cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t1g1jx2z
title: Data for: Implications of plant N/P stoichiometry influenced by arbuscular mycorrhizal fungi for stability of plant species and community in response to nutrient limitation

description: Arbuscular mycorrhizal fungi (AMF) influence plant nitrogen/phosphorus
 (N/P) by modifying plant N and P uptake, which further affects plant
 stoichiometric N/P homeostasis. Plant species and community stoichiometric
 N/P homeostasis can impact plant species and community stability,
 respectively, in response to variations of soil N and P availabilities. We
 investigated interspecific plant interactions via AMF in regard to plant
 and soil microbial N/P stoichiometry across different soil N and P
 availabilities induced by N and P addition (0 mg N kg-1, 25 mg N kg-1, 50
 mg N kg-1, 30 mg P kg-1, and 100 mg P kg-1). We selected one dominant
 (Bothriochloa ischaemum; C4 grass) and one subordinate (Lespedeza
 davurica; legume) species in a natural grassland climax community. We
 examined how AMF influences stoichiometric N/P homeostasis in monoculture
 and mixed culture systems, and the resulting consequences for temporal
 stability of plant species and community in response to variations in soil
 N and P availability. The AMF mitigated the P limitation of soil microbial
 communities and decreased the degree of stoichiometric N/P homeostasis of
 host plants in monoculture. Through their resource-scavenging and soil
 organic matter mineralisation functions, AMF enhances plant ‘luxury
 consumption’, promoting species stability in monoculture in response to
 soil N and P availability variations. Compared with plants in monoculture,
 the interaction between B. ischaemum and L. davurica via AMF increased
 shoot N/P under soil N-poor conditions, leading to an enhanced degree of
 stoichiometric N/P homeostasis in both plant species, especially the
 legume. Our results suggest that interspecific plant interaction between
 C4 grass and legume mediated by AMF confers an advantage in
 complementarity in plant N acquisition under N-poor conditions, leading to
 increased stability of plant communities and better maintenance of
 subordinate species (legume) in response to soil N deficiency.
DOI: 10.5061/dryad.8kprr4xs0
title: Data from: Hedging at the rear edge: Intraspecific trait variability drives the trajectory of marginal populations in a widespread boreal tree species

description: Rear-edge populations at the warm margin of species distribution are
 small, isolated and face environmental conditions at the limit of species
 bioclimatic envelope. Intraspecific phenotypic variation contributing to
 the persistence of peripheral populations is expected to become
 increasingly important under future climate conditions in order to avoid
 local extirpation where range shifts lag behind climate change velocity.
 We investigated the putative role of intraspecific phenotypic variation
 for the maintenance of rear-edge populations of fire-prone jack pine
 (Pinus banksiana), an obligate pyriscent boreal species. We assessed
 whether variation in cone serotiny is associated with the population
 trajectory of marginal stands located south of the boreal biome, in the
 temperate forest where natural wildfires are infrequent and unpredictable.
 To this end, we estimated stand-scale serotiny, minimal age and tree size
 structure in 26 jack pine stands from the rear edge (n = 17 sites) and the
 core (n = 9 sites) of the species’ range in eastern Canada. On average,
 rear-edge jack pine populations are less serotinous albeit more variably
 compared to range-core populations where serotiny is more uniformly high.
 Rear-edge stands are generally older and display reverse J-shape tree size
 structure indicative of a multi-aged demographic equilibrium, whereas
 range-core stands are younger and show a unimodal stand structure
 depicting a single aging cohort generally lacking interfire recruitment.
 Eco-evolutionary dynamics shifts from a dependency on wildfires in
 range-core populations to stands that can regenerate and persist without
 recurrent fires at the rear edge, where stand-scale serotiny reaches
 values below 85%. Synthesis: Unlike range-core populations, rear-edge jack
 pine populations can locally rely on a dual life-history strategy to
 ensure both steady recruitment during fire-free intervals and successful
 postfire regeneration. This capacity to cope with infrequent and
 unpredictable fire regime should increase the resilience and resistance of
 jack pine populations as global changes alter fire dynamics of the boreal
 forest. More generally, unique intraspecific phenotypic variation in
 rear-edge populations contributes to long-term species persistence in
 marginal environmental conditions that might scale up with global changes.
 The conservation of rear-edge populations and their genetic legacy appears
 crucial for the resilience of species.
DOI: 10.34740/kaggle/dsv/14651419
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.8cpyrf
title: Occurrence Download

description: A dataset containing 47733 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus"
 ]
}

 The dataset includes 47733 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003364-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v8cuk5
title: Occurrence Download

description: A dataset containing 2671572 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Macro-moth distribution records for the UK from Butterfly Conservation, up to 2019",
 "TaxonKey is Erebidae",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 2671572 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003356-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0p2ngf24z
title: Genomic relationships of Glycine remota, a recently discovered perennial relative of soybean, within the legume genus Glycine

description: The legume genus, Glycine, which includes the Asian annual cultivated
 soybean, also includes a group of Australian perennial species comprising
 the subgenus Glycine. Because the subgenus Glycine represents the tertiary
 gene pool for one of the world’s most important crops, the group has been
 the target of collection and study for decades, resulting in a steady
 growth in the number of formally recognized species, from six in the 1970s
 to over 20 at present, as well as a number of additional informal taxa.
 These studies have also produced a system of nuclear diploid “genome
 groups” corresponding to clades in molecular phylogenies. The aptly named
 G. remota is known only from a single isolated population in the Kimberley
 region of northwestern Australia and was named only in 2015. The species
 is unique within Glycine in having unifoliolate leaves; its discoverers
 hypothesized that G. remota, if diploid, is related to species of the
 I-genome that are also native to the Kimberley region. We produced
 low-coverage short-read genome sequencing data from an herbarium specimen
 of G. remota. Genome size estimates from the sequencing data suggest that
 G. remota is a diploid, while ploidy estimation is inconclusive likely due
 to the history of whole genome duplication in Glycine. Phylogenomic
 analyses of genome-wide SNPs, as well as phylogenetic analyses of the low
 copy nuclear gene (histone H3D), the entire ribosomal RNA cistron, and the
 internal transcribed spacer all placed the species unequivocally in the
 diploid I-genome clade. A complete plastome sequence was also generated
 and its placement with a plastome phylogeny is also consistent with
 membership in the I-genome.
description: GBS-SNPs called wtih GATK and filtered with VCFtools
 Fasta files aligned with MAFFT Maximum
 likelihood phylogeny inference with RAxML SVDquartets
 in PAUP* ABBA-BABA in D-suite
DOI: 10.5061/dryad.70rxwdc2d
title: Apparent thermal acclimation of soil heterotrophic respiration mainly mediated by substrate availability

description: Multiple lines of existing evidence suggest that increasing CO2 emission
 from soils in response to rising temperatures could accelerate global
 warming. However, in experimental studies, the initial positive response
 of soil heterotrophic respiration (RH) to warming often weakens over time
 (referred to apparent thermal acclimation). If the decreased RH is driven
 by the thermal adaptation of soil microbial community, the potential for
 soil carbon (C) losses would be reduced substantially. In the meanwhile,
 the response could equally be caused by substrate depletion, and would
 then reflect the gradual loss of soil C. To address uncertainties
 regarding the causes of apparent thermal acclimation, we carried out
 sterilization and inoculation experiments using the soil samples from an
 alpine meadow with 6-years of warming and nitrogen (N) addition. We
 demonstrate that substrate depletion, rather than microbial adaptation,
 determined the response of RH to long-term warming. Furthermore, N
 addition appeared to alleviate the apparent acclimation of RH to warming.
 Our study provides strong empirical support for substrate availability
 being the cause of the apparent acclimation of soil microbial respiration
 to temperature. Thus, these mechanistic insights could facilitate efforts
 of biogeochemical modeling to accurately project soil C stocks in the
 future climate.
DOI: 10.5061/dryad.mcvdnck4j
title: Interspecific differences in thermal tolerance landscape explain aphid community abundance under climate change

description: A single critical thermal limit is often used to explain and infer the
 impact of climate change on geographic range and population
 abundance. However, it has limited application in describing the temporal
 dynamic and cumulative impacts of extreme temperatures. Here, we
 used a thermal tolerance landscape approach to address the
 impacts of extreme thermal events on the survival of co-existing
 aphid species (Metopolophium dirhodum, Sitobion avenae and
 Rhopalosiphum padi). Specifically, we built the thermal death time (TDT)
 models based on detailed survival datasets of three aphid species
 with three ages across a broad range of stressful high (34–40 ÅãC) and
 low (−3∼-11 ÅãC) temperatures to compare the interspecific and
 developmental stage variations in thermal tolerance. Using these
 TDT parameters, we performed a thermal risk assessment by calculating the
 potential daily thermal injury accumulation associated with the
 regional temperature variations in three wheat-growing sites along a
 latitude gradient. Results showed that M. dirhodum was the most
 vulnerable to heat but more tolerant to low temperatures than R.
 padi and S. avenae. R. padi survived better at high temperatures than
 Sitobion avenae and M. dirhodum but was sensitive to cold. R.
 padi was estimated to accumulate higher cold injury than the other
 two species during winter, while M. dirhodum accrued more heat
 injury during summer. The warmer site had higher risks of heat
 injury and the cooler site had higher risks of cold injury along a
 latitude gradient. These results support recent field
 observations that the proportion of R. padi increases with the increased
 frequency of heat waves. We also found that young nymphs
 generally had a lower thermal tolerance than old nymphs or adults. Our
 results provide a useful dataset and method for modelling and
 predicting the consequence of climate change on the
 population dynamics and community structure of small insects.
description: Please see the README document
 ("README_Dataset-AphidThermalToleranceLandscape.md" )  and the
 accompanying published article:  Li, Y.-J., S.-Y. Chen, L. B. Jørgensen,
 J. Overgaard, D. Renault, H. Colinet, and C.-S. Ma. 2023. Interspecific
 differences in thermal tolerance landscape explain aphid community
 abundance under climate change. Journal of Thermal
 Biology:103583.
DOI: 10.5061/dryad.zgmsbccg7
title: Data for: Advances and critical assessment of machine learning techniques for prediction of docking scores

description: Semi-flexible docking was performed using AutoDock Vina 1.2.2 software on
 the SARS-CoV-2 main protease Mpro (PDB ID: 6WQF). Two data sets are
 provided in the xyz format containing the AutoDock Vina docking scores.
 These files were used as input and/or reference in the machine learning
 models using TensorFlow, XGBoost, and SchNetPack to study their docking
 scores prediction capability. The first data set originally contained
 60,411 in-vivo labeled compounds selected for the training of ML models.
 The second data set,denoted as in-vitro-only, originally contained 175,696
 compounds active or assumed to be active at 10 μM or less in a direct
 binding assay. These sets were downloaded on the 10th of December 2021
 from the ZINC15 database. Four compounds in the in-vivo set and 12 in the
 in-vitro-only set were left out of consideration due to presence of Si
 atoms. Compounds with no charges assigned in mol2 files were excluded as
 well (523 compounds in the in-vivo and 1,666 in the in-vitro-only set).
 Gasteiger charges were reassigned to the remaining compounds using
 OpenBabel. In addition, four in-vitro-only compounds with docking scores
 greater than 1 kcal/mol have been rejected. The provided in-vivo and the
 in-vitro-only sets contain 59,884 (in-vivo.xyz) and 174,014
 (in-vitro-only.xyz) compounds, respectively. Compounds in both sets
 contain the following elements: H, C, N, O, F, P, S, Cl, Br, and I. The
 in-vivo compound set was used as the primary data set for the training of
 the ML models in the referencing study. The file in-vivo-splits-data.csv
 contains the exact composition of all (random) 80-5-15
 train-validation-test splits used in the study, labeled I, II, III, IV,
 and V. Eight additional random subsets in each of the in-vivo 80-5-15
 splits were created to monitor the training process convergence. These
 subsets were constructed in such a manner, that each subset contains all
 compounds from the previous subset (starting with the 10-5-15 subset) and
 was enlarged by one eighth of the entire (80-5-15) train set of a given
 split. These subsets are further referred to as in_vivo_10_(I, II, ...,
 V), in_vivo_20_(I, II, ..., V),..., in_vivo_80_(I, II, ... V).
description: Molecular docking calculations and the machine learning
 approaches are described in the Computational details section of
 [1]. Reference<br>[1] Lukas Bucinsky, Marián
 Gall, Ján Matúška, Michal Pitoňák, Marek Štekláč. Advances and critical
 assessment of machine learning techniques for prediction of docking
 scores. Int. J. Quantum. Chem. (2023) DOI: 10.1002/qua.27110.
DOI: 10.5061/dryad.63xsj3v60
title: Combined measures of mimetic fidelity explain imperfect mimicry in a brood parasite–host system

description: The persistence of imperfect mimicry in nature presents a challenge to
 mimicry theory. Some hypotheses for the existence of imperfect mimicry
 make differing predictions depending on how mimetic fidelity is measured.
 Here, we measure mimetic fidelity in a brood parasite–host system using
 both trait-based and response-based measures of mimetic fidelity. Cuckoo
 finches Anomalospiza imberbis lay imperfectly mimetic eggs that lack the
 fine scribbling characteristic of eggs of the tawny-flanked prinia Prinia
 subflava, a common host species. A trait-based discriminant analysis based
 on Minkowski functionals—that use geometric and topological morphometric
 methods related to egg pattern shape and coverage—reflects this consistent
 difference between host and parasite eggs. These methods could be applied
 to quantify other phenotypes including stripes and waved patterns.
 Furthermore, by painting scribbles onto cuckoo finch eggs and testing
 their rate of rejection compared to control eggs (i.e. a response-based
 approach to quantify mimetic fidelity), we show that prinias do not
 discriminate between eggs based on the absence of scribbles. Overall, our
 results support relaxed selection on cuckoo finches to mimic scribbles,
 since prinias do not respond differently to eggs with and without
 scribbles, despite the existence of this consistent trait difference.
description: The dataset consists of pattern metrics extracted from egg
 images, and egg rejection data, from field experiments conducted from
 2018-2020.
DOI: 10.5061/dryad.9p8cz8wm2
title: Data from: Tablet-based versus presentation-based seminars in radiology: effects of student digital affinity and teacher charisma on didactic quality

description: Aims: Tablets are being adopted as a teaching medium in medical education
 more frequently. Here we compared two teaching formats in a radiology
 seminar using a tablet-based student-centred approach guided by teachers
 and traditional presentation-based, teacher-centred instruction. The aim
 was to investigate the effects on academic performance, estimated learning
 gain, didactic quality, as well as how teacher charisma and student
 digital affinity influence these elements.  Methods: Data from
 366 students were collected. Student digital affinity, didactic quality
 of, and overall satisfaction with the seminars were rated for each
 teaching format over three semesters, whereby in the last semester,
 students additionally estimated their learning gain, took a knowledge and
 image interpretation test, and rated teacher charisma. Results: The
 tablet-based seminars yielded significantly higher ratings for didactic
 quality and overall satisfaction. However, the presentation-based seminars
 proved superior with respect to academic performance as well as estimated
 learning gain. When employing tablets, teacher charisma correlated with
 estimated learning gain, and digital affinity affected didactic quality.
 Additionally, good seminar organization, comprehensible learning
 objectives, and optimal variation of learning activities were identified
 as important factors. Conclusion: This study suggests a complex interplay
 of various factors concerning teachers, students, and didactics that can
 be assessed and improved to assure the successful curricular
 implementation of tablets. Of note, tablet integration and thereby active
 engagement of students with imaging analysis skills does not automatically
 result in greater declarative knowledge. Nevertheless, understanding the
 complexities of structuring and delivering tablet-based, teacher-guided
 instruction is essential to creating meaningful educational experiences.
DOI: 10.15468/dl.c6enkk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Geoffroea spinosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003366-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.pk0p2ngs1
title: Phenotypic plasticity determines differences between the skulls of tigers from mainland Asia

description: Tiger subspecific taxonomy is controversial because of morphological and
 genetic variation found between now fragmented populations, yet the extent
 to which phenotypic plasticity or genetic variation affects phenotypes of
 putative tiger subspecies has not been explicitly addressed. In order to
 assess the role of phenotypic plasticity in determining skull variation,
 we compared skull morphology amongst continental tigers from zoos and the
 wild. In turn, we examine continental tiger skulls from across their wild
 range, to evaluate how the different environmental conditions experienced
 by individuals in the wild can influence morphological variation.
 Fifty-seven measurements from 172 specimens were used to analyse size and
 shape differences amongst wild and captive continental tiger skulls.
 Captive specimens have broader skulls, and shorter rostral depths and
 mandible heights than wild specimens. In addition, sagittal crest size is
 larger in wild Amur tigers compared with those from captivity, and it is
 larger in wild Amur tigers compared to other wild continental tigers. The
 degree of phenotypic plasticity shown by the sagittal crest, skull width,
 and rostral height suggests that the distinctive shape of Amur tiger
 skulls compared with that of other continental tigers is mostly a
 phenotypically plastic response to differences in their
 environments. 
description: This dataset consists of cranial measurements of 172 continental
 tigers (<em>Panthera</em> <em>tigris</em>
 <em>tigris</em>) from museum collections across Europe, from
 both captivity and from wild populations. The captive specimens are
 individuals with known provenance with individual global studbook numbers,
 which had been born and died in zoos. Subadults are defined by the
 basioccipital-basisphenoid suture, and/or frontal suture still being
 unfused, are not included in this dataset. 56 linear
 measurements and cranial volume are provided for each specimen, following
 Barnett et al. (2008) https://doi.org/10.1163/18759866-07701002
DOI: 10.15468/dl.dsa7w3
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "GadmGid is BRA.13_1",
 "TaxonKey is Ocotea odorifera"
 ]
}

 The dataset includes 128 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003367-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h18931zqm
title: The oxidative cost of competing for egg fertilization exceeds the cost of egg production

description: Measuring reproductive costs is crucial to understanding sexual conflict
 and its evolutionary outcomes. Sexual conflict is thought to originate
 from anisogamy – the size difference between male and female gametes; if
 sperm are tiny and not produced in vastly greater numbers than eggs, at
 any mating females’ gametic investment is larger than that of males.
 Testing this prediction has proven difficult, especially because males and
 females differ in many more traits than just gamete size. We overcame this
 difficulty by exposing simultaneously hermaphroditic polychaete
 worms Ophryotrocha diadema (two sexual functions in the
 same body) to two social conditions, pairs and groups&gt;2, where
 hermaphrodites invest either relatively more in the female function or
 relatively more in the male function, respectively. Then we measured four
 markers of cellular oxidative status, a physiological mediator of
 life-history strategies. Less female-biased hermaphrodites produced fewer
 eggs but, unexpectedly, had lower levels of antioxidant protection than
 more female-biased hermaphrodites, which produced more eggs. Male-biased
 hermaphrodites compete for mating as males (hermaphrodites in pairs do
 not) suggesting that in the short-term male competition might be costlier
 than egg production in terms of regulation of oxidative status. These
 results highlight the need of including behavioral traits, namely
 competition over egg fertilization, in the measures of reproductive costs.
description: The archive contains 3 files. The first .csv
 file has the data about egg and cocoon production as a function of
 treatment, density, and level of egg maturity of the worms.
 The second .csv file has the data about oxidative stress
 markers. The third file has the R scripts used in the
 analyses of egg production, cocoon production, and oxidative stress
 measures.