Find research datasets worth reusing

opencc-by-4.0Jun 2017View details →

Research data supporting "Electrospun aniline-tetramer-co-polycaprolactone fibres for conductive, biodegradable scaffolds"

Research data supporting the publication: Guex, A.G. et al., 2017, "Electrospun aniline-tetramer-co-polycaprolactone fibres for conductive, biodegradable scaffolds", MRS Communications. https://doi.org/10.1557/mrc.2017.45

opencc-by-4.0Aug 2017View details →

Species co-occurrences from EuPMC articles related to pines

A dataset containing info on matches from full text searches by ContentMine tools, that can be mapped to Wikidata. See README.md.

opencc-by-4.0Dec 2022View details →

Single-point CLM simulations with hillslope hydrology at Niwot Ridge, CO

In this study, we ran ecosystem-scale Community Land Model (CLM) simulations with a novel hillslope hydrology configuration to represent topographically heterogeneous alpine tundra vegetation across a moisture gradient at Niwot Ridge, Colorado, USA. We used local observations to evaluate our simulations and investigated the role of topography and aspect in mediating patterns of snow, productivity, soil moisture and temperature, as well as the potential exposure to climate change across an alpine tundra hillslope. This dataset contains output files from single-point CLM simulations with the hillslope hydrology for the manuscript titled 'Topographic Heterogeneity and Aspect Moderate Exposure to Climate Change Across an Alpine Tundra Hillslope'. Local observations from Niwot Ridge, CO were used to force and evaluate these simulations to represent alpine tundra vegetation across a moisture gradient. Our control simulations were modified to represent a site at Niwot Ridge referred to as the 'Saddle', with an east and west facing knoll and a lowland area between them. Three columns represent distinct moist, wet, and dry meadow vegetation communities. We used the same model setup to run additional experiments on north- and south-facing slopes. Simulations were run using input data from 2008-2021 (historical) and then extended to year 2100 (future) using an anomaly forcing protocol.

opencc-by-4.0Sep 2021View details →

Intelligent Energy Systems Ontology: Local flexibility market and power system co-simulation demonstration

The Intelligent Energy Systems Ontology (IESO) provides semantic interoperability within a society of multi-agent systems (MAS) developed in the scope of power and energy systems (PES). It leverages the knowledge from existing and publicly available semantic models developed for specific PES subdomains to accomplish a shared vocabulary among the agents of the MAS community, overcoming heterogeneity among the reused ontologies. IESO provides agents with semantic reasoning, constraints validation, and data uniformization. The use of IESO is demonstrated through the simulation of the management of a rural distribution network, considering the validation of the grid’s technical constraints. This dataset publishes files demonstrating: i) a snapshot of the initial semantic knowledge base (KB); ii) queries to the KB to get services inputs; iii) conversions between syntactic and semantic models;  iv) constraints validations; v) automatic conversion of units of measure.

opencc-by-4.0Aug 2023View details →

Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine

Supplementary Table Captions: Supplementary Table S9. Evaluation and parameter determination of host and microbiome RNA read classification using simulation datasets Supplementary Table S10. 40 pathways significantly upregulated in the cecum as compared to the transverse colon Supplementary Table S11. Host-microbiome gene co-expression network edges Supplementary Table S12. Host-host gene co-expression network edges Supplementary Table S13. Microbiome-microbiome gene co-expression network edges Supplementary Table S14. List of genes included in each gene module identified from the gene co-expression network Supplementary Table S15. Results of enrichment analysis for each gene module identified from the gene co-expression network Supplementary Table S16. The top 32 bacterial species in terms of expression abundance based on metatranscriptome profiles Supplementary Table S17. Number of microbiome RNA reads annotated by the KEGG database Supplementary Table S18. Results of enrichment analysis of gene modules for each parameter Supplementary Table S19. Evaluation of modules in each parameter of Newman algorithm Supplementary Table S20. Evaluation of modules in each parameter of Louvain algorithm Supplementary Table S21. Evaluation of modules in each parameter of Leiden algorithm Supplementary Table S22. Evaluation of modules in each parameter of WGCNA

opencc-zeroJan 2024View details →

Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought and defense related genes

Tropical tree communities are among the most diverse in the world. A small number of genera often disproportionately contribute to this diversity. How so many species from a single genus can co-occur represents a major outstanding question in biology. Niche differences are likely to play a major role in promoting congeneric diversity, but the mechanisms of interest are often not well-characterized by the set of functional traits generally measured by ecologists. To address this knowledge gap, we used a functional genomic approach to investigate the mechanisms of co-occurrence in the hyper-diverse genus Ficus. Our study focused on over 800 genes related to drought and defense, providing detailed information on how these genes may contribute to the diversity of Ficus species. We find widespread and consistent evidence of the importance of defense gene dissimilarity in co-occurring species, providing genetic support for what would be expected under the Janzen-Connell mechanism. We also find that drought-related gene sequence similarity is related to Ficus co-occurrence, indicating that similar responses to drought promote co-occurrence. We provide the first detailed functional genomic evidence of how drought- and defense-related genes simultaneously contribute to the local co-occurrence in a hyper-diverse genus. Our results demonstrate the potential of community transcriptomics to identify the drivers of species co-occurrence in hyper-diverse tropical tree genera.

opencc-zeroJan 2024View details →

ASRC Rooftop CO observations, NYCMA observed and simulated ΔCO, and relative NYC surface influence

Carbon monoxide (CO) observations from the Advanced Science Research Center (ASRC) Rooftop Observatory in Hamilton Heights, West Harlem, Manhattan, calculated background CO, observed, and simulated CO enhancements (ΔCO) for the New York City metropolitan area (NYCMA), and relative NYC surface influence from HRRR-STILT (the Stochastic Time-Inverted Lagrangian Transport model coupled to High-Resolution Rapid Refresh meteorology). All values reported hourly for January-May 2019-2022, when available. Observations and analyzed quantities are as described in "Multi-year observations of variable incomplete combustion in the New York megacity" by Luke D. Schiferl, Cong Cao, Bronte Dalton, Andrew Hallward-Driemeier, Ricardo Toledo-Crow, and Róisín Commane.

opencc-zeroMar 2024View details →

Data and trained models for: Human-robot facial co-expression

Large language models are enabling rapid progress in robotic verbal communication, but nonverbal communication is not keeping pace. Physical humanoid robots struggle to express and communicate using facial movement, relying primarily on voice. The challenge is twofold: First, the actuation of an expressively versatile robotic face is mechanically challenging. A second challenge is knowing what expression to generate so that they appear natural, timely, and genuine. Here we propose that both barriers can be alleviated by training a robot to anticipate future facial expressions and execute them simultaneously with a human. Whereas delayed facial mimicry looks disingenuous, facial co-expression feels more genuine since it requires correctly inferring the human's emotional state for timely execution. We find that a robot can learn to predict a forthcoming smile about 839 milliseconds before the human smiles, and using a learned inverse kinematic facial self-model, co-express the smile simultaneously with the human. We demonstrate this ability using a robot face comprising 26 degrees of freedom. We believe that the ability co-express simultaneous facial expressions could improve human-robot interaction.

opencc-zeroMar 2024View details →

Data and code for: Pneumococcus co-colonization and the stress-gradient-hypothesis

Pneumococcus serotype co-colonization, caused by the polymorphic bacteria Streptococcus pneumoniae, has been increasingly investigated and reported in recent years. Yet, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of these bacteria. Here we report on a rich dataset of cross-sectional pneumococcal colonization studies collected from the literature, where we quantified patterns of transmission intensity and co-colonization variation in children populations across different epidemiological settings. Fitting these data to an SIS model with co-colonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity R0 and susceptibility to co-colonization k, in support of the stress-gradient-hypothesis (SGH) in ecology. According to this hypothesis, ecological interactions between organisms shift positively as environmental stress increases. In our model higher environmental stress is represented via lower values of the basic reproduction number R0, and a shift towards positive interactions is represented via higher vulnerability to co-colonization (higher k) between pneumococcus serotypes.

RNA sequencing of macrophages co-cultured with MSCs and RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCs

RNA sequencing of macrophages co-cultured with MSCS Table 5 RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCS Table 8

Understanding the risks of co-exposures in a changing world: A case study of dual monitoring of the biotoxin domoic acid and Vibrio spp. in Pacific oyster

<div> Assessing the co-occurrence of multiple health risk factors in coastal ecosystems is challenging due to the complexity of multi-factor interactions and limited availability simultaneously collected data. Understanding co-occurrence is particularly important for risk factors that may be associated with or occur in similar environmental conditions. In marine ecosystems, the co-occurrence of harmful algal bloom toxins and bacterial pathogens within the genus Vibrio may impact both ecosystem and human health. This study examined the co-occurrence of Vibrio spp. and domoic acid (DA) produced by the harmful algae Pseudonitzschia by 1) analyzing existing California Department of Public Health monitoring data for V. parahaemolyticus and DA in oysters; 2) and conducting a one-year seasonal monitoring of these risk factors across two Southern California embayments. Existing public health monitoring efforts in the state were robust for individual risk factors; however, it was difficult to evaluate the co-occurrence of these risk factors in oysters due to low number of co-monitoring instances between 2015 and 2020. Seasonal co-monitoring of that DA and Vibrio spp. (V. vulnificus or V. parahaemolyticus) at two embayments revealed the co-occurrence of these health risk factors in 35% of sampled oysters in most seasons. Interestingly, both the overall detection frequency and co-occurrence of these risk factors was considerably less frequent in water samples. These findings may in part suggest the slow depuration of Vibrio spp. and DA in oysters as residual levels may be retained. This study expanded our understanding of the simultaneous presence of DA and Vibrio spp. in bivalves and demonstrate the feasibility of co-monitoring different risk factors from the same sample. Individual programs monitoring for different risk factors from the same sample matrix may consider combining efforts to reduce cost, streamline the process, and better understand the prevalence of co-occurring health risk factors. </div>

Co-occurrence of Methods in Co-Creation: A Sankey Diagram

The Co-Creation Methods Sankey Diagram. This diagram was created in an online open-access tool, RAWGraphs 2.0 (DensityDesign Research Lab). This diagram provides a visual representation of the interrelationships among methods occurring together in the titles and/or abstracts of the sourced literature (n=2,590 citations). These citations are derived from a Systematic Method Overview, which encompasses empirical studies, protocols, exploratory studies, and case studies employing co-creation sourced from the Health CASCADE Co-Creation Database version 1.5. This diagram serves as a snapshot of co-creation practices, and the manuscript about this work is under peer review at JMIR (i-JMR): https://preprints.jmir.org/preprint/59772  For a closer examination of the depicted methods, the image file is available for download, allowing zooming in and out to navigate the intricacies of the diagram. For inquiries or additional information regarding this diagram, please reach out to Danielle M. Agnello at <a href="mailto:danielle.agnello@gcu.ac.uk">danielle.agnello@gcu.ac.uk</a>. Additionally, join the conversation and stay updated her research into co-creation, and methods used in co-creation, by following her on X: <a href="https://twitter.com/DannyAgnello_GH">https://twitter.com/DannyAgnello_GH</a> or LinkedIN: <a href="https://www.linkedin.com/in/daniellemagnello/">https://www.linkedin.com/in/daniellemagnello/ </a>  Co-Creation Resources: For additional support in utilizing these co-creation methods in a co-creation process, explore our Draft Evidence-based Co-Creation Guideline: PRODUCES+ at: <a href="../records/8379784">https://zenodo.org/records/8379784</a>. Additionally, engage with critical questions about method selection through my Methods Selector Infographic at: <a href="https://doi.org/10.5281/zenodo.7414470">https://doi.org/10.5281/zenodo.7414470</a>. For insights into how these methods align with co-creation characteristics, please refer to the pre-print manuscript on the Co-Creation Rainbow framework: <a href="../records/10391410">https://zenodo.org/records/10391410</a>. Finally, you can also conduct your study in the Health CASCADE Co-Creation Database: <a href="https://doi.org/10.2196/45059">https://doi.org/10.2196/45059</a>. Unlock the potential of co-creation and embark on a collaborative research journey with confidence, creativity, and innovation!

embargoedcc-zeroFeb 2024View details →

Intraguild interactions and abiotic conditions mediate occupancy of mammalian carnivores: co-occurrence of coyotes-fishers-martens

The widespread eradication of large carnivores and subsequent expansion of top mesopredators have the potential to impact species and community interactions with ecosystem-wide implications. An example of these trophic dynamics is the widespread establishment of coyotes following the extirpation of wolves and mountain lions in eastern North America. Here, we examined the occupancy of three carnivores in northern New York considering both environmental/habitat factors and interspecific interactions. We estimated the co-occurrence of coyotes, fishers, and martens from a landscape-scale winter camera trap survey repeatedly annually for three years. Martens occurred independently of both coyotes and fishers, while fishers and coyotes displayed positive intraguild interactions that were constant across the landscape. Both marten and fisher first-order occupancy was driven by a combination of biotic and abiotic factors, with both species displaying positive associations with forest cover but antithetical responses to average snow depth. The integral and antithetical role of snow depth in driving the occurrence of martens (positive) and fishers (negative) in the landscape indicates that future climatic warming could reduce the availability of current spatial refuges for martens created by severe winter conditions. Climate-driven alterations to established competitive interactions and co-existence patterns between marten and fishers have critical implications for the species' survival and conservation. We provide correlational evidence consistent with the potential for positive top-down effects of dominant mesocarnivores on subordinate species, with fisher occupancy increasing conditional on the presence of coyotes across the landscape. These findings align with the hypothesis that under certain conditions, coyotes may facilitate certain subordinate carnivores. The evidence produced here is consistent with hypotheses on the dynamic nature of trophic niches. We demonstrate the need to consider the interplay between climate, habitat, and interspecific interactions to understand wildlife occupancy patterns and inform wildlife management in a rapidly changing world.

BIR-MicroED: selected area electron diffraction datasets from static microcrystals (Co(II) meso-tetraphenyl porphyrine at high fluence, ~100 electrons per square Angstrom) at 200 keV

This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). Zip files are named according to the format: "CompoundName_AcceleratingVoltage_Temperature.zip" Diffraction datasets within each folder are named according to the format: CompoundName_static_diffraction_AcceleratingVoltage_Temperature_series#.mrc

BIR-MicroED: selected area electron diffraction datasets from static microcrystals (Co(II) meso-tetraphenyl porphyrin) at 200 keV

BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (Co(II) meso-tetraphenyl porphyrin) at 200 keV

<div> This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). For each crystal, multiple subsequent sweeps (passes) at the same incident flux covering the same angular range are given. Zip files are named according to the format: "CompoundName_multipass_RotationSpeed_FrameRate_SpotSize_tiltseries_Temperature.zip" Where spot size 11 = 0.01 electrons per square Angstrom per second incident flux, and spot size 10 = 0.03 electrons per square Angstrom per second incident flux Diffraction datasets within each folder are named according to the format: "CompoundName_tiltseries_AcceleratingVoltage_Temperature_IncidentFlux_crystal#sweep#.mrc" Where crystal1sweep1 and crystal1sweep2 indicate the first and second sweep of data acquired on the same crystal, respectively. </div>

BIR-MicroED: selected area electron diffraction datasets from slowly rotating (0.09 degrees/second) microcrystals (biotin, Zn(II)-methionine, and Co(II)-porphyrin) at 200 keV

This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). Zip files are named according to the format: "CompoundName_slowrotation_0pp09dps_tiltseries_Temperature.zip" Diffraction datasets within each folder are named according to the format: "CompoundName_slowrotation_0p09dps_tiltseries_AcceleratingVoltage_Temperature_series#.mrc"

BIR-MicroED: selected area electron diffraction datasets from static microcrystals (Zn(II)-histidine, Co(II) meso-tetraphenyl porphyrin, AVAAGA) at 300 keV

This deposition contains a series zip files each containing electron diffraction datasets in .tvips file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). Zip files are named according to the format: "CompoundName_AcceleratingVoltage_Temperature.zip" Diffraction datasets within each folder are named according to the format: CompoundName_static_diffraction_AcceleratingVoltage_Temperature_series#.tvips

opencc-by-4.0May 2021View details →

Figure 7 in Looks can be deceiving: contrasting temperature characteristics of two morphologically similar kelp species co-occurring in the Arctic

Figure 7: Effect of temperature on the relative abundance of different ontogenetic stages during gametogenesis of Laminaria digitata (left) and Hedophyllum nigripes (right) in a temperature gradient after seven days (above) and 14 days (below; mean of n = 3–4; SD not shown for clarity). Only the most developed stage was counted per female gametophyte. †All gametophytes died.