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openMar 2023View details →

Microhabitat humidity rather than food availability drives thermo-hydroregulation responses to drought in a terrestrial lizard

The content of this archive includes raw data and metadata for the paper "Microhabitat humidity rather than food availability drives thermo-hydroregulation responses to drought in a terrestrial lizard" by Bodineau et al. In this experimental study, we investigated how microclimate conditions and food availability influence thermo-hydroregulation strategies and body condition of lizards (Zootoca vivipara) during a simulated drought. We found that water restriction and food deprivation caused physiological alterations such as muscle catabolism and mobilization of caudal energy reserves. Lizards developed behavioural strategy to counteract water and food deprivation like decreased thermoregulation effort, higher shelter use and increased eye closure behaviours. Hydric quality of the shelter rather than food availability was the main modulator of trade-offs between thermoregulatory and hydroregulatory activities and an important buffer against the deleterious effects of water restriction. These original findings challenge the assumptions of mechanistic models of ectotherms, which are currently calibrated on the thermal biology of ectotherms. They demonstrate the urgent need to take into account the dual effect of warming and drought events, behavioural interactions between thermoregulation and hydroregulation and the buffering role of microclimatic conditions.

Data for: Responses of soil phosphorus cycling and bioavailability to plant invasion in river-lake ecotones

The invasion of exotic plants in the river-lake ecotone has seriously affected the nutrient cycling processes in wetland soil. The South American species Alternanthera philoxeroides (Mart.) Griseb. is rapidly invading the river-lake ecotone in subtropical China, and has become the dominant species in the river-lake ecotone. However, there have been few studies on the effects of A. philoxeroides invasion on soil phosphorus (P) cycling and bioavailability in this ecotone. Herein, we measured the bioavailable P fractions, physicochemical properties and nutrient content in the surface soils of the native plant (Zizania latifolia (Griseb.) Turcz and Nelumbo nucifera Gaertn.) communities and the adjacent invasive A. philoxeroides communities in three river-lake ecotones with different nutrient substrates in the subtropical Dongting Lake basin over a three-year period to reveal the effects of A. philoxeroides invasion on the morphology and concentrations of soil bioavailable P. The principal coordinate analysis results showed that A. philoxeroides invasion significantly altered the bioavailable P concentrations in the soil of native plant communities in the different river-lake ecotones, and this effect was not disturbed by the heterogeneity of the soil matrix. However, the effects of invasion into different native plant communities on the fractions of soil bioavailable P were different. Compared with native Z. latifolia and N. nucifera communities, A. philoxeroides invasion increased the concentration of inorganic P by 39.5% and 3.7%, respectively, and the concentration of organic P decreased by 32.7% and 31.9%, respectively. Meanwhile, the invasion promoted P cycling and accumulation in the river-lake ecotone, which resulted in average decreases in the soil N:P and C:P ratios of 7.9% and 12.5%, respectively. These results highlight the impact of exotic plant invasions on nutrient cycling in wetland ecosystems in the river-lake ecotone, and this process may be detrimental to the late recovery of native plants.

opencc-by-4.0Mar 2023View details →

Nonlinear response of productivity to precipitation extremes in the Inner Mongolia grassland

As precipitation (PPT) regimes are becoming more extreme worldwide, our understanding of how terrestrial ecosystems will respond to this aspect of climate change remains unclear. We addressed this research gap by a PPT gradient experiment that included PPT amounts simulating extremely dry and wet years in combination with a long-term (40 years) observational study in a grassland ecosystem. This study illustrates how a grassland responded to greater PPT variability and highlights the role of limiting resource shift in ecosystem responses to climate extremes. Thus, to accurately forecast future ecosystem feedbacks to climate change, we should take into account the negative asymmetric feature of ecosystem response to stronger climate variability.

opencc-by-4.0Sep 2022View details →

Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

In the human gut, the growth of Clostridioides difficile is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of C. difficile to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter C. difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species Desulfovibrio piger increases metronidazole tolerance of C. difficile. Competition with species that display higher sensitivity to the antibiotic than C. difficile leads to enhanced growth of C. difficile at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping C. difficile’s response to antibiotics, which could inform therapeutic interventions.

opencc-by-4.0Jan 2023View details →

Dataset for "Supramolecular design of CO2-responsive lipid nanomaterials"

This dataset provides the raw data supporting the paper: Supramolecular design of CO2-responsive lipid nanomaterials. It comprises SAXS data (Figure 4 on the manuscript), cryo-TEM images (Figure 5), Zeta-potential measurment (Table 1) and  DLS data (Table1 and Figure S8).

Mixed-species groups of herbivorous reef fish show variable responses to ecosystem perturbations in the Lakshadweep Islands, India

This dataset contains data on mixed-species groups of herbivorous reef fish and local species composition in the Lakshadweep Islands, India. Herbivorous reef fish provide a vital function in reef ecosystems by removing algae and making space available to coral recruits. The high abundance of herbivores in the reefs of the Lakshadweep islands has potentially aided in reef recovery and helped avoid a phase shift to an algal-dominated system, despite most areas having suffered massive coral losses. Mixed-species grouping in herbivores could potentially benefit both the participant species and the reef ecosystem by improving foraging efficiency. We examined the grouping propensity and species richness for three types of herbivore groups after a mass-bleaching event in 2010 and a mass recruitment event in 2015. The species richness and number of parrotfish groups, as well as the grouping propensity of common species, declined starkly across years, indicating that these groups may have formed in response to the mass-bleaching event, slowly diminishing as the reefs recovered. Conversely, large surgeonfish, which varied in richness and propensity across islands and aspect, are likely influenced by local processes. Small surgeonfish only increased in species richness and number in 2015, which may have been in response to the recruitment event. Thus, herbivorous fish may respond differently to local ecosystem perturbations and play different roles in reef recovery.

opencc-by-4.0Mar 2023View details →

Data set for D6.7 with questionnaire responses

Response from a survey of LTA industry partners on the use of monitoring in their activities.

openmit-licenseMar 2023View details →

A genome-wide optical pooled screen reveals regulators of antiviral responses

Supplementary Datasets for "A genome-wide optical pooled screen reveals regulators of antiviral responses" Supplementary Dataset 1. Mean per-gene extracted features for all channels of genome-wide screen Supplementary Dataset 2. Features from single cells in secondary antibody screen Supplementary Dataset 3. Features from single cells in secondary reporter screen Supplementary Dataset 4. IRF3 translocation scores from primary and secondary IRF3 antibody and IRF3 reporter screens (the latter upon both Sendai virus and VSV infection) and SeV intensity scores from secondary antibody screen. Supplementary Dataset 5. Peroxisome and Sendai virus feature scores from genome-wide screen

Comparative transcriptomics reveals divergence in pathogen response gene families amongst twenty forest tree species

Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity is key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, we used the RNA-seq data of twenty co-occurring forest tree species from genera including Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, and Ulmus sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.

opencc-by-4.0Nov 2022View details →

Modeling the Sequence Dependence of Differential Antibody Binding in the Immune Response to Infectious Disease

Raw peptide microarray data of fluorescence intensities representing relative binding of antibodies in sera samples collected from different cohorts of patients diagnosed with a number of viral infections. Healthy controls are also included. Columns: Sequence - peptide sequence HCV - Hepatitis Virus C Dengue - Dengue virus WNV - West Nile Virus HBV - Hepatitis Virus B Chagas - Chagas disease ND - negative/healthy donor LowCV - low coefficient of variation HighCV - high coefficient of variation

opencc-by-4.0Feb 2023View details →

Cellular uptake of silica particles influences EGFR signaling pathway and is affected in response to EGF

Background: The human epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that is involved in several key cellular processes such as cell proliferation and differentiation, and it has been linked to the development and progression of various cancers (e.g. breast and lung). Researchers have attempted to improve current cancer-targeted therapies by conjugating molecules on the surface of (nano)particles to efficiently target and inhibit EGFR. However, very few in vitro studies have investigated the effect of particles per se on EGFR signaling and dynamics. Furthermore, the impact of concomitant exposure of particles and EGFR ligands, such as epidermal growth factor (EGF) on cellular uptake efficiency has received little attention.  Purpose: The purpose of this research was to determine the effects of silica (SiO2) particles on EGFR expression and intracellular signaling pathways in A549 lung epithelial cells, in the presence or absence of epidermal growth factor (EGF). Results: We showed that A549 cells are able to internalize SiO2 particles with core diameters of 130 nm and 1 µm without affecting cell proliferation or migration. However, both SiO2 particles interfere with the EGFR signaling pathway by raising the endogenous levels of extracellular signal-regulated kinase (ERK) 1/2. Furthermore, both in the presence and absence of SiO2 particles, the addition of EGF increased cell migration. EGF also stimulated cellular uptake of 130 nm SiO2 particles but not 1 µm particles. The increased uptake is primarily associated with EGF-stimulated macropinocytosis. Conclusion: This study shows that SiO2 particle uptake interferes with cellular signaling pathways and can be boosted by concurrent exposure to the bioactive molecule EGF. SiO2 particles, both alone and in combination with the ligand EGF, interfere with EGFR signaling pathway in a size-dependent manner.

opencc-by-4.0Mar 2023View details →

Data of Forced-response characterization of PBF-LB/AlSi10Mg particle dampers with thin and flat cavities

Powder Bed Fusion (PBF) enables the production of complex geometries which offer the opportunity to manufacture lightweight, stiffness-optimised or integrally designed components. Although these properties are usually advantageous for the performance in many applications, they pose disadvantages under vibration as they lead to low damped components. These are prone to high vibration amplitudes which result in higher sound radiation and a reduced lifetime. Particle damping can counteract these disadvantages. By including cavities during the design process, unmelted powder remains inside the component after its production. This powder dissipates energy under vibration by inelastic impacts and friction in particle-–particle or particle-–wall-interactions, increasing the damping characteristics of the component. In this work, additively manufactured AlSi10Mg specimens with cavities are investigated with respect to their damping characteristics by experimental modal analysis. The focus of the investigation is on thin and flat cavities that can be easily integrated into components without adapting the external geometry. The damping characteristics in dependence on excitation amplitude and mode are quantified. The extent to which settling effects of the powder during shaking influence the damping is analysed. The vibration of the specimens is forced by an electrodynamic shaker and their response is measured contactlessly via Scanning Laser Doppler Vibrometry (SLDV). A damping effect of up to 564% depending on the mode, excitation amplitude and specimen can be achieved. In addition, a significant settling effect of the powder which hampers the damping effect is identified by CT scans and modal analysis. The data of the CT scans as well as the data of the modal analysis is uploaded here.

opencc-by-4.0Jul 2020View details →

Pain et al. 2020 Behavioral and Physiological Responses to Instability in Group Membership in Wild Male Woolly Monkeys (Lagothrix lagotricha poeppigii)

Data for Pain et al. 2020 Behavioral and Physiological Responses to Instability in Group Membership in Wild Male Woolly Monkeys (Lagothrix lagotricha poeppigii)

Behavioral responses to a series of similar but distinct novel objects in house sparrows

Generalization refers to the process by which animals assign different stimuli into cognitive categories based on their similarity/dissimilarity to previously experienced stimuli. Stimuli which strongly deviate from previous experience may be avoided due to their novelty (i.e., neophobia), while stimuli which are sufficiently similar to a known/recognized cue may elicit the same response as that cue (i.e., generalization). While generalization has been widely researched, few studies have examined among-individual variance in its expression. Our study quantified among-individual variation in neophobia and generalization in house sparrows (Passer domesticus) by placing a series of different objects next to each subject's food source on successive days and measuring the subject's latency to approach the food source in the presence vs. absence of each object. Similarly to previous work, we found that house sparrows are neophobic on average and exhibit significant among-individual variance in neophobia. More interestingly, we found that the neophobic response declined across presentations of different novel objects. This implies that the sparrows generalized some aspect(s) of the objects. We also found significant among-individual variance in the rate at which approach latency changed across this series, possibly reflecting individual differences in propensity to generalize. These results raise new questions about how neophobia, habituation, and generalization are linked and about the potential for selection to act on these traits under different ecological conditions.

opencc-by-4.0Dec 2022View details →

Review of Open Call Record Datasets concerning the U.S. 911 Emergency Response System

The data available here identifies and describes a sampling of publicly available datasets about the 911 emergency response system. This list of datasets is a resource for researchers, civic technologists, activists, and journalists seeking to learn more about the 911 emergency response system. The list helps to identify relevant datasets that could be used to understand various types of 911 activity. During the first quarter of 2021, the R911 NAT created a list of priority cities including the top 100 cities by population, all state capitals, and the 82 cities that are home to Code for America Brigades. The team then conducted internet searches for each city using terms like “911 calls for service” and “open 911 data.” The dataset and a codebook defining each of these fields are provided as .csv files within a zip file. Note: this file does not contain the actual 911 datasets, which often number in the millions of records. The data_link field contains the URL of the site where each dataset is publicly available. See also: The Reimagine 911 knowledge base at: <a href="https://reimagine-911.gitbook.io/knowledge-base">https://reimagine-911.gitbook.io/knowledge-base</a> Contributors: This open data review was performed by the Code for America Reimagine 911 National Action Team. Contributing team members include: Aleks Hatfield, Brandon Bolton, Chizo Nwagwu, Dan Stormont, Elaine Chow, Em Spalti, Erica Pauls, Gio Sce, Gregory Janesch, Iva Momcheva, Ivelina Momcheva, Jamie Klenetsky Fay, Jason Trout, Jaya Prasad Jayakumar, Jennifer Miller, Jim Grenadier, Joanna Smith, Jonathan Melvin, Katlyn McGraw, Margaret Fine, Mariah Lynch, Micah Mutrux, Michelle Hoogenhout, Patina Herring, Peter Zeglen, Sarah Graham, Sebastian Barajas

opencc-zeroDec 2022View details →

Data from: Genome-wide epitope mapping reveals significant diversity in antibody responses to Coxiella burnetii vaccination and infection

Coxiella burnetii is an important zoonotic bacterial pathogen of global importance, causing the disease Q fever in a wide range of animal hosts. Ruminant livestock, in particular sheep and goats, are considered the main reservoir of infection. Vaccination is a key control measure and two commercial vaccines based on formalin-inactivated C. burnetii bacterins are currently available. However, their deployment is limited due to significant reactogenicity in individuals previously sensitized to C. burnetii antigens. Furthermore, these vaccines interfere with available serodiagnostic tests which are also based on C. burnetii bacterin preparations. Subunit vaccines based on recombinant proteins offer significant advantages, as they can be designed to reduce reactogenicity and can be co-designed with defined antigen serodiagnostic tests to allow discrimination between vaccinated and infected individuals. This study aimed to investigate the diversity of antibody responses to C. burnetii vaccination and/or infection in cattle, goats, humans, and sheep through genome-wide linear epitope mapping to identify candidate vaccine and diagnostic antigens within the predicted bacterial proteome. Using high-density peptide microarrays, we analyzed the seroreactivity in 156 serum samples from vaccinated and infected individuals to peptides derived from 2,092 ORFs in the C. burnetii genome. We found significant diversity in the antibody responses within and between species and across different C. burnetii exposure statuses. However, C. burnetii exposure did result in more uniform seroreactivity across species. Through the implementation of three different vaccine candidate methods, we identified 493 candidate protein antigens for protein subunit vaccine design or serodiagnostic, out of which 65 have been previously described. This is the first study to investigate seroreactivity against the entire C. burnetii genome presented as overlapping linear peptides and provides the basis for selection of antigen targets for next generation Q fever vaccines and diagnostic tests.

opencc-by-4.0Feb 2023View details →

Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response

We examined the role of the plant vs the environment in selecting for beneficial microbes to plants in their home moisture environment, in either wet vs dry conditions. To this end, we first conditioned soil microbial communities, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After 3 plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants, using the soil from the prior 3 generations as an inoculum. From plants inoculated with these ‘evolved’ soils, we measured plant biomass and height. We also measured soil nitrogen of the inoculum, and measured inoculum respiration across a water content gradient.

opencc-by-4.0May 2023View details →

Integrated Study on the natural variation in Arabidopsis thaliana responses to alkaline salinity

Supplementary Datasets of the doctoral thesis entitled "Integrated Study on the natural variation in Arabidopsis thaliana responses to alkaline salinity", comprising genomic and transcriptomic data from growth, nutritional and gene enrichment analyses of natural populations of A. thaliana in response to neutral and alkaline salinity treatments.

opencc-zeroApr 2023View details →

Data from: Trait-specific indirect effects underlie variation in the response of spiders to cannibalistic social partners

Organisms may respond in different ways to the risk posed by conspecifics, but the cause of such variation remains elusive. Here, we use a half-sib/full-sib design to evaluate the contribution of (indirect) genetic or environmental effects to the behavioral response of the cannibalistic wolf spider Lycosa fasciiventris (Dufour, 1835) towards conspecific cues. Spiders showed variation in relative occupancy time, activity, and velocity on patches with or without conspecific cues, but direct genetic variance was only found for occupancy time. These three traits were correlated and could be lumped in a principal component: spiders spending more time in patches with conspecific cues moved less and at a lower rate in those areas. Genetic and/or environmental components of carapace width and weight loss in the social partner were significantly correlated with the principal component of focal individuals. Individual Variation in these traits may reflect the quality and/or quantity of cues produced by social partners, hence focal individuals were likely behaving along a continuum of strategies in response to the risk posed by social partners. Therefore, environmental and genetic trait variation in the social partners may be key to maintain trait diversity in focal individuals, even in the absence of direct genetic variation.