cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4xgxd2573
title: Evolutionary variation in MADS-box dimerization affects floral development and protein abundance in maize

description: Interactions between MADS-box transcription factors are critical in the
 regulation of floral development, and shifting MADS-box protein-protein
 interactions are predicted to have influenced floral evolution. However,
 precisely how evolutionary variation in protein-protein interactions
 affects MADS-box protein function remains unknown. To assess the impact of
 changing MADS-box protein-protein interactions on transcription factor
 function, we turned to the grasses, where interactions between B-class
 MADS-box proteins vary. We tested the functional consequences of this
 evolutionary variability using maize as an experimental system. We found
 that differential B-class dimerization was associated with subtle,
 quantitative differences in stamen shape. In contrast, differential
 dimerization resulted in large-scale changes to downstream gene
 expression. Differential dimerization also affected B-class complex
 composition and abundance, independent of transcript levels. This
 indicates that differential B-class dimerization affects protein
 degradation, revealing an important consequence for evolutionary
 variability in MADS-box interactions. Our results highlight complexity in
 the evolution of developmental gene networks - changing protein-protein
 interactions could affect not only the composition of transcription factor
 complexes, but also their degradation and persistence in developing
 flowers. Our results also show how coding change in a pleiotropic master
 regulator could have small, quantitative effects on development.
DOI: 10.13140/rg.2.2.33990.13125
title: Рецензия 2 на монографию Модифицированные материалы с использованием золошлаковых отходов ТЭЦ для строительства автомобильных дорог
DOI: 10.15468/dl.3ccspu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Taeniochauliodes minutus, Taeniochauliodes, Taeniochauliodes natalensis, Taeniochauliodes attenuatus, Platychauliodes, Platychauliodes thornei, Platychauliodes capensis, Platychauliodes woodi, Platychauliodes pusillus, Leptosialis, Leptosialis africana, Sialis, Haplosialis afra, Haplosialis, Taeniochauliodes angustus, Madachauliodes bicuspidatus, Madachauliodes, Chloroniella, Chloroniella peringueyi, Taeniochauliodes fuscus, Euchauliodes distinctus, Euchauliodes, Leptosialis necopinata, Taeniochauliodes esbenpeterseni, Madachauliodes torrentialis, Taeniochauliodes ochraceopennis, Madachauliodes ranomafana, Taeniochauliodes barnardi)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "Issue" : [
 "is one of (Recorded date invalid, Recorded date mismatch, Recorded date unlikely, Modified date invalid)"
 ]
 }
 },
 "Geometry MULTIPOLYGON (((43.888 -16.3914, 43.9114 -16.4108, 43.9142 -16.4125, 43.9447 -16.4246, 43.9775 -16.4261, 44.0091 -16.4169, 44.0359 -16.398, 44.0552 -16.3714, 44.0648 -16.3402, 43.8646 -16.3402, 43.8716 -16.3658, 43.888 -16.3914)), ((45.1136 -25.6939, 45.1495 -25.7051, 45.187 -25.7022, 46.5135 -25.3402, 44.4503 -25.3402, 45.1136 -25.6939)), ((44.3278 -25.3729, 44.3587 -25.3676, 44.3884 -25.3575, 44.4115 -25.3402, 44.2371 -25.3402, 44.2444 -25.3489, 44.2694 -25.3652, 44.298 -25.3735, 44.3278 -25.3729)), ((37.6272 -46.8232, 37.5487 -46.8519, 37.5408 -46.8564, 37.5408 -47.0354, 37.5639 -47.044, 37.5962 -47.045, 37.9207 -47.0019, 37.9523 -46.9922, 37.979 -46.9727, 37.9979 -46.9455, 38.0069 -46.9137, 38.005 -46.8807, 37.9925 -46.8501, 37.9706 -46.8252, 37.9065 -46.773, 37.8765 -46.7562, 37.8427 -46.7506, 37.809 -46.7566, 37.8063 -46.7576, 37.7981 -46.7468, 37.77 -46.7282, 37.7374 -46.72, 37.7338 -46.7197, 37.7042 -46.7219, 37.6766 -46.7326, 37.6533 -46.7509, 37.6364 -46.7753, 37.6274 -46.8035, 37.6272 -46.8232)), ((38.0062 -46.5737, 37.9938 -46.5464, 37.974 -46.5239, 37.9483 -46.5083, 37.946 -46.5074, 37.9134 -46.4998, 37.8801 -46.5035, 37.85 -46.5179, 37.8456 -46.5222, 37.8272 -46.5314, 37.8006 -46.5507, 37.7817 -46.5777, 37.7726 -46.6093, 37.7743 -46.6422, 37.7865 -46.6728, 37.808 -46.6977, 37.8693 -46.7488, 37.8973 -46.7652, 37.9291 -46.7719, 37.9614 -46.7679, 37.9906 -46.7539, 38.0139 -46.7312, 38.0286 -46.7023, 38.0333 -46.6701, 38.0275 -46.6382, 38.0071 -46.5814, 38.0062 -46.5737)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002523-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.wh70rxwkj
title: A novel TNFR2 agonist antibody expands highly potent regulatory T cells

description: Regulatory T cells (Treg cells) restrict immune system activity,
 such as in response to self-antigens, and are switched on by tumor
 necrosis factor receptor 2 (TNFR2). Therapeutic activation of TNFR2,
 thereby expanding Treg cells and suppressing immune activity, may
 be beneficial to patients with various inflammatory diseases. Here, we
 characterized a new human TNFR2-directed antibody agonist isolated from
 mice. We found that the antibody agonist expanded the number of
 Treg cells within cultures of primary human CD4+ T cells
 from healthy donors and patients with type 1 diabetes or Sézary syndrome.
 These Treg cells had increased metabolic gene expression and
 intracellular itaconate concentrations, characteristics associated with
 maximally suppressive, anti-inflammatory Treg cells. Furthermore,
 antibody-expanded Treg cells repressed the activity of primary
 human CD8+ effector T cells (Teff cells). Epitope
 mapping suggested that the antibody bound to TNFR2 through a natural
 cross-linking surface and that Treg cell expansion was
 independent of the antibody Fc region. In addition, Treg cell expansion
 was not increased by adding either supplemental TNF ligand or a
 cross-linking reagent, suggesting that the antibody agonist by itself can
 elicit maximal activity, a notion that was confirmed by increased
 secretion of soluble TNFR2. Pending in vivo tests, these features indicate
 that this TNFR2 antibody agonist has the potential to safely and
 effectively treat various inflammatory disorders.
description: Isolated human CD4 cells were cultured for 10 hours in the presence of IL2 only or IL-2 and agonist antibody. The cells were then washed with PBS, total RNA isolated and processed for RNAseq on NextSeq flow cells.
DOI: 10.5061/dryad.ttdz08kw0
title: Data from the study: Effect of experimental DNA demethylation on phytohormones production and palatability of a clonal plant after induction via jasmonic acid

description: Many plant species protect themselves against herbivores through
 mechanical or chemical so-called inducible defences (ID). These are
 regulated via a hormonal cascade which may be under epigenetic control and
 in which jasmonic acid (JA) plays a prominent role. In this study, we
 indirectly tested the role of DNA methylation in the production of ID and
 the synthesis of hormones involved in the ID signalling cascade. Using
 different intensities of 5-azacytidine application, we aimed to produce
 plants of Trifolium repens with different levels of DNA methylation
 alteration. We then elicited the plants together with controls, i.e.
 plants with natural DNA methylation status, with JA and then indirectly
 recorded ID production in herbivore-choice trials in which the leaves of
 plants with different DNA methylation statuses were provided to
 caterpillars of a generalist herbivore, Spodoptera littoralis. We also
 analysed the balance of several key defence hormones such as jasmonates,
 abscisic acid (ABA), indole-3-acetic acid (IAA) and salicylic acid in the
 plants. We found that the Spodoptera littoralis preferred demethylated
 plants over non-demethylated controls. Demethylation also reduced
 production of JA, ABA and IAA. We conclude that DNA methylation modulates
 expression of ID likely via regulation of signalling hormones involved in
 the establishment of defence.
description: Cafeteria data collected as an area eaten by caterpillars.
 Endogenous levels of jasmonates, IAA, ABA and SA were determined in plant
 tissue (20 mg of fresh weight) according to the method described by
 Floková et al. (2014). These phytohormones were extracted using an aqueous
 solution of methanol (10% MeOH/H<sub>2</sub>O, v/v). A
 cocktail of stable isotope-labelled standards was added as follows: 5 pmol
 of [<sup>13</sup>C<sub>6</sub>]IAA, 10 pmol of
 [<sup>2</sup>H<sub>6</sub>]JA,
 [<sup>2</sup>H<sub>2</sub>]JA-Ile, and
 [<sup>2</sup>H<sub>6</sub>]ABA, 20 pmol of
 [<sup>2</sup>H<sub>4</sub>]SA and
 [<sup>2</sup>H<sub>5</sub>]OPDA (all from Olchemim
 Ltd, Czech Republic) per sample to validate the LC-MS method. The extracts
 were purified using Oasis HLB columns (30 mg/1 ml, Waters) and targeted
 analytes were eluted using 80% MeOH. Eluent containing all compounds was
 gently evaporated to dryness under a stream of nitrogen. Neutral and
 acidic phytohormones were determined using ultra-high-performance liquid
 chromatography-electrospray tandem mass spectrometry (an Acquity UPLC
 I-Class System coupled to a Xevo TQ-S MS, all from Waters).
DOI: 10.5061/dryad.kprr4xh2s
title: Do meristic characters used in phylogenetic analysis evolve in an ordered manner?

description: The use of ordered characters in phylogenetic analysis has been
 inconsistent through research history. It has become more widespread in
 recent years, and some have advocated that all characters representing
 continuous or meristic traits should be ordered as a matter of course.
 Here, using the example of dental evolution, we examine two factors that
 may impact on whether meristic characters actually evolve in an ordered
 manner: the regulatory hierarchy governing the development of teeth that
 allows large sections of the entire tooth-row to be supressed in a single
 transition, and regionalisation of the tooth row where different modules
 have a degree of independence in their evolution. These are studied using
 both empirical and simulated data. Models of evolution of such characters
 are examined over molecular phylogenies to see if ordered or unordered
 models fit best. Simulations of tooth-row evolution are designed to
 incorporate changes in region size and multiple levels developmental
 control to supress individual regions or the entire row. The empirical
 analyses show that in a clade with largely homodont dentition the
 characters evolve in an ordered manner, but if dentition is heterodont
 with distinct regionalisation their evolution better fits an unordered
 model. In the simulations, even if teeth are added and removed from the
 tooth row in an ordered manner, dividing the row into independently
 evolving modules can lead to characters covering multiple modules better
 fitting an unordered model of evolution. Adding the ability to suppress
 regions or the entire tooth row has a variable effect depending on the
 rates of suppression relative to the rates of addition and subtraction of
 individual teeth. We therefore advise not following a single policy when
 deciding whether to order meristic traits, but to base the decision on the
 evolution and developmental biology of the clade under study.
DOI: 10.6086/d1px0k
title: Oahu windward beaches microplastics survey

description: We report microplastic densities on windward beaches of Oahu, Hawai`i,
 USA. Microplastic densities, surveyed on six Oahu beaches, were highest on
 the beaches with the coarsest sands, associated with high wave energy. On
 those beaches, densities were very high (700-1700 particles m-2), as high
 as those recorded on other remote island beaches worldwide.
description: We collected microplastics on six beaches on the windward side of
 Oahu. Sampling was carried out in October 2017 during low tides. At each
 beach, the high tide line was identified by a strip of debris or
 discoloration from the previous high tide, and inland and parallel to the
 high tide line, the storm tide line was identified by a linear
 concentration of debris such as branches, twigs or seeds. Three 15-m
 transect lines were haphazardly laid along the high tide line, and storm
 tide lines, end to end. Random coordinates were generated to locate three
 30 cm x 30 cm quadrats along each transect, and in each quadrat the first
 two cm of sand was collected (Fig 3B). In this study we quantified
 microplastics 500 µm - 5 mm in size. Larger plastic pieces were separated
 out. Sand was sieved with a 500 µm mesh, collecting only plastics and
 other materials larger than that size. In total there were 18 samples from
 each beach, nine each from high and storm tide lines. Individual pieces of
 microplastic collected per sample were counted by pouring samples through
 a 5 mm sieve, discarding larger materials caught in the sieve, and
 retaining materials that passed through.We used density separation
 (floating in water) and visual inspection with a stereomicroscope to
 separate plastics from organic (shells, sand, wood) and inorganic (metal)
 materials. Previous studies have shown that other i.e. spectroscopic
 methods can identify small-sized microplastics overlooked using microscopy
 but by restricting our analysis to particles &gt;500 µm we are
 unlikely to have significantly undercounted microplastics. The number of
 plastic pieces was then divided by the quadrat size to find the density of
 plastic pieces per unit area. Size distribution of microplastics was
 characterized using stacked sieve shakers with mesh sizes of 4 mm, 2 mm
 and 1 mm. Samples collected from the same tide line at the same site were
 combined. The stack was shaken for 30 s and then the number of plastics in
 each size range were counted. One sample of sand was
 collected at each beach near the transect lines by collecting the first 2
 cm to be analyzed for particle size distribution as a measure of texture.
 Sand samples from each beach were weighed and distributed through the
 stacked sieve shaker with mesh sizes 4 mm, 2 mm, 1 mm, 500 mm, 250 mm, 100
 mm, 63 mm. The sieve shaker was run for 3 minutes. The portion from each
 sieve was weighed.
DOI: 10.15468/dl.tmnk58
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Roscoea debilis"
 ]
}

 The dataset includes 62 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002525-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4yec4
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calobota saharae",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 10 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002524-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d51c5b015
title: Geometric morphometrics of endophytic oviposition traces of Odonata (Eocene, Argentina)

description: The insertion of the Odonata ovipositor in the plant tissue generates a
 scar that surrounds the eggs (trace). In insects, individual egg
 traces are known to vary in size, but their variation in individual shape
 is mostly unknown. Twenty four specimens were obtained from the Laguna del
 Hunco (Lower Eocene, Chubut) and Río Pichileufú (Middle Eocene, Río
 Negro), Argentina, which had 1346 oviposition traces (MEF Collection). For
 the first time, a study of the shape and size of a large number of
 individual Odonata endophytic egg traces was carried out using traditional
 (general and mixed linear models) and geometric morphometrics (Fourier
 elliptical series) to elucidate whether there are changes in size or shape
 of the individual endophytic egg traces associated with the substrate used
 at the time of oviposition, if the Lower Eocene traces have varied in
 relation to those of the Middle Eocene, and if the ichnological
 classification (Paleoovoidus arcuatus, P. bifurcatus and P. rectus)
 reflects such variations. We found differences in size ( p &lt; 0.05),
 but not in shape, in relation to the variables studied. This could reflect
 that the shape of Odonata eggs (inferred from the traces), unlike their
 size, could have a strong evolutionary constraint already observed since
 the Eocene.
description: This dataset has: Twenty-five figures (images captions in a word
 document) and two excel files:<br> a) Geometric morphometrics. Raw
 data of Fourier coefficient values estimated based on 20 harmonics for
 each material.<br> b) Traditional morphometrics. Raw data of each
 material. Values are expressed in mm. The area is expressed in
 mm<sup>2</sup>.
DOI: 10.5061/dryad.bzkh1896k
title: Positive effects of fast growth on locomotor performance in pelagic fish juveniles

description: Many laboratory experiments on aquatic vertebrates that inhabit closed
 water or coastal areas have highlighted negative effects of fast growth on
 swimming performance. Nonetheless, field studies on pelagic fishes have
 provided evidence of survival advantages of faster growing individuals. To
 reconcile this contradiction, we examined the relationship between growth
 rate and swimming performance as a continuous function for juveniles of
 chub mackerel (scomber japonicus) using 3D tracking analysis. For
 experiments, 20, 24, 27, and 30 days post-hatch individuals within the
 size range of 14.5­­­­­­–25.3 mm were used. We found that the
 growth–swimming (burst speed) relationship in chub mackerel was
 substantially positive and it was supported by morphological traits such
 as muscle area, which were also positively related with growth rate. This
 finding is consistent with field observations showing selective survival
 of fast-growing individuals of this species, reconciling the current
 contradiction between laboratory experiments and field observations. A
 dome-shaped quadratic curve described the relationship between growth rate
 and burst speed better than a linear or cubic function, suggesting that
 growth may trade off with swimming performance, as reported in many
 previous studies, when it is extremely fast. These results, obtained from
 the rarely tested offshore species, strongly suggests the importance of
 experimental verification using animals that inhabit various types of
 habitats in understanding the principles underlying the evolution of
 growth–locomotor relationship.
description: These data were generated to investigate the
 relationship between growth rate and swimming performance and related
 traits for juveniles of chub mackerel (<em>scomber
 japonicus</em>).  To clarify whether SL and growth rate had a
 significant effect on routine and burst speeds, generalized linear mixed models
 (GLMMs) were applied.  In addition, two generalized linear models (GLMs) and an GLMM were applied to determine
 whether there were any significant relationships between morphological
 traits and growth rate or burst speed.
DOI: 10.5061/dryad.zkh18937z
title: Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting

description: Environmental enteropathy is a major contributor to growth faltering in
 millions of children in Africa and South Asia. We carried out a
 longitudinal, observational and interventional study in Lusaka, Zambia, of
 297 children with stunting (aged 2–17 months at recruitment) and 46
 control children who had good growth (aged 1–5 months at recruitment).
 Control children contributed data only at baseline. Children were provided
 with nutritional supplementation of daily cornmeal-soy blend, an egg and a
 micronutrient sprinkle, and were followed up to 24 months of age. Children
 whose growth did not improve over 4–6 months of nutritional
 supplementation were classified as having non-responsive stunting. We
 monitored microbial translocation from the gut lumen to the bloodstream in
 the cohort with non-responsive stunting (n = 108) by measuring circulating
 lipopolysaccharide (LPS), LPS-binding protein and soluble CD14 at baseline
 and when non-response was declared. We found that microbial translocation
 decreased with increasing age, such that LPS declined in 81 (75%) of 108
 children with non-responsive stunting, despite sustained pathogen pressure
 and ongoing intestinal epithelial damage. We used confocal laser
 endomicroscopy and found that mucosal leakiness also declined with age.
 However, expression of brush border enzyme, nutrient transporter and
 mucosal barrier genes in intestinal biopsies did not change with age or
 correlate with biomarkers of microbial translocation. We propose that
 environmental enteropathy arises through adaptation to pathogen-mediated
 epithelial damage. Although environmental enteropathy reduces microbial
 translocation, it does so at the cost of impaired growth. The reduced
 epithelial surface area imposed by villus blunting may explain these
 findings.
description: Two datasets are provided. The first contains data on pathogens
 present. in stool samples, analysed by Luminex xTAG GPP. The second
 contains analysis of plasma biomarkers, analysed by commercial ELISA kits.
 These biomarkers include lipolpolysaccharide (LPS), LPS-binding protein
 (LBP), soluble CD14, and intestinal fatty acid binding protein
 (iFABP).
description: The ID numbers used are not the ID numbers used for each child in
 the study, but allow the two databases to be cross-linked. There are
 missing values where, for example, the plasma was insufficient to do all
 assays. In the pathogens file, avpos is adenovirus positive,
 nvpos is norovirus, rvapos is rotavirus A positive, etecpos is positive
 for Enterotoxigenic Escherichia coli (ETEC), salmo1pos is positive for
 Salmonella spp, shigpos is positive for Shigella spp., campypos is
 positive for Campylobacter spp., giardiapos is positive for Giardia
 intestinalis, and cryptopos is positive for Cryptosporidium
 spp.