cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p4238
title: Data from: A sex-linked supergene controls sperm morphology and swimming speed in a songbird

description: Sperm are perhaps the most diverse cells in the animal kingdom, with
 enormous morphological variation between taxa, between species, between
 males and within an ejaculate. Considerable interest in sperm diversity
 has arisen following the realisation that sperm competition
 (post-copulatory sexual selection) is a powerful selective force in many
 organisms, and that sperm morphology has co-evolved with female
 reproductive tract morphology. However, the relationship between sperm
 morphology, sperm motility and fertilisation success is only partially
 understood. The extent to which between-male variation is heritable is
 largely unknown, and remarkably few studies have investigated the genetic
 architecture of sperm traits, especially sperm morphology. Here we use
 high-density genotyping and gene expression profiling to explore the
 considerable sperm trait variation that exists in the zebra finch
 Taeniopygia guttata. We show that nearly all of the genetic variation in
 sperm morphology is caused by an inversion polymorphism on the Z
 chromosome acting as a ‘supergene’. These results provide a striking
 example of two evolutionary genetic predictions. First, that in species
 where females are the heterogametic sex, genetic variation affecting
 sexually dimorphic traits will accumulate on the Z chromosome. Second,
 recombination suppression at the inversion allows beneficial dominant
 alleles to become fixed on whichever haplotype they first arise, without
 being exchanged onto other haplotypes. Finally, we show that the inversion
 polymorphism will be stably maintained by heterozygote advantage, because
 heterozygous males have the fastest and most successful sperm with no
 apparent fitness cost.
description: Data from Kim et al
 2017. Nat. Eco. Evol.
DOI: 10.5061/dryad.5km60
title: Data from: Origin of tensile strength of a woven sample cut in bias directions

description: Textile fabrics are highly anisotropic, so that their mechanical
 properties including strengths are a function of direction. An extreme
 case is when a woven fabric sample is cut in such a way where the bias
 angle and hence the tension loading direction is around 45° relative to
 the principal directions. Then, once loaded, no yarn in the sample is held
 at both ends, so the yarns have to build up their internal tension
 entirely via yarn–yarn friction at the interlacing points. The overall
 fabric strength in such a sample is a result of contributions from the
 yarns being pulled out and those broken during the process, and thus
 becomes a function of the bias direction angle θ, sample width W and
 length L, along with other factors known to affect fabric strength tested
 in principal directions. Furthermore, in such a bias sample when the major
 parameters, e.g. the sample width W, change, not only the resultant
 strengths differ, but also the strength generating mechanisms (or failure
 types) vary. This is an interesting problem and is analysed in this study.
 More specifically, the issues examined in this paper include the exact
 mechanisms and details of how each interlacing point imparts the
 frictional constraint for a yarn to acquire tension to the level of its
 strength when both yarn ends were not actively held by the testing grips;
 the theoretical expression of the critical yarn length for a yarn to be
 able to break rather than be pulled out, as a function of the related
 factors; and the general relations between the tensile strength of such a
 bias sample and its structural properties. At the end, theoretical
 predictions are compared with our experimental data.
description: SubmittedDataFiles
DOI: 10.5061/dryad.1611
title: Data from: Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae)

description: Analyses of genome scale data sets are beginning to clarify the
 phylogenetic relationships of species with complex evolutionary histories.
 Broad sampling across many genes allows for both large concatenated data
 sets to improve genome-scale phylogenetic resolution and also for
 independent analysis of gene trees and detection of phylogenetic
 incongruence. Recent sequencing projects in Oryza sativa and its wild
 relatives have positioned rice as a model system for such “phylogenomic”
 studies. We describe the assembly of a phylogenomic data set from 800,000
 bacterial artificial chromosome (BAC) end sequences, producing an
 alignment of 2.4 million nucleotides for 10 diploid species of Oryza. A
 supermatrix approach confirms the broad outline of previous phylogenetic
 studies, although the non-phylogenetic signal and high levels of missing
 data must be handled carefully. Phylogenetic analysis of 12 chromosomes
 and nearly 2000 genes finds strikingly high levels of incongruence across
 different genomic scales, a result that is likely to apply to other
 low-level phylogenies in plants. We conclude that there is great potential
 for phylogenetic inference using data from next-generation sequencing
 protocols but that attention to methodological issues arising inevitably
 in these data sets is critical.
description: AA
 chromosomesConcatenated sequences
 for each of the 12 chromosomes for the AA speciesaachromosomes.tar.gzORYZA chromosomesConcatenated sequences for 12 chromosomes across all 10 ORYZA speciesoryzachromosomes.tar.gzAA alignment and treesConcatenated alignment for the AA genome species; include trees block corresponding to Figure 3A and 3B.aa.nexAA (gapless) alignment and treesSequences for AA species, all sites with missing data removed. Includes trees block corresponding to Figure 3C.aagapless.nexORYZA alignment and treesConcatenated sequences for all 10 ORYZA species. Includes trees block corresponding to Figure 2A, 2B and 2C.oryza.nex
DOI: 10.5061/dryad.1br2n
title: Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

description: Ecological understanding of the role of consumer-resource interactions in
 natural food webs is limited by the difficulty of accurately and
 efficiently determining the complex variety of food types animals have
 eaten in the field. We developed a method based on DNA metabarcoding
 multiplexing and next-generation sequencing to uncover different taxonomic
 groups of organisms from complex diet samples. We validated this approach
 on 91 faeces of a large omnivorous mammal, the brown bear, using DNA
 metabarcoding markers targeting the plant, vertebrate, and invertebrate
 components of the diet. We included internal controls in the experiments
 and performed PCR replication for accuracy validation in post-sequencing
 data analysis. Using our multiplexing strategy, we significantly
 simplified the experimental procedure and accurately and concurrently
 identified different prey DNA corresponding to the targeted taxonomic
 groups, with ≥60% of taxa of all diet components identified to
 genus/species level. The systematic application of internal controls and
 replication was a useful and simple way to evaluate the performance of our
 experimental procedure, standardize the selection of sequence filtering
 parameters for each marker data, and validate the accuracy of the results.
 Our general approach can be adapted to the analysis of dietary samples of
 various predator species in different ecosystems, for a number of
 conservation and ecological applications entailing large-scale population
 level diet assessment through cost effective screening of multiple DNA
 metabarcodes, and the detection of fine dietary variation among samples or
 individuals and of rare food items.
description: GH_P3V5_P3MAV_P3Ast_P3Cyp_P3Poa_P3Ros_P3alignment_refDBcdSequence alignment of the chloroplast trnL (UAA) intron of 62 plantsalignment_refDBits2Sequence alignment of the internal transcribed spacer 2 (ITS2) of 30 plants of the family Rosaceae
DOI: 10.5061/dryad.g1q8p
title: Data from: A new crustacean from the Herefordshire (Silurian) Lagerstätte, UK, and its significance in malacostracan evolution

description: Cascolus ravitis gen. et sp. nov. is a three-dimensionally preserved
 fossil crustacean with soft parts from the Herefordshire (Silurian)
 Lagerstätte, UK. It is characterized by a head with a head shield and five
 limb pairs, and a thorax (pereon) with nine appendage-bearing segments
 followed by an apodous abdomen (pleon). All the appendages except the
 first are biramous and have a gnathobase. The post-mandibular appendages
 are similar one to another, and bear petal-shaped epipods that probably
 functioned as a part of the respiratory–circulatory system. Cladistic
 analysis resolves the new taxon as a stem-group leptostracan
 (Malacostraca). This well-preserved arthropod provides novel insights into
 the evolution of appendage morphology, tagmosis and the possible
 respiratory–circulatory physiology of a basal malacostracan.
description: Cascolus ravitis
 holotype (VAXML/STL format)Virtual specimen of
 OUMNH C.29698, holotype of Cascolus ravitis. Reconstructed from
 physical-optical tomographic dataset using SPIERS
 (http://www.spiers-software.org). For method see Sutton, Rahman and
 Garwood 2014. Techniques for Virtual Palaeontology. Wiley Blackwell,
 208pp. For details of VAXML/STL format see
 http://palaeo-electronica.org/content/issue-2-2012-technical-articles/226-virtual-palaeontology-toolkit.Cascolus_VAXML.zipNEXUS file for analysis of CascolusNEXUS format data file associated with Proceedings B articleESI TABLE 1 Siveter et al Cascolus ravitis NEXUS.txtCharacter list for phylogenetic analysis - PDF formatCharacter list for phylogenetic analysis associated with Proceedings B publicationESI TABLE 2. Siveter et al Character list (as used in Briggs et al. 2016).pdfCharacter list for phylogenetic analysis - DOC formatCharacter list for phylogenetic analysis associated with Proceedings B publicationSiveter et al Character list as used in Briggs et al. (2016).doc
DOI: 10.5061/dryad.g12k7
title: Data from: Distribution and bioinformatic analysis of the cerato-platanin protein family in Dikarya

description: The cerato-platanin family is a group of small cysteine-rich fungal
 proteins new to science. They usually are abundantly secreted
 extracellularly and are involved in fungus-host interactions. With the
 advance of available fungal genome sequences, we performed a genomewide
 study of the distribution of this family in fungi and analyzed the common
 characteristics of the protein sequences. A total of 55 fungal genomes,
 including 27 from Ascomycota and 28 from Basidiomycota, were used. A total
 of 130 cerato-platanin homolog protein sequences were obtained and
 analyzed. Our results showed that cerato-platanin homologs existed in both
 Ascomycota and Basidiomycota but were lost in early branches of jelly
 fungi as well as in some groups with yeast or yeast-like forms in their
 life cycle. Homolog numbers varied considerably between Ascomycota and
 Basidiomycota. Phylogenetic analysis suggested that the ancestor of the
 Dikarya possessed multiple copies of cerato-platanins, which sorted
 differently in Ascomycota and Basidiomycota, and that this gene family
 might have expanded in the Basidiomycota. Almost all homologs contained
 signal peptide sequences, and the length of mature proteins were mainly
 105-134 amino acids. Four cysteines involved in forming two disulfide
 bridges and signature sequences (CSD or CSN) were highly conserved in most
 homologs. These results indicated a higher diversity of the
 cerato-platanin family in Basidiomycota than Ascomycota.
description: FIGURE. 1. Distribution
 of cerato-platanin homologs in Dikarya.Distribution of
 cerato-platanin homologs in Dikarya.All cerato-platanin
 mature proteinsFASTA file of all
 cerato-platanin mature proteinsAll cerato-platanin
 mature proteins alignments for phylogenetic analysisFASTA files of all the
 alignments used for both phylogenetic analysesFIGURE. 2.
 Neighbor-joining phylogenetic tree of cerato-platanin family proteins from
 Dikarya.Neighbor-joining
 phylogenetic tree of cerato-platanin family proteins from
 Dikarya.FIGURE. 3. Maximum
 likelihood phylogenetic tree of cerato-platanin family proteins from
 Dikarya.Maximum likelihood
 phylogenetic tree of cerato-platanin family proteins from
 Dikarya.Legends for FIGURE
 1-3Legends for FIGURE
 1-3
DOI: 10.7910/dvn/uboe1n
title: Regional Organizations‘ Competencies (ROCO) Database, version 2.0

description: The Regional Organizations’ (ROCO) databases have been developed as part of the research project “Towards an Increasing Regionalization of International Politics? Comparing the Development of External and Internal Competencies of Regional Organizations over Time”, which was funded by the Fritz-Thyssen-Foundation (grant number Az.10.16.1012IB). 
The update version 2.0 was implemented with funding from the German Research Council, as part of the research project “Overlapping Regionalism in Africa, the Americas, Asia and Europe Compared” (grant number PA 1257/7-1; 421167407)
The ROCO datasets 2.0 provide information on 73 regional international organizations (RIOs) from 1945 to 2020 and the policy competencies which are specified in the RIOs’ primary law documents. While the project’s primary focus is on external policy competencies of RIOs, the dataset entails information about both internal and external policy competencies. 
The research questions guiding the development of the datasets are: how have RIOs’ internal and external policy mandates change over time? 
This codebook provides an overview of the datasets. In the following first part, the codebook introduces the datasets, describes the included cases and information, clarifies the coding procedure and coding decisions, and explains how to use the datasets. The second part of the codebook provides an alphabetical list of all variables in the databases, while the variables are described in detail in part 3, ordered after categories.
description: The Regional Organizations’ (ROCO) databases have been developed as part of the research project “Towards an Increasing Regionalization of International Politics? Comparing the Development of External and Internal Competencies of Regional Organizations over Time”, which was funded by the Fritz-Thyssen-Foundation (grant number Az.10.16.1012IB). 
The update version 2.0 was implemented with funding from the German Research Council, as part of the research project “Overlapping Regionalism in Africa, the Americas, Asia and Europe Compared” (grant number PA 1257/7-1; 421167407)
The ROCO datasets 2.0 provide information on 73 regional international organizations (RIOs) from 1945 to 2020 and the policy competencies which are specified in the RIOs’ primary law documents. While the project’s primary focus is on external policy competencies of RIOs, the dataset entails information about both internal and external policy competencies. 
The research questions guiding the development of the datasets are: how have RIOs’ internal and external policy mandates change over time? 
This codebook provides an overview of the datasets. In the following first part, the codebook introduces the datasets, describes the included cases and information, clarifies the coding procedure and coding decisions, and explains how to use the datasets. The second part of the codebook provides an alphabetical list of all variables in the databases, while the variables are described in detail in part 3, ordered after categories.
DOI: 10.5061/dryad.r1vp879
title: Data from: Biallelic SQSTM1 mutations in early-onset, variably progressive neurodegeneration

description: Objective: To characterize clinically and molecularly an early-onset,
 variably progressive neurodegenerative disorder characterized by a
 cerebellar syndrome with severe ataxia, gaze palsy, dyskinesia, dystonia,
 and cognitive decline affecting 11 individuals from 3 consanguineous
 families. Methods: We used whole-exome sequencing (WES) (families 1 and 2)
 and a combined approach based on homozygosity mapping and WES (family 3).
 We performed in vitro studies to explore the effect of the nontruncating
 SQSTM1 mutation on protein function and the effect of impaired SQSTM1
 function on autophagy. We analyzed the consequences of sqstm1
 down-modulation on the structural integrity of the cerebellum in vivo
 using zebrafish as a model. Results: We identified 3 homozygous
 inactivating variants, including a splice site substitution
 (c.301+2T&gt;A) causing aberrant transcript processing and accelerated
 degradation of a resulting protein lacking exon 2, as well as 2 truncating
 changes (c.875_876insT and c.934_936delinsTGA). We show that loss of
 SQSTM1 causes impaired production of ubiquitin-positive protein aggregates
 in response to misfolded protein stress and decelerated autophagic flux.
 The consequences of sqstm1 down-modulation on the structural integrity of
 the cerebellum in zebrafish documented a variable but reproducible
 phenotype characterized by cerebellum anomalies ranging from depletion of
 axonal connections to complete atrophy. We provide a detailed clinical
 characterization of the disorder; the natural history is reported for 2
 siblings who have been followed up for &gt;20 years. Conclusions: This
 study offers an accurate clinical characterization of this recently
 recognized neurodegenerative disorder caused by biallelic inactivating
 mutations in SQSTM1 and links this phenotype to defective selective
 autophagy.
description: video_NEUROLOGY ID#
 2018_879940VIDEOSupplemental
 Data_Neurology #2018-879940supplemental
 data
DOI: 10.5061/dryad.4cp98
title: Data from: A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals

description: Recent studies have reported multiple cases of molecular adaptation in
 cetaceans related to their aquatic abilities. However, none of these has
 included the hippopotamus, precluding an understanding of whether
 molecular adaptations in cetaceans occurred before or after they split
 from their semi-aquatic sister taxa. Here, we obtained new transcriptomes
 from the hippopotamus and humpback whale, and analysed these together with
 available data from eight other cetaceans. We identified more than 11 000
 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA
 sequences among 23 mammals, to our knowledge the largest phylogenomic
 dataset to date for cetaceans. We found positive selection in nine genes
 on the branch leading to the common ancestor of hippopotamus and whales,
 and 461 genes in cetaceans compared to 64 in hippopotamus. Functional
 annotation revealed adaptations in diverse processes, including lipid
 metabolism, hypoxia, muscle and brain function. By combining these
 findings with data on protein–protein interactions, we found evidence
 suggesting clustering among gene products relating to nervous and muscular
 systems in cetaceans. We found little support for shared ancestral
 adaptations in the two taxa; most molecular adaptations in extant
 cetaceans occurred after their split with hippopotamids.
description: Tsagkogeorga_et_al_alignmentsCoding DNA Sequence (CDS) alignments including 23 mammals.
DOI: 10.5061/dryad.3qm0152
title: Data from: Smartphone motor testing to distinguish idiopathic REM sleep behavior disorder, controls, and PD

description: Objective: We sought to identify motor features that would allow the
 delineation of individuals with sleep study-confirmed idiopathic rapid eye
 movement sleep behaviour disorder (iRBD) from controls and Parkinson’s
 disease (PD) using a customised smartphone application. Methods: 334 PD,
 104 iRBD, and 84 control participants performed seven tasks to evaluate
 voice, balance, gait, finger tapping, reaction time, rest tremor, and
 postural tremor. Smartphone recordings were collected both in clinic and
 at home under non-controlled conditions over several days. All
 participants underwent detailed parallel in-clinic assessments. Using only
 the smartphone sensor recordings, we sought to: (1) discriminate whether
 the participant had iRBD or PD and, (2) identify which of the above seven
 motor tasks were most salient in distinguishing groups. Results:
 Statistically significant differences based on these seven tasks were
 observed between the three groups. For the three pairwise discriminatory
 comparisons: (1) Controls versus iRBD, (2) Controls versus PD, and (3)
 iRBD versus PD, mean sensitivity and specificity values ranged from 84.6%
 to 91.9%. Postural tremor, rest tremor, and voice were the most
 discriminatory tasks overall, while reaction time was least
 discriminatory. Conclusions: Prodromal forms of PD include the sleep
 disorder iRBD, where subtle motor impairment can be detected using
 clinician based rating scales (e.g UPDRS), which may lack the sensitivity
 to detect and track granular change. Consumer grade smartphones can be
 used not only to accurately separate iRBD from controls, but also iRBD
 from PD participants, providing growing consensus for the utility of
 digital biomarkers in early and prodromal PD.
description: Supplementary
 Text-NEUROLOGY-2018-902841Supplementary
 textSupplementary Figure
 1Supplementary text
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DOI: 10.5061/dryad.s3443
title: Data from: Rapid quantitative pharmacodynamic imaging by a novel method: theory, simulation testing and proof of principle

description: Pharmacological challenge imaging has mapped, but rarely quantified, the
 sensitivity of a biological system to a given drug. We describe a novel
 method called rapid quantitative pharmacodynamic imaging. This method
 combines pharmacokinetic-pharmacodynamic modeling, repeated small doses of
 a challenge drug over a short time scale, and functional imaging to
 rapidly provide quantitative estimates of drug sensitivity including EC50
 (the concentration of drug that produces half the maximum possible
 effect). We first test the method with simulated data, assuming a typical
 sigmoidal dose-response curve and assuming imperfect imaging that includes
 artifactual baseline signal drift and random error. With these few
 assumptions, rapid quantitative pharmacodynamic imaging reliably estimates
 EC50 from the simulated data, except when noise overwhelms the drug effect
 or when the effect occurs only at high doses. In preliminary fMRI studies
 of primate brain using a dopamine agonist, the observed noise level is
 modest compared with observed drug effects, and a quantitative EC50 can be
 obtained from some regional time-signal curves. Taken together, these
 results suggest that research and clinical applications for rapid
 quantitative pharmacodynamic imaging are realistic.
description: Simulated 4D images for
 testing the QuanDyn(TM) programThis .7z file can be
 opened using the freely available tool 7-Zip (www.7-zip.org). It contains
 78 image files in NIFTI format. Most image files contain 288 volumes, each
 containing 1000 voxels, and are about 1MB in size. The file is a
 4-dimensional image representing simulated functional image data from 1000
 voxels (i = 1 to 1000) over 288 points in time (t = 1 to 288). See the
 ReadMe file and the PeerJ article text for further
 information.apo_val2a.7z