples, part 2.understory_ecuador_part3.tarIndividual .fastq files for understory Ecuador samples, part 3.understory_peru_part1.tarIndividual .fastq files for understory Peru samples, part 1.understory_peru_part2.tarIndividual .fastq files for understory Peru samples, part 2.understory_peru_part3.tarIndividual .fastq files for understory Peru samples, part 3.understory_peru_part4.tarIndividual .fastq files for understory Peru samples, part 4.
DOI: 10.5061/dryad.165r8
title: Data from: Model-based acceleration of Look-Locker T1 mapping

description: Mapping the longitudinal relaxation time T1 has widespread applications in
 clinical MRI as it promises a quantitative comparison of tissue properties
 across subjects and scanners. Due to the long scan times of conventional
 methods, however, the use of quantitative MRI in clinical routine is still
 very limited. In this work, an acceleration of Inversion-Recovery
 Look-Locker (IR-LL) T1 mapping is presented. A model-based algorithm is
 used to iteratively enforce an exponential relaxation model to a highly
 undersampled radially acquired IR-LL dataset obtained after the
 application of a single global inversion pulse. Using the proposed
 technique, a T1 map of a single slice with 1.6mm in-plane resolution and
 4mm slice thickness can be reconstructed from data acquired in only 6s. A
 time-consuming segmented IR experiment was used as gold standard for T1
 mapping in this work. In the subsequent validation study, the model-based
 reconstruction of a single-inversion IR-LL dataset exhibited a T1
 difference of less than 2.6% compared to the segmented IR-LL reference in
 a phantom consisting of vials with T1 values between 200ms and 3000ms. In
 vivo, the T1 difference was smaller than 5.5% in WM and GM of seven
 healthy volunteers. Additionally, the T1 values are comparable to standard
 literature values. Despite the high acceleration, all model-based
 reconstructions were of a visual quality comparable to fully sampled
 references. Finally, the reproducibility of the T1 mapping method was
 demonstrated in repeated acquisitions. In conclusion, the presented
 approach represents a promising way for fast and accurate T1 mapping using
 radial IR-LL acquisitions without the need of any segmentation.
description: MAPboxThis package
 "MAPbox.rar" contains all raw data and reconstruction code (in
 MATLAB) that is needed to reconstruct the T1 maps of the phantom &
 volunteer study of the Manuscript "Model-Based Acceleration of
 Look-Locker T1 Mapping" which is to be published in PLOS ONE in 2015.
 If you only need the reconstructed data, please additionally download
 "MAPrecon.rar".MAPreconThis package "MAPrecon.rar" is an addition to the package "MAPbox.rar". In case you don't want to do any reconstructions yourself and only want to perform the data analysis using already reconstructed data, additionally download this file and follow the instructions in "readme2.txt".
DOI: 10.35079/hbm865.cbtk.346
title: Visium (no probes) data from the uterus of a 30-year-old white female
DOI: 10.5061/dryad.kc5b8
title: Data from: Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

description: PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular
 markers have yielded various insights into the evolutionary history across
 Brassicales, but many relationships between families remain poorly
 supported or unresolved. A recent phylotranscriptomic approach utilizing
 1155 nuclear markers obtained robust estimates for relationships among 14
 of 17 families. Here we report a complete family‐level phylogeny estimated
 using the plastid genome. METHODS - We conducted phylogenetic analyses on
 a concatenated data set comprising 44,926 bp from 72 plastid genes for
 species distributed across all 17 families. Our analysis includes three
 additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae,
 that were omitted in the previous phylotranscriptomic study. KEY RESULTS -
 Our phylogenetic analyses obtained fully resolved and strongly supported
 estimates for all nodes across Brassicales. Importantly, these findings
 are congruent with the topology reported in the phylotranscriptomic study.
 This consistency suggests that future studies could utilize plastid
 genomes as markers for resolving relationships within some notoriously
 difficult clades across Brassicales. We used this new phylogenetic
 framework to verify the placement of the At‐α event near the origin of
 Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago
 and restrict the At‐β event to one of two nodes with median date estimates
 between 85 to 92.2 million years ago. These events ultimately gave rise to
 novel chemical defenses and are associated with subsequent shifts in net
 diversification rates. CONCLUSIONS - We anticipate that these findings
 will aid future comparative evolutionary studies across Brassicales,
 including selecting candidates for whole‐genome sequencing projects.
description: Brassicales Illumina
 data and Final AlignmentThe directory contains
 the raw illumina data (*.fastq) for each of the species plus the final
 alignment titled 'V4 - Brassicales Plastid CDS' with a
 'Datamatrix-ID' file to decode each fasta
 sequence.Brassicales_GSS.zip
DOI: 10.35079/hbm232.kgrq.548
title: Visium (no probes) data from the uterus of a 30-year-old white female
DOI: 10.35079/hbm257.bngt.952
title: Visium (no probes) data from the uterus of a 30-year-old white female
DOI: 10.5061/dryad.8546kv0
title: Data from: Hit probability as a function of foul-ball accumulation

description: In a day and age where professional baseball has implemented the use of
 countdown timers between innings, and restricted batter movement away from
 the batter’s box during at-bats–all in an effort to truncate drawn-out
 games—the foul ball at present, remains untouched. Despite some calls by
 fans for a rule change on foul balls so as to curb the amount of time they
 expend in a game, the foul ball has an interesting tale to tell when one
 actually looks at the data. Foul balls are ubiquitously portrayed as
 devalued events that merely slow down baseball games. However, despite its
 ‘do-over’ game-dragging reputation, the foul ball event can provide
 potential insight into the fatigue status of a pitcher, while also
 functioning as a predictor of hitter success. This paper investigates
 historical Retrosheet Major League Baseball (MLB) foul ball event data
 from 1945 through 2015 so as to analyze the historical nature of foul ball
 occurrence with respect to two states: [1] foul-ball accumulation when
 foul ball strikes occurred ‘inside-the-count’ (ITC); and [2] foul ball
 accumulation when foul balls only occurred ‘outside the count’ (OTC) and
 thus did not count as strikes. It is hypothesized that the foul ball as an
 event can predict hitting success, but that the probability of such
 success is dependent upon when foul balls occur with respect to the
 ball-strike count, and how many foul ball events accumulate during an
 at-bat.
description: retrosheet19452015MySQL database file comprised of Retrosheet public database Major League Baseball game event data compiled for 71 years from 1945 to 2015. Data were obtained free of charge from Retrosheet.