cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rv15dv4dg
title: Effects of litter quality on foraging behaviour and demographic parameters in Folsomia candida (Collembola)

description: Litter quality has long been associated with demographic parameters of
 Collembola populations. However, little is known about the capacity of
 Collembola to perceive and seek better litter quality. To address this
 gap, three complementary laboratory experiments were carried out with the
 Collembola Folsomia candida. First, populations were fed on three
 different types of leaf litters (Quercus pubescens, Acer opalus and Prunus
 avium) and a control (agar-agar-brewer’s yeast mixture) for six weeks to
 assess their impacts on demography (reproduction rate and population
 size). Second, the body length of individuals differentially fed with the
 same four types of resources was measured to assess a functional trait
 that can potentially affect movement parameters such as prospected area or
 foraging speed. Third, F. candida isolated individuals were exposed to the
 same litter quality gradient and placed at increasing distances from the
 litter (from 1 to 5 cm). For ten minutes, their foraging behaviours were
 recorded which included their prospected area, foraging speed, perception
 distance and success in reaching the litter (foraging success). As
 expected, low-quality litter (i.e., Q. pubescens) contributed to low
 population growth compared to the control treatment and the high-quality
 litters (P. avium and A. opalus). In the third experiment, the probability
 of finding the resource was negatively correlated to the distance but was
 unrelated to the litter quality and the Collembola body length. When
 resource was perceived, F. candida was able to switch from non-directional
 to directional movements, with a large variability in the perception
 distance from a few millimeters to several centimeters. Taken together,
 our results indicate that litter quality plays a relevant role on
 Collembola demographic parameters once the population settles on litter
 patch, but not on foraging behaviour to select high-quality resources.
DOI: 10.5281/zenodo.18404205
title: MESA inlist for "On the contradictory case of the binary system HD 81809 hosting two pulsating solar-like stars observed by TESS"

description: This inlist contains the physics inputs to compute the models in the paper "On the contradictory case of the binary system HD 81809 hosting two pulsating solar-like stars observed by TESS"

The models were computed with MESAS version: mesa-r12778.

The implementation of the SVP routine for radiative acceleration is available in https://zenodo.org/records/14678036
DOI: 10.5281/zenodo.18399940
title: MESA inlist for "On the contradictory case of the binary system HD 81809 hosting two pulsating solar-like stars observed by TESS"

description: This inlist contains the physics inputs to compute the models in the paper "On the contradictory case of the binary system HD 81809 hosting two pulsating solar-like stars observed by TESS"

The models were computed with MESAS version: mesa-r12778.

The implementation of the SVP routine for radiative acceleration is available in https://zenodo.org/records/14678036
DOI: 10.5061/dryad.69p8cz96z
title: Trait value of Stipa krylovii populations in control and drought treatments

description: Understanding patterns of intraspecific trait variation can help us
 understand plant adaptability to environmental changes. To explore the
 underlying adaptation mechanisms of zonal plant species, we selected seven
 populations of Stipa krylovii, a dominant species in the Inner
 Mongolia Steppe of China, and evaluated the effects of phenotypic
 plasticity and genetic differentiation, the effects of climate variables
 on population trait differentiation, and traits coordinated patterns under
 each soil moisture treatment. We selected seeds from seven populations of
 S. krylovii in the Inner Mongolia Steppe, China, and carried out a soil
 moisture (2) × population origin (7) common garden experiment at Tianjin
 City, China, and measured ten plant traits of S. krylovii.
 General linear analyses were used to analyze how soil moisture and
 population origin affect each trait variation, Mantel tests were used to
 analyze population trait differentiation - geographic distance (or
 climatic difference) relationships, regression analyses were used to
 evaluate the trait-climatic variable relationships, and plant trait
 networks (PTNs) were used to evaluate the traits coordinated patterns.
 Both soil moisture and population origin showed significant effects on
 most of the traits. Aboveground biomass, root-shoot ratio, leaf width,
 specific leaf area, and leaf nitrogen (N) content were significantly
 correlated with climate variables under the control condition. Specific
 leaf area and leaf N content were significantly correlated with climate
 variables under drought conditions. By PTNs, the hub trait(s) was plant
 height under the control treatment and were aboveground biomass, root
 length, and specific leaf area under drought conditions. This study
 indicates that both phenotypic plasticity and genetic differentiation can
 significantly affect the adaptability of S. krylovii. In addition, soil
 moisture treatments show significant effects on trait-climate
 relationships and trait-coordinated patterns. These findings provide new
 insights into the adaptive mechanisms of zonal species in the semi-arid
 grassland region.
description: # Trait value of *Stipa krylovii* populations in control and drought
 treatment. *** Original measurement data of 10 traits in 7 populations of
 *Stipa krylovii* in a soil moisture (2) × population origin (7) common
 garden experiment. In the data cell, only 7 samples were set up to
 specific leaf area and Leaf N content, so “null” means no measurement data
 here. The sample size was set to 10 for all other traits (initial tiller
 number, plant height, length of root, aboveground biomass, belowground
 biomass, specific root length, Root-shoot ratio, leaf length, leaf width),
 so "n/a" means the measurement data missing.
DOI: 10.5061/dryad.mkkwh715m
title: Data from: Navigating Polycrisis: long-run socio-cultural factors shape response to changing climate

description: These data are part of a data portal that accompanies the special issue
 ‘Climate change adaptation needs a science of culture,’ published in
 Philosophical Transactions of the Royal Society B in 2023. To access the
 data portal, please visit 10.5061/dryad.bnzs7h4h4. We have systematically
 collected information about the nature and consequences of societal crisis
 in over 150 cases covering different regions in the world in the
 preindustrial period. In this contribution, we discuss some critical
 insights arising from initial analysis of this material, which has
 informed the basis of our work.
description: Our data has been systematically and thoroughly researched
 through a multitude of sources including scholarly publications, social
 datasets, archeological information, and government organisations. The
 research that has been undertaken has employed a unique combination of
 quantitative and qualitative approaches to the study of history. This
 method of applying quantitative 'big data' tracking across more
 than 150 cases of crisis periods allows us to analyse macro-level patterns
 across polities spanning from the Neolithic to the pre-industrial world
 and covering a wide sample of global regions. For this
 publication, we have applied the following 'crisis' variables to
 inform our data: decline, collapse, epidemic, downward mobility,
 extermination, uprising, civil war, century plus, fragmentation, capital,
 conquest, assassination, and deposition. The variables have been coded on
 a present-absent scale as follows: 1 (present), 0 (absent), 1.inf
 (inferred present), 0.inf (inferred absent), U.susp (unknown).
 Forthcoming work by the Seshat: Global Databank will delve more
 deeply into the patterns revealed by the wider data.
DOI: 10.5061/dryad.b8gtht7jf
title: Mapping SARS-CoV-2 antigenic relationships and serological responses

description: During the SARS-CoV-2 pandemic, multiple variants escaping pre-existing
 immunity emerged, causing concerns about continued protection. Here, we
 use antigenic cartography to analyze patterns of cross-reactivity among a
 panel of 21 variants and 15 groups of human sera obtained following
 primary infection with 10 different variants or after mRNA-1273 or
 mRNA-1273.351 vaccination. We find antigenic differences among pre-Omicron
 variants caused by substitutions at spike protein positions 417, 452, 484,
 and 501. Quantifying changes in response breadth over time and with
 additional vaccine doses, our results show the largest increase between 4
 weeks and &gt;3 months post-2nd dose. We find changes in
 immunodominance of different spike regions depending on the variant an
 individual was first exposed to, with implications for variant risk
 assessment and vaccine strain selection.
DOI: 10.5061/dryad.866t1g1wj
title: Data for: RNA-Seq dataset of RBL-2H3 (RPKM)

description: The coordination between actin and microtubule network is crucial, yet our
 understanding of the underlying mechanisms remains limited. In this study,
 we used travelling waves in the cell cortex to characterize the collective
 dynamics of cytoskeletal networks. Our findings show that Cdc42 and
 F-BAR-dependent actin waves in mast cells are mainly driven by
 formin-mediated actin polymerization, with the microtubule-binding formin
 FH2 domain-containing protein 1 (FHDC1) as an early regulator. FHDC1, as
 well as its interaction with microtubule is required for actin waves. In
 addition, the phase of microtubule depolymerization coincides with the
 nucleation of actin waves and microtubule stabilization inhibit actin
 waves, leading us to propose that microtubule shrinking and the concurrent
 release of FHDC1 locally regulate actin nucleation. Lastly, we show that
 FHDC1 is crucial for multiple cellular processes such as cell division and
 migration. Our data provided molecular insights into the nucleation
 mechanisms of actin waves and uncover an antagonistic interplay between
 microtubule and actin polymerization in their collective dynamics.
description: RNA-Seq data for RBL-2H3 cells. [1]Content Introduction: The coverage of
 each gene, expression of gene(RPKM), total number of reads that aligned to
 gene, the description of gene are provided in this analysis. [2]format
 description: RNA-Seq results are presented in xlsx table, named
 \*.Gene.rpkm.xlsx, each independent sample correspond to a xls file. The
 meanings of each column are as follow: Column A: GeneID. Column B:
 Uniq\_reads\_num(\*\*\*\*). This provides the number of reads which are
 aligned to just one position of gene. The total uniq\_reads is shown in
 the parentheses in Cell B1. Here, we refer to all genes and not the
 transcriptome. One gene can correspond to several transcripts. Column C:
 Length of gene. Column D: Coverage. This provides the coverage of gene. It
 is derived by base number of all Uniq\_reads in the gene/the base number
 of gene. Column E: RPKM. This provides the transcript expression levels.
 Column F: KEGG Orthology. Column G: GO Component. Column H: GO Function.
 Column I: GO Process. Column J: BLAST NR. The symbol "-" in
 cells indicates that no matches were found in the respective database.
DOI: 10.5061/dryad.pc866t1vd
title: A public mid-density genotyping platform for alfalfa (Medicago sativa L.)

description: Small public breeding programs have many barriers to adopting technology,
 particularly creating, and using genetic marker panels for genomic-based
 decisions in selection.  Here we report the creation of a DArTag
 panel of 3,000 loci distributed across the alfalfa genome for use in
 molecular breeding and genomic prediction. The creation of this marker
 panel brings cost-effective and rapid genotyping capabilities to public
 breeding programs.  The open access provided by this platform
 will allow genetic data sets generated on the marker panel to be compared
 and joined across projects, institutions, and countries. This genotyping
 resource has the power to bring genotyping equity to breeders in
 alfalfa.  This is the first installment of a series of papers on
 creating affordable public genotyping resources for underserved
 agricultural plant and animal species.
description: The
 haplotype fasta file was created by aggregating microhaplotypes discovered
 in various alfalfa populations, germplasms, and its wild relatives using a
 3K DArTag genotyping marker panel. This alfalfa 3K DArTag panel was
 developed from a diversity panel of 40 alfalfa genotypes, focusing on
 elite breeding and stress-resistant genotypes used in North America. This
 panel consisted of 17 elite parents with various fall dormancy levels, six
 samples of diploid-cultivated alfalfa, 13 genotypes with abiotic stress
 resistance, one genotype with Aphanomyces root rot disease resistance, and
 three other genotypes.
description: The haplotype FASTA file can be opened with any text editor or
 linux command line. The readme file can be opened with any text
 editor.
DOI: 10.5061/dryad.6t1g1jx4j
title: Metallic behavior of T-graphene nanotubes

description: The band structure, density of states (DOS), and Pauli magnetic
 susceptibility (PMS) of T-graphene nanotubes (TGNT) with diﬀerent
 chiralities and diameters are investigated using the tight-binding
 Hamiltonian model and the Green’s function formalism. Two various edges
 are considered: zigzag and armchair (zTGNT and aTGNT). Both types of TGNTs
 show metallic behaviors regardless of their diameter. Additionally, Dirac
 points are observed in the band structure of aTGNTs, with their number
 increasing as the diameter of the nanotubes increases. Furthermore, with
 increasing the diameter of the tubes, additional sub-bands and van-Hove
 singularities appear in the band structure and DOS diagrams, respectively.
 As a result, the PMS curves exhibit a crossover and can be divided into
 two parts at diﬀerent temperature ranges, namely high- and
 low-temperature. The metallic properties of both types of TGNTs are also
 demonstrated in the PMS curves, which is due to the proportionality of PMS
 with the DOS. Moreover, the convergence of the DOS curves towards the
 monolayer is clearly evident as the diameter of both types of TGNT
 increases to signiﬁcant values.
description: Computational codes have been provided in the Fortran 90, and we
 have computed the eigenvalues of matrices and the band structures
 numerically using the LAPACK library. The data file contains two folders
 of zig zag and armchair T-graphene nanotube data. In each folder, there
 are three data files of band structure, DOS, and PMS for each
 diameter.
DOI: 10.5061/dryad.5x69p8d90
title: Precision agricultural data and ecosystem services: can we put the pieces together?

description: Ecosystem services can maintain or increase crop yield in agricultural
 systems, but data to support management decisions is expensive and
 time-consuming to collect. Furthermore, relationships derived from
 small-scale plot data may not apply to ecosystem services operating at
 larger spatial scales (fields, landscapes). Precision yield data can be
 used to improve the accuracy and geographic range of ecosystem service
 studies, but have been underused in previous studies: out of 370
 literature records, we found that less than 2% of all records were used to
 study biotic or landscape effects on yield. We argue that this is likely
 due to low data accessibility and a lack of familiarity with spatial data
 analysis. We provide examples of analysis using simulated and real
 precision yield data and outline two case studies of ecosystem services
 using precision yield data. Ecologists and agronomists should consider
 using precision yield data more broadly, as it can be used to test
 hypotheses about ecosystem services across multiple spatial scales, and
 could be used to inform the design of multifunctional farming landscapes.
description: The combined yield monitor data for Supplemental 1
 was donated by Trent Clark (the absolution location of the spatial data
 has been anonymized for privacy). Supplemental 2 uses
 entirely generated data (see script for details).
 Supplemental 3 uses a correlation matrix created from
 unpublished yield data collected by Hector Cárcamo.
description: All scripts were written in RMarkdown (Allaire et al 2023) using
 R version 4.3.1 (R Core Team 2023).<br><br>Allaire J, Xie Y,
 Dervieux C, McPherson J, Luraschi J, Ushey K, Atkins A, Wickham H, Cheng
 J, Chang W, Iannone R (2023). <em>rmarkdown: Dynamic Documents for
 R</em>. R package version 2.22, https://github.com/rstudio/rmarkdown.  R Core Team (2023). <em>R: A Language and Environment for Statistical Computing</em>. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
DOI: 10.5061/dryad.zkh1893fv
title: Mysterious microsporidians: springtime outbreaks of disease in Daphnia communities in shallow pond ecosystems

description: Parasites can play key roles in ecosystems, especially when they infect
 common hosts that play important ecological roles. Daphnia are critical
 grazers in many lentic freshwater ecosystems and typically reach peak
 densities in early spring. Daphnia have also become prominent model host
 organisms for the field of disease ecology, although most well-studied
 parasites infect them in summer or fall. Here, we report field patterns of
 virulent microsporidian parasites that consistently infect Daphnia in
 springtime, in a set of seven shallow ponds in Georgia, USA, sampled every
 3–4 weeks for 18 months. We detected two distinct parasite taxa, closely
 matching sequences of Pseudoberwaldia daphniae and Conglomerata obtusa,
 both infecting all three resident species of Daphnia: D. ambigua, D.
 laevis, and D. parvula. To our knowledge, neither parasite has been
 previously reported in any of these host species or anywhere in North
 America. Infection prevalence peaked consistently in February-May, but the
 severity of these outbreaks differed substantially among ponds. Moreover,
 host species differed markedly in terms of their maximum infection
 prevalence (5% [D. parvula] to 72% [D. laevis]), mean reduction of
 fecundity when infected (70.6% [D. ambigua] to 99.8% [D. laevis]), mean
 spore yield (62,000 [D. parvula] to 377,000 [D. laevis] per host), and
 likelihood of being infected by each parasite. The timing and severity of
 the outbreaks suggest that these parasites could be impactful members of
 these shallow freshwater ecosystems and that the strength of their effects
 is likely to hinge on the composition of ponds' zooplankton
 communities.
DOI: 10.15468/dl.ydszp2
title: Occurrence Download

description: A dataset containing 2823 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Furcraea foetida)",
 "OccurrenceStatus is Present",
 "SpeciesKey is not null",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2026",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)"
 ]
}

 The dataset includes 2823 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003592-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5068/d1339f
title: Data files associated with: Evolution of the mutation spectrum across a mammalian phylogeny

description: Although evolutionary biologists have long theorized that variation in DNA
 repair efficacy might explain some of the diversity of lifespan and cancer
 incidence across species, we have little data on the variability of normal
 germline mutagenesis outside of humans. Here, we shed light on the
 spectrum and etiology of mutagenesis across mammals by quantifying
 mutational sequence context biases using polymorphism data from thirteen
 species of mice, apes, bears, wolves, and cetaceans. After normalizing the
 mutation spectrum for reference genome accessibility and k-mer content, we
 use the Mantel test to deduce that mutation spectrum divergence is highly
 correlated with genetic divergence between species, whereas life history
 traits like reproductive age are weaker predictors of mutation spectrum
 divergence. Potential bioinformatic confounders are only weakly related to
 a small set of mutation spectrum features. We find that clocklike
 mutational signatures previously inferred from human cancers cannot
 explain the phylogenetic signal exhibited by the mammalian mutation
 spectrum, despite the ability of these clocklike signatures to fit each
 species’ 3-mer spectrum with high cosine similarity. In contrast, parental
 aging signatures inferred from human de novo mutation data appear to
 explain much of the mutation spectrum’s phylogenetic signal when fit to
 non-context-dependent mutation spectrum data in combination with a novel
 mutational signature. We posit that future models purporting to explain
 the etiology of mammalian mutagenesis need to capture the fact that more
 closely related species have more similar mutation spectra; a model that
 fits each marginal spectrum with high cosine similarity is not guaranteed
 to capture this hierarchy of mutation spectrum variation among species.
description: Mutation spectra were generated based on publicly-available whole
 genome sequencing polymorphism data (VCF format) from 13 mammal species
 (house mouse, Algerian mouse, humans, Bornean orangutan, Sumatran
 orangutan, chimpanzee, gorilla, bonobo, gray wolf, polar bear, brown bear,
 vaquita porpoise, and fin whale).  Spectra were
 generated for each species at the 1-mer, 3-mer, 5-mer and 7-mer level
 using the program mutyper and a pipeline that is described extensively in
 the paper's SI Methods section and on the project's GitHub
 repository (https://github.com/harrispopgen/mammal_mutation_spectra/). Data files are described in depth in the Dryad repository's README file.
description: All code that was used to process the data, carry out analyses,
 and generate figures is on the projects GitHub repository (https://github.com/harrispopgen/mammal_mutation_spectra/).
DOI: 10.34740/kaggle/dsv/14653595
title: Mahanagar Yatayat Transport Dataset