cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9p8cz8wgs
title: Toba Caldera geochronological and modelling dataset

description: Bayesian statistical analysis and inverse thermal history modeling of
 feldspar 40Ar/39Ar and zircon (U-Th)/He ages reveal that post-caldera dome
 eruptions at Toba Caldera, Sumatra occurred up to ca. 13.6
 kyr later than indicated by 40Ar/39Ar feldspar ages. This
 discordance implies cold storage of feldspar antecrysts prior to eruption
 for a maximum duration of ca. 5 and 13 kyr at between 280°C and
 500°C. These findings connote that the solidified carapace of remnant
 magma after the Youngest Toba Tuff (YTT) eruption ~74 ka erupted in a
 subsolidus state, without being thermally remobilized or rejuvenated. Our
 data mean that resurgent uplift and volcanism initiated approximately 5
 kyrs after the climactic YTT eruption, thus providing rare constraints on
 resurgence after a cataclysmic supereruption. Our approach has the
 potential to reveal complexities in pre-eruptive storage and eruption at
 unprecedented temporal resolution with implications for active restless
 calderas and young silicic volcanoes worldwide.
DOI: 10.5061/dryad.5mkkwh76f
title: High-resolution mapping of the period landscape reveals polymorphism in cell cycle frequency tuning

description: Biological oscillators adapt to environmental changes with widely tunable
 frequencies, a property theoretical studies attributed to positive
 feedbacks. However, no experiments have tested this theory. Here, we
 created synthetic cells to independently tune the frequency and feedback
 strength of a cell-cycle oscillator, enabling continuous mapping of period
 landscape in response to network perturbations. We found that although
 inhibiting positive feedback of cyclin-dependent kinase (Cdk1) reduces the
 tunability, the reduction is not as significant as theoretically
 predicted, and the Cdk1-counteracting phosphatase, PP2A, provides
 additional machinery to ensure frequency regulation. Additionally, cells
 exhibit polymorphic responses to PP2A inhibition, showing a monomodal
 distribution of oscillatory cells at low or high PP2A inhibition or a
 bimodal distribution at both low and high inhibitions. We explained the
 polymorphism by a model of two interlinked bistable switches of Cdk1 and
 PP2A where cell-cycle oscillations exhibit two modes in the presence or
 absence of PP2A bistability.
description: This dataset contains metadata after image segmentation and
 tracking. Segmentation was achieved by a watershed algorithm with a seed
 generated from the Hough circle detection. Tracking was performed by
 maximizing the segmentation feature correlation between two consecutive
 time frames. Average fluorescent intensity profiles of droplets were then
 extracted for further analysis. All analysis above is performed on MatLab
 2019a. This dataset contains 3 different levels of
 simplification, 1. raw data right after image processing. 2. cycle
 description after semi-automatic peak detection and oscillatory feature
 calculation. 3. droplet level statistics after peak detection. For each
 independent experiment, one or more levels of simplification may be
 provided. See 'readMe.doc' for detailed information about the
 simplification level of the dataset and data structure
 annotation. 
description: This dataset is mainly consisted of two types of files, MatLab
 metadata (*.mat ) after image processing and MatLab scripts (*.m) to
 generate figures.  The dataset is categorized based on
 figures. Each script controls metadata import, data analysis, and figure
 generation. The scripts and corresponding figures are listed in readMe
 file.
DOI: 10.5061/dryad.zgmsbccc3
title: Identification of species by combining molecular and morphological data using convolutional neural networks

description: Integrative taxonomy is central to modern taxonomy and systematic biology,
 including behavior, niche preference, distribution, morphological
 analysis, and DNA barcoding. However, decades of use demonstrate that
 these methods can face challenges when used in isolation, for instance,
 potential misidentifications due to phenotypic plasticity for
 morphological methods, and incorrect identifications because of
 introgression, incomplete lineage sorting, and horizontal gene transfer
 for DNA barcoding. Although researchers have advocated the use of
 integrative taxonomy, few detailed algorithms have been proposed. Here, we
 develop a convolutional neural network method (morphology-molecule network
 [MMNet]) that integrates morphological and molecular data for species
 identification. The newly proposed method (MMNet) worked better than four
 currently available alternative methods when tested with 10 independent
 data sets representing varying genetic diversity from different taxa. High
 accuracies were achieved for all groups, including beetles (98.1% of 123
 species), butterflies (98.8% of 24 species), fishes (96.3% of 214
 species), and moths (96.4% of 150 total species). Further, MMNet
 demonstrated a high degree of accuracy (&gt;98%) in four data sets
 including closely related species from the same genus. The average
 accuracy of two modest subgenomic (single nucleotide polymorphism) data
 sets, comprising eight putative subspecies respectively, is 90%.
 Additional tests show that the success rate of species identification
 under this method most strongly depends on the amount of training data,
 and is robust to sequence length and image size. Analyses on the
 contribution of different data types (image vs. gene) indicate that both
 morphological and genetic data are important to the model, and that
 genetic data contribute slightly more. The approaches developed here serve
 as a foundation for the future integration of multimodal information for
 integrative taxonomy, such as image, audio, video, 3D scanning, and
 biosensor data, to characterize organisms more comprehensively as a basis
 for improved investigation, monitoring, and conservation of biodiversity.
DOI: 10.5061/dryad.w3r2280rd
title: 2D Macro-XRF to reveal redacted sections of French queen Marie-Antoinette secret correspondence with Swedish count Axel von Fersen

description: During the French Revolution, Marie-Antoinette, queen of France and wife
 of Louis the XVIth, maintained a highly secret correspondence with the
 Swedish count Axel von Fersen, her close friend and rumored lover. An
 unidentified censor later redacted certain sections of the exchanged
 letters. This presumably sensitive content has been puzzling historians
 for almost 150 years. We report on the methodology that successfully
 unraveled this historical mystery. X-ray fluorescence spectroscopy was
 used in macro scanning mode on the redacted sections. Specific data
 processing was applied to improve the legibility of the hidden writings
 (elemental ratios, statistical data reduction, multimodal images fusion,
 unmixing procedure; image treatments). This methodology successfully
 revealed the redacted contents of 8 letters, shedding new lights on
 Marie-Antoinette and Fersen relationship but also on the author of the
 redactions. It will also be of great interest for other historical and
 forensic cases involving the disentanglement of superimposed
 multi-elemental materials.
description: 2D Macro-XRF scans of the letters were carried out with a Bruker
 M6 Jetstream. The instrument consists of a measuring head made of a
 Rh-target X-ray tube and a 30 mm<sup>2</sup> XFlash silicon
 drift detector; mounted on a XY-motorized stage. The X-rays are focused
 through polycapillary optics, which allows to set the beam size by
 changing the working distance. Pixel size of the elemental maps -
 determined by the step size - was the same as the beam size and set
 between 50 and 180 µm, depending on the required resolution. Voltage and
 current in the X-ray tube were set to 50 kV and 600 µA, respectively;
 dwell times varied between 100 ms and 3 s per pixel. A first phase of the
 project consisted in optimizing the acquisition parameters (beam size,
 dwell time per pixel) in order to allow the text to be read while
 minimizing analysis time. For this purpose, one word from each letter was
 analyzed under different conditions. The redacted passages of each letter
 were then fully analyzed with this choice of parameters. In certain cases,
 the initial dataset quality had to be improved from a spatial (pixel size)
 and spectral (dwell time) standpoint, requiring much longer (up to 30
 times) acquisition durations. 95 days of analysis were necessary for this
 project. Data were collected and treated with the Bruker M6 software.
 Additional data analyses and image treatments were carried out with ENVI
 (Excelis) and ImageJ softwares. Point analyses were
 performed with the multi-point option of the M6 Jetstream (dwell time of
 200 s, beam size 100 µm).
DOI: 10.5061/dryad.ncjsxksvp
title: Do the predicted suitability scores from species distribution models correlate with species performance on-ground?

description: Species distribution models are a very popular statistical tool for
 inferring potential distribution range of species across space and time
 and are thought to be a good predictor for habitat suitability. Some
 studies have suggested that if these models are reliable, predicted
 habitat suitability (PHS) should relate to species traits
 visualization, growth potential, body size, abundance. We
 validated this hypothesis by estimating association between the PHS and
 species abundance for 17 avian species endemic to the Western Ghats - Sri
 Lanka biodiversity hotspot. Additionally, we compared the PHS of sites
 where species were detected in both seasons (wet and dry) against sites
 where they were detected in the dry season alone. As a proxy for
 abundance, we estimated single-season occupancy estimates (ψ) using
 detection/non-detection data from multiple visits to the survey sites. We
 report significant and positive PHS-ψ correlation, though the strength of
 this association varied across species and models. Half of the
 species showed higher suitability scores for the sites where they
 were detected year round. The results presented here suggest that the
 predictive models can be used as a proxy for habitat quality, in addition
 to inferring the potential distribution.
description: The present work utilises the Kerala Bird Atlas dataset available
 at (https://zenodo.org/record/4920550). Species of interest were selected,
 presence and absence files were created and five different SDM algorithms
 were run in the R platform. Input files for occupancy analysis in PRESENCE
 software were generated. Correlation between the predicted habitat
 suitability and species occupancy estimates (a proxy for abundance) was
 estimated.
description: This folder consists of four input files (.RDS), three raster
 stacks files (.grd) and one R script file (.R) for the analyses performed
 using the Kerala Bird Atlas: 2015-2020 dataset. <br> These files are
 part of the publication "Do the predicted suitability scores from
 Species Distribution Models correlate with species performance
 on-ground?". 1) Download all the files provided
 here as well as the Kerala Bird Atlas files available at
 https://zenodo.org/record/4920550.<br> 2) Create following folders
 in the working directory: 'INPUT', 'OCCUPANCY',
 'PREDICTORS' and 'RESULTS'<br> 3) All raster
 stacks will be in the PREDICTORS folder.<br> 4) Transfer all other
 files to the INPUT folder except the 'R script.R'<br> 5)
 Run the R script. All input files will be called from the folder
 'INPUT'. Raster layers will be called from the folder
 'PREDICTORS'.<br> 6) Files for Occupancy analysis in the
 program 'PRESENCE' will be saved in the folder
 'OCCUPANCY'.<br> 7) SDM results will be saved as ASCII
 files in the folder 'RESULTS'.<br> 8) Result tables will
 be save as csv files in the working directory. The
 figures generated in the R platform were exported in svg format and
 annotated in Inkscape software.
DOI: 10.5061/dryad.0gb5mkm1q
title: Utilizing woody materials for fungal-based management of soil nitrogen pools

description: Application of nitrogen fertilizers to reach high crop production is
 common practice. However, this can come with an environmental cost,
 irrespectively of the synthetic or organic origin of the nitrogen
 fertilizer. Intensively managed soils often fail to retain excess
 nitrogen, which leads to contamination of ground- and surface water. Next
 to abiotic factors like soil texture, limited nitrogen retention is
 ascribed to low activity of saprotrophic fungi. It has been shown that
 amendment of arable soils with cellulose-rich materials can effectively
 stimulate resident saprotrophic fungi. The current study investigated the
 relationship between fungal dynamics (biomass, composition) and nitrogen
 immobilization-remobilization dynamics upon soil amendment with woody
 materials Mineral  nitrogen pools, ergosterol and ITS2 amplicon
 sequences were analyzed during a 6-months pot experiment. Carbon-rich
 amendments included sawdusts of deciduous (beech, willow) and coniferous
 (Douglas fir, larch) tree species, beech wood chips, wheat straw and
 combinations of these materials. Excess nitrogen derived from addition of
 either mineral or organic fertilizer. Deciduous wood sawdust resulted in
 rapid stimulation of fungal biomass, mainly consisting of saprotrophic
 Sordariomycetes. This was accompanied by a reduction in the mineral N pool
 equivalent to  24–60 kg N ha-1 for four to over six months. The
 intensity of nitrogen immobilization depended on sawdust application rate
 and the type of fertilizer. Single amendments of coniferous sawdust and
 beech wood chips had minor effects, but led to prolonged nitrogen
 retention when combined with beech sawdust. Our conclusion is that,
 fungus-stimulating woody soil amendments  have great potential to
 increase nitrogen use efficiency in arable soils.
DOI: 10.5061/dryad.h44j0zpkp
title: Epitope-specific anti-C1Q autoantibodies in systemic Lupus Erythematosus

description: Objective In patients with systemic lupus erythematosus (SLE) complement
 C1q is frequently targeted by autoantibodies (anti-C1q), that correlate
 best with active renal disease. Anti-C1q bind to largely unknown epitopes
 on the collagen-like region (CLR) of this highly functional molecule. Here
 we aimed at exploring the role of epitope-specific anti-C1q in SLE
 patients. Methods First, 22 sera of SLE patients, healthy controls and
 anti-C1q positive patients without SLE were screened for anti-C1q epitopes
 by a PEPperMAP® microarray, expressing CLR of C1q derived peptides with
 one amino acid (AA) shift in different lengths and conformations.
 Afterwards, samples of 378 SLE patients and 100 healthy blood donors were
 analyzed for antibodies against the identified epitopes by peptide-based
 ELISA. Relationships between peptide-specific autoantibodies and SLE
 disease manifestations were explored by logistic regression models.
 Results The epitope mapping showed increased IgG binding to three peptides
 of the C1q A- and three of the C1q B-chain. In subsequent peptide-based
 ELISAs, SLE sera showed significantly higher binding to two N-terminally
 located C1q A-chain peptides than controls (p &lt; 0.0001), but not to
 the other peptides. While anti-C1q were associated with a broad spectrum
 of disease manifestations, some of the peptide-antibodies were associated
 with selected disease manifestations, and antibodies against the
 N-terminal C1q A-chain showed a stronger discrimination between SLE and
 controls than conventional anti-C1q. Conclusion In this large explorative
 study anti-C1q correlate with SLE overall disease activity. In contrast,
 peptide-antibodies are associated with specific aspects of the disease
 suggesting epitope-specific effects of anti-C1q in patients with SLE.
DOI: 10.5061/dryad.rfj6q57b8
title: Test scanner images for ARATA_v2

description: Using a root auto tracing and analysis (ARATA), we succeeded in extracting
 fine roots from soil images and calculating the length and projected area
 of fine roots. The test images for ARATA and extracted black-white images
 by ARATA are available in the repository.
description: Images (.jpg) were taken by flatbed image
 scanners GT-S650 and GT-S600 (EPSON, Tokyo, Japan) inserted into the soil
 of a <em>Chamaecyparis obtusa </em>(image names starting with
 C), and <em>Quercus serrata</em> (image names starting with Q)
 stands in the Ryukoku forest (Shiga, Japan; image names including RKK), a
 deciduous mixture forest in Himeji nature observation forest (Hyogo,
 Japan; image names including HMJ) , an<em> Ilex
 pedunculosa</em> stand (image names starting with I) area in
 Yamashiro forest (Kyoto, Japan; image names including YMS). The size of
 these images is 1180*1180 pixels. The scanners were buried at a depth of
 approximately 20 cm from the soil surface and image was collected as
 described in Dannoura et al., 2009 and 2011. Proceeded images (files
 with_arata) by ARATA were also uploaded.
description: Proceeded images by ARATA are indicated as file name
 with_arata.
DOI: 10.5061/dryad.vt4b8gtsg
title: Single versus repeated human trampling events: Responses of ground vegetation in sub-urban beech forests

description: Forests provide important ecosystem services and are often the only
 natural areas that are freely accessible to the public for outdoor
 recreation. Large numbers of forest visitors can cause severe damage to
 forest ecosystems, which in turn can affect the ecosystem functioning. We
 aimed to assess whether experimental short-term and long-term trampling
 affect the ground vegetation in deciduous forests and its recovery to a
 different extent. We used a standard experimental trampling procedure to
 simulate single and repeated human trampling events of different
 intensity. Experimental trampling of different intensity was conducted on
 a single day (single trampling) or on five days at intervals of four weeks
 (repeated trampling) in three suburban beech forests on different soil
 types. We recorded the cover, height, species density and species
 composition of the ground vegetation in the trampling lanes. We also
 assessed the recovery of the ground vegetation one and two years after
 trampling. Trampling intensity and the type of trampling (single vs.
 repeated) affected the ground vegetation in the three forests. Vegetation
 cover, plant height and species density all decreased with increasing
 trampling intensity, but to a different extent in the three forests. Most
 vegetation characteristics were more severely affected by repeated
 trampling than single trampling of equal intensity. A longer trampling
 period strengthened the effects of trampling on ground vegetation, except
 in one forest. Two years after experimental trampling, most vegetation
 characteristics still differed from those of undisturbed ground vegetation
description: We used a standard experimental trampling procedure to simulate
 single and repeated human trampling events of different intensity.
 Experimental trampling of different intensity was conducted on a single
 day (single trampling) or on five days at intervals of four weeks
 (repeated trampling) in three suburban beech forests on different soil
 types. We recorded the cover, height, species density and species
 composition of the ground vegetation in the trampling lanes. We also
 assessed the recovery of the ground vegetation one and two years after
 trampling.
description: Within the data sets: Four data files for each
 of the three study sites Allschwil, Liestal and Sissach:
 For example for the field site Allschwil:
 Allwschwil_Ground_Vegetation data includes trampling intensity,
 type of trampling on vegetation characteristics, and the data file
 Allwschwil_Ground_Vegetation includes data on changes in vegetation
 composition expressed as Euclidian distance. The files, which ended with
 the extension recovery, include the corresponding recovery data.
 For more details, see Material and Method section in the article
 with the same title.
DOI: 10.5061/dryad.866t1g1r7
title: Naivety dies with the calf: Learning effects in a heavily harvested ungulate

description: In animals, habitat selection and movement strategies may affect survival
 and this may be key agents in selection affection the evolution of a
 species. To test for learning capabilities of previous experience of
 hunting in a long-lived, solitary and heavily harvested ungulate, we
 combined longitudinal GPS-data from 84 female moose (Alces alces) with
 data on calf and adult survival. We tested the prediction that long-lived
 moose individuals would adapt their behavior over time due to experience
 from hunting in the absence of natural predators. We found that female
 moose may learn from having their calf harvested and alters their behavior
 the following hunting season in response to previous experience. We also
 found that females were more likely to be harvested when selecting more
 for open habitats. As a consequence, surviving females increased their use
 of cover in the following hunting season after losing a calf to harvest.
 Use of habitat with cover furthermore increases as female moose aged,
 indicating that learning effects are reinforced over time. Our study
 highlights that losing an offspring imposes a strong learning effect in a
 solitary ungulate and those learning effects may influence future harvest
 success and tools available within ungulate management.
description: Please find additional information in the readme file.
DOI: 10.15468/dl.g6ws9y
title: Occurrence Download

description: A dataset containing 1515 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cynometra ramiflora"
 ]
}

 The dataset includes 1515 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002902-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.