cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kr846
title: Data from: A cross sectional study of the relationship between the exposure of pregnant women to military attacks in 2014 in Gaza and the load of heavy metal contaminants in the hair of mothers and newborns

description: OBJECTIVE: Metal contamination of humans in wars areas was rarely
 investigated. Weaponry’s heavy-metals become environmentally stable
 war-remnants and accumulate in livings. They pose health risks also by
 prenatal intake and potential long-term risks for reproductive and
 children’s health. We studied the contribution by military attacks to the
 load of 23 metals in the hair of Palestinian women in the Gaza Strip,
 pregnant at the time of military attacks in 2014, and their newborns. We
 compared the metal load in the mothers with values of adult hair from
 outside war area (RHS), as reference. We investigated heavy metals
 trans-passing in utero and assessed if risky heavy metals intake could
 come from not war-related sources. DESIGN: Cross-sectional study.
 PARTICIPANTS AND SETTING: Random cohort of 502 mothers delivering in the
 Gaza Strip and their newborns. MAIN OUTCOME MEASURED: Measure of the load
 of heavy-metals in mother and newborn hair by Inductively Coupled Plasma
 Mass Spectrometry (ICP/MS). Comparison of metal load with RHS, between
 groups with different exposures to attacks and house/agriculture
 chemicals, and between mothers and newborns. Data for birth registry and
 for exposures to war and other known risk factors were obtained at
 interviews with mothers. Photo documentation of damage from military
 attacks. RESULTS: The whole cohort had significantly higher load of heavy
 metals than RHS. Women exposed to military attacks had significantly
 higher load of heavy metals than those not exposed; the load in newborns
 correlated positively with mothers’; no significant difference was found
 between users/not users of house/agriculture chemicals; no other known
 confounder was identified. CONCLUSIONS: High heavy-metals loads in
 mothers, reflected in those of their newborns, are associated with
 exposure to military attacks posing risk of immediate and long-term
 negative outcomes for pregnancy and child health. Surveillance,
 biomonitoring and further research are recommended. Implications for
 general and public health are discussed.
description: 23 Metal load, median
 values, for mothers and their babies with different exposure to military
 attacks in 2014 in Gaza, Palestine23 Metal load (median
 values) for mothers and their babies with different exposure to military
 attacks in 2014 in Gaza, Palestine.The whole cohort; exposed and resident
 women (group 1); exposed and relocated after the attacks women (group2);
 not exposed women and their newborns in 2015. analysis by
 ICP/MSManduca et al. supplementary
 Table I.docx
DOI: 10.5061/dryad.r5rh1
title: Data from: Do ‘passive’ medical titanium surfaces deteriorate in service in the absence of wear?

description: Globally, more than 1000 tonnes of titanium (Ti) is implanted into
 patients in the form of biomedical devices on an annual basis. Ti is
 perceived to be ‘biocompatible’ owing to the presence of a robust passive
 oxide film (approx. 4 nm thick) at the metal surface. However, surface
 deterioration can lead to the release of Ti ions, and particles can arise
 as the result of wear and/or corrosion processes. This surface
 deterioration can result in peri-implant inflammation, leading to the
 premature loss of the implanted device or the requirement for surgical
 revision. Soft tissues surrounding commercially pure cranial anchorage
 devices (bone-anchored hearing aid) were investigated using synchrotron
 X-ray micro-fluorescence spectroscopy and X-ray absorption near edge
 structure. Here, we present the first experimental evidence that minimal
 load-bearing Ti implants, which are not subjected to macroscopic wear
 processes, can release Ti debris into the surrounding soft tissue. As such
 debris has been shown to be pro-inflammatory, we propose that such
 distributions of Ti are likely to effect to the service life of the
 device.
description: Figure 2 map
 dataTitanium fluorescence
 intensity data for Figure 2, saved in Origin 8.1 (Originlab). See ReadMe
 for further details.Figure 3
 XANESFigure 5 map
 data
DOI: 10.5061/dryad.578jd
title: Data from: Species identity and depth predict bleaching severity in reef building corals: shall the deep inherit the reef?

description: Mass bleaching associated with unusually high sea temperatures represents
 one of the greatest threats to corals and coral reef ecosystems. Deeper
 reef areas are hypothesized as potential refugia, but the susceptibility
 of Scleractinian species over depth has not been quantified. During the
 most severe bleaching event on record, we found up to 83% of coral cover
 severely affected on Maldivian reefs at a depth of 3–5 m, but
 significantly reduced effects at 24–30 m. Analysis of 153 species'
 responses showed depth, shading and species identity had strong,
 significant effects on susceptibility. Overall, 73.3% of the shallow-reef
 assemblage had individuals at a depth of 24–30 m with reduced effects,
 potentially mitigating local extinction and providing a source of recruits
 for population recovery. Although susceptibility was phylogenetically
 constrained, species-level effects caused most lineages to contain some
 partially resistant species. Many genera showed wide variation between
 species, including Acropora, previously considered highly susceptible.
 Extinction risk estimates showed species and lineages of concern and those
 likely to dominate following repeated events. Our results show that deeper
 reef areas provide refuge for a large proportion of Scleractinian species
 during severe bleaching events and that the deepest occurring individuals
 of each population have the greatest potential to survive and drive reef
 recovery.
description: bleaching_data_FINALspecies-specific bleaching dataRHIS_benthic_FINALCommunity-level bleaching impact data
DOI: 10.5061/dryad.6r138b0h
title: Data from: Fisher's geometrical model of fitness landscape and variance in fitness within a changing environment

description: The fitness of an individual can be simply defined as the number of its
 offspring in the next generation. However, it is not well understood how
 selection on the phenotype determines fitness. In accordance with Fisher’s
 fundamental theorem, fitness should have no or very little genetic
 variance, whereas empirical data suggest that is not the case. To bridge
 these knowledge gaps, we follow Fisher’s geometrical model and assume that
 fitness is determined by multivariate stabilizing selection towards an
 optimum that may vary among generations. We assume random mating, free
 recombination, additive genes, and uncorrelated stabilizing selection and
 mutational effects on traits. In a constant environment, we find that
 genetic variance in fitness under mutation-selection balance is a U-shaped
 function of the number of traits (i.e. of the so-called “organismal
 complexity”). Because the variance can be high if the organism is of
 either low or high complexity, this suggests that complexity has little
 direct costs. Under a temporally varying optimum, genetic variance
 increases relative to a constant optimum and increasingly so when the
 mutation rate is small. Therefore mutation and changing environment
 together can maintain high genetic variance. These results therefore lend
 support to Fisher’s geometric model of a fitness landscape.
description: Data-Code-Zhang2012Data for Figures 1-6 and tables. Fortran code.
DOI: 10.5061/dryad.t0b62
title: Data from: Genetic and morphometric divergence in threespine stickleback in the Chignik catchment, Alaska

description: Divergent selection pressures induced by different environmental
 conditions typically lead to variation in life history, behaviour and
 morphology. When populations are locally adapted to their current
 environment, selection may limit movement into novel sites, leading to
 neutral and adaptive genetic divergence in allopatric populations.
 Subsequently, divergence can be reinforced by development of pre- or
 post-zygotic barriers to gene flow. The threespine stickleback,
 Gasterosteus aculeatus, is a primarily marine fish that has invaded
 freshwater repeatedly in postglacial times. After invasion, the
 established freshwater populations typically show rapid diversification of
 several traits as they become reproductively isolated from their ancestral
 marine population. In this paper we examine the genetic and morphometric
 differentiation between sticklebacks living in an open system comprising a
 brackish water lagoon, two freshwater lakes, and connecting rivers. By
 applying a set of microsatellite markers, we disentangled the genetic
 relationship of the individuals across the diverse environments and
 identified two genetic populations: one associated with brackish and the
 other with the freshwater environments. The ‘brackish’ sticklebacks were
 larger and had a different body shape than those in freshwater. However,
 we found evidence for upstream migration from the brackish lagoon into the
 freshwater environments, as fish that were genetically and
 morphometrically similar to the lagoon fish were found in all freshwater
 sampling sites. Regardless, few F1-hybrids were identified and it
 therefore appears that some pre- and/or post-zygotic barriers to gene flow
 rather than geographic distance are causing the divergence in this system.
description: Chignik_sticklebacksMicrosatellite- and landmark information for Chignik Stickleback collected 2009
DOI: 10.5061/dryad.dc965
title: Data from: Bony labyrinth morphometry indicates locomotor adaptations in the squirrel-related clade (Rodentia, Mammalia)

description: The semicircular canals (SCs) of the inner ear detect angular acceleration
 and are located in the bony labyrinth of the petrosal bone. Based on
 high-resolution computed tomography, we created a size-independent
 database of the bony labyrinth of 50 mammalian species especially rodents
 of the squirrel-related clade comprising taxa with fossorial, arboreal and
 gliding adaptations. Our sampling also includes gliding marsupials,
 actively flying bats, the arboreal tree shrew and subterranean species.
 The morphometric anatomy of the SCs was correlated to the locomotion mode.
 Even if the phylogenetic signal cannot entirely be excluded, the main
 significance for functional morphological studies has been found in the
 diameter of the SCs, whereas the radius of curvature is of minor interest.
 Additionally, we found clear differences in the bias angle of the canals
 between subterranean and gliding taxa, but also between sciurids and
 glirids. The sensitivity of the inner ear correlates with the locomotion
 mode, with a higher sensitivity of the SCs in fossorial species than in
 flying taxa. We conclude that the inner ear of flying and gliding mammals
 is less sensitive due to the large information flow into this sense organ
 during locomotion.
description: suppl01_dataset bony
 labyrinth_Pfaff ETALRaw data and
 measurements of the investigated specimenssuppl02_taxa scan
 informationInformation of the
 investigated specimens and the respective CT scans
DOI: 10.5061/dryad.8988840
title: Data from: Intraspecific predator inhibition, not a prey size refuge, enables oyster population persistence during predator outbreaks

description: Predators commonly structure natural communities, but predation effects
 can vary greatly. For example, increasing predator densities may not
 reduce prey populations as expected if intraspecific predator interactions
 suppress foraging efficiency or if prey size refuges exist. In
 northeastern Florida (USA), outbreaks of the predatory crown conch
 Melongena corona have contributed to declines in oyster populations and
 the commercial oyster fishery. However, despite expectations of oyster
 population collapse, reefs have persisted, albeit with reduced adult
 oyster size and living reef biomass. To investigate the mechanism(s)
 underlying this unexpected persistence, we used field observations and
 experiments to examine the effects of predator density and prey size on
 predation rates. Multi-year surveys indicated that large oysters did not
 experience a predation size refuge, and further suggested that predation
 rates declined with increased predator density. Consistent with field
 surveys, field experiments demonstrated that conchs selectively consumed
 larger oysters (potentially explaining the absence of large oysters on
 natural reefs) and that high conch densities suppressed per capita
 predation rates, likely due to intraspecific antagonistic interactions. A
 Type III ratio-dependent model best described the experimental conch
 functional response, explaining &gt;50% of the variation in per capita
 prey consumption and including a signal of reduced attack rates at high
 predator densities. Thus, although large aggregations of predators have
 the potential to deplete prey populations, our study illustrates
 intraspecific predator interactions that possibly prevent the local
 extirpation of an important habitat-forming prey species.
description: Booth_et_al_2018_MEPS_Data_and_CodeThis file contains both the data files and code associated with each figure and analysis from this study (including supplemental information). Each folder within the file contains the data file(s) for each figure, and the .R file contains all the code used for analyses except that used for Figure 5 (a Matlab file, extension .m, stored with the data in the 'Fig.5' folder). The data and code for the supplemental information are stored together in the SI folder.Booth_et_al_2018_MEPS.zip
DOI: 10.5061/dryad.986kd
title: Data from: Genetic species delineation among branching Caribbean Porites corals

description: Coral species are difficult to discern because of their morphological
 plasticity, long generation times, and slow rates of mitochondrial DNA
 evolution. Amongst Caribbean representatives of the genus Porites are
 three named species (P. divaricata, P. furcata, and P. porites) with
 branching colony morphologies whose validity as genetically isolated
 species has been debated. We present sequence data from the mitochondrial
 control region, nuclear ITS, and nine single copy nuclear loci for the
 Caribbean Porites and a related eastern Pacific species. mtDNA sequences
 were nearly invariant amongst the three branching species and their
 crustose sister P. branneri, and ITS sequences from these four were
 intermingled. An information theoretic analysis provided no support for
 upholding the three named Caribbean branching species. Both a clustering
 analysis and an analysis of molecular variance showed that sequence
 variation from the three branching forms is partitioned geographically
 rather than taxonomically. Multi-locus coalescent phylogenetic analysis
 provided a calibrated estimate for the nuclear DNA substitution rate
 (0.14%/Ma) close to that for other corals. Because no generalities have
 emerged from genetic investigations of the validity of morphologically
 defined coral species, the use of single copy nuclear data is likely to be
 important in testing problematic species designations.
description: ITS2 fasta
 aligmentITS4.fastaATPbREJ Receptor for egg jelly 5'UTRREJ.fastaAnn1 Anonymous 1Ann1.fastaMM100 Major yolk proteinMM100.fastaCR Control RegionCR.fastaMM32 Major yolk proteinMM32.fastaPbr27 AnonymousPbr27.fastaPbr28 AnonymousPbr28.fastaPbr44 AnonymousPbr44.fastaPbr74 AnonymousPbr74.fasta
DOI: 10.5061/dryad.8cg8h
title: Data from: Insecticide applications to soil contribute to development of Burkholderia mediating insecticide resistance in stinkbugs

description: Some soil Burkholderia strains are capable of degrading the
 organophosphorus insecticide, fenitrothion, and establish symbiosis with
 stinkbugs, making the host insects fenitrothion-resistant. However, the
 ecology of the symbiotic degrading Burkholderia adapting to fenitrothion
 in the free-living environment is unknown. We hypothesized that
 fenitrothion applications affect the dynamics of fenitrothion-degrading
 Burkholderia, thereby controlling the transmission of symbiotic degrading
 Burkholderia from the soil to stinkbugs. We investigated changes in the
 density and diversity of culturable Burkholderia (i.e. symbiotic and
 nonsymbiotic fenitrothion degraders and nondegraders) in
 fenitrothion-treated soil using microcosms. During the incubation with
 five applications of pesticide, the density of the degraders increased
 from less than the detection limit to around 106/g of soil. The number of
 dominant species among the degraders declined with the increasing density
 of degraders; eventually, one species predominated. This process can be
 explained according to the competitive exclusion principle using Vmax and
 Km values for fenitrothion metabolism by the degraders. We performed a
 phylogenetic analysis of representative strains isolated from the
 microcosms and evaluated their ability to establish symbiosis with the
 stinkbug Riptortus pedestris. The strains that established symbiosis with
 R. pedestris were assigned to a cluster including symbionts commonly
 isolated from stinkbugs. The strains outside the cluster could not
 necessarily associate with the host. The degraders in the cluster
 predominated during the initial phase of degrader dynamics in the soil.
 Therefore, only a few applications of fenitrothion could allow symbiotic
 degraders to associate with their hosts and may cause the emergence of
 symbiont-mediated insecticide resistance.
description: Tago_Burks_alignment_file16S rRNA gene sequences of the Burkholderia spp. were aligned using MEGA 6.Tago_Burks_MLtree_fileMaximum Likelihood tree of the Burkholderia spp. based on 16S rRNA gene sequences using MEGA 6.Tago_Colony_counting_dataTago_Community_pattern_dataTago_Oxygen_consumption_data
DOI: 10.5061/dryad.9m808
title: Data from: Avoiding erroneous citations in ecological research: read before you apply

description: The Shannon–Wiener index is a popular nonparametric metric widely used in
 ecological research as a measure of species diversity. We used the Web of
 Science database to examine cases where papers published from 1990 to 2015
 mislabelled this index. We provide detailed insights into causes
 potentially affecting use of the wrong name ‘Weaver’ instead of the
 correct ‘Wiener’. Basic science serves as a fundamental information source
 for applied research, so we emphasize the effect of the type of research
 (applied or basic) on the incidence of the error. Biological research,
 especially applied studies, increasingly uses indices, even though some
 researchers have strongly criticized their use. Applied research papers
 had a higher frequency of the wrong index name than did basic research
 papers. The mislabeling frequency decreased in both categories over the
 25-year period, although the decrease lagged in applied research.
 Moreover, the index use and mistake proportion differed by region and
 authors’ countries of origin. Our study also provides insight into
 citation culture, and results suggest that almost 50% of authors have not
 actually read their cited sources. Applied research scientists in
 particular should be more cautious during manuscript preparation,
 carefully select sources from basic research, and read theoretical
 background articles before they apply the theories to their research.
 Moreover, theoretical ecologists should liaise with applied researchers
 and present their research for the broader scientific community.
 Researchers should point out known, often-repeated errors and phenomena
 not only in specialized books and journals but also in widely used and
 fundamental literature.
description: Dataset for analyses of
 patterns of mislabeling of the Shannon-Wiener diversity
 indexData of 2098 papers
 mentioning Shannon-Wiener (S-Wi), Shannon-Weaver (S-We) or both names
 concurrently (S-Wi + S-We) between 1990-2015, downloaded from Web of
 Science database. Metadata of every paper originally included
 authors' names, title, journal and year of publishing, database
 accession number, first author's address, and affiliation to focal
 research area(s). We added information concerning research type (applied
 vs basic), affiliation to country and region of origin, if the first
 author is a native or non-native speaker (language), and impact on a
 scientific community (H-index of particular country - higher (&gt; 200),
 lower (&lt; 200)).Web of Science
 data.xlsx
DOI: 10.5061/dryad.g6b2f
title: Data from: Composition of micro-eukaryotes on the skin of the Cascades frog (Rana cascadae) and patterns of correlation between skin microbes and Batrachochytrium dendrobatidis

description: Global amphibian decline linked to fungal pathogens has galvanized
 research on applied amphibian conservation. Skin-associated bacterial
 communities of amphibians have been shown to mediate fungal skin
 infections and the development of probiotic treatments with antifungal
 bacteria has become an emergent area of research. While exploring the role
 of protective bacteria has been a primary focus for amphibian
 conservation, we aim to expand and study the other microbes present in
 amphibian skin communities including fungi and other micro-eukaryotes.
 Here, we characterize skin-associated bacteria and micro-eukaryotic
 diversity found across life stages of Cascades frog (Rana cascadae) and
 their associated aquatic environments using culture independent 16S and
 18S rRNA marker-gene sequencing. Individuals of various life stages of
 Cascades frogs were sampled from a population located in the Trinity Alps
 in Northern California during an epidemic of the chytrid fungus,
 Batrachochytrium dendrobatidis. We filtered the bacterial sequences
 against a published database of bacteria known to inhibit B. dendrobatidis
 in co-culture to estimate the proportion of the skin bacterial community
 that is likely to provide defense against B. dendrobatidis. Tadpoles had a
 significantly higher proportion of B. dendrobatidis-inhibitory bacterial
 sequence matches relative to subadult and adult Cascades frogs. We applied
 a network analysis to examine patterns of correlation between bacterial
 taxa and B. dendrobatidis, as well as micro-eukaryotic taxa and B.
 dendrobatidis. Combined with the published database of bacteria known to
 inhibit B. dendrobatidis, we used the network analysis to identify
 bacteria that negatively correlated with B. dendrobatidis and thus could
 be good probiotic candidates in the Cascades frog system.
description: Cascadae_Bd_inhibitory_taxa_Summarized_by_liefestage_Test_significant_OTUsCascadae_Bd_inhibitory_taxa_Summarized_by_liefestage_significant_OTUsCascadae_biom_file_16_18s_fungi_combinedCascadae_Supplemental_Table_2_Positive_Co_occurance_w_BdCascadae_Supplemental_Table_2_Positive_Co_occurance_w_BdCascadae_Supplemental_Table_3_Negitive_Co_occurance_w_BdCascadae_Supplemental_Table_3_Negitive_Co_occurance_w_BdCascadae_Supplemental_Table_4_Complete_list_Bd_inhibitory_OTUs_Ids_7459Cascadae_Supplemental_Table_4_Complete_list_Bd_inhibitory_OTUs_Ids_7459Cascadae_Supplemental_Table_5_Results_of_ANCOMCascadae_Supplemental_Table_5_Results_of_ANCOM