cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ttdz08kvs
title: Functional groups of wild bees respond differently to faba bean (Vicia faba L.) cultivation at landscape scale

description: 1.  Concerns about insect declines are growing and the
 provisioning of ecosystem services like pollination may be threatened. To
 safeguard biodiversity, greening measures were introduced within the
 reform of the EU’s Common Agricultural Policy. One measure commonly
 applied by farmers is the cultivation of nitrogen fixing crops. Although
 underlying studies are largely missing, this measure is criticized as
 providing no significant biodiversity benefit. 2.  Using a
 landscape-scale approach, we selected 30 paired study landscapes (1km x
 1km) in Germany, i.e. 15 study landscapes with faba bean (FB) fields
 (Vicia faba L.) and 15 without any grain legumes. Flower-visiting wild
 bees were recorded with transect walks at the field margins of different
 crops using a stratified sampling approach. We analyzed the effect of FB
 cultivation and landscape composition on the abundance and species
 richness of wild bees as well as on the functional composition of the bee
 communities. 3.  Bumblebee densities (Bombus spp. Latreille) were
 more than twice as high in FB compared to control landscapes after the
 flowering of the beans. Non-Bombus wild bee densities, however, were not
 affected by FB cultivation, but were enhanced by increasing amounts of
 semi-natural habitats (SNH). 4.  After the beans` blooming had
 ceased, FB landscapes had a higher proportion of wild bees collecting
 pollen from Fabaceae than control landscapes. The community weighted means
 for bee size, measured as intertegular distance, were not affected by FB
 cultivation, but we found smaller species and species with shorter tongues
 with an increasing percentage of SNH. 5.  Synthesis and
 applications. The cultivation of faba bean (V. faba L.) strongly increased
 bumblebee densities throughout the season. This indicates that also
 on-field greening measures can support biodiversity. Nevertheless, since
 only functional groups adapted to faba bean benefit, measures to promote
 semi-natural habitats in agricultural landscapes need to be implemented.
 We conclude that the combination of on- and off-field measures is
 essential to maintain farmland biodiversity and the Common Agricultural
 Policy should furthermore promote both.
description: The excel sheet contains data on bumblebee and
 non-<em>Bombus</em> wild bee densities, species richness of
 all wild bees and their functional traits (foraging preferences, community
 weighted means (CWM) of intertegular distance (ITD) and of tongue length)
 for landscapes with and without faba bean cultivation in three different
 regions of Germany.
DOI: 10.5061/dryad.sj3tx962w
title: Lasionycteris noctivagans mitochondrial genomes raw data

description: The geographic distributions of eastern and western Lasionycteris
 noctivagans populations suggest they could be geneticially isolated from
 each other, but this has rarely been assessed using genetic data. Here, we
 evaluate this possibility by sequencing the complete mitochondrial genome
 of four silver-haired bats from eastern and western populations. The three
 usable mitogenomes were closely associated with other Vespertilionid bats
 and the phylogenetic tree revealed the two western individuals grouping
 together to form their own clade. Our results support the idea that small
 but significant genetic differences exist between eastern and western
 populations of these bats.
description: Sequenced using Illumina NOVOseq, PE 150
description: Only three of the datasets were able to be successfully assembled
 into complete genomes, but all four are provdied for a complete record.
 The one labeled 'RI' did not have sufficient coverage.
DOI: 10.5061/dryad.zpc866t6r
title: Soil organic carbon accumulation modes between pioneer and old-growth forest ecosystems

description: 1. Increasing evidence suggests that high biomass and litterfall do not
 necessarily bring about soil organic carbon (SOC) sinks, contrary to the
 assumption that higher litterfall implies higher SOC when designing carbon
 models. The underlying mechanism is related to the quality of litter. 2.
 We conducted 15 years (2000–2015) of consecutive field measurements of
 δ13C values in SOC and plants in a pioneer forest (Pinus massoniana
 forest, PF) and an old-growth forest (monsoon evergreen broadleaved
 forest, BF), using an isotope mixing model based on mass balance to
 quantify the effects of vegetation on SOC stock and soil characteristics.
 3. The carbon to nitrogen (C/N) ratio of litter in BF was lower than that
 in PF. The proportion of organic carbon yield input to the soil (Cinput)
 to the total litter carbon loss during decomposition was 38.7 ± 3.3% and
 28.0 ± 2.1% in BF and PF, respectively. New carbon input was higher in BF
 (148.7 ± 8.8 g C m−2 yr−1) than PF (99.7 ± 4.5 g C m−2 yr−1), though there
 was a non-significant difference in annual litterfall between the two
 forests. Moreover, the Cinput was concentrated in the topsoil layer in PF
 but distributed in a more dispersed state across the whole soil profile in
 BF. Consequently, only the δ13C values of SOC decreased in the topsoil
 layer of PF, whereas these decreased at both soil depths in BF from 2000
 to 2015. 4. Compared with PF, BF exhibited higher carbon input and a more
 favourable soil environment for carbon storage. It was the amount of
 intermediate product (i.e., Cinput) of litter decomposition, not the
 amount of litterfall itself, that drove the contrasting differences in SOC
 status. 5. Synthesis and applications. Litter quality controls SOC
 accumulation by regulating the fate of decomposing litter, which may
 explain why old-growth forests can sustainably accumulate carbon in soil.
 This finding questions the carbon models that predict the dependence of
 SOC accumulation on biomass and litter yield and suggests that litter
 quality should be valued in future carbon cycling models.30-Jul-2020
DOI: 10.5061/dryad.n02v6wwvb
title: Synaptic and intrinsic mechanisms underlying development of cortical direction selectivity

description: Modifications of synaptic inputs and cell-intrinsic properties both
 contribute to neuronal plasticity and development. To better understand
 these mechanisms, we undertook an intracellular analysis of the
 development of direction selectivity in the ferret visual cortex, which
 occurs rapidly over a few days after eye opening. We found strong evidence
 of developmental changes in linear spatiotemporal receptive fields of
 simple cells, implying alterations in circuit inputs. Further, this
 receptive field plasticity was accompanied by increases in
 near-spike-threshold excitability and input-output gain that resulted in
 dramatically increased spiking responses in the experienced state.
 Increases in subthreshold membrane responses induced by the receptive
 field plasticity and the increased input-output spiking gain were both
 necessary to explain the elevated firing rates in experienced ferrets.
 These results demonstrate that cortical direction selectivity develops
 through a combination of plasticity in inputs and in cell-intrinsic
 properties.
description: Please see the Methods section of 10.7554/eLife.58509
 The data were processed with functions in https://github.com/VH-Lab/vhlab-publishedstudies. In order to run those functions, one would need to install several libraries, which can be installed with our lab's installer at https://github.com/VH-Lab/vhlab_vhtools/wiki/Installation.
description: Each experiment was performed on a different date, and the data
 are organized by folder. In each folder, each recording
 epoch is a folder (t00001, t00002, etc). The full
 description of what each file type in each epoch is given at http://wiki.vhlab.org/our-basic-rig-plan/data-format (copied below). See http://wiki.vhlab.org/our-basic-rig-plan/data-format/directory-structure-and-reference-txt-files and http://wiki.vhlab.org/our-basic-rig-plan/data-format/files-created-by-vhlabtools-during-acquisition The results of analyses are stored in "documents" of a new prototype data interface standard called Neuroscience Data Interface (NDI). The documents are in a subfolder of each experiment called ".ndi". The documents have a JSON portion (with extension .json) and a binary portion (with extension .binary). If the libraries at https://github.com/VH-Lab/vhlab_vhtools/wiki/Installation are installed, then the files can be opened in NDI in Matlab using E = ndi_session_dir(PATHNAME) To retreive all documents from an experiment, use docs = E.database_search({'ndi_document.id','(.*)'}) Please see the documentation at http://github.com/VH-Lab/NDI-matlab. This prototype is under development and it is expected that a GUI will be developed and available in 2021.
DOI: 10.5061/dryad.ns1rn8pqc
title: Mechanics of walking and running up and downhill: A joint-level perspective to guide design of lower-limb exoskeletons

description: Lower-limb wearable robotic devices can improve clinical gait and reduce
 energetic demand in healthy populations. To help enable real-world use, we
 sought to examine how assistance should be applied in variable gait
 conditions and suggest an approach derived from knowledge of human
 locomotion mechanics to establish a ‘roadmap’ for wearable robot design.
 We characterized the changes in joint mechanics during walking and running
 across a range of incline/decline grades and then provide an analysis that
 informs the development of lower-limb exoskeletons capable of operating
 across a range of mechanical demands. We hypothesized that the
 distribution of limb-joint positive mechanical power would shift to the
 hip for incline walking and running and that the distribution of
 limb-joint negative mechanical power would shift to the knee for decline
 walking and running. Eight subjects (6M,2F) completed five walking (1.25 m
 s -1 ) trials at -8.53º, -5.71º, 0º, 5.71º, and 8.53º grade and five
 running (2.25 m s -1 ) trials at -5.71º, -2.86º, 0º, 2.86º, and 5.71º
 grade on a treadmill. We calculated time-varying joint moment and power
 output for the ankle, knee, and hip. For each gait, we examined how
 individual limb-joints contributed to total limb positive, negative and
 net power across grades. For both walking and running, changes in grade
 caused a redistribution of joint mechanical power generation and
 absorption. From level to incline walking, the ankle’s contribution to
 limb positive power decreased from 44% on the level to 28% at 8.53º uphill
 grade ( p &lt; 0.0001) while the hip’s contribution increased from 27%
 to 52% ( p &lt; 0.0001). In running, regardless of the surface
 gradient, the ankle was consistently the dominant source of lower-limb
 positive mechanical power (47-55%). In the context of our results, we
 outline three distinct use-modes that could be emphasized in future
 lower-limb exoskeleton designs 1) Energy injection: adding positive work
 into the gait cycle, 2) Energy extraction: removing negative work from the
 gait cycle, and 3) Energy transfer: extracting energy in one gait phase
 and then injecting it in another phase (i.e., regenerative braking).
DOI: 10.5061/dryad.z8w9ghx96
title: Data from: Functional and phylogenetic diversity promotes litter decomposition across terrestrial ecosystems

description: Aim: Litter decomposition is a vital process of carbon and nutrient
 cycling in terrestrial ecosystems. Despite rapid declines in plant
 diversity worldwide, the plant diversity effects on litter decomposition,
 along with the factors driving their directions and magnitudes, remain
 uncertain. Location: Globe. Time period: 1985-2018. Major taxa studied:
 Plants. Methods: By synthesizing 492 paired observations of leaf litter
 mixtures and monocultures from 110 studies, we conducted a global
 meta-analysis of the effects of litter mixtures on litter decomposition
 rates, which were calculated as k coefficients from mt/m0 =e-kt, where
 mt/m0 was litter mass remaining proportion corresponding to time t.
 Results: Litter mixtures on average increased litter decomposition rates
 by 5.6% (95% confident intervals, 3.0%-8.1%), and the effects of litter
 mixtures increased with litter species richness, the functional diversity
 of chemical traits (leaf C, N, P contents and C:N ratio) and phylogenetic
 diversity consistently across terrestrial ecosystems. The decomposer
 abundance and function, including soil fauna abundance, microbial biomass,
 and extracellular enzyme activities were positively associated with litter
 mixture effects on decomposition rates. The structural equation models
 accounted for 48.6% of the global variation in litter decomposition rates
 and revealed that the positive effects of litter functional diversity on
 decomposer abundance and function led to increased litter decomposition
 rates, while litter phylogenetic diversity had a direct effect on litter
 decomposition rates. Main conclusions: The functional diversity of the
 chemical traits and phylogenetic diversity, both as indicators for
 complementarity effects, are important drivers for increasing litter
 mixture effects on decomposition. The positive litter diversity effects on
 decomposition rates are mechanistically linked with soil fauna abundance,
 microbial biomass, and extracellular enzyme activities. Our results
 suggest that plant diversity, especially functional and phylogenetic
 diversity, increases decomposer abundance and function, and thus plays a
 key role in the carbon and nutrient cycling across terrestrial ecosystems.
DOI: 10.5281/zenodo.18395493
title: Fractal dimension complexity of gravitational fractals based on hexagonal and  square lattices: Christaller and Lösch revisited.

description: Data generąted and used in our paper
DOI: 10.5281/zenodo.18395492
title: Fractal dimension complexity of gravitational fractals based on hexagonal and  square lattices: Christaller and Lösch revisited.

description: Data generąted and used in our paper
DOI: 10.17605/osf.io/2dxcy
title: Quantitative data on teacher competencies in online multicultural teaching

description: Anonymous responses from 106 respondents regarding online multicultural teaching competencies, using a five-point Likert scale, were coded as follows: “Strongly disagree” was coded as 1, and “Strongly agree” was coded as 5.
DOI: 10.5061/dryad.qz612jmcf
title: Bitcoin Transaction Network

description: This Bitcoin transaction network data as extracted with the bitcoind
 client. Due to the nature of Bitcoin, all transactions are published to a
 P2P network. These can be downloaded and extracted with any of the
 available client programs. This dataset includes the data used in our
 papers: Kondor, D., Pósfai, M., Csabai, I., & Vattay, G. (2014).
 Do the rich get richer? An empirical analysis of the BitCoin transaction
 network. PLoS ONE, 9(2), e86197.
 https://doi.org/10.1371/journal.pone.0086197 Kondor, D., Csabai, I.,
 Szüle, J., Pósfai, M., & Vattay, G. (2014). Inferring the
 interplay between network structure and market effects in Bitcoin. New
 Journal of Physics, 16(12), 125003.
 https://doi.org/10.1088/1367-2630/16/12/125003
description: Data was downloaded and extracted with a modified version of the
 bitcoind client, available at https://github.com/dkondor/bitcoin/. For the
 ease of use, addresses were converted to numeric IDs.
description: This dataset includes three versions: 
 2013 version: this is the original dataset that was used in our
 papers and originally available under http://www.vo.elte.hu/bitcoin (not
 available anymore) 2018 version: updated dataset
 including transactions up to 2018 February, originally available under
 https://senseable2015-6.mit.edu/bitcoin/ (will become unavailable
 soon) 2020 version: updated dataset including
 transactions up to 2020 February Note that
 the three versions are not compatible with each other. Specifically,
 numeric IDs for addresses differ. To reproduce the
 results of the first paper (https://doi.org/10.1371/journal.pone.0086197),
 use the 2013 version of the dataset and limit analysis for the first
 235000 blocks. To reproduce the results of the second
 paper (https://doi.org/10.1088/1367-2630/16/12/125003), use the full 2013
 version of the dataset.
DOI: 10.5061/dryad.8pk0p2nk9
title: Optimizing whole-genomic prediction for autotetraploid blueberry breeding

description: Blueberry (Vaccinium spp.) is an important autopolyploid crop
 with significant benefits for human health. Apart from its genetic
 complexity, the feasibility of genomic prediction has been proven for
 blueberry, enabling a reduction in the breeding cycle time and
 increasing genetic gain. However, as for other polyploid
 crops, sequencing costs still hinder the implementation
 of genome-based breeding methods for blueberry. This motivated us
 to evaluate the effect of training population sizes and composition, as
 well as the impact of marker density and sequencing depth on phenotype
 prediction for the species. For this, data from a large real breeding
 population of 1 804 individuals was used. Genotypic data from 86 930
 markers and three traits with different genetic architecture (fruit
 firmness, fruit weight, and total yield) were evaluated. Herein, we
 suggested that marker density, sequencing depth, and training population
 size can be substantially reduced with no significant impact on model
 accuracy. Our results can help guide decisions towards resource allocation
 (e.g., genotyping and phenotyping) in order to maximize prediction
 accuracy. These findings have the potential to allow for a faster and more
 accurate release of varieties with a substantial reduction of
 resources for the application of genomic prediction in blueberry.
 We anticipate that the benefits and pipeline described in our
 study can be applied to optimize genomic prediction for other
 diploid and polyploid species.
description: Genotypes were obtained using capture-seq and processed as described by Benevenuto et al. (2019). In summary, 15,663 120-mer biotinylated probes designed based on the 2013 blueberry draft genome sequence were used (Bian et al. 2014; Gupta et al. 2015). Probes were aligned to a high-quality draft genome (Colle et al. 2019), using BLAST (Altschul et al. 1990). Probes that aligned uniquely and within homologous groups were selected, resulting in 9,390 probes used during single nucleotide polymorphisms (SNP) calling steps. A total of 276,212 SNPs were identified using FreeBayes v.1.0.1 (Garrison and Marth 2012), considering the tetraploid option. Only SNPs that met the following criteria were retained for further analysis: i) minimum mapping quality score of 20; ii) minimum SNP phred quality score of 10; iii) biallelic markers; iv) maximum genotype and marker missing data of 0.2; and v) minor population allele frequency of 0.05. In addition, markers were kept when presenting average sequencing depth per site across all individuals of 60X. To avoid the use of imputation methods, it was required that all data points presented a minimum sequencing depth of 2X. A total of 87,628 SNPs were obtained after filtering, and the sequencing depth data for the alternative and reference are presented here.
DOI: 10.15468/dl.wzzx23
title: Occurrence Download

description: A dataset containing 4019 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lasioglossum oblongum"
 ]
}

 The dataset includes 4019 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002506-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7d7wm37sk
title: The roles of wing color pattern and geography in the evolution of Neotropical Preponini butterflies

description: Diversification rates and evolutionary trajectories are known to be
 influenced by phenotypic traits and the geographic history of the
 landscapes that organisms inhabit. One of the most conspicuous traits in
 butterflies is their wing color pattern, which has been shown to be
 important in speciation. The evolution of many taxa in the Neotropics has
 also been influenced by major geological events. Using a dated,
 species-level molecular phylogenetic hypothesis for Preponini, a colorful
 Neotropical butterfly tribe, we evaluated if diversification rates were
 constant or varied through time, and how they were influenced by color
 pattern evolution and biogeographic events. We found that Preponini
 originated approximately 28 million years ago and that diversification has
 increased through time consistent with major periods of Andean uplift.
 Even though some clades show evolutionarily rapid transitions in
 coloration, contrary to our expectations, these shifts were not correlated
 with shifts in diversification. Involvement in mimicry with other
 butterfly groups might explain the rapid changes in dorsal color patterns
 in this tribe, but such changes have not increased species diversification
 in this group. However, we found evidence for an influence of major
 Miocene and Pliocene geological events on the tribe's evolution.
 Preponini apparently originated within South America and range evolution
 has since been dynamic, congruent with Andean geologic activity, closure
 of the Panama Isthmus and Miocene climate variability.
description: Molecular data was obtained from museum speciemens which were
 processed in the laboratory. DNA was extracted, amplified and sequenced
 and then analyzed using computational tools. Locality data was obtained
 from museum specimens from different major collections, the database was
 then curated to make sure the locality data was accurate. Color data was
 also obtained from museum specimens by taking high quality photographs
 using standardized equipment to make sure images were comparable. The
 photographs were analyzed using computational tools and a color database
 was created.