cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cb5cf20
title: Data from: Short-term sleep loss alters cytokine gene expression in brain and peripheral tissues and increases plasma corticosterone of zebra finch (Taeniopygia guttata)

description: Lack of sleep incurs physiological costs that include increased
 inflammation and alterations in the hypothalamic-pituitary-adrenal (HPA)
 axis. Specifically, sleep restriction or deprivation leads to increased
 pro-inflammatory cytokine expression and elevated glucocorticoids in
 rodent models, but whether birds exact similar costs is unknown. In this
 study, we examined whether zebra finch (Taeniopygia guttata), an avian
 model species, exhibits physiological costs of sleep loss using a novel
 automated sleep fragmentation/deprivation method; a horizontal wire sweeps
 across a test cage to disrupt sleep every 120 s. We measured
 pro-inflammatory (IL-1β and IL-6) and anti-inflammatory (IL-10) cytokine
 gene expression in the periphery (fat, liver, spleen, and heart) and brain
 (hypothalamus, hippocampus, and apical hyperpallium) of captive finches
 after 12 h of exposure to a moving or stationary (control) bar during the
 night or the day. Plasma corticosterone, body mass, and behavioral
 profiles were also assessed. We predicted that birds undergoing sleep loss
 would exhibit elevated pro-inflammatory and reduced anti-inflammatory gene
 expression in brain and peripheral tissues compared with control birds. In
 addition, we predicted an increase in plasma corticosterone levels after
 sleep loss. As predicted, sleep loss increased pro-inflammatory gene
 expression, specifically in adipose tissue (IL-6), spleen (IL-1), and
 hippocampus (IL-6), but a decrease in anti-inflammatory expression (IL-10)
 was not detected. However, sleep loss elevated baseline concentrations of
 plasma corticosterone. Taken together, these results suggest that a
 diurnal, non-migratory songbird is sensitive to the costs of sleep loss.
description: Supplemental table
 1Raw
 statisticsraw.statistics.csvDark moving barClip of zebra finch exposed to moving wire during the dark phaseDark.Moving.Bar.aviLight Moving BarVideo clip of zebra finch exposed to moving wire during the light phaseLight.Moving.Bar.avi
DOI: 10.5061/dryad.4qq0v
title: Data from: Echidna venom gland transcriptome provides insights into the evolution of monotreme venom

description: Monotremes (echidna and platypus) are egg-laying mammals. One of their
 most unique characteristic is that males have venom/crural glands that are
 seasonally active. Male platypuses produce venom during the breeding
 season, delivered via spurs, to aid in competition against other males.
 Echidnas are not able to erect their spurs, but a milky secretion is
 produced by the gland during the breeding season. The function and
 molecular composition of echidna venom is as yet unknown. Hence, we
 compared the deeply sequenced transcriptome of an in-season echidna crural
 gland to that of a platypus and searched for putative venom genes to
 provide clues into the function of echidna venom and the evolutionary
 history of monotreme venom. We found that the echidna venom gland
 transcriptome was markedly different from the platypus with no correlation
 between the top 50 most highly expressed genes. Four peptides found in the
 venom of the platypus were detected in the echidna transcriptome. However,
 these genes were not highly expressed in echidna, suggesting that they are
 the remnants of the evolutionary history of the ancestral venom gland.
 Gene ontology terms associated with the top 100 most highly expressed
 genes in echidna, showed functional terms associated with steroidal and
 fatty acid production, suggesting that echidna “venom” may play a role in
 scent communication during the breeding season. The loss of the ability to
 erect the spur and other unknown evolutionary forces acting in the echidna
 lineage resulted in the gradual decay of venom components and the
 evolution of a new role for the crural gland.
description: transcripts.fatranscripts_over_500_bpcontig-orderingsplicing_events
DOI: 10.5061/dryad.2b5f7
title: Data from: Blood tracer kinetics in the arterial tree

description: Evaluation of blood supply of different organs relies on labeling blood
 with a suitable tracer. The tracer kinetics is linear: Tracer
 concentration at an observation site is a linear response to an input
 somewhere upstream the arterial flow. The corresponding impulse response
 functions are currently treated empirically without incorporating the
 relation to the vascular morphology of an organ. In this work we address
 this relation for the first time. We demonstrate that the form of the
 response function in the entire arterial tree is reduced to that of
 individual vessel segments under approximation of good blood mixing at
 vessel bifurcations. The resulting expression simplifies significantly
 when the geometric scaling of the vascular tree is taken into account.
 This suggests a new way to access the vascular morphology in vivo using
 experimentally determined response functions. However, it is an ill-posed
 inverse problem as demonstrated by an example using measured arterial spin
 labeling in large brain arteries. We further analyze transport in
 individual vessel segments and demonstrate that experimentally accessible
 tracer concentration in vessel segments depends on the measurement
 principle. Explicit expressions for the response functions are obtained
 for the major middle part of the arterial tree in which the blood flow in
 individual vessel segments can be treated as laminar. When applied to the
 analysis of regional cerebral blood flow measurements for which the
 necessary arterial input is evaluated in the carotid arteries, present
 theory predicts about 20% underestimation, which is in agreement with
 recent experimental data.
description: Blood_tracer_kinetics_in_the_arterial_tree
DOI: 10.5061/dryad.5b331
title: Data from: Autocorrelation structure at rest predicts value correlates of single neurons during reward-guided choice

description: Correlates of value are routinely observed in the prefrontal cortex (PFC)
 during reward-guided decision making. In previous work (Hunt et al.,
 2015), we argued that PFC correlates of chosen value are a consequence of
 varying rates of a dynamical evidence accumulation process. Yet within
 PFC, there is substantial variability in chosen value correlates across
 individual neurons. Here we show that this variability is explained by
 neurons having different temporal receptive fields of integration, indexed
 by examining neuronal spike rate autocorrelation structure whilst at rest.
 We find that neurons with protracted resting temporal receptive fields
 exhibit stronger chosen value correlates during choice. Within
 orbitofrontal cortex, these neurons also sustain coding of chosen value
 from choice through the delivery of reward, providing a potential neural
 mechanism for maintaining predictions and updating stored values during
 learning. These findings reveal that within PFC, variability in temporal
 specialisation across neurons predicts involvement in specific
 decision-making computations.
description: Data and MATLAB Scripts
 for reproducing figuresThis ZIP archive
 contains the raw data and MATLAB scripts for reproducing the figures in
 the paper. To generate the figures, run Make_Cavanagh_figures.m. To find
 out more about the file contents, please read the Readme
 file.Cavanagh_eLife_data.zip
DOI: 10.5061/dryad.v23s994
title: Data from: Tampa Bay (Florida, USA): documenting seagrass recovery since the 1980’s and reviewing the benefits

description: In 1995, the Tampa Bay Estuary Program adopted a goal of restoring
 seagrass areal coverage to 1950s levels after decades of decline. Reaching
 this goal required collaboration from public and private sectors, and the
 implementation of over 450 projects (e.g., wastewater upgrades, stormwater
 improvements, habitat restoration, education, and many others) at an
 estimated cost of $649 M. Nutrient loading has been cut in half, water
 clarity is now similar to 1950s levels, and in 2016, 16,857 ha of
 seagrasses were reported baywide – about 1,480 ha above the original
 restoration goal. Ongoing monitoring and assessments continue to describe
 both the total extent and composition of Tampa Bay seagrass beds which
 guide current management efforts. In addition, ancillary benefits of Tampa
 Bay’s seagrass resource recovery have started to emerge that will provide
 additional support and guidance for future management and recovery
 efforts.
description: TB_SEAGRASS_TRANSECT_DATASET_thru_2015ArcGIS 9.3 compatible geodatabase containing Tampa Bay seagarss transect data collected from 1997-2015. The geodatabase contains transect and discrete point, route-event features collected by partner agencies of the Tampa Bay Estuary Program. Updated databases are maintained here: https://tbeptech.org/data/gis-data/31-tbep-tech-databases.
DOI: 10.5061/dryad.f76nv
title: Data from: Continuum of vasodilator stress from rest to contrast medium to adenosine hyperemia for fractional flow reserve assessment

description: OBJECTIVES: We compared the diagnostic performance with adenosine-derived
 fractional flow reserve (FFR) #0.8 of contrast-based FFR (cFFR), resting
 distal pressure (Pd)/aortic pressure (Pa), and the instantaneous wave-free
 ratio (iFR). BACKGROUND: FFR objectively identifies lesions that benefit
 from medical therapy versus revascularization. However, FFR requires
 maximal vasodilation, usually achieved with adenosine. Radiographic
 contrast injection causes submaximal coronary hyperemia. Therefore,
 intracoronary contrast could provide an easy and inexpensive tool for
 predicting FFR. METHODS: We recruited patients undergoing routine FFR
 assessment and made paired, repeated measurements of all physiology
 metrics (Pd/Pa, iFR, cFFR, and FFR). Contrast medium and dose were per
 local practice, as was the dose of intracoronary adenosine. Operators were
 encouraged to perform both intracoronary and intravenous adenosine
 assessments and a final drift check to assess wire calibration. A central
 core lab analyzed blinded pressure tracings in a standardized fashion.
 RESULTS: A total of 763 subjects were enrolled from 12 international
 centers. Contrast volume was 8 +- 2 ml per measurement, and 8 different
 contrast media were used. Repeated measurements of each metric showed a
 bias &lt;0.005, but a lower SD (less variability) for cFFR than
 resting indexes. Although Pd/Pa and iFR demonstrated equivalent
 performance against FFR #0.8 (78.5% vs. 79.9% accuracy, p ¼ 0.78; area
 under the receiver-operating characteristic curve: 0.875 vs. 0.881, p ¼
 0.35), cFFR improved both metrics (85.8% accuracy and 0.930 area, p
 &lt; 0.001 for each) with an optimal binary threshold of 0.83. A
 hybrid decision-making strategy using cFFR required adenosine less often
 than when based on either Pd/Pa or iFR. CONCLUSIONS: cFFR provides
 diagnostic performance superior to that of Pd/Pa or iFR for predicting
 FFR. For clinical scenarios or health care systems in which adenosine is
 contraindicated or prohibitively expensive, cFFR offers a universal
 technique to simplify invasive coronary physiological assessments. Yet FFR
 remains the reference standard for diagnostic certainty as even cFFR
 reached only ~85% agreement.
description: CONTRAST
 tracingsCONTRAST.tgz
DOI: 10.5061/dryad.57ms3
title: Data from: A revised design for microarray experiments to account for experimental noise and uncertainty of probe response

description: Background: Although microarrays are analysis tools in biomedical
 research, they are known to yield noisy output that usually requires
 experimental confirmation. To tackle this problem, many studies have
 developed rules for optimizing probe design and devised complex
 statistical tools to analyze the output. However, less emphasis has been
 placed on systematically identifying the noise component as part of the
 experimental procedure. One source of noise is the variance in probe
 binding, which can be assessed by replicating array probes. The second
 source is poor probe performance, which can be assessed by calibrating the
 array based on a dilution series of target molecules. Using model
 experiments for copy number variation and gene expression measurements, we
 investigate here a revised design for microarray experiments that
 addresses both of these sources of variance. Results: Two custom arrays
 were used to evaluate the revised design: one based on 25 mer probes from
 an Affymetrix design and the other based on 60 mer probes from an Agilent
 design. To assess experimental variance in probe binding, all probes were
 replicated ten times. To assess probe performance, the probes were
 calibrated using a dilution series of target molecules and the signal
 response was fitted to an adsorption model. We found that significant
 variance of the signal could be controlled by averaging across probes and
 removing probes that are nonresponsive or poorly responsive in the
 calibration experiment. Taking this into account, one can obtain a more
 reliable signal with the added option of obtaining absolute rather than
 relative measurements. Conclusion: The assessment of technical variance
 within the experiments, combined with the calibration of probes allows to
 remove poorly responding probes and yields more reliable signals for the
 remaining ones. Once an array is properly calibrated, absolute
 quantification of signals becomes straight forward, alleviating the need
 for normalization and reference hybridizations.
description: array_25merDatabase containing intensities and probe calibration information for 25-mer array.array_60merDatabase containing signal intensities and probe calibration information for 60-mer array.CNV_ProbeInAllExpts_apGene copy number values calculated based on hybridization with the calibrated 60-mer array.
DOI: 10.5061/dryad.nd4dp
title: Data from: Resistance to RHD virus in wild Australian rabbits: comparison of susceptible and resistant individuals using a genomewide approach

description: Deciphering the genes involved in disease resistance is essential if we
 are to understand host–pathogen coevolutionary processes. The rabbit
 haemorrhagic disease virus (RHDV) was imported into Australia in 1995 as a
 biocontrol agent to manage one of the most successful and devastating
 invasive species, the European rabbit (Oryctolagus cuniculus). During the
 first outbreaks of the disease, RHDV caused mortality rates of up to 97%.
 Recently, however, increased genetic resistance to RHDV has been reported.
 Here, we have aimed to identify genomic differences between rabbits that
 survived a natural infection with RHDV and those that died in the field
 using a genomewide next-generation sequencing (NGS) approach. We detected
 72 SNPs corresponding to 133 genes associated with survival of a RHD
 infection. Most of the identified genes have known functions in virus
 infections and replication, immune responses or apoptosis, or have
 previously been found to be regulated during RHD. Some of the genes
 identified in experimental studies, however, did not seem to play a role
 under natural selection regimes, highlighting the importance of field
 studies to complement the genomic background of wildlife diseases. Our
 study provides a set of candidate markers as a tool for the future
 scanning of wild rabbits for their resistance to RHDV. This is important
 both for wild rabbit populations in southern Europe where RHD is regarded
 as a serious problem decimating the prey of endangered predator species
 and for assessing the success of currently planned RHDV variant biocontrol
 releases in Australia.
description: STACKS
 outputOutput of the STACKS
 ref_map.pl pipeline run for mapped reads of 78 samples (reads archived at
 ENA, accession PRJEB20958). Details about the analysis can be found at
 https://github.com/hdetering/orycun.stacks_output.tar.gzPLINK outputOutput files generated by PLINK association test for 78 samples in two groups (36 dead, 42 survivors). Details about the analysis are at https://github.org/hdetering/orycun.plink_output.tar.gz
DOI: 10.5061/dryad.tn873
title: Data from: Inferior cerebellar hypoplasia resembling a Dandy-Walker-like malformation in purebred Eurasier dogs with familial non-progressive ataxia: a retrospective and prospective clinical cohort study

description: Cerebellar malformations can be inherited or caused by insults during
 cerebellar development. To date, only sporadic cases of cerebellar
 malformations have been reported in dogs, and the genetic background has
 remained obscure. Therefore, this study`s objective was to describe the
 clinical characteristics, imaging features and pedigree data of a familial
 cerebellar hypoplasia in purebred Eurasier dogs. A uniform cerebellar
 malformation characterized by consistent absence of the caudal portions of
 the cerebellar vermis and, to a lesser degree, the caudal portions of the
 cerebellar hemispheres in association with large retrocerebellar fluid
 accumulations was recognized in 14 closely related Eurasier dogs.
 Hydrocephalus was an additional feature in some dogs. All dogs displayed
 non-progressive ataxia, which had already been noted when the dogs were 5
 – 6 weeks old. The severity of the ataxia varied between dogs, from mild
 truncal sway, subtle dysmetric gait, dysequilibrium and pelvic limb ataxia
 to severe cerebellar ataxia in puppies and episodic falling or rolling.
 Follow-up examinations in adult dogs showed improvement of the cerebellar
 ataxia and a still absent menace response. Epileptic seizures occurred in
 some dogs. The association of partial vermis agenesis with an enlarged
 fourth ventricle and an enlarged caudal (posterior) fossa resembled a
 Dandy-Walker-like malformation in some dogs. Pedigree analyses were
 consistent with autosomal recessive inheritance.
description: Raw image
 dataRaw image data from dog
 4 and all prospectively examined dogs (dogs 6 - 11) from the publication
 Bernardino et al. (Plos One).mrt
 data.zip
DOI: 10.5061/dryad.4fk53
title: Data from: Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia

description: The widely used herbicide glyphosate inhibits the shikimate pathway enzyme
 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Globally, the
 intensive use of glyphosate for weed control has selected for glyphosate
 resistance in 31 weed species. Populations of suspected
 glyphosate-resistant Kochia scoparia were collected from fields located in
 the US central Great Plains. Glyphosate dose response verified glyphosate
 resistance in nine populations. The mechanism of resistance to glyphosate
 was investigated using targeted sequencing, quantitative PCR,
 immunoblotting, and whole transcriptome de novo sequencing to characterize
 the sequence and expression of EPSPS. Sequence analysis showed no mutation
 of the EPSPS Pro106 codon in glyphosate-resistant K. scoparia, whereas
 EPSPS genomic copy number and transcript abundance were elevated three- to
 ten-fold in resistant individuals relative to susceptible individuals.
 Glyphosate-resistant individuals with increased relative EPSPS copy
 numbers had consistently lower shikimate accumulation in leaf disks
 treated with 100 μM glyphosate and EPSPS protein levels were higher in
 glyphosate-resistant individuals with increased gene copy number compared
 to glyphosate-susceptible individuals. RNA sequence analysis revealed
 seven nucleotide positions with two different expressed alleles in
 glyphosate-susceptible reads. However, one nucleotide at the seven
 positions was predominant in glyphosate-resistant sequences, suggesting
 that only one of two EPSPS alleles was amplified in glyphosate-resistant
 individuals. No alternatively spliced EPSPS transcripts were detected.
 Expression of five other genes in the chorismate pathway was unaffected in
 glyphosate-resistant individuals with increased EPSPS expression. These
 results indicate increased EPSPS expression is a mechanism for glyphosate
 resistance in these K. scoparia populations.
description: transcriptsFasta file containing all loci and transcripts from de novo assembly of Kochia scoparia Illumina HiSeq data using Oases.pseudomoleculeFasta file containing a pseudomolecule for the Kochia scoparia de novo transcriptome. The single longest transcript for each locus was concantenated into a single pseudomolecule to be used for RNA-Seq alignments.AA_AB_AC_AD_AE_AF_01_02_33.faPseudomolecule annotationGTF version 3 annotation file for the Fasta file containing a pseudomolecule for the Kochia scoparia de novo transcriptome. The single longest transcript for each locus was concantenated into a single pseudomolecule to be used for RNA-Seq alignments.AA_AB_AC_AD_AE_AF_01_02_33.gtfPseudomolecule annotationGFF versoion 3 annotation for the Fasta file containing a pseudomolecule for the Kochia scoparia de novo transcriptome. The single longest transcript for each locus was concantenated into a single pseudomolecule to be used for RNA-Seq alignments.AA_AB_AC_AD_AE_AF_01_02_33.gff3
DOI: 10.5061/dryad.82fd8
title: Data from: Brain transcriptional profiles of male alternative reproductive tactics and females in bluegill sunfish

description: Bluegill sunfish (Lepomis macrochirus) are one of the classic systems for
 studying male alternative reproductive tactics (ARTs) in teleost fishes.
 In this species, there are two distinct life histories: parental and
 cuckolder, encompassing three reproductive tactics, parental, satellite,
 and sneaker. The parental life history is fixed, whereas individuals who
 enter the cuckolder life history transition from sneaker to satellite
 tactic as they grow. For this study, we used RNAseq to characterize the
 brain transcriptome of the three male tactics and females during spawning
 to identify gene ontology (GO) categories and potential candidate genes
 associated with each tactic. We found that sneaker males had higher levels
 of gene expression differentiation compared to the other two male tactics.
 Sneaker males also had higher expression in ionotropic glutamate receptor
 genes, specifically AMPA receptors, compared to other males, which may be
 important for increased spatial working memory while attempting to cuckold
 parental males at their nests. Larger differences in gene expression also
 occurred among male tactics than between males and females. We found
 significant expression differences in several candidate genes that were
 previously identified in other species with ARTs and suggest a previously
 undescribed role for cAMP-responsive element modulator (crem) in
 influencing parental male behaviors during spawning.
description: Fish sampling
 informationA text file detailing
 sampling information for fish used in this study. It includes the sex,
 tactic, total and standard length, sampling colony, sampling location, and
 RNA integrity numbers.Fish_sampling_info.txtTranscript CountsRaw transcripts counts produced from eXpress for all samplesMerged.results.xprsR scriptContains the R scripts used with edgeR for differential gene expression analysisRscript_DE_Analysis.txtAssembled transcriptomeAssembled bluegill transcriptome. Assembled de novo using Trinity.bluegill.final.fa