cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rd465
title: Data from: Composite linkage map and enhanced genome map for Culex pipiens complex mosquitoes

description: We report here the development of 65 novel microsatellite loci and
 construction of a composite genetic linkage map for Culex pipiens complex
 mosquitoes. Microsatellites were identified by in silico screening of the
 Culex quinquefasciatus genome assembly. Cross-species utility of 73
 microsatellites for population studies in C. pipiens sensu stricto and C.
 quinquefasciatus was evaluated by genotyping a subset of samples collected
 in Indiana, United States, and Point Fortin, Trinidad. Allele frequencies
 of 67 microsatellites were within Hardy–Weinberg expectations in both
 population subsets. A composite linkage map was constructed based on
 restriction fragment length polymorphism and microsatellite polymorphisms
 in 12 independent F1 intercross mapping populations. The composite map
 consists of 61 marker loci totaling 183.9 cM distributed across the 3
 linkage groups. These loci cover 29.5, 88.8, and 65.6 cM on chromosomes
 I–III, respectively, and allow for assignment of 10.4% of the genome
 assembly and 13.5% of the protein coding genes to chromosome position. Our
 results suggest that these microsatellites will be useful for mapping and
 population studies of 2 pervasive species in the C. pipiens complex.
 Moreover, the composite map presented here will serve as a basis for the
 construction of high-resolution genetic and physical maps, as well as
 detection of quantitative trait loci to aid in the investigation of
 complex genetic traits influencing phenotypes of interest.
description: Mapping data: two point
 linkage estimates and standard errors.Composite two point
 linkage estimates and standard errors for each linkage group in the Culex
 pipiens genetic map.Mapping
 data.txt
DOI: 10.5061/dryad.m53q0
title: Data from: Starvation effects on nitrogen and carbon stable isotopes of animals: an insight from meta-analysis of fasting experiments

description: Nitrogen and carbon stable isotopic compositions (δ15N and δ13C) of
 consumers have been used for physiological and food web studies. Previous
 studies have shown δ15N and δ13C values are affected by several biological
 and environmental factors during starvation, but the generality of the
 effect of starvation on δ15N and δ13C values has not yet been tested.
 Here, we performed a meta-analysis to evaluate the effects of starvation
 on δ15N and δ13C values of consumers, and the underlying factors that may
 explain the observed variation. The δ15N and δ13C values were calculated
 as the differences between the final δ15N and δ13C values of consumers
 (post-starvation) and the pre-starvation values on each experiment. Our
 meta-analysis showed a large variation in the δ15N and δ13C values of
 consumers (δ15N range: –0.82 to 4.30‰; mean: 0.47‰ and δ13C range: –1.92
 to 2.62‰; mean: 0.01‰). The δ15N values of most consumers increased along
 the length of the starvation period and were influenced by nitrogen
 excretion and thermoregulation types, probably because differences in
 nitrogen metabolism and thermoregulation affect nitrogen processing and
 excretion rates. None of our predictor variables accounted for the
 variation in δ13C values, which showed both increases and decreases due to
 fasting. Our findings suggest that starvation results in changes in
 consumer δ15N values which are mainly explained by the length of the
 fasting period and by nitrogen and energy metabolism, but the underlying
 mechanisms of the starvation effects on δ13C values seem to be more
 complex than previously thought.
description: Table
 S1The
 all data of the meta-analysis on starvation effects on nitrogen and carbon
 stable isotopes of animalsDoietal.-Appendix1.xlsx
DOI: 10.5061/dryad.fq228
title: Data from: Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA genes (rDNA) organisation

description: In higher eukaryotes, the 5S rRNA genes occur in tandem units and are
 arranged either separately (S-type arrangement) or linked to other
 repeated genes, in most cases to rDNA locus encoding 18S–5.8S–26S genes
 (L-type arrangement). Here we used Southern blot hybridisation, PCR and
 sequencing approaches to analyse genomic organisation of rRNA genes in all
 large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and
 Cycadales. The data are provided for 27 species (21 genera). The 5S units
 linked to the 35S rDNA units occur in some but not all Gnetales,
 Coniferales and in Ginkgo (~30% of the species analysed), while the
 remaining exhibit separate organisation. The linked 5S rRNA genes may
 occur as single-copy insertions or as short tandems embedded in the
 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may be encoded by
 the same (Ginkgo, Ephedra) or opposite (Podocarpus) DNA strand as the
 18S–5.8S–26S genes. In addition, pseudogenised 5S copies were also found
 in some IGS types. Both L- and S-type units have been largely homogenised
 across the genomes. Phylogenetic relationships based on the comparison of
 5S coding sequences suggest that the 5S genes independently inserted IGS
 at least three times in the course of gymnosperm evolution. Frequent
 transpositions and rearrangements of basic units indicate relatively
 relaxed selection pressures imposed on genomic organisation of 5S genes in
 plants.
description: IGS and 5S sequences
 from Ginkgo bilobaAlignment of IGS and 5S
 sequences in FASTA format. Only the first 3 sequences contain 5S rDNA.
 Sequences could be only partially aligned due large deletions (Figure
 S6).Ginkgo
 IGS clones and 5S rRNA.fas
DOI: 10.5281/zenodo.18382623
title: Differences in Microphysical Structures Between Continental and Oceanic Thunderstorms: A GPM/DPR-Based Comparison Over South China and the South China Sea
DOI: 10.5281/zenodo.18382622
title: Differences in Microphysical Structures Between Continental and Oceanic Thunderstorms: A GPM/DPR-Based Comparison Over South China and the South China Sea
DOI: 10.5061/dryad.rr42f
title: Data from: Pneumococcal colonisation density: a new marker for disease severity in HIV-infected adults with pneumonia

description: Objective: A high genomic load of Pneumococcus from blood or cerebrospinal
 fluid has been associated with increased mortality. We aimed to analyse
 whether nasopharyngeal colonisation density in HIV-infected patients with
 community-acquired pneumonia (CAP) is associated with markers of disease
 severity or poor outcome. Methods: Quantitative lytA real-time PCR was
 performed on nasopharyngeal swabs in HIV-infected South African adults
 hospitalised for acute CAP at Chris Hani Baragwanath Hospital, Soweto,
 South Africa. Pneumonia aetiology was considered pneumococcal if any
 sputum culture or Gram stain, urinary pneumococcal C-polysaccharide-based
 antigen, blood culture or whole blood lytA real-time PCR revealed
 pneumococci. Results: There was a moderate correlation between the mean
 nasopharyngeal colonisation densities and increasing CURB65 scores among
 all-cause patients with pneumonia (Spearman correlation coefficient
 r=0.15, p=0.06) or with the Pitt bacteraemia score among patients with
 pneumococcal bacteraemia (p=0.63). In patients with pneumococcal
 pneumonia, nasopharyngeal pneumococcal colonisation density was higher
 among non-survivors than survivors (7.7 vs 6.1 log10 copies/mL,
 respectively, p=0.02) and among those who had pneumococci identified from
 blood cultures and/or by whole blood lytA real-time PCR than those with
 non-bacteraemic pneumococcal pneumonia (6.6 vs 5.6 log10 copies/mL,
 p=0.03). Nasopharyngeal colonisation density correlated positively with
 the biomarkers procalcitonin (Spearman correlation coefficient r=0.37,
 p&lt;0.0001), proadrenomedullin (r=0.39, p=0.008) and copeptin
 (r=0.30, p=0.01). Conclusions: In addition to its previously reported role
 as a diagnostic tool for pneumococcal pneumonia, quantitative
 nasopharyngeal colonisation density also correlates with mortality and
 prognostic biomarkers. It may also be useful as a severity marker for
 pneumococcal pneumonia in HIV-infected adults.
description: Database_BMJ_Open_25Jul2014Data spreadsheet
DOI: 10.5061/dryad.q3g37
title: Data from: The availability of research data declines rapidly with article age

description: Policies ensuring that research data are available on public archives are
 increasingly being implemented at the government, funding agency, and
 journal level. These policies are predicated on the idea that authors are
 poor stewards of their data, particularly over the long term, and indeed
 many studies have found that authors are often unable or unwilling to
 share their data. However, there are no systematic estimates of how the
 availability of research data changes with time since publication. We
 therefore requested datasets from a relatively homogenous set of 516
 articles published between 2 and 22 years ago, and found that availability
 of the data was strongly affected by article age. For papers where the
 authors gave the status of their data, the odds of a dataset being extant
 fell by 17% per year. In addition, the odds that we could find a working
 email address for the first, last or corresponding author fell by 7% per
 year. Our results reinforce the notion that, in the long term, research
 data cannot be reliably preserved by individual researchers, and further
 demonstrate the urgent need for policies mandating data sharing via public
 archives.
description: Vines_et_al R
 codeThe R code used for the
 analysesCurrentBiologyDatathe data used in the analyses. This does not contain any identifying information for any of the manuscripts - please contact the first author for access to the raw data.
DOI: 10.5061/dryad.p066m
title: Data from: Hepatoprotective effect of wheat-based solid-state fermented Antrodia cinnamomea in carbon tetrachloride-induced liver injury in rat

description: Antrodia cinnamomea (A. cinnamomea) is an indigenous medical fungus in
 Taiwan and has multiple biological functions, including hepatoprotective
 and immune-modulatory effects. Currently, the commercially available A.
 cinnamomea are mainly liquid- and solid-state fermented A. cinnamomea.
 However, the hepatoprotective effect of solid-state fermented A.
 cinnamomea has never been reported. Here we evaluate the ability of
 air-dried, ground and non-extracted wheat-based solid-state fermented A.
 cinnamomea (WFAC) to protect against carbon tetrachloride (CCl4)-induced
 hepatic injury in vivo. The results showed that oral administration of
 WFAC dose dependently (180, 540 and 1080 mg/kg) ameliorated the increase
 in plasma aspartate aminotransferase and alanine aminotransferase levels
 caused by chronic repeated CCl4 intoxication in rats. WFAC significantly
 reduced the CCl4-induced increase in hepatic lipid peroxidation levels and
 hydroxyproline contents, as well as reducing the spleen weight and water
 content of the liver. WFAC also restored the hepatic soluble protein
 synthesis and plasma albumin concentration in CCl4-intoxicated rats, but
 it did not affect the activities of superoxide dismutase, catalase, or
 glutathione peroxidase. In addition, a hepatic morphological analysis
 showed that the hepatic fibrosis and necrosis induced by CCl4 were
 significantly ameliorated by WFAC. Furthermore, the body weights of
 control rats and WFAC-administered rats were not significantly different,
 and no adverse effects were observed in WFAC-administered rats. These
 results indicate that WFAC is a nontoxic hepatoprotective agent against
 chronic CCl4-induced hepatic injury.
description: Raw data and statistical
 analysisRaw data and statistical
 analysis of all results in this paper
DOI: 10.5061/dryad.hg6vs
title: Data from: Oceanographic drivers of offspring abundance may increase or decrease variance in reproductive success in a temperate marine fish

description: In species that reproduce into uncertain environments, the relationship
 between mean reproductive success (the abundance of new recruits) and the
 variance in reproductive success (whether adults contribute
 disproportionally more offspring) may not be straightforward because of
 stochastic environmental processes that create high variance in
 reproductive success among adults. In this study we investigated the
 relationships between oceanography, reproductive success, and reproductive
 variance in the black rockfish, Sebastes melanops, a long-lived temperate
 reef fish with pelagic larvae. We quantified black rockfish recruitment,
 genetic diversity, and growth rates from otolith microstructure over 5
 years (2005-2009) during which oceanographic conditions differed. We used
 cross-correlations to determine windows of time during which oceanographic
 variables were significantly correlated with the resulting abundance or
 genetic diversity of recruits. We found that warmer ocean temperatures
 were positively correlated with the abundance of recruits, as well as the
 effective number of breeders. In contrast, the strength of coastal
 upwelling during settlement was positively correlated with the annual
 abundance of new recruits, but was negatively correlated with the
 effective number of breeders. Larval growth rates were explained
 substantially more by temperature than by upwelling, and suggested that
 temperature affected survival through growth, while upwelling affected
 survival through transport. Our results indicated that cold ocean
 temperatures and intense upwelling caused sweepstakes-like processes to
 operate on black rockfish populations, despite high abundances of
 recruits. We propose that a decoupling of the mean and variance in
 reproductive success may be characteristic of organisms that reproduce
 into uncertain environments.
description: Data_Recruits.Genotypes.ByYearMicrosatellite genotypes of Sebastes melanops recruits collected from Barkley Sound, British Columbia in GENEPOP format.
DOI: 10.5061/dryad.vn2sh
title: Data from: Lichen traits responding to aridity

description: 1. Climate change is expected to cause several impacts at the global scale
 and drylands will be among the most affected areas. Thus, investigating
 how these changes will affect the composition, structure and functioning
 of dryland ecosystems has become a priority. From an ecological indicator
 point of view, several works have shown that functional diversity is
 better than species richness to understand ecosystem functioning or
 response to environmental factors. However most of these works focus on
 plants while those of other organisms remain largely unknown. Lichens are
 amongst the ecosystem components more sensitive to climatic changes due to
 several physiological and ecological characteristics. Their poikilohydric
 nature (therefore highly dependent on the atmosphere for water supply) and
 their ubiquity on terrestrial ecosystems underlie their potential as
 indicators of climate. Nonetheless, works specifically aiming to identify
 lichen functional traits that respond to aridity remain poorly explored,
 particularly in drylands. 2. We proposed to identify lichen functional
 traits and respective functional groups responding to aridity in a
 Mediterranean drylands ecosystem. 3. Lichen diversity was sampled in open
 holm-oak woodlands along an aridity gradient in SW Europe (Iberian
 Peninsula). Lichen functional traits that could be easily identified and
 related to water uptake were selected to be tested: type of photobiont,
 growth form and reproduction strategy. 4. Lichen species composition was
 related to the aridity gradient. The three traits chosen were related with
 the community's response to aridity, but with contrasting responses
 in different functional groups. More specifically crustose and fruticose
 lichens, isidiate species and the ones with Trentepohlia as photobiont
 were related to the less arid part of the gradient. Foliose species and
 cyanolichens, on the contrary, were associated with the most arid areas.
 5. Synthesis We were able to identify lichen traits responding to aridity.
 Type of photobiont was particularly responsive, with Trentepohlia and
 cyanobacteria functional groups, responding clearly in contrasting ways to
 aridity in this drylands ecosystem. This work emphasizes functional
 diversity role on understanding and assessing the response to
 environmental factors, namely to climate. It also highlights the potential
 use of lichen functional groups as ecological indicators of climate
 change.
description: Relative percentage of
 species LDV (lichen diversity value) per sampling siteRelative percentage of
 species LDV (lichen diversity value) collected along an aridity gradient
 in SW Europe (Iberian Península). Columns are species, sows are sampling
 sites. Species can be decoded in the ReadMe file.Species
 LDV.csv
DOI: 10.5061/dryad.3539k
title: Data from: Is it becoming harder to secure reviewers for peer review? A test with data from five ecology journals

description: Background: There is concern in the academic publishing community that it
 is becoming more difficult to secure reviews for peer-reviewed
 manuscripts, but much of this concern stems from anecdotal and rhetorical
 evidence. Methods: We examined the proportion of review requests that led
 to a completed review over a 6-year period (2009–2015) in a mid-tier
 biology journal (Molecular Ecology). We also re-analyzed previously
 published data from four other mid-tier ecology journals (Functional
 Ecology, Journal of Ecology, Journal of Animal Ecology, and Journal of
 Applied Ecology), looking at the same proportion over the period 2003 to
 2010. Results: The data from Molecular Ecology showed no significant
 decrease through time in the proportion of requests that led to a review
 (proportion in 2009 = 0.47 (95 % CI = 0.43 to 0.52), proportion in
 2015 = 0.44 (95 % CI = 0.40 to 0.48)). This proportion did decrease for
 three of the other ecology journals (changes in proportions from 2003 to
 2010 = −0.10, −0.18, and −0.09), while the proportion for the fourth
 (Functional Ecology) stayed roughly constant (change in
 proportion = −0.04). Conclusions: Overall, our data suggest that reviewer
 agreement rates have probably declined slightly but not to the extent
 suggested by the anecdotal and rhetorical evidence.
description: ripr_analysis_code_annotatedThe R code used for the analysis in the paper, including drawing the figures.reviewer data from Molecular EcologyThis file contains the reviewer data for Molecular Ecology. The other data files called by the analysis code are from Petchey et al (2014), see http://dx.doi.org/10.5061/dryad.36r69ripr for R.csv
DOI: 10.5061/dryad.p5614
title: Data from: Overexpression of Dyrk1A is implicated in several cognitive, electrophysiological and neuromorphological alterations found in a mouse model of Down syndrome

description: Down syndrome (DS) phenotypes result from the overexpression of several
 dosage-sensitive genes. The DYRK1A (dual-specificity
 tyrosine-(Y)-phosphorylation regulated kinase 1A) gene, which has been
 implicated in the behavioral and neuronal alterations that are
 characteristic of DS, plays a role in neuronal progenitor proliferation,
 neuronal differentiation and long-term potentiation (LTP) mechanisms that
 contribute to the cognitive deficits found in DS. The purpose of this
 study was to evaluate the effect of Dyrk1A overexpression on the
 behavioral and cognitive alterations in the Ts65Dn (TS) mouse model, which
 is the most commonly utilized mouse model of DS, as well as on several
 neuromorphological and electrophysiological properties proposed to
 underlie these deficits. In this study, we analyzed the phenotypic
 differences in the progeny obtained from crosses of TS females and
 heterozygous Dyrk1A (+/−) male mice. Our results revealed that
 normalization of the Dyrk1A copy number in TS mice improved working and
 reference memory based on the Morris water maze and contextual
 conditioning based on the fear conditioning test and rescued hippocampal
 LTP. Concomitant with these functional improvements, normalization of the
 Dyrk1A expression level in TS mice restored the proliferation and
 differentiation of hippocampal cells in the adult dentate gyrus (DG) and
 the density of GABAergic and glutamatergic synapse markers in the
 molecular layer of the hippocampus. However, normalization of the Dyrk1A
 gene dosage did not affect other structural (e.g., the density of mature
 hippocampal granule cells, the DG volume and the subgranular zone area) or
 behavioral (i.e., hyperactivity/attention) alterations found in the TS
 mouse. These results suggest that Dyrk1A overexpression is involved in
 some of the cognitive, electrophysiological and neuromorphological
 alterations, but not in the structural alterations found in DS, and
 suggest that pharmacological strategies targeting this gene may improve
 the treatment of DS-associated learning disabilities.
description: Data
 PONE-D-14-18420This is an excel file
 containing the data underlying the results described in each manuscript.
 This file contains 11 spreadsheets, containing the raw data of 1) Dyrk1A
 protein levels, 2) MWM performance, 3) CFC performance, 4) Rotarod
 Performance, 5) Open Field performance, 6) LTP results, 7) GAD65/67 and
 VGLUT levels and VGLUT/GAD65/67 ratio, 8) Ki67, DCX, CLR and DAPI values,
 9) DG volume and SGZ ratio, 10) Body weight and 11) Motor tests
 data
DOI: 10.5061/dryad.k6d43
title: Data from: Song learning and cognitive ability are not consistently related in a songbird

description: Learned aspects of song have been hypothesized to signal cognitive ability
 in songbirds. We tested this hypothesis in hand-reared song sparrows
 (Melospiza melodia) that were tutored with playback of adult songs during
 the critical period for song learning. The songs developed by the 19 male
 subjects were compared to the model songs to produce two measures of song
 learning: the proportion of notes copied from models and the average
 spectrogram cross-correlation between copied notes and model notes. Song
 repertoire size, which reflects song complexity, was also measured. At 1
 year of age, subjects were given a battery of five cognitive tests that
 measured speed of learning in the context of a novel foraging task, color
 association, color reversal, detour-reaching, and spatial learning.
 Bivariate correlations between the three song measures and the five
 cognitive measures revealed no significant associations. As in other
 studies of avian cognition, different cognitive measures were for the most
 part not correlated with each other, and this result remained true when 22
 hand-reared female song sparrows were added to the analysis. General
 linear mixed models controlling for effects of neophobia and nest of
 origin indicated that all three song measures were associated with better
 performance on color reversal and spatial learning but were associated
 with worse performance on novel foraging and detour-reaching. Overall, the
 results do not support the hypothesis that learned aspects of song signal
 cognitive ability.
description: song sparrow cognition
 dataSheet1 gives data on 19
 hand-reared male song sparrows including their neophobia scores, their
 results on five cognitive tests (novel foraging, color association, color
 reversal, spatial learning, and detour reaching) and three measures of
 song (proportion of notes copied, average cross correlation, and
 repertoire size). Sheet2 gives data on cognitive test results for the 19
 hand-reared male plus 22 hand-reared female song sparrows, including
 neophobia scores and scores on the same five cognitive
 tests.