cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3xsj3txd0
title: Data from: The diversity of post-fire regeneration strategies in the cerrado ground layer

description: 1. Disentangling species strategies that confer resilience to natural
 disturbances is key to conserving and restoring savanna ecosystems. Fire
 is a recurrent disturbance in savannas, and savanna vegetation is highly
 adapted to, and often dependent on fire. However, although the woody
 component of tropical savannas is well studied, we still do not understand
 how ground-layer plant communities respond to fire, limiting conservation
 and management actions. 2. We investigated the effects of prescribed fire
 on community structure and composition, and evaluated which traits are
 involved in plant community regeneration after fire in the cerrado ground
 layer. We assessed traits related to species persistence and colonization
 capacity after fire, including resprouter type, underground structure,
 fire-induced flowering, regeneration strategy and growth form. We searched
 for functional groups related to response to fire, to shed light on the
 main strategies of post-fire recovery among species in the ground layer.
 3. Fire changed ground-layer community structure and composition in the
 short term, leading to greater plant species richness, population
 densities, and increasing bare soil, compared with unburned communities.
 Eight months after fire, species abundance did not differ from
 pre-disturbance values for 86% of the species, demonstrating the
 resilience of this layer to fire. Only one ruderal species was
 disadvantaged by fire and 13% of the species benefited. Rapid recovery of
 soil cover by native vegetation in burned areas was driven by species with
 high capacity to resprout and spread vegetatively. Recovery of the savanna
 ground-layer community, as a whole, resulted from a combination of
 different species traits. We summarized these traits into five large
 groups, encompassing key strategies involved in ground layer regeneration
 after fire. Synthesis: Fire dramatically changes the ground layer of
 savanna vegetation in the short term, but the system is highly resilient,
 quickly recovering the pre-fire state. Recovery involves different
 strategies, which we categorized into five functional groups of plant
 species: grasses, seeders, bloomers, undergrounders, and resprouters.
 Knowledge of these diverse strategies should be used as a tool to assess
 conservation and restoration status of fire-resilient ecosystems in the
 cerrado.
DOI: 10.5061/dryad.dncjsxkwv
title: Odorant choice experiment of Tylonycteris Pachypus

description: Insectivorous bats are mostly amblyope, however, they have very strong
 echolocation and olfactory systems. They use ultrasonic sounds to avoid
 pray and to locate food; they use scent alone to discriminate between
 colony and non-colony-mates, males and females and individuals of
 different age. Previous studies show that olfactory cues serve an
 important role in animal close-up recognition, however, there are still
 many unknowns to be clarified. We designed three main experiments in order
 to understand the role of olfactory cues in bat social communication.
 These comprise the pup odorant choice experiment (POC), the colony-mate
 odorant choice experiment (COC) and the gender odorant choice experiment
 (GOC) which were all carried out on the lesser flat-headed bat,
 Tylonycteris pachypus. Our results suggest that olfactory cues play an
 important role in T. pachypus mother-pup, colony-mate and gender
 recognition, however, the POC experiment shows that there was no
 significant difference between a newborn and a weaning pup. In the COC
 experiment, we found that bats were more attracted to colony-mates except
 for subadults, whilst in the GOC experiment, female bats were more
 attracted to female colony-mates. This is the first time that recognition
 behaviour of bats has been studied in multiple aspects.
DOI: 10.15468/dl.mbnb9a
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.99114 20.50417,-100.95234 20.50417,-100.95234 20.52096,-100.99114 20.52096,-100.99114 20.50417))",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002422-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3j9kd51fn
title: Priority determines tribolium competitive outcome in a food-limited environment

description: Flour beetles are a classic model system for studying competitive dynamics
 between species occupying the same ecological niche. Competitive
 performance is often interpreted in terms of biological species traits
 such as fecundity, resource use, and predation. However, many studies only
 measure competitive ability when species enter an environment
 simultaneously, and thus do not consider how the relative timing of
 species’ arrival may determine competitive outcome (i.e., priority
 effects). Whether priority effects may influence competition in Tribolium
 remains to be tested. The present study examined the importance of
 priority effects in competitions between two common species of flour
 beetle (Coleoptera: Tenebrionidae): Tribolium castaneum and T. confusum.
 To investigate whether priority effects confer competitive advantages to
 Tribolium beetles, relative introduction times of T. castaneum and T.
 confusum to competitive arenas were manipulated, and adult populations
 were measured for seven months. Four important patterns were noted: (1)
 Tribolium species given two-weeks priority access to experimental arenas
 attained larger populations than their late-arriving competitor, (2) when
 founding adults were introduced simultaneously, T. castaneum was
 competitively dominant, (3) T. castaneum benefited more from priority
 arrival than T. confusum, and (4) available bran resources largely
 predicted population decline in adult beetles toward the end of the
 experiment. These results suggest competitive outcome in Tribolium is not
 always predicted by species’ identity, and that performance could instead
 be determined by the timing of species’ arrivals and available resources.
DOI: 10.5061/dryad.6wwpzgmw3
title: Data Management and Sharing: Practices and Perceptions of Psychology Researchers

description: Research data is increasingly viewed as an important scholarly output.
 While a growing body of studies have investigated researcher practices and
 perceptions related to data sharing, information about data-related
 practices throughout the research process (including data collection and
 analysis) remains largely anecdotal. Building on our previous study of
 data practices in neuroimaging research, we conducted a survey of data
 management practices in the field of psychology. Our survey included
 questions about the type(s) of data collected, the tools used for data
 analysis, practices related to data organization, maintaining
 documentation, backup procedures, and long-term archiving of research
 materials. Our results demonstrate the complexity of managing and sharing
 data in psychology. Data is collected in multifarious forms from human
 participants, analyzed using a range of software tools, and archived in
 formats that may become obsolete. As individuals, our participants
 demonstrated relatively good data management practices, however they also
 indicated that there was little standardization within their research
 group. Participants generally indicated that they were willing to change
 their current practices in light of new technologies, opportunities, or
 requirements. 
description: To investigate the data-related practices of psychology
 researchers, we adapted a survey developed as part of our previous study
 of neuroimaging researchers. The survey was distributed via Qualtrics
 (http://www.qualtrics.com) from January 25 to March 25, 2019. Before
 beginning the survey, participants were required to verify that they were
 at least 18 years old and gave their informed consent to participate.
 Participants who did not meet these inclusion criteria or who did not
 complete at least the first section of the survey were not included in the
 final data analysis. After filtering, 274 psychology researchers from 31
 countries participated in our survey.  All code for
 data collection and visualization is included in the Jupyter notebooks
 included here.
description: The following materials are included in this dataset:
 Borghi_VanGulick_PsychRDM_Survey - This file contains the text of
 our survey instrument. This file is available in both .docx and .pdf
 format. Borghi_VanGulick_PsychRDM_Notebook - This file
 contains all code used for data analysis and visualization. This file is
 available in both .ipynb and .html format.
 Borghi_VanGulick_PsychRDM_Data - This file contains all data used
 as part of the data analysis and visualization process. This file is
 available in .csv format.
 Borghi_VanGulick_PsychRDM_Dictionary - This file describes what
 each variable in the dataset corresponds to (i.e. which variables relate
 to each survey question). This file is available in .csv format.
DOI: 10.6078/d1j40m
title: Settlement-era public land survey data: Six Rivers National Forest

description: Historical baselines of forest conditions provide reference states to
 assess how forests have changed through time. In California, the Public
 Land Survey System (PLSS) provides tree inventory data between 1872-1884
 at 93.2 km2 (36mi2) resolution. Although these data provide a spatially
 extensive record of settlement-era forest conditions, reconstructions
 using PLSS data have been limited and controversial in western landscapes.
 Recent improvements in the application of plotless density estimators
 (PDE) have made reconstructions more accurate and robust. The purpose of
 this study was to use PDE to reconstruct the settlement-era forest
 conditions in Six Rivers National Forest – a floristically diverse
 temperate forest in the Klamath Mountains of northwestern California – to
 quantify differences with modern conditions. Records of fires and harvests
 were used in conjunction with the PLSS data to understand the influence of
 forest management during the previous century. The contemporary forest in
 Six Rivers contains three times more trees than in the settlement-era with
 a comparable increase in tree basal area. Forest composition during the
 settlement-era was predominantly Douglas-fir (34.4%), pine (24.2%) and oak
 (21.9%) by basal area. Contemporary forests support more Douglas-fir
 (45.2%) and a similar amount of pine (26.1%), while oaks have decreased by
 more than half (9.3%). These increases in tree abundance occurred despite
 extensive, mid-century timber harvesting in Six Rivers. Although large
 fires have burned in Six Rivers between 2000 and 2019, far fewer fires
 occurred during the twentieth century. Our results suggest that effective
 fire suppression contributed to the densification of the contemporary
 forests in Six Rivers.  
description: This dataset contains all the witness tree data available for Six
 Rivers Nationa Forest that was collected through the public land survey in
 the 1880s. Witness tree data were extracted from the handwritten archive
 into digital datasets for this analysis. Surveyors commented sporadically
 about rock type, soil texture, land features, and shrub cover in the
 original notes, but these details were not transcribed. Although the vast
 majority of trees were recorded with distance, direction, species, and
 stem diameter information, surveyors' notes contained three distinct
 types of omitted/absent data. Surveyors reported ‘no trees within limits’
 when trees were present but were too far away for measurement. They
 reported ‘pits impractical’ when field conditions prevented physical
 demarcation of witness trees. Lastly, some entries were blank without
 explanation. These distinctions were recorded into as ‘NTWL’, ‘PI’, and
 ‘NA’, respectively.
DOI: 10.7291/d1nt0s
title: Data from: Geographic structuring of Antarctic penguin populations

description: We hypothesized that regional spatial organization of Antarctic penguin
 breeding populations was affected by social factors, i.e., proximity and
 size of adjacent colonies, and by physical factors, i.e., availability of
 breeding habitat and proximity of polynyas and submarine canyons where
 prey is abundant. The hypothesis of Furness & Birkhead (1984),
 that forage competition and density-dependence affect geographic structure
 of seabird populations, was tested previously for Antarctic penguins when
 biologging to quantify colony foraging areas was less common and when
 assessments of colony size reflected a compendium of historical counts.
 These data on foraging areas and colony size are now available following
 20 years of frequent biologging and real-time satellite data on colony
 locations and sizes. We prepared a literature summary on the basis of
 biologging studies to improve assessment of foraging ranges. We collated
 colony sizes from recent sources and integrated them with data on
 submarine canyon systems and polynyas. We used geospatial models to assess
 the relations of the latter features to colony size, clustering, and
 distribution around Antarctica. The equal spacing of emperor penguin
 colonies was constant, with spacing a function of foraging range. In
 contrast, colonies of other penguin species were clustered, with small
 colonies adjacent to one another and within outer edge of the foraging
 area of large colonies. Colonies and especially clusters occurred near
 polynyas and canyons around Antarctica. Density-dependent processes and
 geography explained penguin colony distribution. We conclude that inter-
 and intraspecific trophic competition affects a geographic structuring of
 colony distribution and size, although not necessarily in the same way
 among species. Results are relevant to assessing effects of climate and
 other factors on penguin population trends at regional scales. We suggest
 that considering penguin colony distribution and abundance at the regional
 or cluster level is necessary to understand changes in these attributes
description: See Methods and Supplemental Materials for description of data
 summary and processing.
description: A ReadMe file is included in the data package describing the
 various data layers.
DOI: 10.15468/dl.tm3waw
title: Occurrence Download

description: A dataset containing 184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Barnebydendron riedelii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 184 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002423-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48505/nims.6164
title: Benchmark Dataset used in the paper "Fast Evaluation of Unbiased Atomic Forces in ab initio Variational Monte Carlo via the Lagrangian Technique"

description: This repository provides the **structures**, **input files**, **output files**, and a **Jupyter notebook** used for the paper [arXiv:2511.05222](https://doi.org/10.48550/arXiv.2511.05222)
DOI: 10.5061/dryad.4b8gtht99
title: Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

description: The ARPA-E funded TERRA-REF project is generating open-access reference
 datasets for the study of plant sensing, genomics, and phenomics. Sensor
 data were generated by a field scanner sensing platform that captures
 color, thermal, hyperspectral, and active flourescence imagery as well as
 three dimensional structure and associated environmental measurements.
 This dataset is provided alongside data collected using traditional field
 methods in order to support calibration and validation of algorithms used
 to extract plot level phenotypes from these datasets. Data were collected
 at the University of Arizona Maricopa Agricultural Center in Maricopa,
 Arizona.  This site hosts a large field scanner with fifteen
 sensors, many of which are capable of capturing mm-scale images and point
 clouds at daily to weekly intervals. These data are intended to be
 re-used, and are accessible as a combination of files and databases linked
 by spatial, temporal, and genomic information. In addition to providing
 open access data, the entire computational pipeline is open source, and we
 enable users to access high-performance computing environments. The study
 has evaluated a sorghum diversity panel, biparental cross populations, and
 elite lines and hybrids from structured sorghum breeding
 populations.  In addition, a durum wheat diversity panel was
 grown and evaluated over three winter seasons. The initial release
 includes derived data from from two seasons in which the sorghum diversity
 panel was evaluated. Future releases will include data from additional
 seasons and locations. The TERRA-REF reference dataset can be used to
 characterize phenotype-to-genotype associations, on a genomic scale, that
 will enable knowledge-driven breeding and the development of
 higher-yielding cultivars of sorghum and wheat.  The data is also
 being used to develop new algorithms for machine learning, image analysis,
 genomics, and optical sensor engineering.
description: See terraref-dryad.pdf, metadata/methods.csv, and
 metadata/docs.terraref.org_2020_04_06.pdf
description: See terraref-dryad.pdf
DOI: 10.7910/dvn/48afkl
title: Replication Data for: Generative Interpretable Visual Design: Using Disentanglement for Visual Conjoint Analysis

description: Code to replicate results in, "Generative Interpretable Visual Design: Using Disentanglement for Visual Conjoint Analysis."
description: torch, 1.7.1
description: torchvision, 0.8.2
description: matplotlib, 3.1.3
description: scipy, 1.5.3
description: imageio, 2.8.0
description: scikit-image, 0.16.2
description: pandas, 1.0.3
description: seaborn, 0.10.0
description: Pillow, 6.1.0
description: tqdm, 4.45.0
description: configparser, 5.0.2
description: numpy, 1.20.3
DOI: 10.5061/dryad.05qfttf0s
title: Using genomics to optimise and evaluate the performance of underwater forest restoration

description: 1. Restoration is an emerging intervention to reverse the degradation and
 loss of marine habitat-formers and the ecosystem services they underpin.
 Current best practice seeks to restore populations by transplanting donor
 individuals chosen to replicate genetic diversity and structure of extant,
 nearby populations. However, genetic characteristics are rarely
 empirically examined across generations, despite their potential role in
 influencing restoration success. 2. We used genomics to design a
 restoration program for lost underwater forests of Phyllospora comosa, a
 dominant forest-forming macroalga that went locally extinct from reefs off
 Sydney, Australia. Population genetic diversity and structure of nearby
 extant populations informed choice of donor sites. We tested whether donor
 provenance influenced adult transplant survival, condition (via metrics of
 epibiosis) and the genetic characteristics of recruits at restoration
 sites. 3. Extant populations of Phyllospora within a 100 km radius of
 Sydney comprised three distinct genetic clusters with similar levels of
 genetic diversity. We transplanted reproductive adults from two of these
 sites, with the aim of restoring five Phyllospora forests with levels of
 genetic structure and diversity similar to donor populations. 4. Donor
 provenance influenced survival and condition of transplanted adults and
 recruitment levels varied significantly among restoration sites. Yet,
 recruitment was rapid and genetic diversity and structure of the F1
 generation resembled extant populations. This likely occurred because
 transplanted individuals reproduced synchronously and rapidly
 post-transplantation, prior to mortality of adult donor transplants. 5.
 Synthesis and applications: As restoration and the need to “future-proof”
 marine ecosystems increase globally, it will be critical to understand the
 role of genetic diversity and structure in restoration success. This study
 demonstrates that evidence-based selection of donor macroalgal forests for
 restoration using genomics can result in levels of genetic diversity and
 structure in the F1 generation that resemble extant populations. However,
 further refinement of transplantation techniques to maximise recruitment
 is also needed.02-Jun-2020
description: Seaweed genomic data from a panel of 354 SNP loci genotyped using
 an Agena Bioscience MassARRAY with iPlex GOLD technology.
 Morphology data from potential seaweed restoration donor
 sites. Survival, condition and recruitment data from 5
 seaweed restoration sites in Sydney, Australia.
DOI: 10.5061/dryad.59zw3r24s
title: Plant density from Environmental drivers of femaleness of an inter-Andean monoecious shrub

description: Hetero-and conspecific interactions, nutrient availability, climate,
 habitat heterogeneity and disturbances can generate variation and spatial
 patterns of femaleness in plants. We assessed whether year, site, plant
 size, plant density and canopy area of conspecific neighbors influenced
 the expression and spatial aggregation of femaleness in Croton aff.
 wagneri, a monoecious shrub from dry shrublands of the inter-Andean
 valleys in Ecuador. We georeferenced in two sites (1,700 and 1,400
 m.a.s.l) in five 10x10 m plots, within each site, the position of each
 Croton reproductive plant during first part of flowering season in two
 years, and measured their height, length and width. The femaleness index
 of each plant was determined by the number of female and male buds and
 flowers. Plant density was determined for each plot, along with the number
 of neighbors and the summed canopy area of conspecific neighbors (at 1.0,
 2.0, and 2.5 m radius, and the five closest plants) from each focal plant.
 Croton's femaleness at the lower elevation site was greater than at
 the higher elevation site and increased with plant size and with canopy of
 the closest five neighbors. Soil at the lower elevation site had higher
 temperatures and lower water content. Aggregate patterns of femaleness
 were found in more plots at the lower elevation site. Our results indicate
 that location, plant size and canopies of conspecific neighbors of Croton
 can affect femaleness and its aggregation and support the hypothesis that
 femaleness can be influenced by facilitative interactions.
description: In November and December 2013 and 2016, the reproductive
 individuals were selected and counted in each 10x10 m subplot at two sites
 with different elevations (1,700 and 1,400 m). Plants with buttons and
 female and male flowers were considered. Plant density was calculated as
 number of reproductive individuals in 10x10 m plots (10 density values
 were obtained for each year). All individuals, reproductive and
 non-reproductive, were counted within 10x10 plots. In 2016 only breeding
 plants were counted, for this reason NA is registered in number of
 individuals in 2016.