cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q4d2v6h
title: Data from: Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum

description: Well-characterised examples of homoploid hybrid speciation (HHS) are rare
 in nature yet they offer the potential to study a number of evolutionary
 processes. In this study we investigate putative homoploid hybrid species
 in the genus Argyranthemum (Asteraceae), a group of plants endemic to the
 Macaronesian archipelagos of the North Atlantic Ocean. We specifically
 address a number of knowledge gaps surrounding the origin(s) of A.
 sundingii and A. lemsii, which are thought to be derived from the same
 parental cross. Comparisons of leaf morphology suggest that A. sundingii
 and A. lemsii are distinct from their parental progenitors and
 distinguishable from each other based on leaf area. Ecological niche
 modelling (ENM) demonstrated that the homoploid hybrid species occupy
 novel habitats that are intermediate relative to the parental species.
 Nuclear SSRs and SNP data indicate that the homoploid hybrid species are
 distinct from the parental taxa, whilst population level sampling of
 chloroplast SSRs and Approximate Bayesian Computation show that A.
 sundingii and A. lemsii are independently derived from the same parental
 cross. As such, Argyranthemum represents an example of independent
 homoploid hybrid speciation events with evidence of divergence in leaf
 morphology and adaptation to novel intermediate habitats. On oceanic
 islands, which are often typified by steep ecological gradients and
 inhabited by recently derived species with weak reproductive barriers,
 multiple HHS events from the same parental cross are not only possible but
 are likely to have played a more important role in oceanic island
 radiations than we currently think.
description: Argy-HHS-demuliplexed-GBS-dataArgy-HHS-demuliplexed-GBS-data.tar.gz contains demultiplexed reads for the samples used in this study, that were created following step one of the ipyrad assembly pipeline.
DOI: 10.5061/dryad.n0m260p
title: Data from: Genome-wide association analysis of stalk biomass and anatomical traits in maize

description: Background: Maize stover is an important source of crop residues and a
 promising sustainable energy source in the United States. Stalk is the
 main component of stover, representing about half of stover dry weight.
 Characterization of genetic determinants of stalk traits provide a
 foundation to optimize maize stover as a biofuel feedstock. We
 investigated maize natural genetic variation in genome-wide association
 studies (GWAS) to detect candidate genes associated with traits related to
 stalk biomass (stalk diameter and plant height) and stalk anatomy (rind
 thickness, vascular bundle density and area). Results: Using a panel of
 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide
 polymorphism (SNP) markers were identified. Stalk traits were measured on
 800 members of the panel in replicated field trials across years. GWAS
 revealed 16 candidate genes associated with four stalk traits. Most of the
 detected candidate genes were involved in fundamental cellular functions,
 such as regulation of gene expression and cell cycle progression. Two of
 the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated
 with plant height were previously shown to be involved in regulating the
 vegetative to floral transition. The association of Zmm22 with plant
 height was confirmed using a transgenic approach. Transgenic lines with
 increased expression of Zmm22 showed a significant decrease in plant
 height as well as tassel branch number, indicating a pleiotropic effect of
 Zmm22. Conclusion: Substantial heritable variation was observed in the
 association panel for stalk traits, indicating a large potential for
 improving useful stalk traits in breeding programs. Genome-wide
 association analyses detected several candidate genes associated with
 multiple traits, suggesting common regulatory elements underlie various
 stalk traits. Results of this study provide insights into the genetic
 control of maize stalk anatomy and biomass.
description: widiv_942g_899784SNPs_imputed_filteredGenos_noRTA_AGPv4.hmp.txtImputed data of 899,784 SNPs generated from RNA-Seq reads of 942 inbred lines. SNPs were called from mapping to the version 4 maize B73 (AGPv4) reference sequence. Imputation was done using fastPHASE v1.4.0 (Scheet and Stephens, 2006).62biomAP_v_B73_SNPMatrix.txt.gzSNP calls generated from high quality whole genome resequencing of 56 inbreds (Brohammer et al., 2018). This dataset was used to validate imputation results of 899,784 SNPs detected in this study.
DOI: 10.5061/dryad.6t7b8
title: Data from: Sequence co-evolution gives 3D contacts and structures of protein complexes

description: Protein-protein interactions are fundamental to many biological processes.
 Experimental screens have identified tens of thousands of interactions and
 structural biology has provided detailed functional insight for select 3D
 protein complexes. An alternative rich source of information about protein
 interactions is the evolutionary sequence record. Building on earlier
 work, we show that analysis of correlated evolutionary sequence changes
 across proteins identifies residues that are close in space with
 sufficient accuracy to determine the three-dimensional structure of the
 protein complexes. We evaluate prediction performance in blinded tests on
 76 complexes of known 3D structure, predict protein-protein contacts in 32
 complexes of unknown structure, and demonstrate how evolutionary couplings
 can be used to distinguish between interacting and non-interacting protein
 pairs in a large complex. With the current growth of sequences, we expect
 that the method can be generalized to genome-wide elucidation of
 protein-protein interaction networks and used for interaction predictions
 at residue resolution.
description: EVcomplex Supplementary
 DataThis archive contains
 all supplementary data described in the manuscript "Sequence
 co-evolution gives 3D contacts and structures of protein complexes".
 This includes the input alignments for the method, EVcomplex results,
 docking in- and outputs as well as data for predicted monomer models of
 ATP synthase subunit a and UMUC.EVcomplex.tar.gzEVcomplex Supplementary Data: AlignmentsA subset of the full supplementary archive containing only the concatenated sequence alignments.01_Alignments.tar.gzEVcomplex Supplementary Data: Coupling PredictionsA subset of the full supplementary data archive containing the EVcomplex output for the test set and the de novo prediction set.03_EVcomplex_dataset.tar.gzEVcomplex Supplementary Data: Genome distance distributionA subset of the full EVcomplex supplementary data archive with only the genome distance distribution plots showing the distance for each concatenated sequence pair.02_Genome_distance_plots.tar.gzEVcomplex Supplementary Data: Protein-protein dockingA subset of the full EVcomplex supplementary data archive containing the input files used for HADDOCK docking and the best models for each of the docking runs.04_Docking.tar.gzEVcomplex Supplementary Data: ATP synthase dataA subset of the full EVcomplex supplementary data archive containing all ATP synthase related data including EVcomplex predictions and the EVfold de novo ATP synthase subunit a models.05_ATP_synthase_predictions.tar.gzEVcomplex Supplementary Data: UmuC modelA subset of the full EVcomplex supplementary data archive containing the data related to the EVfold de novo prediction of UmuC.06_UmuC_model.tar.gz
DOI: 10.5061/dryad.nh109
title: Data from: Noninvasive electroencephalogram based control of a robotic arm for reach and grasp tasks

description: Brain-computer interface (BCI) technologies aim to provide a bridge
 between the human brain and external devices. Prior research using
 non-invasive BCI to control virtual objects, such as computer cursors and
 virtual helicopters, and real-world objects, such as wheelchairs and
 quadcopters, has demonstrated the promise of BCI technologies. However,
 controlling a robotic arm to complete reach-and-grasp tasks efficiently
 using non-invasive BCI has yet to be shown. In this study, we found that a
 group of 13 human subjects could willingly modulate brain activity to
 control a robotic arm with high accuracy for performing tasks requiring
 multiple degrees of freedom by combination of two sequential low
 dimensional controls. Subjects were able to effectively control reaching
 of the robotic arm through modulation of their brain rhythms within the
 span of only a few training sessions and maintained the ability to control
 the robotic arm over multiple months. Our results demonstrate the
 viability of human operation of prosthetic limbs using non-invasive BCI
 technology.
description: Virtual Cursor
 TaskLeft and right virtual
 cursor control data set.1D_PreRun.rarVirtual Cursor TaskTwo-dimensional virtual cursor control task.2D_PreRun.rarRobotic Arm Reach and Grasping taskRobotic Arm Reach and Grasping task of four fixed targetsF4Targets.rarRobotic Arm Reach and Grasping taskRobotic Arm Reach and Grasping task of five fixed targetsF5Targets.rarRobotic Arm Reach and Grasping taskRobotic Arm Reach and Grasping task of a randomly located targetF1RandTarget.rarRobotic Arm Reach and Grasping taskRobotic Arm Reach and Grasping task of moving a target from table onto a shelf.4STEP3DGrasping.rarReadmeInstruction of how to use the data
DOI: 10.5517/ccdc.csd.cc255gys
title: CCDC 2001265: Experimental Crystal Structure Determination

description: Related Article: Dedong Wu,  Faraj Atassi|2021|Z.Naturforsch.,B:Chem.Sci.|76|45|doi:10.1515/znb-2020-0083
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc255gzt
title: CCDC 2001266: Experimental Crystal Structure Determination

description: Related Article: Dedong Wu,  Faraj Atassi|2021|Z.Naturforsch.,B:Chem.Sci.|76|45|doi:10.1515/znb-2020-0083
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc255h0w
title: CCDC 2001267: Experimental Crystal Structure Determination

description: Related Article: Dedong Wu,  Faraj Atassi|2021|Z.Naturforsch.,B:Chem.Sci.|76|45|doi:10.1515/znb-2020-0083
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc255h1x
title: CCDC 2001268: Experimental Crystal Structure Determination

description: Related Article: Dedong Wu,  Faraj Atassi|2021|Z.Naturforsch.,B:Chem.Sci.|76|45|doi:10.1515/znb-2020-0083
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.n08t0
title: Data from: VLUIS, a land use data product for Victoria, Australia, covering 2006 to 2013

description: Land Use Information is a key dataset required to enable an understanding
 of the changing nature of our landscapes and the associated influences on
 natural resources and regional communities. The Victorian Land Use
 Information System (VLUIS) data product has been created within the State
 Government of Victoria to support land use assessments. The project began
 in 2007 using stakeholder engagement to establish product requirements
 such as format, classification, frequency and spatial resolution. Its
 genesis is significantly different to traditional methods, incorporating
 data from a range of jurisdictions to develop land use information
 designed for regular on-going creation and consistency. Covering the
 entire landmass of Victoria, the dataset separately describes land tenure,
 land use and land cover. These variables are co-registered to a common
 spatial base (cadastral parcels) across the state for the period 2006 to
 2013; biennially for land tenure and land use, and annually for land
 cover. Data is produced as a spatial GIS feature class.
description: Victorian Land Use
 Information System Data files 2006-2013The Victorian Land Use
 Information System (VLUIS) dataset has been created by the Spatial
 Information Sciences Group of the Agriculture Research Division in the
 Department of Economic Development, Jobs, Transport, and Resources. The
 method used to create VLUIS is significantly different to traditional
 methods used to create land use information and has been designed to
 create regular and consistent data over time. It covers the entire
 landmass of Victoria and separately describes the land tenure, land use
 and land cover for each cadastral parcel across the state, biennially for
 land tenure and use and annually for land cover; for each year from 2006
 to 2013. The data is in the form of a shapefile.VLUIS2006to2013_zipped_shapefiles.zip
DOI: 10.5061/dryad.2h0q3
title: Data from: Differential neural processing during motor imagery of daily activities in chronic low back pain patients

description: Chronic low back pain (chronic LBP) is both debilitating for patients but
 also a major burden on the health care system. Previous studies reported
 various maladaptive structural and functional changes among chronic LBP
 patients on spine- and supraspinal levels including behavioral
 alterations. However, evidence for cortical reorganization in the
 sensorimotor system of chronic LBP patients is scarce. Motor Imagery (MI)
 is suitable for investigating the cortical sensorimotor network as it
 serves as a proxy for motor execution. Our aim was to investigate
 differential MI-driven cortical processing in chronic LBP compared to
 healthy controls (HC) by means of functional magnetic resonance imaging
 (fMRI). Twenty-nine subjects (15 chronic LBP patients, 14 HC) were
 included in the current study. MI stimuli consisted of randomly presented
 video clips showing every-day activities involving different whole-body
 movements as well as walking on even ground and walking downstairs and
 upstairs. Guided by the video clips, subjects had to perform MI of these
 activities, subsequently rating the vividness of their MI performance.
 Brain activity analysis revealed that chronic LBP patients exhibited
 significantly reduced activity compared to HC subjects in MI-related brain
 regions, namely the left supplementary motor area and right superior
 temporal sulcus. Furthermore, psycho-physiological-interaction analysis
 yielded significantly enhanced functional connectivity (FC) between
 various MI-associated brain regions in chronic LBP patients indicating
 diffuse and non-specific changes in FC. Current results demonstrate
 initial findings about differences in MI-driven cortical processing in
 chronic LBP pointing towards reorganization processes in the sensorimotor
 network.
description: Raw fMRI data of
 controls and patientsRaw fMRI data of 14
 healthy controls (HC) and 15 chronic low back pain patients (CLBP).
 Subject had to perform a motor imagery (MI) task during scanning
 session.Raw_Data.zip
DOI: 10.5061/dryad.q6h2n
title: Data from: Specificity of fungal associations of Pyroleae and Monotropa hypopitys during germination and seedling development

description: Mycoheterotrophic plants obtain organic carbon from associated mycorrhizal
 fungi, fully or partially. Angiosperms with this form of nutrition possess
 exceptionally small 'dust seeds' which after germination develop
 'seedlings' that remain subterranean for several years, fully
 dependent on fungi for supply of carbon. Mycoheterotrophs which as adults
 have photosynthesis thus develop from full to partial mycoheterotrophy, or
 autotrophy, during ontogeny. Mycoheterotrophic plants may represent a
 gradient of variation in a parasitism-mutualism continuum, both among and
 within species. Previous studies on plant-fungal associations in
 mycoheterotrophs have focused on either germination or the adult life
 stages of the plant. Much less is known about the fungal associations
 during development of the subterranean seedlings. We investigated
 germination and seedling development and the diversity of fungi associated
 with germinating seeds and subterranean seedlings (juveniles) in five
 Monotropoideae (Ericaceae) species, the full mycoheterotroph Monotropa
 hypopitys and the putatively partial mycoheterotrophs Pyrola chlorantha,
 P. rotundifolia, Moneses uniflora and Chimaphila umbellata. Seedlings
 retrieved from seed sowing experiments in the field were used to examine
 diversity of fungal associates, using pyrosequencing analysis of ITS2
 region for fungal identification. The investigated species varied with
 regard to germination, seedling development and diversity of associated
 fungi during juvenile ontogeny. Results suggest that fungal host
 specificity increases during juvenile ontogeny, most pronounced in the
 fully mycoheterotrophic species, but a narrowing of fungal associates was
 found also in two partially mycoheterotrophic species. We suggest that
 variation in specificity of associated fungi during seedling ontogeny in
 mycoheterotrophs represents ongoing evolution along a parasitism-mutualism
 continuum.
description: Sample
 infoSample descriptions and
 id.tag
 primersTag primers used in the
 pyrosequencing with corresponding samples and sequencing plate
 id.Pyrosequencing plate
 1fasta, qual and sff file
 from pyrosequencing plate 1.Veronika3.zippyrosequencing plate 2fasta, qual and sff file from pyrosequencing plate 2.Veronika4.zipPyrosequencing plate 3fasta, qual and sff file from pyrosequencing plate 3.Veronika5.zipPyrosequencing plate 4fasta, qual and sff file from pyrosequencing plate 4.Veronika6.zip
DOI: 10.5061/dryad.f8m84
title: Data from: Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone

description: Studies of hybridization and introgression and, in particular, the
 identification of admixed individuals in natural populations benefit from
 the use of diagnostic genetic markers that reliably differentiate pure
 species from each other and their hybrid forms. Such diagnostic markers
 are often infrequent in the genomes of closely related species, and
 genomewide data facilitate their discovery. We used whole-genome data from
 Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years)
 and hybridizing, avian, sister species, the Saltmarsh (Ammodramus
 caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of
 diagnostic markers for high-resolution identification of pure and admixed
 individuals. We compared the microsatellite repeat regions identified in
 the genomes of the two species and selected a subset of 37 loci that
 differed between the species in repeat number. We screened these loci on
 12 pure individuals of each species and report on the 34 that successfully
 amplified. From these, we developed a panel of the 12 most diagnostic
 loci, which we evaluated on 96 individuals, including individuals from
 both allopatric populations and sympatric individuals from the hybrid
 zone. Using simulations, we evaluated the power of the marker panel for
 accurate assignments of individuals to their appropriate pure species and
 hybrid genotypic classes (F1, F2, and backcrosses). The markers proved
 highly informative for species discrimination and had high accuracy for
 classifying admixed individuals into their genotypic classes. These
 markers will aid future investigations of introgressive hybridization in
 this system and aid conservation efforts aimed at monitoring and
 preserving pure species. Our approach is transferable to other study
 systems consisting of closely related and incipient species.
description: SparrowGenotypesGenotypes at 12 diagnostic microsatellite loci of 96 Ammodramus caudacutus and A. nelsoni. Sparrows were sampled from sympatric and allopatric populations.SimulatedGenotypesGenotypes, simulated in HYBRIDLAB, at 12 diagnostics microsatellite loci for six genotypic classes of Ammodramus sparrows: pure caudacutus, backcrossed caudacutus, F1, F2, backcrossed nelsoni, and pure nelsoni.Assembled N50 contigs Ammodramus caudacutusFasta file of assembled contigs that were &gt; the N50contig size of assembled Ammodramus caudacutus reads from Illumina sequencing.SALS-2-29-2012-assembly.fastaAssembled N50 contigs Ammodramus nelsoniFasta file of assembled contigs &gt; than the N50 contig length for Illumina sequencing reads of Ammodramus nelsoni.Nelson-3-26-2012-assembly.fasta
DOI: 10.5061/dryad.q35s1
title: Data from: Biologically and diagenetically derived peptide modifications in Moa collagens

description: The modifications that occur on proteins in natural environments over time
 are not well studied, yet characterizing them is vital to correctly
 interpret sequence data recovered from fossils. The recently extinct moa
 (Dinornithidae) is an excellent candidate for investigating the
 preservation of proteins, their post-translational modifications (PTMs)
 and diagenetic alterations during degradation. Moa protein extracts were
 analysed using mass spectrometry, and peptides from collagen I, collagen
 II and collagen V were identified. We also identified biologically derived
 PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation,
 fucosylation) on amino acids at locations consistent with extant proteins.
 In addition to these in vivo modifications, we detected novel
 modifications that are probably diagenetically derived. These include loss
 of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide
 backbone cleavage, as well as previously noted deamidation. Moa collagen
 sequences and modifications provide a baseline by which to evaluate
 proteomic studies of other fossils, and a framework for defining the
 molecular relationship of moa to other closely related taxa.
description: Moa-HCl-1Moa HCl extraction run #1 on Orbitrap XLMoa-1-60111-1.RAWMoa HCl-2Moa HCl extraction run #2 on Orbitrap XLMoa-1-60111-2.RAWMoa Ammonium Bicarbonate-1Moa ammonium bicarbonate extraction run #1 on Orbitrap XLMoa-2-60111-1.RAWMoa Ammonium Bicarbonate-2Moa ammonium bicarbonate extraction run #2 on Orbitrap XLMoa-2-60111-2.RAWMoa HCl controlMoa HCl extraction buffer control on Orbitrap XLMoa-C1-60111-2.RAWMoa ammonium bicarbonate controlMoa ammonium bicarbonate buffer controlMoa-C2-60111-2.RAW