cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70f4t
title: Data from: Tracking time evolution of collective attention clusters in twitter: time evolving nonnegative matrix factorisation

description: Micro-blogging services, such as Twitter, offer opportunities to analyse
 user behaviour. Discovering and distinguishing behavioural patterns in
 micro-blogging services is valuable. However, it is difficult and
 challenging to distinguish users, and to track the temporal development of
 collective attention within distinct user groups in Twitter. In this
 paper, we formulate this problem as tracking matrices decomposed by
 Nonnegative Matrix Factorisation for time-sequential matrix data, and
 propose a novel extension of Nonnegative Matrix Factorisation, which we
 refer to as Time Evolving Nonnegative Matrix Factorisation (TENMF). In our
 method, we describe users and words posted in some time interval by a
 matrix, and use several matrices as time-sequential data. Subsequently, we
 apply Time Evolving Nonnegative Matrix Factorisation to these
 time-sequential matrices. TENMF can decompose time-sequential matrices,
 and can track the connection among decomposed matrices, whereas previous
 NMF decomposes a matrix into two lower dimension matrices arbitrarily,
 which might lose the time-sequential connection. Our proposed method has
 an adequately good performance on artificial data. Moreover, we present
 several results and insights from experiments using real data from
 Twitter.
description: Dataset from Tracking
 Time Evolution of Collective Attention Clusters in Twitter: Time Evolving
 Nonnegative Matrix FactorisationThis dataset contains
 tweets ID posted before and after one week Tohoku Earthquake and iPhone 4
 announcement. We collected 11,418,600 tweets posted in the interval of 301
 from 4th March 2011 to 16th March and 2,319,874 tweets posted in the
 interval of from 1st June 2010 to 17th June 2010 by 438,464 users, which
 are mainly Japanese tweets, to know the dynamics in Twitter when Japan had
 huge earthquakes in 11th March 2011 and iPhone announcement in 7th June
 2010.datatenmf.zip
DOI: 10.15468/dl.rqxypp
title: Occurrence Download

description: A dataset containing 638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ladislavella emarginata"
 ]
}

 The dataset includes 638 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000416-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.70mv450r
title: Data from: De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.

description: Adaptation to different ecological environments can promote speciation.
 Although numerous examples of such ‘ecological speciation’ exist, the
 genomic basis of the process, and the role of gene flow in it, remains
 less understood. This is, at least in part, because systems that are well
 characterized in terms of their ecology often lack genomic resources. In
 this study we characterize the transcriptome of Timema cristinae stick
 insects, a system that has been researched intensively in terms of
 ecological speciation, but for which genomic resources have not been
 previously developed. Specifically, we obtained &gt;1 million 454
 sequencing reads that assembled into 84,937 contigs representing
 approximately 18,282 unique genes and tens of thousands of potential
 molecular markers. Second, as an illustration of their utility, we used
 these genomic resources to assess multi-locus genetic divergence within
 both an ecotype pair and a species pair of Timema stick insects. The
 results suggest variable levels of genetic divergence and gene flow among
 taxon pairs and genes and illustrate a first step towards future genomic
 work in Timema.
description: timema454_contigstimema454_singletons_1sthalftimema454_singletons_2ndhalfCaliPopp_allo_IMaCaliPopp_para_complete_IMacris_allo_CO1_IMa
DOI: 10.5061/dryad.43h8c
title: Data from: Monoallelic chromatin conformation flanking long-range silenced domains in cancer-derived and normal cells

description: Epigenetic inactivation of chromatin plays an important role in
 determining cell phenotype in both normal and cancer cells, but our
 knowledge is still incomplete with respect to any potential monoallelic
 nature of the phenomenon. We have genotyped DNA isolated from chromatin of
 two colorectal cancer-derived lines and a culture of normal human
 intestinal epithelial cells (HIEC), which was immunoprecipitated with
 antibodies to acetylated vs. methylated histone H3K9, and presented the
 data as B allele frequency differences over multiple single-nucleotide
 polymorphism (SNP) moving window averages. [B allele is an arbitrary term
 defined as one of the two alleles at any given SNP, named A and B]. Three
 different validation tests confirmed that peaks exhibiting differences
 represented monoallelic domains. These complementary tests confirmed the
 following: 1) genes in the regions of high B allele frequency difference
 were expressed monoallelically; 2) in normal cells all five imprinting
 control regions which carried heterozygous SNPs were characterized by B
 allele difference peaks; and 3) the haplotypes in the B allele difference
 peaks were faithfully maintained in the chromatin immunoprecipitated with
 the respective antibodies. In both samples most of the monoallelic domains
 were found at the boundaries between regions of open and closed chromatin.
 With respect to the cancer line, this supports the established concept of
 conformation spreading, but the results from the normal cells were
 unexpected. Since these cells were polyclonal, the monoallelic structures
 were probably not determined by random choice as occurs in X-inactivation,
 so we propose that epigenetic inactivation in some domains may be
 heritable and polymorphic in normal human cells.
description: Chr1Chr2Chr3Chr4Chr5Chr6Chr7Chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22
DOI: 10.15468/dl.jy4866
title: Occurrence Download

description: A dataset containing 638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ladislavella emarginata"
 ]
}

 The dataset includes 638 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000418-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ff138
title: Data from: Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands

description: The effect of plant species composition on soil microbial communities was
 studied at the multiregional level. We compared the soil microbial
 communities of alpine natural grasslands dominated by Carex curvula and
 anthropogenic subalpine pastures dominated by Nardus stricta. We conducted
 paired sampling across the Carpathians and the Alps and used Illumina
 sequencing to reveal the molecular diversity of soil microbes. We found
 that bacterial and fungal communities exhibited contrasting regional
 distributions and that the distribution in each grassland is well
 discriminated. Beta diversity of microbial communities was much higher in
 C. curvula grasslands due to a marked regional effect. The composition of
 grassland-type core microbiomes suggest that C. curvula, and N. stricta to
 a lesser extent, tend to select a cohort of microbes related to
 antibiosis/exclusion, pathogenesis and endophytism. We discuss these
 findings in light of the postglacial history of the studied grasslands,
 the habitat connectivity and the disturbance regimes. Human-induced
 disturbance in the subalpine belt of European mountains has led to
 homogeneous soil microbial communities at large biogeographical scales.
 Our results confirm the overarching role of the dominant grassland plant
 species in the distribution of microbial communities and highlight the
 relevance of biogeographical history.
description: Fasta file of fungal
 unique sequencesFungal unique sequences
 from soils of alpine grasslands dominated by Carex curvula or C. curvula
 sp roase and subalpine pastures dominated by Nardus
 strictaUNITE_annot_fungal_mcl.fastaFasta file of bacterial unique sequencesBacterial unique sequences from soils of alpine grasslands dominated by Carex curvula or C. curvula sp roase and subalpine pastures dominated by Nardus strictaBacterial_abu_uniq.fastaFungi_unique_sequence_abundanceAbundance of each unique sequence in each sampleBacteria_unique_sequence_abundanceAbundance of unique bacterial sequences in each sampleExperimental designCorrespondance between plant species, sampling site and sampleexp_des.txtrarefied microbial communiy matrixesExcell file containing the rarefied microbial communities matrix used in this studyMatrix_core_community.xlsxSoil data for multivariate analysis,Solid chemical parameters by samplng site and grassland typeSoil_chemistry.xlsxPlant communities' occurrence matrixThis file contains a matrix of occurrence of plant species (in columns) for each site (in rows)Plant_communities.xlsx
DOI: 10.5061/dryad.d6508
title: Data from: Expression variants of the lipogenic AGPAT6 gene affect diverse milk composition phenotypes in Bos taurus

description: Milk is composed of a complex mixture of lipids, proteins, carbohydrates
 and various vitamins and minerals as a source of nutrition for young
 mammals. The composition of milk varies between individuals, with lipid
 composition in particular being highly heritable. Recent reports have
 highlighted a region of bovine chromosome 27 harbouring variants affecting
 milk fat percentage and fatty acid content. We aimed to further
 investigate this locus in two independent cattle populations, consisting
 of a Holstein-Friesian x Jersey crossbreed pedigree of 711 F2 cows, and a
 collection of 32,530 mixed ancestry Bos taurus cows. Bayesian genome-wide
 association mapping using markers imputed from the Illumina BovineHD chip
 revealed a large quantitative trait locus (QTL) for milk fat percentage on
 chromosome 27, present in both populations. We also investigated a range
 of other milk composition phenotypes, and report additional associations
 at this locus for fat yield, protein percentage and yield, lactose
 percentage and yield, milk volume, and the proportions of numerous milk
 fatty acids. We then used mammary RNA sequence data from 212 lactating
 cows to assess the transcript abundance of genes located in the milk fat
 percentage QTL interval. This analysis revealed a strong eQTL for AGPAT6,
 demonstrating that high milk fat percentage genotype is also additively
 associated with increased expression of the AGPAT6 gene. Finally, we used
 whole genome sequence data from six F1 sires to target a panel of novel
 AGPAT6 locus variants for genotyping in the F2 crossbreed population.
 Association analysis of 58 of these variants revealed highly significant
 association for polymorphisms mapping to the 5′UTR exons and intron 1 of
 AGPAT6. Taken together, these data suggest that variants affecting the
 expression of AGPAT6 are causally involved in differential milk fat
 synthesis, with pleiotropic consequences for a diverse range of other milk
 components.
description: Genotype, phenotype, and
 pedigree primary dataFiles include genotype
 (*_gens.txt & *_map.txt), phenotype (*_phens.txt), and pedigree
 (*_ped.txt) files for the MA, FJX, RNAseq, and qPCR animal subsets.
 Genotype files are space delimited, all other files tab delimited.
 Phenotype files include covariates used for statistical analyses. Animal
 Identifiers are common to each analysis set only.Primary_data.zip
DOI: 10.5061/dryad.bh84vs3
title: Data from: Global geographic patterns in the colours and sizes of animal‐dispersed fruits

description: Aim. Fruit colours attract animal seed dispersers, yet the causes of fruit
 colour diversity remain controversial. The lack of knowledge of
 large-scale spatial patterns in fruit colours has limited our ability to
 formulate and test alternative hypotheses to explain fruit colour, fruit
 size, and fruit colour diversity. We describe spatial (especially
 latitudinal) variation in fruit colour, colour diversity, and length, and
 test for correlations between fruit colour, length, and plant habit.
 Location. Global. Time period. Present-day. Major taxa studied. Seed
 plants. Methods. We assembled a database of fruit traits for 13,178
 fleshy-fruited plant species spanning 136 sites around the world. To
 assess whether fruit colour categories correspond with spectral
 reflectances, we tested for clustering of hue, chroma, and saturation for
 236 species for which we had reflectance data. We then quantified
 latitudinal gradients in fruit colour, fruit length, and fruit colour
 diversity while controlling for the effects of plant habit, and whether
 colour categories varied with respect to average fruit size. Results.
 Colour categories corresponded well with reflectance data. The tropics
 show high colour diversity, while red fruits progressively constitute a
 higher proportion of the fleshy-fruited plant community towards high
 latitudes. All mammal-associated colours (green, orange, brown, and
 yellow) are more common in the tropics than at high latitudes. Fruit
 length also increases towards the tropics. Main conclusions. Tropical
 communities tend to have diverse fruit colours, including many
 mammal-associated fruit colours, while high latitude communities contain a
 higher percentage of red-fruited species. The correlation between colour
 and size is strong, and some latitudinal patterns may be partly driven by
 changes in fruit size. Differences in geography and in the history of
 plant lineages in the southern versus the northern hemisphere may help to
 explain some biogeographic patterns, but alternative hypotheses related to
 fruit defence, development, and metabolic costs are plausible.
description: Data and code (zip
 file)This file contains the
 data and code used to produce the figures and results. The primary data
 file, all_data.csv, contains the fruit trait-related information (fruit
 color, fruit length, and plant habit, as well as taxonomic and geographic
 information). The primary analysis file, Analyses_final.R, can be run to
 produce all figures and tables. The remaining files and scripts are
 described in the README.txt file.data_code_package.zip
DOI: 10.5281/zenodo.17429140
title: Merged E3SMv3 PPE, surrogate predictions, and coarsened reference data

description: E3SMv3 Autocalibration data including E3SMv3 simulations, E3SMv3 parameter values, surrogate model predictions, and observational/reanalysis data. The data are climatologies for four seasons (DJF, MAM, JJA, SON), or sometimes annual means (ANN). Some field are defined on a lat x lon grid, while others are zonal means with a vertical dimension (lev) in the atmosphere. 

This is a merged dataset composed of model, surrogate, and reference datasets. All sources have been merged onto the same grid for easy comparison. Fields are filled with "nan" if they are not defined for a given season or product. 

Data can be indexed by:

time = ["ANN", "DJF", "JJA", "MAM", "SON"], 

product = ["mod", "obs", "sur"]*,

*sur is shorthand for surrogate model,

input_param = ['clubb_c1', 'clubb_gamma_coef', 'zmconv_tau', 'zmconv_dmpdz',       'zmconv_micro_dcs', 'nucleate_ice_subgrid', 'p3_nc_autocon_expon',       'p3_qc_accret_expon', 'zmconv_auto_fac', 'zmconv_accr_fac', 'zmconv_ke',       'cldfrc_dp1', 'p3_embryonic_rain_size', 'p3_mincdnc'], 

and lat, lon, and lev. 

Model and surrogate data can also be indexed by the "workdir", i.e. a string name assigned to each simulation in the PPE:

workdir[ens_idx]: [..."ens/workdir.399/20230802.v3alpha02.F2010.pmcpu.intel.8N",     "ens/workdir.400/20230802.v3alpha02.F2010.pmcpu.intel.8N", "ctrl",     "L001", "L002", "L003", "H001", "H002", "H003"]

SWCRE_ano_grd_adj and LWCRE_ano_grd_adj (gridded shortwave cloud feedback and gridded longwave cloud feedback, respectively) are per Kelvin, such that the correct units are Watts meter^(-2) Kelvin^(-1).

Any errors or misrepresentations of the observational data as they were remapped from their native grids to the merged grid are the fault of the author. See references. 

This research used computing resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility located at Lawrence Berkeley National Laboratory, operated under Contract No. DE-AC02-05CH11231, using the NERSC award to project E3SM.
DOI: 10.5061/dryad.dg027
title: Data from: A new titanosaurian braincase from the Cretaceous “Lo Hueco” locality in Spain sheds light on neuroanatomical evolution within Titanosauria

description: Despite continuous improvements, our knowledge of the neurocranial anatomy
 of sauropod dinosaurs as a whole is still poor, which is especially true
 for titanosaurians even though their postcranial remains are common in
 many Upper Cretaceous sites worldwide. Here we describe a braincase from
 the uppermost Cretaceous locality of ‘‘Lo Hueco” in Spain that is one of
 the most complete titanosaurian braincases found so far in Europe.
 Although the titanosaurian Ampelosaurus sp. is known from the same
 locality, this specimen is clearly a distinct taxon and presents a number
 of occipital characters found in Antarctosaurus and Jainosaurus, which are
 approximately coeval taxa from southern Gondwana. The specimen was
 subjected to X-ray computed tomographic (CT) scanning, allowing the
 generation of 3D renderings of the endocranial cavity enclosing the brain,
 cranial nerves, and blood vessels, as well as the labyrinth of the inner
 ear. These findings add considerable knowledge to the field of sauropod
 paleoneuroanatomy in general and titanosaurian endocast diversity in
 particular. Compared with that of many sauropodomorphs, the endocast
 appears only slightly flexed in lateral view and bears similarities (e.g.,
 reduction of the rostral dural expansion) with Gondwanan titanosaurians
 such as Jainosaurus, Bonatitan, and Antarctosaurus. The vestibular system
 of the inner ear is somewhat contracted (i.e., the radius of the
 semicircular canals is small), but less so than expected in derived
 titanosaurians. However, as far as the new specimen and Jainosaurus can be
 contrasted, and with the necessary caution due to the small sample of
 comparative data currently available, the two taxa appear more similar to
 one another in endocast morphology than to other titanosaurians. Recent
 phylogenetic analyses of titanosaurians have not included virtually any of
 the taxa under consideration here, and thus the phylogenetic position of
 the new Spanish titanosaurian—even its generic, let alone specific,
 identification—is not possible at the moment. Nevertheless, both the
 braincase osteology and the endocast morphology suggest that the specimen
 represents a derived titanosaurian that presumably branched further from
 the base of Lithostrotia, potentially even near Saltasauridae, comparable
 in evolutionary terms with Jainosaurus.
description: CT scan data (DICOM) for
 Spanish titanosaur braincase (MCCM-HUE-1667)CT scan data (DICOM) for
 Spanish titanosaur braincase (MCCM-HUE-1667). This specimen was collected
 from the Villalba de la Sierra Formation at a locality named “Lo Hueco,”
 near the village of Fuentes, Castile-La Mancha, Spain. Cretaceous (late
 Campanian-early Maastrichtian). The specimen was scanned on an Yxlon CT
 Compact (Yxlon International, Hamburg, Germany) with a voltage of 180 kV
 and a current of 2.8 mA. The in-plane pixel size was 0.18 mm, with an
 inter-slice spacing of 0.20 mm.Spanish_titanosaur_MCCM-HUE-1667_DICOM.zip
DOI: 10.5061/dryad.p8s0j
title: Data from: Women are seen more than heard in online newspapers

description: Feminist news media researchers have long contended that masculine news
 values shape journalists’ quotidian decisions about what is newsworthy. As
 a result, it is argued, topics and issues traditionally regarded as
 primarily of interest and relevance to women are routinely marginalised in
 the news, while men’s views and voices are given privileged space. When
 women do show up in the news, it is often as “eye candy,” thus reinforcing
 women’s value as sources of visual pleasure rather than residing in the
 content of their views. To date, evidence to support such claims has
 tended to be based on small-scale, manual analyses of news content. In
 this article, we report on findings from our large-scale, data-driven
 study of gender representation in online English language news media. We
 analysed both words and images so as to give a broader picture of how
 gender is represented in online news. The corpus of news content examined
 consists of 2,353,652 articles collected over a period of six months from
 more than 950 different news outlets. From this initial dataset, we
 extracted 2,171,239 references to named persons and 1,376,824 images
 resolving the gender of names and faces using automated computational
 methods. We found that males were represented more often than females in
 both images and text, but in proportions that changed across topics, news
 outlets and mode. Moreover, the proportion of females was consistently
 higher in images than in text, for virtually all topics and news outlets;
 women were more likely to be represented visually than they were mentioned
 as a news actor or source. Our large-scale, data-driven analysis offers
 important empirical evidence of macroscopic patterns in news content
 concerning the way men and women are represented.
description: URLs of news
 articles.URLs for the 2,353,652
 news articles covered in the study, as collected from the main feeds of
 the online news outlets.article-urls.tar.gz