cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t748p
title: Data from: Forward genetic screen of human transposase genomic rearrangements

description: Background: Numerous human genes encode potentially active DNA
 transposases or recombinases, but our understanding of their functions
 remains limited due to shortage of methods to profile their activities on
 endogenous genomic substrates. Results: To enable functional analysis of
 human transposase-derived genes, we combined forward chemical genetic
 hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1) screening with
 massively parallel paired-end DNA sequencing and structural variant genome
 assembly and analysis. Here, we report the HPRT1 mutational spectrum
 induced by the human transposase PGBD5, including PGBD5-specific signal
 sequences (PSS) that serve as potential genomic rearrangement substrates.
 Conclusions: The discovered PSS motifs and high-throughput forward
 chemical genomic screening approach should prove useful for the
 elucidation of endogenous genome remodeling activities of PGBD5 and other
 domesticated human DNA transposases and recombinases.
description: laSV_SV_filesSomatic structural variants in BJ cells before and after 6-Thioguanine selectionHPRT_laSV_SV_files.zipCRISPResso analysisHPRT1 structural variant analysis using CRISPResso. Formated accoriding to CRISPResso output. http://dx.doi.org/10.1101/031203HPRT_CRISPResso_files.zipAnalysis_breakpoints_laSVTable containing all sequences from breakpoints called by laSV +/- 50bp from hg19 used to identify PGBD5 signal sequence.PWM_PSS_and_RSSPosition weight matrix of putative PGBD5 signal sequence (PSS) and recombination signal sequence of RAG1 (RSS).Metadata_HPRT1Metadata file describing all files uploaded to dryad.
DOI: 10.5061/dryad.pc8m3
title: Data from: The multilayer temporal network of public transport in Great Britain

description: Despite the widespread availability of information concerning public
 transport coming from different sources, it is extremely hard to have a
 complete picture, in particular at a national scale. Here, we integrate
 timetable data obtained from the United Kingdom open-data program together
 with timetables of domestic flights, and obtain a comprehensive snapshot
 of the temporal characteristics of the whole UK public transport system
 for a week in October 2010. In order to focus on multi-modal aspects of
 the system, we use a coarse graining procedure and define explicitly the
 coupling between different transport modes such as connections at
 airports, ferry docks, rail, metro, coach and bus stations. The resulting
 weighted, directed, temporal and multilayer network is provided in simple,
 commonly used formats, ensuring easy access and the possibility of a
 straightforward use of old or specifically developed methods on this new
 and extensive dataset.
description: The Multilayer Temporal
 Network of Public Transport in Great BritainThe dataset describes
 the Public Transport Network of Great Britain by use of a Multilayer
 node-list and edge-list, where each layer is associated to a mode of
 transport. Each node is geo-referenced, thus defining a spatial network,
 and associated to a wide list of administrative meta-data. For each edge,
 the minimal travel-time in minutes is indicated. For the case of
 inter-layer edges, this is defined as the walking time needed for the
 inter-modal connection. For each intra-layer edge, we also specify a list
 of temporal events representing the vehicles' rides along the edges,
 with origin time and travel duration expressed in minutes with a precision
 of one minute. In Multilayer networks, each node may have several ‘copies’
 in different layers. For that reason, nodes are identified by two numbers,
 one specifying the node itself, and another the layer where it belongs. As
 a consequence, the edges are identified by four numbers, two for the
 origin and two for the destination (node and layer). The ordering of the
 fields in edge-list has been chosen to conform to the tensorial notation
 widely used for this kind of networks. There is no established standard
 format for the temporal event list. Therefore, we decided to use a format,
 derived from the idea of adjacency lists, which has been specifically
 adapted to this dataset.ML_PT_GB_v1.11.zip
DOI: 10.5061/dryad.kc75n
title: Data from: A long PCR based approach for DNA enrichment prior to next-generation sequencing for systematic studies

description: Premise of the study: We present an alternative approach for molecular
 systematic studies that combines long PCR and next-generation sequencing
 (NGS). Our approach can be used to generate templates from any DNA source
 for NGS. Here we test our approach by amplifying complete chloroplast
 genomes and we present a set of 58 potentially universal primers for
 angiosperms to do so. Additionally, this approach is likely to be
 particularly useful for nuclear regions. Methods and Results: Chloroplast
 genomes of 30 species across angiosperms were amplified to test our
 approach. Amplification success varied depending on whether PCR conditions
 were optimized for a given taxon. To further test our approach, some
 amplicons were sequenced on an Illumina HiSeq 2000. Conclusions: Although
 here we tested this approach by sequencing plastomes, long PCR amplicons
 could be generated using DNA from any genome, expanding the possibilities
 of this approach for molecular systematic studies.
description: Files resulting from
 chloroplast assemblies in three genera in OrobanchaceaeContigs, ACE files, and
 other resulting files from chloroplast assemblies in three genera in
 Orobanchaceae (Bartsia, Castilleja, Lamourouxia). These assemblies were
 done by combining long PCR amplicons and NGS data from an Illumina HiSeq
 2000. The Alignreads pipeline v2.25 (Straub et al., 2011) was
 used.Uribe-Convers_Chloroplast_Assemblies.zip
DOI: 10.5061/dryad.vp312
title: Data from: Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments

description: Segmented RNA viruses are ubiquitous pathogens, which include influenza
 viruses and rotaviruses. A major challenge in understanding their assembly
 is the combinatorial problem of a non-random selection of a full genomic
 set of distinct RNAs. This process involves complex RNA-RNA and
 protein-RNA interactions, which are often obscured by non-specific binding
 at concentrations approaching in vivo assembly conditions. Here, we
 present direct experimental evidence of sequence-specific inter-segment
 interactions between rotavirus RNAs, taking place in a complex RNA- and
 protein-rich milieu. We show that binding of the rotavirus-encoded
 non-structural protein NSP2 to viral ssRNAs results in the remodeling of
 RNA, which is conducive to formation of stable inter-segment contacts. To
 identify the sites of these interactions, we have developed an RNA-RNA
 SELEX approach for mapping the sequences involved in inter-segment
 base-pairing. Our findings elucidate the molecular basis underlying
 inter-segment interactions in rotaviruses, paving the way for delineating
 similar RNA-RNA interactions that govern assembly of other segmented RNA
 viruses.
description: Bdata_aptConcatenated HTS sequencing data file, containing unique SELEX-enriched sequences after filtering to remove any sequences of size not matching N, where N = 30 nts (size of the random region in the naive RNA library). Bdata_apt contains the sequences enriched in the presence of NSP2.Cdata_aptConcatenated HTS sequencing data file, containing unique SELEX-enriched sequences after filtering to remove any sequences of size not matching N, where N = 30 nts (size of the random region in the naive RNA library). Cdata_apt contains the sequences enriched during the RNA-RNA SELEX against Seg11 without NSP2.
DOI: 10.5061/dryad.22dr1
title: Data from: The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes

description: The first virtual cranial endocast of a lungfish from the Early Devonian,
 Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth
 Devonian lungfish for which a near complete cranial endocast is known, is
 a key taxon for clarifying primitive character states within the group. A
 ventrally-expanded telencephalic cavity is present in the endocast of
 Dipnorhynchus demonstrating that this is the primitive state for “true”
 Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated
 from the sacculolagenar pouch like that seen in stratigraphically younger
 lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the
 dipnomorph Youngolepis. We do not find separate pineal and para-pineal
 canals in contrast to a reconstruction from previous authors. We conduct
 the first phylogenetic analysis of Dipnoi based purely on endocast
 characters, which supports a basal placement of Dipnorhynchus within the
 dipnoan stem group, in agreement with recent analyses. Our analysis
 demonstrates the value of endocast characters for inferring phylogenetic
 relationships.
description: Dsussmilchi_skull_small_tiffsTIFF stack of tomographic scan data of the skull of Dipnorhynchus sussmilchi (Devonian lungfish)sussmilchi_skull_small_tiffs.zip
DOI: 10.5061/dryad.5vs40
title: Data from: Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis

description: Ploidy levels sometimes vary among individuals or populations,
 particularly in plants. When such variation exists, accurate determination
 of cytotype can inform studies of ecology or trait variation and is
 required for population genetic analyses. Here we propose and evaluate a
 statistical approach for distinguishing low-level ploidy variants (e.g.,
 diploids, triploids and tetraploids) based on genotyping-by-sequencing
 data. The method infers cytotypes based on observed heterozygosity and the
 ratio of DNA sequences containing different alleles at thousands of
 heterozygous SNPs (i.e., allelic ratios). Whereas the method does not
 require prior information on ploidy, a reference set of samples with known
 ploidy can be included in the analysis if it is available. We explore the
 power and limitations of this method using simulated data sets and GBS
 data from natural populations of aspen (Populus tremuloides) known to
 include both diploid and triploid individuals. The proposed method was
 able to reliably discriminate among diploids, triploids and tetraploids in
 simulated data sets, and this was true for different levels of genetic
 diversity, inbreeding and population structure. Power and accuracy were
 minimally affected by low coverage (i.e., 2X), but did sometimes suffer
 when simulated mixtures of diploids, autotetraploids and allotetraploids
 were analyzed. Cytotype assignments based on the proposed method closely
 matched those from previous microsatellite and flow cytometry data when
 applied to GBS data from aspen. An R package (gbs2ploidy) implementing the
 proposed method is available from CRAN.
description: R script to run
 gbs2ploidy on the aspen dataThis script formats and
 summarizes the aspen data and then runs gbs2ploidy on the data set. The
 files needed for analysis are included in this Dryad
 submission.aspenAnalysis.RAspen ID fileThis csv text file contains population and individual IDs for the aspen samples, as well as ploidy levels inferred from microsatellites or flow cytometry.DT_aspen_1Jul16.csvSimulation codeR script to generate the simulated data used to test gbs2ploidy.ploidySims.RSimulation dataThis is a R workspace object. It contains the simulation output from the allo- and autotetraploid simulations. It was generated with the ploidySims.R code also included with this Dryad submission.simsAlloTet.RdataAllele sepecific read countsThis file contains the allele specific read counts for the aspen data. Each row contains the data for one SNP and each pair of columns has the data for an individual. These two columns contain the number of reads of each allele (one allele per column) if the individual was heterozygous at that SNP. Otherwise there is a NA for each column.hetAlleleDepth.txtVariant file for the aspen dataThis vcf (variant call format) contains the filtered variant data for the aspen samples.filtered2x_aspenvariants.vcf
DOI: 10.15468/pnk64c
title: Birds of the Lower: URUGUAY

description: This dataset contains the digitized treatments in Plazi based on the original book chapter Barrows, Walter B. (1883): Birds of the Lower: URUGUAY. In: BULLETIN OF THE NUTTALL ORNITHOLOGICAL CLUB: A Quarterlg Journal of Ornitlhology. W. H. Wheeler, Printer, 17 Brighton St., Cambridge, Mass.: ORNITHOLOGICAL CLUB: 80-94, DOI: 10.5281/zenodo.18380240
DOI: 10.5061/dryad.d7s1183
title: Data from: Computational biomechanical analyses demonstrate similar shell-crushing abilities in modern and ancient arthropods

description: The biology of the extant American horseshoe crab, Limulus polyphemus, is
 well documented—including its dietary habits, particularly the ability to
 crush shell with its gnathobasic walking appendages—but virtually nothing
 is known about the feeding biomechanics of this iconic arthropod. This
 species is also considered the archetypal functional analogue for a range
 of extinct groups that have gnathobasic appendages, including eurypterids,
 trilobites, and some of the earliest arthropods, especially Sidneyia
 inexpectans from the middle Cambrian (508 million-year-old) Burgess Shale
 of Canada. Exceptionally-preserved specimens of S. inexpectans show
 intriguing evidence suggestive of durophagous (shell-crushing)
 tendencies—including thick gnathobasic spine cuticle and shelly gut
 contents—but this feeding mode has never been substantiated using advanced
 computational techniques, such as Finite Element Analysis (FEA). Here we
 present a unique application of 3D FEA by modelling the feeding mechanics
 of L. polyphemus and S. inexpectans, representing the first such analysis
 of a modern horseshoe crab, or indeed any fossil arthropod. Results show
 that mechanical performance of the feeding appendages in both arthropods
 is remarkably similar, confirming that S. inexpectans was a durophagous
 predator. This biomechanical solution to processing shelled prey therefore
 has a history extending over 500 million years, almost dating back to the
 first appearance of shell-bearing animals themselves. The arrival of
 durophagous predators such as S. inexpectans during the early phase of
 animal evolution undoubtedly fuelled the Cambrian ‘arms race’ that
 encompasses the rapid increase in diversity and abundance of
 biomineralised prey species.
description: Figure
 S2Figure S2: 3D PDF of
 Sidneyia inexpectans thoracic biramous appendage, showing the endopod,
 exopod lobes and protopodite.Figure
 S1Figure S1: 3D PDF of
 Limulus polyphemus showing cephalothoracic appendage set V, the
 endosternite and the part of the cephalothorax.Supplemental File 1
 Limulus polyphemus coxaSupplemental File 1: DAT
 file of Limulus polyphemus coxa volume mesh used in FEA
 analysis.Supplemental File 2
 Sidneyia inexpectans protopoditeSupplemental File 2: DAT
 file of Sidneyia inexpectans protopodite volume mesh used in FEA
 analysis.
DOI: 10.5061/dryad.719bt
title: Data from: Calorespirometry reveals that goldfish prioritize aerobic metabolism over metabolic rate depression in all but near-anoxic environments

description: Metabolic rate depression (MRD) has long been proposed as the key
 metabolic strategy of hypoxic survival, but surprisingly the effects of
 changes in hypoxic O2 tensions (PwO2) on MRD are largely unexplored. We
 simultaneously measured the O2 consumption rate (ṀO2) and metabolic heat
 of goldfish using calorespirometry to test the hypothesis that MRD is
 employed at hypoxic PwO2s and initiated just below Pcrit, the PwO2 below
 which ṀO2 is forced to progressively decline as the fish oxyconforms to
 decreasing PwO2. Specifically, we used closed-chamber and flow-through
 calorespirometry together with terminal sampling experiments to examine
 the effects of PwO2 and time on ṀO2, metabolic heat and anaerobic
 metabolism (lactate and ethanol production). The closed-chamber and
 flow-through experiments yielded slightly different results. Under
 closed-chamber conditions with a continually decreasing PwO2, goldfish
 showed a Pcrit of 3.0±0.3 kPa and metabolic heat production was only
 depressed at PwO2 between 0 and 0.67 kPa. Under flow-through conditions
 with PwO2 held at a variety of oxygen tensions for 1 and 4 h, goldfish
 also initiated MRD between 0 and 0.67 kPa but maintained ṀO2 to 0.67 kPa,
 indicating that Pcrit is at or below this PwO2. Anaerobic metabolism was
 strongly activated at PwO2 ≤1.3 kPa, but only used within the first hour
 at 1.3 and 0.67 kPa as anaerobic end-products did not accumulate between 1
 and 4 h exposure. Taken together, it appears that goldfish reserve MRD for
 near-anoxia, supporting routine metabolic rate at sub-Pcrit PwO2s with the
 help of anaerobic glycolysis in the closed-chamber experiments, and
 aerobically after an initial (&lt;1 h) activation of anaerobic
 metabolism in the flow-through experiments, even at 0.67 kPa PwO2.
description: Calorespirometry raw
 data filesExcel files of raw data
 from closed-chamber and flow-through calorespirometry
 experiments.REGAN_data.zip
DOI: 10.5061/dryad.8b146
title: Data from: A statistical framework for neuroimaging data analysis based on mutual information estimated via a gaussian copula

description: We begin by reviewing the statistical framework of information theory as
 applicable to neuroimaging data analysis. A major factor hindering wider
 adoption of this framework in neuroimaging is the difficulty of estimating
 information theoretic quantities in practice. We present a novel
 estimation technique that combines the statistical theory of copulas with
 the closed form solution for the entropy of Gaussian variables. This
 results in a general, computationally efficient, flexible, and robust
 multivariate statistical framework that provides effect sizes on a common
 meaningful scale, allows for unified treatment of discrete, continuous,
 unidimensional and multidimensional variables, and enables direct
 comparisons of representations from behavioral and brain responses across
 any recording modality. We validate the use of this estimate as a
 statistical test within a neuroimaging context, considering both discrete
 stimulus classes and continuous stimulus features. We also present
 examples of analyses facilitated by these developments, including
 application of multivariate analyses to MEG planar magnetic field
 gradients, and pairwise temporal interactions in evoked EEG responses. We
 show the benefit of considering the instantaneous temporal derivative
 together with the raw values of M/EEG signals as a multivariate response,
 how we can separately quantify modulations of amplitude and direction for
 vector quantities, and how we can measure the emergence of novel
 information over time in evoked responses. Open-source Matlab and Python
 code implementing the new methods accompanies this article.
description: Figure source
 dataSource data for results
 figures.figure_data.zipeeg_face_vs_noiseThis is an EEG data set used in Section 4.1. Two classes of stimulus images were presented (faces or noise). Data are from a single subject.meg_speechThis is an MEG data set used in Section 4.2. MEG was recorded during a 7.5 minute auditory presentation of speech. Data are from a single subject.eeg_eye_visibilityThis is an EEG data set used in Section 4.3. EEG was recorded while images of faces were presented sampled with bubbles (Gaussian apertures). We consider here the visibility of the eye region. Data are from a single subject.
DOI: 10.5061/dryad.g3v15
title: Data from: Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation

description: Alternative splicing enhances transcriptome diversity in all eukaryotes
 and plays a role in plant tissue identity and stress adaptation. To
 catalog new maize (Zea mays) transcripts and identify genomic loci that
 regulate alternative splicing, we analyzed over 90 RNA-seq libraries from
 maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines
 (progenies from B73 × Mo17). Transcript discovery was augmented with
 publicly available data from 14 maize tissues, expanding the maize
 transcriptome by more than 30,000 and increasing the percentage of
 intron-containing genes that undergo alternative splicing to 40%. These
 newly identified transcripts greatly increase the diversity of the maize
 proteome, sometimes coding for entirely different proteins compared with
 their most similar annotated isoform. In addition to increasing proteome
 diversity, many genes encoding novel transcripts gained an additional
 layer of regulation by microRNAs, often in a tissue-specific manner. We
 also demonstrate that the majority of genotype-specific alternative
 splicing can be genetically mapped, with cis-acting quantitative trait
 loci (QTLs) predominating. A large number of trans-acting QTLs were also
 apparent, with nearly half located in regions not shown to contain genes
 associated with splicing. Taken together, these results highlight the
 currently underappreciated role that alternative splicing plays in tissue
 identity and genotypic variation in maize.
description: RNA-seq libraries used
 for transcript discovery and alternative splicing
 analysisRNA-seq libraries used
 for transcript discovery and alternative splicing
 analysistpc130773_SupplementalDS1.xlsKnown and novel transcripts' cDNA, protein and expression informationKnown and novel transcripts' cDNA, protein and expression informationtpc130773_SupplementalDS2.txtNovel transcripts which gained or lost miRNA target sites relative to their most similar known isoformNovel transcripts which gained or lost miRNA target sites relative to their most similar known isoformtpc130773_SupplementalDS3.xlsExpression of genes with Gene Ontology (GO) categories associated with alternative splicingExpression of genes with Gene Ontology (GO) categories associated with alternative splicingtpc130773_SupplementalDS4.xlsExpression and mapping results for genes with statistically significant (q &lt; 0.05) genotype-dependent alternative splicing variationsExpression and mapping results for genes with statistically significant (q &lt; 0.05) genotype-dependent alternative splicing variationstpc130773_SupplementalDS5.xlsExpression of genes with statistically significant expression differences in tissue and genotypic testsExpression of genes with statistically significant expression differences in tissue and genotypic teststpc130773_SupplementalDS6.xlsPrimers used to amplify known and novel isoformsPrimers used to amplify known and novel isoformstpc130773_SupplementalDS7.xls