cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.65h9g
title: Data from: Downregulation of endometrial mesenchymal marker SUSD2 causes cell senescence and cell death in endometrial carcinoma cells

description: The cause of death among the majority of endometrial cancer patients
 involves migration of cancer cells within the peritoneal cavity and
 subsequent implantation of cancer spheroids into neighbouring organs. It
 is, thereby, important to identify factors that mediate metastasis. Cell
 adhesion and migration are modified by the mesenchymal stem cell (MSC)
 marker Sushi domain containing 2 (SUSD2), a type I transmembrane protein
 that participates in the orchestration of cell adhesion and migration
 through interaction with its partner Galactosidase-binding soluble-1
 (LGALS1). MSCs have emerged as attractive targets in cancer therapy. Human
 endometrial adenocarcinoma (Ishikawa) cells were treated with TGFβ
 (10ng/ml) for 72h. SUSD2, LGALS1 and MKI67 transcript levels were
 quantified using qRT-PCR. The proportion of SUSD2 positive (SUSD2+) cells
 and SMAD2/3 abundance were quantified by FACS and Western blotting,
 respectively. Senescent cells were identified with β-galactosidase
 staining; cell cycle and cell death were quantified using Propidium Iodide
 staining. Treatment of endometrial cancer cells (Ishikawa cells) with TGFβ
 (10ng/ml) significantly decreased SUSD2 transcript levels and the
 proportion of SUSD2 positive cells. Silencing of SUSD2 using siRNA
 resulted in senescence and cell death of Ishikawa cells via activation of
 SMAD2/3. These findings suggest that SUSD2 counteracts senescence and cell
 death and is thus a potential chemotherapeutic target in human endometrial
 cancer.
description: Zhang et al 2017 SUSD2
 ENCa Data filesFACS histograms, Western
 blot, qPCR and cell death prism files, photographs of cell
 senescence.Zhang_et_al_2017_SUSD2_final.zip
DOI: 10.5061/dryad.qp667
title: Data from: Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines)

description: [No abstract entered]
description: 539.nexThe 539-locus concatenated data set in interleaved nexus alignment format from "Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines)." The alignment contains 605,087 bp for each of 26 in-group turtle species and two outgroup species (Alligator mississippiensis and Gallus gallus).
DOI: 10.6084/m9.figshare.30763463.v4
title: <b>Mild decade-warming shifts soil organic carbon composition without altering total stock in temperate and subtropical forests</b>

description: <b>Mild decade-warming shifts soil organic carbon composition without altering total stock in temperate and subtropical forests</b>
DOI: 10.5061/dryad.bs632
title: Data from: Complexity of possibly gapped histogram and analysis of histogram

description: We demonstrate that gaps and distributional patterns embedded within
 real-valued measurements are inseparable biological and mechanistic
 information contents of the system. Such patterns are discovered through
 data-driven possibly gapped histogram, which further leads to the
 geometry-based analysis of histogram (ANOHT). Constructing a possibly
 gapped histogram is a complex problem of statistical mechanics due to the
 ensemble of candidate histograms being captured by a two-layer Ising
 model. This construction is also a distinctive problem of Information
 Theory from the perspective of data compression via uniformity. By
 defining a Hamiltonian (or energy) as a sum of total coding lengths of
 boundaries and total decoding errors within bins, this issue of computing
 the minimum energy macroscopic states is surprisingly resolved by applying
 the hierarchical clustering algorithm. Thus, a possibly gapped histogram
 corresponds to a macro-state. And then the first phase of ANOHT is
 developed for simultaneous comparison of multiple treatments, while the
 second phase of ANOHT is developed based on classical empirical process
 theory for a tree-geometry that can check the authenticity of branches of
 the treatment tree. The well-known Iris data are used to illustrate our
 technical developments. Also, a large baseball pitching dataset and a
 heavily right-censored divorce data are analysed to showcase the
 existential gaps and utilities of ANOHT.
description: 3pitchersdataThe data is on all Baseball pitches thrown by Arrieta, Dickey, and Hendricks during 2015-16. The zipped folder contains three RData files for the corresponding three pitchers.
DOI: 10.5061/dryad.1pm20
title: Data from: Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea

description: Relatively small volumes of water may contain sufﬁcient environmental DNA
 (eDNA) to detect target aquatic organisms via genetic sequencing. We
 therefore assessed the utility of eDNA to document the diversity of coral
 reef fishes in the central Red Sea. DNA from seawater samples was
 extracted, amplified using fish-specific 16S mitochondrial DNA primers,
 and sequenced using a metabarcoding workflow. DNA sequences were assigned
 to taxa using available genetic repositories or custom genetic databases
 generated from reference fishes. Our approach revealed a diversity of
 conspicuous, cryptobenthic, and commercially relevant reef fish at the
 genus level, with select genera in the family Labridae over-represented.
 Our approach, however, failed to capture a significant fraction of the
 fish fauna known to inhabit the Red Sea, which we attribute to limited
 spatial sampling, amplification stochasticity, and an apparent lack of
 sequencing depth. Given an increase in fish species descriptions,
 completeness of taxonomic checklists, and improvement in species-level
 assignment with custom genetic databases as shown here, we suggest that
 the Red Sea region may be ideal for further testing of the eDNA approach.
description: Unfiltered 16S fish
 mitochondrial DNA sequences amplified from seawater samples collected in
 the Red SeaUnfiltered 16S fish
 mitochondrial DNA sequences amplified from seawater samples collected at
 inshore, midshore, and offshore coral reefs, as well as a boat harbor
 along the central Red Sea coastline near Thuwal, Saudi Arabia. File names
 are structured as follows:
 sequencingrun_gene_samplesource_sitename_sampleID_forwardMIDtag_reverseMIDtag. Example: FTP77_Fish16S_Water_TahlaNorthExposed_AWFSF151469_F750_R637.Unfiltered_sequences_16Sfish_eDNA_RedSea_CoralReefs_DiBattista_et_al_2017.zip
DOI: 10.5061/dryad.t91s5
title: Data from: Investigation of the acid/base behaviour of the opium alkaloid thebaine in LC-ESI-MS mobile phase by NMR spectroscopy

description: As part of a research program to establish an analytical method for the
 simultaneous detection of the five major opium alkaloids in poppy seeds by
 liquid chromatography-electrospray ionization-mass spectrometry
 (LC-ESI-MS) it was discovered that the inclusion of thebaine produced two
 peaks for the same compound. This was in contrast to the effective
 simultaneous detection, by LC-ESI-MS, of morphine, codeine, papaverine and
 noscapine. The presence of these two peaks for thebaine was investigated
 using nuclear magnetic resonance (NMR) spectroscopy with deuterated
 solvents to emulate the mobile phase conditions experienced. It was found
 that the presence of 80%, or higher ratios of, water caused two epimeric
 forms of thebaine to be formed; this explained the presence of two peaks
 on the chromatogram. In contrast, when a lower water content was used with
 1% acetic acid, one stable form of thebaine could be analyzed and resulted
 in a single peak visible in the subsequent chromatography.
description: ESMThebaine NMR
 data
DOI: 10.5061/dryad.20257
title: Data from: The grass was greener: repeated evolution of specialized morphologies and habitat shifts in ghost spiders following grassland expansion in South America

description: While grasslands, one of Earth’s major biomes, are known for their close
 evolutionary ties with ungulate grazers, these habitats are also paramount
 to the origins and diversification of other animals. Within the primarily
 South American spider subfamily Amaurobioidinae (Anyphaenidae), several
 species are found living in the continent’s grasslands, with some
 displaying putative morphological adaptations to dwelling unnoticed in the
 grass blades. Here, a dated molecular phylogeny provides the backbone for
 analyses revealing the ecological and morphological processes behind these
 spiders’ grassland adaptations. The multiple switches from Patagonian
 forests to open habitats coincide with the expansion of South America’s
 grasslands during the Miocene, while the specialized morphology of several
 grass-dwelling spiders originated at least three independent times and is
 best described as the result of different selective regimes operating on
 macroevolutionary timescales. Although grass-adapted lineages evolved
 towards different peaks in adaptive landscape, they all share one
 characteristic: an anterior narrowing of the prosoma allowing spiders to
 extend the first two pairs of legs, thus maintaining a slender resting
 posture in the grass blade. By combining phylogenetic, morphological, and
 biogeographic perspectives we disentangle multiple factors determining the
 evolution of a clade of terrestrial invertebrate predators alongside their
 biomes.
description: Supporting Information
 File 1Supplementary
 TablesSupporting Information
 File 2Extra Materials and
 MethodsSupporting Information
 File 3R scripts and input
 filesSupporting Information
 File 4Supplementary
 Figures
DOI: 10.5061/dryad.03v3n
title: Data from: Identifying the most surprising victims of mass extinction events: an example using Late Ordovician brachiopods

description: Mass extinction events are recognized by increases in extinction rate and
 magnitude and, often, by changes in the selectivity of extinction. When
 considering the selective fingerprint of a particular event, not all taxon
 extinctions are equally informative: some would be expected even under a
 ‘background’ selectivity regime, whereas others would not and thus require
 special explanation. When evaluating possible drivers for the extinction
 event, the latter group is of particular interest. Here, we introduce a
 simple method for identifying these most surprising victims of extinction
 events by training models on background extinction intervals and using
 these models to make per-taxon assessments of ‘expected’ risk during the
 extinction interval. As an example, we examine brachiopod genus
 extinctions during the Late Ordovician Mass Extinction and show that
 extinction of genera in the deep-water ‘Foliomena fauna’ was particularly
 unexpected given preceding Late Ordovician extinction patterns.
description: Appendix
 S1Spreadsheet with local
 stratigraphic ranges of Late Ordovician-Early Silurian
 brachiopods.Local.Ranges.csvAppendixS2R code to reproduce all analyses and figures.
DOI: 10.5061/dryad.pn5kg
title: Data from: Evidence for complex life cycle constraints on salamander body form diversification

description: Metazoans display a tremendous diversity of developmental patterns,
 including complex life cycles composed of morphologically disparate
 stages. In this regard, the evolution of life cycle complexity promotes
 phenotypic diversity. However, correlations between life cycle stages can
 constrain the evolution of some structures and functions. Despite the
 potential macroevolutionary consequences, few studies have tested the
 impacts of life cycle evolution on broad-scale patterns of trait
 diversification. Here we show that larval and adult salamanders with a
 simple, aquatic-only (paedomorphic) life cycle had an increased rate of
 vertebral column and body form diversification compared to lineages with a
 complex, aquatic-terrestrial (biphasic) life cycle. These differences in
 life cycle complexity explain the variations in vertebral number and adult
 body form better than larval ecology. In addition, we found that lineages
 with a simple terrestrial-only (direct developing) life cycle also had a
 higher rate of adult body form evolution than biphasic lineages, but still
 10-fold lower than aquatic-only lineages. Our analyses demonstrate that
 prominent shifts in phenotypic evolution can follow long-term transitions
 in life cycle complexity, which may reflect underlying stage-dependent
 constraints.
description: 1000 Salamander
 ChronogramsPosterior distribution
 of 1000 (post burnin) Bayesian chronograms including 516 salamander taxa.
 Analysis was performed in BEAST and based on 7401 character states derived
 from seven protein-coding genes: three mitochondrial (Co1, Cytb, ND2) and
 four nuclear (BDNF, Pomc, RAG1, Slc8a3). See paper and Supplemental
 Appendix 1 for details.Bonett and Blair
 PNAS_2017_Salamander_Chronograms_Dryad.nex
DOI: 10.15468/dl.atrr7t
title: Occurrence Download

description: A dataset listing the 53101 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 53101 records were derived from 901 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001492-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b20ps
title: Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

description: Chromosomal rearrangements such as inversions can play a crucial role in
 maintaining polymorphism underlying complex traits and contribute to the
 process of speciation. In Atlantic cod (Gadus morhua), inversions of
 several megabases have been identified that dominate genomic
 differentiation between migratory and non-migratory ecotypes in the
 Northeast Atlantic. Here, we show that the same genomic regions display
 elevated divergence and contribute to ecotype divergence in the Northwest
 Atlantic as well. The occurrence of these inversions on both sides of the
 Atlantic Ocean reveals a common evolutionary origin, predating the more
 than 100,000 years old trans-Atlantic separation of Atlantic cod. The
 long-term persistence of these inversions indicates that they are
 maintained by selection, possibly facilitated by co-evolution of genes
 underlying complex traits. Our data suggest that migratory behaviour is
 derived from more stationary, ancestral ecotypes. Overall, we identify
 several large genomic regions - each containing hundreds of genes – likely
 involved in the maintenance of genomic divergence in Atlantic cod on both
 sides of the Atlantic Ocean.
description: BergEtAl2017_AtlanticCod_TransatlanticDataset_PLINK-formatSNP array data for 316 individuals of Atlantic cod (Gadus morhua), genotyped at 8,165 loci in standard PLINK file format. The PLINK file format consists of two files, a map file and a ped file. In the map file, the first column defines the linkage group, the second column contains the loci names (dbSNP accession numbers), the third line describes the position within the linkage groups (here all are set to 0) and the fourth column defines the order of the SNPs within each linkage group. In the ped file, column one is used to separate the populations (pop-1 to pop-9), column 2 defines the individuals within each population (denoted as the population abbreviation followed by the individual number) where the populations are abbreviated as follows: Can-N_PB = Placentia Bay, Can-N_SG = Southern Gulf of St. Lawrence, Can-S_SB = Sambro, Can-S_GM = Gulf of Maine, Can-S_BB = Browns Bank, Ice_F = Iceland Frontal, Ice_C = Iceland Coastal, NEAC = Northeast Arctic cod, NCC = Norwegian coastal cod. The genotypes are given as numbers from column 7 and onwards, where 1=A, 2=C, 3=G, 4=T. (For a thorough description of the PLINK format, please see https://www.cog-genomics.org/plink). All SNPs are referred to by their database of Single Nucleotide Polymorphisms (dbSNP) accession numbers, available from: http://www.ncbi.nlm.nih.gov/SNP.BergEtAl2017_AtlanticCod_TransatlanticDataset.zip
DOI: 10.15468/dl.4v8nfv
title: Occurrence Download

description: A dataset containing 654411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation, Observation)",
 "Continent is Oceania",
 "Country is Australia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Orchidaceae"
 ]
}

 The dataset includes 654411 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001490-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q6p50
title: Data from: Centennial-scale reductions in nitrogen availability in temperate forests of the United States

description: Forests cover 30% of the terrestrial Earth surface and are a major
 component of the global carbon (C) cycle. Humans have doubled the amount
 of global reactive nitrogen (N), increasing deposition of N onto forests
 worldwide. However, other global changes—especially climate change and
 elevated atmospheric carbon dioxide concentrations—are increasing demand
 for N, the element limiting primary productivity in temperate forests,
 which could be reducing N availability. To determine the long-term,
 integrated effects of global changes on forest N cycling, we measured
 stable N isotopes in wood, a proxy for N supply relative to demand, on
 large spatial and temporal scales across the continental U.S.A. Here, we
 show that forest N availability has generally declined across much of the
 U.S. since at least 1850 C.E. with cool, wet forests demonstrating the
 greatest declines. Across sites, recent trajectories of N availability
 were independent of recent atmospheric N deposition rates, implying a
 minor role for modern N deposition on the trajectory of N status of North
 American forests. Our results demonstrate that current trends of global
 changes are likely to be consistent with forest oligotrophication into the
 foreseeable future, further constraining forest C fixation and potentially
 storage.
description: InputData15Nmaster data fileInputDataSiteSite level dataInputBAI01Basal Area Index data for trees from tree ringsModelPlot.ContinentalNR code for running analyses. Includes analyses and plots. Will output to pdf and output text file.
DOI: 10.5061/dryad.707kc
title: Data from: Identification of the Beagle 2 lander on Mars

description: The 2003 Beagle 2 Mars lander has been identified in Isidis Planitia at
 90.43° E, 11.53° N, close to the predicted target of 90.50° E, 11.53° N.
 Beagle 2 was an exobiology lander designed to look for isotopic and
 compositional signs of life on Mars, as part of the European Space Agency
 Mars Express (MEX) mission. The 2004 recalculation of the original landing
 ellipse from a 3-sigma major axis from 174 km to 57 km, and the
 acquisition of Mars Reconnaissance Orbiter High Resolution Imaging Science
 Experiment (HiRISE) imagery at 30 cm per pixel across the target region,
 led to the initial identification of the lander in 2014. Following this,
 more HiRISE images, giving a total of 15, including red and blue-green
 colours, were obtained over the area of interest and searched, which
 allowed sub-pixel imaging using super high-resolution techniques. The size
 (approx. 1.5 m), distinctive multilobed shape, high reflectivity relative
 to the local terrain, specular reflections, and location close to the
 centre of the planned landing ellipse led to the identification of the
 Beagle 2 lander. The shape of the imaged lander, although to some extent
 masked by the specular reflections in the various images, is consistent
 with deployment of the lander lid and then some or all solar panels.
 Failure to fully deploy the panels—which may have been caused by damage
 during landing—would have prohibited communication between the lander and
 MEX and commencement of science operations. This implies that the main
 part of the entry, descent and landing sequence, the ejection from MEX,
 atmospheric entry and parachute deployment, and landing worked as planned
 with perhaps only the final full panel deployment failing.
description: Beagle2 Appendix_Search
 Study detailsSpreadsheet with details
 of search and red:blue-green colour characterisation of the
 lander.Beagle2_and_RDR Appendix_Search
 Study details_V6.xlsxBeagle 2 lander animated
 GIFBeagle 2 lander animated
 GIF from HiRISE imagesRear Cover candidate
 animated GIFRear Cover candidate
 animated GIF from HiRISE imagesParachute candidate
 animated GIFRear Cover candidate
 animated GIF from HiRISE images
DOI: 10.5061/dryad.s7h6b
title: Data from: Phylogenetic and morphological diversity of the Etheostoma zonistium species complex with the description of a new species endemic to the Cumberland Plateau of Alabama

description: We provide a description of the Blueface Darter, Etheostoma cyanoprosopum,
 which is distributed in the upper Sipsey Fork of the Mobile Basin and the
 upper portion of the Bear Creek system in the Tennessee River Drainage.
 The distinctiveness of Etheostoma cyanoprosopum is assessed through
 analysis of morphological variation and molecular phylogenetic diversity
 within the Etheostoma zonistium species complex. In addition to analyzing
 disparity of morphometric and meristic traits, we present phylogenetic
 analyses of a mitochondrial gene and two nuclear genes and identify
 genetic clusters through analysis of 25 microsatellite loci. In the
 mitochondrial DNA (mtDNA) gene tree, Etheostoma cyanoprosopumis resolved
 as the sister lineage to a clade containing all other species of the
 Etheostoma zonistium complex. Etheostoma zonistium is paraphyletic with
 respect to both Etheostoma pyrrhogaster and Etheostoma cervus, which do
 not resolve as sister species in the mtDNA gene tree. The two nuclear gene
 trees are much less resolved, but the S7 ribosomal protein intron 1 (S7)
 gene tree resolves Etheostoma cyanoprosopum and all sampled populations of
 Etheostoma zonistium as a clade with strong Bayesian posterior node
 support. Etheostoma cyanoprosopum is morphologically differentiated from
 Etheostoma zonistium by a shallower body, a more elongate nape, a higher
 number of lateral line scales, a higher number of transverse scale rows,
 and differences in coloration.
description: data_from_E_cyanoprosopum_descriptionData used in species description and phylogenetic analyses.cyanoprosopum_description_data.zip