cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.125p4
title: Data from: Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands

description: Global biodiversity is declining rapidly as a consequence of anthropogenic
 changes to the environment. Traditional diversity indices such as species
 richness have been used to assess biodiversity, but recent arguments call
 for a more comprehensive assessment that includes both phylogenetic and
 functional diversity (PD and FD, respectively). Many PD metrics have been
 developed, but few empirical studies have compared metrics across sites
 with the goal of understanding their application to characterizing
 biodiversity. In this study, 17 PD metrics, four traditional diversity
 indices, and one measure of FD were calculated and compared between two
 Nebraska grasslands. PD metrics were calculated from robust phylogenies
 estimated from next-generation sequencing data of 45 species. Traditional
 indices were calculated using species abundance data, and FD was
 quantified by measuring the phylogenetic signal, K, of specific leaf area
 (SLA). Results showed that PD metrics and traditional indices were not
 always correlated, and various PD metrics characterized biodiversity
 differently. In addition, phylogenies estimated from &gt;80 genes were
 more robust than single- or dual-gene phylogenies resulting in more
 reliable PD metrics. K of SLA indicated random trait assembly in all
 sites. Results suggested that metrics that identify phylogenetic structure
 and relatedness can provide information to conservation planners about the
 ability of a community to persist in an unpredictable future. A
 combination of these results with those of future investigations applying
 PD and FD metrics to varying communities will support concrete
 recommendations to conservation planners about how to incorporate these
 metrics into the selection of priority regions.
description: rosids-cpmtnucSequence alignment of 73 plastid genes, nine mitochondrial genes, and three nuclear repeat regions for 42 rosid taxa plus 3 outgroupsrosids-matKSequence alignment of the plastid matK gene for 42 rosid taxa plus 3 outgroupsrosids-rbcLSequence alignment of the plastid rbcL gene for 42 rosid taxa plus 3 outgroupsrosids-matKrbcLSequence alignment of concatenated plastid matK and rbcL genes for 42 rosid taxa plus 3 outgroups
DOI: 10.5061/dryad.s5q88
title: Data from: Temporal transcriptomics suggest that twin-peaking genes reset the clock

description: The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior
 and physiology, yet a detailed understanding of its coordinated
 transcriptional programmes is lacking. To reveal the finer details of
 circadian variation in the mammalian SCN transcriptome we combined
 laser-capture microdissection and RNA-seq over a 24-hour light/dark cycle.
 We show that 7-times more genes exhibited a classic sinusoidal expression
 signature than previously observed in the SCN. Another group of 766 genes
 unexpectedly peaked twice, near both the start and end of the dark phase;
 this twin-peaking group is significantly enriched for synaptic
 transmission genes that are crucial for light-induced phase shifting of
 the circadian clock. 341 intergenic non-coding RNAs, together with novel
 exons of annotated protein-coding genes, including Cry1, also show
 specific circadian expression variation. Overall, our data provide an
 important chronobiological resource (www.wgpembroke.com/shiny/SCNseq/) and
 allow us to propose that transcriptional timing in the SCN is gating clock
 resetting mechanisms.
description: Primer_list_S1Primer listGeneInfo_S2Table with statistics and general information for each gene surveyed in the SCN.LincInfo_S3Table with statistics and general information for each multi-exonic lincRNA expressed in the SCN.NovelExons_S4Table with coordinates and additional information for identified novel exons expressed in the SCN.LincRNA_3187A GTF file of the 3187 multi-exonic lincRNA expressed in the SCN.GSE72095All raw fastq data files. Both raw and normalised count tables. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72095
DOI: 10.5061/dryad.3vj50
title: Data from: Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale

description: The evolutionary timescale of angiosperms has long been a key question in
 biology. Molecular estimates of this timescale have shown considerable
 variation, being influenced by differences in taxon sampling, gene
 sampling, fossil calibrations, evolutionary models, and choices of priors.
 Here, we analyze a data set comprising 76 protein-coding genes from the
 chloroplast genomes of 195 taxa spanning 86 families, including novel
 genome sequences for 11 taxa, to evaluate the impact of models, priors,
 and gene sampling on Bayesian estimates of the angiosperm evolutionary
 timescale. Using a Bayesian relaxed molecular-clock method, with a core
 set of 35 minimum and two maximum fossil constraints, we estimated that
 crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a
 range of additional sensitivity and subsampling analyses, we found that
 our date estimates were generally robust to large changes in the
 parameters of the birth-death tree prior and of the model of rate
 variation across branches. We found an exception to this when we
 implemented fossil calibrations in the form of highly informative gamma
 priors rather than as uniform priors on node ages. Under all other
 calibration schemes, including trials of seven maximum age constraints, we
 consistently found that the earliest divergences of angiosperm clades
 substantially predate the oldest fossils that can be assigned
 unequivocally to their crown group. Overall, our results and experiments
 with genome-scale data suggest that reliable estimates of the angiosperm
 crown age will require increased taxon sampling, significant
 methodological changes, and new information from the fossil record.
description: Appendix
 1Appendix 1:
 Supplementary materials and methods: DNA Extraction, Library Preparation,
 and High-Throughput SequencingSI_alignment_195_taxaAlignment (in nexus format) of 76 protein-coding chloroplast genes from 193 angiosperm (including 11 novel taxa) and two gymnosperm outgroup taxa. Gene boundaries are indicated in the character set block under the alignment.Supplementary FiguresThis file contains all of the supplementary figures from the study "Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale". In total, there are 52 supplementary figures within. Of these, 48 are tree files (five phylograms, four rategrams, 39 chronograms) that can be read in FigTree or a similar program. There is also a PDF with figure captions for each of the supplementary figures.Supplementary TablesThis file contains the four supplementary tables that are referred to in the main text of our study "Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale".
DOI: 10.5061/dryad.dh11k
title: Data from: Hollows in living trees develop slowly but considerably influence the estimate of forest biomass

description: The decomposition of wood inside living tree hollows influences forest
 structure and processes. Although the decomposition rate controls the
 formation of hollows, it has not previously been measured. In an
 old-growth subtropical montane evergreen broad-leaved forest in south-west
 China, we measured respiration rates of decaying wood inside living tree
 hollows, logs (downed tree trunks) and snags (standing dead trees) using
 infrared CO2 analysis. We compared stem radial growth rates to the
 horizontal expansion rates of hollows. We also estimated the proportion of
 hollows to total stem volume and the time required to form nesting
 hollows. Overall, decaying wood inside living tree hollows had
 significantly higher wood density but lower a moisture content and
 respiration rate than logs. Wood moisture content and wood density
 significantly affected the respiration rates of wood inside tree hollows
 and logs and snags. The average respiration rate of wood inside tree
 hollows (0·16 ± 0·02 μmol kg−1 s−1) was 49% lower than in logs and 34%
 lower than in snags. The proportion of stem volume occupied by hollows was
 8·0% in this forest. The radial expansion rate of tree hollows was 2·0 mm
 year−1, which was slightly less than the stem radial growth rate. The rate
 of vertical expansion of hollows was eight times higher than radial
 expansion. At these rates, it would require 50–100 years for the formation
 of hollows large enough for honeybees Apis cerana cerana to nest. We
 conclude that wood decomposition inside tree hollows is more strongly
 limited by moisture content than in logs, and a very long time is required
 to form nesting hollows by decomposition. However, the decomposition of
 wood inside living tree hollows can considerably influence estimates of
 stem biomass in old-growth forests.
description: respiration moisture and
 density dataContains respiration,
 moisture and density of dead wood samples from living tree hollows, snags
 and logs in the rainy and dry seasonsZheng-FE2014-01013 respiration
 moisture and density data 201508013
 submit.xlsrespiration and wood
 type and season dataContains respiration
 rate, moisture content and wood density of individuals of tree hollows,
 snags and logs for different species in the rainy and dry seasons in
 plots.Zheng-FE2014-01013 respiration
 and wood type and season data 20150813
 submit.xlsSample tree
 dataContains height, DBH and
 proportion of hollow volume to stem volume for sample
 trees.Zheng-FE2014-01013 Sample tree
 data 20150813 submit.xlstree growth
 dataContains tree DBH in
 2005 and 2010, and annual increment (mm) of diameter at breast height for
 each tree in a 1-ha plotZheng-FE2014-01013 tree growth
 data 20150813 submit.xlstree hollow proportion
 in six plot dataContains tree DBH, stem
 biomass regression equation, stem biomass and hollow proportion, and stem
 mass loss for each tree in six plotZheng-FE2014-01013 tree hollow
 proportion in six plot data 20150813
 submit.xls
DOI: 10.5061/dryad.6r4j8
title: Data from: The Beothukis/Culmofrons problem and its bearing on Ediacaran macrofossil taxonomy: evidence from an exceptional new fossil locality

description: The late Ediacaran siliciclastic successions of eastern Newfoundland,
 Canada, are renowned for their fossils of soft-bodied macro-organisms,
 which may include some of the earliest animals. Despite the potential
 importance of such fossils for evolutionary understanding, the taxonomic
 framework within which Ediacaran macrofossils are described is not clearly
 defined. Rangeomorphs from a newly discovered fossil surface on the
 Bonavista Peninsula, Newfoundland, require us to reconsider contemporary
 use of morphological characters to distinguish between genera and species
 within Ediacaran taxa. The new surface exhibits remarkable preservational
 fidelity, resolving features smaller than 0.1 mm in dimension in both
 frondose and non-frondose taxa. Such preservation permits the recognition
 of rarely observed fourth- and fifth-order rangeomorph branching, offering
 unparalleled opportunities to investigate the fine-scale construction of
 rangeomorph taxa including Culmofrons plumosa Laflamme et al., 2012. Our
 observations enable resolution of taxonomic issues relating to
 rangeomorphs, specifically overlap between the diagnoses of the frondose
 genera Beothukis Brasier and Antcliffe, 2009 and Culmofrons. We propose a
 taxonomic framework for all Ediacaran macrofossils whereby gross
 architecture, the presence/absence of discrete morphological characters
 and consideration of growth programme are used to distinguish genera,
 whereas morphometric or continuous characters define taxa at the species
 level. On the basis of its morphological characters, Culmofrons plumosa is
 herein synonymized to a species (Beothukis plumosa comb. nov.) within the
 genus Beothukis. This discussion emphasizes the need to standardize the
 taxonomic approach used to describe Ediacaran macrofossil taxa at both the
 genus and species levels, and raises important considerations for future
 formulation of higher-level taxonomic groups.
description: Liu et al Appendix
 S1Information on the
 sedimentology and stratigraphic setting of the MUN Surface, and six
 additional figures.MUN Beothukis
 plateHigh resolution image of
 Supplementary Figure 6.
DOI: 10.5061/dryad.521j5
title: Data from: Characterization of a novel fusion gene EML4-NTRK3 in a case of recurrent congenital fibrosarcoma

description: We describe the clinical course of a recurrent case of congenital
 fibrosarcoma diagnosed in a 9-mo-old boy with a history of hemimelia.
 Following complete surgical resection of the primary tumor, the patient
 subsequently presented with bulky bilateral pulmonary metastases 6 mo
 following surgery. Molecular characterization of the tumor revealed the
 absence of the prototypical ETV6-NTRK3 translocation. However, tumor
 characterization incorporating cytogenetic, array comparative genomic
 hybridization, and RNA sequencing analyses, revealed a somatic
 t(2;15)(2p21;15q25) translocation resulting in the novel fusion of EML4
 with NTRK3. Cloning and expression of EML4-NTRK3 in murine fibroblast NIH
 3T3 cells revealed a potent tumorigenic phenotype as assessed in vitro and
 in vivo. These results demonstrate that multiple fusion partners targeting
 NTRK3 can contribute to the development of congenital fibrosarcoma.
description: 1328201287_253058711593_1_4Agilent array comparative genomic hybridization data for the described tumor.
DOI: 10.5061/dryad.1jc33
title: Data from: Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood

description: Phragmotic or “door head” ants have evolved independently in several ant
 genera across the world, but in Africa only one case has been documented
 until now. Carebara elmenteitae (Patrizi) is known from only a single
 phragmotic major worker collected from sifted leaf-litter near Lake
 Elmenteita in Kenya, but here the worker castes of two species collected
 from Kakamega Forest, a small rainforest in Western Kenya, are studied.
 Phragmotic major workers were previously identified as Carebara
 elmenteitae and non-phragmotic major and minor workers were assigned to C.
 thoracica (Weber). Using evidence of both morphological and
 next-generation sequencing analysis, it is shown that phragmotic and
 non-phragmotic workers of the two different species are actually the same
 and that neither name – C. elmenteitae or C. thoracica – correctly applies
 to them. Instead, this and another closely related species from Ivory
 Coast are both morphologically different from C. elmenteitae, and thus
 they are described as the new species Carebara phragmotica sp. n. and
 Carebara lilith sp. n.
description: Fischer et al. Carebara
 phragmotica ML tree fileThis file contains the
 ML tree, generated with the alignment file and the described
 methods.Fischer_etal_Carebara_MLtree.treFischer_et al_Carebara phragmotica_alignmentThis file contains the full alignment used to generate the ML tree.Fischer_etal_Carebara_alignment.nexCarebara specimens collection data + extraction codesThis file contains all relevant identification and collection data as well as CASENT and DNA extractions codes.Carebara specimens coll data+extraction codes.xlsx
DOI: 10.5061/dryad.g4n5m
title: Data from: Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome

description: Reconstructing the feeding mode of the latest common ancestor of
 deuterostomes is key to elucidating the early evolution of feeding in
 chordates and allied phyla; however, it is debated whether the ancestral
 deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To
 address this, we evaluated the hydrodynamics of feeding in a group of
 fossil stem-group echinoderms (cinctans) using computational fluid
 dynamics. We simulated water flow past three-dimensional digital models of
 a Cambrian fossil cinctan in a range of possible life positions, adopting
 both passive tentacular feeding and active pharyngeal filter feeding. The
 results demonstrate that an orientation with the mouth facing downstream
 of the current was optimal for drag and lift reduction. Moreover, they
 show that there was almost no flow to the mouth and associated marginal
 groove under simulations of passive feeding, whereas considerable flow
 towards the animal was observed for active feeding, which would have
 enhanced the transport of suspended particles to the mouth. This strongly
 suggests that cinctans were active pharyngeal filter feeders, like modern
 enteropneust hemichordates and urochordates, indicating that the ancestral
 deuterostome employed a similar feeding strategy.
description: Model_S1Digital reconstruction of Protocinctus in VAXML format, compressed in a ZIP archive. To view, unzip the .zip file and open the unpacked .vaxml file with SPIERSview (program and documentation available from www.spiers-software.org).Model S2Digitally restored model of Protocinctus (operculum in ‘closed’ position) in IGES format, compressed in a ZIP archive. To view, unzip the .zip file and open the unpacked .igs file with FreeCAD (program and documentation available from www.freecadweb.org).Model_S2.zipModel S3Digitally restored model of Protocinctus (operculum in ‘open’ position) in IGES format, compressed in a ZIP archive. To view, unzip the .zip file and open the unpacked .igs file with FreeCAD (program and documentation available from www.freecadweb.org).Model_S3.zipVideo S1Results of a CFD simulation using a time-dependent solver to show flow time-evolution. Simulation of passive tentacular feeding with Protocinctus oriented at 180° to the current (ambient velocity of 0.2 m/s) and with the ventral swelling buried within the sediment, visualized as two-dimensional plots (horizontal cross-sections) of flow velocity magnitude (false-colour scale different for each ambient flow velocity) with streamlines over the first 10 s with a time step size of 0.01 s.Video_S1.avi
DOI: 10.5061/dryad.8br20
title: Data from: Selection of Pairings Reaching Evenly Across the Data (SPREAD): a simple algorithm to design maximally informative fully crossed mating experiments

description: We present a novel algorithm for the design of crossing experiments. The
 algorithm identifies a set of individuals (a "crossing-set")
 from a larger pool of potential crossing-sets by maximizing the diversity
 of traits of interest, for example, maximizing the range of genetic and
 geographic distances between individuals included in the crossing-set. To
 calculate diversity, we use the mean nearest neighbor distance of crosses
 plotted in trait space. We implement our algorithm on a real dataset of
 Neurospora crassa strains, using the genetic and geographic distances
 between potential crosses as a two-dimensional trait space. In simulated
 mating experiments, crossing-sets selected by our algorithm provide better
 estimates of underlying parameter values than randomly chosen
 crossing-sets.
description: Mating Types of
 StrainsThis file contains the
 mating type information for all the Neurospora crassa strains used to test
 the SPREAD algorithm. The column labelled "FGSC" lists the
 Fungal Genetics Stock Center strain IDs and the column labelled
 "mat" lists the mating type. "AA" = mating type
 "A", "a" = mating type
 "a".strain_mating_type.csvAll pairwise matings with genetic and geographic distance dataThis CSV contains all 576 possible pairwise matings between the 24 mat-a and 24 mat-A Neurospora crassa strains used to test the SPREAD algorithm. FGSC1 and FGSC2 are the strain IDs of the pair, GeneticDistance is the genetic distance between the pair (number of different SNPs between parents) and GeographicDistance is km between strain isolation locales.all_matings_distance.csvSimulated spore production data for all pairwise matingsThis CSV contains the simulated spore production data used to compute the population GLMM. Subsets of this data-set were used to calculate sample GLMMs. Please see readme file for information on column names.all_matings_spore_simulations.csvFigure2 R ScriptR script to produce figure 2 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.Figure2_SPREAD.RFigure3 Table2 R scriptR script to produce figure 3 and table 2 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.Figure3_Table2_SPREAD.RFigure4 R ScriptR script to produce figure 4 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.Figure4_SPREAD.RTable1 R ScriptR script to produce Table 2 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.Table1_SPREAD.RSPREAD_RdataThis zip file contains 6 rdata files and one CSV file used to produce the figures. Please refer to the ReadMe for descriptions.
DOI: 10.5061/dryad.d6rh9
title: Data from: Utility of real-time shear wave elastography in the assessment of testicular torsion

description: Real-time shear-wave elastography (SWE) is a newly developed method which
 can obtain the stiffness of tissues and organs based on tracking of shear
 wave propagation through a structure. Several studies have demonstrated
 its potential in the differentiation between diseased and normal tissue in
 clinical practices, however the applicability to testicular disease has
 not been well elucidated. We investigated the feasibility and
 reproducibility of SWE in the detection of testicular torsion. This
 prospective study comprised 15 patients with complete testicular torsion.
 Results obtained from SWE along with conventional gray-scale and color
 Doppler sonography and post-operative pathology were compared. The results
 revealed that (i) the size of injured testis was increased and the twisted
 testis parenchyma was heterogeneous. The blood flow signals in injured
 testis were barely visible or absent; (ii) The Young’s modulus, including
 Emean, Emax, Emin and SD values in the border area of torsional testis
 were higher than those of normal testis (Emean, 78.07±9.01kPa vs
 22.0±5.10kPa; Emax,94.07±6.53kPa vs 27.87±5.78kPa; Emin, 60.73±7.84 kPa vs
 18.90±4.39kPa; SD, 7.67±0.60 kPa vs 2.30±0.36 kPa, [P&lt;0.05]); The
 Emax and SD values in the central area of the torsional testis were higher
 than the corresponding area of the normal testis (Emax, 8.23±0.30 kPa vs
 3.97±0.95kPa; SD, 1.5±0.26kPa vs 0.67±0.35kPa,[P&lt;0.05]) and Emin
 values was lower than those of normal testicles(0.93±0.51kPa vs
 1.6±0.36kPa; [P&lt;0.05]); (iii) The Young's modulus measurement
 between two physicians showed good agreement. The pathological findings
 were accordance with SWE measurement. SWE is a non-invasive, convenient
 and high reproducible method and may serve as an important alternative
 tool in the diagnosis and monitoring the progression of the acute
 scrotums, in additional to conventional Doppler sonography.
description: Figure