cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.46st5
title: Data from: Dataset of human medial temporal lobe single neuron activity during declarative memory encoding and recognition

description: We present a dataset of 1,576 single neurons recorded from the human
 amygdala and hippocampus in 65 sessions from 42 patients undergoing
 intracranial monitoring for localization of epileptic seizures. Subjects
 performed a recognition memory task with pictures as stimuli. Subjects
 were asked to identify whether they had seen a particular image the first
 time (‘new’) or second time (‘old’) on a 1–6 confidence scale. This
 comprehensive dataset includes the spike times of all neurons and their
 extracellular waveforms, behavior, electrode locations determined from
 post-operative MRI scans, demographics, and the stimuli shown. As
 technical validation, we provide spike sorting quality metrics and
 assessment of tuning of cells to verify the presence of visually-and
 memory selective cells. We also provide analysis code that reproduces key
 scientific findings published previously on a smaller version of this
 dataset. Together, this large dataset will facilitate the investigation of
 the neural mechanism of declarative memory by providing a substantial
 number of hard to obtain human single-neuron recordings during a well
 characterized behavioral task.
description: Data, Code,
 StimuliThis file contains a set
 of 1576 single neurons recorded from the human MTL during a recognition
 memory "new/old" task with confidence ratings. This data was
 acquired using hybrid depth electrodes from human epilepsy patients
 undergoing invasive monitoring for localizing seizures. All data is
 provided in *.mat files (Matlab format). Also part of this file is code
 that reproduces the plots of the data descriptor and the stimuli (images)
 shown to patients. Please refer to the accompanying data descriptor paper
 for details on how to use this data.RecogMemory_MTL_release_v2.zip
DOI: 10.5061/dryad.f6r55
title: Data from: The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis)

description: Interactions between extrinsic factors, such as disruptive selection, and
 intrinsic factors, such as genetic incompatibilities among loci, often
 contribute towards the maintenance of species boundaries. The relative
 roles of these factors in the establishment of reproductive isolation can
 be examined using species pairs characterized by gene flow throughout
 their divergence history. We investigated the process of speciation and
 the maintenance of species boundaries between Pinus strobiformis and P.
 flexilis. Utilizing ecological niche modeling, demographic modeling, and
 genomic cline analyses, we illustrated a divergence history with
 continuous gene flow. Our results supported an abundance of advanced
 generation hybrids and a lack of loci exhibiting steep transition in
 allele frequency across the hybrid zone. Additionally, we found evidence
 for climate-associated variation in the hybrid index and niche divergence
 between parental species and the hybrid zone. These results are consistent
 with extrinsic factors, such as climate, being an important isolating
 mechanism. A buildup of intrinsic incompatibilities and of co-adapted gene
 complexes is also apparent, although these appear to be in the earliest
 stages of development. This supports previous work in coniferous species
 demonstrating the importance of extrinsic factors in facilitating
 speciation. Overall, our findings lend support to the hypothesis that
 varying strengths and directions of selection pressures across the long
 lifespans of conifers, in combination with their life history strategies,
 delay the evolution of strong intrinsic incompatibilities.
description: Genotype
 fileThis file contains
 genotype information for all 51633 SNPs coded as 0,1,2 (based on the
 number of minor alleles).Gdata012.txtSDM_locationsFiltered occurrence records for Core, Periphery & P. flexilis used in ENM.Demographic_ModelsPython scripts used to run 11 demographic models for SWWP (core and periphery) & LPDemographicModels.zip
DOI: 10.5281/zenodo.18381185
title: ЛИНГВИСТИЧЕСКИЕ ОСОБЕННОСТИ ФРАЗЕОЛОГИЗМОВ РУССКОГО И УЗБЕКСКОГО ЯЗЫКОВ

description: В данной статье рассматриваются лингвистические особенности фразеологических единиц русского и узбекского языков в сопоставительном аспекте. Анализируются структурные, семантические, грамматические и стилистические характеристики фразеологизмов, выявляются универсальные и национально-специфические черты фразеологических систем. Особое внимание уделяется проблемам классификации фразеологизмов, их роли в формировании языковой картины мира и специфике функционирования в речи. Сопоставительное исследование позволяет определить типологические сходства и различия в фразеологических системах двух неродственных языков.
DOI: 10.5281/zenodo.18381186
title: ЛИНГВИСТИЧЕСКИЕ ОСОБЕННОСТИ ФРАЗЕОЛОГИЗМОВ РУССКОГО И УЗБЕКСКОГО ЯЗЫКОВ

description: В данной статье рассматриваются лингвистические особенности фразеологических единиц русского и узбекского языков в сопоставительном аспекте. Анализируются структурные, семантические, грамматические и стилистические характеристики фразеологизмов, выявляются универсальные и национально-специфические черты фразеологических систем. Особое внимание уделяется проблемам классификации фразеологизмов, их роли в формировании языковой картины мира и специфике функционирования в речи. Сопоставительное исследование позволяет определить типологические сходства и различия в фразеологических системах двух неродственных языков.
DOI: 10.5061/dryad.874p9
title: Data from: Wolf in sheep's clothing: model misspecification undermines tests of the neutral theory for life histories

description: Understanding the processes behind change in reproductive state along
 life-history trajectories is a salient research program in evolutionary
 ecology. Two processes, state dependence and heterogeneity, can drive the
 dynamics of change among states. Both processes can operate
 simultaneously, begging the difficult question of how to tease them apart
 in practice. The Neutral Theory for Life Histories (NTLH) holds that the
 bulk of variations in life-history trajectories is due to state dependence
 and is hence neutral: Once previous (breeding) state is taken into
 account, variations are mostly random. Lifetime reproductive success
 (LRS), the number of descendants produced over an individual's
 reproductive life span, has been used to infer support for NTLH in natura.
 Support stemmed from accurate prediction of the population-level
 distribution of LRS with parameters estimated from a state dependence
 model. We show with Monte Carlo simulations that the current reliance of
 NTLH on LRS prediction in a null hypothesis framework easily leads to
 selecting a misspecified model, biased estimates and flawed inferences.
 Support for the NTLH can be spurious because of a systematic positive bias
 in estimated state dependence when heterogeneity is present in the data
 but ignored in the analysis. This bias can lead to spurious positive
 covariance between fitness components when there is in fact an underlying
 trade-off. Furthermore, neutrality implied by NTLH needs a clarification
 because of a probable disjunction between its common understanding by
 evolutionary ecologists and its translation into statistical models of
 life-history trajectories. Irrespective of what neutrality entails,
 testing hypotheses about the dynamics of change among states in life
 histories requires a multimodel framework because state dependence and
 heterogeneity can easily be mistaken for each other.
description: misspecification in
 individual life history modelsThe files in this folder
 allow to replicate the results of the analyses presented in "Wolf in
 Sheep’s Clothing: Model Misspecification Undermines Tests of The Neutral
 Theory for Life Histories". The statistical software R (R Core Team,
 2016) is needed, along with a few libraries. Please, make sure to change
 the path to your working directory. The version of R used at the time of
 the original analysis was R version 3.2.3 (2015-12-10) "Wooden
 Christmas-Tree". All figures from the main manuscript can be
 replicated using the data file "20161204_summary_stat.txt" and
 scripts "03_Tile_plots_main.txt" &
 "04_Tile_plots_suppl.txt". Functions for simulating data are in
 the script "LRS_simul.txt". These scripts were last checked on
 2017-02-22. Please, send me an email (authierm at gmail dot com) if you
 have any remarks or questions. References R Core Team (2016). R: A
 language and environment for statistical computing. R Foundation for
 Statistical Computing, Vienna, Austria. URL
 https://www.R-project.org/.misspecification.zip
DOI: 10.5061/dryad.32md8
title: Data from: Variability of Symbiodinium communities in waters, sediments, and corals of thermally distinct reef pools in American Samoa

description: Reef-building corals host assemblages of symbiotic algae (Symbiodinium
 spp.) whose diversity and abundance may fluctuate under different
 conditions, potentially facilitating acclimatization to environmental
 change. The composition of free-living Symbiodinium in reef waters and
 sediments may also be environmentally labile and may influence symbiotic
 assemblages by mediating supply and dispersal. The magnitude and spatial
 scales of environmental influence over Symbiodinium composition in
 different reef habitat compartments are, however, not well understood. We
 used pyrosequencing to compare Symbiodinium in sediments, water, and ten
 coral species between two backreef pools in American Samoa with
 contrasting thermal environments. We found distinct compartmental
 assemblages of clades A, C, D, F, and/or G Symbiodinium types, with strong
 differences between pools in water, sediments, and two coral species. In
 the pool with higher and more variable temperatures, abundance of various
 clade A and C types differed compared to the other pool, while abundance
 of D types was lower in sediments but higher in water and in Pavona
 venosa, revealing an altered habitat distribution and potential linkages
 among compartments. The lack of between-pool effects in other coral
 species was due to either low overall variability (in the case of Porites)
 or high within-pool variability. Symbiodinium communities in water and
 sediment also showed within-pool structure, indicating that environmental
 influences may operate over multiple, small spatial scales. This work
 suggests that Symbiodinium composition is highly labile in reef waters,
 sediments, and some corals, but the underlying drivers and functional
 consequences of this plasticity require further testing with high spatial
 resolution biological and environmental sampling.
description: Cunning_PLoSONE_Dryad_ArchiveThis archive file contains all data and scripts necessary to reproduce the analyses and figures presented in this manuscript.
DOI: 10.5061/dryad.v7f30
title: Data from: Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America

description: The Tremarctinae are a subfamily of bears endemic to the New World,
 including two of the largest terrestrial mammalian carnivores that have
 ever lived: the giant, short-faced bears Arctodus simus from North America
 and Arctotherium angustidens from South America (greater than or equal to
 1000 kg). Arctotherium angustidens became extinct during the Early
 Pleistocene, whereas Arctodus simus went extinct at the very end of the
 Pleistocene. The only living tremarctine is the spectacled bear
 (Tremarctos ornatus), a largely herbivorous bear that is today only found
 in South America. The relationships among the spectacled bears
 (Tremarctos), South American short-faced bears (Arctotherium) and North
 American short-faced bears (Arctodus) remain uncertain. In this study, we
 sequenced a mitochondrial genome from an Arctotherium femur preserved in a
 Chilean cave. Our molecular phylogenetic analyses revealed that the South
 American short-faced bears were more closely related to the extant South
 American spectacled bear than to the North American short-faced bears.
 This result suggests striking convergent evolution of giant forms in the
 two groups of short-faced bears (Arctodus and Arctotherium), potentially
 as an adaptation to dominate competition for megafaunal carcasses.
description: BEAST_filesBEAST files, including input .xml and final maximum clade credibility tree.RAxML_filesRAxML files, including input alignment & partition file and final tree.PartitionFinder_filesInput & output from PartitionFinder analyses.Arctotherium_SeqData_Filtered_Collapsed.fastqFASTQ file containing filtered, de-mulitplexed, and collapsed MiSeq (Illumina) sequencing reads corresponding to the Arctotherium enriched genomic library. See main publication for full details on data processing.
DOI: 10.5061/dryad.kn1n1
title: Data from: Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera

description: The causes of exceptionally high plant diversity in Mediterranean-climate
 biodiversity hotspots are not fully understood. We asked whether a
 mechanism similar to the tropical niche conservatism hypothesis could
 explain the diversity of four large genera (Protea, Moraea, Banksia, and
 Hakea) with distributions within and adjacent to the Greater Cape
 Floristic Region (South Africa) or the Southwest Floristic Region
 (Australia). Using phylogenetic and spatial data we estimated the
 environmental niche of each species, and reconstructed the mode and
 dynamics of niche evolution, and the geographic history, of each genus.
 For three genera there were strong positive relationships between the
 diversity of clades within a region and their inferred length of
 occupation of that region. Within genera, there was evidence for strong
 evolutionary constraint on niche axes associated with climatic seasonality
 and aridity, with different niche optima for hotspot and non-hotspot
 clades. Evolutionary transitions away from hotspots were associated with
 increases in niche breadth and elevated rates of niche evolution. Our
 results point to a process of “hotspot niche conservatism” whereby the
 accumulation of plant diversity in Mediterranean-type ecosystems results
 from longer time for speciation, with dispersal away from hotspots limited
 by narrow and phylogenetically-conserved environmental niches.
description: banksia.climateOccurrence data from AVH and climate data from CLiMOND for the genus Banksia.hakea.climateOccurence data from AVH and climate data from CLiMond for the genus Hakeaprotea.climateOccurrence records from SANBi and climate data from CLiMond for the genus Proteamoraea.climateOccurrence records from SANBi and climate data from CLiMond for the genus MoraeaOUwie_model_comparison_results_all_generaThis compressed folder contains results from an evolutionary model comparison of 5 OU (OU1, OUM, OUMA, OUMV, OUMVA) and 2 BM (BMS, BMM) models in the R package OUwie. We investiagted 9 environmental niche axes in each of the four genera. for each niche axis we reran the model comparison 50 times across 50 different stochastic maps derived from a BioGeoBEARS analysis in R. So here we present, for each genus, nine .csv files containing the results of 50 different model comparisons.
DOI: 10.5061/dryad.7qm89
title: Data from: The Golgi-localized γ-ear-containing ARF-binding (GGA) proteins alter amyloid-β precursor protein (APP) processing through interaction of their GAE domain with the beta-site APP cleaving enzyme 1 (BACE1)

description: Proteolytic processing of amyloid-β precursor protein (APP) by beta-site
 APP cleaving enzyme 1 (BACE1) is the initial step in the production of
 amyloid beta (Aβ), which accumulates in senile plaques in Alzheimer’s
 disease (AD). Essential for this cleavage is the transport and sorting of
 both proteins through endosomal/Golgi compartments. Golgi-localized
 γ-ear-containing ARF-binding (GGA) proteins have striking cargo-sorting
 functions in these pathways. Recently, GGA1 and GGA3 were shown to
 interact with BACE1, to be expressed in neurons, and to be decreased in AD
 brain, whereas little is known about GGA2. Since GGA1 impacts Aβ
 generation by confining APP to the Golgi and perinuclear compartments, we
 tested whether all GGAs modulate BACE1 and APP transport and processing.
 We observed decreased levels of secreted APP alpha (sAPPα), sAPPβ, and Aβ
 upon GGA overexpression, which could be reverted by knockdown. GGA-BACE1
 co-immunoprecipitation was impaired upon GGA-GAE but not VHS domain
 deletion. Autoinhibition of the GGA1-VHS domain was irrelevant for BACE1
 interaction. Our data suggest that all three GGAs affect APP processing
 via the GGA-GAE domain.
description: uncropped and unadjusted
 Westernblotsuncropped and unadjusted
 Westernblotuncropped
 blots.zip
DOI: 10.5061/dryad.00v07
title: Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

description: Whether species can respond evolutionarily to current climate change is
 crucial for the persistence of many species. Yet, very few studies have
 examined genetic responses to climate change in manipulated experiments
 carried out in natural field conditions. We examined the evolutionary
 response to climate change in a common annelid worm using a controlled
 replicated experiment where climatic conditions were manipulated in a
 natural setting. Analyzing the transcribed genome of 15 local populations,
 we found that about 12% of the genetic polymorphisms exhibit differences
 in allele frequencies associated to changes in soil temperature and soil
 moisture. This shows an evolutionary response to realistic climate change
 happening over short-time scale, and calls for incorporating evolution
 into models predicting future response of species to climate change. It
 also shows that designed climate change experiments coupled with genome
 sequencing offer great potential to test for the occurrence (or lack) of
 an evolutionary response.
description: Filtered
 ContigsFile (FASTA format)
 containing the sequence of all contigs obtained from de novo assembly of
 transcriptome sequencing. Only contigs of at least 200 nt and having
 average coverage of 20x are included.FilteredContigs_200nt20x_cognettiq.fasRaw counts of minor allele frequency at each SNP positionCSV file with counts of reads supporting each allele at each SNP position and in each populationPoisRegFinal_New.csvRaw counts of minor allele frequency at each SNP position (5' UTR)CSV file with counts of reads supporting each allele at each SNP position and in each populationPoisReg_5UTR_final_withSampleTags.csvRaw counts of minor allele frequency at each SNP position (3' UTR)CSV file with counts of reads supporting each allele at each SNP position and in each populationPoisReg_3UTR_final_withSampleTags.csvCOX-I multiple alignment for barcodingAlignment of the Cox-1 reference sequence we used to barcode our samples– labelled JN259763 – with a set of Cox-1 sequences published more recently: http://datadryad.org/resource/doi:10.5061/dryad.6mh29COI_CognettiaPlusJN259763.nex
DOI: 10.5061/dryad.v9b30
title: Data from: Applications of three-dimensional box modeling to paleontological functional analysis

description: Functional analysis through computer modeling can inform on how extinct
 organisms moved and fed, allowing us to test long-standing paleobiological
 hypotheses. Many such studies are based on digital models derived from
 computed tomography or surface scanning, but these methods are not
 appropriate for all fossils. Here, we show that box modeling—3-D modeling
 of complex shapes based on simple objects—can be used to reconstruct the
 morphology of various fossil specimens. Moreover, the results of
 computational functional analyses utilizing such models are very similar
 to those for models derived from tomographic or surface-based techniques.
 Box modeling is more broadly applicable than alternative methods for
 digitizing specimens; hence, there is great potential for this approach in
 paleontological functional analysis. Possible applications include
 large-scale comparative studies, analyses of hypothetical morphologies,
 and virtually restoring incomplete/distorted specimens.
description: Supplemental Data
 13-D
 model (in STL format) of the skull of the theropod dinosaur Allosaurus
 fragilis (MOR 693) generated using box modeling.Supplemental_Data_1.stlSupplemental Data 23-D model (in STL format) of the skull of the theropod dinosaur Allosaurus fragilis (MOR 693) based on computed tomography (CT).Supplemental_Data_2.stlSupplemental Data 33-D model (in STL format) of a dorsal vertebra of the ornithischian dinosaur Stegosaurus stenops (NHMUK R36730) generated using box modeling.Supplemental_Data_3.stlSupplemental Data 43-D model (in STL format) of a dorsal vertebra of the ornithischian dinosaur Stegosaurus stenops (NHMUK R36730) based on photogrammetry.Supplemental_Data_4.stlSupplemental Data 53-D model (in STL format) of a complete individual of the cinctan echinoderm Protocinctus mansillaensis (MPZ 2004/170) generated using box modeling.Supplemental_Data_5.stlSupplemental Data 63-D model (in STL format) of a complete individual of the cinctan echinoderm Protocinctus mansillaensis (MPZ 2004/170) based on computed tomography (CT).Supplemental_Data_6.stl
DOI: 10.5061/dryad.2pt83
title: Data from: Mutual stabilization of rhythmic vocalization and whole-body movement

description: The current study investigated the rhythmic coordination between
 vocalization and whole-body movement. Previous studies have reported that
 spatiotemporal stability in rhythmic movement increases when coordinated
 with a rhythmic auditory stimulus or other effector in a stable
 coordination pattern. Therefore, the present study conducted two
 experiments to investigate (1) whether there is a stable coordination
 pattern between vocalization and whole-body movement and (2) whether a
 stable coordination pattern reduces variability in whole-body movement and
 vocalization. In Experiment 1, two coordination patterns between
 vocalizations and whole-body movement (hip, knee, and ankle joint
 flexion-on-the-voice vs. joint extension-on-the-voice) in a standing
 posture were explored at movement frequencies of 80, 130, and 180 beats
 per minute. At higher movement frequencies, the phase angle in the
 extension-on-the-voice condition deviated from the intended phase angle.
 However, the angle of the flexion-on-the-voice was maintained even when
 movement frequency increased. These results suggest that there was a
 stable coordination pattern in the flexion-on-the-voice condition. In
 Experiment 2, variability in whole-body movement and voice-onset intervals
 was compared between two conditions: one related to tasks performed in the
 flexion-on-the-voice coordination (coordination condition) that was a
 stable coordination pattern, and the other related to tasks performed
 independently (control condition). The results showed that variability in
 whole-body movement and voice-onset intervals was smaller in the
 coordination condition than in the control condition. Overall, the present
 study revealed mutual stabilization between rhythmic vocalization and
 whole-body movement via coordination within a stable pattern, suggesting
 that coupled action systems can act as a single functional unit or
 coordinative structure.
description: Mutual_stabilizationReadme file for data used in study: "Mutual Stabilization of Rhythmic Vocalization and Whole-Body Movement " K. Miyata, K. Kudo PLOS ONE For questions regarding the data, please contact the authors: K. Miyata (still.kzn@gmail.com)