cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t1f5
title: Data from: Association of extracellular dNTP utilization with a GmPAP1-like protein in cell wall proteomic analysis of soybean roots

description: Plant root cell walls are dynamic systems that serve as the first plant
 compartment responsive to soil conditions, such as phosphorus (P)
 deficiency. To date, evidence for the regulation of root cell wall
 proteins by P deficiency remains sparse. In order to facilitate
 understanding of roles played by soybean (Glycine max) root cell wall
 proteins (CWPs) in adaptation to P deficiency, iTRAQ proteomic analysis
 was conducted. A total of 53 CWPs with differential accumulation in
 response to P deficiency were identified. Subsequent qRT-PCR analysis
 correlated the accumulation of 21 of 27 up-regulated proteins, and 8 of 26
 down-regulated proteins with corresponding gene expression patterns in
 response to P deficiency. One up-regulated CWP, the purple acid
 phosphatase 1-like (GmPAP1-like), was functionally characterized. Bean
 (Phaseolus vulgaris) transgenic hairy roots overexpressing GmPAP1-like
 displayed increased root associated acid phosphatase activity. Plus,
 relative growth and P content were significantly enhanced in GmPAP1-like
 overexpression lines compared to control lines when dNTP was applied as
 the sole external P source. Taken together, it suggests that modulation of
 cell wall proteins possibly regulates complex root system changes in
 response to P deficiency, and that the cell wall localized GmPAP1-like
 protein is involved in extracellular dNTP utilization in soybean.
description: RawData_mgf.tarRaw data with mass spectrometry (MS/MS) spectra information for the iTRAQ analysis of soybean cell wall proteins.Supllemental figure S1 to S4Supllemental figure S1 to S4Supplementary Table S1Supplementary Table S1Supplementary Table S2Supplementary Table S2Supplementary Table S3Supplementary Table S3
DOI: 10.5281/zenodo.18380717
title: Geometric Confinement from Torsion Flux Tubes: An Algebraic Unification of QCD and Gravity

description: We present a mathematically rigorous geometric unification where gauge fields emerge as componentsof an extended Cartan connection. The key innovation is the introduction of dynamicalcontraction operators Cn[Θn] that selectively couple spacetime torsion to specific gauge sectors. Thisframework naturally explains confinement in QCD as a geometric phenomenon arising from torsion flux tubes, while electroweak sectors remain non-confining due to symmetry breaking. Startingfrom a unified variational principle with exact dimensional consistency, we derive all fundamentalequations – Einstein–Cartan, Yang–Mills, Dirac, and Higgs. The model predicts the Nambu–Gotostring action emerges from transverse integration of localized torsion, exhibits Z3 flux quantization,and matches all lattice QCD predictions with mathematical precision. All gauge sectors are cleanlyseparated through an extended algebraic structure without ad hoc assumptions. The framework employs dimensionless variables to ensure exact dimensional consistency, with all physical predictionsexpressed as dimensionless ratios of natural scales.
DOI: 10.5061/dryad.jr08b
title: Data from: Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

description: We combined restriction site associated DNA sequencing (RADseq) using a
 hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to
 develop molecular markers for the 16 gigabase genome of Cedrus atlantica,
 a conifer tree species. With each method, Illumina® reads from one
 individual were used to generate de novo assemblies. SNPs from the RADseq
 data set were detected in a panel of one single individual and three pools
 of three individuals each. We developed a flexible script to estimate the
 ascertainment bias in SNP detection considering the pooling and sampling
 effects on the probability of not detecting an existing polymorphism. Gene
 Ontology (GO) and transposable element (TE) search analyses were applied
 to both data sets. The RADseq and the mRNAseq assemblies represented 0.1%
 and 0.6% of the genome, respectively. Genome complexity reduction resulted
 in 17% of the RADseq contigs potentially coding for proteins. This rate
 was doubled in the mRNAseq data set, suggesting that RADseq also explores
 noncoding low-repeat regions. The two methods gave very similar GO-slim
 profiles. As expected, the two assemblies were poor in TE-like sequences
 (&lt;4% of contigs length). We identified 17,348 single nucleotide
 polymorphisms (SNPs) in the RADseq data set and 5,714 simple sequence
 repeats (SSRs) in the transcriptome. A subset of 282 SNPs was validated
 using the Fluidigm genotyping technology, giving a conversion rate of
 50.4%, falling within the expected range for conifers. Increasing sample
 size had the greatest effect for ascertainment bias reduction. These
 results validated the utility of the RADseq approach for highly complex
 genomes such as conifers.
description: C_atl_RADseq_de_novo_assemblySpecies: Cedrus atlantica Manetti Number of individuals: one single adult individual coming from the Luberon forest(43°47' N / 5°12' E, France) Plant tissue: needles (diploid) Sequencing method: Restriction site Associated DNA sequencing, paired-end sequencing using the Illumina HiSeq2000 platform (Illumina Inc., San Diego, CA) (2 x 101 bp) Data description: 66,656 contigs generated by de novo assembly Assembly tool: Velvet 1.2.06 (Zerbino & Birney 2008)C_atl_mRNAseq_de_novo_assemblySpecies: Cedrus atlantica Manetti Number of indiivudals: one single 2-year-old seedling that originated from the the Luberon forest (43°47' N / 5°12' E, France) and was grown in a greenhouse in a pot Plant tissues: needles and roots (diploid) Sequencing method: transcriptome sequencing, paired-end sequencing using the Illumina HiSeq2000 platform (Illumina Inc., San Diego, CA) (2 x 101 bp) Data description: 130,184 contigs generated by de novo assembly Assembly tool: CLC Genomics Workbench 4.8 (CLC bio, Cambridge, MA)
DOI: 10.5061/dryad.vq700
title: Data from: Muscle contributions to the acceleration of the whole body centre of mass during recovery from forward loss of balance by stepping in young and older adults

description: The purpose of this study was to determine the muscular contributions to
 the acceleration of the whole body centre of mass (COM) of older compared
 to younger adults that were able to recover from forward loss of balance
 with a single step. Forward loss of balance was achieved by releasing
 participants (14 older adults and 6 younger adults) from a static
 whole-body forward lean angle of approximately 18 degrees. 10 older adults
 and 6 younger adults were able to recover with a single step and included
 in subsequent analysis. A scalable anatomical model consisting of 36
 degrees-of-freedom was used to compute kinematics and joint moments from
 motion capture and force plate data. Forces for 92 muscle actuators were
 computed using Static Optimisation and Induced Acceleration Analysis was
 used to compute individual muscle contributions to the three-dimensional
 acceleration of the whole body COM. There were no significant differences
 between older and younger adults in step length, step time, 3D COM
 accelerations or muscle contributions to 3D COM accelerations. The stance
 and stepping leg Gastrocnemius and Soleus muscles were primarily
 responsible for the vertical acceleration experienced by the COM. The
 Gastrocnemius and Soleus from the stance side leg together with bilateral
 Hamstrings accelerated the COM forwards throughout balance recovery while
 the Vasti and Soleus of the stepping side leg provided the majority of
 braking accelerations following foot contact. The Hip Abductor muscles
 provided the greatest contribution to medial-lateral accelerations of the
 COM. Deficits in the neuromuscular control of the Gastrocnemius, Soleus,
 Vasti and Hip Abductors in particular could adversely influence balance
 recovery and may be important targets in interventions to improve balance
 recovery performance.
description: Muscle Induced
 Acceleration during Balance RecoveryThe data included within
 the compressed file include the kinematic, kinetic, muscle force and
 muscle induced acceleration results from simulations of each individual
 participant within the associated study published in PLOS
 ONE.Plos
 Data Set.zip
DOI: 10.5061/dryad.4467407
title: Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)

description: With the continued adoption of genome-scale data in evolutionary biology
 comes the challenge of adequately harnessing the information to make
 accurate phylogenetic inferences. Coalescent-based methods of species tree
 inference have become common, and concatenation has been shown in
 simulation to perform well, particularly when levels of incomplete lineage
 sorting are low. However, simulation conditions are often overly
 simplistic, leaving empiricists with uncertainty regarding analytical
 tools. We use a large ultraconserved element (UCE) data set (&gt;3000
 loci) from rattlesnakes of the Crotalus triseriatus group to delimit
 lineages and estimate species trees using concatenation and several
 coalescent-based methods. Unpartitioned and partitioned maximum-likelihood
 and Bayesian analysis of the concatenated matrix yield a topology
 identical to coalescent analysis of a subset of the data in bpp. ASTRAL
 analysis on a subset of the more variable loci also result in a tree
 consistent with concatenation and bpp, whereas the SVDquartets phylogeny
 differs at additional nodes. The size of the concatenated matrix has a
 strong effect on species-tree inference using SVDquartets, warranting
 additional investigation on optimal data characteristics for this method.
 Species-delimitation analyses suggest up to 16 unique lineages may be
 present within the C. triseriatus group, with divergences occurring during
 the Neogene and Quaternary. Network analyses suggest hybridization within
 the group is relatively rare. Altogether, our results reaffirm the Mexican
 highlands as a biodiversity hotspot and suggest that coalescent-based
 species-tree inference on data subsets can provide a strongly supported
 species tree consistent with concatenation of all loci with a large amount
 of missing data.
description: triseriatus75finalConcatenated alignment file of all 3384 loci.UCE-lociZip file containing individual alignments for each UCE locus.RAxML tree with supportML tree inferred through concatenated analysis of all 3384 loci. Node values represent bootstrap values.RAxML_bipartitions.triseriatus_raxml_newASTRAL treeASTRAL species tree inferred from 351 UCE loci.triseriatus_1_speciesTree_ASTRAL.treBPP_SpeciesTreesSpecies trees inferred from BPP analysis of 500 UCE loci.ExaBayes_ConsensusExtendedMajorityRuleNewickConsensus tree from concatenated ExaBayes analysis of all 3384 UCE loci.besttrees_3384Best trees file (ML gene trees) used as input for SNaQ analyses.triseriatus75final-53-SVDQ-ladderizedSVDquartets species tree inferred using all 3384 loci.triseriatus75final_svdquartets_bSTreeSVDquartets bootstrap consensus tree inferred using all loci.
DOI: 10.5061/dryad.879c0
title: Data from: Towards a framework for agent-based image analysis of remote-sensing data

description: Object-based image analysis (OBIA) as a paradigm for analysing remotely
 sensed image data has in many cases led to spatially and thematically
 improved classification results in comparison to pixel-based approaches.
 Nevertheless, robust and transferable object-based solutions for automated
 image analysis capable of analysing sets of images or even large image
 archives without any human interaction are still rare. A major reason for
 this lack of robustness and transferability is the high complexity of
 image contents: Especially in very high resolution (VHR) remote-sensing
 data with varying imaging conditions or sensor characteristics, the
 variability of the objects’ properties in these varying images is hardly
 predictable. The work described in this article builds on so-called rule
 sets. While earlier work has demonstrated that OBIA rule sets bear a high
 potential of transferability, they need to be adapted manually, or
 classification results need to be adjusted manually in a post-processing
 step. In order to automate these adaptation and adjustment procedures, we
 investigate the coupling, extension and integration of OBIA with the
 agent-based paradigm, which is exhaustively investigated in software
 engineering. The aims of such integration are (a) autonomously adapting
 rule sets and (b) image objects that can adopt and adjust themselves
 according to different imaging conditions and sensor characteristics. This
 article focuses on self-adapting image objects and therefore introduces a
 framework for agent-based image analysis (ABIA).
description: IJIDF_ABIA_Towards_a_Framework_supplementThe Supplement contains: a short description file, the rule set of the simulation executable with eCognition 9.2 or higher (Trial Version) which can be downloaded from www.ecognition.com; the image data, elevation data and further derived data used in ERDAS Imagine Format; JPEG and ESRI shape files containing all intermediate results. The Shape files additionally contain object feature values and membership degrees.supplement.zip
DOI: 10.5061/dryad.jb0t7
title: Data from: A Silurian short-great-appendage arthropod

description: A new arthropod, Enalikter aphson gen. et sp. nov., is described from the
 Silurian (Wenlock Series) Herefordshire Lagerstätte of the UK. It belongs
 to the Megacheira (=short-great-appendage group), which is recognized
 here, for the first time, in strata younger than mid-Cambrian age.
 Discovery of this new Silurian taxon allows us to identify a Devonian
 megacheiran representative, Bundenbachiellus giganteus from the Hunsrück
 Slate of Germany. The phylogenetic position of megacheirans is
 controversial: they have been interpreted as stem chelicerates, or stem
 euarthropods, but when Enalikter and Bundenbachiellus are added to the
 most comprehensive morphological database available, a stem euarthropod
 position is supported. Enalikter represents the only fully
 three-dimensionally preserved stem-group euarthropod, it falls in the
 sister clade to the crown-group euarthropods, and it provides new insights
 surrounding the origin and early evolution of the euarthropods.
 Recognition of Enalikter and Bundenbachiellus as megacheirans indicates
 that this major arthropod group survived for nearly 100 Myr beyond the
 mid-Cambrian.
description: OUM
 C.29631Holotype of Enalikter
 aphson in VAXML format (see ReadMe file)OUM_C29631.zipOUM C.29632Specimen of Enalikter aphson in VAXML format (see ReadMe file)OUM_C29632.zipOUM C.29633Specimen of Enalikter aphson in VAXML format (see ReadMe file).OUM_C29633.zip
DOI: 10.5061/dryad.6m8nt
title: Data from: Ultra-low and ultra-broad-band nonlinear acoustic metamaterials

description: Linear acoustic metamaterials (LAMs)are widely used to manipulate sound,
 but it is challenging to obtain bandgaps withthe generalized width (the
 ratio of the bandgap width to its start frequency) γ&gt;1 based on
 linear mechanisms.Here, we adopt both theoretical and experimental
 approaches todescribe the nonlinear chaotic mechanism in both
 one-dimensional (1D) and two-dimensional (2D)nonlinear acoustic
 metamaterials (NAMs). This mechanismenables the strongly NAMsto reduce the
 transmission of wave by as much as 20-40dB in an ultra-low and ultra-broad
 bandthat consists of bandgaps and chaotic bands.With the subwavelength
 cells, the generalized width reachesγ=21 in a 1D NAM and it goes up to
 γ=39 in a 2D NAM, which overcomesthe limit of bandwidth for wave
 suppression in current LAMs.Our work allows for further progress in the
 understanding of the dynamics of NAMs and it opens up
 avenuesindouble-ultra acoustic manipulations.
description: Open
 dataAll these data files are
 experimental data on a nonlinear acoustic metamaterial Beam and a Plate.
 The experiment apparatus and measuring methods are described in the
 Article. The position of the measuring points are also defined in the
 Article.open data -Xin
 Fang.zip
DOI: 10.5061/dryad.c75j9
title: Data from: Estimating cranial musculoskeletal constraints in theropod dinosaurs

description: Many inferences on the biology, behaviour and ecology of extinct
 vertebrates are based on the reconstruction of the musculature and rely
 considerably on its accuracy. Although the advent of digital
 reconstruction techniques has facilitated the creation and testing of
 musculoskeletal hypotheses in recent years, muscle strain capabilities
 have rarely been considered. Here, a digital modelling approach using the
 freely available visualization and animation software BLENDER is applied
 to estimate cranial muscle length changes and optimal and maximal possible
 gape in different theropod dinosaurs. Models of living archosaur taxa
 (Alligator mississippiensis, Buteo buteo) were used in an extant
 phylogenetically bracketed framework to validate the method. Results of
 this study demonstrate that Tyrannosaurus rex, Allosaurus fragilis and
 Erlikosaurus andrewsi show distinct differences in the recruitment of the
 jaw adductor musculature and resulting gape, confirming previous dietary
 and ecological assumptions. While the carnivorous taxa T. rex and Allo.
 fragilis were capable of a wide gape and sustained muscle force, the
 herbivorous therizinosaurian E. andrewsi was constrained to small gape
 angles.
description: S1 Blender setup example
 for Alligator mississippiensisS2 Blender setup example
 for Buteo buteoS3 Blender setup example
 for Allosaurus fragilisS4 Blender setup example
 for Tyrannosaurus rexS5 Blender setup example
 for Erlikosaurus andrewsiS6 Muscle strain script
 for Alligator mississipiensisPython script for strain
 analysis for Alligator mississippiensis (.txt)S7 Muscle strain script
 for Buteo buteoPython script for strain
 analysis for Buteo buteo (.txt)S8 Muscle strain script
 for Allosaurus fragiliisPython script for strain
 analysis for Allosaurus fragilis (.txt)S9 Muscle strain script
 for Tyrannosaurus rexPython script for strain
 analysis for Tyrannosaurus rex (including comments)
 (.txt)S10 Muscle strain script
 for Erlikosaurus andrewsiS11 Data with strain
 factors for studied taxaS12 Movie showing gape
 cycles and strain factors with a muscle resting length at 3
 degreesMovie showing gape
 cycles and strain factors with a muscle resting length at 3 degrees
 (.mov)S13 Movie showing gape
 cycles and strain factors with a muscle resting length at 6
 degreesMovie showing gape
 cycles and strain factors with a muscle resting length at 6 degrees
 (.mov)
DOI: 10.5061/dryad.h68bj
title: Data from: Evaluating conservation and fisheries management strategies by linking spatial prioritisation software and ecosystem and fisheries modelling tools

description: 1. Well-designed marine protected area (MPA) networks can deliver a range
 of ecological, economic and social benefits, and so a great deal of
 research has focused on developing spatial conservation prioritization
 tools to help identify important areas. 2. However, whilst these software
 tools are designed to identify MPA networks that both represent
 biodiversity and minimize impacts on stakeholders, they do not consider
 complex ecological processes. Thus, it is difficult to determine the
 impacts that proposed MPAs could have on marine ecosystem health,
 fisheries and fisheries sustainability. 3. Using the eastern English
 Channel as a case study, this paper explores an approach to address these
 issues by identifying a series of MPA networks using the Marxan and Marxan
 with Zones conservation planning software and linking them with a
 spatially explicit ecosystem model developed in Ecopath with Ecosim. We
 then use these to investigate potential trade-offs associated with
 adopting different MPA management strategies. 4. Limited-take MPAs, which
 restrict the use of some fishing gears, could have positive benefits for
 conservation and fisheries in the eastern English Channel, even though
 they generally receive far less attention in research on MPA network
 design. 5. Our findings, however, also clearly indicate that no-take MPAs
 should form an integral component of proposed MPA networks in the eastern
 English Channel, as they not only result in substantial increases in
 ecosystem biomass, fisheries catches and the biomass of commercially
 valuable target species, but are fundamental to maintaining the
 sustainability of the fisheries. 6. Synthesis and applications. Using the
 existing software tools Marxan with Zones and Ecopath with Ecosim in
 combination provides a powerful policy-screening approach. This could help
 inform marine spatial planning by identifying potential conflicts and by
 designing new regulations that better balance conservation objectives and
 stakeholder interests. In addition, it highlights that appropriate
 combinations of no-take and limited-take marine protected areas might be
 the most effective when making trade-offs between long-term ecological
 benefits and short-term political acceptability.
description: Conservation planning
 and ecosystem modelling dataMarxan and Marxan with
 Zones conservation planning software files and Ecospace model output files
 (Marxan software and associated manuals freely available from:
 http://www.uq.edu.au/marxan/). Ecopath, Ecosim and Ecospace models and
 supporting technical documentation on parameterisation available on
 request from Cefas and Ifremer (Ecopath, Ecosim and Ecospace input data,
 composition of functional groups and model parameters included with online
 supporting information associated with publication).Marxan_Ecospace_Files.zip
DOI: 10.15468/dl.kcce99
title: Occurrence Download

description: A dataset containing 654 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oophaga granulifera"
 ]
}

 The dataset includes 654 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000414-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.