cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v1d30
title: Data from: Unidirectional pulmonary airflow patterns in the savannah monitor lizard

description: The unidirectional airflow patterns in the lungs of birds have long been
 considered a unique and specialized trait associated with the oxygen
 demands of their volant lifestyle, endothermic metabolism and unusual
 pulmonary architecture; however, the discovery of similar flow patterns in
 the lungs of crocodilians indicates that this character is likely
 ancestral for all archosaurs, the group that includes extant birds and
 crocodilians as well as their extinct relatives, such as pterosaurs and
 dinosaurs. Unidirectional flow in birds results from aerodynamic valves,
 rather than from sphincters or other physical mechanisms, and similar
 aerodynamic valves appear to be at work in crocodilians. Due to anatomical
 and developmental similarities in the primary and secondary bronchi of
 birds and crocodilians, these structures and airflow patterns may be
 homologous. Thus the origin of this pattern is at least as old as the
 split between crocodilians and birds, which occurred in the Triassic;
 however, it is possible that this pattern of flow is even older. This
 constitutes an alternative hypothesis, which can be tested by
 investigating patterns of airflow in members of the outgroup to birds and
 crocodilians, the Lepidosauromorpha (tuatara, lizards, and snakes). Here
 we show region-specific unidirectional airflow in the lungs of the
 savannah monitor lizard (Varanus exanthematicus). The presence of
 unidirectional flow in the lungs of V. exanthematicus thus gives rise to
 two possible evolutionary scenarios: (1) unidirectional airflow evolved
 independently in archosaurs and monitor lizards, or (2) these flow
 patterns are homologous in archosaurs and V. exanthematicus, having
 evolved only once in ancestral diapsids. If unidirectional airflow is
 plesiomorphic for Diapsida, this respiratory character can be
 reconstructed for extinct diapsids, and evolved in a small ectothermic
 tetrapod during the Paleozoic Era at least 100 million years before the
 origin of birds.
description: Full body CT scan of a
 live Varanus exanthematicus (V1)Full body CT scan of a
 live female Varanus exanthematicus (V1; mass: 930g). Scanned at scanned at
 100 kVp 400 Ma (0.6 x 0.4 mm). The animal was scanned without sedation
 during apnea.V1.zipFull body CT scan of a live Varanus exanthematicus (V3)Full body CT scan of a live female Varanus exanthematicus (V3; mass: 680g). Scanned at scanned at 100 kVp 400 Ma (0.6 x 0.4 mm). The animal was scanned without sedation during apnea.V3.zipFull body CT scan of a deceased Varanus exanthematicusFull body CT scan of a deceased Varanus exanthematicus. Scanned at scanned at 100 kVp 400 Ma (0.6 x 0.4 mm). The animal was donated to the University of Utah by James Dix (Utah's Reptile Rescue Service). The animal was intubated and the lungs inflated with a 60 cc syringe prior to scanning. The animal died from unknown natural causes.V_Fatty.zip
DOI: 10.5061/dryad.t6096
title: Data from: Maintenance of age in human neurons generated by microRNA-based neuronal conversion of fibroblasts

description: Aging is a major risk factor in many forms of late-onset neurodegenerative
 disorders. The ability to recapitulate age-related characteristics of
 human neurons in culture will offer unprecedented opportunities to study
 the biological processes underlying neuronal aging. Here, we show that
 using a recently demonstrated microRNA-based cellular reprogramming
 approach, human fibroblasts from postnatal to near centenarian donors can
 be efficiently converted into neurons that maintain multiple
 age-associated signatures. Application of an epigenetic biomarker of aging
 (referred to as epigenetic clock) to DNA methylation data revealed that
 the epigenetic ages of fibroblasts were highly correlated with
 corresponding age estimates of reprogrammed neurons. Transcriptome and
 microRNA profiles reveal genes differentially expressed between young and
 old neurons. Further analyses of oxidative stress, DNA damage and telomere
 length exhibit the retention of age-associated cellular properties in
 converted neurons from corresponding fibroblasts. Our results collectively
 demonstrate the maintenance of age after neuronal conversion.
description: Datasets_Transcriptome_And_microRNAomeCompressed datasets for Agilent_Human4X44K_v1 microarray transcriptome and Affymetrix miRNA V4 microarray microRNAome data. When unzipped, three folders will appear: Raw_Data, Processed_data and DEGs. Raw_Data folder contains raw datasets for Agilent and Affy chips. Processed_data folder contains Agilent and Affy datasets processed for downstream differentially expressed genes (DEG) analyses. DEGs folder contains mRNA (transcriptome) and miRNA (microRNAome) sub-directories containing DEG analyses for mRNAs and microRNAs.GO terms described in Figure 3- Figure Supplement 1-2Full list of gene ontology terms and corresponding genes from figure 3 supplement 1 and figure 3 supplement 2. Includes GO terms for age-downregulated genes in reprogrammed neurons (sheet 1), GO terms for age-upregulated genes in reprogrammed neurons (sheet 2), GO terms for predicted targets of miR-497-5p from list of downregulated genes (sheet 3), GO terms for predicted targets of miR-10a from the list of downregulated genes (sheet 4)GO terms.xlsxZipped folder of DNA methylation data and annotationThis zipped package contains 4 files.• The file dat0NoobUpload.csv contains the "Noob" normalized beta values (i.e. the DNA methylation data) from the Illumina 450K array platform. We used the Noob normalization described in TJ Triche et al (2013) Nucleic Acids Res 41, e90. • The sample annotation file (datSampleNoobUpload.csv) reports the chronological age (Age) and the DNA methylation age (DNAmAge) which was calculated with the epigenetic clock method described in Horvath S (2013) Genome Biol. 2013 • The file datPairedData.csv reports the DNAm age estimates before and after conversion.DNAmethylation.zip
DOI: 10.5061/dryad.hm5vs13
title: Data from: Genome sequencing and analysis of the peanut b-genome progenitor (Arachis ipaensis)

description: Peanut (Arachis hypogaea L.), an important leguminous crop, is widely
 cultivated in tropical and subtropical regions. Peanut is an
 allotetraploid, having A and B subgenomes that maybe have originated in
 its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis
 (B-genome), respectively. We previously sequenced the former and here
 present the draft genome of the latter, expanding our knowledge of the
 unique biology of Arachis. The assembled genome of A. ipaensis is ~1.39 Gb
 with 39,704 predicted protein-encoding genes. A gene family analysis
 revealed that the FAR1 family may be involved in regulating peanut special
 fruit development. Genomic evolutionary analyses estimated that the two
 progenitors diverged ~3.3 million years ago and suggested that A. ipaensis
 experienced a whole-genome duplication event after the divergence of
 Glycine max. We identified a set of disease resistance-related genes and
 candidate genes for biological nitrogen fixation. In particular, two and
 four homologous genes that may be involved in the regulation of nodule
 development were obtained from A.ipaensis and A.duranensis, respectively.
 We outline a comprehensive network involved in drought adaptation.
 Additionally, we analyzed the metabolic pathways involved in oil
 biosynthesis and found genes related to fatty acid and triacylglycerol
 synthesis. Importantly, three new FAD2 homologous genes were identified
 from A. ipaensis and one was completely homologous at the amino acid level
 with FAD2 from A.hypogaea. The availability of the A. ipaensis and A.
 duranensis genomic assemblies will advance our knowledge of the peanut
 genome.
description: Arachis_ipaensis_Genome_V1.0.tarArachis_ipaensis_Genome_V1.0.tar
DOI: 10.5061/dryad.58c73
title: Data from: Use of anisotropy, 3D segmented atlas, and computational analysis to identify gray matter subcortical lesions common to concussive injury from different sites on the cortex

description: Traumatic brain injury (TBI) can occur anywhere along the cortical mantel.
 While the cortical contusions may be random and disparate in their
 locations, the clinical outcomes are often similar and difficult to
 explain. Thus a question that arises is, do concussions at different sites
 on the cortex affect similar subcortical brain regions? To address this
 question we used a fluid percussion model to concuss the right caudal or
 rostral cortices in rats. Five days later, diffusion tensor MRI data were
 acquired for indices of anisotropy (IA) for use in a novel method of
 analysis to detect changes in gray matter microarchitecture. IA values
 from over 20,000 voxels were registered into a 3D segmented, annotated rat
 atlas covering 150 brain areas. Comparisons between left and right
 hemispheres revealed a small population of subcortical sites with altered
 IA values. Rostral and caudal concussions were of striking similarity in
 the impacted subcortical locations, particularly the central nucleus of
 the amygdala, laterodorsal thalamus, and hippocampal complex. Subsequent
 immunohistochemical analysis of these sites showed significant
 neuroinflammation. This study presents three significant findings that
 advance our understanding and evaluation of TBI: 1) the introduction of a
 new method to identify highly localized disturbances in discrete gray
 matter, subcortical brain nuclei without postmortem histology, 2) the use
 of this method to demonstrate that separate injuries to the rostral and
 caudal cortex produce the same subcortical, disturbances, and 3) the
 central nucleus of the amygdala, critical in the regulation of emotion, is
 vulnerable to concussion.
description: FA_L1_RA_ComparisonMeasures of Diffusion paramerers (FA, RD, AD, ADC..) following lateral fluid percussion injury to the forebrain (n=5) and hindbrain (n=8) cortex. Statistical differences between 150 brain regions comparing values between the affected ipsilateral side (right) and the contralateral side (left) are rank order for significance. Values are presented as the mean and standard deviation (SD). Areas shown in blue are common to both sites of cortical injury. Arrows denote the direction of the difference between the affected and control sides.Rostral_TBI.tarRaw and Analyzed DTI dataCaudal_TBI.tarRaw and Analyzed DTI data of Caudal Insult.
DOI: 10.5061/dryad.66840
title: Data from: A computational method for sharp interface advection

description: We devise a numerical method for passive advection of a surface, such as
 the interface between two incompressible fluids, across a computational
 mesh. The method is called isoAdvector, and is developed for general
 meshes consisting of arbitrary polyhedral cells. The algorithm is based on
 the volume of fluid (VOF) idea of calculating the volume of one of the
 fluids transported across the mesh faces during a time step. The novelty
 of the isoAdvector concept consists in two parts: First, we exploit an
 isosurface concept for modelling the interface inside cells in a geometric
 surface reconstruction step. Second, from the reconstructed surface, we
 model the motion of the face-interface intersection line for a general
 polygonal face to obtain the time evolution within a time step of the
 submerged face area. Integrating this submerged area over the time step
 leads to an accurate estimate for the total volume of fluid transported
 across the face. The method was tested on simple 2D and 3D interface
 advection problems both on structured and unstructured meshes. The results
 are very satisfactory both in terms of volume conservation, boundedness,
 surface sharpness, and efficiency. The isoAdvector method was implemented
 as an OpenFOAM® extension and is published as open source.
description: Unstructured meshes for
 interface advection testsAn important feature of
 our newly developed Volume-of-Fluid interface advection method,
 isoAdvector, is its ability to advect surfaces across unstructured meshes.
 This is demonstrated in the article with a number of simple standard test
 cases. The unstructured meshes used in these cases are provided here to
 allow readers to verify our results and to allow researchers to test other
 interface advection methods on these meshes. Using the exact same meshes
 makes it easier to compare the performance of different
 methods.meshes.tar.gz
DOI: 10.5061/dryad.2qc64
title: Data from: A novel algorithm to enhance P300 in single trials: application to lie detection using F-score and SVM

description: The investigation of lie detection methods based on P300 potentials has
 drawn much interest in recent years. We presented a novel algorithm to
 enhance signal-to-noise ratio (SNR) of P300 and applied it in lie
 detection to increase the classification accuracy. Thirty-four subjects
 were divided randomly into guilty and innocent groups, and the EEG signals
 on 14 electrodes were recorded. A novel spatial denoising algorithm (SDA)
 was proposed to reconstruct the P300 with a high SNR based on independent
 component analysis. The differences between the proposed method and
 our/other early published methods mainly lie in the extraction and feature
 selection method of P300. Three groups of features were extracted from the
 denoised waves; then, the optimal features were selected by the F-score
 method. Selected feature samples were finally fed into three classical
 classifiers to make a performance comparison. The optimal parameter values
 in the SDA and the classifiers were tuned using a grid-searching training
 procedure with cross-validation. The support vector machine (SVM) approach
 was adopted to combine with an F-score because this approach had the best
 performance. The presented model F-score_SVM reaches a significantly
 higher classification accuracy for P300 (specificity of 96.05%) and
 non-P300 (sensitivity of 96.11%) compared with the results obtained
 without using SDA and compared with the results obtained by other
 classification models. Moreover, a higher individual diagnosis rate can be
 obtained compared with previous methods, and the presented method requires
 only a small number of stimuli in the real testing application.
description: All data for 14
 electrodes and 30 subjectsone can epoch each txt
 file using toolbox suchas EEGLAB
DOI: 10.5061/dryad.j68v33v
title: Data from: Multiple origins of sexual dichromatism and aposematism within large carpenter bees

description: The evolution of reversed sexual dichromatism and aposematic coloration
 have long been of interest to both theoreticians and empiricists. Yet
 despite the potential connections between these phenomena, they have
 seldom been jointly studied. Large carpenter bees (genus Xylocopa) are a
 promising group for such comparative investigations as they are a diverse
 clade in which both aposematism and reversed sexual dichromatism can occur
 either together or separately. We investigated the evolutionary history of
 dichromatism and aposematism and a potential correlation of these traits
 with diversification rates within Xylocopa, using a newly-generated
 phylogeny for 179 Xylocopa species based on ultraconserved elements
 (UCEs). A monochromatic, inconspicuous ancestor is indicated for the
 genus, with subsequent convergent evolution of sexual dichromatism and
 aposematism in multiple lineages. Aposematism is found to co-vary with
 reversed sexual dichromatism in many species; however, reversed
 dichromatism also evolved in non-aposematic species. Bayesian Analysis of
 Macroevolutionary Models (BAMM) did not show increased diversification in
 any specific clade in Xylocopa, whereas support from Hidden State
 Speciation and Extinction (HiSSE) models remained inconclusive regarding
 an association of increased diversification rates with dichromatism or
 aposematism. We discuss the evolution of color patterns and
 diversification in Xylocopa by considering potential drivers of
 dichromatism and aposematism.
description: Data matrices and
 treesDataMatrices_and_trees_from_Blaimer_et_al_2018.zipFiles associated with trait evolution and diversification analysesTraitEvolution_and_Diversification_analyses_from_Blaimer_et_al_2018.zipTrinity assembled contig files used for phylogenetic analysesXylocopaAssembledTrinityContigs_from_Blaimer_et_al_2018.zip
DOI: 10.5061/dryad.3fm645g
title: Data from: Acute maneb exposure significantly alters both glycolysis and mitochondrial function in neuroblastoma cells

description: The pesticides paraquat (PQ) and maneb (MB) have been described as
 environmental risk factors for Parkinson’s disease (PD), with mechanisms
 associated with mitochondrial dysfunction and reactive oxygen species
 generation. A combined exposure of PQ and MB in murine models and
 neuroblastoma cells has been utilized to further advance understanding of
 the PD phenotype. MB acts as a redox modulator through alkylation of
 protein thiols and has been previously characterized to inhibit complex
 III of the electron transport chain and uncouple the mitochondrial proton
 gradient. The purpose of this study was to analyze ATP-linked respiration
 and glycolysis in human neuroblastoma cells utilizing the Seahorse
 extracellular flux platform. Employing an acute, subtoxic exposure of MB,
 this investigation revealed a MB-mediated decrease in mitochondrial oxygen
 consumption at baseline and maximal respiration, with inhibition of ATP
 synthesis and coupling efficiency. Additionally, MB-treated cells showed
 an increase in nonmitochondrial respiration and proton leak. Further
 investigation into mitochondrial fuel flex revealed an elimination of fuel
 flexibility across all 3 major substrates, with a decrease in pyruvate
 capacity as well as glutamine dependency. Analyses of glycolytic function
 showed a substantial decrease in glycolytic acidification caused by lactic
 acid export. This inhibition of glycolytic parameters was also observed
 after titrating the MB dose as low as 6 μM, and appears to be dependent on
 the dithiocarbamate functional group, with manganese possibly potentiating
 the effect. Further studies into cellular ATP and NAD levels revealed a
 drastic decrease in cells treated with MB. In summary, MB significantly
 impacted both aerobic and anaerobic energy production; therefore, further
 characterization of MB’s effect on cellular energetics may provide insight
 into the specificity of PD to dopaminergic neurons.
description: 24 HR - DMSO (10
 fps)_A3_224 HR treatment of 0.5%
 DMSO control on neuroblastoma cells.24 HR - 50 uM
 MB24
 HR treatment of 50 uM MB on neuroblastoma cells.
DOI: 10.5061/dryad.q0740kp8
title: Data from: Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens)

description: Modern pyrosequencing has the potential to uncover many interesting
 aspects of genome evolution, even in lineages where genomic resources are
 scarce. In particular, 454 pyrosequencing of nonmodel species has been
 used to characterize expressed sequence tags, xenobiotics, gene
 ontologies, and relative levels of gene expression. Herein, we use
 pyrosequencing to study the evolution of genes expressed in the gonads of
 a polyploid fish, the lake sturgeon (Acipenser fulvescens). Using 454
 pyrosequencing of transcribed genes, we produced more than 125 MB of
 sequence data from 473,577 high-quality sequencing reads. Sequences that
 passed stringent quality control thresholds were assembled into 12,791
 male contigs and 32,629 female contigs. Average depth of coverage was 4.2x
 for the male assembly and 5.5x for the female assembly. Analytical
 rarefaction indicates that our assemblies include most of the genes
 expressed in lake sturgeon gonads. Over 86,700 sequencing reads were
 assigned gene ontologies, many to general housekeeping genes like protein,
 RNA, and ion binding genes. We searched specifically for sex determining
 genes and documented significant sex differences in the expression of two
 genes involved in vertebrate sex determination, DMRT1 and TRA-1. DMRT1 is
 the master sex determining gene in birds and in medaka (Oryzias latipes)
 whereas TRA-1 helps direct sexual differentiation in nematodes. We also
 searched the lake sturgeon assembly for evidence of xenobiotic organisms
 that may exist as endosymbionts. Our results suggest that exogenous
 parasites (trematodes) and pathogens (protozoans) apparently have infected
 lake sturgeon gonads, and the trematodes have horizontally transferred
 some genes to the lake sturgeon genome.
description: Sturgeon_F.fastaraw 454 sequences for the female lake sturgeonSturgeon_F.qualquality data for sequences in the female sturgeon file.Sturgeon_M.fastaraw 454 sequence data for male sturgeon.Sturgeon_M_qualquality file for sequences generated from the male lake sturgeonSturgeon_M.qualfemale_contigsContigs assembled with PCAP from the female assemblymale_contigsContigs constructed in PCAP from the male lake sturgeon
DOI: 10.5061/dryad.622q4
title: Data from: Nuclear genomic signals of the "microturbellarian" roots of platyhelminth evolutionary innovation

description: Flatworms number among the most diverse invertebrate phyla, and represent
 the most biomedically significant branch of the major bilaterian clade
 Spiralia, but to date, deep evolutionary relationships within this group
 have been studied using only a single locus (the rRNA operon), leaving the
 origins of many key clades unclear. Here, using a survey of genomes and
 transcriptomes representing all free-living flatworm orders, we provide
 resolution of platyhelminth interrelationships based on hundreds of
 nuclear protein-coding genes, exploring phylogenetic signal through
 concatenation as well as recently developed consensus approaches. These
 analyses robustly support a modern hypothesis of flatworm phylogeny, one
 which emphasizes the primacy of the often-overlooked
 'microturbellarian' groups in understanding the major
 evolutionary transitions within Platyhelminthes: perhaps most notably, we
 propose a novel scenario for the interrelationships between free-living
 and vertebrate-parasitic flatworms, providing new opportunities to shed
 light on the origins and biological consequences of parasitism in these
 iconic invertebrates.
description: eLife_datadryadA zip archive containing all trees, supernetworks, gene and concatenated alignments inferred as part of our article, "Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation". Trees are organized with reference to the Figures of the paper; alignments are in a separate directory.trinity_assembliesThese are FASTA files containing the raw output of the Trinity RNA-Seq de novo assembler for the cDNA libraries sequenced as part of our paper in eLife, DOI: http://dx.doi.org/10.7554/eLife.05503