cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d3qh5c8
title: Data from: Genomic signatures of GPCR expansions reveal functional transitions in the evolution of cephalopod signal transduction

description: Coleoid cephalopods show unique morphological and neural novelties, such
 as arms with tactile and chemosensory suckers and a large complex nervous
 system. The evolution of such cephalopod novelties has been attributed at
 a genomic level to independent gene family expansions, yet the exact
 association and the evolutionary timing remain unclear. In the octopus
 genome, one such expansion occurred in the G-protein coupled receptors
 (GPCRs) repertoire, a superfamily of proteins that mediate signal
 transduction. Here we assessed the evolutionary history of this expansion
 and its relationship with cephalopod novelties. Using phylogenetic
 analyses, two cephalopod- and two octopus-specific GPCR expansions were
 identified. Signatures of positive selection were analysed within the four
 groups, and the locations of these sequences in the Octopus bimaculoides
 genome were inspected. Additionally, the expression profiles of octopus
 GPCRs across various tissues were extracted from available transcriptomic
 data. Our results reveal the evolutionary history of cephalopod GPCRs.
 Unexpanded cephalopod GPCRs shared with other bilaterians were found to be
 mainly nervous tissue-specific. In contrast, duplications that are shared
 between octopus and the bobtail squid or specific to the octopus’ lineage
 generated copies with divergent expression patterns devoted to tissues
 outside of the brain. The acquisition of novel expression domains was
 accompanied by gene order rearrangement either through translocation or
 duplication and gene loss. Lastly, expansions showed signs of positive
 selection and some were found to form tandem clusters with shared
 conserved expression profiles in cephalopod innovations such as the axial
 nerve cord. Altogether, our results contribute to the understanding of the
 molecular and evolutionary history of signal transduction and provide
 insights into the role of this expansion during the emergence of
 cephalopod novelties and/or adaptations.
description: Input and output files
 of the positive selection analysisFolder contains peptide
 and CDS sequences, CDS alignment, input topologies, control files and
 codeml outputs for each analysis performed. An additional excel's
 spreadsheet with the Likelihood Ratio Test calculations is
 given.PositiveSelectionAnalysis.zipInput and output files of the phylogenetic analysesFolder contains peptide sequences, cleaned alignment and resulting tree for each of the 5 analyses performed (i.e., all-GPCRs, class A, B, C and F).PhylogeneticAnalyses.zipCalculations for the expression analysesExcel file containing the normalized expression values used for the expression analyses, the resulting proportions of expression and Tau values. Cells contain the formulas used for the calculations of the latter two parameters.ExpressionAnalysis_calculations.xlsx
DOI: 10.5061/dryad.2sq2d9m
title: Data from: Positive effects of liana cutting on seedlings are reduced during El Niño-induced drought

description: 1. Liana cutting is a management practice currently applied to encourage
 seedling regeneration and tree growth in some logged tropical forests.
 However, there is limited empirical evidence of its effects on forest
 demographic rates in Southeast Asia. 2. We used 22 four-hectare plots in
 the Sabah Biodiversity Experiment (a reduced impact logging site)
 enrichment line planted with 16 dipterocarp species to assess the effects
 of complete liana cutting on tree growth and survival. We compared plots
 where lianas were only cut along planting lines (standard enrichment line
 planting) with those with one (2014) or two rounds (2011 and 2014) of
 complete liana cutting. 3. We found increased seedling growth following
 the first complete liana cut in 2011 relative to the enrichment line
 planting, consistent with previous studies. The response after three years
 to the cutting in 2014 depended on whether lianas had been previously cut
 or not: in twice-cut plots, seedling growth was not significantly
 different from the standard enrichment planting controls, whereas growth
 in plots with only one complete cut in 2014 was significantly slower.
 Seedling survival decreased through time for both once- and twice-cut
 liana treatments but remained stable in controls. 4. Sapling growth after
 the 2014 liana cutting showed a similar pattern to seedling growth, while
 tree growth following the 2014 liana cutting was significantly lower than
 controls regardless of whether lianas were cut twice (2011 and 2014) or
 once (2014). 5. Differences in response between the two rounds of liana
 cutting were likely due to changes in precipitation - 2011 was followed by
 consistent rainfall while 2014 was followed by two severe droughts within
 2 years. 6. Synthesis and applications. Our results generally support the
 widely-reported positive effects of liana cutting on tree growth and
 survival. However, reduced growth and survival after the 2015/16 El Niño
 suggests that drought may temporarily undermine the benefits of liana
 cutting in logged tropical forests. Managers of similar areas in SE Asia
 should consider halting liana cutting during El Niño events. In other
 tropical areas, seedling survival should be monitored to assess to what
 extent results from SE Asia are transferable.
description: LianaCanopyDynamicsFinalLiana density and canopy openness after liana cutting. Metadata included as sheet in excel file.SeedlingGrowthFirstCutFinalSeedling growth from 2011 to 2014. Metadata included as sheet in excel file.SeedlingGrowthSecondCutFinalSeedling growth from 2014 to 2017. Metadata included as sheet in excel file.SeedlingSurvivalFinalSeedling survival following liana cutting in 2014. Metadata included as sheet in excel file.TreeSaplingGrowthFinalTree and sapling growth following 2014 liana cutting. Metadata included as sheet in excel file.
DOI: 10.5061/dryad.b4dn0mn
title: Data from: Phylogeography, population genetics, and distribution modeling reveal vulnerability of Scirpus longii (Cyperaceae) and the Atlantic Coastal Plain Flora to climate change.

description: A proactive approach to conservation must be predictive, anticipating how
 habitats will change and which species are likely to decline or prosper.
 We use composite species distribution modeling to identify suitable
 habitats for 18 members of the North American Atlantic Coastal Plain Flora
 (ACPF) since the Last Glacial Maximum and project these into the future.
 We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge
 with many of the characteristics of extinction vulnerability, as a case
 study. We integrate phylogeographic and population genetic analyses and
 species distribution modeling to develop a broad view of its current
 condition and prognosis for conservation. We use genotyping-by-sequencing
 to characterize the genomes of 142 S. longii individuals from twenty
 populations distributed throughout its range (New Jersey to Nova Scotia).
 We measure the distribution of genetic diversity in the species and
 reconstruct its phylogeographic history using SNAPP and RASE. Extant
 populations of S. longii originated from a single refugium south of the
 Laurentide ice sheet around 25 thousand years ago. The genetic diversity
 of S. longii is exceedingly low, populations exhibit little genetic
 structure, and the species is slightly inbred. Projected climate scenarios
 indicate that nearly half of extant populations of S. longii will be
 exposed to unsuitable climate by 2070. Similar changes in suitable habitat
 will occur for many other northern ACPF species – centers of diversity
 will shift northward and Nova Scotia may become the last refuges for those
 species not extinguished.
description: Scirpus_longii_SNPSNexus alignment of SNPs from all sequenced individuals of Scirpus long.MAXENT_input_distributionsSpecies distribution data used for MAXENT species distribution modeling.
DOI: 10.5061/dryad.t72v91c
title: Data from: A journey on plate tectonics sheds light on European crayfish phylogeography

description: Crayfish can be used as model organisms in phylogeographic and divergence
 time studies if reliable calibrations are available. This study presents a
 comprehensive investigation into the phylogeography of the European stone
 crayfish (Austropotamobius torrentium) and includes samples from
 previously unstudied sites. Two mitochondrial markers were used to reveal
 evolutionary relationships among haplogroups throughout the species’
 distributional range and to estimate the divergence time by employing both
 substitution rates and geological calibration methods. Our haplotype
 network reconstruction and phylogenetic analyses revealed the existence of
 a previously unknown haplogroup distributed in Romania's Apuseni
 Mountains. This haplogroup is closely related to others that are endemic
 in the Dinarides, despite their vast geographical separation (~600 km).
 The separation is best explained by the well-dated tectonic displacement
 of the Tisza-Dacia microplate, which started in the Miocene (~16 Ma) and
 possibly carried part of the A. torrentium population to the current
 location of the Apuseni Mountains. This population may thus have been
 isolated from the Dinarides for a period of ca. 11 m.y. by marine and
 lacustrine phases of the Pannonian Basin. The inclusion of this geological
 event as a calibration point in divergence time analyses challenges
 currently accepted crayfish evolutionary time frames for the region,
 constraining the evolution of this area’s crayfish to a much earlier date.
 We discuss why molecular clock calibrations previously employed to date
 European crayfish species divergences should therefore be reconsidered.
description: Crayfish Geological
 CalibrationThese are the file
 associated with the geological time calibration analysis including the
 BEAST XML files.Strict Clock
 FilesThese are the files
 associated with the strict molecular clock analyses including the BEAST
 XML files.Strcit Clock
 Files.zipNexus and
 partitionfinderThese are the nexus
 files for the 16S and COI data along with partitionfinder
 results.
DOI: 10.5061/dryad.sc673ds
title: Data from: Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

description: Marine ecosystems are changing rapidly as the oceans warm and become more
 acidic. The physical factors and the changes to ocean chemistry that they
 drive can all be measured with great precision. Changes in the biological
 composition of communities in different ocean regions are far more
 challenging to measure because most biological monitoring methods focus on
 a limited taxonomic or size range. Environmental DNA (eDNA) analysis has
 the potential to solve this problem in biological oceanography, as it is
 capable of identifying a huge phylogenetic range of organisms to species
 level. Here we develop and apply a novel multi-gene molecular toolkit to
 eDNA isolated from bulk plankton samples collected over a five-year period
 from a single site. This temporal scale and level of detail is
 unprecedented in eDNA studies. We identified consistent seasonal
 assemblages of zooplankton species, which demonstrates the ability of our
 toolkit to audit community composition. We were also able to detect clear
 departures from the regular seasonal patterns that occurred during an
 extreme marine heatwave. The integration of eDNA analyses with existing
 biotic and abiotic surveys delivers a powerful new long-term approach to
 monitoring the health of our world’s oceans in the context of a rapidly
 changing climate.
description: Marine environmental DNA
 biomonitoring reveals seasonal patterns in biodiversity and identifies
 ecosystem responses to anomalous climatic eventsUnique DNA sequences
 obtained from IMOS zooplankton samples, using eight different
 metabarcoding assays, taken from Rottnest Island Western Australian on 55
 occasions over five years.
DOI: 10.5061/dryad.g6k20t0
title: Data from: A potential role for GSK3beta in glucose-driven intrauterine catch-up growth in maternal obesity

description: Obesity and an unhealthy nutrition are on the rise and affect also women
 in childbearing age and hence, during pregnancy. Despite normal or even
 high birth weight the offspring suffers from long term metabolic risks. We
 hypothesized that fetal growth is disturbed during different intrauterine
 phases. Underlying molecular events remain elusive. Female mice were fed
 either a control diet (SD) or a high fat diet (HFD) after weaning until
 mating and during pregnancy. Pregnant mice were sacrificed at gestational
 time points G15.5 and G18.5 and fetuses and placentas were removed for
 analysis. HFD fetuses displayed intrauterine growth restriction (IUGR) at
 G15.5, which disappeared until G18.5, indicating an intrauterine catch-up
 growth during that time period. Main placental findings indicate decreased
 canonical Wnt-GSK3beta signaling and lower proliferation rates at G18.5
 which goes along with a smaller placental transfer zone. On the other
 hand, glucose depots (glycogen cluster) in HFD placentas decreased
 stronger between G15.5 and G18.5 compared to placentas from SD mothers,
 and the glucose transporter protein GLUT-1 was increased at G18.5 in the
 HFD group. Maternal diet-induced obesity causes an IUGR phenotype at the
 beginning of the third week (G15.5) in our mouse model. This phenotype is
 reversed by the end of the third week (G18.5) despite of a smaller
 placental transfer zone, probably based on GSK3beta-mediated increased
 glucose mobilization in the placenta and hence an increased glucose supply
 to the fetus.
description: Appel et al
 2018_supplemental materialSupplemental material
 for publication 'A potential role for GSK3beta in glucose-driven
 intrauterine catch-up growth in maternal obesity'.Appel et al_supplemental
 material.pdf
DOI: 10.5061/dryad.32c2qh4
title: Data from: Oral anticoagulation in patients with chronic kidney disease: a systematic review and meta-analysis

description: Objective: Data regarding the efficacy and safety of warfarin and
 Non-Vitamin K Antagonist Oral Anticoagulant (NOAC) among patients with
 chronic kidney disease (CKD) remain scarce. Methods: Systematic review and
 meta-analysis of studies involving CKD patients treated on OACs was
 conducted to evaluate following outcomes: ischemic stroke, intracerebral
 hemorrhage (ICH), combined ischemic and hemorrhagic stroke
 (strokecombined), stroke or systemic embolism, mortality, and major
 bleeding events. CKD was defined based on creatinine clearance (CrCl)
 ranging from mild (CrCl: 60-89 ml/min), moderate (CrCl: 30-59 ml/min) and
 severe (CrCl: 15-29 ml/min). Results: Fifteen studies (7 comparing NOAC
 vs. warfarin & 8 comparing warfarin vs. no anticoagulant) were
 identified comprising 87,291 patients. Warfarin (vs. no anticoagulant) was
 associated with reduced risk of ischemic stroke [RR=0.68 (95%CI:
 0.55-0.84)] and mortality [RR=0.70 (95%CI: 0.62-0.78)]. In comparison to
 warfarin, NOAC use lowered the risk of ICH [RR=0.43 (95%CI: 0.33-0.56)],
 strokecombined [RR=0.83 (95%CI: 0.72-0.96)], stroke or systemic embolism
 [RR=0.73 (95%CI: 0.62-0.85)] and major bleeding [RR=0.77 (95%CI:
 0.66-0.90)]. In adjusted analyses, warfarin use (vs. no anticoagulant) was
 associated with reduced mortality [HRadj=0.68 (95%CI: 0.61-0.76)], whereas
 NOAC (vs. warfarin) use reduced the risk of ICH [HRadj=0.39 (95%CI:
 0.30-0.50)] and stroke or systemic embolism [HRadj=0.75 (95%CI:
 0.65-0.88)]. Our sensitivity analyses comparing different NOACs exhibited
 that factor Xa inhibitors (compared to warfarin) consistently reduced
 strokecombined [RR=0.84 (95%CI: 0.73-0.96)], mortality [RR=0.84 (95%CI:
 0.70-1.00)], ICH [RR=0.45 (95%CI: 0.24-0.85)] and major bleeding [RR=0.76
 (95%CI: 0.64-0.91)]. Conclusions: Amongst CKD patients treated with OAC,
 NOACs present with a more favorable safety and efficacy profile for
 various cardiovascular outcomes.
description: Online
 supplementSupplemental
 file
DOI: 10.5281/zenodo.18389681
title: Synthetic Dataset for Sequential Learning-Based Optimisation of Bio-Ash  Binder Formulations under Seasonal Availability Constraints

description: This dataset accompanies the study on sequential learning–based optimisation of bio-ash–cement binder formulations under seasonally varying material availability. It provides a fully synthetic but chemically inspired benchmark design space for evaluating data-driven optimisation strategies in cementitious materials research.

The dataset comprises 5,006 unique binder formulations, each defined by the mass fractions of cement and five bio-based ash components (A1–A5). Ash components represent generic bio-ash types derived from agricultural residues (e.g. rice husk ash, cassava peel ash), and their internal proportions are systematically varied under mass-balance constraints. Cement content ranges from 0 to 100 wt% in discrete steps.

To reflect dynamic supply conditions, the dataset includes season-specific ash usage metrics for four seasons (S1–S4), expressing the fraction of available ash resources consumed by each formulation. A synthetic compressive strength value is assigned to every formulation using a nonlinear scoring function based on chemically inspired descriptors, with added noise to generate a structured yet non-trivial optimisation landscape. These strength values do not represent calibrated physical predictions and are intended solely as a hidden objective function for benchmarking sequential learning algorithms.

The dataset is designed for in silico benchmarking, reproducibility studies, and methodological comparisons of optimisation and active learning strategies. It enables systematic evaluation of algorithmic performance without the need for physical experiments.

Column description





Index_Sample: Unique sample identifier




A1_m% – A5_m%: Mass fractions (wt%) of five bio-ash components




Cement_m%: Mass fraction (wt%) of cement in the binder




Ash_Usage_Percentage_S1 – S4: Normalised ash usage metrics for four seasonal availability scenarios




Compressive_Strength (MPa): Synthetic compressive strength value used as optimisation target
DOI: 10.5281/zenodo.18389682
title: Synthetic Dataset for Sequential Learning-Based Optimisation of Bio-Ash  Binder Formulations under Seasonal Availability Constraints

description: This dataset accompanies the study on sequential learning–based optimisation of bio-ash–cement binder formulations under seasonally varying material availability. It provides a fully synthetic but chemically inspired benchmark design space for evaluating data-driven optimisation strategies in cementitious materials research.

The dataset comprises 5,006 unique binder formulations, each defined by the mass fractions of cement and five bio-based ash components (A1–A5). Ash components represent generic bio-ash types derived from agricultural residues (e.g. rice husk ash, cassava peel ash), and their internal proportions are systematically varied under mass-balance constraints. Cement content ranges from 0 to 100 wt% in discrete steps.

To reflect dynamic supply conditions, the dataset includes season-specific ash usage metrics for four seasons (S1–S4), expressing the fraction of available ash resources consumed by each formulation. A synthetic compressive strength value is assigned to every formulation using a nonlinear scoring function based on chemically inspired descriptors, with added noise to generate a structured yet non-trivial optimisation landscape. These strength values do not represent calibrated physical predictions and are intended solely as a hidden objective function for benchmarking sequential learning algorithms.

The dataset is designed for in silico benchmarking, reproducibility studies, and methodological comparisons of optimisation and active learning strategies. It enables systematic evaluation of algorithmic performance without the need for physical experiments.

Column description





Index_Sample: Unique sample identifier




A1_m% – A5_m%: Mass fractions (wt%) of five bio-ash components




Cement_m%: Mass fraction (wt%) of cement in the binder




Ash_Usage_Percentage_S1 – S4: Normalised ash usage metrics for four seasonal availability scenarios




Compressive_Strength (MPa): Synthetic compressive strength value used as optimisation target
DOI: 10.5061/dryad.18p3h04
title: Data from: Repeat variants for the SbMATE transporter protect sorghum roots from aluminum toxicity by transcriptional interplay in cis and trans

description: Acidic soils, where aluminum (Al) toxicity is a major agricultural
 constraint, are globally widespread and are prevalent in developing
 countries. In sorghum, the root citrate transporter SbMATE confers Al
 tolerance by protecting root apices from toxic Al3+, but can exhibit
 reduced expression when introgressed into different lines. We show that
 allele-specific SbMATE transactivation occurs and is caused by factors
 located away from SbMATE. Using expression-QTL mapping and -GWAS, we
 establish that SbMATE transcription is controlled in a bipartite fashion,
 primarily in cis but also in trans. Multi-allelic promoter transactivation
 and ChIP analyses demonstrated that intermolecular effects on SbMATE
 expression arise from a WRKY and a zinc finger-DHHC transcription factor
 (TF) that bind to and trans-activate the SbMATE promoter. A haplotype
 analysis in sorghum RILs indicate that the TFs influence SbMATE expression
 and Al tolerance. Variation in SbMATE expression likely results from
 changes in tandemly repeated cis sequences flanking a transposable element
 (MITE) insertion in the SbMATE promoter, which are recognized by the
 Al3+-responsive TFs. According to our model, repeat expansion in
 Al-tolerant genotypes increases TF recruitment and, hence, SbMATE
 expression, which is, in turn, lower in Al-sensitive genetic backgrounds
 due to lower TF expression and fewer binding sites. We thus show that even
 dominant cis regulation of an agronomically-important gene can be
 subjected to precise intermolecular fine-tuning. These concerted cis/trans
 interactions, which allow the plant to sense and respond to environmental
 cues, such as Al3+ toxicity, can now be used to increase yields and food
 security on acidic soils.
description: Melo et
 al_2018_PNAS_QTL-GWAS datasetThis dataset includes
 SNP physical positions (pos in bp, v1.4 of the sorghum genome) and
 association P-values with Al tolerance (RNRG) and SbMATE expression (RQ)
 obtained from biparental mapping (QTL) and genome wide association mapping
 (GWAS) (Fig. 2). Data was generated with TASSEL. Quantitative trait
 mapping in recombinant inbred lines: QTL.csv. Genome wide association
 mapping: GWAS.csv. Al tolerance was measured as RNRG: relative net root
 growth (see supplementary methods) SbMATE expression: RQ - relative
 quantification using the ddCt method (see supplementary
 methods).Melo et
 al_2018_PNAS_QTL-GWAS.zip