cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2tg0c
title: Data from: Transcriptome analyses reveal genes and pathways associated with fatty acid composition traits in pigs

description: Fatty acid composition is associated with meat quality in pigs as well as
 with obesity- and diabetes-related traits in humans. Liver and muscle are
 important tissues for fatty acid metabolism. In this study, we evaluated
 correlations between liver and muscle transcriptomes and fatty acid
 composition traits in muscle and abdominal fat tissues in 335 F2 pigs from
 a White Duroc × Erhualian F2 pig resource population. Transcripts
 significantly correlated with fatty acid composition traits were enriched
 for genes involved in the categories of triglyceride catabolic process,
 mitochondrial function, hematological and immune system, and disease such
 as Type II diabetes. Gene co-expression network analysis further
 identified liver network modules relevant to fatty acid unsaturation index
 that were enriched in platelet activation and the type I interferon
 signaling pathway and highlighted the connections between variations in
 fatty acid composition and genes involved in hematological and immune
 system. Integrative analysis of the expression QTL identified ELOVL6 and
 SCD as plausible candidate genes underlying the loci for muscle
 C18:1n-9/C16:1n-7 values on chromosome 8 and the loci for muscle
 C18:1n-9/C18:0 contents on chromosome 14 respectively.
description: DGE_Tag.tar
DOI: 10.5061/dryad.4dv48
title: Data from: Using relatedness networks to infer contemporary dispersal: application to the endangered mammal Galemys pyrenaicus

description: Information about the degree of contemporary dispersal is important when
 trying to understand how populations interchange individuals and identify
 the specific barriers that prevent these movements. In the case of
 endangered species, this can represent crucial information when designing
 appropriate strategies that favor natural genetic exchange between
 populations. Here we analyze the parentage relationships between
 individuals from different localities and use these data to infer
 dispersal occurred in recent generations. We applied this approach to the
 Pyrenean desman (Galemys pyrenaicus), a semiaquatic and endangered species
 endemic to the Iberian Peninsula. We studied this species in four primary
 rivers in the Iberian Range, where two ancient mitochondrial lineages are
 separated by a strict contact zone but whose populations are more
 homogeneous at the genome level, suggesting the existence of complex
 dispersal patterns. Using next generation sequencing, we obtained 912 SNPs
 from each sample and estimated relatedness values between them. While
 relatedness networks were very dense within each river, we found
 surprisingly few relationships between individuals from different rivers
 despite their close proximity in some cases, indicating that dispersal
 between rivers is extremely low compared to dispersal within a single
 river. In agreement with this, the degree of inbreeding was exceedingly
 high in most individuals. These data show that relatedness information can
 be crucial to understand the contemporary dispersal patterns and
 conservation status of specific populations of endangered species.
description: ddRAD
 readsQuality-filtered reads
 for each sample in FASTA format.ddRAD_reads.zipDataset 1 SNPsSNPs from Dataset 1 in PLINK format.Dataset_1_SNPs.plink.pedDataset 2 SNPsSNPs from Dataset 2 in PLINK format.Dataset_2_SNPs.plink.pedGetCrosses.plPerl script for generation of offspring from a SNPs file.
DOI: 10.5061/dryad.fm67n
title: Data from: IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries

description: Motivation: 16S rDNA hypervariable tag sequencing has become the de facto
 method for accessing microbial diversity. Illumina paired-end sequencing,
 which produces two separate reads for each DNA fragment, has become the
 platform of choice for this application. However, when the two reads do
 not overlap, existing computational pipelines analyze data from read
 separately and underutilize the information contained in the paired-end
 reads. Results: We created a workflow known as Illinois Mayo Taxon
 Organization from RNA Dataset Operations (IM-TORNADO) for processing
 non-overlapping reads while retaining maximal information content. Using
 synthetic mock datasets, we show that the use of both reads produced
 answers with greater correlation to those from full length 16S rDNA when
 looking at taxonomy, phylogeny, and beta-diversity. Availability and
 Implementation: IM-TORNADO is freely available at
 http://sourceforge.net/projects/imtornad​o and produces BIOM format output
 for cross compatibility with other pipelines such as QIIME, mothur, and
 phyloseq.
description: Files for taxonomy
 comparisonSynthetic mock dataset
 used for taxonomy assignment comparison, across multiple read lengths.
 File includes scripts used and raw validation data.comparison_taxonomy.tar.bz2Files for comparison of sequence alignersSynthetic mock datasets used to compare the mulitple sequence aligners cmalign (from the infernal package) versus the NAST algorithm (from the PyNAST implementation). File includes R scripts and resulting raw validation data.comparison_aligners.tar.bz2Files for validation with realistic synthetic readsSynthetic mock datasets used for validation based on a realistic human stool microbiome dataset. These are NOT real bacterial reads. Those reads are available as example data from the IM-TORNADO pipeline. File includes scripts and raw validation data.validation_realistic.tar.bz2Files for taxonomy comparison using reads with errorsSynthetic mock datasets (100 replicates) used for validation of taxonomy using reads with errors and different length. File also includes scripts and resulting raw data for the validation.validation_taxonomy_errors.tar.bz2Files for validation of beta diversity using 16S rDNA regions V3 to V5Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V3 to V5. File also includes scripts and resulting raw data for the validation.validation_V3V5.tar.bz2Files for validation of beta diversity using 16S rDNA regions V6 to V9Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V6 to V9. File also includes scripts and resulting raw data for the validation.validation_V6V9.tar.bz2
DOI: 10.5061/dryad.11m62
title: Data from: Behavioural responses of naked mole rats to acute hypoxia and anoxia

description: Naked mole rats (NMRs) are among the most hypoxia-tolerant mammals. Other
 species respond to hypoxia by either escaping the hypoxic environment or
 drastically decreasing behavioural activity and body temperature (Tb) to
 conserve energy. However, NMRs rarely leave their underground burrows,
 which are putatively hypoxic and thermally stable near the NMRs'
 preferred Tb. Therefore, we asked whether NMRs are able to employ
 behavioural and thermoregulatory strategies in response to hypoxia despite
 their need to remain active and the minimal thermal scope in their
 burrows. We exposed NMRs to progressively deeper levels of hypoxia (from
 21 to 0% O2) while measuring their behaviour and Tb. Behavioural activity
 decreased 40–60% in hypoxia and Tb decreased slightly in moderate hypoxia
 (5–9%) and then further with deeper hypoxia (3% O2). However, even at 3%
 O2 NMRs remained somewhat active and warm, and continued to explore their
 environment. Remarkably, NMRs were active for greater than 90 s in acute
 anoxia and Tb and metabolic rate decreased rapidly. We conclude that NMRs
 are adapted to remain awake and functional even at the extremes of their
 hypoxia-tolerance. This adaptation likely reflects variable and
 challenging levels of environmental hypoxia in the natural habitat of this
 species.
description: Behavioural and
 metabolic dataEthovision files contain
 video and analysis of experiments. Loggerpro files contain metabolic data
 including O2, CO2 and flow readings. Files are separated into hypoxia
 (video + metabolism) and anoxia (metabolism) data.Raw
 data.7z
DOI: 10.5061/dryad.p68f8
title: Data from: Three-dimensional trajectories and network analyses of group behaviour within chimney swift flocks during approaches to the roost

description: Chimney swifts (Chaetura pelagica) are highly manoeuvrable birds notable
 for roosting overnight in chimneys, in groups of hundreds or thousands of
 birds, before and during their autumn migration. At dusk, birds gather in
 large numbers from surrounding areas near a roost site. The whole flock
 then employs an orderly, but dynamic, circling approach pattern before
 rapidly entering a small aperture en masse. We recorded the
 three-dimensional trajectories of ≈1 800 individual birds during a 30 min
 period encompassing flock formation, circling, and landing, and used these
 trajectories to test several hypotheses relating to flock or group
 behaviour. Specifically, we investigated whether the swifts use local
 interaction rules based on topological distance (e.g. the n nearest
 neighbours, regardless of their distance) rather than physical distance
 (e.g. neighbours within x m, regardless of number) to guide interactions,
 whether the chimney entry zone is more or less cooperative than the
 surrounding flock, and whether the characteristic subgroup size is
 constant or varies with flock density. We found that the swift flock is
 structured around local rules based on physical distance, that subgroup
 size increases with density, and that there exist regions of the flock
 that are less cooperative than others, in particular the chimney entry
 zone.
description: A_nodesPlease refer to Readme.rtfB_nodesPlease refer to Readme.rtfC_nodesPlease refer to Readme.rtfMovie A part 1Please see movie_notes.txt; first part of 20140901/blue/MVI_0011.MOVAaamovie_notes.txtMovie A part 2Aabmovie_notes.txtMovie A part 3Aacmovie_notes.txtMovie A part 4Aadmovie_notes.txtMovie A part 5Aaemovie_notes.txtMovie B part 120140901/blue/MVI_0012.MOVBaamovie_notes.txtMovie B part 2Babmovie_notes.txtMovie B part 3Bacmovie_notes.txtMovie B part 4Badmovie_notes.txtMovie B part 5Baemovie_notes.txtMovie C part 1201409101/blue/MVI_0013.MOVCaamovie_notes.txtMovie C part 2Cabmovie_notes.txtMovie C part 3Cacmovie_notes.txtMovie C part 4Cadmovie_notes.txt
DOI: 10.5061/dryad.br14k
title: Data from: Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab

description: Identification of arthropods important in disease transmission is a
 crucial, yet difficult, task that can demand considerable training and
 experience. An important case in point is that of the 150+ species of
 Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas
 disease across the Americas. We present a fully automated system that is
 able to identify triatomine bugs from Mexico and Brazil with an accuracy
 consistently above 80%, and with considerable potential for further
 improvement. The system processes digital photographs from a photo
 apparatus into landmarks, and uses ratios of measurements among those
 landmarks, as well as (in a preliminary exploration) two measurements that
 approximate aspects of coloration, as the basis for classification. This
 project has thus produced a working prototype that achieves reasonably
 robust correct identification rates, although many more developments can
 and will be added, and—more broadly—the project illustrates the value of
 multidisciplinary collaborations in resolving difficult and complex
 challenges.
description: VVL packet
 1VVL.zip.001VVL packet 2VVL.zip.002VVL packet 3VVL.zip.003VVL packet 4VVL.zip.004VVL packet 5VVL.zip.005VVL packet 6VVL.zip.006VVL packet 7VVL.zip.007VVL packet 8VVL.zip.008VVL packet 9VVL.zip.009VVL packet 10VVL.zip.010VVL packet 11VVL.zip.011VVL packet 12VVL.zip.012VVL packet 13VVL.zip.013VVL packet 14VVL.zip.014VVL packet 15VVL.zip.015
DOI: 10.21942/uva.28846991
title: Dutch ADE corpus

description: The corpus contains 102 anonymised Dutch Intensive Care progress notes with 16,470 labels, consisting of 8,914 Disorder entities, 5,307 Drug entities, 134 Qualitative Concept entities, 1,501 Indication relations, and 614 Adverse Drug Event (ADE) relations. Annotation reached high agreement for all entities (F1 score 0.7724) with an expected lower agreement for relations (F1 score 0.4327). The Dutch ADE corpus is a real-world data set that can be used to evaluate natural language processing pipelines for ADE detection tasks. Although the corpus was developed for drug-related acute-kidney injury, 158 additional ADEs were identified. The combination of iterative annotation guideline development and double annotation followed by adjudication produced high quality annotations.Re-use of the Dutch ADE Corpus is possible upon reasonable request and subject to certain limitations. Access requests and terms of use can be found <b>here</b><b>.</b>Please use the following citation to give the authors credit for their work, should you use or refer to the Dutch ADE Corpus: Murphy, R.M., Dongelmans, D.A., de Keizer, N.F. <i>et al.</i> Creation of a gold standard Dutch corpus of clinical notes for adverse drug event detection: the Dutch ADE corpus. <i>Lang Resources & Evaluation</i> (2025). https://doi.org/10.1007/s10579-025-09832-5
DOI: 10.21942/uva.28846991.v2
title: Dutch ADE corpus

description: The corpus contains 102 anonymised Dutch Intensive Care progress notes with 16,470 labels, consisting of 8,914 Disorder entities, 5,307 Drug entities, 134 Qualitative Concept entities, 1,501 Indication relations, and 614 Adverse Drug Event (ADE) relations. Annotation reached high agreement for all entities (F1 score 0.7724) with an expected lower agreement for relations (F1 score 0.4327). The Dutch ADE corpus is a real-world data set that can be used to evaluate natural language processing pipelines for ADE detection tasks. Although the corpus was developed for drug-related acute-kidney injury, 158 additional ADEs were identified. The combination of iterative annotation guideline development and double annotation followed by adjudication produced high quality annotations.Re-use of the Dutch ADE Corpus is possible upon reasonable request and subject to certain limitations. Access requests and terms of use can be found <b>here</b><b>.</b>Please use the following citation to give the authors credit for their work, should you use or refer to the Dutch ADE Corpus: Murphy, R.M., Dongelmans, D.A., de Keizer, N.F. <i>et al.</i> Creation of a gold standard Dutch corpus of clinical notes for adverse drug event detection: the Dutch ADE corpus. <i>Lang Resources & Evaluation</i> (2025). https://doi.org/10.1007/s10579-025-09832-5
DOI: 10.5061/dryad.pk8dv
title: Data from: Spatial and quantitative datasets of the pancreatic β-cell mass distribution in lean and obese mice

description: A detailed understanding of pancreatic β-cell mass distribution is a key
 element to fully appreciate the pathophysiology of models of diabetes and
 metabolic stress. Commonly, such assessments have been performed by
 stereological approaches that rely on the extrapolation of two-dimensional
 data and provide very limited topological information. We present ex vivo
 optical tomographic data sets of the full β-cell mass distribution in
 cohorts of obese ob/ob mice and their lean controls, together with
 information about individual islet β-cell volumes, their three-dimensional
 coordinates and shape throughout the volume of the pancreas between 4 and
 52 weeks of age. These data sets offer the currently most comprehensive
 public record of the β-cell mass distribution in the mouse. As such, they
 may serve as a quantitative and topological reference for the planning of
 a variety of in vivo or ex vivo experiments including computational
 modelling and statistical analyses. By shedding light on intra- and
 inter-lobular variations in β-cell mass distribution, they further provide
 a powerful tool for the planning of stereological sampling assessments.
description: Data record
 A_tomographic images.zipOPT generated
 tomographic image stacks (*.bmp) throughout the volume of the splenic,
 duodenal and gastric lobes of ob/ob and control Mus Musculus pancreas for
 the insulin and the anatomy channel. The individual image files are
 annotated to indicate phenotype, age (weeks), ID, pancreatic lobe, channel
 (insulin or anatomy) and sequential stack number using the following
 format: “XXXX_XXw_IDX_XL_XXXXXX_XXXX.bmp”. (Note, when unzipped the data
 file will be 218 GB.)Data record A_Tomographic
 images.zipData record
 B_Isosurfaced 3D volumes.zipImaris (*.ims) files
 with segmented islet volumes (here defined as a continuous body of insulin
 positive cells) based on the signal from insulin specific antibodies and
 pancreatic lobular volumes based on the signal from endogenous tissue
 autofluorescence. These files contain both the anatomy and insulin
 channels and are annotated to indicate phenotype, age (weeks), ID and
 pancreatic lobe using the following format:
 “XXXX_XXw_IDX_XL.ims”.Data record C Volumetric
 and spatial statisticsExcel sheets (*.xls)
 providing information about individual the islet β-cell volumes, their
 corresponding 3D coordinates and related aspect ratio information,
 together with information on pancreatic lobular volumes. These files are
 annotated to indicate phenotype, age (weeks), ID, pancreatic lobe and
 channel (XXXX_XXw_IDX_XL_XXXXXX.xls)Data record D_Visual
 reference imagesRepresentative
 iso-surfaced reconstruction images of each sample for visual reference
 (*.jpg). These files are annotated to indicate phenotype, age (weeks), ID
 and lobe (XXXX_XXw_IDX_XL.jpg).
DOI: 10.21942/uva.28846991.v1
title: Dutch ADE corpus

description: The corpus contains 102 anonymised Dutch Intensive Care progress notes with 16,470 labels, consisting of 8,914 Disorder entities, 5,307 Drug entities, 134 Qualitative Concept entities, 1,501 Indication relations, and 614 Adverse Drug Event (ADE) relations. Annotation reached high agreement for all entities (F1 score 0.7724) with an expected lower agreement for relations (F1 score 0.4327). The Dutch ADE corpus is a real-world data set that can be used to evaluate natural language processing pipelines for ADE detection tasks. Although the corpus was developed for drug-related acute-kidney injury, 158 additional ADEs were identified. The combination of iterative annotation guideline development and double annotation followed by adjudication produced high quality annotations. Re-use of the Dutch ADE Corpus is possible upon reasonable request and subject to certain limitations. Access requests and terms of use can be found <b>here</b><b>.</b>Please use the following citation [<i>will add after publication</i>] to give the authors credit for their work, should you use or refer to the Dutch ADE Corpus.
DOI: 10.5061/dryad.84q8c68
title: Data from: A comprehensive assessment of inbreeding and laboratory adaptation in Aedes aegypti mosquitoes

description: Modified Aedes aegypti mosquitoes reared in laboratories are being
 released around the world to control wild mosquito populations and the
 diseases they transmit. Several efforts have failed due to poor
 competitiveness of the released mosquitoes. We hypothesized that colonized
 mosquito populations could suffer from inbreeding depression and adapt to
 laboratory conditions, reducing their performance in the field. We
 established replicate populations of Ae. aegypti mosquitoes collected from
 Queensland, Australia, and maintained them in the laboratory for twelve
 generations at different census sizes. Mosquito colonies maintained at
 small census sizes (≤100 individuals) suffered from inbreeding depression
 due to low effective population sizes which were only 25% of the census
 size as estimated by SNP markers. Populations that underwent full-sib
 mating for 9 consecutive generations had greatly reduced performance
 across all traits measured. We compared the established laboratory
 populations with their ancestral population resurrected from quiescent
 eggs for evidence of laboratory adaptation. The overall performance of
 laboratory populations maintained at a large census size (400 individuals)
 increased, potentially reflecting adaptation to artificial rearing
 conditions. However most individual traits were unaffected, and patterns
 of adaptation were not consistent across populations. Differences between
 replicate populations may indicate that founder effects and drift affect
 experimental outcomes. Though we find limited evidence of laboratory
 adaptation, mosquitoes maintained at low population sizes can clearly
 suffer fitness costs, compromising the success of “rear and release”
 strategies for arbovirus control.
description: Experimental
 dataResults from all
 laboratory experiments conducted in this study.Pooled ddRADseq
 library_R1.7zRaw sequencing data
 archived here represents raw Read1 and Read2 paired-end Illumina data from
 a single sequencing run. Original R1 and R2 *.fastq files have been
 compressed using 7Zip (available at
 https://www.7-zip.org/download.html).Perran_CB12LANXX_NoIndex_L005_R1.7zPooled ddRADseq library_R2.7zRaw sequencing data archived here represents raw Read1 and Read2 paired-end Illumina data from a single sequencing run. Original R1 and R2 *.fastq files have been compressed using 7Zip (available at https://www.7-zip.org/download.html).Perran_CB12LANXX_NoIndex_L005_R2.7z
DOI: 10.5061/dryad.kc2vj64
title: Data from: Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico

description: Identifying genetic connectivity and discrete population boundaries is an
 important objective for man- agement of declining Caribbean reef-building
 corals. A double digest restriction-associated DNA sequencing pro- tocol
 was utilized to generate 321 single nucleotide poly- morphisms to estimate
 patterns of horizontal and vertical gene flow in the brooding Caribbean
 plate coral, Agaricia lamarcki. Individual colonies (n = 59) were sampled
 from eight locations throughout southwestern Puerto Rico from six shallow
 (* 10–20 m) and two mesophotic habitats (* 30–40 m). Descriptive summary
 statistics (Fixation index, FST), analysis of molecular variance, and
 analysis through landscape and ecological associations and dis- criminant
 analysis of principal components estimated high population connectivity
 with subtle subpopulation structure among all sampling localities.
description: alam_reads.tar.gzalam_reads_part2.tar