cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xd2547dkt
title: Local field potentials reflect cortical population dynamics in a region-specific and frequency-dependent manner

description: The spiking activity of populations of cortical neurons is well described
 by a small number of population-wide covariance patterns, the “latent
 dynamics”. These latent dynamics are largely driven by the same correlated
 synaptic currents across the circuit that determine the generation of
 local field potentials (LFP). Yet, the relationship between latent
 dynamics and LFPs remains largely unexplored. Here, we characterised this
 relationship for three different regions of primate sensorimotor cortex
 during reaching. The correlation between latent dynamics and LFPs was
 frequency-dependent and varied across regions. However, for any given
 region, this relationship remained stable across behaviour: in each of the
 primary motor and premotor cortices, the LFP-latent dynamics correlation
 profile was remarkably similar between movement planning and execution.
 These robust associations between LFPs and neural population latent
 dynamics help bridge the wealth of studies reporting neural correlates of
 behaviour using either type of recording.
description: This data set includes behavioral recordings and extracellular
 neural recordings from the motor cortex, premotor cortex, and area 2 of
 the primary somatosensory cortex of Rhesus macaques during an
 instructed-delayed reaching task. Matthew Perich and Raeed Chowdhury
 collected and processed the data in the laboratory of Lee Miller for use
 in Gallego-Carracedo et al. 2022, which characterised the relationship
 between neural population activity and local field potentials across these
 sensorimotor cortical regions. Results and methodology from these
 experiments are described in Gallego-Carracedo et al. 2022.
 In these experiments, monkeys controlled a cursor on a screen
 using a two-link, planar manipulandum. Monkeys performed a simple
 center-out task to one of the eight possible targets, after a variable
 delayed period. During this reaching task, we tracked the endpoint
 position of the hand using sensors on the manipulandum. In addition to the
 behavioral data, we collected neural data from one or two of these areas
 using Blackrock Utah multielectrode arrays, yielding ~100 to ~200 channels
 of extracellular recordings per monkey. Recordings from these channels
 were thresholded online to detect spikes, which were sorted offline into
 putative single units. Analysis code used to produce
 figures for Gallego-Carracedo et al. 2022 provides useful examples for how
 to work with this dataset. See https://github.com/BeNeuroLab/Relationship_between_latent_dynamics_and_LFP.git for code and README. If you publish any work using the data, please cite the publication above (Gallego-Carracedo et al. 2022) and also cite this data set.
DOI: 10.25338/b8kk91
title: Prior parental experience attenuates hormonal stress responses and alters hippocampal glucocorticoid receptors in biparental rock doves

description: In the face of challenges, animals must balance investments in
 reproductive effort versus their own survival. Physiologically, this
 tradeoff may be mediated by glucocorticoid release by the
 hypothalamic-pituitary-adrenal (HPA) axis and prolactin release from the
 pituitary to maintain parental care. The degree to which animals react to
 and recover from stressors likely affects maintenance of parental behavior
 and ultimately, fitness. However, less is known about how gaining parental
 experience may alter hormonal stress responses and their underlying
 neuroendocrine mechanisms. To address this gap, we measured the
 corticosterone (CORT) and prolactin (PRL) stress response in both sexes of
 the biparental rock dove (Columba livia) that had never raised chicks
 versus birds that had fledged at least one chick. We measured both CORT
 and PRL at baseline and after an acute stressor (30 minutes restraint). We
 also measured negative feedback ability by administering dexamethasone, a
 synthetic glucocorticoid that suppresses CORT release, and measured CORT
 and PRL after 60 minutes. All hormones we measured when birds were not
 actively nesting to assess whether effects of parental experience extend
 beyond the breeding bout. Experienced birds had lower stress-induced and
 negative-feedback CORT, and higher stress-induced PRL than inexperienced
 birds. In a separate experiment, we measured glucocorticoid receptor
 subtype expression in the hippocampus, a key site of negative feedback
 regulation. Experienced birds expressed higher glucocorticoid receptors
 than inexperienced controls, which may mediate their ability to attenuate
 CORT release. Together, these results shed light on potential mechanisms
 by which gaining experience may improve parental performance and fitness.
description: This dataset includes plasma hormone data collected before and
 after a classic restraint-stressor in captive rock doves (Columba livia),
 with information on baseline, stress-induced, and negative
 feedback/recovery levels of corticosterone (CORT) and prolactin.
 Additionally, there is a dataset on gene expression of glucocorticoid and
 mineralocorticoid hormone receptors measured in hippocampi microdissected
 from brain tissue.
DOI: 10.5061/dryad.tdz08kq2r
title: Data from: Optimal mating of Pinus taeda L. under different scenarios using differential evolution algorithm

description: A newly developed software, AgMate, was used to perform optimized mating
 for monoecious Pinus taeda L. breeding. Using a
 computational optimization procedure called differential evolution (DE),
 AgMate was applied under different breeding population sizes scenarios
 (50, 100, 150, 200, 250) and candidate contribution scenarios (max use of
 each candidate was set to 1 or 8), to assess its efficiency in maximizing
 the genetic gain while controlling inbreeding. Real pedigree data set from
 North Carolina State University Tree Improvement Co-op with
 962 Pinus taeda were used to optimize objective functions
 accounting for coancestry of parents and expected genetic gain and
 inbreeding of the future progeny. AgMate results were compared with those
 from another widely used mating software called MateSel (Kinghorn, 1999).
 For the proposed mating list for 200 progenies, AgMate resulted in an
 83.7% increase in genetic gain compared with the candidate population.
 There was evidence that AgMate performed similarly to MateSel in managing
 coancestry and expected genetic gain, but MateSel was superior in avoiding
 inbreeding in proposed mate pairs. The developed algorithm was
 computationally efficient in maximizing the objective functions and
 flexible for practical application in monoecious diploid conifer breeding.
description: Agmate, an R software that utilizes the
 Differential Evolution algorithm and Second-order Cone Programming for the
 optimization of mate pair decisions and contributions for monoecious
 diploid species like <em>Pinus taeda</em> was used to analyze
 the data.  AgMate is a
 multi-functional software able to Process pedigree information Complete
 and order pedigrees Generate numerator relationship matrices
 Optimize selection
 and contribution of candidates Design optimal matings between
 candidates Provide visualization of results
 Detailed R code is available at https://github.com/khushigoda/AgMate. The ShinyApp version is available here: https://khushigoda.shinyapps.io/AgMate/ MateSel licensed version was used to analyze the same data to validate AgMate for this study. MateSel is available at http://matesel.une.edu.au/
DOI: 10.5061/dryad.51c59zwbn
title: Data from: Latent generative landscapes as maps of functional diversity in protein sequence space

description: Variational autoencoders are unsupervised learning models with generative
 capabilities, when applied to protein data, they classify sequences by
 phylogeny and generate de novo sequences which preserve statistical
 properties of protein composition. While previous studies focus on
 clustering and generative features, here, we evaluate the underlying
 latent manifold in which sequence information is embedded. To investigate
 properties of the latent manifold, we utilize direct coupling analysis and
 a Potts Hamiltonian model to construct a latent generative landscape. We
 showcase how this landscape captures phylogenetic groupings, functional
 and fitness properties of several systems including Globins, β-lactamases,
 ion channels, and transcription factors. We provide support on how the
 landscape helps us understand the effects of sequence variability observed
 in experimental data and provides insights on directed and natural protein
 evolution. We propose that combining generative properties and functional
 predictive power of variational autoencoders and coevolutionary analysis
 could be beneficial in applications for protein engineering and design.
description: Homologs were found and aligned using the HMMER suite and PFAM
 seeds or a single seed sequence. Other datasets are associated with cited
 papers and are aligned also using HMMER. De novo sequences are generated
 using the LGL model. GO annotations were retrieved using
 QuickGO.
description: All fasta files can be opened using any text editor.
DOI: 10.5061/dryad.9cnp5hqn4
title: Sample metadata for feline leukemia virus dataset

description: Feline leukemia virus (FeLV) is a gammaretrovirus with horizontally
 transmitted and endogenous forms. Domestic cats are the primary reservoir
 species, but FeLV outbreaks in endangered Florida panthers and Iberian
 lynx have resulted in mortalities. To assess prevalence and
 interspecific/intraspecific transmission, we conducted an extensive survey
 and phylogenetic analysis of FeLV infection in free-ranging pumas (n=641),
 bobcats (n=212) and shelter domestic cats (n=304). Samples were collected
 from coincident habitats across the United States between
 1985-2018.  FeLV infection was detected in 3.12% puma, 6.25%
 domestic cat, and 0.47% bobcat samples analyzed. Puma prevalence varied by
 location, with Florida having the highest rate of infection. 
 FeLV env sequences revealed variation among isolates, and we identified
 two distinct clades.  Both progressive and regressive infections
 were identified in cats and pumas. Based upon time and location of
 sampling and phylogenetic analysis, we inferred 3 spillover events between
 domestic cats and puma; 3 puma-to-puma transmissions were inferred in
 Florida. An additional 14 infections in pumas likely represented spillover
 events following contact with reservoir host domestic cat populations. Our
 data provides evidence that FeLV transmission from domestic cats to pumas
 occurs widely across the US, and puma-to-puma transmission may occur in
 genetically and geographically constrained populations.
description: All samples in the dataset were screened for feline leukemia
 virus with an FeLV-A specific qPCR. The proviral load of positive samples
 was quantified via qPCR by normalizing against the puma or domestic cat
 CCR5 housekeeping gene, depending upon the species of the sample.
 Additionally, we used conventional PCR to isolate the FeLV env gene from
 FeLV positive samples, cloned the PCR product, and Sanger sequenced the
 clones for a phylogenetic analysis of the env gene. This dataset
 identifies all samples screened and which individuals tested positive. For
 positive animals, this dataset lists the proviral load and if FeLV
 isolates from the invidual were sequenced. FeLV sequences for this study
 are published to GenBank.
DOI: 10.25349/d9s90s
title: Climatology of Sundowner Winds in Coastal Santa Barbara, California, Based on 30 yr High Resolution WRF Downscaling

description: Weather Research and Forecasting (WRF) model version 4.0.1 was used to
 produce a 32 yr high-resolution (1km horizontal grid spacing and hourly
 resolution) downscaling climatology over Santa Barbara County. Data in
 this repository contain surface meteorological variables from WRF
 downscaling simulations during a series of Sundowner wind events.
 The list of events is: -- Painted Cave Fire 1990: 26-June,
 27-June, 28-June-- Tea Fire 2008: 13-November, 14-November-- 2004:
 24-April, 27-April, 28-April, 2-May, 3-May-- Jesusita Fire 2009: 5-May,
 6-May, 7-May, 8-May, -- Sherpa Fire 2016: 15-June, 16-June--
 Whittier Fire 2017: 6-July, 8-July-- 2017: 11-March, 12-March Users
 interested in accessing the entire 32-year WRF downscaling dataset, please
 contact: Charles Jones at cjones@eri.ucsb.edu  
  
description: WRF model version 4.0.1 was used to produce a 32 yr
 high-resolution downscaling climatology over Santa Barbara County. WRF was
 configured with 4 two-way nested grids with 27 km, 9 km, 3 km and 1 km
 horizontal grid spacings. WRF was configured with 55 vertical levels and
 model top at 50 hPa. The configuration used numerical parameterizations
 for microphysics (Single moment 6-class, Hong and Lim, 2006), long-wave
 and short-wave radiation transfer (RRTMG, Iacono et al., 2008), Noah
 multi-parameterization options (Noah-MP) (Niu et al., 2011), surface layer
 physics and planetary boundary layer (MYNN, Nakanishi and Niino, 2009; 
 Olson et al., 2019). Initial and boundary conditions were obtained from
 the European Centre for Medium-Range Weather Forecasts Interim Reanalysis
 (ERA Interim) (Dee et al., 2011). WRF was initialized on 1 July 00UTC of a
 given year and integrated continuously until 1 September 00UTC of the
 following year and repeated for 32 yr. Sea surface temperature (SST) from
 ERA Interim was updated every 6 h. Grid nudging was applied in all model
 levels of the 27 km grid (nudging coefficient 0.0003 s−1) so that WRF was
 forced to follow large-scale features from the reanalysis.
 Additional details can be found in the associate
 manuscript.  
description: Data can be accessed with any software capable of processing
 NetCDF format files. Examples include: -- python and
 wrf-python https://wrf-python.readthedocs.io/en/latest/
 -- Interactive Data Language (IDL) --
 Matlab For more usage notes data, refer to the
 README.txt file.
DOI: 10.5061/dryad.7m0cfxpxd
title: Data derived state probabilities for Z. noltei monitoring study. Observed variables were shoot density at four sites in this study

description: 1. In general, it is not feasible to collect enough empirical data to
 capture the entire range of processes that define a complex system, either
 intrinsically or when viewing the system from a different geographical or
 temporal perspective. In this context, an alternative approach is to
 consider model transferability, which is the act of translating a model
 built for one environment to another less well-known situation. Model
 transferability and adaptability may be extremely beneficial - approaches
 that aid in the reuse and adaption of models, particularly for sites with
 limited data, would benefit from widespread model uptake. Besides the
 reduced effort required to develop a model, data collection can be
 simplified when transferring a model to a different application context.
 2. The research presented in this paper focused on a case study to
 identify and implement guidelines for model adaptation. Our study adapted
 a general Dynamic Bayesian Networks (DBN) of a seagrass ecosystem to a new
 location where nodes were similar, but the conditional probability tables
 varied. We focused on two species of seagrass (Zostera noltei and Zostera
 marina) located in Arcachon Bay, France. Expert knowledge was used to
 complement peer-reviewed literature to identify which components needed
 adjustment including parameterisation and quantification of the model, and
 desired outcomes. We adopted both linguistic labels and scenario-based
 elicitation to elicit from experts the conditional probabilities used to
 quantify the DBN. 3. Following the proposed guidelines, the model
 structure of the general DBN was retained, but the conditional probability
 tables were adapted for nodes that characterised the growth dynamics in
 Zostera spp. population located in Arcachon Bay, as well as the seasonal
 variation on their reproduction. Particular attention was paid to the
 light variable as it is a crucial driver of growth and physiology for
 seagrasses. 4. Our guidelines provide a way to adapt a general DBN to
 specific ecosystems to maximise model reuse and minimise re-development
 effort. Especially important from a transferability perspective are
 guidelines for ecosystems with limited data, and how simulation and prior
 predictive approaches can be used in these contexts.
description: Data-derived state probabilities for the seagrass monitoring
 study (Cognat et al., 2018) were used to validate the DBN model for
 Zostera noltei in Arcachon Bay. Shoot density was observed at four sites
 in this study (Supporting Information Table S4).
DOI: 10.5061/dryad.zcrjdfngd
title: Relationship between eDNA concentration from metabarcoding method and stream fish density under field conditions

description: Estimating abundance or biomass using eDNA metabarcoding is a powerful
 emerging tool that may provide an alternative to conventional laborious
 methods for biological monitoring. However, inferring aquatic
 macroorganism abundance or biomass using eDNA concentrations remains
 challenging, especially in lotic environments, because of several
 potential confounding factors. In this study, we tested whether
 quantitative eDNA metabarcoding that uses internal standard DNA can be
 used to estimate the abundance of four fish species. We collected eDNA
 samples and concurrently estimated fish densities using the conventional
 removal method in small tributaries in four seasons during a year. The
 effects of potential confounding factors, including the body mass of the
 individuals, water temperature, and discharge volume, were assessed using
 an allometric scaling model. We found an increasing trend of eDNA
 concentration against the increase in abundance across all species. In the
 most abundant species, a significant increase in the precision of
 predicted abundance was achieved by considering confounding factors, such
 as season and discharge. Although this study successfully determined the
 relationships between eDNA concentration and fish abundance under lotic
 field conditions, it also identified several limitations of quantitative
 eDNA metabarcoding. The relationship between eDNA concentration and fish
 abundance in rare species showed significant variances in the regression.
 More sequencing depth may be necessary to detect rare species
 sufficiently. The eDNA concentration estimation error effect was
 significant, particularly among the samples that showed the same abundance
 figures by direct capture estimation. The utilization of quantitative eDNA
 metabarcoding may be suitable for organisms that are expected to have a
 substantial variation in their population density. More comparative
 studies with various conventional methods would be informative, especially
 in lotic field environments, to overcome these limitations and achieve
 wider applications of eDNA metabarcoding in future research and
 monitoring.
DOI: 10.5061/dryad.wwpzgmsn6
title: Data and code for: Dog lifespans and the evolution of ageing

description: The basic tenets of the evolutionary theories of senescence are well
 supported. However, there has been little progress in determining the
 relative influences of mutation accumulation and life history
 optimisation. The causes of the well-established inverse relationship
 between lifespan and body size across dog breeds are used here to test
 these two classes of theories. The lifespan-body size relationship is
 confirmed for the first time after controlling for breed phylogeny. The
 lifespan-body size relationship cannot be explained by evolutionary
 responses to differences in extrinsic mortality, either of contemporary
 breeds or of breeds at their establishment. The development of breeds
 larger and smaller than ancestral grey wolves has occurred through changes
 in early growth rate. This may explain the increase in the minimum
 age-dependent mortality rate with breed body size and thus higher
 age-dependent mortality throughout adult life. The main cause of this
 mortality is cancer. These patterns are consistent with the optimisation
 of life history as described by the disposable soma theory of the
 evolution of ageing. The dog breed lifespan-body size relationship may be
 the result of the evolution of greater defence against cancer lagging
 behind the rapid increase in body size during recent breed establishment.
description: Data are from published sources.
description: Data were analysed using R.
DOI: 10.15468/dl.bx9v25
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Padaungiella",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 71 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003179-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gxd2547q2
title: Supplemental text for: Wuchiapingian (Lopingian, Late Permian) brachiopod fauna from Guangdong Province, southeastern China: systematics and contribution to the Lopingian recovery

description: A most diversified Wuchiapingian brachiopod fauna, which contains 57
 species in 28 genera, is described from the Shuizhutang Formation at
 Liannan section, Guangdong province, southeastern China. Four new species
 are proposed. Among these 57 species, many of them have been fully
 described in recent papers and thus are only illustrated in the manuscript
 and described herein.
description: All species have been systematically described and the
 classification above genus level follows Kaesler (2000a, 2000b, 2002,
 2006) and Selden (2007).
description: Please refer to ReadMe file.
DOI: 10.5061/dryad.2fqz612s1
title: SnRNA-seq and mRNA hybridization indicate key bud events and LcFT1 and LcTFL1-2 mRNA transportability during floral transition in litchi

description: In flowering plants, floral induction signals intersect at the shoot apex
 to modulate meristem determinacy and growth form. Herein, we reported a
 snRNA-seq analysis of litchi apical buds at different developmental
 stages. A total of 41,641 nuclei expressing 21,402 genes were analyzed,
 revealing 35 cell clusters corresponding to 12 broad populations. We
 signature genes associated with floral transition and propose a model that
 profiles the key events associated with litchi floral meristem identity by
 analyzing 567 identified floral meristem cells at single-cell resolution.
 Interestingly, snRNA-seq data indicated that all putative FT and TFL1
 genes were not expressed in bud nuclei, but significant expressions of
 them were detected in bud samples using RT-PCR. Based on the expression
 patterns and gene silencing results, we highlight the critical role of
 LcTFL1-2 in inhibiting flowering and propose that LcFT1/LcTFL1-2
 expression ratio may determine the success of flower transition. The
 transport of LcFT1 and LcTFL1-2 mRNA from the leaf to the shoot apical
 meristem was proposed based on in-situ and dot blot hybridization results.
 These findings allowed for a more comprehensive understanding of the
 molecular events that occur during the litchi floral transition, as well
 as the identification of new regulators.