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Highlighting health consequences of racial disparities sparks support for action
<p>Racial disparities arise across many vital areas of American life, including employment, health, and interpersonal treatment. For example, 1 in 3 Black children live in poverty (vs. 1 in 9 White children) and on average, Black Americans live 4 fewer years than White Americans. Which disparity is more likely to spark reduction efforts? We find that highlighting disparities in health-related (vs. economic) outcomes spurs greater social media engagement and support for disparity-mitigating policy. Further, reading about racial health disparities elicits greater support for action (e.g., protesting) than economic or belonging-based disparities. This occurs, in part, because people view health disparities as violating morally-sacred values which enhances perceived injustice. This work elucidates which manifestations of racial inequality are most likely to prompt Americans to action.</p>
Data from: Friction and instability of glaucophane gouges at blueschist temperatures support abundance of intermediate-depth earthquakes
<p>Fluid release from the hydraulically-confined dehydration of blueschist minerals may significantly elevate fluid pressures and concomitantly reduce effective stresses. This is a viable mechanism to explain brittle failure and frictional instability, and it is a possible explanation for intermediate-depth earthquakes in cold subduction zones. We examine this hypothesis for glaucophane – a key index mineral for blueschist facies – at lower confining stresses where behavior is poorly understood. We conduct laboratory shear tests on glaucophane gouge at temperatures of 100–500<em>℃</em> and effective normal stresses of 50–200 <em>MPa</em>, to explore the controls of temperature, stresses and excess pore fluid pressures on fault friction. Frictional strength of glaucophane gouge at representative temperatures and stresses is ~0.70 and insensitive to temperature with a slight increase in friction coefficient at lower effective stresses. Elevating temperature promotes a transition from velocity-strengthening to mild velocity-weakening behavior, indicating the destabilizing effect of high-temperature downdip in subduction zones. Reducing effective normal stress or concomitantly elevating pore fluid pressure, potentially sourced from dehydration reactions, further strengthens the velocity-weakening response and would be manifest as moderate-sized earthquakes. This observed instability at higher temperatures or lower stresses is indexed with and accompanied by denser distributions of strongly- to moderately-localized shears in the microstructures – congruent with the observed mechanical response. Our results support the potential for enhanced unstable sliding of glaucophane gouges at lower effective stresses and at blueschist facies temperatures - and have significant implications for understanding the abundance of intermediate-depth earthquakes apparent in cold subduction zones.</p>
Supporting data for: The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
<p>Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene-concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.</p>
Supporting data for assessing impacts of satellite GPS transmitters on survival, nesting propensity, and nest success of greater sage-grouse
<p>Telemetry technology and data are commonly used to study behavior and demography of wildlife. Satellite-based, global positioning system (GPS) telemetry allows researchers to remotely collect a high volume of fine-resolution animal location data but may also come with hidden costs. For example, recent studies suggested GPS transmitters attached via backpacks may reduce survival of greater sage-grouse (<em>Centrocercus urophasianus</em>) relative to very high frequency (VHF) telemetry transmitters attached via collars. While some evidence suggests GPS backpacks can reduce survival, no studies examined their effects on sage-grouse breeding behavior and success. We compared survival, breeding behavior, and nest success for sage-grouse hens marked with either VHF collars or GPS backpack transmitters in central Idaho, USA. GPS backpacks reduced spring-summer survival relative to VHF collars, yet GPS backpacks did not consistently affect nest success or the likelihood or timing of nest initiation relative to VHF collars. Daily nest survival varied annually and with timing of nest initiation and nest age, but marginal effects of transmitter type were statistically insignificant, and interactions between transmitter type and study year were inconsistent. These results demonstrate the effect of GPS backpacks on sage-grouse survival but also suggest GPS backpacks do not appear to affect components of fecundity. </p>
Supporting data: Functional plasticity of the swim bladder as an acoustic organ for communication in a vocal fish
<div> <p>In this study, we show that the swim bladder of male plainfin midshipman fish (<em>Porichthys notatus</em>) exhibits reproductive state-dependent changes in morphology and function for sound production and reception. We quantified swim bladder morphometrics and utilized psuedolandmarking to identify differences in nonreproductive and reproductive male swim bladders. We utilized auditory evoked potential recordings, to measure the auditory sensitivity of saccular hair cells in response to sound pressure levels ranging from 97 - 154 dB re: 1 µPa to determine how the swim bladder contributes to midshipman auditory sensitivity. Finally, we used finite element modeling to explore the frequency response of nonreproductive and reproductive male swim bladders.</p> </div>
Supporting data for "Space weather in the popular media, and the opportunities the upcoming solar maximum brings"
<p>This contains the supporting data for the Space Weather Editorial "Space weather in the popular media, and the opportunities the upcoming solar maximum brings". It contains the Google Trends data (multiTimeline.csv) and the F10.7 and Kp data (omniweb.txt). </p>
Livestock guardian dogs establish a landscape of fear for wild predators: implications for the role of guardian dogs in reducing human-wildlife conflict and supporting biodiversity conservation
<ol> <li>Livestock guardian dogs (LGDs) are increasingly used to protect livestock from predators, but their effects on the distribution and behaviour of wild predators are mostly unknown. A key question is whether LGDs exclude predators from grazing land, or if predators continue to use areas with LGDs but modify their behaviour in ways that reduce impacts on livestock.</li> <li>We studied effects of LGDs (Maremma sheepdogs) on distribution and behaviour of red foxes Vulpes vulpes in north-eastern Victoria, Australia. We mapped the activity of LGDs across the study areas using GPS tracking and measured fox activity using remote cameras. We also measured risk-sensitive foraging in foxes to test if they reduced feeding time at sites regularly used by LGDs.</li> <li>Foxes occurred throughout areas occupied by LGDs, but their probability of detection was negatively related to probability of LGD presence. Foxes extracted fewer food items from experimental food stations in proportion to the intensity of local activity of LGDs. This indicates that though foxes overlapped with LGDs, they responded to risk of encountering LGDs by allocating less time to foraging. </li> <li>While LGDs do not necessarily exclude wild predators from areas used for livestock production, they can have strong effects on predator behaviour. Reduction in time allocated to foraging in areas regularly used by LGDs could lead to suppression of hunting behaviour and therefore a reduction in attacks on livestock. The flexible response of predators to LGDs should facilitate coexistence of wild predators with livestock farming, by allowing predators to continue to use areas occupied by livestock while still preventing attacks on those livestock. Our results therefore strengthen the case for use of LGDs in the conservation of predators threatened by conflict with farming. Suppression of hunting behaviour should also mean that prey species experience reduced rates of predation on farmland with LGDs. This effect could be valuable for conservation of threatened species of prey.</li> </ol>
Data supporting "Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly-Polarized Light"
<p>This repository contains the set of data to reproduce the computational results shown in "Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly-Polarized Light" published on Journal of the American Chemical Society (DOI: to be assigned).</p>
Supporting data for: Development of alternate climate divisions for Colorado based on gridded data
<p>The official climate divisions for the contiguous United States are used for a wide range of purposes, including ongoing climate monitoring, and through NOAA's long-standing nClimDiv dataset. In Colorado, the climate divisions are based around the basins of the large rivers that flow out of the state. However, considering the complex topography and climate of the state, these divisions do not always represent key climate variations and changes. This study builds upon an approach first developed by Wolter and Allured to establish alternate climate divisions that more closely reflect observed climate variability across Colorado. Hierarchical cluster analysis is applied to gridded temperature and precipitation data (NOAA's nClimGrid) from 1950–2021 to identify areas with similar climate variability, then manual inspection is used to establish 11 divisions. These resulting divisions are being used in an updated state-level climate change assessment. The method is flexible and uses open-source tools that could be extended to other regions or datasets.</p>
UKESM1 data supporting manuscript "Marine isoprene emissions in the Southern Ocean are significantly larger than expected"
<p>Model output and README from simulations performed for study "Marine isoprene emissions in the Southern Ocean are significantly larger than expected" (Ferracci and Weber et al) </p>
Data to support: Anthropogenic influence on tropospheric reactive bromine since the pre-industrial: Implications for ice-core bromine trends
<p>Tropospheric reactive bromine (Br<sub>y</sub>) influences the oxidation capacity of the atmosphere by acting as a sink for ozone and nitrogen oxides. Aerosol acidity plays a crucial role in Br<sub>y</sub> abundances through acid-catalyzed debromination from sea-salt-aerosol, the largest global source. Bromine concentrations in a Russian Arctic ice-core, Akademii Nauk, show a 3.5-fold increase from pre-industrial (PI) to the 1970s (peak acidity, PA), and decreased by half to 1999 (present day, PD). Ice-core acidity mirrors this trend, showing robust correlation with bromine, especially after 1940 (<em>r</em>=0.9). Model simulations considering anthropogenic emission changes alone show that atmospheric acidity is the main driver of Br<sub>y</sub> changes, consistent with the observed relationship between acidity and bromine. The influence of atmospheric acidity and Br<sub>y</sub> should be considered in interpretation of ice-core bromine trends.</p>
Supporting Data for "Local exposure misclassification in national models: relationships with urban infrastructure and demographics"
<p><strong>Overview:</strong> This dataset accompanies the recent publication "Local exposure misclassification in national models: relationships with urban infrastructure and demographics" (DOI: 10.1038/s41370-023-00624-z). It provides essential data for replicating and extending the analysis conducted in the study. The script for the analysis is available at https://github.com/SEChambliss-AQ/LD-analysis. The dataset consists of four key files.</p> <p><strong>Files Included:</strong></p> <ol> <li> <p><strong>Gridded OSM and GSV Data (gridded_OSM_GSV.RDS):</strong></p> <ul> <li>This R object offers a 100mx100m grid covering select neighborhoods in the San Francisco Bay Area.</li> <li>Each grid cell includes average air pollution levels (Ultrafine Particle Count in thousand count per cubic meter; Nitrogen Dioxide in ppb) from mobile monitoring.</li> <li>The file also provides normalized z-scores of local density of urban infrastructure related to air pollutants based on OpenStreetMap (OSM) data.</li> <li>Further details can be found in the associated publication.</li> </ul> </li> <li> <p><strong>BartMachine Outputs (bartMachine R objects.zip):</strong></p> <ul> <li>A collection of R object outputs from the bartMachine package, an R-Java Bayesian Additive Regression Trees implementation.</li> <li>These objects, which can be regenerated using the provided script, are included to reduce computational requirements for future analyses.</li> <li>The script for generating these outputs is available at the above <a href="https://github.com/SEChambliss-AQ/LD-analysis">GitHub Repository</a>.</li> </ul> </li> <li> <p><strong>NO2 Predictions (CACES_criteria.csv):</strong></p> <ul> <li>Land Use Regression (LUR) data for Nitrogen Dioxide, provided by the Center for Air, Climate, and Energy Solutions.</li> <li>Methodologies for integrating these data with the gridded dataset are described in the publication and script.</li> </ul> </li> <li> <p><strong>UFP Predictions (CACES_UFP.csv):</strong></p> <ul> <li>Similar to the NO2 dataset, this file contains LUR data for Ultrafine Particle predictions.</li> <li>Methods for data integration are detailed in the publication and available script.</li> </ul> </li> </ol> <p><strong>Usage:</strong> These files are intended for researchers and analysts aiming to replicate or build upon the study's findings. They provide a source of data for exploring the complex interplay between air pollution, urban infrastructure, and demographic factors in urban environments. For detailed methodology and analysis, refer to the original publication and the accompanying GitHub repository.</p>
Data from: Genome-wide support for incipient Tula orthohantavirus species within a single rodent host lineage
<p>Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host-shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from 42 locations in the contact region between clades for TULV infection by RT-PCR. Sequencing yielded 23 TULV Central North and 21 TULV Central South genomes which differed by 14.9-18.5% at the nucleotide and 2.2-3.7% at the amino acid level without evidence of recombination or reassortment. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis and genomic SNPs showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating of the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.</p>
Supporting information for: Discrimination ability of central visual field testing using stimulus size I, II, and III and relationship with macular ganglion cell thickness in chiasmal compression
<p><strong>Purpose</strong><strong>: </strong>To compare the relationship between macular ganglion cell layer (mGCL) thickness and 10-2 visual field (VF) sensitivity using different stimulus sizes in patients with temporal hemianopia from chiasmal compression.</p> <p><strong>Methods:</strong><strong> </strong>A cross-sectional study was conducted involving 30 eyes from 25 patients with temporal VF loss on 24-2 SITA standard automated perimetry due to previous chiasmal compression and 30 healthy eyes (23 controls). Optical coherence tomography (OCT) of the macular area and 10-2 VF testing using Goldmann stimulus size I (GI), II (GII), and III (GIII) were performed in the Octopus 900 perimeter. For the sake of analysis, mGCL thickness and VF data were segregated into four quadrants (two temporal and two nasal) and two halves (temporal and nasal) centered on the fovea, and the groups were compared using generalized estimated equations. The discrimination ability of GI, GII, and GIII was evaluated, as was the correlation between mGCL and 10-2 VF sensitivity using GI, GII, and GIII. </p> <p><strong>Results:</strong><strong> </strong>All mGCL parameters were significantly reduced in patients compared to controls. 10-2 VF test sensitivity using GI, GII, and GIII was significantly lower in patients than in controls (p≤0.008) for all parameters, except the three nasal divisions when using GI (p=0.41, 0.07 and 0.18) Significant correlations were found between temporal VF sectors (all stimulus sizes) and the corresponding nasal mGCL measurements, with similar discrimination ability. Significant correlations were also observed between all three nasal VF divisions and the corresponding temporal mGCL thickness when using stimulus sizes I and II, but not stimulus size III.</p> <p><strong>Conclusions</strong><strong>:</strong> On 10-2 VF testing, GII outperformed GI and GIII with regard to discrimination ability and structure-function correlation with mGCL thickness in chiasmal compression. Our findings suggest that the use of GII can enhance the diagnostic power of 10-2 VF testing, although further studies are necessary to support this conclusion.</p>
A Refined Supply-demand Framework to Quantify variability in Ecosystem Services Related to Surface Water in support of Sustainable Development Goals
<p>The file named 'Results' stores the data produced in this study. The file named 'Scripts' stores the python codes used in this study. The file named 'Software' stores the software installation package (Windows 64-bit system). The file named '3basin' stores the shapefile data of Level 3 basin in Xinjiang.</p>
Supporting information for "Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni"
<ul> <li>Files “CG_Ro_1_High Sensitivity DNA Assay_DE13805677_2019-06-20_09-10-48.pdf” and “CG_Ro_2_High Sensitivity DNA Assay_DE13805677_2019-06-20_10-12-12.pdf” uncropped files used in figure 2</li> <li>File “gel qpcr test input sds_01.tif” : uncropped file used in figure 8.</li> <li>File "20200612-1_Report.pdf" : qPCR report for inputs 1µL and available chromatine ("Row7"), figure 6 </li> <li>File "20200919-1_Report.pdf" : qPCR report for for testing SDS after Tn5, figure 7B and figure 8</li> <li>File "20200921-1_Report.pdf" : qPCR report for for comparing inputs with enzyme of Diagenode kit and our protocol with other enzyme Tn5 </li> <li>File "wilcoxon_curves.tgz" contains compressed versions of R-script "wilcoxon_curves.Rmd" that was used to compared metagene profiles and generate "wilcoxon_curves.html" and underlying ressources that are also in this compressed archive</li> </ul> <p>Produced at IHPE (http://ihpe.univ-perp.fr)</p>
Research data supporting article on implementation and validation of OpenMC cell-based R2S shutdown dose rate capabilities
<p>This file contains an archive of all research data that supports the article on implementation and validation of a cell-based R2S shutdown dose rate workflow in OpenMC.</p>
Data for: Male, female and mixed-sex poplar plantations support divergent soil microbial communities
<p>Mixed-species forests are often more productive than monocultures because of a lower niche overlap and higher taxonomic and functional diversity of soil microbial communities. Males and females of dioecious plants have sex-specific adaptations to diverse habitats. The potential of using sexual differences in establishing more diverse poplar plantations has not been explored in degraded areas. We conducted a series of greenhouse and field experiments to investigate how belowground competition, soil microbial communities and seasonal variation nitrogen content differ among female, male and mixed-sex <em>Populus cathayana</em> plantations. In the greenhouse experiment, female neighbors suppressed the growth of males under optimal nitrogen conditions. However, male neighbors enhanced δ<sup>15</sup>N of females under inter-sexual competition. In the field, the root length density, root area density and biomass of fine roots were lower in female plantations than in male or mixed-sex plantations. Bacterial networks of female, male and mixed-sex plantations were characterized by different composition of hub nodes, including connectors, module and network hubs. The sex composition of plantations altered bacterial and fungal community structures according to Bray-Curtis distances, with 44% and 65% of variance explained by the root biomass, respectively. The total soil nitrogen content of mixed-sex plantation was higher than that in female plantation in spring and summer. The mixed-sex plantation also had a higher β-1,4-N-acetyl-glucosaminidase activity in summer and a higher nitrification rate in autumn than the other two plantations. The seasonal soil N content, nitrification rate and root distribution traits demonstrated spatiotemporal niche separation in the mixed-sex plantation. We argue that a strong female-female competition and limited nitrogen content could strongly impede plant growth and reduce the resistance of monosex plantations to climate change and the mixed-sex plantations constitutes a promising way to restore degraded land.</p>
Supporting data for the paper "Investigating Potential Ecological Benefits from Mariculture"
<p>This dataset provides the parameter data used for calculation, the generated resulting data, and data files uploaded as Supporting Information.</p>
Behavioral response of delphinids to sonar - supporting acoustic data
<p>Oceanic delphinids around naval operations are regularly exposed to intense military sonar broadcast within the frequency range of their hearing. However, empirically measuring the impact of sonar on the behavior of highly social, free-ranging dolphins is challenging. Additionally, baseline variability or the frequency of vocal state-switching among social oceanic dolphins during undisturbed conditions is lacking, making it difficult to attribute changes in vocal behavior to anthropogenic disturbance. Using a network of drifting acoustic buoys in controlled exposure experiments, we investigated the effects of mid-frequency (3-4 kHz) active sonar (MFAS) on whistle production in short-beaked (<em>Delphinus delphis delphis</em>) and long-beaked common dolphins (<em>Delphinus delphis bairdii</em>) in southern California. Given the complexity of acoustic behavior exhibited by these group-living animals, we conducted our response analysis over varying temporal windows (10 min – 5 s) to describe both longer-term and instantaneous changes in sound production. We found that common dolphins exhibited acute and pronounced changes in whistle rate in the 5 s following exposure to simulated Navy MFAS. This response was sustained throughout sequential MFAS exposures within experiments simulating operational conditions, suggesting that dolphins may not habituate to this disturbance. These results indicate that common dolphins exhibit brief yet clearly detectable acoustic responses to MFAS. They also highlight how variable temporal analysis windows – tuned to key aspects of baseline vocal behavior as well as experimental parameters related to MFAS exposure – enable the detection of behavioral responses. We suggest future work with oceanic delphinids explore baseline vocal rates a-priori and use information on the rate of change in vocal behavior to inform the analysis time window over which behavioral responses are measured.</p>
ScienceDex guides
Understand access before you commit
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.