cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8n2d374
title: Data from: Genomic selection of juvenile height across a single generational gap in Douglas-fir

description: Here we perform cross-generational GS analysis on coastal Douglas-fir
 (Pseudotsuga menziesii), reflecting trans-generational selective breeding
 application. 1,321 trees, representing 37 full-sib F1 families from 3
 environments in British Columbia, Canada, were used as the training
 population for 1) EBVs (estimated breeding values) of juvenile height
 (HTJ) in the F1 generation predicting genomic EBVs of HTJ of 136
 individuals in the F2 generation, 2) deregressed EBVs of F1 HTJ predicting
 deregressed genomic EBVs of F2 HTJ, 3) F1 mature height (HT35) predicting
 HTJ EBVs in F2, and 4) deregressed F1 HT35 predicting genomic deregressed
 HTJ EBVs in F2. Ridge regression best linear unbiased predictor (RR-BLUP),
 generalized ridge regression (GRR), and Bayes-B GS methods were used and
 compared to pedigree-based (ABLUP) predictions. GS accuracies for
 scenarios 1 (0.92, 0.91, and 0.91) and 3 (0.57, 0.56, and 0.58) were
 similar to their ABLUP counterparts (0.92 and 0.60 respectively) (using
 RR-BLUP, GRR, and Bayes-B). Results using deregressed values fell
 dramatically for both scenarios 2 and 4 which approached zero in many
 cases. Cross-generational GS validation of juvenile height in Douglas-fir
 produced predictive accuracies almost as high as that of ABLUP. Without
 capturing LD, GS cannot surpass the prediction of ABLUP. Here we tracked
 pedigree relatedness between training and validation sets. More markers or
 improved distribution of markers are required to capture LD in
 Douglas-fir. This is essential for accurate forward selection among
 siblings as markers that track pedigree are of little use for forward
 selection of individuals within controlled pollinated families.
description: validation
 genotypesSNP data for 136 samples
 from Jordan River validation population (69951 SNPs).validation_geno.txtJordan River phenotypesF2 samples of juvenile height phenotypesJordan_val_pheno.txt
DOI: 10.5061/dryad.8dc747r
title: Data from: Strain specific differences in rates of Photosystem II repair in picocyanobacteria correlate to differences in FtsH protein levels and isoform expression patterns

description: Picocyanobacteria are the numerically dominant photoautotrophs of the
 oligotrophic regions of Earth’s oceans. These organisms are characterized
 by their small size and highly reduced genomes. Strains partition to
 different light intensity and nutrient level niches, with differing
 photosynthetic apparatus stoichiometry, light harvesting machinery and
 susceptibility to photoinactivation. In this study, we grew three strains
 of picocyanobacteria: the low light, high nutrient strain Prochlorococcus
 marinus MIT 9313; the high light, low nutrient Prochlorococcus marinus MED
 4; and the high light, high nutrient marine Synechococcus strain WH 8102;
 under low and high growth light levels. We then performed matched
 photophysiology, protein and transcript analyses. The strains differ
 significantly in their rates of Photosystem II repair under high light and
 in their capacity to remove the PsbA protein as the first step in the
 Photosystem II repair process. Notably, all strains remove the PsbD
 subunit at the same rate that they remove PsbA. When grown under low
 light, MIT 9313 loses active Photosystem II quickly when shifted to high
 light, but has no measurable capacity to remove PsbA. MED 4 and WH 8102
 show less rapid loss of Photosystem II and considerable capacity to remove
 PsbA. MIT 9313 has less of the FtsH protease thought to be responsible for
 the removal of PsbA in other cyanobacteria. Furthermore, by transcript
 analysis the predominant FtsH isoform expressed in MIT 9313 is homologous
 to the FtsH 4 isoform characterized in the model strain Synechocystis PCC
 6803, rather than the FtsH 2 and 3 isoforms thought to be responsible for
 PsbA degradation. MED 4 on the other hand shows high light inducible
 expression of the isoforms homologous to FtsH 2 and 3, consistent with its
 faster rate of PsbA removal. MIT 9313 has adapted to its low light
 environment by diverting resources away from Photosystem II content and
 repair.
description: Data for Strain specific
 differences in PSII repair in picocyanobacteriaContains bioinformatic,
 physiology, protein and RT PCR data. Includes README files in each
 subfolder.Dryad
 Submission.zip
DOI: 10.5061/dryad.rg27v0h
title: Data from: Preparation of modified pomelo peel’s pulp adsorbent and its adsorption to uranyl ions

description: Using Pomelo peel’s pulp (PPP) as raw materials, the new chemically
 modified PPP was prepared by the process of fermentation, cooking,
 freeze-drying, and so on. The adsorbent were characterized by SEM, IR, BET
 and EDS. The effects of different adsorption conditions such as pH value,
 adsorption temperature, mass of adsorbent, adsorption time, and initial
 concentration of UO22+ were studied. The adsorption mechanism was explored
 through adsorption thermodynamics and adsorption kinetics experiments. The
 results show that the pH value is 6.0, the dosage of adsorbent is 10 mg,
 the temperature is 50℃ and the adsorption time is 90 min, which is the
 best adsorption condition. When the initial concentration of UO22+ is 35
 mg/L, the adsorbed capacity of uranyl ion by the modified PPP adsorbent
 can reach 42.733 mg/g, 26.8% higher than the adsorption capacity of
 unmodified adsorbent (31.276 mg/g), which is obviously enhanced. The
 kinetic and thermodynamic experiments show that the adsorption process
 accords with the pseudo-second-order kinetics model and is an endothermic
 reaction, and the reaction is spontaneous. The adsorption process is
 dominated by entropic. The Freundlich adsorption isotherm can describe the
 adsorption process more accurately.
description: Data
DOI: 10.5061/dryad.p2qq2d0
title: Data from: Network-targeted stimulation engages neurobehavioral hallmarks of age-related memory decline

description: Objective: To test whether targeting hippocampal-cortical brain networks
 with high-frequency transcranial magnetic stimulation (TMS) in older
 adults influences behavioral and neural measures characteristic of
 age-related memory impairment. Methods: Fifteen adults aged 64 – 80 years
 (mean = 72 years) completed a single-blind, sham-controlled experiment.
 Stimulation targets in parietal cortex were determined based on functional
 magnetic resonance imaging (fMRI) connectivity with the hippocampus.
 Recollection and recognition memory were assessed after five consecutive
 daily sessions of full-intensity stimulation versus low-intensity sham
 stimulation using a within-subjects crossover design. Neural correlates of
 recollection and recognition memory formation were obtained via fMRI,
 measured within the targeted hippocampal-cortical network versus a control
 frontal-parietal network. These outcomes were measured ~24 hours after the
 final stimulation session. Results: Recollection was specifically impaired
 in older adults compared to a young-adult control sample at baseline.
 Relative to sham, stimulation improved recollection to a greater extent
 than recognition. Stimulation increased recollection fMRI signals
 throughout the hippocampal-cortical network, including at the targeted
 location of the hippocampus. Effects of stimulation on fMRI recollection
 signals were greater than those for recognition and were greater in the
 targeted network compared to the control network. Conclusions: Age-related
 recollection impairments were causally related to hippocampal-cortical
 network function in older adults. Stimulation selectively modified neural
 and behavioral hallmarks of age-related memory impairment, indicating
 effective engagement of memory intervention targets in older adults.
description: Supplementary
 MaterialsdervishDO_NeurologyBRIEF_supplement_R1_v6.docx
DOI: 10.5061/dryad.h5h7v20
title: Data from: Age‐dependent habitat relationships of a burned forest specialist emphasise the role of pyrodiversity in fire management

description: 1. Variation in fire characteristics, termed pyrodiversity, plays an
 important role in structuring post-fire communities, but little is known
 about the importance of pyrodiversity for individual species. The
 availability of diverse post-fire habitats may be key for fire-associated
 species if they require different resources at different life history
 stages. 2. We tested for age-specific habitat relationships in the
 black-backed woodpecker, a post-fire specialist. We used radio-telemetry
 to track fledgling and adult woodpeckers in burned forests and built
 resource selection functions to compare the effect of stand-, tree-, and
 snag-level covariates between adults and fledglings. 3. Fledgling
 black-backed woodpeckers selected habitat with more live trees than
 adults, and used more heterogeneous habitats burned at lower severity,
 illustrating strong age-dependent effects on habitat selection. Within
 selected stands, fledglings were less likely to use snags and more likely
 to use live trees when compared to adults, but both age classes showed
 strong positive selection for larger-diameter trees (live and dead). Over
 the 60 days after leaving their nests, fledglings showed an increasing
 propensity to use snags rather than live trees. 4. Our results provide
 evidence that the predation–starvation hypothesis, which posits a
 trade-off between foraging efficiency and the need to minimize predation
 risk, plays a role in structuring the age-dependent habitat use of a
 burned forest specialist. Adult black-backed woodpeckers selected
 resources associated with food availability, but these resources occurred
 in relatively open, exposed habitat. Fledglings selected habitat that
 provided increased cover, perhaps as a strategy to reduce predation risk.
 5. Synthesis and applications. Globally, fires are increasing in severity
 and extent, leading to increased focus on fire-associated species that
 play keystone roles in facilitating biodiversity resilience. Our findings
 suggest that a diversity of patches burned at different severities may
 benefit post-fire specialists like the black-backed woodpecker at multiple
 life history stages. The increasing prevalence of large, homogeneously
 high-severity “megafires” may present an emerging threat even to post-fire
 specialists, and we urge land managers to consider opportunities to
 promote pyrodiversity in the face of novel fire regimes.
description: MetadataMetadata describing .csv files used in this analysisStand-level DataData used in stand-level resource selection functionTree-level DataData used in tree-level resource selection functionSnag-level DataData used in snag-level resource selection function
DOI: 10.5061/dryad.tk8774f
title: Data from: Genome-wide association study of an unusual dolphin mortality event reveals candidate genes for susceptibility and resistance to cetacean morbillivirus

description: Infectious diseases are significant demographic and evolutionary drivers
 of populations, but studies about the genetic basis of disease resistance
 and susceptibility are scarce in wildlife populations. Cetacean
 morbillivirus (CeMV) is a highly contagious disease that is increasing in
 both geographic distribution and incidence, causing unusual mortality
 events (UME) and killing tens of thousands of individuals across multiple
 cetacean species worldwide since the late 1980’s. The largest CeMV
 outbreak in the Southern Hemisphere reported to date occurred in Australia
 in 2013, where it was a major factor in a UME, killing mainly young
 Indo-Pacific bottlenose dolphins (Tursiops aduncus). Using cases
 (non-survivors) and controls (putative survivors) from the most affected
 population, we carried out a genome-wide association study to identify
 candidate genes for resistance and susceptibility to CeMV. The genomic
 dataset consisted of 278,147,988 sequence reads and 35,493 high quality
 SNPs genotyped across 38 individuals. Association analyses found highly
 significant differences in allele and genotype frequencies amongst cases
 and controls at 65 SNPs, and Random Forests conservatively identified
 eight as candidates. Annotation of these SNPs identified five candidate
 genes (MAPK8, FBXW11, INADL, ANK3, and ACOX3) with functions associated
 with stress, pain and immune responses. Our findings provide the first
 insights into the genetic basis of host defence to this highly contagious
 disease, enabling the development of an applied evolutionary framework to
 monitor CeMV resistance across cetacean species. Biomarkers could now be
 established to assess potential risk factors associated with these genes
 in other CeMV affected cetacean populations and species. These results
 could also possibly aid in the advancement of vaccines against
 morbilliviruses.
description: Tursiops SNP
 datasetSNP genotype, vcf file.
 Mapped to the Tursiops truncatus genome
 (GCA_001922835.1).mappedQC.fil5.vcfTursiops ref_seqFForward reference sequencesTur_1.fastaTursiops ref_seqRReverse reference sequencesTur_2.fasta
DOI: 10.5061/dryad.bh14n51
title: Data from: Linking life-history theory and metabolic theory explains the offspring size-temperature relationship

description: Temperature often affects maternal investment in offspring. Across and
 within species, mothers in colder environments generally produce larger
 offspring than mothers in warmer environments, but the underlying drivers
 of this relationship remain unresolved. We formally evaluated the ubiquity
 of the temperature-offspring size relationship and found strong support
 for a negative relationship across a wide variety of ectotherms. We then
 tested an explanation for this relationship that formally links
 life-history and metabolic theories. We estimated the costs of development
 across temperatures using a series of laboratory experiments on model
 organisms, and a meta-analysis across 72 species of ectotherms spanning
 five phyla. We found that both metabolic and developmental rates increase
 with temperature, but development rate is more temperature-sensitive than
 metabolic rate, such that the overall costs of development decrease with
 temperature. Hence, within a species’ natural temperature range,
 development at relatively cooler temperatures requires mothers to produce
 larger, better provisioned offspring.
description: Bugula_neritina_DTMRR markdown file PDF for Bugula neritina: temperature dependence of development time and metabolic rateBugula_DTBugula neritina development time with temperature dataBugula_MRBugula neritina metabolic rate with temperature dataBugula_RepmeasuresBugula neritina metabolic rate repeated measures analysis dataDanio_rerio_DTMRR markdown file PDF for Danio rerio: temperature dependence of development time and metabolic rateDanio_DTDanio rerio development time with temperature dataDanio_MRDanio rerio metabolic rate with temperature dataDanio_RepmeasuresDanio rerio metabolic rate repeated measures analysis dataOffspring size and temperature meta-analysisR file for meta-analysis 1: offspring size and temperaturematched data1Data for meta-analysis 1: offspring size and temperaturematched tree1Tree for meta-analysis 1: offspring size and temperatureCosts of development and temperature meta-analysisR file for meta-analysis 2: costs of development and temperaturematched data2Data for meta-analysis 2: costs of development and temperaturematched tree2Tree for meta-analysis 2: costs of development and temperaturepinPin file required to run both meta-analyses
DOI: 10.5061/dryad.cj4733b
title: Data from: Flexibility, variability and constraint in energy management strategies across vertebrate taxa revealed by long-term heart rate measurements

description: 1) Animals are expected to be judicious in the use of the energy they gain
 due to the costs and limits associated with its intake. The management of
 energy expenditure (EE) exhibited by animals has previously been
 considered in terms of three patterns: the constrained, independent and
 performance patterns of energy management. These patterns can be
 interpreted by regressing daily EE against maintenance EE measured over
 extended periods. From the multiple studies on this topic, there is
 equivocal evidence about the existence of universal patterns in certain
 aspects of energy management. 2) The implicit assumption that animals
 exhibit specifically one of three discrete energy management patterns, and
 without variation, seems simplistic. We suggest that animals can exhibit
 gradations of different energy management patterns and that the exact
 pattern will fluctuate as their environmental context changes. 3) To
 investigate these ideas, and for possible large-scale patterns in energy
 management pattern, we analysed long-term heart rate data – a strong proxy
 for EE – across and within individuals in 16 species of birds, mammals,
 and fish. 4) Our analyses of 292 individuals representing 46 539
 observation-days suggest that vertebrates typically exhibit predominantly
 the independent or performance energy patterns at the across-individual
 level, and that the pattern does not associate with taxonomic group.
 Within individuals, however, animals generally exhibit some degree of
 energy constraint. Together, these findings indicate that across diverse
 species, some individuals supply more energy to all aspects of their life
 than do others, however all individuals must trade-off deployment of their
 available energy between competing functions. This demonstrates that
 within-individual analyses are essential for interpretation of energy
 management patterns. 5) We also found that species do not necessarily
 exhibit a fixed energy management pattern but rather temporal variation in
 their energy management over the year. Animals’ energy management
 exhibited stronger energy constraint during periods of higher EE, which
 typically coincided with clear and key life cycle events such as
 reproduction, suggesting an adaptive plasticity to respond to fluctuating
 energy demands.
description: Heart_rate_long_format_13Complete data set used in the analyses presented in the article.
DOI: 10.5061/dryad.20j465p
title: Data from: Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer

description: Using an ORF kinome screen in MCF-7 cells treated with the CDK4/6
 inhibitor ribociclib plus fulvestrant, we identified FGFR1 as a mechanism
 of drug resistance. FGFR1-amplified/ER+ breast cancer cells and MCF-7
 cells transduced with FGFR1 were resistant to fulvestrant ± ribociclib or
 palbociclib. This resistance was abrogated by treatment with the FGFR
 tyrosine kinase inhibitor (TKI) lucitanib. Addition of the FGFR TKI
 erdafitinib to palbociclib/fulvestrant induced complete responses of
 FGFR1-amplified/ER+ patient-derived-xenografts. Next generation sequencing
 of circulating tumor DNA (ctDNA) in 34 patients after progression on
 CDK4/6 inhibitors identified FGFR1/2 amplification or activating mutations
 in 14/34 (41%) post-progression specimens. Finally, ctDNA from patients
 enrolled in MONALEESA-2, the registration trial of ribociclib, showed that
 patients with FGFR1 amplification exhibited a shorter progression-free
 survival compared to patients with wild type FGFR1. Thus, we propose
 breast cancers with FGFR pathway alterations should be considered for
 trials using combinations of ER, CDK4/6 and FGFR antagonists.
description: RNAseq
 CAMA1RNA-seq
 CAMA1Final
 ReportCell cycle array Fig.
 5Afinal_report.xlsCCND1CCND1 quantification by PCR Fig. 5Bccnd1.xlsNanostring analysis in PDX modelNanostring analysis in PDX modelNanostring Fig6D.csvFigure 7ActDNA analysis in Fig. 7asanitized_vcf.zipFigure 7B Figure 7CFGFR1_NatureComm.zip
DOI: 10.5517/cc3z8dq
title: CCDC 118463: Experimental Crystal Structure Determination

description: Related Article: L.J.Barbour, G.W.Orr, J.L.Atwood|1998|Nature (London)|393|671|doi:10.1038/31441
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25574/30504
title: Chandra X-ray Observatory ObsId 30504

description: Emission Line Driving in Vela X-1
DOI: 10.5061/dryad.c90m738
title: Data from: Have Welsh agri-environment schemes delivered for focal species? Results from a comprehensive monitoring programme

description: 1. Agri-environment schemes (AES) have been criticised for being
 inadequately monitored and for not delivering the expected benefits to
 nature. Consequently, the Welsh Government funded a comprehensive
 programme of monitoring of Welsh AES, which took place between 2009 and
 2012. The AES assessment focused primarily on Tir Gofal (which translates
 as “Land in Care”), but also included the Organic Farming Scheme, and
 monitoring focused on a range of taxa of conservation importance: arable
 plants, grassland fungi, bats (six species), butterflies (three species),
 birds (five species), water vole and brown hare. 2. Field work was
 undertaken to survey these taxa on matched farms and fields within and
 outside of AES. Response variables consisted of spatial trends of
 abundance, occurrence and species richness, which were modelled against
 AES status. Existing data were also available for two bird species. 3. Few
 differences were observed between AES and non-AES farms and fields. Those
 that were observed were for species that use arable habitats (which are
 uncommon in Wales): arable plants, yellowhammers, and brown hares. The
 lack of differences in non-arable habitats may reflect the smaller
 contrast between AES and non-AES management in these habitats. It may also
 reflect the original condition of habitat entered into AES prescriptions,
 as most non-arable prescriptions were defined by mandatory management of
 existing habitats, rather than optional habitat creation or restoration,
 which is the case for most arable prescriptions. 4. Despite the lack of
 differences observed, AES may help to maintain populations of species,
 making it more likely that they will persist in the landscape. There is
 evidence, from this monitoring programme and elsewhere, that AES can
 increase the populations of species, when well targeted and implemented.
 5. Policy applications. The results indicate that Welsh AES have been only
 partly successful in achieving their stated aim of “maintaining and
 enhancing species abundance.” These results can be used to improve AES
 design and management, both in Wales and more widely, by identifying and
 promoting effective management interventions, and by identifying
 ineffective management interventions and seeking alternatives. In
 particular, we highlight the importance of comprehensive monitoring of
 AES, and we recommend that this be combined with specific targets
 regarding the expected outcomes of AES management. This is essential to
 determine whether AES are providing value for money.28-Nov-2018
description: Data_from_MacDonald_et_al_Welsh_AES_species_J_Appl_EcolThese are the data files used in the analysis for the article: Have Welsh agri-environment schemes delivered for focal species? Results from a comprehensive monitoring programme, by MacDonald et al.data_for_archiving.xlsx