cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h9w0vt4qp
title: d13C and d15N of Pacific halibut skeletal muscle tissue from the Gulf of Alaska, 2018

description: In 2018, white muscle samples were collected from the lateral musculature
 of a random sample of up to 4 fish from each survey station of the
 International Pacific Halibut Commission's Fishery Independent
 Setline Survey (total n = 1653). Muscle samples were stored at -20°C,
 thawed, oven-dried to a constant mass at 42°C, and ground to a fine
 powder. Approximately 0.5 to 1.0 mg of each powdered sample was loaded
 into a tin capsule for stable isotope analysis. d13C and d15N values were
 determined using a Carlo Erba 1110 Elemental Analyzer (Carlo Erba
 Reagents, CE Instruments, ThermoQuest Italia S.p.A. Milan, Italy) coupled
 to a Thermo Delta Plus XP IRMS (Thermo Finnigan, Bremen, German) at the
 University of Wyoming’s Stable Isotope Facility (Laramie, Wyoming, USA).
 Long-term analyses of quality control standards have yielded precisions of
 0.3‰ for d13C and 0.4‰ for d15N. Stable isotope data are presented in ‰
 relative to Pee Dee Belemnite for 13C and atmospheric nitrogen for 15N.
description: Muscle samples were stored at -20°C, thawed, oven-dried to a
 constant mass at 42°C, and ground to a fine powder. Approximately 0.5 to
 1.0 mg of each powdered sample was loaded into a tin capsule for stable
 isotope analysis. d<sup>13</sup>C and
 d<sup>15</sup>N values were determined using a Carlo Erba 1110
 Elemental Analyzer (Carlo Erba Reagents, CE Instruments, ThermoQuest
 Italia S.p.A. Milan, Italy) coupled to a Thermo Delta Plus XP IRMS (Thermo
 Finnigan, Bremen, German) at the University of Wyoming’s Stable Isotope
 Facility (Laramie, Wyoming, USA). Long-term analyses of quality control
 standards have yielded precisions of 0.3‰ for d<sup>13</sup>C
 and 0.4‰ for d<sup>15</sup>N. Stable isotope data are
 presented in ‰ relative to Pee Dee Belemnite for
 <sup>13</sup>C and atmospheric nitrogen for
 <sup>15</sup>N.
description: # d13C and d15N of Pacific halibut skeletal muscle tissue from the Gulf of
 Alaska, 2018
 [https://doi.org/10.5061/dryad.h9w0vt4qp](https://doi.org/10.5061/dryad.h9w0vt4qp) ## Description of the data and file structure Data are provided as a CSV file with rows representing individual fish and columns representing 1) age (years; as determined by otolith), 2) sex, 3) fork length (cm), 4) d15N (per mil), 5) d13C (per mil), 6) nitrogen concentration ([N]), 7) carbon concentration ([C]), and 8) C:N concentration ratio. ## Sharing/Access information Corresponding data for each fish including 1) International Pacific Halibut Commission Fisheries Independent Setline Survey Station, 2) latitude of first anchor of capture gear, 3) longitude of first anchor of capture gear, 4) minimum depth at which capture gear was placed (fathoms) are publicly available on the International Pacific Halibut Commission's website ([https://iphc.int/data/datatest/fishery-independent-setline-survey-fiss](https://iphc.int/data/datatest/fishery-independent-setline-survey-fiss).
DOI: 10.15468/dl.3rsnmz
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "GadmGid is BRA.13_1",
 "TaxonKey is Grammitis fluminensis"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003809-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.80gb5mkx4
title: Data from: Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)

description: Genome skimming (shallow whole-genome sequencing) offers time- and
 cost-efficient production of large amounts of DNA data that can be used to
 address unsolved evolutionary questions. Here we address phylogenetic
 relationships and topological incongruence in the tribe Anthospermeae
 (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear
 ribosomal cistron, and the plastome. All three genomic compartments
 resolve relationships in the Anthospermeae; the tribe is monophyletic and
 consists of three major subclades. Carpacoce Sond. is sister to the
 remaining clade, which comprises an African subclade and a Pacific
 subclade. Most results, from all three genomic compartments, are
 statistically well-supported; however, not fully consistent. Intergenomic
 topological incongruence is most notable in the Pacific subclade but
 present also in the African subclade. Hybridization and introgression
 followed by organelle capture may explain these conflicts but other
 processes, such as incomplete lineage sorting (ILS), can yield similar
 patterns and cannot be ruled out based on the results. Whereas the null
 hypothesis of congruence among all sequenced loci in the individual
 genomes could not be rejected for nuclear and mitochondrial data, it was
 rejected for plastid data. Phylogenetic analyses of three subsets of
 plastid loci identified using hierarchical likelihood ratio test
 demonstrated statistically supported intragenomic topological
 incongruence. Given that plastid genes are thought to be fully linked,
 this result is surprising and may suggest modelling or sampling error.
 However, biological processes such as biparental inheritance and
 inter-plastome recombination have been reported and may be responsible for
 the observed intragenomic incongruence. Mitochondrial insertions into the
 plastome are rarely documented in angiosperms. Our results indicate that a
 mitochondrial insertion event in the plastid trnSGGA-rps4 IGS region
 occurred in the common ancestor of the Pacific clade of Anthospermeae.
 Exclusion/inclusion of this locus in phylogenetic analyses had strong
 impact on topological results in the Pacific clade.
description: # Data from: Phylogenomics and topological conflicts in the tribe
 Anthospermeae (Rubiaceae) 
 This dataset contains mitochondrial, nuclear ribsomal, and plastid
 marker/locus alignments.See primary article for details on data generation
 and processing. ## Description of the data and file structure This
 repository has three (compressed) folders. Each folder includes
 marker/locus alignments (FASTA format) from the associated genomic
 compartment. <br>
DOI: 10.5061/dryad.g79cnp5wq
title: Extravascular administration of IGF1R antagonists protects against aortic aneurysm in rodent and porcine models

description: Aortic aneurysm is a life-threatening cardiovascular disease with high
 mortality. Herein, we first identified that plasma IGF1 was an independent
 risk factor in patients with abdominal aortic aneurysm. The IGF1 receptor
 was also activated in aneurysmal aortas from humans and mice, and SMC- or
 fibroblast-specific knockout of IGF1R attenuated AAA formation in mouse
 models, indicating the potential of IGF1R as a therapeutic target.
 Systemic administration of IGF1C peptide exerted an evident inhibitory
 effect on AAA formation and progression via competitive inhibition of IGF1
 binding to its receptor and modulation of downstream AKT/mTOR signaling.
 However, global inhibition of IGF1R signaling induces side effects,
 including abnormal glucose metabolism, muscular disorder, and pain
 hypersensitivity observed after systemic administration of IGF1C or the
 commercialized IGF1R antagonists. Accordingly, local administration of
 IGF1C was realized via ultrasound-guided percutaneous injection of an
 IGF1C-loaded hydrogel, and the therapeutic efficacy was confirmed in a pig
 AAA model, demonstrating its translational potential for AAA therapy.
description: Aneurysmal aortas were harvested from different groups (Control,
 GelMa, and IGF1C/GelMa) and mRNA was isolated from four aortas per sample
 using Trizol. Then, samples were sequenced by BGI using the DNBSEQ
 platform. The average mapping ratio with reference genome is 93.56%, and
 the average mapping ratio with gene is 74.53%; 18819 genes were
 identified. The complete dataset has not been processed.
description: # Extravascular administration of IGF1R antagonists protects against
 aortic aneurysm in rodent and porcine models
 [https://doi.org/10.5061/dryad.g79cnp5wq](https://doi.org/10.5061/dryad.g79cnp5wq) ## Description of the data and file structure In total, 3 groups (control, GelMa, IGF1C/GelMa) of datasets have been sequenced. In each group, aortic samples were taken from four different individuals. Each group corresponds to one .fq sequence file.
DOI: 10.15468/dl.6uk2cb
title: Occurrence Download

description: A dataset containing 176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Intsia palembanica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 176 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003810-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pc866t1wg
title: Hibernating female big brown bats (Eptesicus fuscus) adjust huddling and drinking behaviour, but not arousal frequency, in response to low humidity

description: Many mammals hibernate during winter, reducing energy expenditure via
 bouts of torpor. The majority of a hibernator’s energy reserves are used
 to fuel brief, but costly, arousals from torpor. Although arousals likely
 serve multiple functions, an important one is to restore water stores
 depleted during torpor. Many hibernating bat species require high
 humidity, presumably to reduce torpid water loss, but big brown bats
 (Eptesicus fuscus) appear tolerant of a wide humidity range. We tested the
 hypothesis that hibernating female E. fuscus use behavioural flexibility
 during torpor and arousals to maintain water balance and reduce energy
 expenditure. We predicted: (1) E. fuscus hibernating in dry conditions
 would exhibit more compact huddles during torpor and drink more frequently
 than bats in high humidity conditions; and (2) frequency and duration of
 torpor bouts and arousals, and thus, total loss of body mass would not
 differ between bats in both environments. We housed hibernating E. fuscus
 in temperature- and humidity-controlled incubators at 50% or 98% relative
 humidity (8°C, 110 days). Bats in the dry environment maintained a more
 compact huddle during torpor and drank more frequently during arousals.
 Bats in both environments had a similar number of arousals, but arousal
 duration was shorter in the dry environment. However, total loss of body
 mass over hibernation did not differ between treatments indicating that
 both groups used similar amounts of energy. Our results suggest that
 behavioural flexibility allows hibernating E. fuscus to maintain water
 balance and reduce energy costs across a wide range of hibernation
 humidities.
description: # Hibernating female big brown bats (Eptesicus fuscus) adjust huddling and
 drinking behaviour, but not arousal frequency, in response to low humidity
 ## Description of the data
 and file structure The excel file has four different sheets that contains
 (listed in order): **Sheet1_Video Data - arousals**: arousal begin and end
 time/date, bat ID, humidity treatment, drinking bouts, and associated
 starting body mass (prior to hibernation) and ending body mass (end of
 hibernation)) **Sheet2_Video Data - torpor:** torpor begin and end
 time/date, bat ID, humidity treatment, and associated starting body mass
 (prior to hibernation) and ending body mass (end of hibernation))
 **Sheet3_Arousal Definition Data**: bat ID, humidity treatment, arousal
 begining and end data/time, and associated skin temperature threshold.
 Note: arousals for video data do not have an associated skin temperature
 threshold. **Sheet4_Huddle Size Index**: photo date and time, humidity
 treatment, file name, and huddle measurements by observer 1 and 2.
DOI: 10.5281/zenodo.15561180
title: eZooMS analyses of medieval Danish and Swedish parchment charters

description: A total of 194 medieval parchment charters, issued in (medieval) Denmark and Sweden, were analysed for species identification with eZooMS. The research was carried out as part of my PhD at Lund University: "Parchment: demand and supply in medieval Scandinavia". The vast majority were calf parchment.

The dataset consists of .txt-files of all samples in triplicate, as well as a .csv-file that correlates the sample numbers with the Swedish National Archive's charter id, year of issue, location of issue, species, parchment glutamine index and bacollite scores, and a .txt-file for metadata.
DOI: 10.5061/dryad.n02v6wx44
title: Synergistic polyploidization and long-distance dispersal enable the global diversification of yellowcress herbs

description: Aim: Long-distance dispersal (LDD) plays an important role in shaping the
 distribution of global biodiversity. Polyploidy could favor invasion and
 thereby facilitate LDD. However, how and to what extent polyploidy
 interacts with LDD is unclear. Here, we test the putative role of
 polyploidy in the global dispersal of a cosmopolitan genus Rorippa.
 Location: Global. Time period: Late Miocene to present. Major taxa
 studied: Rorippa Scop., Brassicaceae. Methods: We traced the biogeographic
 and speciation history for 17 diploids and 41 polyploids of Rorippa using
 variation from plastid genomes and multiple nuclear loci. The ploidy role
 in dispersal rate difference was demonstrated using trait-dependent
 biogeographic modeling. Results: LDD shaped the amphitropical disjunction
 of Rorippa, during which polyploids showed higher dispersal rates than
 those of diploids, with 5.6× increase under the best-fitted model. Five
 diploids and 21 polyploids were identified as products of transoceanic
 speciation events. Polyploidy-involved LDD was more common in terms of
 polyploidization following LDD than those preceding LDD. Main conclusions:
 We demonstrate that polyploidy would be not only a driver but also a
 responder of LDD in Rorippa, highlighting a synergistic relationship
 between them. Our results provide a framework to uncover the biogeographic
 consequences of polyploidization and the joint roles of polyploidy and LDD
 in shaping the distribution of biodiversity.
description: This is the R scripts used in the project asr\_ploidy.R The R script used
 for ancestral ploidy state reconstruction under two or multiple ploidy
 level models (TPL or MPL model). RorippaBAYAREA\_ploidy.R The R script
 used for ploidy-based biogeographic modeling under BAYAREA model.
 RorippaDEC\_ploidy.R The R script used for ploidy-based biogeographic
 modeling under DEC model. RorippaDIVA\_ploidy.R The R script used for
 ploidy-based biogeographic modeling under DIVA model. phylomap.r The R
 script used to plot phylogenetic tree on map. rescale branch length.r The
 R script used to rescale branch length of phylogenetic tree. Appendix S1
 The appendix described the methods used for phylogenetic analyses, trait
 evolution of ploidy state, and collection of lifespan and mating system.
 ploidy.txt Ploidy data used for trait-based biogeographic modelling.
 rorippa\_cp.tre Tree data used for phylogenetic analysis. Supplement
 Figures S1-13.zip Supplement Figures in high-resolution PDF format.
DOI: 10.5061/dryad.d51c5b09b
title: Chromosome-level genome assembly of the bay scallop Argopecten irradians

description: The bay scallop, Argopecten irradians, is a species of major commercial,
 cultural, and ecological importance. It is endemic to the eastern coast of
 the United States but has also been introduced to China, where it supports
 a significant aquaculture industry. Here, we provide an annotated
 chromosome-level reference genome assembly for the bay scallop, assembled
 using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed
 over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%)
 of the assembled genome is contained within the 16 largest scaffolds,
 corresponding to the 16 chromosomes confirmed by Hi-C analysis. The
 assembly also includes the complete mitochondrial genome. Approximately
 36.2% of the genome consists of repetitive elements. The BUSCO analysis
 showed a completeness of 96.2%. We identified 33,772 protein-coding genes.
 This genome assembly will be a valuable resource for future research on
 evolutionary dynamics and adaptive mechanisms and will support
 genome-assisted breeding, contributing to the conservation and management
 of this iconic species in the face of environmental and pathogenic
 challenges.
description: # Chromosome-level genome assembly of the bay scallop *Argopecten
 irradians*
 [https://doi.org/10.5061/dryad.d51c5b09b](https://doi.org/10.5061/dryad.d51c5b09b) ### Files and variables #### File: Argopecten\_irradians\_NY.gff3 **Description:** GFF3 file of the *Argopecten irradians* NY genome #### File: Argopecten\_irradians\_NY\_proteins.fasta **Description:** Annotated proteins of the *Argopecten irradians* NY genome #### File: Argopecten\_irradians\_NY\_genome\_with\_mito.fasta.gz **Description:** FASTA file of the *Argopecten irradians* NY genome
DOI: 10.5281/zenodo.18405198
title: Table 1. Morphometric data for Liosomadoras oncinus and L. morrowi. n in Systematics of the Jaguar catfish genus Liosomadoras Fowler, 1940 (Auchenipteridae: Siluriformes)

description: Table 1. Morphometric data for Liosomadoras oncinus and L. morrowi. n = number of analized specimens; SD = Standard Deviation.
Liosomadoras oncinusLiosomadoras morrowinMeanRangeSDnMeanRangeSDStandard Length (mm)2598.7445.30 - 142.97673.0445.80 - 103.3Percentage of standard lengthHead length2530.6927.88 - 34.331.76633.0530.80 - 37.652.53Body depth2527.3423.80 - 31.971.98629.0624.89 - 33.783.81Body width2537.2833.87 - 39.831.76639.6136.96 - 42.802.21Predorsal length2540.9637.82 - 43.371.66642.3038.94 - 45.722.87Prepectoral length2528.2625.24 - 31.811.77630.7227.72 - 32.641.69Pectoral-fin spine length2532.6528.15 - 37.972.37633.3530.13 - 36.622.82Dorsal-fin spine length2425.4720.16 - 31.473.00626.6724.09 - 28.622.04First pelvic-fin ray length2517.7513.86 - 23.402.43617.2912.88 - 21.653.04Caudal-peduncle depth2512.8110.09 - 14.811.03612.7811.35 - 15.111.40Caudal-peduncle length2514.3412.21 - 17.351.12612.4211.34 - 14.631.23Percentages of head lengthHorizontal eye diameter2516.2113.57 - 18.121.13616.1114.01 - 19.732.10Snout length2534.7029.92 - 40.272.03634.9732.14 - 39.232.33Bony interorbital width2551.8446.21 - 56.502.36654.3150.48 - 56.462.06
description: Published as part of Birindelli, José L. O. & Zuanon, Jansen, 2012, Systematics of the Jaguar catfish genus Liosomadoras Fowler, 1940 (Auchenipteridae: Siluriformes), pp. 3 in Neotropical Ichthyology 10 (1) on page 3, DOI: 10.1590/S1679-62252012000100001, http://zenodo.org/record/10660768
DOI: 10.5281/zenodo.18405197
title: Table 1. Morphometric data for Liosomadoras oncinus and L. morrowi. n in Systematics of the Jaguar catfish genus Liosomadoras Fowler, 1940 (Auchenipteridae: Siluriformes)

description: Table 1. Morphometric data for Liosomadoras oncinus and L. morrowi. n = number of analized specimens; SD = Standard Deviation.
Liosomadoras oncinusLiosomadoras morrowinMeanRangeSDnMeanRangeSDStandard Length (mm)2598.7445.30 - 142.97673.0445.80 - 103.3Percentage of standard lengthHead length2530.6927.88 - 34.331.76633.0530.80 - 37.652.53Body depth2527.3423.80 - 31.971.98629.0624.89 - 33.783.81Body width2537.2833.87 - 39.831.76639.6136.96 - 42.802.21Predorsal length2540.9637.82 - 43.371.66642.3038.94 - 45.722.87Prepectoral length2528.2625.24 - 31.811.77630.7227.72 - 32.641.69Pectoral-fin spine length2532.6528.15 - 37.972.37633.3530.13 - 36.622.82Dorsal-fin spine length2425.4720.16 - 31.473.00626.6724.09 - 28.622.04First pelvic-fin ray length2517.7513.86 - 23.402.43617.2912.88 - 21.653.04Caudal-peduncle depth2512.8110.09 - 14.811.03612.7811.35 - 15.111.40Caudal-peduncle length2514.3412.21 - 17.351.12612.4211.34 - 14.631.23Percentages of head lengthHorizontal eye diameter2516.2113.57 - 18.121.13616.1114.01 - 19.732.10Snout length2534.7029.92 - 40.272.03634.9732.14 - 39.232.33Bony interorbital width2551.8446.21 - 56.502.36654.3150.48 - 56.462.06
description: Published as part of Birindelli, José L. O. & Zuanon, Jansen, 2012, Systematics of the Jaguar catfish genus Liosomadoras Fowler, 1940 (Auchenipteridae: Siluriformes), pp. 3 in Neotropical Ichthyology 10 (1) on page 3, DOI: 10.1590/S1679-62252012000100001, http://zenodo.org/record/10660768
DOI: 10.5061/dryad.pk0p2ngvx
title: Flying, nectar-loaded honey bees conserve water and improve heat tolerance by reducing wingbeat frequency and metabolic heat production

description: Heat waves are becoming increasingly common due to climate change, making
 it crucial to identify and understand the capacities for insect
 pollinators, such as honey bees, to avoid overheating. We examined the
 effects of hot, dry air temperatures on the physiological and behavioral
 mechanisms that honey bees use to fly when carrying nectar loads, to
 assess how foraging is limited by overheating or desiccation. We found
 that flight muscle temperatures increased linearly with load mass at air
 temperatures of 20 or 30°C, but, remarkably, there was no change with
 increasing nectar loads at an air temperature of 40°C. Flying,
 nectar-loaded bees were able to avoid overheating at 40°C by reducing
 their flight metabolic rates and increasing evaporative cooling. At high
 body temperatures, bees apparently increase flight efficiency by lowering
 their wingbeat frequency and increasing stroke amplitude to compensate,
 reducing the need for evaporative cooling. However, even with reductions
 in metabolic heat production, desiccation likely limits foraging at
 temperatures well below bees’ critical thermal maxima in hot, dry
 conditions.
description: To determine how high air temperatures affect thermoregulation,
 water balance, and force generation during foraging flight, we measured
 flight muscle temperatures, flight metabolic rates, and water loss rates
 of honey bees carrying nectar loads at three different air temperatures
 (20, 30, and 40 °C), and measured wing kinematics with high-speed video at
 air temperatures of 25 and 40 °C. We then used these data and the prior
 literature to model heat-limits on honey bee flight.
description: # Flying, nectar-loaded honey bees conserve water and improve heat
 tolerance by reducing wingbeat frequency and metabolic heat production
 To determine how high air
 temperatures affect thermoregulation, water balance, and force generation
 during foraging flight, we measured flight muscle temperatures, flight
 metabolic rates, and water loss rates of honey bees carrying nectar loads
 at three different air temperatures (20, 30, and 40°C), and measured wing
 kinematics with high-speed video at air temperatures of 25 and 40°C. We
 then used these data and the prior literature to model heat-limits on
 honey bee flight. ## Description of the data and file structure There are
 multiple pages within the included dataset, labelled accordingly. ##
 Sharing/Access information If problems arise while downloading the
 corresponding dataset, feel free to contact the corresponding author. ##
 Code/Software The code used in our analysis can be made available upon
 request.
DOI: 10.15468/dl.zjpejw
title: Occurrence Download

description: A dataset containing 997 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Prosopis nigra, Prosopis affinis, Prosopis alba)",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 997 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003811-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.