cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nt40m53
title: Data from: A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change

description: Plant-herbivore interactions provide critical insights into the mechanisms
 that govern the spatiotemporal distributions of organisms. These
 interactions are crucial to understanding the impacts of climate change,
 which are likely to have an effect on the population dynamics of alpine
 herbivores. The Royle’s pika (Ochotona roylei, hereafter pika) is a
 lagomorph found in the western Himalaya, and is dependent on alpine plants
 that are at risk from climate change. As the main prey of many carnivores
 in the region, the pika plays a crucial role in trophic interactions. We
 examined topographical features, plant genera presence, and seasonal
 dynamics as drivers of the plant richness in the pika’s diet across an
 elevational gradient (2600−4450 m). We identified 79 plant genera in the
 faecal pellets of pikas, of which 89% were forbs, &gt; 60% were
 endemic to the Himalaya and 97.5% of the plant genera identified followed
 the C3 photosynthetic pathway. We found that during the pre-monsoon
 season, the plant richness of the pika’s diet decreased with increasing
 elevation. We demonstrate that a large area of talus supports greater
 plant diversity and, not surprisingly, results in higher species richness
 in the pika’s diet. However, in talus habitat with deep crevices, pikas
 consumed fewer plant genera suggesting they may be foraging sub-optimally
 due to predation risk. The continued increase in global temperature is
 expected to have an effect on the distribution dynamics of C3 plants and
 consequently influence pika diet and distribution, resulting in a
 significant negative cascading effect on the Himalayan ecosystem.
description: GPS location of sample
 collectionGPS location of faecal
 sample meta barcoded during the studyDATA for GLM
 modellingData used to test the
 various ecological hypothesis to understand the influence of habitat
 structure on diet diversityCode for GLM
 modelR code used to test
 various ecological hypothesis using GLM modelsList of meta barcode
 sample name with illumina tag and locationList of meta barcode
 sample name with corresponding illumina tag and sample collection
 locationsList of sample name_illumina
 tag_location.xlsxRoyle pika faecal DNA
 meta barcode dataRoyle pika faecal DNA
 meta barcode dataPika DNA meta barcode RAW
 data.zip
DOI: 10.5061/dryad.02c47
title: Data from: Neutral processes forming large clones during colonization of new areas

description: In species reproducing both sexually and asexually clones are often more
 common in recently established populations. Earlier studies have suggested
 that this pattern arises due to natural selection favouring generally or
 locally successful genotypes in new environments. Alternatively, as we
 show here, this pattern may result from neutral processes during species’
 range expansions. We model a dioecious species expanding into a new area
 in which all individuals are capable of both sexual and asexual
 reproduction, and all individuals have equal survival rates and dispersal
 distances. Even under conditions that favour sexual recruitment in the
 long run, colonisation starts with an asexual wave. After colonisation is
 completed, a sexual wave erodes clonal dominance. If individuals reproduce
 more than one season, and with only local dispersal, a few large clones
 typically dominate for thousands of reproductive seasons. Adding
 occasional long-distance dispersal, more dominant clones emerge, but they
 persist for a shorter period of time. The general mechanism involved is
 simple: edge effects at the expansion front favour asexual (uniparental)
 recruitment where potential mates are rare. Specifically, our model shows
 that neutral processes (with respect to genotype fitness) during the
 population expansion, such as random dispersal and demographic
 stochasticity, produce genotype patterns that differ from the patterns
 arising in a selection model. The comparison with empirical data from a
 postglacially established seaweed species (Fucus radicans) shows that in
 this case a neutral mechanism is strongly supported.
description: Code_for_the_main_modelCode for the main model in the paper. The ReadMe file is contained in the folder.Code_for_model_with_males_sexual_onlyCode for the model with males reproducing only sexually and females reproducing both sexually and asexually. The ReadMe file is contained in the folder.Code_for_relocation_of_sexual_seedsCode used to simulate the model with long-range dispersal of seeds instead of adults, or asexual fragments. The ReadMe file is contained in the folder.Data_for_Fig2Data used to generate Fig. 2.Data_for_Fig3Data used to generate Fig. 3.Data_for_Fig4Data used to generate Fig. 4.Data_for_Fig5Data used to generate Fig. 5.Data_for_Fig6Data used to generate Fig. 6.Data_for_Fig7Data used to generate Fig. 7.
DOI: 10.5061/dryad.50k60
title: Data from: Using optimal control to disambiguate the effect of depression on sensorimotor, motivational and goal-setting functions

description: Differentiating the ability from the motivation to act is of central
 importance to psychiatric disorders in general and depression in
 particular. However, it has been difficult to develop quantitative
 approaches to relate depression to poor motor performance in goal-directed
 tasks. Here, we use an inverse optimal control approach to provide a
 computational framework that can be used to infer and factorize
 performance deficits into three components: sensorimotor speed, goal
 setting and motivation. Using a novel computer-simulated driving
 experiment, we found that (1) severity of depression is associated with
 both altered sensorimotor speed and motivational function; (2) moderately
 to severely depressed individuals show an increased distance from the stop
 sign indicating aversive learning affecting goal setting functions. Taken
 together, the inverse optimal control framework can disambiguate on an
 individual basis the sensorimotor from the motivational dysfunctions in
 depression, which may help to develop more precisely targeted
 interventions.
description: PlosOne_DR_DataThis .mat file includes experimental data (data{i} for subject i, in which data{i}.mg for task 1 and data{i}.ss for task 2), and model output of sensorimotor speed and motivation.
DOI: 10.34740/kaggle/dsv/14631078
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.ps70b
title: Data from: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate

description: Olfactory cues play an integral, albeit underappreciated, role in
 mediating vertebrate social and reproductive behaviour. These cues
 fluctuate with the signaller's hormonal condition, coincident with
 and informative about relevant aspects of its reproductive state, such as
 pubertal onset, change in season and, in females, timing of ovulation.
 Although pregnancy dramatically alters a female's endocrine profiles,
 which can be further influenced by fetal sex, the relationship between
 gestation and olfactory cues is poorly understood. We therefore examined
 the effects of pregnancy and fetal sex on volatile genital secretions in
 the ring-tailed lemur (Lemur catta), a strepsirrhine primate possessing
 complex olfactory mechanisms of reproductive signalling. While pregnant,
 dams altered and dampened their expression of volatile chemicals, with
 compound richness being particularly reduced in dams bearing sons. These
 changes were comparable in magnitude with other, published chemical
 differences among lemurs that are salient to conspecifics. Such olfactory
 ‘signatures’ of pregnancy may help guide social interactions, potentially
 promoting mother–infant recognition, reducing intragroup conflict or
 counteracting behavioural mechanisms of paternity confusion; cues that
 also advertise fetal sex may additionally facilitate differential sex
 allocation.
description: GCMS
 FilesGCMS files generated
 using Shimadzu QP2010 GC/MS. Files are compressed in RAR format.
 'PC' corresponds to preconceptive; 'Preg' corresponds
 to pregnant.GCMSfiles.rarChemical richness analysesThis file contains the data and analytical script for analyses relating chemical richness to reproductive condition and fetal sex, compressed in RAR format. Open ChemicalAnalyses.jsl in JMP (SAS Institute) and run the script by clicking "Edit, Run Script".ChemicalAnalyses.rarEndocrine analysesThis file contains the data and analytical script for analyses relating serum steroid concentrations to reproductive condition and fetal sex, compressed in RAR format. Open EndocrineAnalyses.jsl in JMP (SAS Institute) and run the script by clicking "Edit, Run Script".EndocrineAnalyses.rar
DOI: 10.5061/dryad.85p80
title: Data from: Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

description: Global climate change is projected to accelerate during the next century,
 altering oceanic patterns in temperature, pH and oxygen concentrations.
 Documenting patterns of genetic adaptation to these variables in locations
 that currently experience geographic variation in them is an important
 tool in understanding the potential for natural selection to allow
 populations to adapt as climate change proceeds. We sequenced the mantle
 transcriptome of 39 red abalone (Haliotis rufescens) individuals from
 three regions (Monterey Bay, Sonoma, north of Cape Mendocino) distinct in
 temperature, aragonite saturation, exposure to hypoxia and disease
 pressure along the California coast. Among 1.17 × 10^6 Single Nucleotide
 Polymorphisms (SNPs) identified in this study (1.37% of the
 transcriptome), 21 579 could be genotyped for all individuals. A principal
 components analysis concluded that the vast majority of SNPs show no
 population structure from Monterey, California to the Oregon border, in
 corroboration with several previous studies. In contrast, an F_ST outlier
 analysis indicated 691 SNPs as exhibiting significantly higher than
 expected differentiation (experiment-wide P &lt; 0.05). From these, it
 was possible to identify 163 genes through BLAST annotation, 34 of which
 contained more than one outlier SNP. A large number of these genes are
 involved in biomineralization, energy metabolism, heat-, disease- or
 hypoxia-tolerance. These genes are candidate loci for spatial adaptation
 to geographic variation that is likely to increase in the future.
description: supplementary_materialsCombined zip archive of supplementary materials.
DOI: 10.5061/dryad.rd247
title: Data from: A new family of Cambrian rhynchonelliformean brachiopods (Order Naukatida) with an aberrant coral-like morphology

description: Tomteluva perturbata gen. et sp. nov. and Nasakia thulensis gen. et sp.
 nov., two new rhynchonelliformean brachiopod taxa, are described from
 carbonate beds from the lower middle Cambrian (Series 3, Stage 5) basinal
 Stephen Formation, Canada, and the upper lower Cambrian (Series 2, Stage
 4) Henson Gletscher Formation, North Greenland, respectively. The two taxa
 are characterized by an unusual coral-like morphology typified by a high
 conical ventral valve with an anteriorly curved umbo and a tube-like
 structure inside the ventral valve, interpreted as pedicle tube. Both
 resemble the problematic late middle Cambrian (Drumian) species
 Anomalocalyx cawoodi Brock from Australia, whose systematic affiliation is
 controversial. Together, the three genera are interpreted as
 representatives of a new family of rhynchonelliformean brachiopods, the
 Tomteluvidae fam. nov., which is interpreted as an aberrant or derived
 taxon within the Order Naukatida. Convergence between the Tomteluvidae and
 the coralla of small solitary Cambrian coralimorphs, as well as the late
 Palaeozoic reef-building richthofenioid brachiopods, might indicate
 adaptation to a similar life habits and environments. However, their small
 size (length 4 mm), well-developed pedicle and perfect morphological
 symmetry make it more likely that tomteluvids lived attached to frondose
 algae or sponges, above the seafloor, in a similar fashion to the
 acrotretoid brachiopods with which they show a high degree of
 morphological convergence. Morphological features of the pedicle tube of
 N. thulensis suggest that the tomteluvid pedicle is homologous to that in
 modern rhynchonelliformean brachiopods. This is the first evidence of the
 pedicle type within the Naukatida and represents the oldest confirmation
 of a rhynchonellate pedicle.
description: 3D reconstruction of
 Tomteluva perturbataStreng_et_al_2016_.mpg
DOI: 10.5061/dryad.dr216
title: Data from: Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing

description: Freshwaters ecosystems are critical but fragile environments directly
 affecting society and its welfare. However, our understanding of genuinely
 freshwater microbial communities, constrained by our capacity to
 manipulate its prokaryotic participants in axenic cultures, remains very
 rudimentary. Even the most abundant components, freshwater Actinobacteria,
 remain largely unknown. Here, applying deep metagenomic sequencing to the
 microbial community of a freshwater reservoir, we were able to circumvent
 this traditional bottleneck and reconstruct de novo seven distinct
 streamlined actinobacterial genomes. These genomes represent three new
 groups of photoheterotrophic, planktonic Actinobacteria. We describe for
 the first time genomes of two novel clades, acMicro (Micrococcineae,
 related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides,
 an aggregate of contigs belonged to a new branch of the Acidimicrobiales.
 All are estimated to have small genomes (~1.2 Mb) and their GC content
 varied from 40-61%. One of the Micrococcineae genomes encodes a
 proteorhodopsin, a rhodopsin type reported for the first time in
 Actinobacteria.The remarkable potential capacity of some of these genomes
 to transform recalcitrant plant detrital material, particularly lignin
 derived compounds, suggests close linkages between the terrestrial and
 aquatic realms. Moreover, abundances of Actinobacteria correlate inversely
 to those of Cyanobacteria that are responsible for prolonged and
 frequently irretrievable damage to freshwater ecosystems. This suggests
 that they might serve as sentinels of impending ecological catastrophes.
description: CytometryThis readme file describes the raw data files for cytometry as performed in the above publication For any further queries please contact antonio.picazo-mozo@uv.esRAW_Actino_Amadorio_FISHThis readme file describes the data file for FISH as performed in the above publication For any further queries please contact antonio.picazo-mozo@uv.esphylogenetic-treesThis readme file describes the tree files for all phylogenetic analyses as performed in the above publication For any further queries please contact ghai.rohit@gmail.com16S-alignmentsThis readme file describes the 16S alignments as performed in the above publication For any further queries please contact ghai.rohit@gmail.com
DOI: 10.5061/dryad.4480g
title: Data from: Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery

description: Using rice (Oryza sativa) as a model crop species, we performed an
 in-depth temporal transcriptome analysis, covering the early and late
 stages of Pi deprivation as well as Pi recovery in roots and shoots, using
 next-generation sequencing. Analyses of 126 paired-end RNA sequencing
 libraries, spanning nine time points, provided a comprehensive overview of
 the dynamic responses of rice to Pi stress. Differentially expressed genes
 were grouped into eight sets based on their responses to Pi starvation and
 recovery, enabling the complex signaling pathways involved in Pi
 homeostasis to be untangled. A reference annotation-based transcript
 assembly was also generated, identifying 438 unannotated loci that were
 differentially expressed under Pi starvation. Several genes also showed
 induction of unannotated splice isoforms under Pi starvation. Among these,
 PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi
 starvation–induced isoform, which was associated with increased
 translation activity. In addition, microRNA (miRNA) expression profiles
 after long-term Pi starvation in roots and shoots were assessed,
 identifying 20 miRNA families that were not previously associated with Pi
 starvation, such as miR6250. In this article, we present a comprehensive
 spatio-temporal transcriptome analysis of plant responses to Pi stress,
 revealing a large number of potential key regulators of Pi homeostasis in
 plants.
description: tpc117325SupplementalDS1FPKM and fold changes of all genes, in rootstpc117325SupplementalDS2FPKM and fold changes of all genes, in shootstpc117325SupplementalDS3FPKM and fold changes of significantly regulated genes, in roots and shoots.tpc117325SupplementalDS4List of genes forming class 1 to 6, in roots and shoots, with expression levels (FPKM).
DOI: 10.5061/dryad.1rr57
title: Data from: Temporal specificity of the initial adaptive response in motor adaptation

description: Repeated exposure to a novel physical environment eventually leads to a
 mature adaptive response whereby feedforward changes in motor output
 mirror both the amplitude and temporal structure of the environmental
 perturbations. However, adaptive responses at the earliest stages of
 learning have been found to be not only smaller, but systematically less
 specific in their temporal structure compared to later stages of learning.
 This observation has spawned a lively debate as to whether the temporal
 structure of the initial adaptive response is, in fact, stereotyped and
 non-specific. To settle this debate, we directly measured the adaptive
 responses to velocity-dependent and position-dependent force-field
 perturbations (vFFs and pFFs) at the earliest possible stage of motor
 learning in humans–after just a single-movement exposure. In line with
 previous work, we found these earliest stage adaptive responses to be more
 similar than the perturbations that induced them. However, the
 single-trial adaptive responses for vFF and pFF perturbations were clearly
 distinct, and the disparity between them reflected the difference between
 the temporal structure of the perturbations that drove them. Critically,
 we observed these differences between single-trial adaptive responses when
 vFF and pFF perturbations were randomly intermingled from one trial to the
 next within the same block, indicating perturbation response specificity
 at the single trial level. These findings demonstrate that the initial
 adaptive responses to physical perturbations are not stereotyped. Instead,
 the neural plasticity in sensorimotor areas is sensitive to the temporal
 structure of a movement perturbation even at the earliest stage in
 learning. This insight has direct implications for the development of
 computational models of early-stage motor adaptation and the evolution of
 this adaptive response with continued training.
description: Motion and force
 dataMATLAB data file (.MAT)
 with experimental data for Joiner et al 2017joineretal2017data.mat
DOI: 10.5061/dryad.150nm
title: Data from: Allatostatin A signalling in Drosophila regulates feeding and sleep and is modulated by PDF

description: Feeding and sleep are fundamental behaviours with significant
 interconnections and cross-modulations. The circadian system and
 peptidergic signals are important components of this modulation, but still
 little is known about the mechanisms and networks by which they interact
 to regulate feeding and sleep. We show that specific thermogenetic
 activation of peptidergic Allatostatin A (AstA)-expressing PLP neurons and
 enteroendocrine cells reduces feeding and promotes sleep in the fruit fly
 Drosophila. The effects of AstA cell activation are mediated by AstA
 peptides with receptors homolog to galanin receptors subserving similar
 and apparently conserved functions in vertebrates. We further identify the
 PLP neurons as a downstream target of the neuropeptide pigment-dispersing
 factor (PDF), an output factor of the circadian clock. PLP neurons are
 contacted by PDF-expressing clock neurons, and express a functional PDF
 receptor demonstrated by cAMP imaging. Silencing of AstA signalling and
 continuous input to AstA cells by tethered PDF changes the sleep/activity
 ratio in opposite directions but does not affect rhythmicity. Taken
 together, our results suggest that pleiotropic AstA signalling by a
 distinct neuronal and enteroendocrine AstA cell subset adapts the fly to a
 digestive energy-saving state which can be modulated by PDF.
description: READMEData_Chenetal_PLOSGeneticsThe file contains the data of the experiments described in the publication incl. supplements, Chen et al. 2016
DOI: 10.15468/dl.e5gjqh
title: Occurrence Download

description: A dataset containing 1505 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Kinosternon integrum Le Conte, 1854"
 ]
}

 The dataset includes 1505 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010111-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g3z4rh
title: Occurrence Download

description: A dataset containing 11654915 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 11654915 records from 1353 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010087-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/14662734
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.25345/c5gb1xw8c
title: MassIVE MSV000100635 - Chronic Stress Accelerates Aging in the Young but Reverses Aging in Aged Mice - liver MandF
title: Chronic stress is thought to accelerate brain aging. We find this is true in the brains of young mice, but reversed in the old. Using chronic variable stress in young (2-month) and aged (24-month) mice, we show that aged animals perceive stress physiologically but exhibit stress-responses that oppose those of young mice on behavioral, synaptic, and molecular levels. Multi-Omics profiling of prefrontal cortex and nucleus accumbens and 3D vasculature measurements reveals that stress in aged mice activates angiogenic programs that are opposite to aging. Our results demonstrate that stress cannot be universally conceptualized as an aging accelerator, but instead engages age-specific programs whose directionality reverses in late life.
DOI: 10.5281/zenodo.15766751
title: STOPUP. WP2. Pollution modelling. Task2.2 – 2.4. Hydrological, hydraulic and water quality modelling of surface runoff and sewer networks

description: This dataset combines the results of hydrological, hydraulic, and water quality modelling from Tasks 2.2 and 2.4, as presented in Deliverable D2.5 – Water Quantity and Quality Modelling for Case Studies. It includes collected and generated data from six urban case studies and supports risk assessment, pollution control, and decision-making. The models are not part of the dataset as several of them are classified as critical infrastructure. The measured data are available depending on the restriction on the case study.

The dataset covers:



Input data: rainfall, flow, water depth, and water quality measurements.

Outputs: calibrated models, simulation results (timeseries of flow, waterlevel or water quality variable).


The modelling work aims to simulate the flow and pollutant dynamics in urban sewer systems under wet weather conditions, with the goal of supporting risk assessment, pollution control strategies, and design of monitoring campaigns.