cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ttdz08m35
title: Data from: High vascular plant species richness in the Usumacinta River Basin: a comprehensive floristic checklist for a natural region in the Mesoamerican biodiversity hotspot

description: Background: Mesoamerica is one of the most important biodiversity hotspots
 on the planet. Despite significant efforts made over two centuries to
 contribute to the floristic knowledge of this region, our understanding of
 its flora is still scattered and uneven. Questions: What is the magnitude
 of the vascular plant species richness in the Usumacinta River Basin?
 Study site and dates: Usumacinta River Basin (Guatemala and Mexico),
 1838–2018. Methods: We compiled the checklist by systematizing the
 floristic information acquired from various sources derived from numerous
 floristic and ecological studies. Results: We recorded 6,977 species,
 1,892 genera, and 274 families. The largest numbers of species (5,746) and
 records (58,859) correspond to the Mexican portion of the Usumacinta River
 Basin, compared to its Guatemalan counterpart (4,445 species and 19,952
 records). The most species-rich families were Orchidaceae (598 species),
 Fabaceae (512), and Asteraceae (476). The prevalence of these and all
 other families with significant contributions to the flora varied among
 three elevation-defined sectors into which the Usumacinta River Basin was
 subdivided (lower, middle, and upper basin). Conclusions: The Usumacinta
 River Basin is a strategic region for plant biodiversity conservation as
 it hosts almost one-third of all vascular plant species known for
 Mesoamerica and ca. 6 % of the entire flora in the Americas. Further
 botanical exploration should focus on those areas of the basin for which
 little or no information is available in order to gain a better
 appreciation of its flora.
description: The database contains 78,811
 records of vascular plant from localities within the polygon corresponding
 to the Usumacinta River Basin, which includes territories in both
 Guatemala and Mexico. The database was compiled by consulting digital
 collections, herbarium specimens, literature review, and ecological field
 studies. Please refer to the article published in <em>Botanical
 Sciences </em>(DOI: 10.17129/botsci.3253) for a detailed description
 of the taxonomic and geographical treatments performed on the data.
 Location coordinates (latitude/longitude) of species or groups of species
 under a risk of extinction status were omitted, following national
 (Guatemala and Mexico), and international norms (IUCN Red List of
 Threatened Species).
DOI: 10.5061/dryad.4mw6m90fb
title: Dataset for testing the Adaptive Source Term Estimation algorithm

description: The objective of this work is to study the Adaptive Source Term Estimation
 algorithm developed by the authors and that will be presented in a future
 article. Briefly, source term estimation (STE) is a mathematical tool
 aimed to characterize the source parameters of some gas hazard based on
 its measurements at given positions. The adaptive STE (ASTE) is aimed to
 perform this procedure iteratively, i.e. based on the received
 measurements at a given set of deployed detectors, the algorithm proposes
 the location for the next detector in order to optimally solve the STE
 problem.
DOI: 10.5061/dryad.nzs7h44wd
title: Wide-field fluorescence lifetime imaging of neuron spiking and sub-threshold activity in vivo

description: The development of voltage-sensitive fluorescent probes suggests
 fluorescence lifetime as a promising readout for electrical activity in
 biological systems. Existing approaches fail to achieve the speed and
 sensitivity required for voltage imaging in neuroscience applications.
 Here we demonstrate that wide-field electro-optic fluorescence lifetime
 imaging (EO-FLIM) allows lifetime imaging at kHz frame acquisition rates,
 spatially resolving action potential propagation and sub-threshold neural
 activity in live adult Drosophila. Lifetime resolutions of &lt; 5 ps
 at 1 kHz were achieved for single cell voltage recordings. Lifetime
 readout is limited by photon shot noise and the method provides strong
 rejection of motion artifacts and technical noise sources. Recordings
 revealed local transmembrane depolarizations, two types of spikes with
 distinct fluorescence lifetimes, and phase locking of spikes to an
 external mechanical stimulus.
description: Datasets are provided for all manuscript figures along with
 analysis code (Matlab R2021b).
DOI: 10.5061/dryad.dr7sqvb36
title: Multi-decadal stability of fish productivity despite increasing coral reef degradation

description: 1.     Under current
 trajectories, it is unlikely that the coral reefs of the future will
 resemble those of the past. As multiple stressors, such as climate change
 and coastal development, continue to impact coral reefs, understanding the
 changes in ecosystem functioning is imperative to protect key ecosystem
 services. 2.     We used a
 26-year dataset of benthic reef fishes (including cryptobenthic fishes) to
 identify multi-decadal trends in fish biomass production on a degraded
 coral reef. We converted fish abundances into estimates of community
 productivity to track the long-term trend of fish biomass production
 through time.
 3.     Following the first
 mass coral bleaching event in 1998, the abundance, standing biomass, and
 productivity of fish communities remained remarkably constant through
 time, despite the occurrence of multiple stressors, including extreme
 sedimentation, cyclones, and mass coral bleaching events. Species richness
 declined following the 1998 bleaching event, but rebounded to
 pre-bleaching levels and also remained relatively stable. 4. 
    Although the species composition of the communities
 changed over time, these new community configurations still maintain a
 steady level of fish biomass production. While these highly dynamic and
 increasingly degraded systems can still provide some critical ecosystem
 functions, it is unclear whether these patterns will remain stable over
 future decades.
description: We sampled benthic reef fishes annually from 1993-2021 (excluding
 2014, 2017, and 2020) at approximately 3-5 m depth. Sampling always
 occurred during the Austral winter to avoid sampling during the peak
 summer recruitment (Bellwood et al., 2012, 2006). Each year, 2-4 coral
 outcrops (hereon referred to as stations) of roughly equal sizes were
 sampled (approximately 2 m<sup>3</sup>; Bellwood et al., 2012,
 2006). Because cryptobenthic reef fishes cannot be surveyed adequately
 using visual surveys, we used enclosed ichthyocide stations to sample the
 entire small benthic fish communities (e.g. Ackerman and Bellwood, 2000;
 Brandl et al., 2019; Morais and Bellwood, 2019). Each station was enclosed
 in a 2 mm-mesh mosquito net (double bed), weighed along the perimeter by a
 2.3 m long steel chain. The net was sown over the chain to avoid coral
 abrasion. The net was then enclosed in a 2-man tent, again weighed down by
 a chain. All fishes within the net were euthanized with rotenone or (after
 2000) anesthetized with clove oil (cf. Ackerman and Bellwood, 2000); both
 rotenone and clove oil equally sample benthic fishes (Ackerman and
 Bellwood, 2002). After five minutes, the divers slowly removed the tent
 and net, searching for anesthetized fishes. All fishes were collected in
 plastic bags and placed on ice. In the lab, the fishes were identified to
 species, where possible, and counted.
DOI: 10.5061/dryad.3tx95x6m2
title: Age, but not an immune challenge, triggers terminal investment in the Pacific field cricket

description: The terminal investment hypothesis proposes that, when individuals are
 faced with a threat to survival, they will increase investment in current
 reproduction. The level of the threat necessary to elicit terminal
 investment (the dynamic terminal investment threshold) may vary based on
 other factors that also influence future reproduction. Here, we tested
 whether there is an interactive effect of age and an immune challenge on
 the dynamic terminal investment threshold in the Pacific field cricket,
 Teleogryllus oceanicus. We measured the courtship call, mating
 attractiveness, ejaculate size and offspring production of T. oceanicus
 males. We found only limited support for the dynamic terminal investment
 threshold: there was no consistent evidence of a positive interaction
 between male age and immune challenge intensity. However, we found
 evidence for age-related terminal investment: older males produced a
 larger spermatophore than younger males. Older males also had a slower
 calling rate compared to younger males, suggesting a potential trade-off
 between these two pre- and post-copulatory traits. As some, but not, all
 reproductive traits responded plastically to cues for terminal investment,
 our research highlights the importance of considering a broad range of
 pre-and post-copulatory traits when exploring the potential for terminal
 investment to occur.
DOI: 10.5281/zenodo.8340160
title: AN OPEN-SOURCE, THREE-DIMENSIONAL GROWTH MODEL OF THE MANDIBLE

description: This repository contains all geometrical data and metadata belonging to the paper AN OPEN-SOURCE, THREE-DIMENSIONAL GROWTH MODEL OF THE MANDIBLE by the MAGIC Amsterdam research consortium. The following contents are uploaded:
shapeVectors_original.csv | shape vectors of the original datashapeVectors_rescaled.csv | shape vectors of the rescaled data678 x 62589 matrices where the rows are samples and the columns are shape vectors. The shape vectors are formatted [x1, x2, x3, ..., y1, y2, y3, ..., z1, z2, z3, ...].
PCA_coeff_original.csv | principal component coefficients of the original dataPCA_coeff_rescaled.csv | principal component coefficients of the rescaled data62589 x 677 matrices where each row of these matrices is a variable (x-, y-, or z-coordinate of a vertex) and each column is a principal component.
PCA_score_original.csv | principal component scores of the original dataPCA_score_rescaled.csv | principal component scores of the rescaled data678 x 677 matrices where rows correspond to samples and columns correspond to principal components.
PCA_latent_original.csv | principal component variances of the original dataPCA_latent_rescaled.csv | principal component variances of the rescaled data677 x 1 vectors where each element is an eigenvalue of a principal component.
PCA_mu_original.csv | mean of the original dataPCA_mu_rescaled.csv | mean of the rescaled data1 x 62589 vectors that represent the average shape vector. All (centered) data can be reconstructed as follows: shapeVectors = PCA_score * PCA_coeff' + PCA_mu.
PCA_standardDeviations_original.csv | standard deviations of each sample for each principal component of the original data.PCA_standardDeviations_rescaled.csv | standard deviations of each sample for each principal component of the rescaled data.677 x 678 matrices where the rows are principal components and the columns are samples. The standard deviations were calculated as follows: PCA_standardDeviations = PCA_score' ./ sqrt(PCA_latent).
metadata.csv | This matrix contains the age in years (first column) and biological sex (second column, 1 = male and 2 = female) for all samples (rows).
connectivityList.csv | This matrix defines the mesh of the 3D model of the mandible. The vector in each row represents which vertices define a triangle. Indexing starts at 0, so for use in e.g. Matlab, add 1 to all elements.
DOI: 10.5281/zenodo.8340161
title: AN OPEN-SOURCE, THREE-DIMENSIONAL GROWTH MODEL OF THE MANDIBLE

description: This repository contains all geometrical data and metadata belonging to the paper AN OPEN-SOURCE, THREE-DIMENSIONAL GROWTH MODEL OF THE MANDIBLE by the MAGIC Amsterdam research consortium. The following contents are uploaded:
shapeVectors_original.csv | shape vectors of the original datashapeVectors_rescaled.csv | shape vectors of the rescaled data678 x 62589 matrices where the rows are samples and the columns are shape vectors. The shape vectors are formatted [x1, x2, x3, ..., y1, y2, y3, ..., z1, z2, z3, ...].
PCA_coeff_original.csv | principal component coefficients of the original dataPCA_coeff_rescaled.csv | principal component coefficients of the rescaled data62589 x 677 matrices where each row of these matrices is a variable (x-, y-, or z-coordinate of a vertex) and each column is a principal component.
PCA_score_original.csv | principal component scores of the original dataPCA_score_rescaled.csv | principal component scores of the rescaled data678 x 677 matrices where rows correspond to samples and columns correspond to principal components.
PCA_latent_original.csv | principal component variances of the original dataPCA_latent_rescaled.csv | principal component variances of the rescaled data677 x 1 vectors where each element is an eigenvalue of a principal component.
PCA_mu_original.csv | mean of the original dataPCA_mu_rescaled.csv | mean of the rescaled data1 x 62589 vectors that represent the average shape vector. All (centered) data can be reconstructed as follows: shapeVectors = PCA_score * PCA_coeff' + PCA_mu.
PCA_standardDeviations_original.csv | standard deviations of each sample for each principal component of the original data.PCA_standardDeviations_rescaled.csv | standard deviations of each sample for each principal component of the rescaled data.677 x 678 matrices where the rows are principal components and the columns are samples. The standard deviations were calculated as follows: PCA_standardDeviations = PCA_score' ./ sqrt(PCA_latent).
metadata.csv | This matrix contains the age in years (first column) and biological sex (second column, 1 = male and 2 = female) for all samples (rows).
connectivityList.csv | This matrix defines the mesh of the 3D model of the mandible. The vector in each row represents which vertices define a triangle. Indexing starts at 0, so for use in e.g. Matlab, add 1 to all elements.
DOI: 10.5061/dryad.d51c5b07h
title: Data from: A transcriptome-based phylogeny of Scarabaeoidea confirms the sister group relationship of dung beetles and phytophagous pleurostict scarabs (Coleoptera)

description: Scarab beetles (Scarabaeidae) are a diverse and ecologically important
 group of angiosperm-associated insects. As conventionally understood,
 scarab beetles comprise two major lineages: dung beetles and the
 phytophagous Pleurosticti. However, previous phylogenetic analyses have
 not been able to convincingly answer the question whether or not the two
 lineages form a monophyletic group. Here we report our results from
 phylogenetic analyses of more than 4,000 genes mined from transcriptomes
 of more than 50 species of Scarabaeidae and non-scarabaeid Scarabaeoidea.
 Our results provide convincing support for the monophyly of Scarabaeidae,
 confirming the debated sister group relationship of dung beetles and
 phytophagous pleurostict scarabs. Supermatrix-based maximum likelihood and
 multispecies coalescent phylogenetic analyses strongly imply the subfamily
 Melolonthinae as currently understood being paraphyletic. We consequently
 suggest various changes in the systematics of Melolonthinae: Sericinae
 Kirby, 1837 stat. rest. and sensu n. to include the tribes Sericini,
 Ablaberini and Diphucephalini, and Sericoidinae Erichson, 1847 stat. rest.
 and sensu n. to include the
 tribes Automoliini, Heteronychini, Liparetrini,
 Maechidiini, Scitalini, Sericoidini, and Phyllotocini. Both subfamilies
 appear to consistently form a monophyletic sister group to all remaining
 subfamilies so far included within pleurostict scarabs except Orphninae.
 Our results represent a major step towards understanding the
 diversification history of one of the largest angiosperm-associated
 radiations of beetles.
description: Universal single-copy orthologs (USCOs) on the Endopterygota
 level as well as Coleoptera-specific orthologs were extracted from
 transcriptomes of scarabaeoid beetles with Orthograph and aligned using
 two different programs (MAFFT and hmmalign). Alignments were analysed both
 on the nucleotide and amino-acid level, and additionally reduced datasets
 were generated that include only positions present in at leats 70% of
 individuals. Phylogenetic trees were created with IQ-TREE both for
 concatenated alignments and for individual genes, and coalescent-based
 analyses were done with ASTRAL based on the individual gene
 trees.
description: All alignments, including SNP datasets, are in FASTA format and
 can be opened with standard alignment viewers. Phylogenetic trees are in
 NEWICK format, files including multiple named trees are in NEXUS format.
 Both can be opened in a standard phylogenetic tree viewer such as
 FigTree.
DOI: 10.5061/dryad.73n5tb323
title: Data from: Sensitivity analysis of collision risk at wind turbines based on flight altitude of migratory waterbirds

description: This dataset contains information on the distribution of geese and swans
 and the three-dimensional flight trajectories. The former was obtained
 through vehicle field surveys, interviews, and a literature review. The
 latter was obtained using ornithodolites.
description: <strong>Collection of
 bird distribution</strong> The foraging and resting flocks of swans and
 geese were located and recorded at the stopover sites and in the wintering
 areas by vehicle. A cumulative total of approximately 60,000
 km<sup>2</sup> of farmland (including pastures, rice fields,
 and cropland), in addition to bodies of water, including rivers, ponds,
 and lakes was covered. The surveys were carried out for a total of 101
 days: nine days in Niigata Prefecture (from November 2018 to February
 2019), four days in Yamagata Prefecture (in February 2019); 10 days in
 Akita Prefecture (in February and November 2017); 11 days in Akita
 Prefecture (in December 2018 and February 2019), 10 days in Aomori
 Prefecture (March 2018 and March 2019); five days in Miyagi Prefecture (in
 November 2017); and 52 days in Hokkaido (in March and April 2017, March
 and April 2018, and March 2019). The surveys were carried out in daylight
 between 08:00, after the birds left their roosts in the morning, and
 16:00, before they roost in the evening. The approximate sunrise and
 sunset times during the study period were from 04:30 to 06:30 am and from
 15:30 to 18:00. During the surveys, species and flock sizes on the ground
 were recorded and locations were mapped. Birds in flight were recorded
 only when they passed directly above the
 researcher. <strong>Fixed-point observation using an
 ornithodolite</strong> We used ornithodolites (VECTOR21, VECTOR21 AERO,
 and MOSKITO manufactured by SAFRAN Vectronix; 1σ distance error: ± 5m, 1σelevation error: ± 0.2°, 1σ azimuth: ± 0.6°) capable of obtaining highly
 accurate three-dimensional location data. These devices accurately measure
 an object's azimuth, elevation, and oblique distance and calculate
 the latitude, longitude, and altitude using the built-in compass and
 infrared laser illuminator. When used for birds, the tracking data is
 acquired at 3 to 6-second intervals. The response of flight altitude to
 terrain and landscape can be understood. During March and April 2018 and
 February and March 2019, fixed-point ornithodolite surveys were conducted
 at 93 sites within the study area to obtain location and flight altitude
 data. We measured flight altitudes in various environments, including
 farmland, water bodies, urban areas, forests, and mountainous areas, to
 elucidate the effects of landscape and terrain factors on flight altitude.
 The maximum measurable range according to the device's specifications
 was 12 km for structures. However, for the target species of geese and
 swans, the measured range was approximately 2 km for individual birds and
 approximately 3 km for flocks.
DOI: 10.5061/dryad.1vhhmgqxp
title: Transcriptional profiling of the response to starvation and fattening reveals differential regulation of autophagy genes in mammals

description: Nutrient deprivation (starvation) induced by fasting and hypercaloric
 regimens are stress factors that can influence cell and tissue homeostasis
 in mammals. One of the key cellular responses to changes in nutrient
 availability is the cell survival pathway, autophagy. While there has been
 much research into the protein networks regulating autophagy, less is
 known about the gene expression networks involved in this fundamental
 process. Here, we applied a network algorithm designed to analyze omics
 datasets, to identify sub-networks that are enriched for induced genes in
 response to starvation. This enabled us to identify two prominent active
 modules composed of key stress-induced transcription factors, including
 members of the Jun, Fos, and ATF families, and the other comprising
 autophagosome sub-network genes, including ULK1. The results were
 validated in the brain, liver, and muscle of fasting mice. Moreover,
 differential expression analysis of autophagy genes in the brain, liver,
 and muscle of high-fat diet-exposed mice, showed significant suppression
 of GABARAPL1 in the liver. Finally, our data provide a resource that may
 facilitate the future identification of regulators of autophagy.
DOI: 10.5061/dryad.s4mw6m9b5
title: Modelling long-distance seed dispersal of Spathodea campanulata in the Society Islands

description: These datasets are related to the paper "Modelling long-distance seed
 dispersal of the invasive tree Spathodea campanulata in the Society
 Islands" published in Ecological Applications. We used a 3-D
 kinematic trajectory model (Computing Atmospheric Trajectory tool (CAT))
 initiated from regional wind field data to assess the potential for
 long-distance seed dispersal (LDD) of a wind-dispersed invasive tree,
 Spathodea campanulata (African tulip tree) across the Society Islands
 (French Polynesia, South Pacific Ocean) following its initial planting and
 spread on the island of Tahiti. The main objective of our study was to
 determine whether S. campanulata can be expected to spread naturally among
 islands. Atmospheric dynamics, seed terminal velocity, precipitation, and
 temperature of air masses were considered to assess the potential for LDD
 between oceanic islands, with the island of Tahiti serving as the island
 source for multiple, geographically distant invasions. These datasets
 contain the number of simulated seed trajectories with Computing
 Atmospheric Trajectory tool (CAT) in the study area as well as all data
 corresponding to each figure found in the paper.
DOI: 10.5061/dryad.s4mw6m9b6
title: Data from: Longitudinal effects of early psychosocial deprivation on macaque executive function: Evidence from computational modelling

description: Executive function (EF) describes a group of cognitive processes
 underlying the organization and control of goal-directed behaviour.
 Environmental experience appears to play a crucial role in EF development,
 with early psychosocial deprivation often linked to EF impairment.
 However, many questions remain concerning the developmental trajectories
 of EF after exposure to deprivation, especially concerning specific
 mechanisms. Accordingly, using an ‘A-not B’ paradigm and a macaque model
 of early psychosocial deprivation, we investigated how early deprivation
 influences EF development longitudinally from adolescence into early
 adulthood. The contribution of working memory and inhibitory control
 mechanisms were examined specifically via the fitting of a computational
 model of decision-making to the choice behaviour of each individual. As
 predicted, peer-reared animals (i.e. those exposed to early psychosocial
 deprivation) performed worse than mother-reared animals across time, with
 the fitted model parameters yielding novel insights into the functional
 decomposition of group-level EF differences underlying task performance.
 Results indicated differential trajectories of inhibitory control and
 working memory development in the two groups. Such findings not only
 extend our knowledge of how early deprivation influences EF
 longitudinally, but also provide support for the utility of computational
 modelling to elucidate specific mechanisms linking early psychosocial
 deprivation to long-term poor outcomes.