cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cm41ff4
title: Data from: Low reversed cyclic loading tests for integrated precast structure of lightweight wall with single-row reinforcement under a lightweight steel frame

description: Given the development of precast structures for low-rise residential
 buildings, this study explores a new structure—namely, an integrated
 precast structure of lightweight recycled-concrete wall with single-row
 reinforcement—under a lightweight steel frame filled with recycled
 concrete (integrated precast structure for short). The lightweight steel
 frame and lightweight wall cooperate to bear the forces. The applied
 concealed bracing, either a rebar bracing or a steel plate bracing,
 increases the shear resistance of the wall. The lightweight steel frame is
 designed to bear the vertical loading, whereas the seismic load in the
 horizontal direction is jointly borne by the frame and wall. This study
 presents the results of low reversed cyclic loading tests on nine
 specimens of integrated precast structures. An analysis is then carried
 out to investigate the mechanical properties of the specimens; based on
 these results, a formula for the force-bearing performance of the inclined
 section is developed. The results show satisfactory performance as an
 integrated piece; the proposed structure has two seismic lines of defence,
 with the lightweight wall restraint by the side frame being the first line
 and the steel frame being the second line. Because the failure of the wall
 can be categorised as shear failure, the restraint of the lightweight
 steel frame significantly reduces the potential damage of the wall. As the
 beams and columns of the steel frame tend to bend against failure, the
 wall filling helps resist sliding. Therefore, the reinforced joints of the
 connecting beams and columns show no visible signs of damage, indicating
 that the connection between the beams and columns is reliable. The narrow
 spacing of rebars and the setting of concealed bracing contribute to the
 increase in ductility and energy efficiency and the evident reduction in
 the failure process. Furthermore, the recycled concrete increases the
 seismic resistance of the structure.
description: Data for Low reversed
 cyclic loading tests for integrated precast structuredata-RSOS-180321.xlsx
DOI: 10.5061/dryad.6s76rp7
title: Data from: Resilience or robustness: identifying topological vulnerabilities in rail networks

description: Many critical infrastructure systems have network structure and are under
 stress. Despite their national importance, the complexity of large-scale
 transport networks means we do not fully understand their vulnerabilities
 to cascade failures. The research in this paper examines the
 interdependent rail networks in Greater London and surrounding commuter
 area. We focus on the morning commuter hours, where the system is under
 the most demand stress. There is increasing evidence that the topological
 shape of the network plays an important role in dynamic cascades. Here, we
 examine whether the different topological measures of resilience
 (stability) or robustness (failure) are more appropriate for understanding
 poor railway performance. The results show that resilience and not
 robustness has a strong correlation to the consumer experience statistics.
 Our results are a way of describing the complexity of cascade dynamics on
 networks without the involvement of detailed agent-based-models, showing
 that cascade effects are more responsible for poor performance than
 failures. The network science analysis hints at pathways towards making
 the network structure more resilient by reducing feedback loops.
description: Passenger network in
 London areaFiles describing the
 passenger network in the London area. The Python code to compute the
 resilience and robustness in also included.Encore_datasets.zip
DOI: 10.5061/dryad.4s3t2p3
title: Data from: On the importance of having a good mother: maternal investment affects duckling mortality risk in wood ducks

description: Most avian populations experience more variation in recruitment than adult
 survival, and twhich drives much of the change in population growth rates
 from year to year. In duck species, the probability of duckling survival
 is an important component of recruitment into the breeding population. We
 investigated how variation in maternal investment in offspring by nesting
 female wood duck Aix sponsa affected duckling mortality (1‐survival) to 60
 days of age using capture‐mark‐recapture techniques. Our primary sample
 consisted of 3,035 ducklings, from 545 nests, that were marked with
 uniquely coded webtags on the day of hatch over nine nesting seasons
 (2008‐2016). We also included 4,437 HY and AHY individuals to increase
 precision on parameter estimates because some ducklings were not
 recaptured until after fledging. Duckling mortality was greatest during
 the first week of life (0.76, 85% C.I. 0.71, 0.81) and approached zero by
 the second week after hatching (0.005, 85% C.I. 0, 0.025). We observed a
 quadratic effect of hatch date on duckling mortality (βHD = 0.013, 85% CI
 0.13, 0.20, βHD2 = 0.12, 85% CI 0.051, 0.017) of hatch date, suggesting
 that successful females improve fitness by nesting early in the year, but
 not too early (15 days before mean hatch). Increased egg volume and
 duckling mass reduced the probability of ducking mortality (βegg volume =
 ‐0.155, 85% CI ‐0.245, ‐0.075. βduckling mass = ‐7.56, 85% CI
 ‐10.67,‐4.45). Our results suggest that risk of mortality for ducklings is
 influenced, at least in part, by maternal effects, which are manifested
 through energy allocation and behavior during the breeding season. As
 such, individual heterogeneity among breeding females affects duckling
 mortality risk and likely the recruitment process for wood ducks.
description: Wood duck
 input
DOI: 10.5061/dryad.rd681sp
title: Data from: Brain myo-inositol as a potential marker of amyloid-related pathology: a longitudinal study.

description: Objective: To investigate the association between longitudinal changes in
 proton magnetic spectroscopy (MRS) metabolites and amyloid pathology in
 non-demented individuals; to explore the relationship between MRS and
 cognitive decline. Methods: In this longitudinal multiple time point study
 (a subset of the Swedish BioFINDER) we included cognitively healthy
 participants, individuals with subjective cognitive decline and mild
 cognitive impairment (MCI). MRS was acquired serially in 294 participants
 (670 individual spectra) from the posterior cingulate/precuneus. Using
 mixed-effects models, we assessed the association between MRS and baseline
 amyloid β42 (Aβ), and between MRS and longitudinal MMSE, accounting for
 APOE, age and sex. Results: While baseline MRS metabolites were similar in
 Aβ positive (Aβ+) and negative (Aβ-) individuals, in the Aβ+ group, the
 estimated rate of change was +1.9%/year for myo-inositol/creatine (mI/Cr)
 and -2.0%/year for N-acetyl-aspartate/myo-inositol (NAA/mI). In the Aβ-
 group, mI/Cr and NAA/mI yearly change was -0.05% and +1.2%, however this
 was not significant across time points. MCI Aβ+ group showed the steepest
 MRS changes, with an estimated rate of +2.93%/year (p=0.07) for mI/Cr and
 -3.55%/year (p&lt;0.01) for NAA/mI. Further, in the entire cohort, we
 found that Aβ+ individuals with low baseline NAA/mI had a significantly
 higher rate of cognitive decline than Aβ+ individuals with high baseline
 NAA/mI. Conclusions: We demonstrate that the longitudinal change in mI/Cr
 and NAA/mI is associated with underlying amyloid pathology. MRS may be a
 useful non-invasive marker of Aβ-related processes over time. Further, we
 show that in Aβ+ individuals, baseline NAA/mI may predict the rate of
 future cognitive decline.
description: Dryad Additional
 MethodsFlowchart describing how
 the final number of s study participants was arrived
 at.Dryad Additional
 Results1) Tables reporting
 concentrations of MRS metabolites in the precuneus/PCC region across the
 different diagnostic/amyloid groups, at baseline, visit 1 and visit 2. 2)
 Boxplots presenting serial spectroscopic data groups based on baseline Aβ
 status.
DOI: 10.5061/dryad.p4mv8t8
title: Data from: Gene regulatory divergence between locally adapted ecotypes in their native habitats

description: Local adaptation is a key driver of ecological specialization and the
 formation of new species. Despite its importance, the evolution of gene
 regulatory divergence among locally-adapted populations is poorly
 understood, especially how that divergence manifests in nature. Here, we
 evaluate gene expression divergence and allele-specific gene expression
 responses for locally-adapted coastal perennial and inland annual
 accessions of the yellow monkeyflower, Mimulus guttatus, in a field
 reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes
 were differentially expressed between coastal and inland habitats, while
 7213 (77%) were differentially expressed between the coastal perennial and
 inland annual accessions. Cis-regulatory variation was pervasive,
 affecting 79% (5532) of differentially expressed genes. We detected trans
 effects for 52% (3611) of differentially expressed genes. Expression
 plasticity of alleles across habitats (GxE interactions) appears to be
 relatively common (affecting 18% of transcripts) and could minimize
 fitness trade-offs at loci that contribute to local adaptation. We also
 found evidence that at least one chromosomal inversion may act as
 supergene by holding together haplotypes of differentially expressed
 genes, but this pattern depends on habitat context. Our results highlight
 multiple key patterns regarding the relationship between gene expression
 and the evolution of locally adapted populations.
description: all_ASE_data_filtered.txtCounts per million reads for assembled transcripts (allele "pairs"). There is one column for each F0 plant and two columns for each F1 plant, one for the S allele and one for the L allele. The columns are labeled as allele-site-generation. So for column "SIF1.3", this is the data for the S allele expressed at the Inland field site in the third F1 plant.CR.faFasta file containing alleleic sequences for all transcripts in the combined parental reference transcriptome.
DOI: 10.5061/dryad.9s03863
title: Data from: Large mammal declines and the incipient loss of mammal-bird mutualisms in an African savanna ecosystem

description: Over the past half-century, large mammal populations have declined
 substantially throughout East Africa, mainly due to habitat loss and
 unsustainable direct exploitation. While it has been acknowledged that the
 loss of large mammals can have direct and cascading effects on community
 composition and ecosystem characteristics, limited quantitative work has
 been done on how declines of large herbivore populations impacts the
 abundance of mutualistic symbionts. Using a space-for-time observational
 approach, we quantified the large mammal community alongside the
 densities, host preferences and behaviors of mutualistic red-billed
 oxpeckers (Buphagus erythrorhynchus), and yellow-billed oxpeckers
 (Buphagus africanus) in northern Tanzania. At the landscape scale, mammal
 community composition was substantially less diverse in highly
 human-dominated areas when compared with more protected areas, with an
 observed complete loss of large wild mammal species in two study areas.
 Mirroring this trend, oxpecker densities were lowest in the least
 protected areas, and highest in fully protected areas. Using resource
 selection functions implemented via generalized linear models at different
 scales, we found that oxpeckers (1) were predominantly (67% of red-billed
 oxpeckers; 70% of yellow-billed oxpeckers) feeding on larger (between
 500kg and 1500kg) ungulate host species within the mammal community, (2)
 usually preferred feeding on larger individuals (adults and males) within
 a specific host species population, and (3) preferred hosts that were more
 tolerant of their presence. In particular, cattle were especially
 intolerant of oxpecker presence and were relatively effective in
 displacing oxpeckers. We found little evidence that oxpecker feeding was
 parasitic across all host species; wound feeding was only observed on
 giraffe, comprising 6% and 4% of feeding behavior in red-billed and
 yellow-billed oxpeckers respectively. Thus, a loss of large-bodied and
 oxpecker tolerant host species is a likely explanation for declines of
 oxpecker populations in human dominated landscapes, which may have further
 cascading effects.
description: Oxpecker
 DataEach row represents a
 five minute observation of an individual mammal and associated number of
 red-billed (RBO) and yellow-billed oxpeckers (YBO). For each individual,
 general data (date, time, location) as well as specific data (group size,
 wound presence, demographics) are provided.
DOI: 10.5061/dryad.cf0hj73
title: Data from: Clinical spectrum of STX1B-related epileptic disorders

description: Objective: The aim of this study was to expand the spectrum of epilepsy
 syndromes related to STX1B, encoding the presynaptic protein syntaxin-1B,
 and establish genotype-phenotype correlations by identifying further
 disease-related variants. Methods: We used next generation sequencing in
 the framework of research projects and diagnostic testing. Clinical data
 and EEGs were reviewed, including already published cases. To estimate the
 pathogenicity of the variants, we used established and newly developed in
 silico prediction tools. Results: We describe 15 new variants in STX1B
 which are distributed across the whole gene. We discerned four different
 phenotypic groups across the newly identified and previously published
 patients (49 patients in 23 families): 1) Six sporadic patients or
 families (31 affected individuals) with febrile and afebrile seizures with
 a benign course, generally good drug response, normal development and
 without permanent neurological deficits; 2) two patients with genetic
 generalized epilepsy without febrile seizures and cognitive deficits; 3)
 13 patients or families with intractable seizures, developmental
 regression after seizure onset and additional neuropsychiatric symptoms;
 4) two patients with focal epilepsy. More often we found loss-of-function
 mutations in benign syndromes, whereas missense variants in the SNARE
 motif of syntaxin-1B were associated with more severe phenotypes.
 Conclusion: These data expand the genetic and phenotypic spectrum of
 STX1B-related epilepsies to a diverse range of epilepsies that span the
 ILAE classification. Variants in STX1B are protean and contribute to many
 different epilepsy phenotypes, similar to SCN1A, the most important gene
 associated with fever-associated epilepsies.
description: Supplements_STX1B_WolkingSupplement_Figures
DOI: 10.5061/dryad.fs4b1b3
title: Data from: Influence of a growth hormone transgene on the genetic architecture of growth-related traits: a comparative analysis between transgenic and wild-type coho salmon

description: Genetic engineering has been increasingly applied to many commercially
 important plant and animal species, generating phenotypic changes that are
 not observed in natural populations and creating genetic interactions that
 have not experienced natural selection. The degree to and way in which
 such human-induced genetic variation interacts with the rest of the genome
 is currently largely unknown. Integrating such information into ecological
 and risk assessment frameworks is crucial to understand the potential
 effects of genetically modified organisms in natural environments. Here,
 we performed QTL mapping to investigate the genetic architecture of
 growth-related traits in non-transgenic (NT) and growth hormone transgenic
 (T) coho salmon with large changes in growth and related physiology, with
 the aim of identifying how an inserted transgene might influence the
 opportunity for selection. These fish shared the same parental genetic
 background, thus allowing us to determine whether the same or different
 loci influence these traits within the two groups. The use of over 1700
 loci, derived from Restriction site Associated DNA Sequencing, revealed
 that different genomic regions were linked with growth over time between
 the two groups. Additionally, the effect sizes of detected QTL appear to
 have been influenced by the transgene. Direct comparison of QTL between
 the T and NT fish during two size-matched periods identified little
 overlap in their location. Taken together, the results showed that the
 transgene altered the genetic basis of growth-related traits in this
 species. The study has important implications for effective conservation
 and management of wild populations experiencing introduction of
 transgenes. Evolutionary changes and their ecological consequences may
 occur at different rates and in different directions in NT versus T
 individuals in response to selection. Thus assessments of phenotypic
 change, and hence ecological risk, should be determined periodically to
 evaluate whether initial estimates made with founder strains remain valid.
description: Genotype and phenotype
 fileGenotype and phenotype
 information for the non-transgenic and transgenic coho salmon used in the
 study. This file consists of 4 sheets: 1) phenotype info for
 non-transgenic siblings with genotype for loci polymorphic in the father
 ("1.NTsib_FatherPolymorphic"), 2) phenotype info for
 non-transgenic siblings with genotype for loci polymorphic in the mother
 ("2.NTsib_MotherPolymorphic"), 3) phenotype info for transgenic
 siblings with genotype for loci polymorphic in the father
 ("3.TGsib_FatherPolymorphic"), 4) phenotype info for transgenic
 siblings with genotype for loci polymorphic in the mother
 ("4.TGsib_MotherPolymorphic").Geno_Pheno_File_MiyakoKodama_8Aug18.xlsx
DOI: 10.5061/dryad.10gk660
title: Data from: Black Queen evolution and trophic interactions determine plasmid survival after the disruption of conjugation network

description: Mobile genetic elements such as conjugative plasmids are responsible for
 antibiotic resistant phenotypes in many bacterial pathogens. The ability
 to conjugate, the presence of antibiotics and ecological interactions all
 have a notable role in the persistence of plasmids in bacterial
 populations. Here, we set out to investigate the contribution of these
 factors when the conjugation network was disturbed by a plasmid-dependent
 bacteriophage. Phage alone effectively caused the population to lose
 plasmids, thus rendering them susceptible to antibiotics. Leakiness of the
 antibiotic resistance mechanism allowing Black Queen evolution (i.e. race
 to the bottom) was a more significant factor over antibiotic concentration
 (lethal vs sub-lethal) in determining plasmid prevalence. Interestingly,
 plasmid loss was also prevented by protozoan predation. These results show
 that the outcome of attempts to re-sensitize bacterial communities by
 disrupting the conjugation network are highly dependent on ecological
 factors and resistance mechanisms.
description: population_dataPopulation data from the experimental evolution experiment.temporal_data.txtCommunity_model_filesContains the JAVA files of the individual based model. Can be run for example in Eclipse using Java runtime environment.conjugation_ability_testsPlates from the experiments where the conjugation ability of the bacteria from the end time point was investigated. Plates are coded with the following letters referring to the experiment setup: B = Bacterium, P = Predator, V = Virus (phage), 0.1K = 0.1 MIC kanamycin, 1.5K = 1.5 MIC kanamycin, 0.1A = 0.1 MIC ampicillin, 1.5A = 1.5 MIC ampicillin. L-malja indicates plates without antibiotics, Amp = ampicillin on the plate, Kana (or Kan) = kanamycin on the plate, Tetra = tetracycline on the plate.
DOI: 10.5061/dryad.63nm407
title: Data from: Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species

description: Next‐generation reduced representation sequencing (RRS) approaches show
 great potential for resolving the structure of wild populations. However,
 the population structure of species that have shown rapid demographic
 recovery following severe population bottlenecks may still prove difficult
 to resolve due to high gene flow between subpopulations. Here, we tested
 the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for
 describing the population structure of the New Zealand fur seal (NZFS,
 Arctocephalus forsteri), a species that was heavily exploited by the 19th
 century commercial sealing industry and has since rapidly recolonized most
 of its former range from a few isolated colonies. Using 26,026 neutral
 single nucleotide polymorphisms (SNPs), we assessed genetic variation
 within and between NZFS colonies. We identified low levels of population
 differentiation across the species range (&lt;1% of variation
 explained by regional differences) suggesting a state of near panmixia.
 Nonetheless, we observed subtle population substructure between West Coast
 and Southern East Coast colonies and a weak, but significant (p = 0.01),
 isolation‐by‐distance pattern among the eight colonies studied.
 Furthermore, our demographic reconstructions supported severe bottlenecks
 with potential 10‐fold and 250‐fold declines in response to Polynesian and
 European hunting, respectively. Finally, we were able to assign
 individuals treated as unknowns to their regions of origin with high
 confidence (96%) using our SNP data. Our results indicate that while it
 may be difficult to detect population structure in species that have
 experienced rapid recovery, next‐generation markers and methods are
 powerful tools for resolving fine‐scale structure and informing
 conservation and management efforts.
description: Stacks and Plink
 CommandsGBS pipeline commands
 for SNP discrovery including Stacks and post-filtering with populations
 and Plinkfiltered-geno-0.2-maf-0.05-mind-0.9169 NZFS - NCBI accession numbers169 NZFS - NCBI accession numbers