cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v7m14
title: Data from: How much of the world is woody?

description: 1.The question posed by the title of this paper is a basic one, and it is
 surprising that the answer is not known. Recently assembled trait datasets
 provide an opportunity to address this, but scaling these datasets to the
 global scale is challenging because of sampling bias. Although we
 currently know the growth form of tens of thousands of species, these data
 are not a random sample of global diversity; some clades are exhaustively
 characterised, while others we know little–to–nothing about. 2.Starting
 with a database of woodiness for 39,313 species of vascular plants (12% of
 taxonomically resolved species, 59% of which were woody), we estimated the
 status of the remaining taxonomically resolved species by randomisation.
 To compare the results of our method to conventional wisdom, we informally
 surveyed a broad community of biologists. No consensus answer to the
 question existed, with estimates ranging from 1% to 90% (mean: 31.7%).
 3.After accounting for sampling bias, we estimated the proportion of
 woodiness among the world's vascular plants to be between 45% and
 48%. This was much lower than a simple mean of our dataset and much higher
 than the conventional wisdom. 4.Synthesis: Alongside an understanding of
 global taxonomic diversity (i.e., number of species globally), building a
 functional understanding of global diversity is an important emerging
 research direction. This approach represents a novel way to account for
 sampling bias in functional trait datasets and to answer basic questions
 about functional diversity at a global scale
description: Results-woodinessAll results from the analyses conducted in the paper and results from our survey of researcherswood-supporting.tar.gz
DOI: 10.5061/dryad.hb4ht
title: Data from: Life-history trait database of European reptile species

description: Life-history data are essential for providing answers to a wide range of
 questions in evolution, ecology, and conservation biology. While life
 history data for many species, especially plants, are available online,
 life history traits of European reptiles are available only widely
 scattered in different languages and primarily in printed media. For this
 reason, we generated a comprehensive trait database covering all European
 reptile species. Data were compiled by searching the peer-reviewed and
 non-peer-reviewed literature. The database covers the whole of Europe and
 neighbouring Asian and African countries. Traits were categorised under
 five main headings: Activity / Energy / Habitat; Phenology; Movement;
 Sexual Maturity; and Morphometry. To ensure that the data were
 standardised, we defined trait data categories before we started compiling
 data. All entries were checked by at least one other person. The dataset
 provides a unique source for meta-analyses and modelling in ecology and
 conservation biology.
description: Life-history trait
 database of European reptile speciesOur database comprises
 two sections: basic information and actual trait data. In the basic
 section, general information about taxonomy, references, and countries is
 stored. The trait data section is divided into the following: Activity /
 Energy / Habitat; Phenology; Sexual Maturity; Movement; and Morphometry.
 Object name: Trait database of reptile life histories Character encoding:
 UTF-16 Format name: Microsoft Access Database Format version: Microsoft®
 Access® 2010 (14.0.7104.5000) SP2 MSO (14.0.7116.5000) as part of
 Microsoft Office Professional Plus 2010 Language: English Licenses of use:
 Data have been made available under the Creative Commons CC-Zero Waiver:
 http://creativecommons.org/publicdomain/zero/1.0/. Thus, the data can be
 freely used for non-commercial purposes provided the source is
 acknowledged. See Creative Commons for more details of the conditions of
 usage.Grimm_etal_Reptile_DB_Update_2015.accdb
DOI: 10.5061/dryad.30j63
title: Data from: An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating

description: Most microbial taxa lack a conventional microfossil or biomarker record,
 and so we currently have little information regarding how old most
 microbial clades and their associated traits are. Building on the
 previously published oxygen age constraint, two new age constraints are
 proposed based on the ability of microbial clades to metabolize chitin and
 aromatic compounds derived from lignin. Using the archaeal domain of life
 as a test case, phylogenetic analyses, along with published metabolic and
 genetic data, showed that members of the Halobacteriales and
 Thermococcales are able to metabolize chitin. Ancestral state
 reconstruction combined with phylogenetic analysis of the genes underlying
 chitin degradation predicted that the ancestors of these two groups were
 also likely able to metabolize chitin or chitin-related compounds. These
 two clades were therefore assigned a maximum age of 1.0 Ga (when chitin
 likely first appeared). Similar analyses also predicted that the ancestor
 to the Sulfolobus solfataricus-Sulfolobus islandicus clade was able to
 metabolize phenol using catechol dioxygenase, so this clade was assigned a
 maximum age of 475 Ma. Inferred ages of archaeal clades using relaxed
 molecular clocks with the new age constraints were consistent with those
 inferred with the oxygen age constraints. This work expands our current
 toolkit to include Paleoproterozoic, Neoproterozoic, and Paleozoic age
 constraints, and should aid in our ability to phylogenetically reconstruct
 the antiquity of a wide array of microbial clades and their associated
 morphological and biogeochemical traits, spanning deep geologic time. Such
 hypotheses-although built upon evolutionary inferences-are fundamentally
 testable.
description: Blank2011.AnExpansionOfAgeConstrA mesquite file containing phylogenetic tree and character matrix.
DOI: 10.48656/0gaj-xb49
title: Multilingual Sequences Dataset
DOI: 10.48656/d22w-s781
title: Multilingual Sequences Dataset
DOI: 10.5061/dryad.45g90h4
title: Data from: Global pattern of nest predation is disrupted by climate change in shorebirds

description: Ongoing climate change is thought to disrupt trophic relationships, with
 consequences for complex interspecific interactions, yet the effects of
 climate change on species interactions are poorly understood, and such
 effects have not been documented at a global scale. Using a single
 database of 38,191 nests from 237 populations, we found that shorebirds
 have experienced a worldwide increase in nest predation over the past 70
 years. Historically, there existed a latitudinal gradient in nest
 predation, with the highest rates in the tropics; however, this pattern
 has been recently reversed in the Northern Hemisphere, most notably in the
 Arctic. This increased nest predation is consistent with climate-induced
 shifts in predator-prey relationships.
description: Data and R codes for
 Global pattern of nest predation is disrupted by climate change in
 shorebirdsAll data files (*26*)
 are in one zip folder (3 scripts, *21* dataset files, 1 file with
 phylogenetic trees, 1 file with all variables description). Choose one of
 the commented scripts (Models, Figures, SuppFigures) and run it. It will
 use all needed data.Kubelka et al. 2018_Global
 pattern of nest predation is disrupted by climate change in
 shorebirds_DATA for Dryad.zip
DOI: 10.5061/dryad.s5p7j
title: Data from: Local adaptation of sex-induction in a facultative sexual crustacean: insights from QTL mapping and natural population of Daphnia magna

description: Dormancy is a common adaptation in invertebrates to survive harsh
 conditions. Triggered by environmental cues, populations produce resting
 eggs that allow them to survive temporally unsuitable conditions. Daphnia
 magna is a crustacean that reproduces by cyclical parthenogenesis,
 alternating between the production of asexual offspring and the sexual
 reproduction of diapausing eggs (ephippia). Prior to ephippia production,
 males (necessary to ensure ephippia fertilization) are produced
 parthenogenetically. Both the production of ephippia and the
 parthenogenetic production of males are induced by environmental factors.
 Here, we test the hypothesis that the induction of Daphnia magna resting
 egg production shows a signature of local adaptation. We postulated that
 Daphnia from permanent ponds would produce fewer ephippia and males than
 Daphnia from intermittent ponds, and that the frequency and season of
 habitat deterioration would correlate with the timing and amount of male
 and ephippia production. To test this, we quantified the production of
 males and ephippia in clonal D. magna populations in several different
 controlled environments. We found that the production of both ephippia and
 males varies strongly among populations in a way that suggests local
 adaptation. By performing QTL mapping with parent clones from contrasting
 pond environments, we identified non-overlapping genomic regions
 associated with male and ephippia production. Since the traits are
 influenced by two different genomic regions and both are necessary for
 successful resting egg production, we suggest that the genes for their
 induction co-evolve.
description: SNP_d.magnaThe file contains SNP data (1324 SNP markers) genotype for 353 F2 clones of D.magna. Details about the parental lines and the cross can be found in Routtu et al. 2010microsat_Dmagnathe file contains the microsatellite markers used to built the first genetic map of D.magnaF2-line phenotypesThis file contains the F2-line phenotypes for ephippia and male production.phenotypes_QTL_mapping_Roulin_etal_MolEcol2013.csv
DOI: 10.5281/zenodo.18391898
title: A dataset of formal proofs in lean from the 1000 theorems project, for integration into the MaRDI knowledge graph.

description: The dataset was created by the following python code in the context of https://github.com/MaRDI4NFDI/MaRDIRoadmap/issues/65:

 



import yamlimport pandas as pd#obtained from https://github.com/leanprover-community/mathlib4/blob/master/docs/1000.yamlwith open("~/1000.yaml",encoding='utf-8') as stream:    theorems_dict = yaml.safe_load(stream)theorems_project_df = pd.DataFrame(theorems_dict).transpose()theorems_project_df.index.name = 'wikidata_qid'sparql_query = 'https://w.wiki/HcXE'#theorems from wikidata with english-language wikipedia article. obtained from wikidata via query https://w.wiki/HcXEnamed_theorems_json = '~/Downloads/named_theorems.json'with open(named_theorems_json, encoding='utf-8') as named_theorems_fh:    named_theorems = json.load(named_theorems_fh)theorems_df = pd.read_json(named_theorems_json)theorems_df['wikidata_qid'] = theorems_df.cid.apply(lambda x:x.split('/')[-1])theorems_df = theorems_df.join(theorems_project_df,how='outer',on='wikidata_qid')theorems_df['P31'] = 'Q6480412'theorems_df['P37']='Q6480413'theorems_df['P1603']=theorems_df.apply(lambda x:x['decl'] if x['decl'] else x['url'],axis=1)theorems_df['P1460'] = 'Q6534201'theorems_df['P12'] = theorems_df['wikidata_qid']theorems_df = theorems_df.rename({'date':'P140','comment':'Den','title':'Len'})theorems_df['P205'] = theorems_df.apply(lambda x:"https://leanprover-community.github.io/1000.html#"+x['P12'] if x['decl'] or x['url'] else '')theorems_df['P1648'] = 'Q27041'formal_proofs_df = theorems_df.drop(columns=['P1460','P37','P31','P1603','cid','label','article','decl','authors','url','statement'])formal_proofs_df = formal_proofs_df.dropna(columns=['P205'])formal_proofs_df.fillna('').to_csv('~/formal_proofs_mardi.csv',index=False)
DOI: 10.5061/dryad.hb8b5
title: Data from: The physical boundaries of public goods cooperation between surface-attached bacterial cells

description: Bacteria secrete a variety of compounds important for nutrient scavenging,
 competition mediation and infection establishment. While there is a
 general consensus that secreted compounds can be shared and therefore have
 social consequences for the bacterial collective, we know little about the
 physical limits of such bacterial social interactions. Here, we address
 this issue by studying the sharing of iron-scavenging siderophores between
 surface-attached microcolonies of the bacterium Pseudomonas aeruginosa.
 Using single-cell fluorescence microscopy, we show that siderophores,
 secreted by producers, quickly reach non-producers within a range of 100
 µm, and significantly boost their fitness. Producers in turn respond to
 variation in sharing efficiency by adjusting their pyoverdine investment
 levels. These social effects wane with larger cell-to-cell distances and
 on hard surfaces. Thus, our findings reveal the boundaries of compound
 sharing, and show that sharing is particularly relevant between nearby yet
 physically separated bacteria on soft surfaces, matching realistic natural
 conditions such as those encountered in soft tissue infections.
description: Data for Weigert et
 al._ManuscriptIncludes raw data for
 all figures (including supplementary figures).Weigert_Kummerli_ProcB_2017_RawData.xlsxCode_Weigert_et_alIncludes the code for single cell analysis. Please refer to the supplementary protocol for instructions.Code_Single_cell_analysis_Weigert_et_al.zipExample_dataContains example images needed for the supplementary protocol.
DOI: 10.6084/m9.figshare.31119181
title: 2026 Quisvirales discovery paper

description: We provide supplemental data for the paper "A large replicase of nidovirus-like complexity in a putative RNA virus order“<i>Quisvirales</i>” expands the known diversity of helicase superfamilies".
DOI: 10.6084/m9.figshare.31119181.v1
title: 2026 Quisvirales discovery paper

description: We provide supplemental data for the paper "A large replicase of nidovirus-like complexity in a putative RNA virus order“<i>Quisvirales</i>” expands the known diversity of helicase superfamilies".
DOI: 10.6084/m9.figshare.31119181.v2
title: 2026 Quisvirales discovery paper

description: We provide supplemental data for the paper "A large replicase of nidovirus-like complexity in a putative RNA virus order“<i>Quisvirales</i>” expands the known diversity of helicase superfamilies".
DOI: 10.5061/dryad.7ss03
title: Data from: Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype

description: Breeding has transformed wild plant species into modern crops, increasing
 the allocation of their photosynthetic assimilate into grain, fiber, and
 other products for human use. Despite progress in increasing the harvest
 index, much of the biomass of crop plants is not utilized. Potential uses
 for the large amounts of agricultural residues that accumulate are animal
 fodder or bioenergy, though these may not be economically viable without
 additional efforts such as targeted breeding or improved processing. We
 characterized leaf and stem tissue from a diverse set of rice genotypes
 (varieties) grown in two environments (greenhouse and field) and report
 bioenergy-related traits across these variables. Among the 16 traits
 measured, cellulose, hemicelluloses, lignin, ash, total glucose, and
 glucose yield changed across environments, irrespective of the genotypes.
 Stem and leaf tissue composition differed for most traits, consistent with
 their unique functional contributions and suggesting that they are under
 separate genetic control. Plant variety had the least influence on the
 measured traits. High glucose yield was associated with high total glucose
 and hemicelluloses, but low lignin and ash content. Bioenergy yield of
 greenhouse-grown biomass was higher than field-grown biomass, suggesting
 that greenhouse studies overestimate bioenergy potential. Nevertheless,
 glucose yield in the greenhouse predicts glucose yield in the field
 (ρ = 0.85, p &lt; 0.01) and could be used to optimize greenhouse (GH)
 and field breeding trials. Overall, efforts to improve cell wall
 composition for bioenergy require consideration of production environment,
 tissue type, and variety.
description: all data files and
 directory structure for processingThis zip file contains
 all raw data in the "input" directory, and the
 fieldvsgh_final/README.md contains instructions on how to obtain and run R
 scripts to process the data. Once the scripts are obtained, a README.md
 file provides further information.AllDataTanger2014.zip
DOI: 10.5061/dryad.4sh70
title: Data from: De novo sequencing and assembly of Azadirachta indica fruit transcriptome

description: Azadirachta indica (neem) is a unique, versatile and important tree
 species. Many parts of the plant are traditionally used as pesticide,
 insecticide, fungicide and for other medicinal purposes. Azadirachta
 fruits and seeds, a good source of oil, are widely used for agriculturally
 important pest management. Neem oil and its derivatives also support
 multiple cottage industries in India. Past efforts have been mostly
 concentrated towards identifying, characterizing and synthesizing one of
 its principal components, i.e. azadirachtin from seed kernels. Despite
 diverse use of the neem plant, a modern drug-development programme which
 systematically exploits the therapeutic ability of Azadirachta fruits
 remains to be fully established. Next generation sequencing technology
 that helps decode genomes and transcriptomes has transformational impact
 on medicine, agriculture, bio-fuel and biodiversity studies. Here, we
 report sequencing, assembly and analysis of Azadirachta fruit
 transcriptome using next-generation sequencing technology. We believe that
 our study shall offer valuable insights towards realizing the larger
 vision of understanding the key medicinally active compounds and their
 pathways.
description: Neem_Fruit_CurrentScience_2011_Supplementary_file_1Supplementary Files described in the manuscript http://www.currentscience.ac.in/Volumes/101/12/1553.pdfSupp_Data_Files.zipfruit_R1.fastqfruit_R2.fastq
DOI: 10.5061/dryad.b6c54q3
title: Data from: Mechanism of Ca2+, Mg2+ and Fe3+ in fine cassiterite flotation using octanohydroxamic acid

description: The existence of metal ion should not be ignored in both hydrometallurgy
 and flotation. In this study, the effects of Ca2+, Mg2+ and Fe3+ on the
 flotation performance of cassiterite using octanohydroxamic acid (OHA) as
 the collector were investigated by the micro-flotation tests, X-ray
 photoelectron spectroscopy (XPS), fourier transform infrared spectroscopy
 (FTIR), contact angle, zeta (ζ) potential measurements and atomic force
 microscopy (AFM) imaging. The results of the flotation and contact angle
 experiments showed that the addition of Ca2+, Mg2+ and Fe3+ significantly
 decreased both the recovery and contact angle of cassiterite within pH
 ranged from 6.0 to 12.0 in the presence of OHA collector. ζ–potential
 measurements, solution chemistry analysis and FTIR measurements indicated
 that the flotation recovery of the cassiterite declined due to the CaOH+,
 MgOH+ and Fe(OH)3 sites on the cassiterite surface. XPS results indicated
 that the chemisorption of OHA on cassiterite surface and its adsorption
 combined with calcium ions effects finally changed the chemical properties
 of cassiterite surface. The AFM images also revealed that new species
 Fe(OH)3 of Fe3+ formed and adsorbed on the cassiterite surface at pH of
 9.0. The adsorption of Fe(OH)3 reduced the adsorption of OHA on the
 cassiterite surface, thus the hydrophobicity of cassiterite was
 deteriorated.
description: Original data and
 descriptionData tool and
 description, including xps fitting process.Final original data and
 description.rar
DOI: 10.5061/dryad.cq5ff51
title: Data from: Evolution of jaw disparity in fishes

description: The morphology of the vertebrate lower jaw has been used to infer feeding
 ecology.; transformations in mandibular shape and structure likely to have
 facilitated the emergence of different feeding behaviours in vertebrate
 evolution. Here we present elliptical Fourier shape and principal
 component analyses, characterizing and comparing the disparity of jaw
 shape in early gnathostomes and their modern primitively aquatic
 counterparts. 83% of shape variation is summarized on the first three
 principal component axes and all component clades of early gnathostomes
 exhibit overlapping morphological variation. Non-tetrapodomorph Palaeozoic
 sarcopterygians are more disparate than their extant counterparts whereas
 extant chondrichthyans are more disparate than their Palaeozoic
 counterparts. More generally, extant jawed fishes are more disparate than
 their Palaeozoic relatives largely because of the extensive shape
 variation exhibited by mandibles of extant actinopterygians. Only some
 areas of shape space vacated by Palaeozoic gnathostomes have been
 convergently refilled by living taxa. Characterization of theoretical jaw
 morphologies demonstrates that less than half of all possible shapes are
 realised by the jawed fishes that comprise our empirical dataset; many of
 these morphologies are realised by unrepresented terrestrial tetrapods,
 implying environmental constraint. Our results are incompatible with the
 early burst model of clade evolution and contradict the hypothesis that
 maximum disparity is reached early in the evolutionary history of jawed
 fishes.
description: Supplementary Tables and
 FiguresSupplementary Tables and
 FiguresData
 from-Evolution of jaw disparity in
 fishes.docxSupplementary Table
 1Table S1. An excel
 spreadsheet composed of taxa information for 138 specimens including
 institutions, museums, and sources where specimen photographs were
 obtained.Supplementary_Table_1.xlsx
DOI: 10.5061/dryad.4kn5j5d
title: Data from: Signatures of microevolutionary processes in phylogenetic patterns

description: Phylogenetic trees are representations of evolutionary relationships among
 species and contain signatures of the processes responsible for the
 speciation events they display. Inferring processes from tree properties,
 however, is challenging. To address this problem we analysed a
 spatially-explicit model of speciation where genome size and mating range
 can be controlled. We simulated parapatric and sympatric (narrow and wide
 mating range, respectively) radiations and constructed their phylogenetic
 trees, computing structural properties such as tree balance and speed of
 diversification. We showed that parapatric and sympatric speciation are
 well separated by these structural tree properties. Balanced trees with
 constant rates of diversification only originate in sympatry and genome
 size affected both the balance and the speed of diversification of the
 simulated trees. Comparison with empirical data showed that most of the
 evolutionary radiations considered to have developed in parapatry or
 sympatry are in good agreement with model predictions. Even though
 additional forces other than spatial restriction of gene flow, genome
 size, and genetic incompatibilities, do play a role in the evolution of
 species formation, the microevolutionary processes modeled here capture
 signatures of the diversification pattern of evolutionary radiations,
 regarding the symmetry and speed of diversification of lineages.
description: Individual-based
 modelThe code for run
 simulations based on the model presented in the paper.ibm.f90inputAn example of input data to run the ibm.f90 code.SM_Costa-SysBio_2017_SysBio_reviewSupplementary MaterialSM_Costa-SysBio_2018_SysBio.pdf