cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.72dk5
title: Data from: Scoring tools for the analysis of infant respiratory inductive plethysmography signals

description: Infants recovering from anesthesia are at risk of life threatening
 Postoperative Apnea (POA). POA events are rare, and so the study of POA
 requires the analysis of long cardiorespiratory records. Manual scoring is
 the preferred method of analysis for these data, but it is limited by low
 intra- and inter-scorer repeatability. Furthermore, recommended scoring
 rules do not provide a comprehensive description of the respiratory
 patterns. This work describes a set of manual scoring tools that address
 these limitations. These tools include: (i) a set of definitions and
 scoring rules for 6 mutually exclusive, unique patterns that fully
 characterize infant respiratory inductive plethysmography (RIP) signals;
 (ii) RIPScore, a graphical, manual scoring software to apply these rules
 to infant data; (iii) a library of data segments representing each of the
 6 patterns; (iv) a fully automated, interactive formal training protocol
 to standardize the analysis and establish intra- and inter-scorer
 repeatability; and (v) a quality control method to monitor scorer ongoing
 performance over time. To evaluate these tools, three scorers from varied
 backgrounds were recruited and trained to reach a performance level
 similar to that of an expert. These scorers used RIPScore to analyze data
 from infants at risk of POA in two separate, independent instances.
 Scorers performed with high accuracy and consistency, analyzed data
 efficiently, had very good intra- and inter-scorer repeatability, and
 exhibited only minor confusion between patterns. These results indicate
 that our tools represent an excellent method for the analysis of
 respiratory patterns in long data records. Although the tools were
 developed for the study of POA, their use extends to any study of
 respiratory patterns using RIP (e.g., sleep apnea, extubation readiness).
 Moreover, by establishing and monitoring scorer repeatability, our tools
 enable the analysis of large data sets by multiple scorers, which is
 essential for longitudinal and multicenter studies.
description: Original and
 pre-processed data, and analysis resultsData acquired from
 infants at risk of Postoperative Apnea (in MATLAB *.mat format). Also,
 results of the analysis of these data by 4 scorers using the RIPScore
 manual scoring tool.StudyData.zip
DOI: 10.5061/dryad.68pk1rv
title: Data from: Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

description: Horseshoe crabs including Tachypleus tridentatus are a group of marine
 arthropods living fossil species which have existed on the earth for 500
 million years. However, the genetic mechanisms underlying their unique
 adaptive ability are still unclear. Here, we assembled the first
 chromosome-level T. tridentatus genome, and proofed that this genome is of
 very high quality with contig N50 1.69 Mb. By comparison with other
 arthropods, some gene families of T. tridentatus experienced significant
 expansion, whichare related to several signaling pathways, endonuclease
 activity, and metabolic processes. Based on the comparative analysis of
 genomics and 27 transcriptomes from 9 tissues, we found that the expanded
 Dscam genes usually locate at the key hub positions of immune network.
 Furthermore, the Dscam genes showed higher levels of expression in the
 yellow connective tissue, the birthplace of blood cells with strong
 differentiation capability, than the other 8 tissues. Besides, Dscam genes
 are positively correlated with the expression of the core immunity gene,
 clotting factor B, which is implicated in the coagulation cascade
 reaction. The effective and unusual immune ability endowed by the
 expansion and expression of Dscam genes in horseshoe crabs may be a factor
 that makes horseshoe crabs having a strong environmental adaptability with
 ~500 million years. The high-quality chromosome-level genome of a
 horseshoe crab and unique genomic features reported in this study provide
 important data resources for future studies on the evolutionary history of
 marine ecological systems.
description: Ttri_cds.tar.gzThe CDS sequence file of horseshoe crab.Ttri_pep.tar.gzThe protein sequence file of horseshoe crab.Ttri_gff3.tar.gzThe gff3 file of horseshoe crab.Ttri_repeat_annotation.gff.tar.gzThe repeats annotation file of horseshoe crab.Ttri_genome.fa.tar.gzThe genome file of horseshoe crab.Ttri_genome.fa.sm.fa.tar.gzThe repeats-masked genome file of horseshoe crab.
DOI: 10.5061/dryad.4q67s
title: Data from: The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long-toed salamander (Ambystoma macrodactylum Baird)

description: The relative importance of ecological versus non-ecological factors for
 the origin and maintenance of species is an open question in evolutionary
 biology. Young lineages—such as the distinct genetic groups that make up
 the ranges of many northern species—represent an opportunity to study the
 importance of ecological divergence during the early stages of
 diversification. Yet, few studies have examined the extent of niche
 divergence between lineages in previously glaciated regions and the role
 of ecology in maintaining the contact zones between them. In this study,
 we used tests of niche overlap in combination with ecological niche models
 to explore the extent of niche divergence between lineages of the
 long-toed salamander (Ambystoma macrodactylum Baird) species complex and
 to determine whether contact zones correspond to (divergent) niche limits.
 We found limited evidence for niche divergence between the different
 long-toed salamander lineages, substantial overlap in the predicted
 distribution of suitable climatic space for all lineages and range limits
 that are independent of niche limits. These results raise questions as to
 the importance of ecological divergence to the development of this
 widespread species complex and highlight the potential for non-ecological
 factors to play a more important role in the maintenance of northern taxa.
description: Data and scripts for
 niche models and other analysesZip file with several
 folders. Please see README file.JEB_Lee-Yaw_Irwin_2015_new.zip
DOI: 10.4121/d2f0b61f-d74a-49c9-8b4c-c69d6d56eb55
title: Data supporting the PhD thesis: Medium-Voltage Medium-Frequency Transformer for Green Hydrogen Applications

description: This dataset supports the PhD research on the design and validation of medium-voltage, medium-frequency transformers (MFTs) for solid-state transformer (SST) applications in large-scale green hydrogen production. The research is applied and experimental, focusing on electromagnetic, insulation, thermal, and parasitic-parameter aspects of high-power MFTs. The dataset includes simulation results (FEM electromagnetic and thermal models), analytical and Python-based calculations, design parameter sets, and experimental measurement data from a downscaled laboratory prototype, including loss measurements, partial-discharge tests, impedance/Bode analysis, and thermal-rise tests. Data were generated through a combination of numerical simulations, controlled laboratory experiments, and post-processing scripts, and are intended to support reproducibility of the reported results and further research on SST-based power conversion systems.
DOI: 10.5061/dryad.d1013
title: Data from: The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

description: The macronuclear genome of the ciliate Oxytricha trifallax displays an
 extreme and unique eukaryotic genome architecture with extensive genomic
 variation. During sexual genome development, the expressed, somatic
 macronuclear genome is whittled down to the genic portion of a small
 fraction (~5%) of its precursor “silent” germline micronuclear genome by a
 process of “unscrambling” and fragmentation. The tiny macronuclear
 “nanochromosomes” typically encode single, protein-coding genes (a small
 portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are
 differentially amplified to an average of ~2,000 copies. We report the
 high-quality genome assembly of ~16,000 complete nanochromosomes (~50 Mb
 haploid genome size) that vary from 469 bp to 66 kb long (mean ~3.2 kb)
 and encode ~18,500 genes. Alternative DNA fragmentation processes ~10% of
 the nanochromosomes into multiple isoforms that usually encode complete
 genes. Nucleotide diversity in the macronucleus is very high (SNP
 heterozygosity is ~4.0%), suggesting that Oxytricha trifallax may have one
 of the largest known effective population sizes of eukaryotes. Comparison
 to other ciliates with nonscrambled genomes and long macronuclear
 chromosomes (on the order of 100 kb) suggests several candidate proteins
 that could be involved in genome rearrangement, including domesticated
 MULE and IS1595-like DDE transposases. The assembly of the highly
 fragmented Oxytricha macronuclear genome is the first completed genome
 with such an unusual architecture. This genome sequence provides
 tantalizing glimpses into novel molecular biology and evolution. For
 example, Oxytricha maintains tens of millions of telomeres per cell and
 has also evolved an intriguing expansion of telomere end-binding proteins.
 In conjunction with the micronuclear genome in progress, the O. trifallax
 macronuclear genome will provide an invaluable resource for investigating
 programmed genome rearrangements, complementing studies of rearrangements
 arising during evolution and disease.
description: Oxytricha trifallax
 macronuclear PE-Assembler/SSAKE assemblyContigs in gzipped fasta
 format.s_all.fastq.high_qual.ssake_m20_o5_r0.8_t0_s-pe-asm.assembly_pid11360.contigs_singlets.gzOxytricha trifallax macronuclear IDBA assemblyContigs in gzipped fasta format.idba_pe_new45_85-contig-mate.fa.gzOxytricha trifallax macronuclear ABySS assemblyoxy-abyss-pese-50-contigs.fa.greater200.bettersplit.gzOxytricha trifallax macronuclear PCAP 2.1.8 assemblyPCAP_2.1.8_assembly.tar.gzOxytricha trifallax macronuclear genome fosmidsoxytricha_mac_fosmids.tar.gzStylonychia lemnae DDE_TNP_is1595 contigsContigs in fasta format.stylonychia_dde_tnp_is1595_contigs.fa
DOI: 10.4121/d2f0b61f-d74a-49c9-8b4c-c69d6d56eb55.v1
title: Data supporting the PhD thesis: Medium-Voltage Medium-Frequency Transformer for Green Hydrogen Applications

description: This dataset supports the PhD research on the design and validation of medium-voltage, medium-frequency transformers (MFTs) for solid-state transformer (SST) applications in large-scale green hydrogen production. The research is applied and experimental, focusing on electromagnetic, insulation, thermal, and parasitic-parameter aspects of high-power MFTs. The dataset includes simulation results (FEM electromagnetic and thermal models), analytical and Python-based calculations, design parameter sets, and experimental measurement data from a downscaled laboratory prototype, including loss measurements, partial-discharge tests, impedance/Bode analysis, and thermal-rise tests. Data were generated through a combination of numerical simulations, controlled laboratory experiments, and post-processing scripts, and are intended to support reproducibility of the reported results and further research on SST-based power conversion systems.
DOI: 10.5061/dryad.g1q85
title: Data from: Reintroduction of locally extinct vertebrates impacts arid soil fungal communities

description: Introduced species have contributed to extinction of native vertebrates in
 many parts of the world. Changes to vertebrate assemblages are also likely
 to alter microbial communities through coextinction of some taxa and the
 introduction of others. Many attempts to restore degraded habitats involve
 removal of exotic vertebrates (livestock and feral animals) and
 reintroduction of locally extinct species, but the impact of such
 reintroductions on microbial communities is largely unknown. We used
 high-throughput DNA sequencing of the fungal internal transcribed spacer I
 (ITS1) region to examine whether replacing exotic vertebrates with
 reintroduced native vertebrates led to changes in soil fungal communities
 at a reserve in arid central Australia. Soil fungal diversity was
 significantly different between dune and swale (interdune) habitats.
 Fungal communities also differed significantly between sites with exotic
 or reintroduced native vertebrates after controlling for the effect of
 habitat. Several fungal operational taxonomic units (OTUs) found
 exclusively inside the reserve were present in scats from reintroduced
 native vertebrates, providing a direct link between the vertebrate
 assemblage and soil microbial communities. Our results show that changes
 to vertebrate assemblages through local extinctions and the invasion of
 exotic species can alter soil fungal communities. If local extinction of
 one or several species results in the coextinction of microbial taxa, the
 full complement of ecological interactions may never be restored.
description: Arid_Recovery_APDP_soil_scats_mapQIIME mapping fileotu_table_mc2_w_taxSoil & scat fungal OTU table generated by open-reference OTU picking with the UNITE database.barcodes_AridRecITS_soilSample-specific MIDs for soil samples.Rev_barcodes_AridRecITS_soil_scats6 bp MID at the 5’ end of the ITS5 primerRev_barcodes_AridRecITS_soil.txtPGM_AridRecITS_soil.fastqFASTQ file of PGM reads for Arid Recovery soil samples.Sample-specific MIDs for scat samples.barcodes_AridRecITS_scats.txtArid recovery soil fungiIonTorrent PGM run for fungi diversity studyPGM_AridRecITS_scat.fastq.gz
DOI: 10.5061/dryad.v99j8
title: Data from: The evolution of scarab beetles tracks the consecutive rise of angiosperms and mammals

description: Extant terrestrial biodiversity arguably is driven by the evolutionary
 success of angiosperm plants, but the evolutionary mechanisms and
 timescales of angiosperm-dependent radiations remain poorly understood.
 The Scarabaeoidea is a diverse lineage of predominantly plant- and
 dung-feeding beetles. Here, we present a phylogenetic analysis of
 Scarabaeoidea based on four DNA markers for a taxonomically comprehensive
 set of specimens and link it to recently described fossil evidence. The
 phylogeny strongly supports multiple origins of coprophagy, phytophagy and
 anthophagy. The ingroup-based fossil calibration of the tree widely
 confirmed a Jurassic origin of the Scarabaeoidea crown group. The crown
 groups of phytophagous lineages began to radiate first (Pleurostict
 scarabs: 108 Ma; Glaphyridae between 101 Ma), followed by the later
 diversification of coprophagous lineages (crown-group age Scarabaeinae: 76
 Ma; Aphodiinae: 50 Ma). Pollen feeding arose even later, at maximally 62
 Ma in the oldest anthophagous lineage. The clear time lag between the
 origins of herbivores and coprophages suggests an evolutionary path driven
 by the angiosperms that first favoured the herbivore fauna (mammals and
 insects) followed by the secondary radiation of the dung feeders. This
 finding makes it less likely that extant dung beetle lineages initially
 fed on dinosaur excrements, as often hypothesized.
description: PhyML
 treesTrees resulting from
 analysis in PhyML 3.0 on the Mafft and Mafft/Aliscore
 alignmentML-Trees.zipData: ConcatenatedAlignmentAligned and concatenated DNA data for the Mafft and the Mafft/Aliscore alignmentsData_ConcatenatedAlignment.zipBEAST-Analysis resultsContains for each Beast run: 1) posterior trees after burnin and thinning; 2) XML files for Beast runs; 3) Final time treeBEAST-Analysis.zipResults MrBayes analysesResults_MrBayes.zip
DOI: 10.5061/dryad.tt550
title: Data from: Caspr3-deficient mice exhibit low motor learning during the early phase of the accelerated rotarod task

description: Caspr3 (Contactin-associated protein-like 3, Cntnap3) is a neural cell
 adhesion molecule belonging to the Caspr family. We have recently shown
 that Caspr3 is expressed abundantly between the first and second postnatal
 weeks in the mouse basal ganglia, including the striatum, external segment
 of the globus pallidus, subthalamic nucleus, and substantia nigra.
 However, its physiological role remains largely unknown. In this study, we
 conducted a series of behavioral analyses on Capsr3-knockout (KO) mice and
 equivalent wild-type (WT) mice to investigate the role of Caspr3 in brain
 function. No significant differences were observed in most behavioral
 traits between Caspr3-KO and WT mice, but we found that Caspr3-KO mice
 performed poorly during the early phase of the accelerated rotarod task in
 which latency to falling off a rod rotating with increasing velocity was
 examined. In the late phase, the performance of the Caspr3-KO mice caught
 up to the level of WT mice, suggesting that the deletion of Caspr3 caused
 a delay in motor learning. We then examined changes in neural activity
 after training on the accelerated rotarod by conducting
 immunohistochemistry using antibody to c-Fos, an indirect marker for
 neuronal activity. Experience of the accelerated rotarod task caused
 increases in the number of c-Fos-positive cells in the dorsal striatum,
 cerebellum, and motor cortex in both Caspr3-KO and WT mice, but the number
 of c-Fos-positive cells was significantly lower in the dorsal striatum of
 Caspr3-KO mice than in that of WT mice. The expression of c-Fos in the
 ventral striatum of Caspr3-KO and WT mice was not altered by the training.
 Our findings suggest that reduced activation of neural cells in the dorsal
 striatum in Caspr3-KO mice leads to a decline in motor learning in the
 accelerated rotarod task.
description: Image files for c-Fos
 immunohistochemistryAll the image files
 (Tiff) used in this paper as well as an excel file in which a list of
 names and short descriptions of the image files are indicated will be
 found in this folder.c-Fos　image.zip
DOI: 10.5061/dryad.n0v6d91
title: Data from: Gene expression is more strongly associated with behavioural specialisation than with age or fertility in ant workers

description: The ecological success of social insects is based on division of labour,
 not only between queens and workers, but also among workers. Whether a
 worker tends the brood or forages is influenced by age, fertility and
 nutritional status, with brood carers being younger, more fecund and more
 corpulent. Here, we experimentally disentangle behavioural specialisation
 from age and fertility in Temnothorax longispinosus ant workers and
 analyse how these parameters are linked to whole-body gene expression. A
 total of 3644 genes were associated with behavioural specialisation which
 is ten times more than associated with age and 50 times more than
 associated with fertility. Brood carers were characterized by an
 upregulation of three Vitellogenin (Vg) genes, one of which, Vg-like A,
 was the most differentially expressed gene that was recently shown
 experimentally to control the switch from brood- to worker-care. The
 expression of Conventional Vg was unlinked to behavioural specialisation,
 age or fertility, which contrasts to studies on bees and some ants.
 Diversity in Vg/Vg-like copy number and expression bias across ants
 supports subfunctionalisation of vitellogenin genes and indicates that
 some regulatory mechanisms of division of labour diverged in different ant
 lineages. Simulations revealed that our experimental dissociation of
 co-varying factors reduced transcriptomic noise, suggesting that
 confounding factors could potentially explain inconsistencies across
 transcriptomic studies of behavioural specialisation in ants. Thus, our
 study reveals that worker gene expression is mainly linked to the worker’s
 function for the colony and provides novel insights into the evolution of
 sociality in ants.
description: Results of blast and
 gene expression analysisEscel sheet with the
 results of the blast search and gene expression analysis for each of the
 three factors tested (Behaviour, age, fertility)Transcriptome and gene
 expression data.xlsxTranscriptomeFasta file with all contig sequencesMIRA_Longi_Transcriptome_plus_Debris_with_split_Vg1.fastaPermutation resultsResult files of the 1000 permutations of the reduced sample size GLMPermutation.rarResults of the age confounded GLMExcel sheet containing the results of the gene expression analysis on the age confounded subdatasetage_confounded_GLM.xlsx
DOI: 10.5061/dryad.83420
title: Data from: Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction

description: Exosomes are small vesicles that are secreted from metazoan cells and may
 convey selected membrane proteins and small RNAs to target cells for the
 control of cell migration, development and metastasis. To study the
 mechanisms of RNA packaging into exosomes, we devised a purification
 scheme based on the membrane marker CD63 to isolate a single exosome
 species secreted from HEK293T cells. Using immunoisolated CD63-containing
 exosomes we identified a set of miRNAs that are highly enriched with
 respect to their cellular levels. To explore the biochemical requirements
 for exosome biogenesis and RNA packaging, we devised a cell-free reaction
 that recapitulates the species-selective enclosure of miR-223 in isolated
 membranes supplemented with cytosol. We found that the RNA-binding protein
 Y-box protein I (YBX1) binds to and is required for the sorting of miR-223
 in the cell-free reaction. Furthermore, YBX1 serves an important role in
 the secretion of miRNAs in exosomes by HEK293T cells.
description: HEK293T cell small
 RNA-seqsmall RNA-seq reads from
 HEK293T cells mapped to human genome hg19.MSRS001A.bamExosomes from HEK293T cells small RNA-seq readsSmall RNA-seq reads from purified exosomes aligned to human genome hg19MSRS001B.bam
DOI: 10.5281/zenodo.17190630
title: Evaluation of Chunk Priority Functions for Point Cloud Out-of-Core Rendering - Evaluation Datasets

description: These datasets were used in experiments for a paper that was not accepted for publication.
DOI: 10.5281/zenodo.17190629
title: Evaluation of Chunk Priority Functions for Point Cloud Out-of-Core Rendering - Evaluation Datasets

description: These datasets were used in experiments for a paper that was not accepted for publication.
DOI: 10.5061/dryad.1pf43rb
title: Data from: Bottlenose dolphins can understand their partner’s role in a cooperative task

description: In recent decades, a number of studies have examined whether various
 non-human animals understand their partner’s role in cooperative
 situations. Yet the relatively tolerant timing requirements of these tasks
 make it theoretically possible for animals to succeed by using simple
 behavioural strategies rather than by jointly intended coordination. Here
 we investigated whether bottlenose dolphins could understand a cooperative
 partner’s role by testing whether they could learn a button-pressing task
 requiring precise behavioural synchronisation. Specifically, members of
 cooperative dyads were required to swim across a lagoon and each press
 their own underwater button simultaneously (within a 1-second time
 window), whether sent together or with a delay between partners of 1-20
 seconds. We found that dolphins were able to work together with extreme
 precision even when they had to wait for their partner, and that their
 coordination improved over the course of the study, with the time between
 button presses in the latter trials averaging 370 milliseconds. These
 findings show that bottlenose dolphins can learn to understand their
 partner’s role in a cooperative situation, and suggest that the
 behavioural synchronisation evident in wild dolphins’ synchronous movement
 and coordinated alliance displays may be a generalized cognitive ability
 that can also be used to solve novel cooperative tasks.
description: Movie S1a_dyad 2_SIM
 TrialMovie S1b_dyad 2_SIM
 TrialMovie S2a_dyad 2_10 Sec
 DelayMovie S2b_dyad 2_10 Sec
 DelayVideo files for dolphin
 cooperation trials submitted as supplementary material