cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jd88rd12
title: Data from: Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow

description: Understanding patterns of connectivity among populations of marine
 organisms is essential for the development of realistic, spatially
 explicit models of population dynamics. Two approaches, theoretical and
 empirical population genetic models, have been used to estimate levels of
 evolutionary connectivity among marine populations but rarely have their
 potentially-complementary insights been combined. Here, a
 spatially-realistic Lagrangian model of larval dispersal and a theoretical
 genetic model are integrated with the most extensive study of gene flow in
 a Caribbean marine organism. The 871 genets collected from 26 sites spread
 over the wider Caribbean sub-sampled 45.8% of the 1900 potential unique
 genets in the model. At a coarse scale, significant consensus between
 modelled estimates of genetic structure and empirical genetic data for
 populations of the reef-building coral Montastraea annularis is observed.
 However, modelled and empirical data differ in their estimates of
 connectivity among northern Mesoamerican reefs indicating that processes
 other than dispersal may dominate here. Further, the geographic location
 and porosity of the previously described east-west barrier to gene flow in
 the Caribbean is refined. A multi-prong approach, integrating genetic data
 and spatially-realistic models of larval dispersal and genetic projection,
 provides complementary insights into the processes underpinning population
 connectivity in marine invertebrates on evolutionary timescales.
description: Montastraea annularis
 microsatellite dataGenotype data for 6
 microsatellite loci for 871 samples of Montastraea annularis collected
 from 26 sites across the wider Caribbean are provided. Montastraea samples
 were collected in the field between 2004 and 2008. Sample ID, region and
 site name are supplied for each individual. Column headings are detailed
 in the ReadMe file.Foster_Montastraea.csv
DOI: 10.5061/dryad.5cc27
title: Data from: Reproducibility of volumetric computed tomography of stable small pulmonary nodules with implications on estimated growth rate and optimal scan interval

description: Purpose: To use clinically measured reproducibility of volumetric CT (vCT)
 of lung nodules to estimate error in nodule growth rate in order to
 determine optimal scan interval for patient follow-up. Methods: We
 performed quantitative vCT on 89 stable non-calcified nodules and 49
 calcified nodules measuring 3–13 mm diameter in 71 patients who underwent
 3–9 repeat vCT studies for clinical evaluation of pulmonary nodules.
 Calculated volume standard deviation as a function of mean nodule volume
 was used to compute error in estimated growth rate. This error was then
 used to determine the optimal patient follow-up scan interval while fixing
 the false positive rate at 5%. Results: Linear regression of nodule volume
 standard deviation versus the mean nodule volume for stable non-calcified
 nodules yielded a slope of 0.057±0.002 (r2 = 0.79, p&lt;0.001). For
 calcified stable nodules, the regression slope was 0.052±0.005 (r2 = 0.65,
 p = 0.03). Using this with the error propagation formula, the optimal
 patient follow-up scan interval was calculated to be 81 days, independent
 of initial nodule volume. Conclusions: Reproducibility of vCT is
 excellent, and the standard error is proportional to the mean calculated
 nodule volume for the range of nodules examined. This relationship
 constrains statistical certainty of vCT calculated doubling times and
 results in an optimal scan interval that is independent of the initial
 nodule volume.
description: PLOS One
 dataMultiple tabs for nodule
 analysis. The Gietema and Veronesi data are calculated values from raw
 data which I do not have permission to share.
DOI: 10.5061/dryad.c25f0
title: Data from: Maize diversity associated to social origin and environmental variation in southern Mexico

description: While prevailing theories of crop evolution suggest that crop diversity
 and cultural diversity should be linked, empirical evidence for such a
 link remains inconclusive. In particular, few studies have investigated
 such patterns on a local scale. Here, we address this issue by examining
 the determinants of maize diversity in a local region of high cultural and
 biological richness in Southern Mexico. We collected maize samples from
 villages at low and middle elevations in two adjacent municipalities of
 differing ethnicity: Mixtec or Chatino. Although morphological traits show
 few patterns of population structure, we see clear genetic differentiation
 among villages, with municipality explaining a larger proportion of the
 differentiation than altitude. Consistent with an important role of social
 origin in patterning seed exchange, metapopulation model-based estimates
 of differentiation match the genetic data within village and ethnically
 distinct municipalities, but underestimate differentiation when all four
 villages are taken together. Our research provides insights about the
 importance of social origin in structuring maize diversity at the local
 scale.
description: morphology data from
 common gardensThis file contains
 morphological maize data from four maize common gardens. Each common
 garden has 60 plots, 20 maize populations with three repetitions. Except
 one garden, which has 40 plots, 20 maize populations with two repetitions.
 It includes information about population and data of thirteen plant
 morphological traits. See detailed abbreviations in the ReadMe
 file.SSR
 dataThis file contains SSR
 data of 20 populations, 10 plants per population, and data for 15 SSR. It
 includes some characteristics of the population, see abbreviations in
 ReadMe file. SSR’s are phi051, phi115, phi015, phi033, phi053, phi072,
 phi093, phi024, phi085, phi034, phi121, phi029, phi073, phi96342,
 phi109275. See publication for details. Data of each plant are in two
 consecutive rows. Missing data is coded as -9
DOI: 10.5061/dryad.2bs8g
title: Data from: The genetic architecture of constitutive and induced trichome density in two new RIL populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response

description: Background: Herbivory imposes an important selective pressure on plants.
 In Arabidopsis thaliana leaf trichomes provide a key defense against
 insect herbivory; however, trichome production incurs a fitness cost in
 the absence of herbivory. Previous work on A. thaliana has shown an
 increase in trichome density in response to leaf damage, suggesting a
 mechanism by which the cost associated with constitutively high trichome
 density might be mitigated; however, the genetic basis of trichome density
 induction has not been studied. Results: Here, we describe the mapping of
 quantitative trait loci (QTL) for constitutive and damage induced trichome
 density in two new recombinant inbred line populations of A. thaliana;
 mapping for constitutive and induced trichome density also allowed for the
 investigation of damage response (plasticity) QTL. Both novel and
 previously identified QTL for constitutive trichome density and the first
 QTL for induced trichome density and response are identified.
 Interestingly, two of the four parental accessions and multiple RILs in
 each population exhibited lower trichome density following leaf damage, a
 response not previously described in A. thaliana. Importantly, a single
 QTL was mapped for the response phenotype and allelic variation at this
 locus appears to determine response trajectory in RILs. The data also show
 that epistatic interactions are a significant component of the genetic
 architecture of trichome density. Conclusions: Together, our results
 provide further insights into the genetic architecture of constitutive
 trichome density and new insights into induced trichome density in A.
 thaliana specifically and to our understanding of the genetic
 underpinnings of natural variation generally.
description: HixOb RIL genotypes for
 dryad - VV SymondsGenotype file for the
 HixOb RIL mapping population.The first row is marker names, second row is
 chromosome number, and third row is position in cM based on linkage maps
 used in the publication.StxSf RIL genotypes for
 dryad - VV SymondsGenotype file for the
 StxSf RIL mapping population.The first row is marker names, second row is
 chromosome number, and third row is position in cM based on linkage maps
 used in the publication.
DOI: 10.5281/zenodo.18382720
title: Structural and elastic properties of W-S-Te and W-Se-Te systems

description: The crystal structure, formation energy, elastic constants, and stress strain curves for W-S-Te and W-Se-Te systems are provided. These were prepared using Quantum ESPRESSO. This dataset was used for studying the structure-property relationships in these systems.

(1) Structure_files.zip includes 55 crystal structures of 1T'-structured W-S-Te and W-Se-Te monolayers with 2x1 supercell in POSCAR format. The indexes 0 and 54 correspond to WS2 (WSe2) and WTe2, respectively, and the other indexes correspond to W-S-Te (W-Se-Te). 

(2) 1Tp_WXTe.csv (X=S, Se) includes the conentration of Te atom, the formation energy (in units of eV/atom), and the y corrdinate (in units of b) for 55 structures of 1T' W-S-Te and W-Se-Te monolayers. 

(3) 1Tp_WXTe_elastic.csv (X=S, Se) includes the elastic constants, epsi_x, epsi_y, and epsi_xy (in units of GPa nm) for 55 structures of 1T' W-S-Te and W-Se-Te monolayers. 

(4) 1Tp_WXTe_nonlinear_i (X=S, Se; i=x, y) includes the in-plane stress (GPa nm) under the uniaxial strain along x and y directions up to 20 % with an increment of 2 % for 1T' structures with the index from 20 to 54.
DOI: 10.5281/zenodo.18382719
title: Structural and elastic properties of W-S-Te and W-Se-Te systems

description: The crystal structure, formation energy, elastic constants, and stress strain curves for W-S-Te and W-Se-Te systems are provided. These were prepared using Quantum ESPRESSO. This dataset was used for studying the structure-property relationships in these systems.

(1) Structure_files.zip includes 55 crystal structures of 1T'-structured W-S-Te and W-Se-Te monolayers with 2x1 supercell in POSCAR format. The indexes 0 and 54 correspond to WS2 (WSe2) and WTe2, respectively, and the other indexes correspond to W-S-Te (W-Se-Te). 

(2) 1Tp_WXTe.csv (X=S, Se) includes the conentration of Te atom, the formation energy (in units of eV/atom), and the y corrdinate (in units of b) for 55 structures of 1T' W-S-Te and W-Se-Te monolayers. 

(3) 1Tp_WXTe_elastic.csv (X=S, Se) includes the elastic constants, epsi_x, epsi_y, and epsi_xy (in units of GPa nm) for 55 structures of 1T' W-S-Te and W-Se-Te monolayers. 

(4) 1Tp_WXTe_nonlinear_i (X=S, Se; i=x, y) includes the in-plane stress (GPa nm) under the uniaxial strain along x and y directions up to 20 % with an increment of 2 % for 1T' structures with the index from 20 to 54.
DOI: 10.5061/dryad.jm40h
title: Data from: Evolution of movement rate increases the effectiveness of marine reserves for the conservation of pelagic fishes

description: Current debates about the efficacy of no-take marine reserves (MR) in
 protecting large pelagic fish such as tuna and sharks have usually not
 considered the evolutionary dimension of this issue, which emerges because
 the propensity to swim away from a given place, like any other biological
 trait, will probably vary in a heritable fashion among individuals. Here,
 based on spatially-explicit simulations, we investigated whether selection
 to remain in MRs to avoid higher fishing mortality can lead to the
 evolution of more philopatric fish. Our simulations, which covered a range
 of life histories among tuna species (skipjack tuna vs. Atlantic Bluefin
 tuna) and shark species (great white sharks vs. spiny dogfish) suggested
 that MRs were most effective at maintaining viable population sizes when
 movement distances were lowest. Decreased movement rate evolved following
 the establishment of marine reserves, and this evolution occurred more
 rapidly with higher fishing pressure. Evolutionary reductions in movement
 rate led to increases in within-reserve population sizes over the course
 of the 50 years following MR establishment, although this varied among
 life-histories, with skipjack responding fastest and great white sharks
 slowest. Our results suggest the evolution of decreased movement can
 augment the efficacy of marine reserves, especially for species, such as
 skipjack tuna, with relatively short generation times. Even when movement
 rates did not evolve substantially over 50 years (e.g., given long
 generation times or little heritable variation), marine reserves were an
 effective tool for the conservation of fish populations when mean movement
 rates were low or MRs were large.
description: R code for simulations
 involving non-migratory pelagic speciesgrid_model_Skip_Dog_displaced.RR code for simulations involving migratory pelagic speciesgrid_model_Blue_White_displaced.RSkipjack_resultsBluefin_resultsDogfish_resultsWhiteShark_results
DOI: 10.6084/m9.figshare.30305325
title: Energy transition through community energy, local energy and smart local energy system initiatives in the UK: a systematic review of technologies, ownership and user engagement

description: The UK energy system is transitioning towards decarbonisation, decentralisation, and digitalisation to meet Net Zero targets. Place-based approaches such as community energy (CE), local energy (LE), and smart local energy systems (SLES) have emerged over the past 15 years to address these goals. SLES integrate electricity, heat, transport, supply, demand, and storage at a local scale to improve efficiency, reduce emissions and costs, and enhance resilience. Yet user engagement, vital to their success, remains limited due to low public trust and weak evaluation. This paper reports a systematic meta-study of 445 CE, LE, and SLES initiatives in the UK (2008–2020), analysing technology, scale, governance, funding, engagement, and evaluation. CE and LE projects focused on generation (52%, 60%) and efficiency (61%, 58%), largely led by community groups and local authorities. SLES, by contrast, centred on smart data (78%) and grid management (89%), with Distribution Network Operators (DNOs) and private actors. Over half of SLES were located in Scotland and Southern England, in areas of grid constraint and renewable penetration. Despite the importance of sustained participation, 14% assessed user engagement longitudinally. The study underscores the need for stronger collaboration between DNOs, local actors and academia to enhance scalability of SLES.
DOI: 10.6084/m9.figshare.30305325.v1
title: Energy transition through community energy, local energy and smart local energy system initiatives in the UK: a systematic review of technologies, ownership and user engagement

description: The UK energy system is transitioning towards decarbonisation, decentralisation, and digitalisation to meet Net Zero targets. Place-based approaches such as community energy (CE), local energy (LE), and smart local energy systems (SLES) have emerged over the past 15 years to address these goals. SLES integrate electricity, heat, transport, supply, demand, and storage at a local scale to improve efficiency, reduce emissions and costs, and enhance resilience. Yet user engagement, vital to their success, remains limited due to low public trust and weak evaluation. This paper reports a systematic meta-study of 445 CE, LE, and SLES initiatives in the UK (2008–2020), analysing technology, scale, governance, funding, engagement, and evaluation. CE and LE projects focused on generation (52%, 60%) and efficiency (61%, 58%), largely led by community groups and local authorities. SLES, by contrast, centred on smart data (78%) and grid management (89%), with Distribution Network Operators (DNOs) and private actors. Over half of SLES were located in Scotland and Southern England, in areas of grid constraint and renewable penetration. Despite the importance of sustained participation, 14% assessed user engagement longitudinally. The study underscores the need for stronger collaboration between DNOs, local actors and academia to enhance scalability of SLES.
DOI: 10.5061/dryad.4v58b
title: Data from: Chemogenetic inhibition of the medial prefrontal cortex reverses the effects of REM sleep loss on sucrose consumption

description: Rapid eye movement (REM) sleep loss is associated with increased
 consumption of weight-promoting foods. The prefrontal cortex (PFC) is
 thought to mediate reward anticipation. However, the precise role of the
 PFC in mediating reward responses to highly palatable foods (HPF) after
 REM sleep deprivation is unclear. We selectively reduced REM sleep in mice
 over a 25–48 hr period and chemogenetically inhibited the medial PFC
 (mPFC) by using an altered glutamate-gated and ivermectin-gated chloride
 channel that facilitated neuronal inhibition through hyperpolarizing
 infected neurons. HPF consumption was measured while the mPFC was
 inactivated and REM sleep loss was induced. We found that REM sleep loss
 increased HPF consumption compared to control animals. However, mPFC
 inactivation reversed the effect of REM sleep loss on sucrose consumption
 without affecting fat consumption. Our findings provide, for the first
 time, a causal link between REM sleep, mPFC function and HPF consumption.
description: Dataset 1: Kissei Comtec
 Data formatKM20150417_EEG5_7_8.kcdDataset 1: European Data FormatKM20150417_EEG5_7_8.edfDataset 2: European Data Format - file 1KM20150420_EEG5_7_8-1.edfDataset 2: European Data Format - file 2KM20150420_EEG5_7_8-2.edfDataset 2: Kissei Comtec Data formatKM20150420_EEG5_7_8.kcd
DOI: 10.5061/dryad.41sk145
title: Data from: Flow of CO2 from soil may not correspond with CO2 concentration in soil

description: The relationship between CO2 flow from soil and soil CO2 concentration was
 investigated at 72 permanent sampling points at two forested post-mining
 sites in the northwest of the Czechia. Based on the entire data set (72
 points sampled monthly during the growing season), CO2 flow from the soil
 was positively correlated with soil CO2 concentration. CO2 concentration
 in deeper soil layers was positively correlated with root biomass and
 negatively correlated with soil microbial respiration. In individual
 sampling points relationship between CO2 flow and soil CO2 concentration
 varied from being significantly positive (30% of points) to significantly
 negative (7%) but mostly being non-significant (63%). The positive
 correlation occurred at points with high root biomass in deeper soil
 layers, while the negative correlation occurred at points with high soil
 microbial respiration per cm3 of soil. Laboratory experiments showed that
 the CO2 produced by microbial respiration can reduce microbial respiration
 but that CO2 produced by root respiration did not reduce root respiration.
 The results indicate that when soil ventilation is poor, microbial
 respiration can sufficiently increase soil CO2 concentration so as to
 reduce microbial respiration, which greatly increases the variability in
 the relationship between CO2 flow from soil and soil CO2 concentration.
description: field_data_flow_concentrationTable describes values of soil CO2 concentration measured at two depth (0-5 cm and 5-20cm) and value of CO2 flow from the soil measured the same spot, in addition, there is soil temperature measured at this spot in the same time. These data are accompanied by set soil physical and biological characteristics, which was measured for each spot at the end of measurement. See fig 1 for scheme of the measurement. The data in the table serve as basis for fig. 3 and 4.labrsp_soilTable describes respiration of soil in laboratory incubation experiments when respiration was measured by incubation of samples in hermetically closed bottle where CO2 was trapped in NaOH. There were two variant of NaOH addition in one he NaOH was added at the beginning of cultivation in second at the end of cultivation. There were two bottle for soil from each spot so this is a pair data. See Fig 2 in the paper for scheme of experiment. Date were basis for Fig 5.lab_spruceTable describes respiration of spruce seedling roots in laboratory incubation experiments when respiration was measured by incubation of samples in hermetically closed bottle where CO2 was trapped in NaOH. There were two variant of NaOH addition in one he NaOH was added at the beginning of cultivation in second at the end of cultivation. There were two comparable groups of seedlings so this is not a pair data. See Fig 2 in the paper for scheme of experiment.
DOI: 10.5061/dryad.5j2v6
title: Data from: Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China

description: Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix)
 are invasive species and listed as US federally injurious species under
 the Lacy Act. They have established populations in much of the Mississippi
 River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are
 capable of producing fertile hybrids and complex introgression.
 Characterizing the composition of this admixture requires a large set of
 high-quality, evolutionarily conserved, diagnostic genetic markers to aid
 in the identification and management of these species in the midst of
 morphological ambiguity. Restriction site-associated DNA (RAD) sequencing
 of 45 barcoded bighead and silver carp from the United States and China
 produced reads that were aligned to the silver carp transcriptome yielded
 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic
 differences between the two species. We selected the highest quality 112
 SNP loci for validation using 194 putative pure-species and F1 hybrids
 from the MRB and putative bighead carp and silver carp pure species from
 China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to
 design/amplification failure or lack of diagnostic utility. A total of 57
 species-diagnostic SNPs conserved between carp species in US and Chinese
 rivers were identified; 32 were annotated to functional gene loci.
 Twenty-seven of the 181 (15%) putative pure species were identified as
 hybrid backcrosses after validation, including three backcrosses from the
 Amur River, where hybridization has not been documented previously. The 57
 SNPs identified through RAD sequencing provide a diagnostic tool to detect
 population admixture and to identify hybrid and pure-species Asian carps
 in the United States and China.
description: SNP genotype file for
 validationData was generated on
 the MassARRAY 4 analyzer system (Sequenom, Inc., San Diego, CA) and tissue
 was collected in the field from the authors and other personnel listed in
 the acknowledgements. The SNP ID's and primer sequences are added in
 the supplementary information of the manuscript for reference. The top
 rows indicate species specific genotypes for Hypophthalmichthys nobilis
 (BH) and H. molitrix (SV). The remaining rows and columns give the
 location, field ID, genetic ID, and genotypes of individual fishes at 57
 SNP loci.