cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.18ng6
title: Data from: Climate suitable planting as a strategy for maintaining forest productivity and functional diversity

description: Within the time frame of the longevity of tree species, climate change
 will change faster than the ability of natural tree migration. Migration
 lags may result in reduced productivity and reduced diversity in forests
 under current management and climate change. We evaluated the efficacy of
 planting climate-suitable tree species (CSP), those tree species with
 current or historic distributions immediately south of a focal landscape,
 to maintain or increase aboveground biomass, productivity, and species and
 functional diversity. We modeled forest change with the LANDIS-II forest
 simulation model for 100 years (2000–2100) at a 2-ha cell resolution and
 five-year time steps within two landscapes in the Great Lakes region
 (northeastern Minnesota and northern lower Michigan, USA). We compared
 current climate to low- and high-emission futures. We simulated a
 low-emission climate future with the Intergovernmental Panel on Climate
 Change (IPCC) 2007 B1 emission scenario and the Parallel Climate Model
 Global Circulation Model (GCM). We simulated a high-emission climate
 future with the IPCC A1FI emission scenario and the Geophysical Fluid
 Dynamics Laboratory (GFDL) GCM. We compared current forest management
 practices (business-as-usual) to CSP management. In the CSP scenario, we
 simulated a target planting of 5.28% and 4.97% of forested area per
 five-year time step in the Minnesota and Michigan landscapes,
 respectively. We found that simulated CSP species successfully established
 in both landscapes under all climate scenarios. The presence of CSP
 species generally increased simulated aboveground biomass. Species
 diversity increased due to CSP; however, the effect on functional
 diversity was variable. Because the planted species were functionally
 similar to many native species, CSP did not result in a consistent
 increase nor decrease in functional diversity. These results provide an
 assessment of the potential efficacy and limitations of CSP management.
 These results have management implications for sites where diversity and
 productivity are expected to decline. Future efforts to restore a specific
 species or forest type may not be possible, but CSP may sustain a more
 general ecosystem service (e.g., aboveground biomass).
description: MN Biomass Succession
 filesMinnesota Biomass
 Succession input files for LANDIS-II including all three associated
 climate scenarios used.MN_biomass-succession-all_climates_combined.txtMI_biomass-succession-all_climates_combinedMichigan Biomass Succession input files for LANDIS-II including all three associated climate scenarios used.MN_Harvest_COMBINEDMinnesota harvest files.MI_harvest_COMBINEDMichigan Harvest FilesMN_DYNAMIC_INPUTS_COMBINED_CLIMATESMinnesota Dynamic Input Files (All three climate scenarios)MI_DYNAMIC_INPUTS_COMBINED_CLIMATESMichigan Dynamic Input Files (All three climate scenarios)ReadMeReadMe file is a general metadata file for all the data associated with the article.
DOI: 10.5061/dryad.gn4hh
title: Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology

description: The self-incompatible species Arabidopsis halleri is a close relative of
 the self-compatible model plant Arabidopsis thaliana. The broad European
 and Asian distribution and heavy metal hyperaccumulation ability make A.
 halleri a useful model for ecological genomics studies. We used
 long-insert mate-pair libraries to improve the genome assembly of the A.
 halleri ssp. gemmifera Tada mine genotype (W302) collected from a site
 with high contamination by heavy metals in Japan. After five rounds of
 forced selfing, heterozygosity was reduced to 0.04%, which facilitated
 subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the
 estimated genome size and achieved scaffold N50 length of 712 kb. To
 validate assembly and annotation, we used synteny of A. halleri Tada mine
 with a previously published high-quality reference assembly of a closely
 related species, Arabidopsis lyrata. Further validation of the assembly
 quality comes from synteny and phylogenetic analysis of the HEAVY METAL
 ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published
 sequences from European A. halleri for comparison. Three tandemly
 duplicated copies of HMA4, key gene involved in cadmium and zinc
 hyperaccumulation, were assembled on a single scaffold. The assembly will
 enhance the genomewide studies of A. halleri as well as the allopolyploid
 Arabidopsis kamchatica derived from A. lyrata and A. halleri.
description: Reciprocal best BLAST
 hits between Arabidopsis halleri and Arabidopsis
 thalianaReciprocal best BLAST
 hits between Arabidopsis halleri ssp. gemmifera Tada mine and Arabidopsis
 thaliana TAIR10.RBH_Ahal_Atha.txt.gzReciprocal best BLAST hits between Arabidopsis halleri and Arabidopsis lyrataReciprocal best BLAST hits between Arabidopsis halleri ssp. gemmifera Tada mine and Arabidopsis lyrata.RBH_Ahal_Alyr.txt.gzRepeatMasker output for the Arabidopsis halleri assemblyAhal_RepeatMaskerTE.out.gzTransposable elements identified by RepeatMasker in the Arabidopsis halleri assemblyTransposable elements identified by RepeatMasker in the Arabidopsis halleri assembly. The output was converted to GFF format.Ahal_RepeatMaskerTE.gff.gzArabidopsis halleri assembly with TE maskingArabidopsis halleri assembly with transposable elements and simple repeats masked by RepeatMasker.Ahal_masked.fa.gzArabidopsis halleri functional annotationFunctional annotation for Arabidopsis halleri ssp. gemmifera Tada mine. The annotation was performed with AUGUSTUS v3.0.3 using RNA-seq data from leaves and roots.annotation.gff.gzArabidopsis halleri TranscriptsCoding sequences of all reported transcripts in Arabidopsis halleritranscripts.fa.gz
DOI: 10.5061/dryad.3019k
title: Data from: Specific membrane capacitance, cytoplasm conductivity and instantaneous Young’s modulus of single tumour cells

description: As label-free biomarkers, biophysical properties of cells are widely used
 for cell type classification. However, intrinsic biophysical markers, e.g.
 specific membrane capacitance (Cspecific membrane), cytoplasm conductivity
 (σconductivity) and instantaneous Young’s modulus (Einstantaneous)
 measured for hundreds of single cells were not yet reported. In this
 study, single cells in suspension (adherent cells treated with trypsin)
 were aspirated through a microfluidic constriction channel at 25°C, and
 the entry processes and impedance profiles were recorded and translated to
 Cspecific membrane, σconductivity and Einstantaneous. Cspecific membrane,
 σconductivity and Einstantaneous of five cell types were quantified as
 2.10±0.38 μF/cm2, 0.91±0.15 S/m and 5.52±0.95 kPa for H460 cells
 (ncell=437); 2.52±0.54 μF/cm2, 0.83±0.12 S/m and 5.54±1.04 kPa for H446
 cells (ncell=410); 2.45±0.57 μF/cm2, 0.99±0.18 S/m and 5.16±1.68 kPa for
 A549 cells (ncell=442); 1.86±0.31 μF/cm2, 1.07±0.18 S/m and 3.86±0.81 kPa
 for 95D cells (ncell=415); 2.03±0.35 μF/cm2, 0.99±0.16 S/m and 3.49±0.70
 kPa for 95C cells (ncell=290). The database of Cspecific membrane,
 σconductivity and Einstantaneous may serve as a reference for future
 studies of cellular biophysical properties.
description: Biophysical Properties
 of Single Tumour CellsThe file is an Excel
 composed of five sheets which are named after five cell lines of H460,
 H446, A549, 95D and 95C, respectively. In each sheet of a specific cell
 type, there are nine columns which are cell number (column A), A1 kHz
 (column B), A100 kHz (column C), Linstantaneous (column D), Ltransitional
 (column E), Lelongation (column F), Cspecific membrane (column G),
 σconductivity (column H) and Einstantaneous (column I). In this file, each
 row represents the quantified biophysical parameters of a biological cell
 including A1 kHz, A100 kHz, Linstantaneous, Ltransitional, Lelongation,
 Cspecific membrane, σconductivity and Einstantaneous.Data Source
 20160830.xlsxRaw Impedance and Image
 Data of Single Tumour CellsThe file is an Excel
 composed of five sheets named after five cell lines of H460, H446, A549,
 95D and 95C, respectively. In each sheet of a specific cell type, the
 first row is the cell number and within each cell number, there are seven
 columns which are time (collected from impedance analyser), amplitude at 1
 kHz, phase at 1 kHz, amplitude at 100 kHz, phase at 100 kHz, time
 (collected from high-speed camera) and aspiration
 length.Raw
 Data 20161109.xlsx
DOI: 10.5061/dryad.r5f7m
title: Data from: A tale of the ciliate tail: investigation into the adaptive significance of this sub-cellular structure

description: Ciliates can form an important link between the microbial loop and higher
 trophic levels primarily through consumption by copepods. This high
 predation pressure has resulted in a number of ciliate species developing
 rapid escape swimming behaviour. Several species of these escaping
 ciliates also possess a long contractile tail for which the functionality
 remains unresolved. We use high-speed video, specialized optics and novel
 fluid visualization tools to evaluate the role of this contractile
 appendage in two free-swimming ciliates, Pseudotontonia sp. and Tontonia
 sp., and compare the performance to escape swimming behaviour of a
 non-tailed species, Strobilidium sp. Here, we show that ‘tailed’ species
 respond to hydrodynamic disturbances with extremely short response
 latencies (less than or equal to 0.89 ms) by rapidly contracting the tail
 which carries the cell body 2–4 cell diameters within a few milliseconds.
 This provides an advantage over non-tailed species during the critical
 first 10–30 ms of an escape. Two small, short-lived vortex rings are
 created during contraction of the tail. The flow imposed by the ciliate
 jumping can be described as two well-separated impulsive Stokeslets and
 the overall flow attenuates spatially as r−3. The high initial velocities
 and spatio-temporal arrangement of vortices created by tail contractions
 appear to provide a means for rapid escape as well as hydrodynamic
 ‘camouflage’ against fast striking, mechanoreceptive predators such as
 copepods.
description: Pseudotontonia PIV data
 for fig 4.micro-PIV data of flows
 created by Pseudotontonia during contraction of tail as seen in Figure
 4.Pseudotontonia
 PIV.aviFig 3
 dataData used in Figure
 3.Video used in Fig
 1.Compressed AVI of Figure
 1 data. Recorded at 1125 fps and played back at 30 fps.compressed_playback 30
 fps.avi
DOI: 10.5061/dryad.55p06
title: Data from: Genome-wide survey of nuclear protein-coding markers for beetle phylogenetics and their application in resolving both deep and shallow-level divergences

description: Beetles (Coleoptera) are the most diverse and species-rich insect group,
 representing an impressive explosive radiation in the evolutionary history
 of insects, and their evolutionary relationships are often difficult to
 resolve. The amount of “traditional markers” (e.g., mitochondrial genes
 and nuclear rDNAs) for beetle phylogenetics is small and these markers
 often lack sufficient signals in resolving relationships for such a
 rapidly radiating lineage. Here, based on the available genome data of
 beetles and other related insect species, we performed a genome-wide
 survey to search nuclear protein-coding (NPC) genes suitable for research
 on beetle phylogenetics. As a result, we identified 1470 candidate loci,
 which provided a valuable data resource to the beetle evolutionary
 research community for NPC marker development. We randomly chose 180
 candidate loci from the database to design primers and successfully
 developed 95 NPC markers which can be PCR amplified from standard genomic
 DNA extracts. These new nuclear markers are universally applicable across
 Coleoptera, with an average amplification success rate of 90%. To test the
 phylogenetic utility, we used them to investigate the backbone phylogeny
 of Coleoptera (18 families sampled) and the family Coccinellidae (39
 species sampled). Both phylogenies are well resolved (average bootstrap
 support &gt; 95%), showing that our markers can be used to address
 phylogenetic questions of various evolutionary depth (from species level
 to family level). In general, the newly developed nuclear markers are much
 easier to use and more phylogenetically informative than the “traditional
 markers”, and show great potential to expedite resolution of many parts in
 the Beetle Tree of Life.
description: data_nexThis zip package includes data matrices used in this study.DataBase_1470candidatesThe database containing a total of 1470 NPC marker candidates for beetle phylogenety, including nucleotide and protein alignments,and summary information of the marker candidates.python_scriptsAutomation Python scripts used in the analysis, including some genome mining procedures (Filter_long_single_copy_seqs,Auto_filter_alignments) and Auto_exclusion_introns. All scripts call module of Biopython. Please install Biopython before use.Supplemental_TablesSupplemental Tables in this study.
DOI: 10.5061/dryad.35hq4
title: Data from: Stability of phase relationships while coordinating arm reaches with whole body motion

description: The human movement repertoire is characterized by the smooth coordination
 of several body parts, including arm movements and whole body motion. The
 neural control of this coordination is quite complex because the various
 body parts have their own kinematic and dynamic properties. Behavioral
 inferences about the neural solution to the coordination problem could be
 obtained by examining the emerging phase relationship and its stability.
 Here, we studied the phase relationships that characterize the
 coordination of arm-reaching movements with passively-induced whole-body
 motion. Participants were laterally translated using a vestibular chair
 that oscillated at a fixed frequency of 0.83 Hz. They were instructed to
 reach between two targets that were aligned either parallel or orthogonal
 to the whole body motion. During the first cycles of body motion, a
 metronome entrained either an in-phase or an anti-phase relationship
 between hand and body motion, which was released at later cycles to test
 phase stability. Results suggest that inertial forces play an important
 role when coordinating reaches with cyclic whole-body motion. For parallel
 reaches, we found a stable in-phase and an unstable anti-phase
 relationship. When the latter was imposed, it readily transitioned or
 drifted back toward an in-phase relationship at cycles without metronomic
 entrainment. For orthogonal reaches, we did not find a clear difference in
 stability between in-phase and anti-phase relationships. Computer
 simulations further show that cost models that minimize energy expenditure
 (i.e. net torques) or endpoint variance of the reach cannot fully explain
 the observed coordination patterns. We discuss how predictive control and
 impedance control processes could be considered important mechanisms
 underlying the rhythmic coordination of arm reaches and body motion.
description: data_subject1data subject 1data_subject2data subject 2data_subject3data subject 3data_subject4data subject 4data_subject5data subject 5data_subject6data subject 6data_subject7data subject 7data_subject8data subject 8data_subject9data subject 9data_subject10data subject 10
DOI: 10.5061/dryad.d27gv
title: Data from: Metabolic depression and the evolution of hypoxia tolerance in threespine stickleback, Gasterosteus aculeatus

description: Anthropogenic increases in global temperature and agricultural runoff are
 increasing the prevalence of aquatic hypoxia throughout the world. We
 investigated the potential for a relatively rapid evolution of hypoxia
 tolerance using two isolated (for less than 11 000 years) populations of
 threespine stickleback: one from a lake that experiences long-term hypoxia
 (Alta Lake, British Columbia) and one from a lake that does not (Trout
 Lake, British Columbia). Loss-of-equilibrium (LOE) experiments revealed
 that the Alta Lake stickleback were significantly more tolerant of hypoxia
 than the Trout Lake stickleback, and calorimetry experiments revealed that
 the enhanced tolerance of Alta Lake stickleback may be associated with
 their ability to depress metabolic rate (as indicated by metabolic heat
 production) by 33% in hypoxia. The two populations showed little variation
 in their capacities for O2 extraction and anaerobic metabolism. These
 results reveal that intraspecific variation in hypoxia tolerance can
 develop over relatively short geological timescales, as can metabolic rate
 depression, a complex biochemical response that may be favoured in
 long-term hypoxic environments.
description: Regan et al.
 (2017)REGAN
 et al. (2017).zip
DOI: 10.5061/dryad.r4026
title: Data from: Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi

description: Hemibiotrophic fungal plant pathogens represent a group of agronomically
 significant disease-causing agents that grow first on living tissue and
 then cause host death in later, necrotrophic growth. Among these,
 Colletotrichum spp. are devastating pathogens of many crops. Identifying
 expanded classes of genes in the genomes of phytopathogenic
 Colletotrichum, especially those associated with specific stages of
 hemibiotrophy, can provide insights on how these pathogens infect a large
 number of hosts. The genomes of C. orbiculare, which infects cucurbits and
 Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range
 of crops, were sequenced and analyzed, focusing on features with potential
 roles in pathogenicity. Regulation of C. orbiculare gene expression was
 investigated during infection of N. benthamiana using a custom
 microarray.Genes expanded in both genomes compared to other fungi included
 sequences encoding small, secreted proteins (SSPs), secondary metabolite
 synthesis genes, proteases and carbohydrate-degrading enzymes. Many SSP
 and secondary metabolite synthesis genes were up-regulated during initial
 stages of host colonization, while the necrotrophic stage of growth is
 characterized by up-regulation of sequences encoding degradative enzymes.
 Hemibiotrophy in C. orbiculare is characterized by distinct stage-specific
 gene expression profiles of expanded classes of potential pathogenicity
 genes.
description: Colletotrichum_gloeosporioides_Nara_gc5_1_assemblyGenome assembly of Colletotrichum gloeosporioides Nara gc5 isolated from strawberry plants. Files include SOAP denovo assembled Colletotrichum gloeosporioides scaffolds and contigs, all predicted proteins and all predicted transcripts in fasta format.Colletotrichum_orbiculare_104T_MAFF_240422_1_assemblyGenome assembly of Colletotrichum orbiculare 104T (MAFF 240422). Files include GS De Novo Assembler assembled Colletotrichum orbiculare scaffolds, all predicted proteins and all predicted transcripts in fasta format.
DOI: 10.5061/dryad.3n08c
title: Data from: Hearables: feasibility of recording cardiac rhythms from head and in-ear locations

description: Mobile technologies for the recording of vital signs and neural signals
 are envisaged to underpin the operation of future health services. For
 practical purposes, unobtrusive devices are favoured, such as those
 embedded in a helmet or incorporated onto an earplug. However, these
 locations have so far been underexplored, as the comparably narrow neck
 impedes the propagation of vital signals from the torso to the head
 surface. To establish the principles behind electrocardiogram (ECG)
 recordings from head and ear locations, we first introduce a realistic
 three-dimensional biophysics model for the propagation of cardiac electric
 potentials to the head surface, which demonstrates the feasibility of
 head-ECG recordings. Next, the proposed biophysics propagation model is
 verified over comprehensive real-world experiments based on head- and
 in-ear-ECG measurements. It is shown both that the proposed model is an
 excellent match for the recordings, and that the quality of head- and
 ear-ECG is sufficient for a reliable identification of the timing and
 shape of the characteristic P-, Q-, R-, S- and T-waves within the cardiac
 cycle. This opens up a range of new possibilities in the identification
 and management of heart conditions, such as myocardial infarction and
 atrial fibrillation, based on 24/7 continuous in-ear measurements. The
 study therefore paves the way for the incorporation of the cardiac
 modality into future ‘hearables’, unobtrusive devices for health
 monitoring.
description: Datazip-folder containing
 the data sets for the simulated and recorded dataScriptszip-folder containing the scripts to process the raw data in the folder Data.zipScripts - readmeThe file "Scripts - readme.txt" explains which MATLAB scripts are the main files and how the parameters in the header need to be set to obtain the diagrams in the paper, based on the supplied data files.
DOI: 10.15468/dl.vjtqct
title: Occurrence Download

description: A dataset containing 619277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Accipitridae"
 ]
}

 The dataset includes 619277 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000425-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.83g2024
title: Data from: Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers

description: Detecting positive selection using genomic data is critical to
 understanding the role of adaptive evolution. Of particular interest in
 this context is sex chromosomes since they are thought to play a special
 role in local adaptation and speciation. We sought to circumvent the
 challenges associated with statistical phasing when using haplotype-based
 statistics in sweep scans by benefitting from that whole-chromosome
 haplotypes of the sex chromosomes can be obtained by re-sequencing of
 individuals of the hemizygous sex. We analyzed whole Z chromosome
 haplotypes from 100 females from several populations of four black and
 white flycatcher species (in birds, females are ZW and males ZZ). Based on
 integrated haplotype score (iHS) and number of segregating sites by length
 (nSL) statistics, we found strong and frequent haplotype structure in
 several regions of the Z chromosome in each species. Most of these sweep
 signalswere population-specific, with essentially no evidence for regions
 under selection shared among species. Some completed sweeps were revealed
 by the cross-population extended haplotype homozygosity (XP-EHH)
 statistic. Importantly, by using statistically phased Z chromosome data
 from re-sequencing of males, we failed to recover the signals of selection
 detected in analyses based on whole-chromosome haplotypes from females;
 instead, what likely represent false signals of selection were frequently
 seen. This highlights the power issues in statistical phasing and cautions
 against conclusions from selection scans using such data. The detection of
 frequent selective sweeps on the avian Z chromosome supports a large role
 of sex chromosomes in adaptive evolution.
description: haplotypes_males