cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6tm5v
title: Data from: Characterization of regional left ventricular function in nonhuman primates using magnetic resonance imaging biomarkers: a test-retest repeatability and inter-subject variability study

description: Pre-clinical animal models are important to study the fundamental
 biological and functional mechanisms involved in the longitudinal
 evolution of heart failure (HF). Particularly, large animal models, like
 nonhuman primates (NHPs), that possess greater physiological, biochemical,
 and phylogenetic similarity to humans are gaining interest. To assess the
 translatability of these models into human diseases, imaging biomarkers
 play a significant role in non-invasive phenotyping, prediction of
 downstream remodeling, and evaluation of novel experimental therapeutics.
 This paper sheds insight into NHP cardiac function through the
 quantification of magnetic resonance (MR) imaging biomarkers that
 comprehensively characterize the spatiotemporal dynamics of left
 ventricular (LV) systolic pumping and LV diastolic relaxation. MR tagging
 and phase contrast (PC) imaging were used to quantify NHP cardiac strain
 and flow. Temporal inter-relationships between rotational mechanics,
 myocardial strain and LV chamber flow are presented, and functional
 biomarkers are evaluated through test-retest repeatability and inter
 subject variability analyses. The temporal trends observed in strain and
 flow was similar to published data in humans. Our results indicate a
 dominant dimension based pumping during early systole, followed by a
 torsion dominant pumping action during late systole. Early diastole is
 characterized by close to 65% of untwist, the remainder of which likely
 contributes to efficient filling during atrial kick. Our data reveal that
 moderate to good intra-subject repeatability was observed for peak strain,
 strain-rates, E/circumferential strain-rate (CSR) ratio, E/longitudinal
 strain-rate (LSR) ratio, and deceleration time. The inter-subject
 variability was high for strain dyssynchrony, diastolic strain-rates, peak
 torsion and peak untwist rate. We have successfully characterized cardiac
 function in NHPs using MR imaging. Peak strain, average systolic
 strain-rate, diastolic E/CSR and E/LSR ratios, and deceleration time were
 identified as robust biomarkers that could potentially be applied to
 future pre-clinical drug studies.
description: Non-Human Primate MRI
 Cardiac Functional DataThis file consists of
 MRI datasets from eight naive non-human primates. The datasets are
 repeated twice for test and retest acquisitions. Each dataset includes
 cardiac structural, tagging, and phase contrast MRI
 images.SUM0030.zip
DOI: 10.5061/dryad.20r9k
title: Data from: Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species

description: The advent of Next Generation Sequencing Technology (NGST) has
 revolutionized molecular biology research, allowing for rapid gene/genome
 sequencing from a multitude of diverse species. As high throughput
 sequencing becomes more accessible, more efficient workflows must be
 developed to deal with the amounts of data produced and better assemble
 the genomes of de novo lineages. We combine traditional laboratory methods
 with Illumina NGST to amplify and sequence the largest mammalian multigene
 family, the Olfactory Receptor gene family, for species with and without a
 reference genome. We develop novel assembly methods to annotate and filter
 these data, which can be utilized for any gene family or any species. We
 find no significant difference between the ratio of genes within their
 respective gene families of our data compared with available genomic data.
 Using simulated data we explore the limitations of short-read sequence
 data and our assembly in recovering this gene family. We highlight the
 benefits and shortcomings of these methods. Compared with data generated
 from traditional polymerase chain reaction, cloning and Sanger sequencing
 methodologies, sequence data generated using our pipeline increases yield
 and sequencing efficiency without reducing the number of unique genes
 amplified. A cloning step is not required, therefore shortening data
 generation time. The novel downstream methodologies and workflows
 described provide a tool to be utilized by many fields of biology, to
 access and analyze the vast quantities of data generated. By combining
 laboratory and in silico methods, we provide a means of extracting genomic
 information for multigene families without complete genome sequencing.
description: 8prPrimers used in study
 (required for trimming script)Ailuropoda_melanoleuca_genomicORsORs found in the giant panda genomefilter_on_QFiltering scriptremove_primersScript to remove primersailurapoda_contigs.tarContigs assembled for giant pandacanis_contigs.tarContigs assembled for doganoura_contigs.tarContigs assembled for Geoffroy's tailless batartibeus_contigs.tarContigs assembled for Jamaican fruit batMyotis_contigs.tarContigs assembled for little brown batNyctimene_contigs.tarContigs assembled for common tube-nosed fruit batRhinolophus_contigs.tarContigs assembled for lesser horseshoe batailuropoda_reads.txtReads used to assemble the Panda ORsanoura_readsReads used to assemble Geoffroy's tailless batartibeus_readsreads used to assemble Jamaican fruit batcanis_readsReads used to assemble Dog datamyotis_readsreads used to assemble little brown bat contigsnyctimene_readsreads used to assemble Common tube-nosed fruit batrhinolophus_readsreads used to assemble the lesser horseshoe batMyotis_lucifugus_genomicORsGenomic ORs mined from little brown bat genome
DOI: 10.5061/dryad.b5j25
title: Data from: Does recognized genetic management in supportive breeding prevent genetic changes in life-history traits?

description: Supportive breeding is one of the last resort conservation strategies to
 avoid species extinction. Management of captive populations is challenging
 because several harmful genetic processes need to be avoided. Several
 recommendations have been proposed to limit these deleterious effects, but
 empirical assessments of these strategies remain scarce. We investigated
 the outcome of a genetic management in a supportive breeding for the
 Houbara Bustard. At the phenotypic level, we found an increase over
 generations in the mean values of gamete production, body mass and
 courtship display rate. Using an animal model, we found that phenotypic
 changes reflected genetic changes as evidenced by an increase in breeding
 values for all traits. These changes resulted from selection acting on
 gamete production and to a lesser extent on courtship display. Selection
 decreased over years for female gametes, emphasizing the effort of
 managers to increase the contribution of poor breeders to offspring
 recruited in the captive breeding. Our results shed light on very fast
 genetic changes in an exemplary captive programme that follows worldwide
 used recommendations and emphasizes the need of more empirical evidence of
 the effects of genetic guidelines on the prevention of genetic changes in
 supportive breeding.
description: breeding values in
 fitness-linked traits in the Houbara bustard captive
 breedingThe ZIP file consists in
 5 files referring to 5 traits (NBJ: display rate, NBO: number of eggs,
 SPZ: number of spermatozoa, PoidsM: male body mass, PoidsF: female body
 mass). Each file contains the breeding values (and other fixed and random
 effects) estimated with MCMCglmm (R). NonInf in the file name to the non
 informative prior used, and Gauss or Poi to the distribution of errors
 (Normal or Poisson). 1000 iterations have been simulated for each
 individual.BV_FEV_2013.zip
DOI: 10.5061/dryad.mt048
title: Data from: Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens

description: The Franklin Parker Preserve within the New Jersey Pine Barrens contains
 5,000 acres of wetlands habitat, including old-growth Atlantic White Cedar
 (or AWC; Chamaecyparis thyoides) swamps, cranberry bogs, and former
 cranberry bogs undergoing restoration into AWC forests. This study showed
 that the C-use efficiency was greater in the old-growth AWC soils than in
 soils from 8-year old mid-stage restored AWC stands, which were greater
 than found in soil from 4-year old AWC stands—the latter two stands being
 restored from long-term cranberry bogs. A metagenomic analysis of eDNA
 extracted from these soils showed that the C-cycle trends were associated
 with increases in the relative numbers of DNA sequences from several
 copiotrophic bacterial groups (Bacteroidetes, and Proteobacteria), complex
 C decomposing fungal groups ( Sordiomycetes, Mortierellales, and
 Thelephorales), and collembolan and formicid invertebrates. All groups are
 indicators of successionally more advanced soils, and critical for soil
 C-cycle activities. These data suggest that the restoration activities
 studied are enhancing critical guilds of soil biota, and increasing C-use
 efficiency in the soils of restored habitats, and that the use of
 metagenomic analysis of soil eDNA can be used in the development of
 assessment models for soil recovery of wetlands following restoration.
description: Eaton_PineBarrens
DOI: 10.5281/zenodo.18379885
title: TABLE 2 in Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana

description: TABLE 2. Comparison of four potential syntypes for Thecla tiasa. The grey table cells indicate which items best fit the original description.
NHMUK 015200801NHMUK 015201058NHMUK 015201062NHMUK 015201063specimen 1specimen 2specimen 3specimen 4(Fig. 21)(Fig. 11)(Fig. 20)(Fig. 19)Original locality: AmazonParáAmazonEga U. AmazonAmazonOriginal collection: HewitsonBates collection?Saunders collectionBates collectionBates collection“tiasa” labelNoYesYesYesOriginal text: postmedian line above the anal angle in a semicircle shapeU-shapedU-shapedV-shapedV-shapedOriginal drawing: cell CuA2-2A filled with a lot of red scalesNoYesYesYesOriginal drawing: VHW postmedian line bent at the apexNoYesNoYesWingspan: 1.4 inches (measured with Photoshop tool)30.25 mm33.09 mm31.91 mm34.80 mmIdentification by DNA comparisonThereus sp. nov.Thereus genenaThereus burisThereus buris
description: Published as part of Faynel, Christophe, Huertas, Blanca, Crom, Jean-François Le, O'Brien, Richard & Fåhraeus, Christer, 2025, Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana, pp. 218 in Zootaxa 5728 (2) on page 218, DOI: 10.11646/zootaxa.5728.2.1, http://zenodo.org/record/17894360
DOI: 10.5281/zenodo.18379886
title: TABLE 2 in Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana

description: TABLE 2. Comparison of four potential syntypes for Thecla tiasa. The grey table cells indicate which items best fit the original description.
NHMUK 015200801NHMUK 015201058NHMUK 015201062NHMUK 015201063specimen 1specimen 2specimen 3specimen 4(Fig. 21)(Fig. 11)(Fig. 20)(Fig. 19)Original locality: AmazonParáAmazonEga U. AmazonAmazonOriginal collection: HewitsonBates collection?Saunders collectionBates collectionBates collection“tiasa” labelNoYesYesYesOriginal text: postmedian line above the anal angle in a semicircle shapeU-shapedU-shapedV-shapedV-shapedOriginal drawing: cell CuA2-2A filled with a lot of red scalesNoYesYesYesOriginal drawing: VHW postmedian line bent at the apexNoYesNoYesWingspan: 1.4 inches (measured with Photoshop tool)30.25 mm33.09 mm31.91 mm34.80 mmIdentification by DNA comparisonThereus sp. nov.Thereus genenaThereus burisThereus buris
description: Published as part of Faynel, Christophe, Huertas, Blanca, Crom, Jean-François Le, O'Brien, Richard & Fåhraeus, Christer, 2025, Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana, pp. 218 in Zootaxa 5728 (2) on page 218, DOI: 10.11646/zootaxa.5728.2.1, http://zenodo.org/record/17894360
DOI: 10.5281/zenodo.18379116
title: Supplementary materials of the article Syninclusions reveal "Ant mosaic" in the Eocene amber forest

description: This page contains the following files:



ASIN.xlsxThe first table, “Number of specimens found in amber samples,” lists the ant species identified in syninclusions and the total number of occurrences for each species.The second table, “Number of co-occurrences of different species,” provides counts of pairwise co-occurrences within eusyninclusions.The third table contains the calculations for the association index.The fourth table presents the computed association indices.

ASIN_script.RR script used to construct the co-occurrence network.

matrix_only_syninclusions_cooccurrences_analysis.xlsxContains the presence/absence matrix of ant species across Baltic amber samples, used as input for the co-occurrence analysisFull results, including observed vs. expected co-occurrences, raw and adjusted p-values, and taxon names for all tested species pairs.

4. cooccurrence_analysis_script.R


R script used to perform the co-occurrence analysis.
DOI: 10.5281/zenodo.18379115
title: Supplementary materials of the article Syninclusions reveal "Ant mosaic" in the Eocene amber forest

description: This page contains the following files:



ASIN.xlsxThe first table, “Number of specimens found in amber samples,” lists the ant species identified in syninclusions and the total number of occurrences for each species.The second table, “Number of co-occurrences of different species,” provides counts of pairwise co-occurrences within eusyninclusions.The third table contains the calculations for the association index.The fourth table presents the computed association indices.

ASIN_script.RR script used to construct the co-occurrence network.

matrix_only_syninclusions_cooccurrences_analysis.xlsxContains the presence/absence matrix of ant species across Baltic amber samples, used as input for the co-occurrence analysisFull results, including observed vs. expected co-occurrences, raw and adjusted p-values, and taxon names for all tested species pairs.

4. cooccurrence_analysis_script.R


R script used to perform the co-occurrence analysis.
DOI: 10.5281/zenodo.18379888
title: TABLE 3 in Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana

description: TABLE 3. Comparison of intra- and interspecific p-distances in percent (average ± SD) for the genena group. The alignment is the same as we used for the Iqtree runs. Number of specimens examined within parenthesis. Species ranking by same order as in the text.
T. endera (12)T. geminus (2)T. cacao (2)T. antecum (3)T. genena (4)T. tiasa (5)T. angulus (4)T. borbaensis (2)T. chontachaca (4)T. ramirezi (2)T. ortaloides (4)T. confusus (6)T. praxioides (8)T. praxis (3)T. ortalus (6)T. aguacatal (6)T. endera (12)1.08 ± 0.53T. geminus (2)3.47 ± 0.340.15 ± 0.00T. cacao (2)2.24 ± 0.222.99 ± 0.100.00 ± 0.00T. antecum (3)6.56 ± 0.366.83 ± 0.255.21 ± 0.230.31 ± 0.27T. genena (4)4.44 ± 0.154.21 ± 0.103.82 ± 0.006.74 ± 0.220.00 ± 0.00T. tiasa (5)4.99 ± 0.264.42 ± 0.204.19 ± 0.087.20 ± 0.242.75 ± 0.260.85 ± 0.46T. angulus (4)4.49 ± 0.313.90 ± 0.373.90 ± 0.146.82 ± 0.252.98 ± 0.352.97 ± 0.351.02 ± 0.53T. borbaensis (2)4.14 ± 0.164.36 ± 0.113.59 ± 0.096.81 ± 0.244.64 ± 0.084.56 ± 0.114.25 ± 0.220.30 ± 0.00T. chontachaca (4)4.82 ± 0.194.53 ± 0.084.45 ± 0.007.12 ± 0.085.07 ± 0.005.31 ± 0.234.93 ± 0.364.22 ± 0.080.00 ± 0.00T. ramirezi (2)4.47 ± 0.144.52 ± 0.114.13 ± 0.007.55 ± 0.074.79 ± 0.175.34 ± 0.174.74 ± 0.294.96 ± 0.092.77 ± 0.020.31 ± 0.00T. ortaloides (4)6.34 ± 0.695.71 ± 0.345.66 ± 0.808.78 ± 0.735.93 ± 0.746.66 ± 0.275.50 ± 0.356.18 ± 0.826.14 ± 0.256.69 ± 0.320.16 ± 0.17T. confusus (6)6.97 ± 0.336.56 ± 0.156.19 ± 0.088.96 ± 0.236.68 ± 0.076.74 ± 0.126.20 ± 0.227.26 ± 0.156.81 ± 0.127.01 ± 0.252.66 ± 0.450.54 ± 0.57T. praxioides (8)6.58 ± 0.385.99 ± 0.376.31 ± 0.309.07 ± 0.366.54 ± 0.246.22 ± 0.295.68 ± 0.486.47 ± 0.426.13 ± 0.426.83 ± 0.204.36 ± 0.746.09 ± 0.371.19 ± 0.64T. praxis (3)8.27 ± 0.377.18 ± 0.127.50 ± 0.1410.07 ± 0.237.84 ± 0.118.41 ± 0.337.69 ± 0.568.63 ± 0.168.31 ± 0.028.42 ± 0.325.08 ± 0.706.70 ± 0.295.31 ± 0.490.61 ± 0.27T. ortalus (6)7.19 ± 0.306.24 ± 0.186.55 ± 0.129.21 ± 0.246.54 ± 0.367.02 ± 0.336.14 ± 0.176.46 ± 0.146.62 ± 0.146.34 ± 0.263.22 ± 1.125.60 ± 0.345.11 ± 0.405.84 ± 0.300.42 ± 0.34T. aguacatal (6)7.42 ± 0.306.55 ± 0.156.87 ± 0.1810.13 ± 0.167.34 ± 0.347.66 ± 0.366.83 ± 0.387.50 ± 0.227.71 ± 0.247.63 ± 0.384.31 ± 0.435.50 ± 0.604.81 ± 0.396.06 ± 0.424.94 ± 0.430.29 ± 0.56
......continued on the next page
description: Published as part of Faynel, Christophe, Huertas, Blanca, Crom, Jean-François Le, O'Brien, Richard & Fåhraeus, Christer, 2025, Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana, pp. 240-241 in Zootaxa 5728 (2) on page 240, DOI: 10.11646/zootaxa.5728.2.1, http://zenodo.org/record/17894360
DOI: 10.5281/zenodo.18379889
title: TABLE 3 in Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana

description: TABLE 3. Comparison of intra- and interspecific p-distances in percent (average ± SD) for the genena group. The alignment is the same as we used for the Iqtree runs. Number of specimens examined within parenthesis. Species ranking by same order as in the text.
T. endera (12)T. geminus (2)T. cacao (2)T. antecum (3)T. genena (4)T. tiasa (5)T. angulus (4)T. borbaensis (2)T. chontachaca (4)T. ramirezi (2)T. ortaloides (4)T. confusus (6)T. praxioides (8)T. praxis (3)T. ortalus (6)T. aguacatal (6)T. endera (12)1.08 ± 0.53T. geminus (2)3.47 ± 0.340.15 ± 0.00T. cacao (2)2.24 ± 0.222.99 ± 0.100.00 ± 0.00T. antecum (3)6.56 ± 0.366.83 ± 0.255.21 ± 0.230.31 ± 0.27T. genena (4)4.44 ± 0.154.21 ± 0.103.82 ± 0.006.74 ± 0.220.00 ± 0.00T. tiasa (5)4.99 ± 0.264.42 ± 0.204.19 ± 0.087.20 ± 0.242.75 ± 0.260.85 ± 0.46T. angulus (4)4.49 ± 0.313.90 ± 0.373.90 ± 0.146.82 ± 0.252.98 ± 0.352.97 ± 0.351.02 ± 0.53T. borbaensis (2)4.14 ± 0.164.36 ± 0.113.59 ± 0.096.81 ± 0.244.64 ± 0.084.56 ± 0.114.25 ± 0.220.30 ± 0.00T. chontachaca (4)4.82 ± 0.194.53 ± 0.084.45 ± 0.007.12 ± 0.085.07 ± 0.005.31 ± 0.234.93 ± 0.364.22 ± 0.080.00 ± 0.00T. ramirezi (2)4.47 ± 0.144.52 ± 0.114.13 ± 0.007.55 ± 0.074.79 ± 0.175.34 ± 0.174.74 ± 0.294.96 ± 0.092.77 ± 0.020.31 ± 0.00T. ortaloides (4)6.34 ± 0.695.71 ± 0.345.66 ± 0.808.78 ± 0.735.93 ± 0.746.66 ± 0.275.50 ± 0.356.18 ± 0.826.14 ± 0.256.69 ± 0.320.16 ± 0.17T. confusus (6)6.97 ± 0.336.56 ± 0.156.19 ± 0.088.96 ± 0.236.68 ± 0.076.74 ± 0.126.20 ± 0.227.26 ± 0.156.81 ± 0.127.01 ± 0.252.66 ± 0.450.54 ± 0.57T. praxioides (8)6.58 ± 0.385.99 ± 0.376.31 ± 0.309.07 ± 0.366.54 ± 0.246.22 ± 0.295.68 ± 0.486.47 ± 0.426.13 ± 0.426.83 ± 0.204.36 ± 0.746.09 ± 0.371.19 ± 0.64T. praxis (3)8.27 ± 0.377.18 ± 0.127.50 ± 0.1410.07 ± 0.237.84 ± 0.118.41 ± 0.337.69 ± 0.568.63 ± 0.168.31 ± 0.028.42 ± 0.325.08 ± 0.706.70 ± 0.295.31 ± 0.490.61 ± 0.27T. ortalus (6)7.19 ± 0.306.24 ± 0.186.55 ± 0.129.21 ± 0.246.54 ± 0.367.02 ± 0.336.14 ± 0.176.46 ± 0.146.62 ± 0.146.34 ± 0.263.22 ± 1.125.60 ± 0.345.11 ± 0.405.84 ± 0.300.42 ± 0.34T. aguacatal (6)7.42 ± 0.306.55 ± 0.156.87 ± 0.1810.13 ± 0.167.34 ± 0.347.66 ± 0.366.83 ± 0.387.50 ± 0.227.71 ± 0.247.63 ± 0.384.31 ± 0.435.50 ± 0.604.81 ± 0.396.06 ± 0.424.94 ± 0.430.29 ± 0.56
......continued on the next page
description: Published as part of Faynel, Christophe, Huertas, Blanca, Crom, Jean-François Le, O'Brien, Richard & Fåhraeus, Christer, 2025, Diagnostic male secondary sexual structures and wing patterns in the Thereus genena species group (Lepidoptera: Lycaenidae: Theclinae) with the description of nine new species from Colombia, Peru, Brazil and French Guiana, pp. 240-241 in Zootaxa 5728 (2) on page 240, DOI: 10.11646/zootaxa.5728.2.1, http://zenodo.org/record/17894360
DOI: 10.5061/dryad.5s32v
title: Data from: Glutathione S-transferase protein expression in different life stages of zebrafish (Danio rerio)

description: Zebrafish is a widely used animal model in biomedical sciences and
 toxicology. Although evidence for the presence of phase I and phase II
 xenobiotic defense mechanisms in zebrafish exists on the transcriptional
 and enzyme activity level, little is known about the protein expression of
 xenobiotic metabolizing enzymes. Given the important role of glutathione
 S-transferases (GSTs) in phase II biotransformation, we analyzed cytosolic
 GST proteins in zebrafish early life stages and different organs of adult
 male and female fish, using a targeted proteomics approach. The
 established Multiple Reaction Monitoring-based assays enable the
 measurement of the relative abundance of specific GST isoenzymes and GST
 classes in zebrafish through a combination of proteotypic peptides and
 peptides shared within the same class. GSTs of the classes alpha, mu, pi
 and rho are expressed in zebrafish embryo as early as 4 hours post
 fertilization (hpf). The majority of GST enzymes are present at 72 hpf
 followed by a continuous increase in expression thereafter. In adult
 zebrafish, GST expression is organ dependent, with most of the GST classes
 showing the highest expression in the liver. The expression of a wide
 range of cytosolic GST isoenzymes and classes in zebrafish early life
 stages and adulthood supports the use of zebrafish as a model organism in
 chemical-related investigations.
description: Data_Evaluation_Skyline