cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z34tmpgb4
title: National Grid frequency trace

description: The attached dataset provides the GB grid frequency every second
 for two hours (02.00-04.00) on 1 September 2015 (at some location that I
 do not remember).  I used it to test some linear stochastic
 process models for the frequency as a function of time.  On the
 2-hour timescale the trace fit reasonably well to an Ornstein-Uhlenbeck
 (OU) process with a decay time of around 30 minutes.  On a
 shorter timescale, in particular the first 3 minutes 20 seconds, the trace
 looked smooth so I fitted it to a first-order filtered OU process, which
 gave me time constants of 11 minutes and 1.9 seconds.  This was
 important evidence that a useful model for power imbalance as a function
 of time is a filtered white noise.  Furthermore, the power
 spectrum of the 2-hour trace showed a regime with slope around -4 for
 periods shorter than 25 seconds, consistent with being a first-order
 filtered OU process, until the Nyquist cutoff at 2 seconds.
description: The data were publicly available from National Grid
 (http://www2.nationalgrid.com/Enhanced-Frequency-Response.aspx) at the
 time.  I downloaded them.  The link is no longer active, so I have made
 the data available here.  I made no changes.
description: The data are in an excel file with three columns: date
 (DD/MM/YEAR), time (HH:MM:SS), frequency (Hz).  A graph is also
 provided.
DOI: 10.25345/c5tq5rt4w
title: MassIVE MSV000100609 - Recognizing In-Source Fragmentation in Ion Mobility-Enabled Data-Independent Acquisition Workflows
title: IM-DIA analysis of chemical standards and human plasma extracts.
DOI: 10.5061/dryad.8w9ghx3jx
title: Sex differences in moral judgements across 67 countries

description: Most of the empirical research on sex differences and cultural variations
 in morality has relied on within-culture analyses or small-scale
 cross-cultural data. To further broaden the scientific understanding of
 sex differences in morality, the current research relies on two
 international samples to provide the first large-scale examination of sex
 differences in moral judgements nested within cultures. Using a sample
 from 67 countries (Study 1; n = 336,691), we found culturally-variable sex
 differences in moral judgements, as conceptualized by Moral Foundations
 Theory. Women consistently scored higher than men on Care, Fairness, and
 Purity. In contrast, sex differences in Loyalty and Authority were
 negligible and highly variable across cultures. Country-level sex
 differences in moral judgements were also examined in relation to
 cultural, socio-economic, and gender-equality indicators revealing that
 sex differences in moral judgements are larger in individualist, Western,
 and gender-equal societies. In Study 2 (19 countries; n = 11,969), these
 results were largely replicated using Bayesian multi-level modeling in a
 distinct sample. The findings were robust even when incorporating cultural
 non-independence of countries into the models. Specifically, women
 consistently showed higher concerns for Care, Fairness, and Purity in
 their moral judgements than did men. Sex differences in moral judgements
 were larger in individualist and gender-equal societies with more flexible
 social norms. We discuss the implications of these findings for the
 ongoing debate about the origin of sex differences and cultural variations
 in moral judgements as well as theoretical and pragmatic implications for
 moral and evolutionary psychology.
DOI: 10.5061/dryad.k98sf7m4g
title: Resource quality determines the evolution of resistance and its genetic basis

description: Parasites impose strong selection on their hosts, but the level of any
 evolved resistance may be constrained by the availability of resources.
 However, studies identifying the genomic basis of such resource-mediated
 selection are rare, particularly in non-model organisms. Here, we
 investigated the role of nutrition in the evolution of resistance to a DNA
 virus (PiGV), and any associated trade-offs in a lepidopteran pest species
 (Plodia interpunctella). Through selection experiments and whole genome
 re-sequencing we identify genetic markers of resistance that vary between
 the nutritional environments during selection. We do not find consistent
 evolution of resistance in the presence of virus but rather see
 substantial variation among replicate populations. Resistance in a low
 nutrition environment is negatively correlated with growth rate,
 consistent with an established trade-off between immunity and development,
 but this relationship is highly context dependent. Whole genome
 resequencing of the host shows that resistance mechanisms are likely to be
 highly polygenic and although the underlying genetic architecture may
 differ between high and low nutrition environments, similar mechanisms are
 commonly used. As a whole, our results emphasise the importance of the
 resource environment on influencing the evolution of resistance.
DOI: 10.5061/dryad.m37pvmd0c
title: Supplementary material of the article “Elevation patterns and critical environmental drivers of the taxonomic, functional and phylogenetic diversity of small mammals in a karst mountain area”.

description: Understanding how biodiversity components are related under different
 environmental factors is a fundamental challenge for ecology studies, yet
 there is little knowledge of this interplay among the biotas, especially
 small mammals, in karst mountain areas. Here, we examine the elevation
 patterns of the taxonomic diversity (TD), phylogenetic diversity (PD) and
 functional diversity (FD) of small mammals in a karst mountain area, the
 Wuling Mountains, Southwest China, and compare these patterns between taxa
 (Rodentia and Eulipotyphla) and scales (broad- and narrow-range species).
 We also disentangle the impacts of the human influence index, net primary
 productivity (NPP), normalized difference vegetation index (NDVI), annual
 precipitation (AP), and annual mean temperature (AMT) on these three
 facets of biodiversity by using structural equation modeling. We recorded
 a total of 39 small mammal species, including 26 rodents and 13 species of
 the order Eulipotyphla. Our study shows that the facets of biodiversity
 are spatially incongruent. Net primary productivity has a positive effect
 on the three facets for most groups, while the effect of the normalized
 difference vegetation index is negative for TD and PD in most groups.
 Annual mean temperature and annual precipitation have negative effects on
 FD and PD, whereas TD is dependent on the species range scale. The human
 influence index effect on TD and PD also depends on the species range
 scale. These findings provide robust evidence that the ecological drivers
 of biodiversity differ among different biotas and different range scales,
 and future research should use multi-facet approach to determine
 biodiversity conservation strategies.
DOI: 10.15468/dl.hkv28x
title: Occurrence Download

description: A dataset containing 2043723 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-99 20,-100 20,-100 19,-99 19,-99 20))",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 2043723 records from 699 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002474-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.15dv41nvs
title: Introgression, admixture and selection facilitate genetic adaptation to high-altitude environments in Chinese cattle

description: Domestication and subsequent selection of cattle to form breeds and
 biological types that can adapt to different environments partitioned
 ancestral genetic diversity into distinct modern lineages. Genome-wide
 selection particularly for adaptation to extreme environments left
 detectable signatures genome-wide. We used high-density genotype data for
 42 cattle breeds and identified the influence of Bos grunniens and Bos
 javanicus on the formation of Chinese indicine breeds that led to their
 divergence from India-origin Zebu. We also found evidence for
 introgression, admixture, and migration in most of the Chinese breeds.
 Selection signature analyses between high-altitude (&gt;1800m) and
 low-altitude adapted breeds (&lt;1500m) revealed candidate genes
 (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively
 involved in hypoxia adaptation. Immunohistochemical, real-time PCR and
 CRISPR/cas9 ACSS2-knockout analyses suggests that the up-regulation of
 ACSS2 expression in the liver promotes the metabolic adaptation of cells
 to hypoxia via the hypoxia-inducible factor pathway. High altitude
 adaptation involved the introgression of alleles from high-altitude
 adapted Yaks into Chinese B. t. taurus prior to their formation into
 recognized breeds and followed by selection. In addition to selection,
 adaptation to high altitude environments has been facilitated by admixture
 and introgression with locally adapted cattle populations.
DOI: 10.5061/dryad.fttdz08qr
title: Pollination ecology, specialization, and genetic isolation in sympatric bee pollinated Salvia (Lamiaceae)

description: Premise of research. Previous pollination ecology studies in Salvia have
 shown that there is low specialization to certain subgroups of bees and
 that pollinator number varies with species and locality. We studied twelve
 Salvia species (three clades with different corolla morphologies and
 staminal lever mechanisms) which in part co-occur and co-flower to examine
 pre-zygotic isolation mechanisms and the degree of specialization vs.
 generalization in pollination ecology. Methodology. Pollinators were
 identified using field observations, photos, and related literature across
 three sites in Turkey. Video documentation of the visitation rate and the
 site of pollen placement on the pollinator body, morphometric measurements
 between flowers and pollinators, flowering time, flower color, handling
 time, and stigma contact ratio were analyzed. Plant-pollinator networks
 were constructed. Pivotal results. Mechanical, phenological, and
 ethological isolation occur among sympatric Salvia species. Morphological
 fit is evident between flower tube length and proboscis length of main
 pollinators. Pollinator networks indicate that most species are ecological
 generalists but only few are specialists. Conclusions. The twelve Salvia
 species, though phenotypically and functionally specialized due to their
 zygomorphic-bilabiate flowers and bee pollination syndrome, differ in the
 degree of ecological specialization. Most of the sympatric Salvia species
 tend to be ecologically generalized with two or more main pollinators and
 a few additional secondary pollinators, while a few Salvia species are
 clearly specialized. Some floral traits (e.g., flower color, morphology,
 size, corolla tube length and width of corolla tube entrance, type and
 size of the staminal lever mechanism, small numbers of flowers in the
 inflorescence), short flowering time, and small population size appear
 correlated to the degree of ecological specialization.
DOI: 10.5061/dryad.66t1g1k0c
title: Soil images in DICOM format including Python programs for data transformation, 3D analysis, CNN traininig, CNN analysis

description: The 'Use of Deep Learning for structural analysis of CT-images of
 soil samples' used a set of soil sample data (CT-images). 
 All the data and programs used here are open source and were created with
 the help of open source software. All steps are made by Python programs
 which are included in the data set.
description: Please download the *.tgz and unpack them (tar -zxvf 3086.tgz).
 Then you have directories with the dataset in DICOM format.<br> To
 read this data and to transfer it into a structure suitable for training
 neural networks the program gen_cube.py must be called. This is done by
 passing parameters on the command line. To get an overview of the
 commands, type: <strong>python gen_cube.py
 -h</strong> gen_cube.py creates the directory
 'npy' and writes the generated data
 "Deutschland_3086.npy" into the directory. In
 the second step the 3D analysis of the data is performed by
 analyse3d.py <strong>python analyse3d.py
 -h</strong> explains the parameters. It needs as
 --file the Deutschland_3086.npy and with the help of --object 1,2,3,4,5,6
 or combinations of these like 1 2 the objects for the visualization can be
 chosen. mayavi is interactive and very interesting insights into the data
 can be created. The third step is the training of deep
 CNN. Here Tensorflow and opencv must be installed first (see Install.txt).
 The training takes some time without a GPU this can be more than one hour.
 The program is used: <strong>python
 ImageGenerator2_VGG16.py -h</strong> It needs
 the  Deutschland_3086.npy (or another file) created in the first step and
 an object from [1,2,3,4,5], where 5 combines the objects 5 and 6. The
 number of epochs was reduced to 10 due to time constraints, in the paper
 100 epochs were used for the training. The model parameters
 (Deutschland_3086_1.h5) and its structure (Deutschland_3086_1.yaml) are
 located in the newly created models directory. The results of the training
 are stored in the directory res (Deutschland_3086_1.dat), which was also
 created. It should be mentioned that regularization like early stoping was
 not used in the example due to the limited number of epochs. It can be
 easily added when a GPU is available. Perhaps the most
 interesting program
 "<strong>model_analyse.py</strong>" evaluates the
 results of the training and visualizes the heatmap or the partial images
 for the CNN. This can be controlled with --method heatmap or --method
 activation. Otherwise the program needs the --file Deutschland_3086.npy
 the --modell Deutschland_3086_1 (without file extension) Furthermore the
 model layer can be created from the block2_conv2, block3_conv1
 block3_conv2,... can be selected. With --slice a slice from 0..399 is
 selected in the spatial structure Deutschland_3086.npy. The parameter
 --thresh allows the adjustment of the threshold value when using the
 method activation.
DOI: 10.5061/dryad.d7wm37pzw
title: Fatigue resistant jaw muscles facilitate long-lasting courtship behavior in the southern alligator lizard (Elgaria multicarinata)

description: The southern alligator lizard (Elgaria multicarinata) exhibits a courtship
 behavior during which the male firmly grips the female’s head in his jaws
 for many hours at a time. This extreme behavior counters the conventional
 wisdom that reptile muscles are fast to fatigue and incapable of powering
 high endurance behaviors. We conducted in situ experiments in which the
 jaw-adductor muscles of lizards were stimulated directly while bite force
 was measured simultaneously with a force transducer. Fatigue tests were
 performed by supramaximally and bilaterally stimulating the muscles for
 several minutes with a series of tetanic trains. Our results show that a
 substantial sustained force gradually develops during the first few
 minutes of the fatigue test. This sustained force persists after peak
 tetanic forces have declined to a fraction of their initial magnitude. The
 observed sustained force during in situ fatigue tests is consistent with
 the natural courtship behavior of these lizards and likely reflects
 physiological specialization. The results of molecular analysis reveal
 that the jaw-adductor muscles contain masticatory myosin and tonic myosin
 fibers. We propose that the presence of tonic fibers may explain the
 unusual sustained force properties during mate-holding behavior. The
 characterization of muscle properties that facilitate extreme performance
 in specialized systems may help reveal general mechanisms, especially when
 done in light of convergently evolved systems exhibiting similar
 performance characteristics.
DOI: 10.5061/dryad.7m0cfxprw
title: The asymptotic behavior of bootstrap support values in molecular phylogenetics

description: The phylogenetic bootstrap is the most commonly used method for assessing
 statistical confidence in estimated phylogenies by non-Bayesian methods
 such as maximum parsimony and maximum likelihood (ML).  It is
 observed that bootstrap support tends to be high in large genomic datasets
 whether or not the inferred trees and clades are correct. Here we study
 the asymptotic behavior of bootstrap support for the ML tree in
 large datasets when the competing phylogenetic trees are equally
 right or equally wrong.  We consider phylogenetic reconstruction
 as a problem of statistical model selection when the compared
 models are nonnested and misspecified. The bootstrap is found to
 have qualitatively different dynamics from Bayesian inference,
 and does not exhibit the polarized behavior of posterior model
 probabilities, consistent with the empirical observation that the
 bootstrap is more conservative than Bayesian probabilities. Nevertheless
 bootstrap support similarly shows fluctuations among large datasets, with
 no convergence to a point value, when the compared models are equally
 right or equally wrong. Thus in large datasets strong support for wrong
 trees or models is likely to occur. Our analysis provides a partial
 explanation for the high bootstrap support values for incorrect clades
 observed in empirical data analysis.
DOI: 10.5061/dryad.x3ffbg7gn
title: Environmental drivers of plant distributions at global and regional scales: occurrence data with associated environmental variables of plant families/genera/species

description: How environmental factors drive plant distribution across globe is one of
 the most fundamental questions in ecology. Plant
 distributions may be shaped by various environmental factors,
 such as climate, topography and edaphic factors. Nevertheless, it is not
 clear about the relative importance of different environmental factors in
 driving plant distribution across spatial scales and among plant groups.
 This study aimed to disentangle how plant–environment
 relationships vary with latitude and among plant taxa including
 angiosperms, gymnosperms, pteridophytes and bryophytes. Location: Global
 Main taxa: Plants Results: Our analyses revealed the primacy of climatic
 variability (temperature seasonality and isothermality) on plant
 distribution at the global scale. The relative contribution of
 temperature
 seasonality and isothermality peaked in
 tropical areas, whereas solar radiation and annual mean temperature had
 stronger influence at high-latitude areas. We also found
 wide-range plant groups tend to occur at area with higher temperature
 variability (isothermality and temperature
 seasonality) and flatter terrain (low slope). Climate
 extremes (low temperature and low solar radiation)
 determined plant distribution range and limits across
 latitude. Soil and topography had diverse thought less
 important effects (related to climate) on broad-scale
 plant distribution patterns. Main Conclusions: Our study
 highlights the significance of climate variability for global
 plant distributions and climate extremes at higher latitude areas.
 Environmental effects of plant distributions vary across latitude. The
 findings imply that our understandings on environmental factors
 affecting plant distributions rely on the geographical scales
 that we focus on, suggesting that different geographcial and local
 ecological processes should be integrated to explain multi-scale
 distribution patterns.
description: We collected global distribution occurrence data of plant groups
 (625 families, 6,221 genera, and 54,101 species) from GBIF database. We
 used random forest to quantify the relative importance of 15 environmental
 factors (including climate, soil and topography) on plant distributions at
 global and regional scales (divided into different latitude zones). We
 also used phylogenetic general least square (PGLS) models to investigate
 the relationship between environmental variables and geographical range
 size, latitudinal range and limits of plants at the global
 scale.
DOI: 10.5061/dryad.vx0k6djpn
title: Anoxia hormesis in cactus moth

description: As part of Sterile Insect Technique (SIT) programs, irradiation can
 effectively induce sterility in insects by damaging germline genomic DNA.
 However, irradiation also induces other off-target side effects that
 reduce the quality and performance of sterilized males, including the
 formation of damaging free radicals that can reduce sterile male
 performance. Thus, treatments that reduce off-target effects of
 irradiation on male performance while maintaining sterility can improve
 the feasibility and economy of SIT programs. We previously found that
 inducing a form of rapid, beneficial plasticity with a one-hour anoxic
 conditioning period (physiological conditioning hormesis) prior to and
 during irradiation improves male field performance in the laboratory while
 maintaining sterility in males of the cactus moth, Cactoblastis cactorum.
 Here we extend this work by testing the extent to which this beneficial
 plasticity may improve male field performance in the field. Based on
 capture rates after a series of mark release-recapture experiments, we
 found that anoxia-conditioned irradiated moths were active in the field
 longer than their irradiated counterparts. In addition, anoxia-conditioned
 moths were captured in traps that were farther away from the release site
 than unconditioned moths, suggesting greater dispersal. These data
 confirmed that beneficial plasticity induced by anoxia hormesis prior to
 irradiation led to lower post-irradiation damage and increased performance
 in field conditions. We recommend greater consideration of
 beneficial plasticity responses in biological control programs, and
 specifically the implementation of anoxia-conditioning treatments applied
 prior to irradiation in area-wide integrated pest management programs that
 use SIT.
DOI: 10.7272/q6tt4p5t
title: Impaired therapeutic efficacy of bone marrow cells from post-myocardial infarction patients in the TIME and lateTIME clinical trials

description: Implantation of bone marrow-derived cells (BMCs) into mouse hearts
 post-myocardial infarction (MI) limits cardiac functional decline.
 However, clinical trials of post-MI BMC therapy have yielded conflicting
 results. While most laboratory experiments use healthy BMC donor mice,
 clinical trials use post-MI autologous BMCs. Post-MI mouse BMCs are
 therapeutically impaired, due to inflammatory changes in BMC composition.
 Thus, therapeutic efficacy of the BMCs progressively worsens after MI but
 recovers as donor inflammatory response resolves. The availability of
 post-MI patient BM mononuclear cells (MNCs) from the TIME and LateTIME
 clinical trials enabled us to test if human post-MI MNCs undergo a similar
 period of impaired efficacy. We hypothesized that MNCs from TIME trial
 patients would be less therapeutic than healthy human donor MNCs when
 implanted into post-MI mouse hearts, and that therapeutic properties would
 be restored in MNCs from LateTIME trial patients. Post-MI SCID mice
 received MNCs from healthy donors, TIME patients, or LateTIME patients.
 Cardiac function improved considerably in the healthy donor group, but
 neither the TIME nor LateTIME group showed therapeutic effect. Conclusion:
 post-MI human MNCs lack therapeutic benefits possessed by healthy MNCs,
 which may partially explain why BMC clinical trials have been less
 successful than mouse studies.
description: Use Vevo ultrasound analysis software for viewing .vsi images and
 videos.