cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4254b
title: Data from: Extending the use of ecological models without sacrificing details: a generic and parsimonious meta-modelling approach

description: Process-based models (PBMs, see table 1 for a list of abbreviations) are
 essential tools to assess ecosystem response to climate change, land use
 changes, extreme weather patterns, or other environmental disturbances.
 PBMs allow to deal with the high level of interactions and feedbacks which
 are intrinsic to ecological processes, but their complexity comes at the
 cost of computation time and memory. Because of that, there is a trade-off
 between the resolution satisfactory to describe ecological processes (e.g.
 organism, population, species, vegetation type …), and the computing
 constraints when applying PBMs at a large spatial extent and/or long time
 periods.
description: This script was used to
 construct metamodel and to perform scale analysisSoftware : R; Packages :
 lattice, polspline, lhs, ade4, caret, neuralnet, nnet, MASS, Hmisc, Cairo;
 functions are loaded from the library.R file.script_analysis_article.RR library where the functions are describedPackages used : lattice, polspline, lhs, ade4, caret, neuralnet, nnet, MASS, Hmisc, Cairo.library.RLatin hypercube design simulationsEach ".res" file is a one day simulation results of noTG model. There are three design of simulation : construct LHS for the construction of the meta-models; test LHS for neural network metamodel and polynomial regression spline optimizations; and Valid LHS for intercomparaison of different metamodel techniques. A readme file is attached to describe variables of ".res" files.LHS_9_inputs.rarConstructed metamodelsA rar file with all constructed meta-models. Meta-model files can be loaded in to R script with the function "load".metamodels.rar50 and 100 years simulations with noTG modelData used to provide a multi-scale validation test. Each simulation is stocked in one repertory. The name of the repertory was generated as follow : "meta" or "mod" for simulation made with or without meta-model; TC is the name of the plot; the number of the sub-plot; the simulated period. Into each repertory, there are five types of output file: - "finals_plant.s" : where dimensions, carbon and nitrogen pools of each tree are recorded at the end of the simulation. - "finals_sol.s" : where carbon, nitrogen, ligin and water content of each pixel are recorded at the end of the simulation. - "XXX_TC_X_XXX.Day1D.res" : where species and soil state variables are recorded for each species and for each day. - "XXX_TC_X_XXXTotal.res" : where cumulated species and soil state variables are recorded for each species and for entire period. - "XXX_TC_X_XXXTree_X.res" : where tree state variables are recorded for each day.Simulations.rar
DOI: 10.5061/dryad.q84m0
title: Data from: A resorbable antibiotic-eluting polymer composite bone void filler for perioperative infection prevention in a rabbit radial defect model

description: Nearly 1.3 million total joint replacement procedures are performed in the
 United States annually, with numbers projected to rise exponentially in
 the coming decades. Although finite infection rates for these procedures
 remain consistently low, device-related infections represent a significant
 cause of implant failure, requiring secondary or revision procedures.
 Revision procedures manifest several-fold higher infection recurrence
 rates. Importantly, many revision surgeries, infected or not, require bone
 void fillers to support the host bone and provide a sufficient tissue bed
 for new hardware placement. Antibiotic-eluting bone void fillers (ABVF),
 providing both osteoconductive and antimicrobial properties, represent one
 approach for reducing rates of orthopedic device-related infections. Using
 a solvent-free, molten-cast process, a polymer-controlled
 antibiotic-eluting calcium carbonate hydroxyapatite (HAP) ceramic
 composite BVF (ABVF) was fabricated, characterized, and evaluated in vivo
 using a bacterial challenge in a rabbit radial defect window model. ABVF
 loaded with tobramycin eliminated the infectious burden in rabbits
 challenged with a clinically relevant strain of Staphylococcus aureus
 (inoculum as high as 107 CFU). Histological, microbiological, and
 radiographic methods were used to detail the effects of ABVF on microbial
 challenge to host bone after 8 weeks in vivo. In contrast to the HAP/BVF
 controls, which provided no antibiotic protection and required euthanasia
 3 weeks post-operatively, tobramycin-releasing ABVF animals showed no
 signs of infection (clinical, microbiological, or radiographic) when
 euthanized at the 8-week study endpoint. ABVF sites did exhibit fibrous
 encapsulation around the implant at 8 weeks. Local antibiotic release from
 ABVF to orthopedic sites requiring bone void fillers eliminated the
 periprosthetic bacterial challenge in this 8-week in vivo study,
 confirming previous in vitro results.
description: Histology
 Filesdocuments-export-2015-01-27.zipRabbit DataThis file contains the information on the rabbits used in the study. Any histories on the rabbit are also recorded in this file.RabbitData.xlsxRabbit Scoring Data RepositoryThis file has scoring informationRabbit data repository.xlsxRadiographsRadiographs
DOI: 10.5061/dryad.g92c4
title: Data from: Multiband semimetallic electronic structure of superconducting Ta2PdSe5

description: We report the electronic structure and related properties of the
 superconductor Ta2PdSe5 as determined from density functional
 calculations. The Fermi surface has two disconnected sheets, both derived
 from bands of primarily chalcogenide p states. These are a corrugated hole
 cylinder and a heavier complex shaped electron sheet. The sheets contain
 0.048 holes and a compensating number of electrons per formula unit,
 making the material a semimetallic superconductor. The results support the
 presence of two band superconductivity, although a discrepancy in the
 specific heat is noted. This discrepancy is discussed as a possible
 consequence of Pd deficiency in samples.
description: Ta2PdSe5-data.tarThis is a gzip tar file containing directories with input and output files from the calculations and data in the figures.
DOI: 10.5061/dryad.q5903
title: Data from: Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters

description: Marine Archaea are important players among microbial plankton and
 significantly contribute to biogeochemical cycles, but details regarding
 their community structure and long-term seasonal activity and dynamics
 remain largely unexplored. In this study, we monitored the inter-annual
 archaeal community composition of abundant and rare biospheres in
 northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA
 and rRNA. A detailed analysis of the rare biosphere structure showed that
 the rare archaeal community was composed of three distinct fractions. One
 contained the rare Archaea that became abundant at different times within
 the same ecosystem; these cells were typically not dormant, and we
 hypothesize that they represent a local seed bank that is specific and
 essential for ecosystem functioning through cycling seasonal environmental
 conditions. The second fraction contained cells that were uncommon in
 public databases and not active, consisting of aliens to the studied
 ecosystem and representing a non-local seed bank of potential colonizers.
 The third fraction contained Archaea that were always rare but actively
 growing; their affiliation and seasonal dynamics were similar to the
 abundant microbes and could not be considered a seed bank. We also showed
 that the major archaeal groups, Thaumarchaeota Marine Group-I (MGI) and
 Euryarchaeota Group-II.B (MGII.B) in winter and Euryarchaeota Group-II.A
 (MGII.A) in summer, contained different ecotypes with varying activities.
 Our findings suggest that archaeal diversity could be associated with
 distinct metabolisms or life strategies, and that the rare archaeal
 biosphere is composed of a complex assortment of organisms with distinct
 histories that affect their potential for growth.
description: archaea_77samples_fastaHugoniB.fnaarchaea_77samples_qualityHugoniB.qualarchaea_3samples_fastaHugoniB.fnaarchaea_3samples_qualityHugoniB.qualarchaea_3samples_barcodesHugoniB.txtarchaea_77samples_barcodesHugoniB.txt
DOI: 10.5061/dryad.5dc12
title: Data from: Environment-dependent prey-capture in the Atlantic mudskipper (Periophthalmus barbarus)

description: Few vertebrates capture prey in both the aquatic and the terrestrial
 environment due to the conflicting biophysical demands of feeding in water
 versus air. The Atlantic mudskipper (Periophthalmus barbarus) is known to
 be proficient at feeding in the terrestrial environment and feeds
 predominately in this environment. Given the considerable forward flow of
 water observed during the mouth opening phase to assist with feeding on
 land, the mudskipper must alter the function of its feeding system to feed
 successfully in water. Here, we quantify the aquatic prey-capture
 kinematics of the mudskipper and compare this with the previously
 described pattern of terrestrial feeding. Prior to feeding in the aquatic
 environment, the gill slits open, allowing water to be expelled through
 the gill slits. The opposite happens in terrestrial feeding during which
 the gill slits remain closed at this point. In water, the expansive
 movements of the head are larger, amounting to a larger volume increase
 and are initiated slightly later than in the terrestrial environment. This
 implies the generation of strong suction flows when feeding in water.
 Consequently, the kinematic patterns of the hydrodynamic tongue during
 terrestrial feeding and aquatic suction feeding are similar, except for
 the amplitude of the volume increase and the active closing of the gill
 slits early during the terrestrial feeding strike. The mudskipper thus
 exhibits the capacity to change the kinematics of its feeding apparatus to
 enable successful prey-capture in two disparate environments.
description: Muskipper_Aquatic_feedingA zip containing High speed vid recording of both lateral and ventral views. Four individuals, two recordings per individual. Mudskippers. Periophthalmus barbarus, feeding underwater.PerioDigi.zip
DOI: 10.5061/dryad.7m645
title: Data from: Information use by humans during dynamic route choice in virtual crowd evacuations

description: We conducted a computer-based experiment with over 450 human participants
 and used a Bayesian model selection approach to explore dynamic exit route
 choice mechanisms of individuals in simulated crowd evacuations. In
 contrast to previous work, we explicitly explore the use of time-dependent
 and time-independent information in decision-making. Our findings suggest
 that participants tended to base their exit choices on time-dependent
 information, such as differences in queue lengths and queue speeds at
 exits rather than on time-independent information, such as differences in
 exit widths or exit route length. We found weak support for similar
 decision-making mechanisms under a stress-inducing experimental treatment.
 However, under this treatment participants were less able or willing to
 adjust their original exit choice in the course of the evacuation. Our
 experiment is not a direct test of behaviour in real evacuations, but it
 does highlight the role different types of information and stress play in
 real human decision-making in a virtual environment. Our findings may be
 useful in identifying topics for future study on real human crowd
 movements or for developing more realistic agent-based simulations.
description: raw_dataPlease refer to 'readme.txt' for additional information. This archive contains the raw data output from the interactive computer-based task for 464 human participantsprocessed_dataPlease refer to 'readme.txt' for additional information. This archive contains processed data for 464 participants that was used for Bayesian model fitting (see associated manuscript).
DOI: 10.5061/dryad.4mh47r7
title: Data from: Do larger individuals cope with resource fluctuations better? An artificial selection approach

description: Size determines the rate at which organisms acquire and use resources but
 it is unclear what size should be favoured under unpredictable resource
 regimes. Some theories claim smaller organisms can grow faster following a
 resource pulse, whereas others argue larger species can accumulate more
 resources and maintain growth for longer periods between resource pulses.
 Testing these theories has relied on interspecific comparisons, which tend
 to confound body size with other life-history traits. As a more direct
 approach, we used 280 generations of artificial selection to evolve a
 10-fold difference in mean body size between small- and large-selected
 phytoplankton lineages of the green microalga Dunaliella tertiolecta,
 while controlling for biotic and abiotic variables. We then quantified how
 body size affected the ability of this species to grow at nutrient-replete
 conditions and following periods of nitrogen or phosphorous deprivation.
 Overall, smaller cells showed slower growth, lower storage capacity and
 poorer recovery from phosphorous depletion, as predicted by the “fasting
 endurance hypothesis”. However, recovery from nitrogen limitation was
 independent of size – a finding unanticipated by current theories.
 Phytoplankton species are responsible for much of the global carbon
 fixation and projected trends of cell size decline could reduce primary
 productivity by lowering the ability of a cell to store resources.
description: Algae Mic Photos -
 OriginalsAll original photos of
 the culturesCodes and
 analysisThis file contains all
 codes, figures and photos generated in the article “DO LARGER INDIVIDUALS
 COPE WITH RESOURCE FLUCTUATIONS BETTER? AN ARTIFICIAL SELECTION APPROACH”,
 by Martino E. Malerba, Maria M. Palacios, and Dustin J. Marshall, in
 Proceeding Royal Society B. Folder “Algae Mic Photos” contains the photos
 taken for each lineage of each size-selection treatment “Codes and
 analysis” includes all codes generated to analyse the size of the cell
 (Fig. 2) and the demographic rates (Fig. 3 and Fig. S7). For each code
 provided, open it with statistical software R. Within the script file: (1)
 check that all packages are installed in the computer (otherwise install
 before running the script), and (2) copy the directory where the script.R
 file is located in the computer and (3) paste the directory after “dir.day
 = “. If done correctly, the command "setwd(dir.day)" should not
 return any error messages. After the setwd(dir.day) works correctly,
 everything else should work too, by simply running the file in R. The
 script will read all data, calculate the statistics, plot the images, and
 save the images in the same folder where the Main script file is. The file
 is designed to run on a Mac computer.
DOI: 10.5061/dryad.jb79430
title: Data from: Sequence clustering threshold has little effect on the recovery of microbial community structure

description: Analysis of microbial community structure by multivariate ordination
 methods, using data obtained by high throughput sequencing of amplified
 markers (i.e., DNA metabarcoding), often requires clustering of DNA
 sequences into operational taxonomic units (OTUs). Parameters for the
 clustering procedure tend not to be justified but are set by tradition
 rather than being based on explicit knowledge. In this study, we explore
 the extent to which ordination results are affected by variation in
 parameter settings for the clustering procedure. Amplicon sequence data
 from nine microbial community studies, representing different sampling
 designs, spatial scales and ecosystems, were subjected to clustering into
 OTUs at seven different similarity thresholds (clustering thresholds)
 ranging from 87% to 99% sequence similarity. The 63 data sets thus
 obtained were subjected to parallel DCA and GNMDS ordinations. The
 resulting community structures were highly similar across all clustering
 thresholds. We explain this pattern by the existence of strong ecological
 structuring gradients and phylogenetically diverse sets of abundant OTUs
 that are highly stable across clustering thresholds. Removing low
 abundance, rare OTUs had negligible effects on community patterns. Our
 results indicate that microbial data sets with a clear gradient structure
 are highly robust to choice of sequence clustering threshold.
description: Dataset4_RawDataTarball containing raw data in the form of 5 .sff.txt files. Corresponding mapping files for demultiplexing of each raw file are provided, in addition to a combined mapping file with treatment information.Dataset4_Dryad.tar.gzDataset7_DryadTar archive containing raw data for Dataset 7 in the form of 4 .sff files. Corresponding mapping files for demultiplexing are provided for each data file.Dataset3_DryadTar archive consisting of 20 .fastq files representing raw, demultiplexed data.Dataset9_DryadTar archive containing 20 .fastq files representing raw, demultiplexed illumina sequencing data.Sequence_Data_For_ClusteringFasta files containing the quality filtered sequences used as the basis for all clustering analyses.sequence_data_for_clustering.tar.gz
DOI: 10.5061/dryad.qs65q
title: Data from: Nonlinear amplitude dynamics in flagellar beating

description: The physical basis of flagellar and ciliary beating is a major problem in
 biology which is still far from completely understood. The fundamental
 cytoskeleton structure of cilia and flagella is the axoneme, a cylindrical
 array of microtubule doublets connected by passive cross-linkers and
 dynein motor proteins. The complex interplay of these elements leads to
 the generation of self-organized bending waves. Although many mathematical
 models have been proposed to understand this process, few attempts have
 been made to assess the role of dyneins on the nonlinear nature of the
 axoneme. Here, we investigate the nonlinear dynamics of flagella by
 considering an axonemal sliding control mechanism for dynein activity.
 This approach unveils the nonlinear selection of the oscillation
 amplitudes, which are typically either missed or prescribed in
 mathematical models. The explicit set of nonlinear equations are derived
 and solved numerically. Our analysis reveals the spatio-temporal dynamics
 of dynein populations and flagellum shape for different regimes of motor
 activity, medium viscosity and flagellum elasticity. Unstable modes
 saturate via the coupling of dynein kinetics and flagellum shape without
 the need of invoking a nonlinear axonemal response. Hence, our work
 reveals a novel mechanism for the saturation of unstable modes in axonemal
 beating.
description: Data_JRSOS_Supplementary_OriolaData_JRSOS_Supplementary_video_1 (MATLAB data files): -t_SV1.mat: Time series. Total time 2000 ms. Time step: 0.5 ms. -X_SV1.mat: X-coordinate of every point along the flagellum at every time step (um). -Y_SV1.mat: Y-coordinate of every point along the flagellum at every time step (um). -dn_SV1.mat: dn value at every point along the flagellum at every time step. Data_JRSOS_Supplementary_video_2 (MATLAB data files): -t_SV2.mat: Time series. Total time 1500 ms. Time step: 0.5 ms. -X_SV2.mat: X-coordinate of every point along the flagellum at every time step (um). -Y_SV2.mat: Y-coordinate of every point along the flagellum at every time step (um). -dn_SV2.mat: dn value at every point along the flagellum at every time step. Data_JRSOS_Supplementary_video_3 (MATLAB data files): -t_SV3.mat: Time series. Total time 1000 ms. Time step: 0.5 ms. -X_SV3.mat: X-coordinate of every point along the flagellum at every time step (um). -Y_SV3.mat: Y-coordinate of every point along the flagellum at every time step (um). -dn_SV3.mat: dn value at every point along the flagellum at every time step.
DOI: 10.5061/dryad.fd24j
title: Data from: Stable recombination hotspots in birds

description: The DNA-binding protein PRDM9 has a critical role in specifying meiotic
 recombination hotspots in mice and apes, but it appears to be absent from
 other vertebrate species, including birds. To study the evolution and
 determinants of recombination in species lacking the gene that encodes
 PRDM9, we inferred fine-scale genetic maps from population resequencing
 data for two bird species: the zebra finch, Taeniopygia guttata, and the
 long-tailed finch, Poephila acuticauda. We found that both species have
 recombination hotspots, which are enriched near functional genomic
 elements. Unlike in mice and apes, most hotspots are shared between the
 two species, and their conservation seems to extend over tens of millions
 of years. These observations suggest that in the absence of PRDM9,
 recombination targets functional features that both enable access to the
 genome and constrain its evolution.
description: Genomes &
 recombination maps for zebra finch and long-tailed finchDataDryad.zip
DOI: 10.5061/dryad.t6m37
title: Data from: Measuring the configurational temperature of a binary disc packing

description: Jammed packings of granular materials differ from systems normally
 described by statistical mechanics in that they are athermal. In recent
 years a statistical mechanics of static granular media has emerged where
 the thermodynamic temperature is replaced by a configurational temperature
 X which describes how the number of mechanically stable configurations
 depends on the volume. Four different methods have been suggested to
 measure X. Three of them are computed from properties of the Voronoi
 volume distribution, the fourth takes into account the contact number and
 the global volume fraction. This paper answers two questions using
 experimental binary disc packings: First we test if the four methods to
 measure compactivity provide identical results when applied to the same
 dataset. We find that only two of the methods agree quantitatively. This
 implies that at least two of the four methods are wrong. Secondly, we test
 if X is indeed an intensive variable; this becomes true only for samples
 larger than roughly 200 particles. This result is shown to be due to
 recently measured correlations between the particle volumes [Zhao et al.,
 Europhys. Lett., 2012, 97, 34004].
description: disc_packing_08175.tarpacking_08175.tar.bz2disc_packing_08183.tarpacking_08183.tar.bz2disc_packing_08209.tarpacking_08209.tar.bz2disc_packing_08229.tarpacking_08229.tar.bz2disc_packing_08218.tarpacking_08218.tar.bz2disc_packing_08231.tarpacking_08231.tar.bz2disc_packing_08277.tarpacking_08277.tar.bz2disc_packing_08315.tarpacking_08315.tar.bz2disc_packing_08337.tarpacking_08337.tar.bz2disc_packing_08356.tarpacking_08356.tar.bz2disc_packing_08366.tarpacking_08366.tar.bz2disc_packing_08380.tarpacking_08380.tar.bz2