cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0jt43
title: Data from: Numerical simulations of targeted delivery of magnetic drug aerosols in the human upper and central respiratory system: a validation study

description: In the present study, we investigate the concept of the targeted delivery
 of pharmaceutical drug aerosols in an anatomically realistic geometry of
 the human upper and central respiratory system. The geometry considered
 extends from the mouth inlet to the 8th generation of the bronchial
 bifurcations and is identical to the phantom model used in the
 experimental studies of [Banko {em et al.} (2015), Exp. Fluids, {bf 56}
 (117):1-12]. In our computer simulations, we combine the transitional
 Reynolds-Averaged Navier-Stokes (RANS) and the wall-resolved Large Eddy
 Simulation (LES) methods for the air phase with the Lagrangian approach
 for the particulate (aerosol) phase. We validated simulations against
 recently obtained magnetic resonance velocimetry (MRV) measurements of
 [Banko {em et al.} (2015), Exp. Fluids, {bf 56} (117):1-12] that provide
 full a 3D mean velocity field for steady inspiratory conditions. Both
 approaches produced good agreement with experiments, and the transitional
 RANS approach is selected for the multi-phase simulations of aerosols
 transport, because of significantly lower computational costs. The local
 and total deposition efficiency are calculated for different classes of
 pharmaceutical particles (in the $0.1mu$m$le d_{rm p} le 10mu$m range)
 without and with a paramagnetic core (the shell-core particles). For the
 latter, an external magnetic field is imposed. The source of the imposed
 magnetic field was placed in the proximity of the first bronchial
 bifurcation. We demonstrated that both total- and local-depositions of
 aerosols at targeted locations can be significantly increased by an
 applied magnetization force. This finding confirms the possible potential
 for further advancement of the magnetic drug targeting (MDT) technique for
 more efficient treatments for respiratory diseases.
description: kenjeres_2017_rans_sst.casANSYS file (in .cas format): results + numerical mesh for RANS-SST modelkenjeres_2017_rans_sst.datANSYS file (in .dat format) results and numerical mesh for RANS-SST model
DOI: 10.5061/dryad.jd183
title: Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species

description: Microsatellites are ubiquitous in Eukaryotic genomes. A more complete
 understanding of their origin and spread can be gained from a comparison
 of their distribution within a phylogenetic context. Although information
 for model species is accumulating rapidly, it is insufficient due to a
 lack of species depth, thus intragroup variation is necessarily ignored.
 As such, apparent differences between groups may be overinflated and
 generalizations cannot be inferred until an analysis of the variation that
 exists within groups has been conducted. In this study, we examined
 microsatellite coverage and motif patterns from 454 shotgun sequences of
 154 Eukaryote species from eight distantly related phyla (Cnidaria,
 Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and
 Streptophyta) to test if a consistent phylogenetic pattern emerges from
 the microsatellite composition of these species. It is clear from our
 results that data from model species provide incomplete information
 regarding the existing microsatellite variability within the Eukaryotes. A
 very strong heterogeneity of microsatellite composition was found within
 most phyla, classes and even orders. Autocorrelation analyses indicated
 that while microsatellite contents of species within clades more recent
 than 200 Mya tend to be similar, the autocorrelation breaks down and
 becomes negative or non-significant with increasing divergence time.
 Therefore, the age of the taxon seems to be a primary factor in degrading
 the phylogenetic pattern present among related groups. The most recent
 classes or orders of Chordates still retain the pattern of their common
 ancestor. However, within older groups, such as classes of Arthropods, the
 phylogenetic pattern has been scrambled by the long independent evolution
 of the lineages.
description: species_listInformation on species and sequencesfasta_files1-5fasta_files6-10fasta_files11-15fasta_files16-20fasta_files21-25fasta_files26-30fasta_files31-35fasta_files36-40fasta_files41-45fasta_files46-50fasta_files51-55fasta_files56-60fasta_files61-65fasta_files66-70fasta_files71-75fasta_files76-80fasta_files81-85fasta_files86-90fasta_files91-95fasta_files96-100fasta_files101-104
DOI: 10.5061/dryad.15249
title: Data from: Leaf form evolution in Viburnum parallels variation within individual plants

description: Few studies have critically evaluated how morphological variation within
 individual organisms corresponds to variation within and among species.
 Sub-individual variation in plants facilitates such studies because their
 indeterminate, modular growth generates multiple serially homologous
 structures along growing axes. Focusing on leaf form, we evaluate how
 sub-individual trait variation relates to leaf evolution across Viburnum,
 a clade of woody angiosperms. In Viburnum we infer multiple independent
 origins of wide/lobed leaves with toothed margins from ancestors with
 elliptical, smooth-margined leaves. We document leaf variation along the
 branches of individual plants of 28 species and among populations across
 the wide range of V. dentatum. We conclude that when novel leaf forms
 evolved in Viburnum, they were intercalated at the beginning of the
 seasonal leaf sequence, which then generated a repeated spectrum of leaf
 forms along each branch (seasonal heteroblasty). We hypothesize that the
 existence of such a spectrum then facilitated additional evolutionary
 shifts, including reversions to more ancestral forms. We argue that the
 recurrent production of alternative phenotypes provides opportunities to
 canalize the production of particular forms, and that this phenomenon has
 played an important role in generating macro-scale patterns.
description: A_priori_morphospace_analysisThis folder contains examples and code for conducting the a prioiri leaf scoring analysis.Heteroblasty_3_speciesFor each of the three focal species, V. dentatum, V. acerifolium, and V. rafinesquianum leaf images, chain code, and a datasheet are included.Aboretum_heteroblasty_surveyThis folder contains data and images for the 25 species collected at the Arnold Arboretum (Figure 6, Table S1).Viburnum-wide_shape_imagesThis folder contains image files for all leaves used in the Viburnum-wide analyses.
DOI: 10.57841/casdc.0007098
title: 建立高温超导材料失超传播测试平台
DOI: 10.26275/f6k1-me0i
title: Reconstructing Human Vagal Anatomy (REVA) (CWRU & Duke) - Cadaver CT

description: Computed tomography (CT) of embalmed human cadavers.
DOI: 10.5061/dryad.kt13g
title: Data from: Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture

description: Poleward range expansions are commonly attributed to global change, but
 could alternatively be driven by rapid evolutionary adaptation. A
 well-documented example of a range expansion during the past decades is
 provided by the European wasp spider Argiope bruennichi. Using ecological
 niche modeling, thermal tolerance experiments and a genome-wide analysis
 of gene expression divergence, we show that invasive populations have
 adapted to novel climatic conditions in the course of their expansion.
 Their climatic niche shift is mirrored in an increased cold tolerance and
 a population-specific and functionally differentiated gene expression
 response. We generated an Argiope reference genome sequence and used
 population genome re-sequencing to assess genomic changes associated with
 the new climatic adaptations. We find clear genetic differentiation and a
 significant admixture with alleles from East Asian populations in the
 invasive Northern European populations. Population genetic modeling
 suggests that at least some of these introgressing alleles have
 contributed to the new adaptations during the expansion. Our results thus
 confirm the notion that range expansions are not a simple consequence of
 climate change, but are accompanied by fast genetic changes and
 adaptations that may be fuelled through admixture between long separated
 lineages.
description: Cold_shock_recoverySummary of the cold shock recovery experimentPopulation_ModellingResults of the population modellingDifferential_gene_expression_BlastRead counts and blast results for the transcriptome assemblyTranscriptome_Blast_Results_Read_Counts.xlsxGenome-wide genetic divergence and genetic diversityFST_Pi_All_Populations.xlsxArgiope_bruennichi_Transcriptome_Assembly.fastaArgiope_bruennichi_Genome_Assembly.fastaGenome assembly of a Madeiran wasp spider (Argiope bruennichi)Argippe_bruennichi_Reference_genome.fasta
DOI: 10.5061/dryad.jr56h
title: Data from: High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus

description: Marine fish species are characterised by a low degree of population
 differentiation at putatively neutral marker genes. This has been
 traditionally attributed to ecological homogeneity and a lack of obvious
 dispersal barriers in marine habitats, as well as to large (effective)
 population sizes of most marine fish species. The herring (Clupea
 harengus) is a case in point – the levels of population differentiation at
 neutral markers, even across vast geographic areas, are typically very low
 (FST ≈ 0.005). We used a RAD-sequencing approach to identify 5985 novel
 SNPs in the herring, and estimated genome-wide levels of divergence using
 pooled DNA-samples between two Baltic Sea populations separated by 387 km.
 We found a total of 4756 divergent SNPs (79% of all SNPs) between the
 populations, of which 117 showed evidence of substantial divergence,
 corresponding to FST = 0.128 (0.125,0.131) after accounting for possible
 biases due to minor alleles and uneven DNA amplification over the pooled
 samples. This estimate - based on screening many genomic polymorphisms -
 suggests the existence of hitherto unrecognized levels of genetic
 differentiation in this commercially important species, challenging the
 view of genetic homogeneity in marine fish species, and in that of the
 Baltic Sea herring in particular.
description: SequenceDataRaw sequence data and pileupsSNP matrixSNP matrix produced from the .vcf genotype calling file by VCFTOOLSout.012allSNPSNP data (5985 SNPs in total) discovered from both herring populations in vcf 4.1 formatfixed_loci_indexFixed loci (1567 in total) on distinct alleles in the two sample locations. Each element in this file is an index of a SNP in "allSNP.vcf".herring_detailsOffice 2010 excel format table of details concerning the BLAST analysis for the study "High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus". The table columns include "RAD_id", "Reference", "E-value", "Similarity" and "Sample sequence in FASTA". The calculated values are collected with Blast2GO program. For additional descriptions, see README.txt.
DOI: 10.5061/dryad.b301d
title: Data from: Selection, periodicity and potential function for highly iterative Palindrome-1 (HIP1) in cyanobacterial genomes

description: Highly Iterated Palindrome 1 (HIP1, GCGATCGC) is hyper-abundant in most
 cyanobacterial genomes. In some cyanobacteria, average HIP1 abundance
 exceeds one motif per gene. Such high abundance suggests a significant
 role in cyanobacterial biology. However, 20 years of study have not
 revealed whether HIP1 has a function, much less what that function might
 be. We show that HIP1 is 15-300 fold over-represented in genomes analysed.
 More importantly, HIP1 sites are conserved both within and between open
 reading frames, suggesting that their overabundance is maintained by
 selection rather than by continual replenishment by neutral processes,
 such as biased DNA repair. This evidence for selection suggests a
 functional role for HIP1. No evidence was found to support a functional
 role as a peptide or RNA motif or a role in the regulation of gene
 expression. Rather, we demonstrate that the distribution of HIP1 along
 cyanobacterial chromosomes is significantly periodic, with periods ranging
 from 10 to 90 kb, consistent in scale with periodicities reported for
 co-regulated, co-expressed, and evolutionarily correlated genes. The
 periodicity we observe is also comparable in scale to chromosomal
 interaction domains previously described in other bacteria. In this
 context, our findings imply HIP1 functions associated with chromosome and
 nucleoid structure.
description: Synechococcus elongatus
 PCC 7942 transcript data derived from Vijayan et al.
 (2011)syf-transcript-info.zipParameters estimated from sine wave fitting for HIP1 and control hexamersHIP1_periodicity_parameters.zipThe genuine and randomized genomic coordinates for HIP1-like motifsThe genuine and randomized genomic coordinates for HIP1-like motifs, for all the 50 genomes in our studyHIP1_from_50_HIP1_rich_genomes.zipThe genuine and randomized genomic coordinates for control motifs - Part 1The genuine and randomized genomic coordinates for control motifs, for genomes with names that begin with A to N.Ctrl_from_50_HIP1_rich_genomes_Part1.zipThe genuine and randomized genomic coordinates for control motifs - Part 2The genuine and randomized genomic coordinates for control motifs, for genomes with names that begin with O to Z.Ctrl_from_50_HIP1_rich_genomes_Part2.zip
DOI: 10.5061/dryad.r984n
title: Data from: A large fraction of HLA class I ligands are proteasome-generated spliced peptides

description: The proteasome generates the epitopes presented on human leukocyte antigen
 (HLA) class I molecules that elicit CD8+ T cell responses. Reports of
 proteasome-generated spliced epitopes exist, but they have been regarded
 as rare events. Here, however, we show that the proteasome-generated
 spliced peptide pool accounts for one-third of the entire HLA class I
 immunopeptidome in terms of diversity and one-fourth in terms of
 abundance. This pool also represents a unique set of antigens, possessing
 particular and distinguishing features. We validated this observation
 using a range of complementary experimental and bioinformatics approaches,
 as well as multiple cell types. The widespread appearance and abundance of
 proteasome-catalyzed peptide splicing events has implications for
 immunobiology and autoimmunity theories and may provide a previously
 untapped source of epitopes for use in vaccines and cancer immunotherapy.
description: RAW files
 C1Rmass spectrometry data
 for immunopeptidome and cell lysate o C1R cell line. File names include
 mass spectrometry method used.C1R.zipT2 mass spectrometry datamass spectrometry data for immunopeptidome and cell lysate o T2 cell line. File names include mass spectrometry method used.T2.zipGRLCL immunopeptidomemass spectrometry data for immunopeptidome of GRLCL cell line. File names include mass spectrometry method used.GRLCL_immunopeptidome.zipGRLCL lysate mass spectrometry datamass spectrometry data for cell lysate of GRLCL cell line. File names include mass spectrometry method used.GRLCL_lysate.zip
DOI: 10.5061/dryad.5gc82
title: Data from: Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients

description: Background: Induced and spontaneous sputum are used to evaluate the
 airways microbiota. Whether the sputum types can be used interchangeably
 in microbiota research is unknown. Our aim was to compare microbiota in
 induced and spontaneous sputum from COPD patients sampled during the same
 consultation. Methods: COPD patients from Bergen, Norway, were followed
 between 2006/2010, examined during the stable state and exacerbations. 30
 patients delivered 36 sample pairs. DNA was extracted by enzymatic and
 mechanical lysis methods. The V3-V4 region of the 16S rRNA gene was
 PCR-amplified and prepared for paired-end sequencing. Illumina Miseq
 System was used for sequencing, and Quantitative Insights Into Microbial
 Ecology (QIIME) and Stata were used for bioinformatics and statistical
 analyses. Results: Approximately 4 million sequences were sorted into 1004
 different OTUs and further assigned to 106 different taxa. Pair-wise
 comparison of both taxonomic composition and beta-diversity revealed
 significant differences in one or both parameters in 1/3 of sample pairs.
 Alpha-diversity did not differ. Comparing abundances for each taxa
 identified, showed statistically significant differences between the mean
 abundances in induced versus spontaneous samples for 15 taxa when disease
 state was considered. This included potential pathogens like Haemophilus
 and Moraxella. Conclusion: When studying microbiota in sputum samples one
 should take into consideration how samples are collected and avoid the
 usage of both induced and spontaneous sputum in the same study.
description: COPDindspon_mapping_DRYADMetadatafile for Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients, allowing rerun of analysis.COPDindspon_commands_DRYADCommand file for correct sample selection and creation of sub populations as in article: Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients.uc_fast_paramsParameter file necessary for OTU-picking.COPD_BERGEN_Fastq175Resulting Illumina fastq files from 175 sputum samples collected as part of the Bergen COPD Cohort Study (BCCS) and its adjunct Bergen COPD Exacerbation Study (BCES).
DOI: 10.5061/dryad.h5g60
title: Data from: Sticky genomes: using NGS evidence to test hybrid speciation hypotheses

description: Hypotheses of hybrid origin are common. Here we use next generation
 sequencing to test a hybrid hypothesis for a non-model insect with a large
 genome. We compared a putative hybrid triploid stick insect species
 (Acanthoxyla geisovii) with its putative paternal diploid taxon
 (Clitarchus hookeri), a relationship that provides clear predictions for
 the relative genetic diversity within each genome. The parental taxon is
 expected to have comparatively low allelic diversity that is nested within
 the diversity of the hybrid daughter genome. The scale of genome
 sequencing required was conveniently achieved by extracting mRNA and
 sequencing cDNA to examine expressed allelic diversity. This allowed us to
 test hybrid-progenitor relationships among non-model organisms with large
 genomes and different ploidy levels. Examination of thousands of
 independent loci avoids potential problems produced by the silencing of
 parts of one or other of the parental genomes, a phenomenon sometimes
 associated with the process of stabilisation of a hybrid genome.
 Transcript assembles were assessed for evidence of paralogs and/or
 alternative splice variants before proceeding. Comparison of transcript
 assemblies was not an appropriate measure of genetic variability, but by
 mapping reads back to clusters derived from each species we determined
 levels of allelic diversity. We found greater cDNA sequence diversity
 among alleles in the putative hybrid species (Acanthoxyla geisovii) than
 the non-hybrid. The allelic diversity within the putative paternal species
 (Clitachus hookeri) nested within the hybrid-daughter genome, supports the
 current view of a hybrid-progenitor relationship for these stick insect
 species. Next generation sequencing technology provides opportunities for
 testing evolutionary hypotheses with non-model organisms, including, as
 here, genomes that are large due to polyploidy
description: contigs from Clitarchus
 hookeriA fasta file listing the
 longest contigs from Clitarchus hookeri used in the
 analysis.longestContigs_Cl.facontigs from Acanthoxyla geisoviiA fasta file listing the longest contigs from Acanthoxyla geisovii used in the analysis.longestContigs_Ac.faIllumina Fastq files from Acanthoxyla geisoviA compressed file for the Illumina short read sequences from the Acanthoxyla geisovii used in the analysis.Ag_sequence.fq.zipIllumina Fastq files from Clitarchus hookeriA compressed file for the Illumina short read sequences from the Clitarchus hookeri used in the analysis.Ch_sequence.fq.zip
DOI: 10.5061/dryad.ch264
title: Data from: Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss

description: Little information has been gathered regarding the ontogenetic changes
 that contribute to differentiation between resident and migrant
 individuals, particularly before the onset of gross morphological and
 physiological changes in migratory individuals. The aim of this study was
 to evaluate gene expression during early development in Oncorhynchus
 mykiss populations with different life histories, in a tissue known to
 integrate environmental cues to regulate complex developmental processes
 and behaviours. We sampled offspring produced from migrant and resident
 parents, collecting whole embryos prior to the beginning of first feeding,
 and brain tissue at three additional time points over the first year of
 development. RNA sequencing for 32 individuals generated a reference
 transcriptome of 30 177 genes that passed count thresholds. Differential
 gene expression between migrant and resident offspring was observed for
 1982 genes. The greatest number of differentially expressed genes occurred
 at 8 months of age, in the spring a full year before the obvious
 physiological transformation from stream-dwelling parr to sea
 water-adaptable smolts begins for migrant individuals. Sex and age
 exhibited considerable effects on differential gene expression between
 migrants and resident offspring. Differential gene expression was observed
 in genes previously associated with migration, but also in genes
 previously unassociated with early life history divergence. Pathway
 analysis revealed coordinated differential expression in genes related to
 phototransduction, which could modulate photoperiod responsiveness and
 variation in circadian rhythms. The role for early differentiation in
 light sensitivity and biological rhythms is particularly intriguing in
 understanding early brain processes involved in differentiation of
 migratory and resident life history types.
description: Full Trinity
 assemblyFull de novo Trinity
 assembly without filtering for read counts.Trinity_full.fastaTable S1Number of total reads generated for each sample and number of read alignments to transcriptome.TableS1.xlsxTable S2Raw read counts, statistical results and annotations from RNAseq expression and differential expression analysis, including EdgeR results for all genes (components) passing filtering for count thresholds.TableS2.xlsxTable S3Results from alignment of RNAseq genes to RADtags and the Oncorhynchus mykiss genome.TableS3.xlsxTable S4Results from qPCR validation of genes, and correlations between RNAseq expression and qPCR expression values.TableS4.xlsxTable S5Results from Ingenuity Pathway Analysis pathway enrichment analysis.TableS5.xlsxTable S6Results from Ingenuity Pathway Analysis biofunction enrichment analysis.TableS6.xlsxFiltered Trinity assemblyContigs contained in the components that passed filtering for read counts, and ultimately used for differential gene expression analyses.Omykiss_filteredTrinityassembly.fasta
DOI: 10.5281/zenodo.17876521
title: SHM_120832_HST_3D

description: Photogrammetric 3D model of a black earthenware jug from the Early or High Middle Ages, collected from Kalmar, Sweden and currently held in the collections of the National Historical Museums in Stockholm.

 

Link to the Dynamic Collection platform 

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=512

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/2C5D7084-B615-4DCF-A163-5C3C0517D84A