cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jwstqjq6t
title: Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae

description: Species within the mint family, Lamiaceae, are widely used for their
 culinary, cultural, and medicinal properties due to production of a wide
 variety of specialized metabolites, especially terpenoids. To further our
 understanding of genome diversity in the Lamiaceae and to provide a
 resource for mining biochemical pathways, we generated high-quality genome
 assemblies of four economically important culinary herbs, namely, sweet
 basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.),
 oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.),
 and characterized their terpenoid diversity through metabolite profiling
 and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were
 identified in leaf tissue from the four species. Genes encoding enzymes
 responsible for the biosynthesis of precursors for mono- and
 sesqui-terpene synthases were identified in all four species. Across all
 four species, a total of 235 terpene synthases were identified, ranging
 from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study
 provides valuable resources for further investigation of the genetic basis
 of chemodiversity in these important culinary herbs.
description: -
 aa.min_10k_final.fa fasta genome assembly with
 minimum 10k scaffold size and no N scaffolds
 -
 aa.working_models.cdna.fa cDNA sequences of all
 isoforms of the working gene set -
 aa.working_models.cds.fa CDS of all isoforms of the
 working gene set -
 aa.working_models.gff3 GFF of all isoforms of the
 working gene set -
 aa.working_models.pep.fa Peptide sequence of all
 isoforms of the working gene set -
 aa.working_models.pep.func_anno.txt
 Functional annotation of
 the working gene set -
 aa.gene_models.hc.cdna.fa cDNA sequences of all high
 confidence gene models -
 aa.gene_models.hc.cds.fa CDS of all high confidence
 gene models -
 aa.gene_models.hc.gff3 GFF of all high confidence
 gene models -
 aa.gene_models.hc.pep.fa Peptide sequences of all
 high confidence gene models -
 aa.gene_models.hc.pep.func_anno.txt
 Functional annotation of
 the high confidence gene set -
 aa.gene_models.hc.repr.gff3 GFF of high confidence
 representative gene models -
 aa.gene_models.hc.repr.pep.fa Peptide sequences of high
 confidence representative gene models
 -
 Cufflinks_FPKMs_functions_all_hc_genes.txt Expression abundances of
 the high confidence gene model set
 -
 Cufflinks_FPKMs_functions_working_genes.txt Expression abundances of
 the working gene model set -
 Readme_culinary_herbs_DataDryad_files.docx Readme
DOI: 10.5061/dryad.mcvdncjzb
title: Non-native species outperform natives in coastal marine ecosystems subjected to warming and freshening events - A meta-analysis of coastal marine native and non-native species responses to experimentally manipulated climatic events

description: Aims: Contemporary climate change and biological invasions are two main
 drivers of biodiversity redistribution. Interactive effects between these
 drivers have been reported in a number of study systems, yet results are
 conflicting. Some studies find that future climate change facilitates the
 spread and success of non-native species, especially those with broad
 physiological tolerances. Other studies conclude that non-natives are
 vulnerable to current and future changes in climatic conditions. Given
 that most studies have focused on terrestrial species, here we contribute
 to this debate by analysing responses of coastal native and non-native
 fauna and flora to key climate-related stressors namely increased
 temperature (warming) and decreased salinity (freshening). Location:
 Global. Time period: 2002 – 2019. Major taxa studied: Marine benthic
 macrophytes and invertebrates. Methods: We conducted a meta-analysis of
 results from experiments investigating the performance (e.g., growth,
 survival and reproduction) of sessile and sedentary species from benthic
 marine communities to warming and freshening. Results: We found
 evidence of positive responses to elevated temperature across a range of
 biological processes on non-native species, whereas the performance of
 native species declined. Similarly, decreased salinity negatively affected
 the biological processes of native species, but non-natives showed no
 positive or negative overall response to freshening. Main conclusions: Our
 study showed that non-native species outperform natives under a wide
 variety of warming and freshening conditions. The growth and reproduction
 of non-natives are enhanced by warmer temperatures, and thus ocean warming
 is expected to facilitate future spread and success of non-native species.
 Increased freshening, however, will likely have a negative impact in the
 future in both native and non-native species and thus is expected to be a
 driver of significant change in coastal marine ecosystems. Our
 comprehensive literature search revealed the need of more studies focusing
 on salinity changes and highlighted the need to expand our understanding
 of climate change drivers beyond warming.
description: Data were extracted from peer-reviewed published literature from
 studies that measured biological responses of native and non-native
 species to experimentally controlled changes in warming (temperature) and
 freshening (salinity).
DOI: 10.15468/dl.byjpdg
title: Occurrence Download

description: A dataset containing 2788 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cajanus cajan",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2788 records from 269 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002494-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5068/d1c38j
title: An incoherent feedforward loop interprets NFkappaB/RelA dynamics to determine TNF-induced necroptosis decisions

description: Balancing cell death is essential to maintain healthy tissue homeostasis
 and prevent disease. Tumor necrosis factor (TNF) not only activates
 nuclear factor kB (NFkappaB), which coordinates the cellular
 response to inflammation, but may also trigger necroptosis, a
 pro-inflammatory form of cell death. Whether TNF-induced NFkappaB affects
 the fate decision to undergo TNF-induced necroptosis is unclear. Live-cell
 microscopy and model-aided analysis of death kinetics identified a
 molecular circuit that interprets TNF-induced NFkappaB/RelA dynamics to
 control necroptosis decisions.Inducible expression of TNFAIP3/A20 forms an
 incoherent feedforward loop to interfere with the RIPK3-containing
 necrosome complex and protect a fraction of cells from transient,
 but not long-term TNF exposure. Furthermore, dysregulated NFkappaB
 dynamics often associated with disease diminish TNF-induced necroptosis.
 Our results suggest that TNF’s dual roles in either coordinating
 cellular responses to inflammation, or further amplifying inflammation are
 determined by a dynamic NFkappaB-A20-RIPK3 circuit, that could be targeted
 to treat inflammation and cancer.
description: This data set is part of submission doi:10.5068/D1W09J
DOI: 10.5061/dryad.37pvmcvh7
title: Serum 25(OH)D level on hospital admission is correlated with COVID-19 mortality

description: Objective: Vitamin D deficiency was previously correlated with incidence
 and severity of COVID-19. We investigated the correlation between
 serum 25(OH)D level on admission and radiological stage and
 outcome of COVID-19 pneumonia.  Methods: Retrospective
 observational trial on 186 SARS-CoV-2-infected individuals hospitalized
 from March 1, 2020 to April 7, 2020 with combined chest CT and 25(OH)D
 measurement on admission. Multivariate analysis was performed to study if
 vitamin D deficiency (25(OH)D &lt; 20 ng/mL) predicts survival
 independently of confounding comorbidities.  Results: 59% of
 COVID-19 patients were vitamin D deficient on admission: 47% of females
 and 67% of males. Particularly male COVID-19 patients showed progressively
 lower 25(OH)D with advancing radiological stage, with deficiency rates
 increasing from 55% in stage 1 to 74% in stage 3. Vitamin D deficiency on
 admission was not confounded by age, chronic lung disease, coronary artery
 disease/hypertension or diabetes and was correlated with mortality
 (OR=3.87, 95%CI 1.30-11.55), independently of other predictors including
 age (OR=1.09, 95%CI 1.03-1.14), chronic lung disease (OR=3.61, 95% CI
 1.18-11.09) and extent of lung damage expressed by chest CT severity score
 (1.12, 95% CI 1.01-1.25).  Conclusions: low 25(OH)D levels on
 admission are associated with COVID-19 disease mortality
description: <b><i>Statistical
 analysis</i></b> Data (not normally distributed) are expressed
 as medians (IQR) and Mann-Whitney test was used to test statistical
 differences between groups. Proportions for categorical variables were
 compared using chi-squared test. Multivariate analysis was done by
 logistic regression or multiple regression as indicated. Odds ratios and
 95% CIs were calculated with bivariable logistic regression for assessment
 of demographic characteristics and comorbidities associated with 25-OH
 vitamin deficiency, and for assessment of demographic characteristics,
 comorbidities, vitamin D status and CT findings on admission associated
 with survival outcome. The authors did not correct for multiple
 comparisons. Statistical analyses were performed using MedCalc (version
 12.2.1, Mariakerke, Belgium) and considered significant if P value was
 less than .05.   <em><strong>Supplementary
 methods:</strong></em> detailed scanning and image analysis
 protocol chest CT <i> </i>
description: This file contains descriptive information on statistical
 analysis (including multivariate analysis to predict COVID-19 outcome) and
 chest CT. Source data (25(OH)D and structured chest CT
 data) are available upon email request to
 geert.martens@azdelta.be
DOI: 10.5061/dryad.fqz612jqs
title: Reduction of elevated proton leak rejuvenates mitochondria in the aged cardiomyocyte

description: Aging-associated diseases, including cardiac dysfunction, are increasingly
 common in the population. However, the mechanisms of physiologic aging in
 general, and cardiac aging in particular, remain poorly understood.
 Age-related heart impairment is lacking a clinically effective treatment.
 Using the model of naturally aging mice and rats, we show direct evidence
 of increased proton leak in the aged heart mitochondria. Moreover, our
 data suggested ANT1 as the most likely site of mediating increased
 mitochondrial proton permeability in old cardiomyocytes. Most importantly,
 the tetra-peptide SS-31 prevents age-related excess proton entry,
 decreases the mitochondrial flash activity and mitochondrial permeability
 transition pore opening, rejuvenates mitochondrial function by direct
 association with ANT1 and the mitochondrial ATP synthasome, and leads to
 substantial reversal of diastolic dysfunction. Our results uncover the
 excessive proton leak as a novel mechanism of age-related cardiac
 dysfunction and elucidate how SS-31 is able to reverse this clinically
 important complication of cardiac aging.
description: Mitochondrial respiration data were collected by Seahorse Assay
 and combined all the data in the attached excel file.
 Confocal imaging data were collceted by Leica SP8X and images
 were analyzed by the Leica LASX or FIJI software.  The
 western blot images were collected by FluoChem Q machine and analyzed by
 AlphaView software.
DOI: 10.5061/dryad.s7h44j14x
title: UV reflectance in poison frog

description: We have identified strong UV reflectance in the white spots of only a
 single population of the polymorphic/polytypic poison frog species Oophaga
 sylvatica. As congeners (O. pumilio) are unable to view UV signals, it
 stands to reason that natural selection, or neutral processes are likely
 to be responsible for these signals. We employ visual modeling techniques
 to estimate the perception of these UV signals, and in a series of
 comparisons we show surprisingly minimal gains in frog contrast due to
 their addition.
description: Digital images were taken using a tripod mounted full spectrum
 quartz converted Canon EOS 7D combined with a metal body Nikkor EL 80mm
 lens (known for high UV transmission), and a series of pass filters. To
 capture the full range of wavelengths visible to UV-sensitive species we
 took two photographs of each frog: one in human-visible wavelengths (VIS)
 and one in the ultraviolet (UV). For human-visible spectra the lens was
 fitted with a Baader UV-IR blocking filter that allowed transmission from
 420-680 nm. For the UV photographs we fitted a Baader UV pass filter that
 allowed transmission from 320-380 nm. To ensure our camera matched known
 sensitivities included in the Multispectral Image Calibration and Analysis
 (MICA) Toolbox, the quartz conversion was undertaken at the same facility
 as the toolbox authors (Troscianko and Stevens, 2015) (Advanced Camera
 Services Limited, Norfolk, UK). Images were taken in RAW format and each
 photograph included 10% and 77% reflectance standards. Downwelling
 illumination was provided by unfiltered full sun local lighting conditions
 within frog microhabitats at peak frog activity. Photograph histograms
 were manually checked for each photograph (UV and visible) to ensure
 proper exposure and prevent data loss due to overexposure.
DOI: 10.5061/dryad.dr7sqv9wd
title: Phylogenomic resolution of sea spider diversification through integration of multiple data classes

description: Despite significant advances in invertebrate phylogenomics over the past
 decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains
 elusive. Due to the inaccessibility of some small-bodied lineages, few
 phylogenetic studies have sampled all sea spider families. Previous
 efforts based on a handful of genes have yielded unstable tree topologies.
 Here, we inferred the relationships of 89 sea spider species using
 targeted capture of the mitochondrial genome, 56 conserved exons, 101
 ultraconserved elements, and three nuclear ribosomal genes. We inferred
 molecular divergence times by integrating morphological data for fossil
 species to calibrate 15 nodes in the arthropod tree of life. This
 integration of data classes resolved the basal topology of sea spiders
 with high support. The enigmatic family Austrodecidae was resolved as the
 sister group to the remaining Pycnogonida and the small-bodied family
 Rhynchothoracidae as the sister group of the robust-bodied family
 Pycnogonidae. Molecular divergence time estimation recovered a basal
 divergence of crown group sea spiders in the Ordovician. Comparison of
 diversification dynamics with other marine invertebrate taxa that
 originated in the Paleozoic suggests that sea spiders and some crustacean
 groups exhibit resilience to mass extinction episodes, relative to mollusk
 and echinoderm lineages.
DOI: 10.5068/d17957
title: Pulsed electromagnetic field (PEMF) transiently stimulates the rate of mineralization in a 3-dimensional ring culture model of osteogenesis

description: Pulsed Electromagnetic Frequencies (PEMF) have shown efficacy in bone
 repair and yet the optimum characteristics of this modality and its
 molecular mechanism remain unclear.  To determine the effects of
 timing of PEMF treatment we present a three-dimensional ring culture model
 of osteogenesis that demonstrates strong de novo generation of collagen
 and mineral matrix and exhibits stimulation by PEMF in multiple stages
 over 62 days of culture.  Mouse postnatal day 2 calvarial
 pre-osteoblasts were cast within and around Teflon rings by polymerization
 of fibrinogen and cultured suspended without contact with tissue culture
 plastic.  Ring constructs were exposed to PEMF for 4h/day for the
 entire culture (Daily), or just during Day1-Day10, Day11-Day 27, or
 Day28-Day63 and cultured without PEMF for the preceding or remaining days,
 and compared to no-PEMF controls. PEMF was conducted as HF Physio, 40.85
 kHz frequency with a 67 ms burst period.  Osteogenesis was
 kinetically monitored by repeated fluorescence measurements of
 continuously present Alizarin Red S (ARS) and periodically confirmed by
 micro-CT.  PEMF treatment induced early-onset and statistically
 significant transient stimulation (~4-fold) of the mineralization rate
 when PEMF was applied Daily, or during D1-D10 and D11-D27. 
 Stimulation was apparent but not significant between D28-D63 by ARS but
 was significant at D63 by micro-CT.  PEMF also shifted the
 micro-CT density profiles to higher densities in each PEMF treatment group
 .  Ring culture generated tissue with a mineral:matrix ratio of
 2.0 by thermogravimetric analysis (80% of the calvaria control) and the
 deposited crystal structure was 50% hydroxyapatite by X-ray diffraction
 (63% of the calvaria and femur controls), independent of PEMF. 
 These results were consistent with backscatter, secondary electron, and
 elemental analysis by scanning electron microscopy.  Thus, in a
 defined, strong osteogenic environment, PEMF applied at different times
 was capable of further stimulation of osteogenesis with the potential to
 enhance bone repair.
DOI: 10.5061/dryad.bvq83bk6g
title: Data from: Changes in aspects of emergent and submerged vegetation cover, richness, and diversity in a fragmenting marsh system

description: Habitat fragmentation is a global environmental challenge, and the marshes
 of southeastern Louisiana are a hotspot for habitat fragmentation.
 Evaluating marsh ecosystems during the transition from intact to
 fragmented is critical to predict future changes and inform effective
 conservation and restoration plans. We sampled three sites in Terrebonne
 Basin, Louisiana to characterize a fragmenting emergent-vegetation
 dominated system, investigate the relationship between plant species
 richness and diversity and marsh fragmentation, and determine the
 relationship between marsh fragmentation and cover of submerged aquatic
 vegetation (SAV). Emergent plant richness and diversity were higher in
 areas with low salinity and high surface elevation. Although these areas
 had relatively low fragmentation, there was no direct relationship between
 richness or diversity and measures of marsh fragmentation. Despite greater
 light availability in highly fragmented areas, SAV was restricted to areas
 with low fragmentation, suggesting light availability was not the factor
 limiting SAV colonization into open water areas. Results from this study
 highlight the complex interactions of geomorphological and biotic
 processes within a fragmenting marsh and suggest that physical drivers
 such as salinity and elevation are a better indicator of emergent plant
 community structure in this system than degree of fragmentation.
DOI: 10.15468/dl.25hg3a
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anolis rivalis"
 ]
}

 The dataset includes 63 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002495-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j0zpc86c6
title: Seasonal patterns of melatonin alter aggressive phenotypes of female Siberian hamsters

description: Many animal species exhibit year-round aggression, a behaviour that allows
 individuals to compete for limited resources in their environment
 (e.g., food and mates). Interestingly, this high degree of territoriality
 persists during the non-breeding season, despite low levels of
 circulating gonadal steroids (i.e., testosterone [T] and oestradiol [E2]).
 Our previous work suggests that the pineal hormone melatonin mediates a
 ‘seasonal switch’ from gonadal to adrenal regulation of
 aggression in Siberian hamsters (Phodopus sungorus); solitary, seasonally
 breeding mammals that display increased aggression during the
 short, ‘winter-like’ days (SDs) of the non-breeding season. To test the
 hypothesis that melatonin elevates non-breeding aggression by increasing
 circulating and neural steroid metabolism, we housed female
 hamsters in long days (LDs) or SDs, administered them timed or mis-timed
 melatonin injections (mimic or do not mimic a SD-like signal,
 respectively), and measured aggression, circulating hormone profiles, and
 aromatase (ARO) immunoreactivity in brain regions associated with
 aggressive or reproductive behaviours (paraventricular
 hypothalamic nucleus [PVN], periaqueductal gray [PAG], and ventral
 tegmental area [VTA]). Females that were responsive to SD
 photoperiods (SD-R) and LD females given timed melatonin injections
 (Mel-T) exhibited gonadal regression and reduced circulating E2, but
 increased aggression and circulating dehydroepiandrosterone
 (DHEA). Furthermore, aggressive challenges differentially altered
 circulating hormone profiles across seasonal
 phenotypes; reproductively inactive females (ie, SD-R and Mel-T
 females) reduced circulating DHEA and T, but increased E2 after an
 aggressive interaction, whereas reproductively active females
 (i.e., LD females, SD non-responder females, and LD females given
 mis-timed melatonin injections) solely increased circulating E2.
 Although no differences in neural ARO abundance were observed, LD
 and SD-R females showed distinct associations between ARO cell
 density and aggressive behaviour in the PVN, PAG, and VTA. Taken
 together, these results suggest that melatonin increases non-breeding
 aggression by elevating circulating steroid metabolism after an aggressive
 encounter and by regulating behaviourally relevant neural
 circuits in a region-specific manner.
DOI: 10.25338/b8xk8r
title: Evolved differences in energy metabolism and growth dictate the impacts of ocean acidification on abalone aquaculture

description: Ocean acidification (OA) poses a major threat to marine ecosystems and
 shellfish aquaculture. A promising mitigation strategy is the
 identification and breeding of shellfish varieties exhibiting resilience
 to acidification stress. We experimentally compared the effects of OA on
 two populations of red abalone (Haliotis rufescens), a marine
 mollusck important to fisheries and global aquaculture. Results
 from our experiments simulating captive aquaculture conditions
 demonstrated that abalone sourced from a strong upwelling region were
 tolerant of ongoing OA, whereas a captive-raised population sourced from a
 region of weaker upwelling exhibited significant mortality and
 vulnerability to OA. This difference was linked to population-specific
 variation in the maternal provisioning of lipids to offspring, with a
 positive correlation between lipid concentrations and survival under OA.
 This relationship also persisted in experiments on second-generation
 animals, and larval lipid consumption rates varied among paternal crosses,
 which is consistent with the presence of genetic variation for
 physiological traits relevant for OA survival. Across experimental trials,
 growth rates differed among family lineages, and the highest mortality
 under OA occurred in the fastest growing crosses. Identifying traits that
 convey resilience to OA is critical to the continued success of abalone
 and other shellfish production, and these mitigation efforts should be
 incorporated into breeding programs for commercial and restoration
 aquaculture.