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7,920 results for “implications”
Counterintuitive scaling between population abundance and local density: implications for modelling transmission of infectious diseases in bat populations
<p>1. Models of host-pathogen interactions help to explain infection dynamics in wildlife populations and to predict and mitigate the risk of zoonotic spillover. Insights from models inherently depend on the way contacts between hosts are modelled, and crucially, how transmission scales with animal density.</p> <p>2. Bats are important reservoirs of zoonotic disease and are among the most gregarious of all mammals. Their population structures can be highly heterogenous, underpinned by ecological processes across different scales, complicating assumptions regarding the nature of contacts and transmission. Although models commonly parameterise transmission using metrics of total abundance, whether this is an ecologically representative approximation of host-pathogen interactions is not routinely evaluated.</p> <p>3. We collected a 13-month dataset of tree-roosting <i>Pteropus </i>spp. from 2,522 spatially referenced trees across eight roosts to empirically evaluate the relationship between total roost abundance and tree-level measures of abundance and density – the scale most likely to be relevant for virus transmission. We also evaluate whether roost features at different scales (roost-level, subplot-level, tree-level) are predictive of these local density dynamics.</p> <p>4. Roost-level features were not representative of tree-level abundance (bats per tree) or tree-level density (bats per m<sup>2</sup> or m<sup>3</sup>), with roost-level models explaining minimal variation in tree-level measures. Total roost abundance itself was either not a significant predictor (tree-level 3-D density) or only weakly predictive (tree-level abundance).</p> <p>5. This indicates that basic measures, such as total abundance of bats in a roost, may not provide adequate approximations for population dynamics at scales relevant for transmission, and that alternative measures are needed to compare transmission potential between roosts. From the best candidate models, the strongest predictor of local population structure was tree density within roosts, where roosts with low tree density had a higher abundance but lower density of bats (more spacing between bats) per tree.</p> <p>6. Together, these data highlight unpredictable and counterintuitive relationships between total abundance and local density. More nuanced modelling of transmission, spread and spillover from bats likely requires alternative approaches to integrating contact structure in host-pathogen models, rather than simply modifying the transmission function.</p>
Both consumptive and non-consumptive effects of predators impact mosquito populations and have implications for disease transmission
<p class="Default">Predator-prey interactions influence prey traits through both consumptive and non-consumptive effects, and variation in these traits can shape vector-borne disease dynamics. Meta-analysis methods were employed to generate predation effect sizes by different categories of predators and mosquito prey. This analysis showed that multiple families of aquatic predators are effective in consumptively reducing mosquito survival, and that the survival of <i>Aedes</i>, <i>Anopheles</i>, and <i>Culex</i> mosquitoes is negatively impacted by consumptive effects of predators. Mosquito larval size was found to play a more important role in explaining the heterogeneity of consumptive effects from predators than mosquito genus. Mosquito survival and body size were reduced by non-consumptive effects of predators, but development time was not significantly impacted. In addition, <i>Culex</i> vectors demonstrated predator avoidance behavior during oviposition. The results of this meta-analysis suggest that predators limit disease transmission by reducing both vector survival and vector size, and that associations between drought and human West Nile virus cases could be driven by the vector behavior of predator avoidance during oviposition. These findings are likely to be useful to infectious disease modelers who rely on vector traits as predictors of transmission.</p>
Dataset for "Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behaviour"
<p>Dataset files include:</p> <p>- Alignment of rhodopsin (Rh1) sequences formatted for PAML</p> <p>- Corresponding species tree in Newick format for PAML</p> <p>- Ancestral Rh1 amino acid sequences (for Cetacean and Whippomorpha nodes) estimated with PAML (random sites, clade, and amino acid models), Datamonkey, and ProtASR</p>
Ignorance is not bliss: Evolutionary naïveté in an endangered desert fish and implications for conservation
<p><span><em>Predator naiveté</em> </span><span>has been invoked to explain the impacts of non-native predators on isolated populations that evolved with limited predation. Such impacts have been repeatedly observed for the endangered Pahrump poolfish, <em>Empetrichthys latos</em>, a desert fish species that evolved in isolation since the end of the Pleistocene. We tested Pahrump poolfish anti-predator responses to conspecific chemical alarm cues released from damaged epidermal tissue in terms of fish activity and water column position. Pahrump poolfish behavioural responses to conspecific alarm cues did not differ from responses to a dechlorinated tap water control. As a positive control, the well-studied fathead minnow, <em>Pimephales promelas</em>, showed significant alarm cue responses in terms of reduced activity and lowered water column position. The density of epidermal club cells, the presumptive source of alarm cues, was significantly lower in Pahrump poolfish relative to fathead minnows. Therefore, anti-predator competence mediated by conspecific alarm cues does not seem to be a component of the ecology of Pahrump poolfish. These findings provide a proximate mechanism for the vulnerability of Pahrump poolfish to non-native predators, with implications for conservation and management of insular species.</span></p>
The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
<p><strong>Datasets</strong>: The trimmed data matrices and partition files as shown in Table 2.</p> <ol> <li>P1P2R_Phylip.phy: 1<sup>st</sup> and 2<sup>nd</sup> positions of PCG nucleotides and rRNAs.</li> <li>P1P2R_partition.txt: Partition scheme for P1P2R_Phylip.phy.</li> <li>P12R_Phylip.phy: the united first two positions of PCG nucleotides plus rRNAs.</li> <li>P12R_partition.txt: Partition scheme for P12R_Phylip.phy.</li> <li>P2R_Phylip.phy: 2<sup>nd</sup> position of PCG nucleotides and rRNAs.</li> <li>P2R_partition.txt: Partition scheme for P2R_Phylip.phy.</li> <li>AA_Phylip.phy: PCG amino acids.</li> <li>AA_partition.txt: Partition scheme for AA_Phylip.phy.</li> </ol> <p><strong>Trees: </strong>The expanded consensus trees constructed by all data compositions, partition schemes, and models shown in Table 2.</p> <ol> <li>P1P2R_FP.tree: edge-unlinked and full partitioned (FP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_MP.tree: edge-unlinked and merged partitioned (MP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_NP.tree: unpartitioned (NP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_NPH4.tree: NP dataset of PCG positions 1 & 2 + rRNAs under +H4 heterotachy model.</li> <li>P12R_FP.tree: FP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_MP.tree: MP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_NP.tree: NP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_NPH4.tree: NP dataset of united PCG positions 1 & 2 + rRNAs under +H4 heterotachy model.</li> <li>P2R_FP.tree: FP dataset of PCG position 2 + rRNAs.</li> <li>P2R_MP.tree: MP dataset of PCG position 2 + rRNAs.</li> <li>P2R_NP.tree: NP dataset of PCG position 2 + rRNAs.</li> <li>P2R_NPH4.tree: NP dataset of PCG position 2 + rRNAs under +H4 heterotachy model.</li> <li>AA_FP.tree: FP dataset of PCG amino acids.</li> <li>AA_MP.tree: MP dataset of PCG amino acids.</li> <li>AA_NP.tree: NP dataset of PCG amino acids.</li> <li>AA_NPC60.tree: NP dataset of PCG amino acids under +C60 mixture model.</li> </ol> <p><strong>Tables S1-2.xlsx:</strong></p> <ol> <li>Table S1: Pairwise similarity of nucleotide alignments between <em>Creophilus maxillosus</em> and the 92 sampled species in the Staphylinoidea.</li> <li>Table S2: Percentage of conserved sites in amino acid alignments between <em>Creophilus maxillosus</em> and the 92 sampled species in the Staphylinoidea.</li> </ol> <p>Data Use Statement. Data on genetic material contained in this paper are published for non-commercial use only. Utilization by third parties for purposes other than non-commercial scientific research may infringe the conditions under which the genetic resources were originally accessed, and should not be undertaken without obtaining consent from the corresponding author of the paper and/or obtaining permission from the original provider of the genetic material.</p> <p> </p>
Data from: Genetic diversity and divergence in the fountain darter (Etheostoma fonticola): implications for conservation of an endangered species
<p>The endangered fountain darter Etheostoma fonticola is found only in the Comal and San Marcos rivers in the Guadalupe River basin in central Texas, USA. Comal River fountain darters were believed to be extir- pated following a severe drought in the 1950s and were reintroduced in the early 1970s using 457 darters from the San Marcos River. In this study we used 23 microsatellite loci to describe and evaluate the genetic diversity, population structure and effective population size (Ne) of fountain darters. We also evaluated the genetic effect of the Comal River reintroduction and the influence of low-head dams (dams) on dispersal in both rivers. Bayesian analysis of individual genotypes and Analysis of Molecular Variation supported two distinct populations concordant with the two rivers. Estimates of Ne were much smaller (<10 %) than census size (Nc) in both rivers but did not indicate the populations are at risk of an immediate and rapid loss of genetic diversity. Coalescent-based estimates of the genetically effective number of founders (Nf) for the Comal River averaged about 49 darters and, together with the indices of genetic diversity and the bottleneck test (heterozygosity excess) results, were consistent with a founder event following the reintroduction in the Comal River. Finally, our results regarding the influence of dams on fountain darter dispersal were equivocal and did not support a conclusion. We recommend this issue be examined further as part of the fountain darter recovery program.</p>
Adaptive and non-adaptive plasticity in changing environments: implications for sexual species with different life history strategies
<p>Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modelled as random noise and linear reaction norms that assume simple one-to-one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and non-adaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directional climate change. Non-adaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (i) smaller phenotypic than genotypic variance in the population (many-to-one genotype-phenotype map) and the coexistence of polymorphisms, and (ii) the maintenance of higher genetic variation – compared to linear reaction norms and genetic determinism – even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations producing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.</p>
A model of digestive tooth corrosion in lizards: experimental tests and taphonomic implications
<p>Abstract </p><p>Corrosion patterns induced by gastric fluids on the skeleton of prey animals may depend on the nature of the corrosive agents (acid, enzymes) as well as on the composition of the hard parts and the soft tissues that surround them. We propose a framework for predicting and interpreting corrosion patterns on lizard teeth, our model system, drawing on the different digestive pathways of avian and non-avian vertebrate predators. We propose that high-acid, low-enzyme systems (embodied by mammalian carnivores) will lead to corrosion of the tooth crowns, whereas low-acid, high-enzyme systems (embodied by owls) will lead to corrosion of the tooth shafts. We test our model experimentally using artificial gastric fluids (with HCl and pepsin) and feeding experiments, and phenomenologically using wild-collected owl pellets with lizard remains. Finding an association between the predictions and the experimental results, we then examine corrosion patterns on nearly 900 fossil lizard jaws. Given an appropriate phylogenetic background, our focus on physiological rather than taxonomic classes of predators allows the extension of the approach into Deep Time.</p><p></p>
Data from: Computed tomographic analysis of dental system of three Jurassic ceratopsians: implications for the evolution of the tooth replacement pattern and diet in early-diverging ceratopsians
<p><span>T</span><span>he </span><span>dental system of ceratops</span><span>ids is among the most specialized structure in Dinosauria</span><span>, and includes high angled wear surfaces, split tooth roots, and multiple teeth in each tooth family. However, the early evolution of this unique dental system is generally poorly understood due to a lack of knowledge of the dental morphology and development in early-diverging ceratopsians.</span><span> Here we study the dental system of </span><span>three</span><span> of the earliest-diverging Chinese ceratopsians</span><span>: </span><em><span>Yinlong</span></em><span> and <em>Hualianceratops</em> from the early Late Jurassic of Xinjiang</span><span>,</span><span> and <em>Chaoyangsaurus</em> from the Late Jurassic of Liaoning. By using micro-computed tomographic analyses, our study has revealed significant new information regarding the dental system of these early ceratopsians, including </span><span>no</span><span> more than five replacement teeth in each jaw quadrant; at most one generation of replacement teeth in each alveolus; nearly full resorption of the functional tooth root during tooth replacement; and occlusion with low-angled, concave wear facets that differs significantly from the shearing occlusal system seen in ceratopsids. <em>Yinlong</em> displays an increase in the number of maxillary tooth alveoli and a decrease in the number of replacement teeth during ontogeny as well as the retention of remnants of functional teeth in the largest individual.</span> <span>Early-diverging ceratopsians thus display a relatively slow tooth replacement rate compared to late-diverging ceratopsians.</span> <span>Combined with paleobotany and palaeoenvironment data, <em>Yinlong</em> likely uses gastroliths to triturate foodstuffs, and t</span><span>he difference in diet strategy might have influenced the pattern of tooth replacement in later-diverging ceratopsians.</span></p>
Data archive for "Rock abundance on the lunar mare on surfaces of different age: Implications for regolith evolution and thickness"
<p>This is associated data for the study "<strong>Rock abundance on the lunar mare on surfaces of different age: Implications for regolith evolution and thickness </strong>" in GRL.</p> <p>The zipfile FT2014-Dense50kmN-n800mto5km.tif.zip is a raster of neighborhood crater frequencies from Fassett and Thomson 2014 (JGR) that are used for the age information in this paper. </p> <p>The csv file is the extracted rock abundance for every frequency pixel in this dataset. </p> <p>A github software release associated with the paper is also available on <a href="https://zenodo.org/badge/latestdoi/417542233">as a Zenodo software repository</a>, as well as on <a href="https://github.com/cfassett/MareRockAbundances">Github</a>.</p>
No evidence for trade-offs between bird diversity, yield and water table depth on oil palm smallholdings: implications for tropical peatland landscape restoration
<p>Tropical peat swamp forests retain large carbon stocks and support unique biodiversity, but clearance and drainage for agriculture have resulted in fires, carbon emissions and biodiversity losses. Initiatives to re-wet cultivated peatlands may benefit biodiversity if this protects remaining forests from fire and agricultural encroachment, but there are concerns that re-wetting could reduce yields and damage livelihoods, as relationships between drainage, on-farm biodiversity, and crop yields have not been studied.</p> <p>We examined oil palm fruit yields and bird diversity on 41 smallholder farms in Jambi (Sumatra, Indonesia), which varied in drainage intensity (12-month mean water table per plot from August 2018 to August 2019: -52 to -3 cm below ground). We also compared farm bird diversity with a neighbouring area of protected forest (11,000 ha, 21 plots; mean water table per plot -3 to +15 cm).</p> <p>Bird species richness (3-18 species per plot), species composition, and oil palm yields (4.5-19.2 t fresh fruit bunch ha-1 yr-1) varied among farms, but were not detectably affected by water table depth, although ground-level vegetation was more complex on wetter farms. Bird richness in oil palm (mean = 10.3 species per plot) was <50% of that in forest (26 species per plot), and only three out of 35 conservation-priority species found in forest were recorded in oil palm.</p> <p>Synthesis & applications: Tropical peatlands in Indonesia have been drained to allow farmer access and improve farm yields, but we found no trade-offs between drainage depth, yields or bird diversity on smallholder oil palm farms in our study landscape. Current restoration initiatives to re-wet peat may benefit farmers by reducing fire risk, without affecting yields. Wetter farms had increased understorey vegetation complexity, but this did not affect bird diversity, so we find no evidence that re-wetting improves on-farm biodiversity within the studied range of drainage depths. However, on-farm fire reduction efforts in cultivated peatlands, including re-wetting, will be vital for reducing the risk of fires escaping into nearby forests, which contain unique and diverse bird species assemblages. Protection of remaining peatland forests from fire and clearance is key for biodiversity conservation, and for providing a source of seed dispersers and genetic material for future forest and landscape restoration efforts. Restoration of more biodiversity-friendly land covers will improve landscape permeability and help conserve species and the ecosystem services they deliver.</p>
Raw Data for the article: miRNA expression analysis in the human heart: Undifferentiated progenitors vs. bioptic tissues-Implications for proliferation and ageing
<p>In developed countries, cardiovascular diseases are currently the first cause of death. Cardiospheres (CSs) and cardiosphere-derived cells (CDCs) have been found to have the ability to regenerate the myocardium after myocardial infarction (MI). In recent years, much effort has been made to gain insight into the human heart repair mechanisms, in which miRNAs have been shown to play an important role. In this regard, to elucidate the involvement of miRNAs, we evaluated the miRNA expression profile across human heart biopsy, CSs and CDCs using microarray and next-generation sequencing (NGS) technologies. We identified several miRNAs more represented in the progenitors, where some of them can be responsible for the proliferation or the maintenance of an undifferentiated state, while others have been found to be downregulated in the undifferentiated progenitors compared with the biopsies. Moreover, we also found a correlation between downregulated miRNAs in CSs/CDCs and patient age (eg miR-490) and an inverse correlation among miRNAs upregulated in CSs/CDCs (eg miR-31).</p>
Raw Data for the article: HCV Interplay With Mir34a: Implications in Hepatocellular Carcinoma
<p>Since its identification, HCV has been considered one of the main causes of hepatitis and liver cancer. Currently, the molecular mechanisms of HCC development induced by HCV infection have not been sufficiently clarified. The recent discovery of novel treatments that inhibit HCV replication gave rise to new questions concerning HCC mechanisms. In particular, the HCV eradication mediated by new direct-acting antiviral (DAAs) drugs does not exclude the possibility of <em>de novo</em> HCC development; this finding opened more questions on the interplay between liver cells and the virus. Different groups have investigated the pathways leading to cancer recurrence in patients treated with DAAs. For this reason, we tried to gain molecular insights into the changes induced by HCV infection in the target liver cells. In particular, we observed an increase in microRNA34a (miR34a) expression following HCV infection of HCC cell line Huh7.5. In addition, Huh7.5 treated with extracellular vesicles (EVs) from the previously HCV-infected Huh7.5 underwent apoptosis. Since miR34 expression was increased in Huh7.5 EVs, we hypothesized a paracrine mechanism of viral infection mediated by miR34a cargo of EVs. The balance between viral infection and cell transformation may raise some questions on the possible use of antiviral drugs in association with antineoplastic treatment.</p>
Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape
<p>This repository includes:</p> <p> </p> <p>SI Appendix</p> <p>GISAID Acknowledgements</p> <p>An example resfile</p> <p>RosettaScripts .xml files</p> <p>Complex conformations (50 each) for WT/Delta/Gamma/Omicron; antibody (NAb) and receptor (ACE2)</p>
Microbiome of domestic water from rural communities in the southern caribbean: water quality and human health implications
<p><strong>LIST OF SUPPLEMENTARY DATA FILES</strong></p> <p>Chapter 4 - The microbiome of domestic water in the rainwater harvesting-dependent island community of Carriacou, Grenada in the Southern Caribbean</p> <p>Chapter 5 - Microbial composition of drinking water in Speightstown, Barbados</p> <p>Chapter 6 - Bacterial diversity of drinking water in Nariva, Trinidad</p> <p>Chapter 7 - A preliminary assessment of protozoans in various water sources in Nariva, Trinidad</p>
Cross-seasonal effects in the American Woodcock: conditions prior to fall migration relate to migration strategy and its implications for conservation
<p>How post-breeding habitat quality and body composition of migratory birds carry over to influence fall migration strategies and residency merits consideration when creating cross-seasonal conservation plans, especially in breeding populations that are partial migrants. We assessed the influence of post-breeding habitat quality on departure body composition and fall migration patterns in a southern New England breeding population of American Woodcock (<em>Scolopax minor</em>). Woodcock that overwintered near breeding areas (<em>n</em>=5) had less fat upon capture in fall and used lower quality habitat during the fall than birds that eventually departed on migration (<em>n</em>=17). Woodcock that departed earlier were long-distance migrants that had inhabited higher-quality landscapes prior to migration, departed with less fat or similar fat stores, stopped over for shorter periods on migration, and arrived earlier on their more southerly wintering areas. In contrast, woodcock that departed later were short-distance migrants that had inhabited lower quality landscapes prior to migration yet stored similar or more fat upon departure, stopped over for longer periods on migration, and arrived relatively late to their more northerly wintering areas. These differences in migration strategies were evident under the same fall environmental conditions and did not appear related to individuals responding to their own condition as would be expected if they were class condition-based carry-over effects. As such, the southern New England breeding population of woodcock are best categorized as non-facultative partial migrants (i.e., includes residents, short-distance migrants, and long-distance migrants) that demonstrate weak connectivity between life stages; such populations are excellent for the study of the costs and benefits of migration. The stopover and wintering areas used by woodcock in the coastal mid-Atlantic deserve conservation and management attention in order to preserve critical habitat throughout their wintering range.</p>
Formation of Hematite Spherules from Metallic Spherules by Oxidative Hydrothermal Alteration: Implications for Hematite Spherules on Martian Surface
<p>Figures used in paper “Formation of Hematite Spherules from Metallic Spherules by Oxidative Hydrothermal Alteration: Implications for Hematite Spherules on Martian Surface”</p>
FIG. 21 in Skeleton of Early Miocene Bathyergoides neotertiarius Stromer, 1923 (Rodentia, Mammalia) from Namibia: behavioural implication
FIG. 21. — Lumbar vertebrae of GT 50'06 (dorsal view). Scale bar: 1 cm.
FIG. 17 in Skeleton of Early Miocene Bathyergoides neotertiarius Stromer, 1923 (Rodentia, Mammalia) from Namibia: behavioural implication
FIG. 17. — Muscular insertions on the left tibia GT 50'06. Scale bars: 1 cm.
FIG. 7 in Skeleton of Early Miocene Bathyergoides neotertiarius Stromer, 1923 (Rodentia, Mammalia) from Namibia: behavioural implication
FIG. 7. — Right lower cheek tooth row of GT 50'06 (p4-m3, occlusal view). Scale bar: 1 mm.
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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.