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Data from: Polarimetry of Pinctada fucata nacre indicates myostracal layer interrupts nacre structure
The inner layer of many bivalve and gastropod molluscs consists of iridescent nacre, a material that is structured like a brick wall with bricks consisting of crystalline aragonite and mortar of organic molecules. Myostracal layers formed during shell growth at the point of muscle attachment to the shell can be found interspersed within the nacre structure. Little has been done to examine the effect the myostracal layer has on subsequent nacre structure. Here we present data on the structure of the myostracal and nacre layers from a bivalve mollusc, Pinctada fucata. Scanning electron microscope imaging shows the myostracal layer consists of regular crystalline blocks. The nacre before the layer consists of tablets approximately 400 nm thick, while after the myostracal layer the tablets are approximately 500 nm thick. A new technique, imaging polarimetry, indicates that the aragonite crystals within the nacre following the myostracal layer have greater orientation uniformity than before the myostracal layer. The results presented here suggest a possible interaction between the myostracal layer and subsequent shell growth.
Data from: Earthworms and cadmium – heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils?
Preservation of the soil resources stability is of high importance for ecosystems, particularly in the current era of environmental change, which presents a severe pollution burden (e.g. by heavy metals) to soil fauna. Gut microbiomes are becoming recognized as important players in organism health, with comprehension of their perturbations in the polluted environment offering new insights into the nature and extent of heavy metal effects on the health of soil biota. Our aim was to investigate the effect of environmentally relevant heavy metal concentrations of cadmium (Cd) on the earthworm (Lumbricus terrestris) gut microbiota. Our results revealed that Cd exposure led to perturbations of earthworm gut microbiota with an increase in bacteria previously described as heavy metal resistant or able to bind heavy metals, revealing the potential of the earthworm-gut microbiota system in overcoming human-caused heavy metal pollution. Furthermore, an 'indicator species analysis' linked the bacterial genera Paenibacillus, Flavobacterium and Pseudomonas, with Cd treatment, suggesting these bacterial taxa as biomarkers of exposure in earthworms inhabiting Cd-stressed soils. The results of this study help to understand the impact of anthropogenic disturbance on soil fauna health and will have implications for environmental monitoring and protection of soil resources.
Data from: Are extraversion and openness indicators of a slow life history strategy?
Theory and data generally concur that a slower Life History Strategy (LHS) is associated with higher Conscientiousness, Agreeableness and Emotional Stability. Whether Extraversion and Openness are indicators of a slow LH, or whether they include both fast and slow LH components, remains unresolved. I addressed these questions in two studies: one of university students observed via periodic brief audio recordings during 72 hours of their daily lives, and the second a re-analysis of data from Block and Block's (2006) longitudinal study. In both studies, I operationalized LHS as the correlation between an individual's California Q-Sort (CAQ) profile and the slow Life History (SLH) CAQ template created by Sherman et al. (2013) and Dunkel et al. (2015). I calculated Five Factor Model dimension scores using McCrae et al's (1986) method. In both samples, individuals whose CAQ profile more closely resembled the SLH template were higher in Conscientiousness, Agreeableness, and Emotional Stability than those pursuing a faster LHS. Extraversion was unrelated to LHS, while Openness in the Block and Block data set was actually associated with a faster LHS. Analysis of individual CAQ items revealed some differences between the studies. Generally, Extraversion-loading items tapping excitement-seeking and self-dramatization, and Openness-loading items tapping nonconformity, were associated with a faster LHS. Participants in the audio recording study also completed a HEXACO personality inventory and the Arizona Life History Battery. LHS as measured by the ALHB was uncorrelated with LHS as measured by the CAQ. Controlling for Extraversion yielded a significant positive relationship between the two LHS measures, suggesting that their poor convergent validity resulted from differences in their coverage of Extraversion-related content.
Data from: Improving estimates of environmental change using multilevel regression models of Ellenberg indicator values
Ellenberg indicator values (EIVs) are a widely used metric in plant ecology comprising a semi-quantitative description of species' ecological requirements. Typically, point estimates of mean EIV scores are compared to infer differences in the environmental conditions structuring plant communities – particularly in resurvey studies with no historical environmental data available. However, the use of point estimates as a basis for inference does not take into account variance among species EIVs within sampled plots, and gives equal weighting to means calculated from sites with differing numbers of species. We present a set of multilevel models – fitted with and without group-level predictors – to improve precision and accuracy of site mean EIV scores, and to provide more reliable inference on changing environmental conditions over spatial and temporal gradients in re-visitation studies. We compare multilevel model performance to GLMM's fitted to point estimates of site mean EIVs. We also test the reliability of this method to improve inferences with incomplete species lists in some or all sample sites. Hierarchical modelling led to more accurate and precise estimates of site-level differences in mean EIV scores between time-periods, particularly for datasets with incomplete records of species occurrence. They also revealed directional environmental change within ecological habitat types, which estimates from GLMM's were inadequate to detect. Multilevel models also highlighted a prominent role of hydrological differences as a driver of community change in our case study, which traditional use of EIVs failed to reveal. We have demonstrated that multilevel modelling of EIVs allows for a nuanced estimation of environmental change underlying ecological communities from plant assemblage data, leading to a better understanding of temporal dynamics of ecosystems. Further, the ability of these methods to perform well with missing data should increase the total set of historical data which can be used to this end.
Data from: Non-monotonic temporal-weighting indicates a dynamically modulated evidence-integration mechanism
Perceptual decisions are thought to be mediated by a mechanism of sequential sampling and integration of noisy evidence whose temporal weighting profile affects the decision quality. To examine temporal weighting, participants were presented with two brightness-fluctuating disks for 1, 2 or 3 seconds and were requested to choose the overall brighter disk at the end of each trial. By employing a signal-perturbation method, which deploys across trials a set of systematically controlled temporal dispersions of the same overall signal, we were able to quantify the participants' temporal weighting profile. Results indicate that, for intervals of 1 or 2 sec, participants exhibit a primacy-bias. However, for longer stimuli (3-sec) the temporal weighting profile is non-monotonic, with concurrent primacy and recency, which is inconsistent with the predictions of previously suggested computational models of perceptual decision-making (drift-diffusion and Ornstein-Uhlenbeck processes). We propose a novel, dynamic variant of the leaky-competing accumulator model as a potential account for this finding, and we discuss potential neural mechanisms.
Data from:Corruption, development and governance indicators predict invasive species risk from trade
Invasive species have an enormous global impact, with international trade being the leading pathway for their introduction. Current multinational trade deals under negotiation will dramatically change trading partnerships and pathways. These changes have considerable potential to influence biological invasions and global biodiversity. Using a database of 47 328 interceptions spanning 10 years, we demonstrate how development and governance socio-economic indicators of trading partners can predict exotic species interceptions. For import pathways associated with vegetable material, a significantly higher risk of exotic species interceptions was associated with countries that are poorly regulated, have more forest cover and have surprisingly low corruption. Corruption and indicators such as political stability or adherence to rule of law were important in vehicle or timber import pathways. These results will be of considerable value to policy makers, primarily by shifting quarantine procedures to focus on countries of high risk based on their socio-economic status. Further, using New Zealand as an example, we demonstrate how a ninefold reduction in incursions could be achieved if socio-economic indicators were used to select trade partners. International trade deals that ignore governance and development indicators may facilitate introductions and biodiversity loss. Development and governance within countries clearly have biodiversity implications beyond borders.
Data from: Molecular data and distribution dynamics indicate a recent and incomplete separation of manakins species of the genus Antilophia (Aves: Pipridae) in response to Holocene climate change
To determine a hypothetical scenario that accounts for the diversification of the two species of the genus Antilophia, we conducted multilocus molecular comparisons and species distribution modeling for the two taxa, which have distinct male plumage coloration patterns and allopatric geographic distributions, despite the high degree of genetic similarity indicated by recent studies. Three mitochondrial and three nuclear fragments were analyzed. The results indicate clear differences in the genetic diversity of the two species, but with ample sharing of haplotypes in all the markers analyzed, reflecting the absence of reciprocal monophyly, presumably due to the relatively recent and still incomplete separation of the two species. The paleoclimatic distribution models, together with the observed genetic profile indicate a recent process of divergence by geographic isolation in the ancestral populations of the two species. This scenario coincides with the recent climatic events of the South American dry diagonal, which involves the gallery forests of the Cerrado biome and the cloud forest enclaves of the seasonal tropical dry forest of the Caatinga between the late Pleistocene and the mid Holocene.
Data from: Plasma pro-atrial natriuretic peptide to indicate fluid balance during cystectomy: a prospective observational study
Objectives: During surgery the volume of administered fluid is debated. Pro-atrial natriuretic peptide (proANP) is released by atrial distension, and we evaluated the relationship between changes in proANP associated with perioperative fluid balance. Design: Prospective observational study. Setting: One university/tertiary centre. Participants: The study included patients who underwent radical cystectomy. Plasma for determination of proANP was obtained before surgery, after resection of the bladder, and at the end of surgery for 20 robotic-assisted radical cystectomy (RARC) and 20 open radical cystectomy (ORC) procedures. Results: The blood loss was 1871 (95% CI 1267 to 2475) vs 589 mL (378 to 801) in the ORC and RARC groups (p=0.001), respectively, and fluid balance was positive by 1518 mL (1215 to 1821) during ORC, and by 1858 mL (1461 to 2255) during RARC (p=0.163). Yet, at the end of ORC, plasma proANP was reduced by 23% (14% to 32%, p=0.001), while plasma proANP did not change significantly during RARC. Thus, plasma proANP was associated both with the perioperative blood loss (r= −0.475 (0.632 to −0.101), p=0.002), and with fluid balance (r=0.561 (0.302 to 0.740), p=0.001), indicating that a stable plasma proANP required a fluid surplus by 2.4 L (2.0 to 2.7). Conclusions: There was a correlation between intraoperative haemorrhage and a decrease in plasma proANP and, taking plasma proANP to indicate filling of the heart, about 2.5 L surplus volume of lactated Ringer's solution appears to maintain cardiac preload during cystectomy.
Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana
Gene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. Using RNA-seq we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in alpha whole genome duplicates, and 33% of AS events in tandem duplicates, are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this divergence. Conserved events had different frequencies, as only 31% of shared AS events in alpha whole genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative divergence. Analysis of published RNA-seq data from nonsense mediated decay (NMD) mutants indicated that 85% of alpha whole genome duplicates and 89% of tandem duplicates have diverged in their AS-induced NMD. Our results indicate that alternative splicing shows a high degree of divergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative divergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level divergence.
Data from: Variation in defence strategies in the metal hyperaccumulator Noccaea caerulescens is indicative of synergies and trade-offs between forms of defence
The metal hyperaccumulator, N. caerulescens, uses metals as a defence against pathogens. Earlier work has suggested both trade-offs and synergies between metals and inducible defences. Different populations of N. caerulescens vary in metal accumulation. Here, we test the hypothesis that this produces different outcomes in trade-offs between defences. We compare zinc concentrations, glucosinolate concentrations, and inducible stress responses, including ROS and cell death, in four N. caerulescens populations, and relate these to the growth of the plant pathogen Pseudomonas syringae, its zinc tolerance mutants, and Pseudomonas pathogens isolated from a natural population of N. caerulescens. The populations display strikingly different defences. Where defences are successful, pathogens are limited primarily by metals, cell death, or organic defences, with evidence of both trade-offs and synergies between these, depending upon population. In addition, we find evidence that Pseudomonas pathogens may evolve to overcome any of these strategies, indicating that the arms race continues. These data indicate that defensive enhancement, joint effects and trade-offs between forms of defence are all plausible explanations for the evolution of metal-based defences, with factors including metal availability and pressures from metal-tolerant pathogens likely shaping the current strategy of each ecotype.
Data from: How to use (and not to use) movement-based indices for quantifying foraging behavior
1. Movement based indices such as Moves Per Minute (MPM) and Proportion Time Moving (PTM) are common methodologies to quantify foraging behavior. We explore fundamental drawbacks of these indices, question the ways scientists have been using them, and propose new solutions. 2. To do so, we combined analytical and simulation models with lizards foraging data at the individual and species levels. 3. We found that the maximal value of MPM is constrained by the minimal durations of moves and stops. As a result, foragers that rarely move and those that rarely stop are bounded to similar low MPM values. This implies that (a) MPM has very little meaning when used alone, (b) MPM and PTM are interdependent, and (c) certain areas in the MPM-PTM plane cannot be occupied. We also found that MPM suffers from inaccuracy and imprecision. 4. We introduced a new bias correction formula for already published MPM data, and a novel index of Changes Per Minute (CPM) that uses the frequency of changes between move and stop bouts. CPM is very similar to MPM, but does not suffer from bias. Finally, we suggested a new foraging plane of Average Move and Average Stop durations. We hope that our guidelines of how to use (and not to use) movement- based indices will add rigor to the study of animals' foraging behavior.
Data from: Sperm divergence in a passerine contact zone: indication of reinforcement at the gametic level
Postcopulatory sexual selection may promote evolutionary diversification in sperm form, but the contribution of between-species divergence in sperm morphology to the origin of reproductive isolation and speciation remains little understood. To assess the possible role of sperm diversification in reproductive isolation, we studied sperm morphology in two closely related species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia), that hybridize in a secondary contact zone spanning Central and Eastern Europe. We found: (1) striking divergence between the species in total sperm length, accompanied by a difference in the length of the mitochondrial sperm component; (2) greater divergence between species in sperm morphology in sympatry than in allopatry, with evidence for character displacement in sperm head length detected in L. megarhynchos; (3) interspecific hybrids showing sperm with a length intermediate between the parental species, but no evidence for decreased sperm quality (the proportion of abnormal spermatozoa in ejaculates). Our results demonstrate that divergence in sperm morphology between the two nightingale species does not result in intrinsic postzygotic isolation, but may contribute to postcopulatory prezygotic isolation. This isolation could be strengthened in sympatry by reinforcement.
Data from: The fitness effects of a pale mutant in the aposematic seed bug Lygaeus simulans indicate pleiotropy between warning coloration and life history
Conspicuous warning colours that signal chemical or other defences are common in the natural world. For instance, such aposematic warning patterns of red-and-black or yellow-and-black are common among insect taxa, particularly in the order Hemiptera, often forming the basis of Batesian and/or Müllerian mimicry rings. In addition, it has been repeatedly noted that colour polymorphisms or mutants that influence pigmentation can show pleiotropy with other behavioural, physiological or life-history traits. Here we describe a pale mutant of the seed bug Lygaeus simulans that appeared in our lab population in 2012, which differs in colour to the wild-type bugs. Through multigenerational experimental crosses between wild-type and pale mutant L. simulans, we first show that the pale phenotype segregates as a single Mendelian locus, with the pale allele being recessive to the wild-type. Next, we show (1) that there is a large heterozygous advantage in terms of fecundity, (2) that pale females suffer reduced longevity, and (3) that pale males have increased body length compared to wild-type homozygotes. Our data therefore suggest that the colour locus is pleiotropic with a number of life-history traits, opening the door for a more complete genetic analysis of aposematic colouration in this species. In addition, this phenotype will be useful as a visible genetic marker, providing a tool for investigating sperm competition and other post-copulatory drivers of sexual selection in this species.
Data from: Quantifying and modelling decay in forecast proficiency indicates the limits of transferability in land-cover classification
1. The ability to provide reliable projections for the current and future distribution patterns of land-covers is fundamental if we wish to protect and manage our diminishing natural resources. Two inter-related revolutions made map productions feasible at unprecedented resolutions- the availability of high-resolution remotely-sensed data and the development of machine-learning algorithms. However, the ground-truth data needed for training models is in most cases spatially and temporally clustered. Therefore, map production requires extrapolation of models from one place to another and the uncertainty cost of such extrapolation is rarely explored. In other words, we focus mainly on projections, and less on quantifying how reliable they are. 2. Following the concept of 'forecast horizon', we suggest that the predictability of land-cover classification models should be methodologically explored with quantitative tools as a continuum against distances measured along multiple dimensions. Focusing on ten agricultural sites from England and using models specifically designed to predict multivariate decay-curves we ask: how does a model's predictive performance decay with distance? More specifically, we explored if we could predict the proficiency (kappa statistics) of a model trained in one site when making predictions in another site based on the spatial, temporal, spectral and environmental distances between sites. 3. We found that model proficiency decays with spatial, temporal, spectral and environmental distance between sites. More importantly, we found for the first time that it is possible to predict the performance a model transferred to or from a novel site will have, based on its distances from known sites. The spatial distance variables where the most important when predicting model transferability. 4. Exploring model transferability as a continuum may have multiple usages including predicting uncertainty values in space and time, prioritization of strategies for ground-truth data collection, and optimizing model characteristics for defined tasks.
Data from: Relating national levels of crop damage to population size indices of large grazing birds: implications for management
1. Populations of large grazing birds have increased in Europe during at least five decades, raising conflicts between conservation and farming interests. Managing these conflicts requires knowledge about the currently unknown relationship between population sizes and crop damage levels. 2. We analyzed unique data on reported, inspected and compensated crop damage caused by geese, swans and cranes together with data from population surveys in Sweden to investigate how bird abundance related to damage levels at the national scale between 2000 and 2015. 3. Over the study period, the annual number of damage reports, yield loss and costs for compensation increased. These crop damage levels were positively related to national population indices of common crane, barnacle and greylag goose. The shape of these relationships varied between species and encompassed considerable uncertainty. However, on a year-to-year basis (detrended data) we found no evident association between damage levels and bird numbers. 4. Yield loss and compensation costs per reported damage did not increase with higher population indices of greylag goose, but they did so for barnacle goose. 5. Synthesis and applications: We present a novel study towards the understanding of the relationships between different crop damage level indicators (damage reports, yield loss and compensation costs) and population numbers of large grazing birds. We identified a positive relationship with high uncertainty for all cases. We also identified the need to 1) better synchronize the monitoring of damages and bird numbers in time and space and 2) further study the relationships between damage levels and bird numbers at smaller (local and regional) and larger (flyway) spatial scales to reduce the uncertainty of the relationship and to gain a more holistic understanding of the system.
Data from: Multi-locus analyses indicate that Melastoma dendrisetosum, an endemic and endangered shrub in Hainan, is a distinct species
Melastoma dendrisetosum is an extremely narrowly distributed taxon endemic to the Diaoluo Mountain region in Hainan, China, and was recently taxonomically incorporated under a widespread species, M. sanguineum. Based on its distinct morphological traits, especially the indumentum on the hypanthium, we propose that it should represent a distinct species. In this study, we sequenced six partial nuclear genes and two chloroplast intergenic spacers of M. dendrisetosum and three other morphologically similar species, M. sanguineum, M. penicillatum, and M. normale, to clarify its taxonomic status. M. dendrisetosum exhibited an extremely low level of genetic diversity, and was well-separated from the three other species with no shared haplotypes at all six nuclear genes, supporting the hypothesis that it is a distinct species. This finding was also supported by the Bayesian clustering-based STRUCTURE analysis, phylogenetic analysis, and Bayesian species delimitation analysis. We further propose that M. dendrisetosum be categorized as 'Critically Endangered' under the IUCN criteria, due to its extremely small population and declining habitat quality. We suggest that the conservation of M. dendrisetosum be prioritized, and road construction in its range should be avoided, to protect this distinct and critically endangered species.
Withdrawing Performance Indicators: Retrospective Analysis of General Practice Performance Under the UKs Quality and Outcomes Framework
<p>No description provided.</p>
FIGURE 26. Leurotrigona, geographic records. The arrow indicates L in Neotropical Meliponini: the genus Leurotrigona Moure — two new species (Hymenoptera: Apidae, Apinae)
FIGURE 26. Leurotrigona, geographic records. The arrow indicates L. crispula sp. nov.
FIGURE 2 in Larvae of Hydropsyche angustipennis (Trichoptera, Hydropsychidae) as indicators of stream contamination by heavy metals in Łódź agglomeration
FIGURE 2. Annual results of the measured water parameters at given sampling sites.
FIGURE 5 in Larvae of Hydropsyche angustipennis (Trichoptera, Hydropsychidae) as indicators of stream contamination by heavy metals in Łódź agglomeration
FIGURE 5. Presence of heavy metals in whole bodies and in water at given sampling sites.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.